From a7934802abea368a2fa4a15d555653d16abb91bc Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Thu, 20 Jan 2011 11:37:12 -0500
Subject: [PATCH 001/282] A test for branches, removed GENBIN

---
 gtfold-mfe/Makefile.in                 |  21 +-
 gtfold-mfe/aclocal.m4                  |  10 +-
 gtfold-mfe/configure                   | 522 ++++++++++++++-----------
 gtfold-mfe/data/Andronescu/Makefile.in |   2 +-
 gtfold-mfe/data/Makefile.in            |   6 +-
 gtfold-mfe/data/Turner04/Makefile.in   |   2 +-
 gtfold-mfe/data/Turner99/Makefile.in   |   2 +-
 gtfold-mfe/gtfold_config.h             |   6 +-
 gtfold-mfe/include/Makefile.in         |   4 +-
 gtfold-mfe/src/Makefile.in             |   7 +-
 gtfold-mfe/src/loader.cc               |   5 -
 11 files changed, 318 insertions(+), 269 deletions(-)
 mode change 100644 => 100755 gtfold-mfe/configure

diff --git a/gtfold-mfe/Makefile.in b/gtfold-mfe/Makefile.in
index 108710a..61df044 100644
--- a/gtfold-mfe/Makefile.in
+++ b/gtfold-mfe/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
@@ -39,8 +39,8 @@ subdir = .
 DIST_COMMON = README $(am__configure_deps) $(include_HEADERS) \
 	$(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(srcdir)/gtfold_config.h.in $(top_srcdir)/configure AUTHORS \
-	COPYING ChangeLog INSTALL NEWS config.guess config.sub depcomp \
-	install-sh missing
+	COPYING ChangeLog INSTALL NEWS TODO config.guess config.sub \
+	depcomp install-sh missing
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/configure.in
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
@@ -320,7 +320,7 @@ uninstall-includeHEADERS:
 #     (which will cause the Makefiles to be regenerated when you run `make');
 # (2) otherwise, pass the desired values on the `make' command line.
 $(RECURSIVE_TARGETS):
-	@failcom='exit 1'; \
+	@fail= failcom='exit 1'; \
 	for f in x $$MAKEFLAGS; do \
 	  case $$f in \
 	    *=* | --[!k]*);; \
@@ -345,7 +345,7 @@ $(RECURSIVE_TARGETS):
 	fi; test -z "$$fail"
 
 $(RECURSIVE_CLEAN_TARGETS):
-	@failcom='exit 1'; \
+	@fail= failcom='exit 1'; \
 	for f in x $$MAKEFLAGS; do \
 	  case $$f in \
 	    *=* | --[!k]*);; \
@@ -509,7 +509,8 @@ distdir: $(DISTFILES)
 	  fi; \
 	done
 	-test -n "$(am__skip_mode_fix)" \
-	|| find "$(distdir)" -type d ! -perm -777 -exec chmod a+rwx {} \; -o \
+	|| find "$(distdir)" -type d ! -perm -755 \
+		-exec chmod u+rwx,go+rx {} \; -o \
 	  ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
 	  ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
 	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
@@ -553,17 +554,17 @@ dist dist-all: distdir
 distcheck: dist
 	case '$(DIST_ARCHIVES)' in \
 	*.tar.gz*) \
-	  GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
-	  bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\
+	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
 	*.tar.lzma*) \
-	  unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\
+	  lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\
 	*.tar.xz*) \
 	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
 	*.tar.Z*) \
 	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
 	*.shar.gz*) \
-	  GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	esac
diff --git a/gtfold-mfe/aclocal.m4 b/gtfold-mfe/aclocal.m4
index d5a87a3..f5a02ce 100644
--- a/gtfold-mfe/aclocal.m4
+++ b/gtfold-mfe/aclocal.m4
@@ -1,4 +1,4 @@
-# generated automatically by aclocal 1.11 -*- Autoconf -*-
+# generated automatically by aclocal 1.11.1 -*- Autoconf -*-
 
 # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
 # 2005, 2006, 2007, 2008, 2009  Free Software Foundation, Inc.
@@ -13,8 +13,8 @@
 
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.64],,
-[m4_warning([this file was generated for autoconf 2.64.
+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.67],,
+[m4_warning([this file was generated for autoconf 2.67.
 You have another version of autoconf.  It may work, but is not guaranteed to.
 If you have problems, you may need to regenerate the build system entirely.
 To do so, use the procedure documented by the package, typically `autoreconf'.])])
@@ -34,7 +34,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION],
 [am__api_version='1.11'
 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.11], [],
+m4_if([$1], [1.11.1], [],
       [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
 ])
 
@@ -50,7 +50,7 @@ m4_define([_AM_AUTOCONF_VERSION], [])
 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.11])dnl
+[AM_AUTOMAKE_VERSION([1.11.1])dnl
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure
old mode 100644
new mode 100755
index 5dd127c..c5acafe
--- a/gtfold-mfe/configure
+++ b/gtfold-mfe/configure
@@ -1,11 +1,13 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.64 for gtfold 1.17.
+# Generated by GNU Autoconf 2.67 for gtfold 1.18.
+#
 #
 # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
 # Foundation, Inc.
 #
+#
 # This configure script is free software; the Free Software Foundation
 # gives unlimited permission to copy, distribute and modify it.
 ## -------------------- ##
@@ -314,7 +316,7 @@ $as_echo X"$as_dir" |
       test -d "$as_dir" && break
     done
     test -z "$as_dirs" || eval "mkdir $as_dirs"
-  } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir"
+  } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
 
 
 } # as_fn_mkdir_p
@@ -354,19 +356,19 @@ else
 fi # as_fn_arith
 
 
-# as_fn_error ERROR [LINENO LOG_FD]
-# ---------------------------------
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
 # Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
 # provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-# script with status $?, using 1 if that was 0.
+# script with STATUS, using 1 if that was 0.
 as_fn_error ()
 {
-  as_status=$?; test $as_status -eq 0 && as_status=1
-  if test "$3"; then
-    as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-    $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3
+  as_status=$1; test $as_status -eq 0 && as_status=1
+  if test "$4"; then
+    as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+    $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
   fi
-  $as_echo "$as_me: error: $1" >&2
+  $as_echo "$as_me: error: $2" >&2
   as_fn_exit $as_status
 } # as_fn_error
 
@@ -524,10 +526,11 @@ as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
 as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
 
 
-exec 7<&0 </dev/null 6>&1
+test -n "$DJDIR" || exec 7<&0 </dev/null
+exec 6>&1
 
 # Name of the host.
-# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
 # so uname gets run too.
 ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
 
@@ -546,8 +549,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='gtfold'
 PACKAGE_TARNAME='gtfold'
-PACKAGE_VERSION='1.17'
-PACKAGE_STRING='gtfold 1.17'
+PACKAGE_VERSION='1.18'
+PACKAGE_STRING='gtfold 1.18'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -775,8 +778,9 @@ do
   fi
 
   case $ac_option in
-  *=*)	ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
-  *)	ac_optarg=yes ;;
+  *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+  *=)   ac_optarg= ;;
+  *)    ac_optarg=yes ;;
   esac
 
   # Accept the important Cygnus configure options, so we can diagnose typos.
@@ -821,7 +825,7 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error "invalid feature name: $ac_useropt"
+      as_fn_error $? "invalid feature name: $ac_useropt"
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -847,7 +851,7 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error "invalid feature name: $ac_useropt"
+      as_fn_error $? "invalid feature name: $ac_useropt"
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -1051,7 +1055,7 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error "invalid package name: $ac_useropt"
+      as_fn_error $? "invalid package name: $ac_useropt"
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -1067,7 +1071,7 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error "invalid package name: $ac_useropt"
+      as_fn_error $? "invalid package name: $ac_useropt"
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -1097,8 +1101,8 @@ do
   | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
     x_libraries=$ac_optarg ;;
 
-  -*) as_fn_error "unrecognized option: \`$ac_option'
-Try \`$0 --help' for more information."
+  -*) as_fn_error $? "unrecognized option: \`$ac_option'
+Try \`$0 --help' for more information"
     ;;
 
   *=*)
@@ -1106,7 +1110,7 @@ Try \`$0 --help' for more information."
     # Reject names that are not valid shell variable names.
     case $ac_envvar in #(
       '' | [0-9]* | *[!_$as_cr_alnum]* )
-      as_fn_error "invalid variable name: \`$ac_envvar'" ;;
+      as_fn_error $? "invalid variable name: \`$ac_envvar'" ;;
     esac
     eval $ac_envvar=\$ac_optarg
     export $ac_envvar ;;
@@ -1124,13 +1128,13 @@ done
 
 if test -n "$ac_prev"; then
   ac_option=--`echo $ac_prev | sed 's/_/-/g'`
-  as_fn_error "missing argument to $ac_option"
+  as_fn_error $? "missing argument to $ac_option"
 fi
 
 if test -n "$ac_unrecognized_opts"; then
   case $enable_option_checking in
     no) ;;
-    fatal) as_fn_error "unrecognized options: $ac_unrecognized_opts" ;;
+    fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;;
     *)     $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;;
   esac
 fi
@@ -1153,7 +1157,7 @@ do
     [\\/$]* | ?:[\\/]* )  continue;;
     NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
   esac
-  as_fn_error "expected an absolute directory name for --$ac_var: $ac_val"
+  as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val"
 done
 
 # There might be people who depend on the old broken behavior: `$host'
@@ -1167,8 +1171,8 @@ target=$target_alias
 if test "x$host_alias" != x; then
   if test "x$build_alias" = x; then
     cross_compiling=maybe
-    $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
-    If a cross compiler is detected then cross compile mode will be used." >&2
+    $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host.
+    If a cross compiler is detected then cross compile mode will be used" >&2
   elif test "x$build_alias" != "x$host_alias"; then
     cross_compiling=yes
   fi
@@ -1183,9 +1187,9 @@ test "$silent" = yes && exec 6>/dev/null
 ac_pwd=`pwd` && test -n "$ac_pwd" &&
 ac_ls_di=`ls -di .` &&
 ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
-  as_fn_error "working directory cannot be determined"
+  as_fn_error $? "working directory cannot be determined"
 test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
-  as_fn_error "pwd does not report name of working directory"
+  as_fn_error $? "pwd does not report name of working directory"
 
 
 # Find the source files, if location was not specified.
@@ -1224,11 +1228,11 @@ else
 fi
 if test ! -r "$srcdir/$ac_unique_file"; then
   test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
-  as_fn_error "cannot find sources ($ac_unique_file) in $srcdir"
+  as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
 fi
 ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
 ac_abs_confdir=`(
-	cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error "$ac_msg"
+	cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
 	pwd)`
 # When building in place, set srcdir=.
 if test "$ac_abs_confdir" = "$ac_pwd"; then
@@ -1254,7 +1258,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures gtfold 1.17 to adapt to many kinds of systems.
+\`configure' configures gtfold 1.18 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1268,7 +1272,7 @@ Configuration:
       --help=short        display options specific to this package
       --help=recursive    display the short help of all the included packages
   -V, --version           display version information and exit
-  -q, --quiet, --silent   do not print \`checking...' messages
+  -q, --quiet, --silent   do not print \`checking ...' messages
       --cache-file=FILE   cache test results in FILE [disabled]
   -C, --config-cache      alias for \`--cache-file=config.cache'
   -n, --no-create         do not create output files
@@ -1325,7 +1329,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of gtfold 1.17:";;
+     short | recursive ) echo "Configuration of gtfold 1.18:";;
    esac
   cat <<\_ACEOF
 
@@ -1345,7 +1349,7 @@ Some influential environment variables:
   LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
               nonstandard directory <lib dir>
   LIBS        libraries to pass to the linker, e.g. -l<library>
-  CPPFLAGS    C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
+  CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
               you have headers in a nonstandard directory <include dir>
   CXX         C++ compiler command
   CXXFLAGS    C++ compiler flags
@@ -1417,10 +1421,10 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-gtfold configure 1.17
-generated by GNU Autoconf 2.64
+gtfold configure 1.18
+generated by GNU Autoconf 2.67
 
-Copyright (C) 2009 Free Software Foundation, Inc.
+Copyright (C) 2010 Free Software Foundation, Inc.
 This configure script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it.
 _ACEOF
@@ -1465,7 +1469,7 @@ sed 's/^/| /' conftest.$ac_ext >&5
 	ac_retval=1
 fi
   eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-  return $ac_retval
+  as_fn_set_status $ac_retval
 
 } # ac_fn_c_try_compile
 
@@ -1503,7 +1507,7 @@ sed 's/^/| /' conftest.$ac_ext >&5
 	ac_retval=1
 fi
   eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-  return $ac_retval
+  as_fn_set_status $ac_retval
 
 } # ac_fn_cxx_try_compile
 
@@ -1549,7 +1553,7 @@ fi
   # left behind by Apple's compiler.  We do this before executing the actions.
   rm -rf conftest.dSYM conftest_ipa8_conftest.oo
   eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-  return $ac_retval
+  as_fn_set_status $ac_retval
 
 } # ac_fn_c_try_link
 
@@ -1574,7 +1578,7 @@ $as_echo "$ac_try_echo"; } >&5
     mv -f conftest.er1 conftest.err
   fi
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; } >/dev/null && {
+  test $ac_status = 0; } > conftest.i && {
 	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
 	 test ! -s conftest.err
        }; then :
@@ -1586,7 +1590,7 @@ sed 's/^/| /' conftest.$ac_ext >&5
     ac_retval=1
 fi
   eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-  return $ac_retval
+  as_fn_set_status $ac_retval
 
 } # ac_fn_c_try_cpp
 
@@ -1628,7 +1632,7 @@ sed 's/^/| /' conftest.$ac_ext >&5
 fi
   rm -rf conftest.dSYM conftest_ipa8_conftest.oo
   eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-  return $ac_retval
+  as_fn_set_status $ac_retval
 
 } # ac_fn_c_try_run
 
@@ -1640,10 +1644,10 @@ fi
 ac_fn_c_check_header_mongrel ()
 {
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+  if eval "test \"\${$3+set}\"" = set; then :
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 fi
 eval ac_res=\$$3
@@ -1679,7 +1683,7 @@ if ac_fn_c_try_cpp "$LINENO"; then :
 else
   ac_header_preproc=no
 fi
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.err conftest.i conftest.$ac_ext
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
 $as_echo "$ac_header_preproc" >&6; }
 
@@ -1706,7 +1710,7 @@ $as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
 esac
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   eval "$3=\$ac_header_compiler"
@@ -1728,7 +1732,7 @@ ac_fn_c_check_header_compile ()
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -1759,7 +1763,7 @@ ac_fn_c_check_type ()
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   eval "$3=no"
@@ -1812,7 +1816,7 @@ ac_fn_c_check_func ()
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -1874,8 +1878,8 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by gtfold $as_me 1.17, which was
-generated by GNU Autoconf 2.64.  Invocation command line was
+It was created by gtfold $as_me 1.18, which was
+generated by GNU Autoconf 2.67.  Invocation command line was
 
   $ $0 $@
 
@@ -1985,11 +1989,9 @@ trap 'exit_status=$?
   {
     echo
 
-    cat <<\_ASBOX
-## ---------------- ##
+    $as_echo "## ---------------- ##
 ## Cache variables. ##
-## ---------------- ##
-_ASBOX
+## ---------------- ##"
     echo
     # The following way of writing the cache mishandles newlines in values,
 (
@@ -2023,11 +2025,9 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
 )
     echo
 
-    cat <<\_ASBOX
-## ----------------- ##
+    $as_echo "## ----------------- ##
 ## Output variables. ##
-## ----------------- ##
-_ASBOX
+## ----------------- ##"
     echo
     for ac_var in $ac_subst_vars
     do
@@ -2040,11 +2040,9 @@ _ASBOX
     echo
 
     if test -n "$ac_subst_files"; then
-      cat <<\_ASBOX
-## ------------------- ##
+      $as_echo "## ------------------- ##
 ## File substitutions. ##
-## ------------------- ##
-_ASBOX
+## ------------------- ##"
       echo
       for ac_var in $ac_subst_files
       do
@@ -2058,11 +2056,9 @@ _ASBOX
     fi
 
     if test -s confdefs.h; then
-      cat <<\_ASBOX
-## ----------- ##
+      $as_echo "## ----------- ##
 ## confdefs.h. ##
-## ----------- ##
-_ASBOX
+## ----------- ##"
       echo
       cat confdefs.h
       echo
@@ -2117,7 +2113,12 @@ _ACEOF
 ac_site_file1=NONE
 ac_site_file2=NONE
 if test -n "$CONFIG_SITE"; then
-  ac_site_file1=$CONFIG_SITE
+  # We do not want a PATH search for config.site.
+  case $CONFIG_SITE in #((
+    -*)  ac_site_file1=./$CONFIG_SITE;;
+    */*) ac_site_file1=$CONFIG_SITE;;
+    *)   ac_site_file1=./$CONFIG_SITE;;
+  esac
 elif test "x$prefix" != xNONE; then
   ac_site_file1=$prefix/share/config.site
   ac_site_file2=$prefix/etc/config.site
@@ -2128,18 +2129,22 @@ fi
 for ac_site_file in "$ac_site_file1" "$ac_site_file2"
 do
   test "x$ac_site_file" = xNONE && continue
-  if test -r "$ac_site_file"; then
+  if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
 $as_echo "$as_me: loading site script $ac_site_file" >&6;}
     sed 's/^/| /' "$ac_site_file" >&5
-    . "$ac_site_file"
+    . "$ac_site_file" \
+      || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "failed to load site script $ac_site_file
+See \`config.log' for more details" "$LINENO" 5 ; }
   fi
 done
 
 if test -r "$cache_file"; then
-  # Some versions of bash will fail to source /dev/null (special
-  # files actually), so we avoid doing that.
-  if test -f "$cache_file"; then
+  # Some versions of bash will fail to source /dev/null (special files
+  # actually), so we avoid doing that.  DJGPP emulates it as a regular file.
+  if test /dev/null != "$cache_file" && test -f "$cache_file"; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
 $as_echo "$as_me: loading cache $cache_file" >&6;}
     case $cache_file in
@@ -2208,7 +2213,7 @@ if $ac_cache_corrupted; then
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
   { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
 $as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
-  as_fn_error "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+  as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
 fi
 ## -------------------- ##
 ## Main body of script. ##
@@ -2229,16 +2234,22 @@ ac_config_headers="$ac_config_headers gtfold_config.h"
 
 ac_aux_dir=
 for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
-  for ac_t in install-sh install.sh shtool; do
-    if test -f "$ac_dir/$ac_t"; then
-      ac_aux_dir=$ac_dir
-      ac_install_sh="$ac_aux_dir/$ac_t -c"
-      break 2
-    fi
-  done
+  if test -f "$ac_dir/install-sh"; then
+    ac_aux_dir=$ac_dir
+    ac_install_sh="$ac_aux_dir/install-sh -c"
+    break
+  elif test -f "$ac_dir/install.sh"; then
+    ac_aux_dir=$ac_dir
+    ac_install_sh="$ac_aux_dir/install.sh -c"
+    break
+  elif test -f "$ac_dir/shtool"; then
+    ac_aux_dir=$ac_dir
+    ac_install_sh="$ac_aux_dir/shtool install -c"
+    break
+  fi
 done
 if test -z "$ac_aux_dir"; then
-  as_fn_error "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
+  as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
 fi
 
 # These three variables are undocumented and unsupported,
@@ -2252,7 +2263,7 @@ ac_configure="$SHELL $ac_aux_dir/configure"  # Please don't use this var.
 
 # Make sure we can run config.sub.
 $SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
-  as_fn_error "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
+  as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
 $as_echo_n "checking build system type... " >&6; }
@@ -2263,16 +2274,16 @@ else
 test "x$ac_build_alias" = x &&
   ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
 test "x$ac_build_alias" = x &&
-  as_fn_error "cannot guess build type; you must specify one" "$LINENO" 5
+  as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
 ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
-  as_fn_error "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
+  as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
 
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
 $as_echo "$ac_cv_build" >&6; }
 case $ac_cv_build in
 *-*-*) ;;
-*) as_fn_error "invalid value of canonical build" "$LINENO" 5;;
+*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;;
 esac
 build=$ac_cv_build
 ac_save_IFS=$IFS; IFS='-'
@@ -2297,7 +2308,7 @@ else
   ac_cv_host=$ac_cv_build
 else
   ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
-    as_fn_error "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
+    as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
 fi
 
 fi
@@ -2305,7 +2316,7 @@ fi
 $as_echo "$ac_cv_host" >&6; }
 case $ac_cv_host in
 *-*-*) ;;
-*) as_fn_error "invalid value of canonical host" "$LINENO" 5;;
+*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;;
 esac
 host=$ac_cv_host
 ac_save_IFS=$IFS; IFS='-'
@@ -2330,7 +2341,7 @@ else
   ac_cv_target=$ac_cv_host
 else
   ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` ||
-    as_fn_error "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5
+    as_fn_error $? "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5
 fi
 
 fi
@@ -2338,7 +2349,7 @@ fi
 $as_echo "$ac_cv_target" >&6; }
 case $ac_cv_target in
 *-*-*) ;;
-*) as_fn_error "invalid value of canonical target" "$LINENO" 5;;
+*) as_fn_error $? "invalid value of canonical target" "$LINENO" 5 ;;
 esac
 target=$ac_cv_target
 ac_save_IFS=$IFS; IFS='-'
@@ -2468,11 +2479,11 @@ am_lf='
 '
 case `pwd` in
   *[\\\"\#\$\&\'\`$am_lf]*)
-    as_fn_error "unsafe absolute working directory name" "$LINENO" 5;;
+    as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;;
 esac
 case $srcdir in
   *[\\\"\#\$\&\'\`$am_lf\ \	]*)
-    as_fn_error "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
+    as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;;
 esac
 
 # Do `set' in a subshell so we don't clobber the current shell's
@@ -2494,7 +2505,7 @@ if (
       # if, for instance, CONFIG_SHELL is bash and it inherits a
       # broken ls alias from the environment.  This has actually
       # happened.  Such a system could not be considered "sane".
-      as_fn_error "ls -t appears to fail.  Make sure there is not a broken
+      as_fn_error $? "ls -t appears to fail.  Make sure there is not a broken
 alias in your environment" "$LINENO" 5
    fi
 
@@ -2504,7 +2515,7 @@ then
    # Ok.
    :
 else
-   as_fn_error "newly created file is older than distributed files!
+   as_fn_error $? "newly created file is older than distributed files!
 Check your system clock" "$LINENO" 5
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
@@ -2676,6 +2687,7 @@ IFS=$as_save_IFS
 
 fi
 
+  test -d ./--version && rmdir ./--version
   if test "${ac_cv_path_mkdir+set}" = set; then
     MKDIR_P="$ac_cv_path_mkdir -p"
   else
@@ -2683,7 +2695,6 @@ fi
     # value for MKDIR_P within a source directory, because that will
     # break other packages using the cache if that directory is
     # removed, or if the value is a relative name.
-    test -d ./--version && rmdir ./--version
     MKDIR_P="$ac_install_sh -d"
   fi
 fi
@@ -2742,7 +2753,7 @@ done
 $as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
 set x ${MAKE-make}
 ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
-if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat >conftest.make <<\_ACEOF
@@ -2750,7 +2761,7 @@ SHELL = /bin/sh
 all:
 	@echo '@@@%%%=$(MAKE)=@@@%%%'
 _ACEOF
-# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
 case `${MAKE-make} -f conftest.make 2>/dev/null` in
   *@@@%%%=?*=@@@%%%*)
     eval ac_cv_prog_make_${ac_make}_set=yes;;
@@ -2784,7 +2795,7 @@ if test "`cd $srcdir && pwd`" != "`pwd`"; then
   am__isrc=' -I$(srcdir)'
   # test to see if srcdir already configured
   if test -f $srcdir/config.status; then
-    as_fn_error "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+    as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
   fi
 fi
 
@@ -2800,7 +2811,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='gtfold'
- VERSION='1.17'
+ VERSION='1.18'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -2846,7 +2857,7 @@ if test "${enable_64bit+set}" = set; then :
   enableval=$enable_64bit; case "${enableval}" in
     "" | y | ye | yes) gtfold_cv_enable_64bit=yes ;;
     n | no) gtfold_cv_enable_64bit=no ;;
-    *) as_fn_error "bad value ${enableval} for --enable-64bit" "$LINENO" 5 ;;
+    *) as_fn_error $? "bad value ${enableval} for --enable-64bit" "$LINENO" 5  ;;
   esac
 else
   gtfold_cv_enable_64bit=no
@@ -2975,8 +2986,8 @@ fi
 
 test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "no acceptable C compiler found in \$PATH
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5 ; }
 
 # Provide some information about the compiler.
 $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
@@ -2997,32 +3008,30 @@ $as_echo "$ac_try_echo"; } >&5
 ... rest of stderr output deleted ...
          10q' conftest.err >conftest.er1
     cat conftest.er1 >&5
-    rm -f conftest.er1 conftest.err
   fi
+  rm -f conftest.er1 conftest.err
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }
 done
 
 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
-#include <stdio.h>
+
 int
 main ()
 {
-FILE *f = fopen ("conftest.out", "w");
- return ferror (f) || fclose (f) != 0;
 
   ;
   return 0;
 }
 _ACEOF
 ac_clean_files_save=$ac_clean_files
-ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out conftest.out"
+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
 # Try to create an executable without -o first, disregard a.out.
 # It will help us diagnose broken compilers, and finding out an intuition
 # of exeext.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
-$as_echo_n "checking for C compiler default output file name... " >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
+$as_echo_n "checking whether the C compiler works... " >&6; }
 ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
 
 # The possible output files:
@@ -3084,62 +3093,28 @@ test "$ac_cv_exeext" = no && ac_cv_exeext=
 else
   ac_file=''
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
-$as_echo "$ac_file" >&6; }
 if test -z "$ac_file"; then :
-  $as_echo "$as_me: failed program was:" >&5
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+$as_echo "$as_me: failed program was:" >&5
 sed 's/^/| /' conftest.$ac_ext >&5
 
 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ as_fn_set_status 77
-as_fn_error "C compiler cannot create executables
-See \`config.log' for more details." "$LINENO" 5; }; }
+as_fn_error 77 "C compiler cannot create executables
+See \`config.log' for more details" "$LINENO" 5 ; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
 fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
+$as_echo_n "checking for C compiler default output file name... " >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
+$as_echo "$ac_file" >&6; }
 ac_exeext=$ac_cv_exeext
 
-# Check that the compiler produces executables we can run.  If not, either
-# the compiler is broken, or we cross compile.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
-$as_echo_n "checking whether the C compiler works... " >&6; }
-# If not cross compiling, check that we can run a simple program.
-if test "$cross_compiling" != yes; then
-  if { ac_try='./$ac_file'
-  { { case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_try") 2>&5
-  ac_status=$?
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; }; }; then
-    cross_compiling=no
-  else
-    if test "$cross_compiling" = maybe; then
-	cross_compiling=yes
-    else
-	{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "cannot run C compiled programs.
-If you meant to cross compile, use \`--host'.
-See \`config.log' for more details." "$LINENO" 5; }
-    fi
-  fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-
-rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out conftest.out
+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
 ac_clean_files=$ac_clean_files_save
-# Check that the compiler produces executables we can run.  If not, either
-# the compiler is broken, or we cross compile.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
-$as_echo_n "checking whether we are cross compiling... " >&6; }
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
-$as_echo "$cross_compiling" >&6; }
-
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
 $as_echo_n "checking for suffix of executables... " >&6; }
 if { { ac_try="$ac_link"
@@ -3169,16 +3144,75 @@ done
 else
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "cannot compute suffix of executables: cannot compile and link
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
-rm -f conftest$ac_cv_exeext
+rm -f conftest conftest$ac_cv_exeext
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
 $as_echo "$ac_cv_exeext" >&6; }
 
 rm -f conftest.$ac_ext
 EXEEXT=$ac_cv_exeext
 ac_exeext=$EXEEXT
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#include <stdio.h>
+int
+main ()
+{
+FILE *f = fopen ("conftest.out", "w");
+ return ferror (f) || fclose (f) != 0;
+
+  ;
+  return 0;
+}
+_ACEOF
+ac_clean_files="$ac_clean_files conftest.out"
+# Check that the compiler produces executables we can run.  If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+if test "$cross_compiling" != yes; then
+  { { ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; }
+  if { ac_try='./conftest$ac_cv_exeext'
+  { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; }; }; then
+    cross_compiling=no
+  else
+    if test "$cross_compiling" = maybe; then
+	cross_compiling=yes
+    else
+	{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details" "$LINENO" 5 ; }
+    fi
+  fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
+ac_clean_files=$ac_clean_files_save
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
 $as_echo_n "checking for suffix of object files... " >&6; }
 if test "${ac_cv_objext+set}" = set; then :
@@ -3221,8 +3255,8 @@ sed 's/^/| /' conftest.$ac_ext >&5
 
 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "cannot compute suffix of object files: cannot compile
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 rm -f conftest.$ac_cv_objext conftest.$ac_ext
 fi
@@ -3761,8 +3795,8 @@ $as_echo "$ac_try_echo"; } >&5
 ... rest of stderr output deleted ...
          10q' conftest.err >conftest.er1
     cat conftest.er1 >&5
-    rm -f conftest.er1 conftest.err
   fi
+  rm -f conftest.er1 conftest.err
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
   test $ac_status = 0; }
 done
@@ -4172,7 +4206,7 @@ else
   # Broken: fails on valid input.
 continue
 fi
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.err conftest.i conftest.$ac_ext
 
   # OK, works on sane cases.  Now check whether nonexistent headers
   # can be detected and how.
@@ -4188,11 +4222,11 @@ else
 ac_preproc_ok=:
 break
 fi
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.err conftest.i conftest.$ac_ext
 
 done
 # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.i conftest.err conftest.$ac_ext
 if $ac_preproc_ok; then :
   break
 fi
@@ -4231,7 +4265,7 @@ else
   # Broken: fails on valid input.
 continue
 fi
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.err conftest.i conftest.$ac_ext
 
   # OK, works on sane cases.  Now check whether nonexistent headers
   # can be detected and how.
@@ -4247,18 +4281,18 @@ else
 ac_preproc_ok=:
 break
 fi
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.err conftest.i conftest.$ac_ext
 
 done
 # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.i conftest.err conftest.$ac_ext
 if $ac_preproc_ok; then :
 
 else
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "C preprocessor \"$CPP\" fails sanity check
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 
 ac_ext=c
@@ -4319,7 +4353,7 @@ esac
   done
 IFS=$as_save_IFS
   if test -z "$ac_cv_path_GREP"; then
-    as_fn_error "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+    as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
   fi
 else
   ac_cv_path_GREP=$GREP
@@ -4385,7 +4419,7 @@ esac
   done
 IFS=$as_save_IFS
   if test -z "$ac_cv_path_EGREP"; then
-    as_fn_error "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+    as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
   fi
 else
   ac_cv_path_EGREP=$EGREP
@@ -4519,8 +4553,7 @@ do :
   as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
 ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
 "
-eval as_val=\$$as_ac_Header
-   if test "x$as_val" = x""yes; then :
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
   cat >>confdefs.h <<_ACEOF
 #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
 _ACEOF
@@ -4534,8 +4567,7 @@ for ac_header in stdlib.h string.h sys/time.h
 do :
   as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
 ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
-eval as_val=\$$as_ac_Header
-   if test "x$as_val" = x""yes; then :
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
   cat >>confdefs.h <<_ACEOF
 #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
 _ACEOF
@@ -5046,8 +5078,7 @@ for ac_func in floor gettimeofday pow
 do :
   as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
 ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
-eval as_val=\$$as_ac_var
-   if test "x$as_val" = x""yes; then :
+if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
   cat >>confdefs.h <<_ACEOF
 #define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
 _ACEOF
@@ -5062,7 +5093,7 @@ if test "${enable_debug+set}" = set; then :
     "" | y | ye | yes) debug=true;
 		       CFLAGS=$(echo $CFLAGS -g | sed -e 's/-O\|-O2\|-O3//g') ;;
     n | no) debug=false ;;
-    *) as_fn_error "bad value ${enableval} for --enable-debug" "$LINENO" 5 ;;
+    *) as_fn_error $? "bad value ${enableval} for --enable-debug" "$LINENO" 5  ;;
   esac
 else
   debug=false
@@ -5165,6 +5196,7 @@ DEFS=-DHAVE_CONFIG_H
 
 ac_libobjs=
 ac_ltlibobjs=
+U=
 for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
   # 1. Remove the extension, and $U if already installed.
   ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
@@ -5188,19 +5220,19 @@ else
 fi
 
 if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
-  as_fn_error "conditional \"AMDEP\" was never defined.
+  as_fn_error $? "conditional \"AMDEP\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5
 fi
 if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
-  as_fn_error "conditional \"am__fastdepCC\" was never defined.
+  as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5
 fi
 if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
-  as_fn_error "conditional \"am__fastdepCXX\" was never defined.
+  as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5
 fi
 if test -z "${GTFOLD_DEBUG_TRUE}" && test -z "${GTFOLD_DEBUG_FALSE}"; then
-  as_fn_error "conditional \"GTFOLD_DEBUG\" was never defined.
+  as_fn_error $? "conditional \"GTFOLD_DEBUG\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5
 fi
 
@@ -5350,19 +5382,19 @@ export LANGUAGE
 (unset CDPATH) >/dev/null 2>&1 && unset CDPATH
 
 
-# as_fn_error ERROR [LINENO LOG_FD]
-# ---------------------------------
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
 # Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
 # provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-# script with status $?, using 1 if that was 0.
+# script with STATUS, using 1 if that was 0.
 as_fn_error ()
 {
-  as_status=$?; test $as_status -eq 0 && as_status=1
-  if test "$3"; then
-    as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-    $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3
+  as_status=$1; test $as_status -eq 0 && as_status=1
+  if test "$4"; then
+    as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+    $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
   fi
-  $as_echo "$as_me: error: $1" >&2
+  $as_echo "$as_me: error: $2" >&2
   as_fn_exit $as_status
 } # as_fn_error
 
@@ -5558,7 +5590,7 @@ $as_echo X"$as_dir" |
       test -d "$as_dir" && break
     done
     test -z "$as_dirs" || eval "mkdir $as_dirs"
-  } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir"
+  } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
 
 
 } # as_fn_mkdir_p
@@ -5611,8 +5643,8 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by gtfold $as_me 1.17, which was
-generated by GNU Autoconf 2.64.  Invocation command line was
+This file was extended by gtfold $as_me 1.18, which was
+generated by GNU Autoconf 2.67.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
   CONFIG_HEADERS  = $CONFIG_HEADERS
@@ -5652,6 +5684,7 @@ Usage: $0 [OPTION]... [TAG]...
 
   -h, --help       print this help, then exit
   -V, --version    print version number and configuration settings, then exit
+      --config     print configuration, then exit
   -q, --quiet, --silent
                    do not print progress messages
   -d, --debug      don't remove temporary files
@@ -5674,12 +5707,13 @@ Report bugs to the package provider."
 
 _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-gtfold config.status 1.17
-configured by $0, generated by GNU Autoconf 2.64,
-  with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
+gtfold config.status 1.18
+configured by $0, generated by GNU Autoconf 2.67,
+  with options \\"\$ac_cs_config\\"
 
-Copyright (C) 2009 Free Software Foundation, Inc.
+Copyright (C) 2010 Free Software Foundation, Inc.
 This config.status script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it."
 
@@ -5697,11 +5731,16 @@ ac_need_defaults=:
 while test $# != 0
 do
   case $1 in
-  --*=*)
+  --*=?*)
     ac_option=`expr "X$1" : 'X\([^=]*\)='`
     ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
     ac_shift=:
     ;;
+  --*=)
+    ac_option=`expr "X$1" : 'X\([^=]*\)='`
+    ac_optarg=
+    ac_shift=:
+    ;;
   *)
     ac_option=$1
     ac_optarg=$2
@@ -5715,12 +5754,15 @@ do
     ac_cs_recheck=: ;;
   --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
     $as_echo "$ac_cs_version"; exit ;;
+  --config | --confi | --conf | --con | --co | --c )
+    $as_echo "$ac_cs_config"; exit ;;
   --debug | --debu | --deb | --de | --d | -d )
     debug=: ;;
   --file | --fil | --fi | --f )
     $ac_shift
     case $ac_optarg in
     *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+    '') as_fn_error $? "missing file argument" ;;
     esac
     as_fn_append CONFIG_FILES " '$ac_optarg'"
     ac_need_defaults=false;;
@@ -5733,7 +5775,7 @@ do
     ac_need_defaults=false;;
   --he | --h)
     # Conflict between --help and --header
-    as_fn_error "ambiguous option: \`$1'
+    as_fn_error $? "ambiguous option: \`$1'
 Try \`$0 --help' for more information.";;
   --help | --hel | -h )
     $as_echo "$ac_cs_usage"; exit ;;
@@ -5742,7 +5784,7 @@ Try \`$0 --help' for more information.";;
     ac_cs_silent=: ;;
 
   # This is an error.
-  -*) as_fn_error "unrecognized option: \`$1'
+  -*) as_fn_error $? "unrecognized option: \`$1'
 Try \`$0 --help' for more information." ;;
 
   *) as_fn_append ac_config_targets " $1"
@@ -5806,7 +5848,7 @@ do
     "data/Turner04/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner04/Makefile" ;;
     "data/Andronescu/Makefile") CONFIG_FILES="$CONFIG_FILES data/Andronescu/Makefile" ;;
 
-  *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
+  *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;;
   esac
 done
 
@@ -5844,7 +5886,7 @@ $debug ||
 {
   tmp=./conf$$-$RANDOM
   (umask 077 && mkdir "$tmp")
-} || as_fn_error "cannot create a temporary directory in ." "$LINENO" 5
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
 
 # Set up the scripts for CONFIG_FILES section.
 # No need to generate them if there are no CONFIG_FILES.
@@ -5861,7 +5903,7 @@ if test "x$ac_cr" = x; then
 fi
 ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
 if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
-  ac_cs_awk_cr='\r'
+  ac_cs_awk_cr='\\r'
 else
   ac_cs_awk_cr=$ac_cr
 fi
@@ -5875,18 +5917,18 @@ _ACEOF
   echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
   echo "_ACEOF"
 } >conf$$subs.sh ||
-  as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5
-ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'`
+  as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
 ac_delim='%!_!# '
 for ac_last_try in false false false false false :; do
   . ./conf$$subs.sh ||
-    as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5
+    as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
 
   ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
   if test $ac_delim_n = $ac_delim_num; then
     break
   elif $ac_last_try; then
-    as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5
+    as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
   else
     ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
   fi
@@ -5908,7 +5950,7 @@ s/'"$ac_delim"'$//
 t delim
 :nl
 h
-s/\(.\{148\}\).*/\1/
+s/\(.\{148\}\)..*/\1/
 t more1
 s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
 p
@@ -5922,7 +5964,7 @@ s/.\{148\}//
 t nl
 :delim
 h
-s/\(.\{148\}\).*/\1/
+s/\(.\{148\}\)..*/\1/
 t more2
 s/["\\]/\\&/g; s/^/"/; s/$/"/
 p
@@ -5975,20 +6017,28 @@ if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
 else
   cat
 fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
-  || as_fn_error "could not setup config files machinery" "$LINENO" 5
+  || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
 _ACEOF
 
-# VPATH may cause trouble with some makes, so we remove $(srcdir),
-# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
 # trailing colons and then remove the whole line if VPATH becomes empty
 # (actually we leave an empty line to preserve line numbers).
 if test "x$srcdir" = x.; then
-  ac_vpsub='/^[	 ]*VPATH[	 ]*=/{
-s/:*\$(srcdir):*/:/
-s/:*\${srcdir}:*/:/
-s/:*@srcdir@:*/:/
-s/^\([^=]*=[	 ]*\):*/\1/
+  ac_vpsub='/^[	 ]*VPATH[	 ]*=[	 ]*/{
+h
+s///
+s/^/:/
+s/[	 ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
 s/:*$//
+x
+s/\(=[	 ]*\).*/\1/
+G
+s/\n//
 s/^[^=]*=[	 ]*$//
 }'
 fi
@@ -6016,7 +6066,7 @@ for ac_last_try in false false :; do
   if test -z "$ac_t"; then
     break
   elif $ac_last_try; then
-    as_fn_error "could not make $CONFIG_HEADERS" "$LINENO" 5
+    as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
   else
     ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
   fi
@@ -6101,7 +6151,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 _ACAWK
 _ACEOF
 cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-  as_fn_error "could not setup config headers machinery" "$LINENO" 5
+  as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
 fi # test -n "$CONFIG_HEADERS"
 
 
@@ -6114,7 +6164,7 @@ do
   esac
   case $ac_mode$ac_tag in
   :[FHL]*:*);;
-  :L* | :C*:*) as_fn_error "invalid tag \`$ac_tag'" "$LINENO" 5;;
+  :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;;
   :[FH]-) ac_tag=-:-;;
   :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
   esac
@@ -6142,7 +6192,7 @@ do
 	   [\\/$]*) false;;
 	   *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
 	   esac ||
-	   as_fn_error "cannot find input file: \`$ac_f'" "$LINENO" 5;;
+	   as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;;
       esac
       case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
       as_fn_append ac_file_inputs " '$ac_f'"
@@ -6169,7 +6219,7 @@ $as_echo "$as_me: creating $ac_file" >&6;}
 
     case $ac_tag in
     *:-:* | *:-) cat >"$tmp/stdin" \
-      || as_fn_error "could not create $ac_file" "$LINENO" 5 ;;
+      || as_fn_error $? "could not create $ac_file" "$LINENO" 5  ;;
     esac
     ;;
   esac
@@ -6306,22 +6356,22 @@ s&@MKDIR_P@&$ac_MKDIR_P&;t t
 $ac_datarootdir_hack
 "
 eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \
-  || as_fn_error "could not create $ac_file" "$LINENO" 5
+  || as_fn_error $? "could not create $ac_file" "$LINENO" 5
 
 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
   { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
   { ac_out=`sed -n '/^[	 ]*datarootdir[	 ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined.  Please make sure it is defined." >&5
+which seems to be undefined.  Please make sure it is defined" >&5
 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined.  Please make sure it is defined." >&2;}
+which seems to be undefined.  Please make sure it is defined" >&2;}
 
   rm -f "$tmp/stdin"
   case $ac_file in
   -) cat "$tmp/out" && rm -f "$tmp/out";;
   *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
   esac \
-  || as_fn_error "could not create $ac_file" "$LINENO" 5
+  || as_fn_error $? "could not create $ac_file" "$LINENO" 5
  ;;
   :H)
   #
@@ -6332,19 +6382,19 @@ which seems to be undefined.  Please make sure it is defined." >&2;}
       $as_echo "/* $configure_input  */" \
       && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs"
     } >"$tmp/config.h" \
-      || as_fn_error "could not create $ac_file" "$LINENO" 5
+      || as_fn_error $? "could not create $ac_file" "$LINENO" 5
     if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then
       { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
 $as_echo "$as_me: $ac_file is unchanged" >&6;}
     else
       rm -f "$ac_file"
       mv "$tmp/config.h" "$ac_file" \
-	|| as_fn_error "could not create $ac_file" "$LINENO" 5
+	|| as_fn_error $? "could not create $ac_file" "$LINENO" 5
     fi
   else
     $as_echo "/* $configure_input  */" \
       && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \
-      || as_fn_error "could not create -" "$LINENO" 5
+      || as_fn_error $? "could not create -" "$LINENO" 5
   fi
 # Compute "$ac_file"'s index in $config_headers.
 _am_arg="$ac_file"
@@ -6494,7 +6544,7 @@ _ACEOF
 ac_clean_files=$ac_clean_files_save
 
 test $ac_write_fail = 0 ||
-  as_fn_error "write failure creating $CONFIG_STATUS" "$LINENO" 5
+  as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
 
 
 # configure is writing to config.log, and then calls config.status.
@@ -6515,7 +6565,7 @@ if test "$no_create" != yes; then
   exec 5>>config.log
   # Use ||, not &&, to avoid exiting from the if with $? = 1, which
   # would make configure fail if this is the last instruction.
-  $ac_cs_success || as_fn_exit $?
+  $ac_cs_success || as_fn_exit 1
 fi
 if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
diff --git a/gtfold-mfe/data/Andronescu/Makefile.in b/gtfold-mfe/data/Andronescu/Makefile.in
index d572ff3..86b4876 100644
--- a/gtfold-mfe/data/Andronescu/Makefile.in
+++ b/gtfold-mfe/data/Andronescu/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
diff --git a/gtfold-mfe/data/Makefile.in b/gtfold-mfe/data/Makefile.in
index 0818588..20b49f3 100644
--- a/gtfold-mfe/data/Makefile.in
+++ b/gtfold-mfe/data/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
@@ -232,7 +232,7 @@ $(am__aclocal_m4_deps):
 #     (which will cause the Makefiles to be regenerated when you run `make');
 # (2) otherwise, pass the desired values on the `make' command line.
 $(RECURSIVE_TARGETS):
-	@failcom='exit 1'; \
+	@fail= failcom='exit 1'; \
 	for f in x $$MAKEFLAGS; do \
 	  case $$f in \
 	    *=* | --[!k]*);; \
@@ -257,7 +257,7 @@ $(RECURSIVE_TARGETS):
 	fi; test -z "$$fail"
 
 $(RECURSIVE_CLEAN_TARGETS):
-	@failcom='exit 1'; \
+	@fail= failcom='exit 1'; \
 	for f in x $$MAKEFLAGS; do \
 	  case $$f in \
 	    *=* | --[!k]*);; \
diff --git a/gtfold-mfe/data/Turner04/Makefile.in b/gtfold-mfe/data/Turner04/Makefile.in
index 7d91d24..60d8467 100644
--- a/gtfold-mfe/data/Turner04/Makefile.in
+++ b/gtfold-mfe/data/Turner04/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in
index bf80b77..d9a1eb3 100644
--- a/gtfold-mfe/data/Turner99/Makefile.in
+++ b/gtfold-mfe/data/Turner99/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
diff --git a/gtfold-mfe/gtfold_config.h b/gtfold-mfe/gtfold_config.h
index fb341ee..56549bc 100644
--- a/gtfold-mfe/gtfold_config.h
+++ b/gtfold-mfe/gtfold_config.h
@@ -53,7 +53,7 @@
 #define PACKAGE_NAME "gtfold"
 
 /* Define to the full name and version of this package. */
-#define PACKAGE_STRING "gtfold 1.17"
+#define PACKAGE_STRING "gtfold 1.18"
 
 /* Define to the one symbol short name of this package. */
 #define PACKAGE_TARNAME "gtfold"
@@ -62,7 +62,7 @@
 #define PACKAGE_URL ""
 
 /* Define to the version of this package. */
-#define PACKAGE_VERSION "1.17"
+#define PACKAGE_VERSION "1.18"
 
 /* Define to 1 if you have the ANSI C header files. */
 #define STDC_HEADERS 1
@@ -74,7 +74,7 @@
 /* #undef TM_IN_SYS_TIME */
 
 /* Version number of package */
-#define VERSION "1.17"
+#define VERSION "1.18"
 
 /* Define to empty if `const' does not conform to ANSI C. */
 /* #undef const */
diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in
index e916841..d049bac 100644
--- a/gtfold-mfe/include/Makefile.in
+++ b/gtfold-mfe/include/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
@@ -155,7 +155,7 @@ target_vendor = @target_vendor@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main-c.h main.h traceback.h
+noinst_HEADERS = algorithms.h algorithms-partition.h constants.h data.h loader.h main-c.h main.h traceback.h
 CLEANFILES = *~
 all: all-am
 
diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in
index 48c25e0..bce43ec 100644
--- a/gtfold-mfe/src/Makefile.in
+++ b/gtfold-mfe/src/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
@@ -49,7 +49,8 @@ CONFIG_CLEAN_VPATH_FILES =
 am__installdirs = "$(DESTDIR)$(bindir)"
 PROGRAMS = $(bin_PROGRAMS)
 am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) \
-	algorithms.$(OBJEXT) traceback.$(OBJEXT)
+	algorithms.$(OBJEXT) algorithms-partition.$(OBJEXT) \
+	traceback.$(OBJEXT)
 gtfold_OBJECTS = $(am_gtfold_OBJECTS)
 gtfold_DEPENDENCIES =
 gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
@@ -182,6 +183,7 @@ gtfold_SOURCES = \
 	main.cc\
 	loader.cc\
 	algorithms.c\
+	algorithms-partition.c\
 	traceback.c
 
 gtfold_LDFLAGS = 
@@ -268,6 +270,7 @@ mostlyclean-compile:
 distclean-compile:
 	-rm -f *.tab.c
 
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/loader.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 773a28a..b081412 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -31,7 +31,6 @@
 #define xstr(s) str(s)
 #define str(s) #s
 
-//#define GENBIN
 
 using namespace std;
 
@@ -84,7 +83,6 @@ void populate(const char *userdatadir,bool userdatalogic) {
 
 	cout << "Loading in GTfold data files from ";
 
-#ifndef GENBIN
 	if (!userdatalogic) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
@@ -92,9 +90,6 @@ void populate(const char *userdatadir,bool userdatalogic) {
 	} else {
 		EN_DATADIR.assign(userdatadir);
 	}
-#else
-	EN_DATADIR = "data";
-#endif
 
 	//Handle the ending forward slash case
 	if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') {

From e615e1525fc0943ed9cb09b65a799f39cfddad5c Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 20 Jan 2011 11:42:05 -0500
Subject: [PATCH 002/282] Clean up some comments on the global variables

---
 gtfold-mfe/src/main.cc | 30 +++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 11 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 87086e5..ded39a7 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -44,23 +44,27 @@
 using namespace std;
 
 /* GLOBAL VARIABLES */
-enum BOOL ILSA; /* A boolean variable to know if we are executing with Internal loop speedup algorithm (ILA) or not. ILSA finds the optimal internal loop by exploring all possibilities. */
+
+enum BOOL ILSA; // enable internal loop speedup algorithm (ILSA)
 enum BOOL NOISOLATE;
-enum BOOL BPP; // calculating base pair probabilities
+enum BOOL BPP; // calculate base pair probabilities
 enum BOOL USERDATA;
 enum BOOL PARAMS;
 enum BOOL LIMIT_DISTANCE;
 #ifdef DYNALLOC
 int LENGTH;
 unsigned char *RNA1; 
-unsigned char *RNA; /* Contains RNA string in terms of 0, 1, 2, 3 for A, C, G and U respectively*/
-int *structure; /* An array to contain the optimal structure */
-int *V; /* int V[LENGTH][LENGTH]; */
+unsigned char *RNA; // the RNA string in terms of 0, 1, 2, 3 for A, C, G and U
+int *structure; // An array to contain the optimal structure
+int *V; // int V[LENGTH][LENGTH];
 int *W;
-int **VBI; /* VBI(i,j) will contain the energy of optimal internal loop closed with (i,j) base pair */
-int **VM; /* VM(i, j) will contain the energy of optimla multiloop closed with (i,j) base pair */
-int **WM; /* This array is introduced to help multiloop calculations. WM(i,j) contains the optimal energy of string segment from si to sj if this forms part of a multiloop */
-int *indx; /* This array is used to index V array. Here V array is mapped from 2D to 1D and indx array is used to get the mapping back.*/
+int **VBI; // VBI(i,j) -- energy of optimal internal loop closed with (i,j) base pair
+int **VM; // VM(i,j) -- energy of optimal multiloop closed with (i,j) base pair
+int **WM; // WM(i,j) -- the optimal energy of string segment from i to j,
+          // if this forms part of a multiloop. Used to speed multiloop
+          // calculations.
+int *indx; // used to index V array. The V array is mapped from 2D to 1D and
+           // the indx array is used to get the mapping back.
 int *constraints;
 
 double **QB;  // QB[i][j] is the sum over all possible loops closed by (i,j),
@@ -103,7 +107,9 @@ double get_seconds() {
 	return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0;
 }
 
-/*Function for printing the sequence*/
+/**
+ * Print out the sequence contained in RNA1
+ */
 void printSequence(int len) {
 	int i = 1;
 	for (i = 1; i <= len; i++) {
@@ -121,7 +127,9 @@ void printSequence(int len) {
 	printf("\n");
 }
 
-/*Function for printing the input constraints*/
+/**
+ * Print out the constraints located in variable: constraints
+ */
 void printConstraints(int len) {
 	int i = 1;
 	for (i = 1; i <= len; i++) {

From b92aec8f24a8eccba1b68f56ff49bf1e7c297d65 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 20 Jan 2011 11:43:15 -0500
Subject: [PATCH 003/282] Split help message out into logical segments

---
 gtfold-mfe/src/main.cc | 29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index ded39a7..1007323 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -87,15 +87,28 @@ int W[LENGTH];
 int indx [LENGTH];
 #endif
 
-
-
-
-
-/* Function for displaying help */
+/**
+ * Print the hep message and quit.
+ */
 void help() {
-	fprintf(
-			stderr,
-			"Usage: gtfold [-ilsa] [-noisolate] [-params setofparameters] [-constraints filename] [-limitCD dist] [-datadir datadirloc] [-basepairprobabilities] filename(sequence)\n\n-ilsa\t\t= Use the Internal Loop Speedup Algorithm for faster calculation\n-noisolate\t= Prevent isolated base pairs from forming\n-params\t\t= Choose thermodynamic parameters to use: Turner99 or Turner04 or Andronescu\n-constraints\t= Force or prohibit particular pairings\n\tConstraint syntax:\n\t\tF i j k  to force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) to pair\n\t\tP i j k  to prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) from pairing\n\t\tP i 0 k  to make bases from i to i+k-1 single stranded bases.\n-limitCD\t= Limit the 'contact distance' for a base pair to the given distance\n-basepairprobabilities\n\t\t= Calculate and output base pair probabilities of the predicted structure\n\nSequence file has to be in one of the two formats: Single line or FASTA\n\n");
+	fprintf(stderr,
+			"Usage: gtfold [-ilsa] [-noisolate] [-params setofparameters] [-constraints filename] [-limitCD dist] [-datadir datadirloc] [-basepairprobabilities] filename(sequence)\n\n");
+    fprintf(stderr,
+            "-ilsa\t\t= Use the Internal Loop Speedup Algorithm for faster calculation\n");
+    fprintf(stderr,
+            "-noisolate\t= Prevent isolated base pairs from forming\n");
+    fprintf(stderr,
+            "-params\t\t= Choose thermodynamic parameters to use: Turner99 or Turner04 or Andronescu\n");
+    fprintf(stderr,
+            "-constraints\t= Force or prohibit particular pairings\n");
+    fprintf(stderr,
+            "\tConstraint syntax:\n\t\tF i j k  to force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) to pair\n\t\tP i j k  to prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) from pairing\n\t\tP i 0 k  to make bases from i to i+k-1 single stranded bases.\n");
+    fprintf(stderr,
+            "-limitCD\t= Limit the 'contact distance' for a base pair to the given distance\n");
+    fprintf(stderr,
+            "-basepairprobabilities\n\t\t= Calculate and output base pair probabilities of the predicted structure\n");
+    fprintf(stderr,
+            "\nSequence file has to be in one of the two formats: Single line or FASTA\n\n");
 	//	[-forceNC] 	-forceNC = an option to force pairing of noncanonical bases \nSyntax for forcing noncanonical bases (example):\n\t\tA-A,A-G,U-U\n\n");
 	exit(-1);
 }

From 6e82fb3b150ec4e1000b221393cd9c9094a15e13 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 20 Jan 2011 11:48:15 -0500
Subject: [PATCH 004/282] Remove auto-generated Makefile.in files

---
 gtfold-mfe/Makefile.in                 | 752 -------------------------
 gtfold-mfe/data/Andronescu/Makefile.in | 399 -------------
 gtfold-mfe/data/Makefile.in            | 536 ------------------
 gtfold-mfe/data/Turner04/Makefile.in   | 405 -------------
 gtfold-mfe/data/Turner99/Makefile.in   | 407 -------------
 gtfold-mfe/include/Makefile.in         | 388 -------------
 gtfold-mfe/src/Makefile.in             | 506 -----------------
 7 files changed, 3393 deletions(-)
 delete mode 100644 gtfold-mfe/Makefile.in
 delete mode 100644 gtfold-mfe/data/Andronescu/Makefile.in
 delete mode 100644 gtfold-mfe/data/Makefile.in
 delete mode 100644 gtfold-mfe/data/Turner04/Makefile.in
 delete mode 100644 gtfold-mfe/data/Turner99/Makefile.in
 delete mode 100644 gtfold-mfe/include/Makefile.in
 delete mode 100644 gtfold-mfe/src/Makefile.in

diff --git a/gtfold-mfe/Makefile.in b/gtfold-mfe/Makefile.in
deleted file mode 100644
index 108710a..0000000
--- a/gtfold-mfe/Makefile.in
+++ /dev/null
@@ -1,752 +0,0 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
-# @configure_input@
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-@SET_MAKE@
-
-VPATH = @srcdir@
-pkgdatadir = $(datadir)/@PACKAGE@
-pkgincludedir = $(includedir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
-pkglibexecdir = $(libexecdir)/@PACKAGE@
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = @build@
-host_triplet = @host@
-target_triplet = @target@
-subdir = .
-DIST_COMMON = README $(am__configure_deps) $(include_HEADERS) \
-	$(srcdir)/Makefile.am $(srcdir)/Makefile.in \
-	$(srcdir)/gtfold_config.h.in $(top_srcdir)/configure AUTHORS \
-	COPYING ChangeLog INSTALL NEWS config.guess config.sub depcomp \
-	install-sh missing
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
- configure.lineno config.status.lineno
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
-	html-recursive info-recursive install-data-recursive \
-	install-dvi-recursive install-exec-recursive \
-	install-html-recursive install-info-recursive \
-	install-pdf-recursive install-ps-recursive install-recursive \
-	installcheck-recursive installdirs-recursive pdf-recursive \
-	ps-recursive uninstall-recursive
-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-am__vpath_adj = case $$p in \
-    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-    *) f=$$p;; \
-  esac;
-am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-am__install_max = 40
-am__nobase_strip_setup = \
-  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-am__nobase_strip = \
-  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-am__nobase_list = $(am__nobase_strip_setup); \
-  for p in $$list; do echo "$$p $$p"; done | \
-  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-    if (++n[$$2] == $(am__install_max)) \
-      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-    END { for (dir in files) print dir, files[dir] }'
-am__base_list = \
-  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__installdirs = "$(DESTDIR)$(includedir)"
-HEADERS = $(include_HEADERS)
-RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
-  distclean-recursive maintainer-clean-recursive
-AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-	$(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
-	distdir dist dist-all distcheck
-ETAGS = etags
-CTAGS = ctags
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-distdir = $(PACKAGE)-$(VERSION)
-top_distdir = $(distdir)
-am__remove_distdir = \
-  { test ! -d "$(distdir)" \
-    || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
-         && rm -fr "$(distdir)"; }; }
-am__relativize = \
-  dir0=`pwd`; \
-  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
-  sed_rest='s,^[^/]*/*,,'; \
-  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
-  sed_butlast='s,/*[^/]*$$,,'; \
-  while test -n "$$dir1"; do \
-    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
-    if test "$$first" != "."; then \
-      if test "$$first" = ".."; then \
-        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
-        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
-      else \
-        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
-        if test "$$first2" = "$$first"; then \
-          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
-        else \
-          dir2="../$$dir2"; \
-        fi; \
-        dir0="$$dir0"/"$$first"; \
-      fi; \
-    fi; \
-    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
-  done; \
-  reldir="$$dir2"
-DIST_ARCHIVES = $(distdir).tar.gz
-GZIP_ENV = --best
-distuninstallcheck_listfiles = find . -type f -print
-distcleancheck_listfiles = find . -type f -print
-ACLOCAL = @ACLOCAL@
-AMTAR = @AMTAR@
-AUTOCONF = @AUTOCONF@
-AUTOHEADER = @AUTOHEADER@
-AUTOMAKE = @AUTOMAKE@
-AWK = @AWK@
-CC = @CC@
-CCDEPMODE = @CCDEPMODE@
-CFLAGS = @CFLAGS@
-CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
-CXX = @CXX@
-CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
-CYGPATH_W = @CYGPATH_W@
-DEFS = @DEFS@
-DEPDIR = @DEPDIR@
-ECHO_C = @ECHO_C@
-ECHO_N = @ECHO_N@
-ECHO_T = @ECHO_T@
-EGREP = @EGREP@
-EXEEXT = @EXEEXT@
-GREP = @GREP@
-INSTALL = @INSTALL@
-INSTALL_DATA = @INSTALL_DATA@
-INSTALL_PROGRAM = @INSTALL_PROGRAM@
-INSTALL_SCRIPT = @INSTALL_SCRIPT@
-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
-LIBOBJS = @LIBOBJS@
-LIBS = @LIBS@
-LTLIBOBJS = @LTLIBOBJS@
-MAKEINFO = @MAKEINFO@
-MKDIR_P = @MKDIR_P@
-OBJEXT = @OBJEXT@
-OPENMP_CFLAGS = @OPENMP_CFLAGS@
-PACKAGE = @PACKAGE@
-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-PACKAGE_NAME = @PACKAGE_NAME@
-PACKAGE_STRING = @PACKAGE_STRING@
-PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
-PACKAGE_VERSION = @PACKAGE_VERSION@
-PATH_SEPARATOR = @PATH_SEPARATOR@
-SET_MAKE = @SET_MAKE@
-SHELL = @SHELL@
-STRIP = @STRIP@
-VERSION = @VERSION@
-abs_builddir = @abs_builddir@
-abs_srcdir = @abs_srcdir@
-abs_top_builddir = @abs_top_builddir@
-abs_top_srcdir = @abs_top_srcdir@
-ac_ct_CC = @ac_ct_CC@
-ac_ct_CXX = @ac_ct_CXX@
-am__include = @am__include@
-am__leading_dot = @am__leading_dot@
-am__quote = @am__quote@
-am__tar = @am__tar@
-am__untar = @am__untar@
-bindir = @bindir@
-build = @build@
-build_alias = @build_alias@
-build_cpu = @build_cpu@
-build_os = @build_os@
-build_vendor = @build_vendor@
-builddir = @builddir@
-datadir = @datadir@
-datarootdir = @datarootdir@
-docdir = @docdir@
-dvidir = @dvidir@
-exec_prefix = @exec_prefix@
-host = @host@
-host_alias = @host_alias@
-host_cpu = @host_cpu@
-host_os = @host_os@
-host_vendor = @host_vendor@
-htmldir = @htmldir@
-includedir = @includedir@
-infodir = @infodir@
-install_sh = @install_sh@
-libdir = @libdir@
-libexecdir = @libexecdir@
-localedir = @localedir@
-localstatedir = @localstatedir@
-mandir = @mandir@
-mkdir_p = @mkdir_p@
-oldincludedir = @oldincludedir@
-pdfdir = @pdfdir@
-prefix = @prefix@
-program_transform_name = @program_transform_name@
-psdir = @psdir@
-sbindir = @sbindir@
-sharedstatedir = @sharedstatedir@
-srcdir = @srcdir@
-sysconfdir = @sysconfdir@
-target = @target@
-target_alias = @target_alias@
-target_cpu = @target_cpu@
-target_os = @target_os@
-target_vendor = @target_vendor@
-top_build_prefix = @top_build_prefix@
-top_builddir = @top_builddir@
-top_srcdir = @top_srcdir@
-SUBDIRS = src include data
-DIST_SUBDIRS = src include data
-include_HEADERS = gtfold_config.h
-CLEANFILES = *~
-MAINTAINERCLEANDIRS = autom4te.cache
-# MAINTAINERCLEANFILES = libtool gtfold_config.h.in
-MAINTAINERCLEANFILES = gtfold_config.h gtfold_config.h.in
-EXTRA_DIST = autogen.sh
-all: gtfold_config.h
-	$(MAKE) $(AM_MAKEFLAGS) all-recursive
-
-.SUFFIXES:
-am--refresh:
-	@:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      echo ' cd $(srcdir) && $(AUTOMAKE) --gnu'; \
-	      $(am__cd) $(srcdir) && $(AUTOMAKE) --gnu \
-		&& exit 0; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    echo ' $(SHELL) ./config.status'; \
-	    $(SHELL) ./config.status;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	$(SHELL) ./config.status --recheck
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	$(am__cd) $(srcdir) && $(AUTOCONF)
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	$(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
-$(am__aclocal_m4_deps):
-
-gtfold_config.h: stamp-h1
-	@if test ! -f $@; then \
-	  rm -f stamp-h1; \
-	  $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
-	else :; fi
-
-stamp-h1: $(srcdir)/gtfold_config.h.in $(top_builddir)/config.status
-	@rm -f stamp-h1
-	cd $(top_builddir) && $(SHELL) ./config.status gtfold_config.h
-$(srcdir)/gtfold_config.h.in:  $(am__configure_deps) 
-	($(am__cd) $(top_srcdir) && $(AUTOHEADER))
-	rm -f stamp-h1
-	touch $@
-
-distclean-hdr:
-	-rm -f gtfold_config.h stamp-h1
-install-includeHEADERS: $(include_HEADERS)
-	@$(NORMAL_INSTALL)
-	test -z "$(includedir)" || $(MKDIR_P) "$(DESTDIR)$(includedir)"
-	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
-	for p in $$list; do \
-	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-	  echo "$$d$$p"; \
-	done | $(am__base_list) | \
-	while read files; do \
-	  echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(includedir)'"; \
-	  $(INSTALL_HEADER) $$files "$(DESTDIR)$(includedir)" || exit $$?; \
-	done
-
-uninstall-includeHEADERS:
-	@$(NORMAL_UNINSTALL)
-	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
-	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-	test -n "$$files" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(includedir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(includedir)" && rm -f $$files
-
-# This directory's subdirectories are mostly independent; you can cd
-# into them and run `make' without going through this Makefile.
-# To change the values of `make' variables: instead of editing Makefiles,
-# (1) if the variable is set in `config.status', edit `config.status'
-#     (which will cause the Makefiles to be regenerated when you run `make');
-# (2) otherwise, pass the desired values on the `make' command line.
-$(RECURSIVE_TARGETS):
-	@failcom='exit 1'; \
-	for f in x $$MAKEFLAGS; do \
-	  case $$f in \
-	    *=* | --[!k]*);; \
-	    *k*) failcom='fail=yes';; \
-	  esac; \
-	done; \
-	dot_seen=no; \
-	target=`echo $@ | sed s/-recursive//`; \
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  echo "Making $$target in $$subdir"; \
-	  if test "$$subdir" = "."; then \
-	    dot_seen=yes; \
-	    local_target="$$target-am"; \
-	  else \
-	    local_target="$$target"; \
-	  fi; \
-	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-	  || eval $$failcom; \
-	done; \
-	if test "$$dot_seen" = "no"; then \
-	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
-	fi; test -z "$$fail"
-
-$(RECURSIVE_CLEAN_TARGETS):
-	@failcom='exit 1'; \
-	for f in x $$MAKEFLAGS; do \
-	  case $$f in \
-	    *=* | --[!k]*);; \
-	    *k*) failcom='fail=yes';; \
-	  esac; \
-	done; \
-	dot_seen=no; \
-	case "$@" in \
-	  distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
-	  *) list='$(SUBDIRS)' ;; \
-	esac; \
-	rev=''; for subdir in $$list; do \
-	  if test "$$subdir" = "."; then :; else \
-	    rev="$$subdir $$rev"; \
-	  fi; \
-	done; \
-	rev="$$rev ."; \
-	target=`echo $@ | sed s/-recursive//`; \
-	for subdir in $$rev; do \
-	  echo "Making $$target in $$subdir"; \
-	  if test "$$subdir" = "."; then \
-	    local_target="$$target-am"; \
-	  else \
-	    local_target="$$target"; \
-	  fi; \
-	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-	  || eval $$failcom; \
-	done && test -z "$$fail"
-tags-recursive:
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-	done
-ctags-recursive:
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
-	done
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	mkid -fID $$unique
-tags: TAGS
-
-TAGS: tags-recursive $(HEADERS) $(SOURCES) gtfold_config.h.in $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	set x; \
-	here=`pwd`; \
-	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
-	  include_option=--etags-include; \
-	  empty_fix=.; \
-	else \
-	  include_option=--include; \
-	  empty_fix=; \
-	fi; \
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    test ! -f $$subdir/TAGS || \
-	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
-	  fi; \
-	done; \
-	list='$(SOURCES) $(HEADERS) gtfold_config.h.in $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	shift; \
-	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-	  test -n "$$unique" || unique=$$empty_fix; \
-	  if test $$# -gt 0; then \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      "$$@" $$unique; \
-	  else \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      $$unique; \
-	  fi; \
-	fi
-ctags: CTAGS
-CTAGS: ctags-recursive $(HEADERS) $(SOURCES) gtfold_config.h.in $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	list='$(SOURCES) $(HEADERS) gtfold_config.h.in $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	test -z "$(CTAGS_ARGS)$$unique" \
-	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$unique
-
-GTAGS:
-	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && $(am__cd) $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) "$$here"
-
-distclean-tags:
-	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
-distdir: $(DISTFILES)
-	$(am__remove_distdir)
-	test -d "$(distdir)" || mkdir "$(distdir)"
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    test -d "$(distdir)/$$subdir" \
-	    || $(MKDIR_P) "$(distdir)/$$subdir" \
-	    || exit 1; \
-	  fi; \
-	done
-	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
-	    $(am__relativize); \
-	    new_distdir=$$reldir; \
-	    dir1=$$subdir; dir2="$(top_distdir)"; \
-	    $(am__relativize); \
-	    new_top_distdir=$$reldir; \
-	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
-	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
-	    ($(am__cd) $$subdir && \
-	      $(MAKE) $(AM_MAKEFLAGS) \
-	        top_distdir="$$new_top_distdir" \
-	        distdir="$$new_distdir" \
-		am__remove_distdir=: \
-		am__skip_length_check=: \
-		am__skip_mode_fix=: \
-	        distdir) \
-	      || exit 1; \
-	  fi; \
-	done
-	-test -n "$(am__skip_mode_fix)" \
-	|| find "$(distdir)" -type d ! -perm -777 -exec chmod a+rwx {} \; -o \
-	  ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
-	  ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
-	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
-	|| chmod -R a+r "$(distdir)"
-dist-gzip: distdir
-	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
-	$(am__remove_distdir)
-
-dist-bzip2: distdir
-	tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2
-	$(am__remove_distdir)
-
-dist-lzma: distdir
-	tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma
-	$(am__remove_distdir)
-
-dist-xz: distdir
-	tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz
-	$(am__remove_distdir)
-
-dist-tarZ: distdir
-	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
-	$(am__remove_distdir)
-
-dist-shar: distdir
-	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
-	$(am__remove_distdir)
-
-dist-zip: distdir
-	-rm -f $(distdir).zip
-	zip -rq $(distdir).zip $(distdir)
-	$(am__remove_distdir)
-
-dist dist-all: distdir
-	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
-	$(am__remove_distdir)
-
-# This target untars the dist file and tries a VPATH configuration.  Then
-# it guarantees that the distribution is self-contained by making another
-# tarfile.
-distcheck: dist
-	case '$(DIST_ARCHIVES)' in \
-	*.tar.gz*) \
-	  GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\
-	*.tar.bz2*) \
-	  bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\
-	*.tar.lzma*) \
-	  unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\
-	*.tar.xz*) \
-	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
-	*.tar.Z*) \
-	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
-	*.shar.gz*) \
-	  GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\
-	*.zip*) \
-	  unzip $(distdir).zip ;;\
-	esac
-	chmod -R a-w $(distdir); chmod a+w $(distdir)
-	mkdir $(distdir)/_build
-	mkdir $(distdir)/_inst
-	chmod a-w $(distdir)
-	test -d $(distdir)/_build || exit 0; \
-	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
-	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
-	  && am__cwd=`pwd` \
-	  && $(am__cd) $(distdir)/_build \
-	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
-	    $(DISTCHECK_CONFIGURE_FLAGS) \
-	  && $(MAKE) $(AM_MAKEFLAGS) \
-	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
-	  && $(MAKE) $(AM_MAKEFLAGS) check \
-	  && $(MAKE) $(AM_MAKEFLAGS) install \
-	  && $(MAKE) $(AM_MAKEFLAGS) installcheck \
-	  && $(MAKE) $(AM_MAKEFLAGS) uninstall \
-	  && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
-	        distuninstallcheck \
-	  && chmod -R a-w "$$dc_install_base" \
-	  && ({ \
-	       (cd ../.. && umask 077 && mkdir "$$dc_destdir") \
-	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
-	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
-	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
-	            distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
-	      } || { rm -rf "$$dc_destdir"; exit 1; }) \
-	  && rm -rf "$$dc_destdir" \
-	  && $(MAKE) $(AM_MAKEFLAGS) dist \
-	  && rm -rf $(DIST_ARCHIVES) \
-	  && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
-	  && cd "$$am__cwd" \
-	  || exit 1
-	$(am__remove_distdir)
-	@(echo "$(distdir) archives ready for distribution: "; \
-	  list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
-	  sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
-distuninstallcheck:
-	@$(am__cd) '$(distuninstallcheck_dir)' \
-	&& test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
-	   || { echo "ERROR: files left after uninstall:" ; \
-	        if test -n "$(DESTDIR)"; then \
-	          echo "  (check DESTDIR support)"; \
-	        fi ; \
-	        $(distuninstallcheck_listfiles) ; \
-	        exit 1; } >&2
-distcleancheck: distclean
-	@if test '$(srcdir)' = . ; then \
-	  echo "ERROR: distcleancheck can only run from a VPATH build" ; \
-	  exit 1 ; \
-	fi
-	@test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
-	  || { echo "ERROR: files left in build directory after distclean:" ; \
-	       $(distcleancheck_listfiles) ; \
-	       exit 1; } >&2
-check-am: all-am
-check: check-recursive
-all-am: Makefile $(HEADERS) gtfold_config.h
-installdirs: installdirs-recursive
-installdirs-am:
-	for dir in "$(DESTDIR)$(includedir)"; do \
-	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-	done
-install: install-recursive
-install-exec: install-exec-recursive
-install-data: install-data-recursive
-uninstall: uninstall-recursive
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-recursive
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-	-test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
-clean: clean-recursive
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-recursive
-	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic distclean-hdr distclean-tags
-
-dvi: dvi-recursive
-
-dvi-am:
-
-html: html-recursive
-
-html-am:
-
-info: info-recursive
-
-info-am:
-
-install-data-am: install-includeHEADERS
-
-install-dvi: install-dvi-recursive
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-recursive
-
-install-html-am:
-
-install-info: install-info-recursive
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-recursive
-
-install-pdf-am:
-
-install-ps: install-ps-recursive
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-recursive
-	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
-	-rm -rf $(top_srcdir)/autom4te.cache
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-recursive
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-recursive
-
-pdf-am:
-
-ps: ps-recursive
-
-ps-am:
-
-uninstall-am: uninstall-includeHEADERS
-
-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
-	ctags-recursive install-am install-strip tags-recursive
-
-.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-	all all-am am--refresh check check-am clean clean-generic \
-	ctags ctags-recursive dist dist-all dist-bzip2 dist-gzip \
-	dist-lzma dist-shar dist-tarZ dist-xz dist-zip distcheck \
-	distclean distclean-generic distclean-hdr distclean-tags \
-	distcleancheck distdir distuninstallcheck dvi dvi-am html \
-	html-am info info-am install install-am install-data \
-	install-data-am install-dvi install-dvi-am install-exec \
-	install-exec-am install-html install-html-am \
-	install-includeHEADERS install-info install-info-am \
-	install-man install-pdf install-pdf-am install-ps \
-	install-ps-am install-strip installcheck installcheck-am \
-	installdirs installdirs-am maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am \
-	uninstall-includeHEADERS
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/gtfold-mfe/data/Andronescu/Makefile.in b/gtfold-mfe/data/Andronescu/Makefile.in
deleted file mode 100644
index d572ff3..0000000
--- a/gtfold-mfe/data/Andronescu/Makefile.in
+++ /dev/null
@@ -1,399 +0,0 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
-# @configure_input@
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-@SET_MAKE@
-
-VPATH = @srcdir@
-pkgdatadir = $(datadir)/@PACKAGE@
-pkgincludedir = $(includedir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
-pkglibexecdir = $(libexecdir)/@PACKAGE@
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = @build@
-host_triplet = @host@
-target_triplet = @target@
-subdir = data/Andronescu
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-am__vpath_adj = case $$p in \
-    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-    *) f=$$p;; \
-  esac;
-am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-am__install_max = 40
-am__nobase_strip_setup = \
-  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-am__nobase_strip = \
-  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-am__nobase_list = $(am__nobase_strip_setup); \
-  for p in $$list; do echo "$$p $$p"; done | \
-  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-    if (++n[$$2] == $(am__install_max)) \
-      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-    END { for (dir in files) print dir, files[dir] }'
-am__base_list = \
-  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
-DATA = $(gtfold_data_DATA)
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = @ACLOCAL@
-AMTAR = @AMTAR@
-AUTOCONF = @AUTOCONF@
-AUTOHEADER = @AUTOHEADER@
-AUTOMAKE = @AUTOMAKE@
-AWK = @AWK@
-CC = @CC@
-CCDEPMODE = @CCDEPMODE@
-CFLAGS = @CFLAGS@
-CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
-CXX = @CXX@
-CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
-CYGPATH_W = @CYGPATH_W@
-DEFS = @DEFS@
-DEPDIR = @DEPDIR@
-ECHO_C = @ECHO_C@
-ECHO_N = @ECHO_N@
-ECHO_T = @ECHO_T@
-EGREP = @EGREP@
-EXEEXT = @EXEEXT@
-GREP = @GREP@
-INSTALL = @INSTALL@
-INSTALL_DATA = @INSTALL_DATA@
-INSTALL_PROGRAM = @INSTALL_PROGRAM@
-INSTALL_SCRIPT = @INSTALL_SCRIPT@
-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
-LIBOBJS = @LIBOBJS@
-LIBS = @LIBS@
-LTLIBOBJS = @LTLIBOBJS@
-MAKEINFO = @MAKEINFO@
-MKDIR_P = @MKDIR_P@
-OBJEXT = @OBJEXT@
-OPENMP_CFLAGS = @OPENMP_CFLAGS@
-PACKAGE = @PACKAGE@
-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-PACKAGE_NAME = @PACKAGE_NAME@
-PACKAGE_STRING = @PACKAGE_STRING@
-PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
-PACKAGE_VERSION = @PACKAGE_VERSION@
-PATH_SEPARATOR = @PATH_SEPARATOR@
-SET_MAKE = @SET_MAKE@
-SHELL = @SHELL@
-STRIP = @STRIP@
-VERSION = @VERSION@
-abs_builddir = @abs_builddir@
-abs_srcdir = @abs_srcdir@
-abs_top_builddir = @abs_top_builddir@
-abs_top_srcdir = @abs_top_srcdir@
-ac_ct_CC = @ac_ct_CC@
-ac_ct_CXX = @ac_ct_CXX@
-am__include = @am__include@
-am__leading_dot = @am__leading_dot@
-am__quote = @am__quote@
-am__tar = @am__tar@
-am__untar = @am__untar@
-bindir = @bindir@
-build = @build@
-build_alias = @build_alias@
-build_cpu = @build_cpu@
-build_os = @build_os@
-build_vendor = @build_vendor@
-builddir = @builddir@
-datadir = @datadir@
-datarootdir = @datarootdir@
-docdir = @docdir@
-dvidir = @dvidir@
-exec_prefix = @exec_prefix@
-host = @host@
-host_alias = @host_alias@
-host_cpu = @host_cpu@
-host_os = @host_os@
-host_vendor = @host_vendor@
-htmldir = @htmldir@
-includedir = @includedir@
-infodir = @infodir@
-install_sh = @install_sh@
-libdir = @libdir@
-libexecdir = @libexecdir@
-localedir = @localedir@
-localstatedir = @localstatedir@
-mandir = @mandir@
-mkdir_p = @mkdir_p@
-oldincludedir = @oldincludedir@
-pdfdir = @pdfdir@
-prefix = @prefix@
-program_transform_name = @program_transform_name@
-psdir = @psdir@
-sbindir = @sbindir@
-sharedstatedir = @sharedstatedir@
-srcdir = @srcdir@
-sysconfdir = @sysconfdir@
-target = @target@
-target_alias = @target_alias@
-target_cpu = @target_cpu@
-target_os = @target_os@
-target_vendor = @target_vendor@
-top_build_prefix = @top_build_prefix@
-top_builddir = @top_builddir@
-top_srcdir = @top_srcdir@
-gtfold_datadir = $(datadir)/@PACKAGE@/Andronescu
-gtfold_data_DATA = \
-	stack.dat\
-	miscloop.dat\
-	dangle.dat\
-	loop.dat\
-	int11.dat\
-	int21.dat\
-	int22.dat\
-	tloop.dat\
-	triloop.dat\
-	tstackh.dat\
-	tstacki.dat
-
-EXTRA_DIST = $(gtfold_data_DATA)
-CLEANFILES = *~
-all: all-am
-
-.SUFFIXES:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Andronescu/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu data/Andronescu/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-install-gtfold_dataDATA: $(gtfold_data_DATA)
-	@$(NORMAL_INSTALL)
-	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	for p in $$list; do \
-	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-	  echo "$$d$$p"; \
-	done | $(am__base_list) | \
-	while read files; do \
-	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
-	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
-	done
-
-uninstall-gtfold_dataDATA:
-	@$(NORMAL_UNINSTALL)
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-	test -n "$$files" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
-tags: TAGS
-TAGS:
-
-ctags: CTAGS
-CTAGS:
-
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-am
-all-am: Makefile $(DATA)
-installdirs:
-	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
-	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-	done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-am
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am: install-gtfold_dataDATA
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-gtfold_dataDATA
-
-.MAKE: install-am install-strip
-
-.PHONY: all all-am check check-am clean clean-generic distclean \
-	distclean-generic distdir dvi dvi-am html html-am info info-am \
-	install install-am install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am \
-	install-gtfold_dataDATA install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am uninstall uninstall-am \
-	uninstall-gtfold_dataDATA
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/gtfold-mfe/data/Makefile.in b/gtfold-mfe/data/Makefile.in
deleted file mode 100644
index 0818588..0000000
--- a/gtfold-mfe/data/Makefile.in
+++ /dev/null
@@ -1,536 +0,0 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
-# @configure_input@
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-@SET_MAKE@
-VPATH = @srcdir@
-pkgdatadir = $(datadir)/@PACKAGE@
-pkgincludedir = $(includedir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
-pkglibexecdir = $(libexecdir)/@PACKAGE@
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = @build@
-host_triplet = @host@
-target_triplet = @target@
-subdir = data
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
-	html-recursive info-recursive install-data-recursive \
-	install-dvi-recursive install-exec-recursive \
-	install-html-recursive install-info-recursive \
-	install-pdf-recursive install-ps-recursive install-recursive \
-	installcheck-recursive installdirs-recursive pdf-recursive \
-	ps-recursive uninstall-recursive
-RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
-  distclean-recursive maintainer-clean-recursive
-AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-	$(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
-	distdir
-ETAGS = etags
-CTAGS = ctags
-DIST_SUBDIRS = $(SUBDIRS)
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-am__relativize = \
-  dir0=`pwd`; \
-  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
-  sed_rest='s,^[^/]*/*,,'; \
-  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
-  sed_butlast='s,/*[^/]*$$,,'; \
-  while test -n "$$dir1"; do \
-    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
-    if test "$$first" != "."; then \
-      if test "$$first" = ".."; then \
-        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
-        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
-      else \
-        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
-        if test "$$first2" = "$$first"; then \
-          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
-        else \
-          dir2="../$$dir2"; \
-        fi; \
-        dir0="$$dir0"/"$$first"; \
-      fi; \
-    fi; \
-    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
-  done; \
-  reldir="$$dir2"
-ACLOCAL = @ACLOCAL@
-AMTAR = @AMTAR@
-AUTOCONF = @AUTOCONF@
-AUTOHEADER = @AUTOHEADER@
-AUTOMAKE = @AUTOMAKE@
-AWK = @AWK@
-CC = @CC@
-CCDEPMODE = @CCDEPMODE@
-CFLAGS = @CFLAGS@
-CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
-CXX = @CXX@
-CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
-CYGPATH_W = @CYGPATH_W@
-DEFS = @DEFS@
-DEPDIR = @DEPDIR@
-ECHO_C = @ECHO_C@
-ECHO_N = @ECHO_N@
-ECHO_T = @ECHO_T@
-EGREP = @EGREP@
-EXEEXT = @EXEEXT@
-GREP = @GREP@
-INSTALL = @INSTALL@
-INSTALL_DATA = @INSTALL_DATA@
-INSTALL_PROGRAM = @INSTALL_PROGRAM@
-INSTALL_SCRIPT = @INSTALL_SCRIPT@
-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
-LIBOBJS = @LIBOBJS@
-LIBS = @LIBS@
-LTLIBOBJS = @LTLIBOBJS@
-MAKEINFO = @MAKEINFO@
-MKDIR_P = @MKDIR_P@
-OBJEXT = @OBJEXT@
-OPENMP_CFLAGS = @OPENMP_CFLAGS@
-PACKAGE = @PACKAGE@
-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-PACKAGE_NAME = @PACKAGE_NAME@
-PACKAGE_STRING = @PACKAGE_STRING@
-PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
-PACKAGE_VERSION = @PACKAGE_VERSION@
-PATH_SEPARATOR = @PATH_SEPARATOR@
-SET_MAKE = @SET_MAKE@
-SHELL = @SHELL@
-STRIP = @STRIP@
-VERSION = @VERSION@
-abs_builddir = @abs_builddir@
-abs_srcdir = @abs_srcdir@
-abs_top_builddir = @abs_top_builddir@
-abs_top_srcdir = @abs_top_srcdir@
-ac_ct_CC = @ac_ct_CC@
-ac_ct_CXX = @ac_ct_CXX@
-am__include = @am__include@
-am__leading_dot = @am__leading_dot@
-am__quote = @am__quote@
-am__tar = @am__tar@
-am__untar = @am__untar@
-bindir = @bindir@
-build = @build@
-build_alias = @build_alias@
-build_cpu = @build_cpu@
-build_os = @build_os@
-build_vendor = @build_vendor@
-builddir = @builddir@
-datadir = @datadir@
-datarootdir = @datarootdir@
-docdir = @docdir@
-dvidir = @dvidir@
-exec_prefix = @exec_prefix@
-host = @host@
-host_alias = @host_alias@
-host_cpu = @host_cpu@
-host_os = @host_os@
-host_vendor = @host_vendor@
-htmldir = @htmldir@
-includedir = @includedir@
-infodir = @infodir@
-install_sh = @install_sh@
-libdir = @libdir@
-libexecdir = @libexecdir@
-localedir = @localedir@
-localstatedir = @localstatedir@
-mandir = @mandir@
-mkdir_p = @mkdir_p@
-oldincludedir = @oldincludedir@
-pdfdir = @pdfdir@
-prefix = @prefix@
-program_transform_name = @program_transform_name@
-psdir = @psdir@
-sbindir = @sbindir@
-sharedstatedir = @sharedstatedir@
-srcdir = @srcdir@
-sysconfdir = @sysconfdir@
-target = @target@
-target_alias = @target_alias@
-target_cpu = @target_cpu@
-target_os = @target_os@
-target_vendor = @target_vendor@
-top_build_prefix = @top_build_prefix@
-top_builddir = @top_builddir@
-top_srcdir = @top_srcdir@
-SUBDIRS = Turner04 Turner99 Andronescu
-all: all-recursive
-
-.SUFFIXES:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu data/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-
-# This directory's subdirectories are mostly independent; you can cd
-# into them and run `make' without going through this Makefile.
-# To change the values of `make' variables: instead of editing Makefiles,
-# (1) if the variable is set in `config.status', edit `config.status'
-#     (which will cause the Makefiles to be regenerated when you run `make');
-# (2) otherwise, pass the desired values on the `make' command line.
-$(RECURSIVE_TARGETS):
-	@failcom='exit 1'; \
-	for f in x $$MAKEFLAGS; do \
-	  case $$f in \
-	    *=* | --[!k]*);; \
-	    *k*) failcom='fail=yes';; \
-	  esac; \
-	done; \
-	dot_seen=no; \
-	target=`echo $@ | sed s/-recursive//`; \
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  echo "Making $$target in $$subdir"; \
-	  if test "$$subdir" = "."; then \
-	    dot_seen=yes; \
-	    local_target="$$target-am"; \
-	  else \
-	    local_target="$$target"; \
-	  fi; \
-	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-	  || eval $$failcom; \
-	done; \
-	if test "$$dot_seen" = "no"; then \
-	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
-	fi; test -z "$$fail"
-
-$(RECURSIVE_CLEAN_TARGETS):
-	@failcom='exit 1'; \
-	for f in x $$MAKEFLAGS; do \
-	  case $$f in \
-	    *=* | --[!k]*);; \
-	    *k*) failcom='fail=yes';; \
-	  esac; \
-	done; \
-	dot_seen=no; \
-	case "$@" in \
-	  distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
-	  *) list='$(SUBDIRS)' ;; \
-	esac; \
-	rev=''; for subdir in $$list; do \
-	  if test "$$subdir" = "."; then :; else \
-	    rev="$$subdir $$rev"; \
-	  fi; \
-	done; \
-	rev="$$rev ."; \
-	target=`echo $@ | sed s/-recursive//`; \
-	for subdir in $$rev; do \
-	  echo "Making $$target in $$subdir"; \
-	  if test "$$subdir" = "."; then \
-	    local_target="$$target-am"; \
-	  else \
-	    local_target="$$target"; \
-	  fi; \
-	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-	  || eval $$failcom; \
-	done && test -z "$$fail"
-tags-recursive:
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-	done
-ctags-recursive:
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
-	done
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	mkid -fID $$unique
-tags: TAGS
-
-TAGS: tags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	set x; \
-	here=`pwd`; \
-	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
-	  include_option=--etags-include; \
-	  empty_fix=.; \
-	else \
-	  include_option=--include; \
-	  empty_fix=; \
-	fi; \
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    test ! -f $$subdir/TAGS || \
-	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
-	  fi; \
-	done; \
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	shift; \
-	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-	  test -n "$$unique" || unique=$$empty_fix; \
-	  if test $$# -gt 0; then \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      "$$@" $$unique; \
-	  else \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      $$unique; \
-	  fi; \
-	fi
-ctags: CTAGS
-CTAGS: ctags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	test -z "$(CTAGS_ARGS)$$unique" \
-	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$unique
-
-GTAGS:
-	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && $(am__cd) $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) "$$here"
-
-distclean-tags:
-	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    test -d "$(distdir)/$$subdir" \
-	    || $(MKDIR_P) "$(distdir)/$$subdir" \
-	    || exit 1; \
-	  fi; \
-	done
-	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
-	    $(am__relativize); \
-	    new_distdir=$$reldir; \
-	    dir1=$$subdir; dir2="$(top_distdir)"; \
-	    $(am__relativize); \
-	    new_top_distdir=$$reldir; \
-	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
-	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
-	    ($(am__cd) $$subdir && \
-	      $(MAKE) $(AM_MAKEFLAGS) \
-	        top_distdir="$$new_top_distdir" \
-	        distdir="$$new_distdir" \
-		am__remove_distdir=: \
-		am__skip_length_check=: \
-		am__skip_mode_fix=: \
-	        distdir) \
-	      || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-recursive
-all-am: Makefile
-installdirs: installdirs-recursive
-installdirs-am:
-install: install-recursive
-install-exec: install-exec-recursive
-install-data: install-data-recursive
-uninstall: uninstall-recursive
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-recursive
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-recursive
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-recursive
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic distclean-tags
-
-dvi: dvi-recursive
-
-dvi-am:
-
-html: html-recursive
-
-html-am:
-
-info: info-recursive
-
-info-am:
-
-install-data-am:
-
-install-dvi: install-dvi-recursive
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-recursive
-
-install-html-am:
-
-install-info: install-info-recursive
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-recursive
-
-install-pdf-am:
-
-install-ps: install-ps-recursive
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-recursive
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-recursive
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-recursive
-
-pdf-am:
-
-ps: ps-recursive
-
-ps-am:
-
-uninstall-am:
-
-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
-	install-am install-strip tags-recursive
-
-.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-	all all-am check check-am clean clean-generic ctags \
-	ctags-recursive distclean distclean-generic distclean-tags \
-	distdir dvi dvi-am html html-am info info-am install \
-	install-am install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am install-html \
-	install-html-am install-info install-info-am install-man \
-	install-pdf install-pdf-am install-ps install-ps-am \
-	install-strip installcheck installcheck-am installdirs \
-	installdirs-am maintainer-clean maintainer-clean-generic \
-	mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \
-	tags-recursive uninstall uninstall-am
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/gtfold-mfe/data/Turner04/Makefile.in b/gtfold-mfe/data/Turner04/Makefile.in
deleted file mode 100644
index 7d91d24..0000000
--- a/gtfold-mfe/data/Turner04/Makefile.in
+++ /dev/null
@@ -1,405 +0,0 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
-# @configure_input@
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-@SET_MAKE@
-
-VPATH = @srcdir@
-pkgdatadir = $(datadir)/@PACKAGE@
-pkgincludedir = $(includedir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
-pkglibexecdir = $(libexecdir)/@PACKAGE@
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = @build@
-host_triplet = @host@
-target_triplet = @target@
-subdir = data/Turner04
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-am__vpath_adj = case $$p in \
-    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-    *) f=$$p;; \
-  esac;
-am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-am__install_max = 40
-am__nobase_strip_setup = \
-  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-am__nobase_strip = \
-  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-am__nobase_list = $(am__nobase_strip_setup); \
-  for p in $$list; do echo "$$p $$p"; done | \
-  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-    if (++n[$$2] == $(am__install_max)) \
-      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-    END { for (dir in files) print dir, files[dir] }'
-am__base_list = \
-  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
-DATA = $(gtfold_data_DATA)
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = @ACLOCAL@
-AMTAR = @AMTAR@
-AUTOCONF = @AUTOCONF@
-AUTOHEADER = @AUTOHEADER@
-AUTOMAKE = @AUTOMAKE@
-AWK = @AWK@
-CC = @CC@
-CCDEPMODE = @CCDEPMODE@
-CFLAGS = @CFLAGS@
-CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
-CXX = @CXX@
-CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
-CYGPATH_W = @CYGPATH_W@
-DEFS = @DEFS@
-DEPDIR = @DEPDIR@
-ECHO_C = @ECHO_C@
-ECHO_N = @ECHO_N@
-ECHO_T = @ECHO_T@
-EGREP = @EGREP@
-EXEEXT = @EXEEXT@
-GREP = @GREP@
-INSTALL = @INSTALL@
-INSTALL_DATA = @INSTALL_DATA@
-INSTALL_PROGRAM = @INSTALL_PROGRAM@
-INSTALL_SCRIPT = @INSTALL_SCRIPT@
-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
-LIBOBJS = @LIBOBJS@
-LIBS = @LIBS@
-LTLIBOBJS = @LTLIBOBJS@
-MAKEINFO = @MAKEINFO@
-MKDIR_P = @MKDIR_P@
-OBJEXT = @OBJEXT@
-OPENMP_CFLAGS = @OPENMP_CFLAGS@
-PACKAGE = @PACKAGE@
-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-PACKAGE_NAME = @PACKAGE_NAME@
-PACKAGE_STRING = @PACKAGE_STRING@
-PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
-PACKAGE_VERSION = @PACKAGE_VERSION@
-PATH_SEPARATOR = @PATH_SEPARATOR@
-SET_MAKE = @SET_MAKE@
-SHELL = @SHELL@
-STRIP = @STRIP@
-VERSION = @VERSION@
-abs_builddir = @abs_builddir@
-abs_srcdir = @abs_srcdir@
-abs_top_builddir = @abs_top_builddir@
-abs_top_srcdir = @abs_top_srcdir@
-ac_ct_CC = @ac_ct_CC@
-ac_ct_CXX = @ac_ct_CXX@
-am__include = @am__include@
-am__leading_dot = @am__leading_dot@
-am__quote = @am__quote@
-am__tar = @am__tar@
-am__untar = @am__untar@
-bindir = @bindir@
-build = @build@
-build_alias = @build_alias@
-build_cpu = @build_cpu@
-build_os = @build_os@
-build_vendor = @build_vendor@
-builddir = @builddir@
-datadir = @datadir@
-datarootdir = @datarootdir@
-docdir = @docdir@
-dvidir = @dvidir@
-exec_prefix = @exec_prefix@
-host = @host@
-host_alias = @host_alias@
-host_cpu = @host_cpu@
-host_os = @host_os@
-host_vendor = @host_vendor@
-htmldir = @htmldir@
-includedir = @includedir@
-infodir = @infodir@
-install_sh = @install_sh@
-libdir = @libdir@
-libexecdir = @libexecdir@
-localedir = @localedir@
-localstatedir = @localstatedir@
-mandir = @mandir@
-mkdir_p = @mkdir_p@
-oldincludedir = @oldincludedir@
-pdfdir = @pdfdir@
-prefix = @prefix@
-program_transform_name = @program_transform_name@
-psdir = @psdir@
-sbindir = @sbindir@
-sharedstatedir = @sharedstatedir@
-srcdir = @srcdir@
-sysconfdir = @sysconfdir@
-target = @target@
-target_alias = @target_alias@
-target_cpu = @target_cpu@
-target_os = @target_os@
-target_vendor = @target_vendor@
-top_build_prefix = @top_build_prefix@
-top_builddir = @top_builddir@
-top_srcdir = @top_srcdir@
-gtfold_datadir = $(datadir)/@PACKAGE@/Turner04
-gtfold_data_DATA = \
-	stack.dat\
-	miscloop.dat\
-	dangle.dat\
-	loop.dat\
-	coaxial.dat\
-	coaxstack.dat\
-	hexaloop.dat\
-	int11.dat\
-	int21.dat\
-	int22.dat\
-	tloop.dat\
-	triloop.dat\
-	tstack.dat\
-	tstackcoax.dat\
-	tstackh.dat\
-	tstacki.dat\
-	tstackm.dat
-
-EXTRA_DIST = $(gtfold_data_DATA)
-CLEANFILES = *~
-all: all-am
-
-.SUFFIXES:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Turner04/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu data/Turner04/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-install-gtfold_dataDATA: $(gtfold_data_DATA)
-	@$(NORMAL_INSTALL)
-	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	for p in $$list; do \
-	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-	  echo "$$d$$p"; \
-	done | $(am__base_list) | \
-	while read files; do \
-	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
-	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
-	done
-
-uninstall-gtfold_dataDATA:
-	@$(NORMAL_UNINSTALL)
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-	test -n "$$files" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
-tags: TAGS
-TAGS:
-
-ctags: CTAGS
-CTAGS:
-
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-am
-all-am: Makefile $(DATA)
-installdirs:
-	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
-	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-	done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-am
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am: install-gtfold_dataDATA
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-gtfold_dataDATA
-
-.MAKE: install-am install-strip
-
-.PHONY: all all-am check check-am clean clean-generic distclean \
-	distclean-generic distdir dvi dvi-am html html-am info info-am \
-	install install-am install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am \
-	install-gtfold_dataDATA install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am uninstall uninstall-am \
-	uninstall-gtfold_dataDATA
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in
deleted file mode 100644
index bf80b77..0000000
--- a/gtfold-mfe/data/Turner99/Makefile.in
+++ /dev/null
@@ -1,407 +0,0 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
-# @configure_input@
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-@SET_MAKE@
-
-VPATH = @srcdir@
-pkgdatadir = $(datadir)/@PACKAGE@
-pkgincludedir = $(includedir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
-pkglibexecdir = $(libexecdir)/@PACKAGE@
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = @build@
-host_triplet = @host@
-target_triplet = @target@
-subdir = data/Turner99
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-am__vpath_adj = case $$p in \
-    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-    *) f=$$p;; \
-  esac;
-am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-am__install_max = 40
-am__nobase_strip_setup = \
-  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-am__nobase_strip = \
-  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-am__nobase_list = $(am__nobase_strip_setup); \
-  for p in $$list; do echo "$$p $$p"; done | \
-  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-    if (++n[$$2] == $(am__install_max)) \
-      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-    END { for (dir in files) print dir, files[dir] }'
-am__base_list = \
-  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
-DATA = $(gtfold_data_DATA)
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = @ACLOCAL@
-AMTAR = @AMTAR@
-AUTOCONF = @AUTOCONF@
-AUTOHEADER = @AUTOHEADER@
-AUTOMAKE = @AUTOMAKE@
-AWK = @AWK@
-CC = @CC@
-CCDEPMODE = @CCDEPMODE@
-CFLAGS = @CFLAGS@
-CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
-CXX = @CXX@
-CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
-CYGPATH_W = @CYGPATH_W@
-DEFS = @DEFS@
-DEPDIR = @DEPDIR@
-ECHO_C = @ECHO_C@
-ECHO_N = @ECHO_N@
-ECHO_T = @ECHO_T@
-EGREP = @EGREP@
-EXEEXT = @EXEEXT@
-GREP = @GREP@
-INSTALL = @INSTALL@
-INSTALL_DATA = @INSTALL_DATA@
-INSTALL_PROGRAM = @INSTALL_PROGRAM@
-INSTALL_SCRIPT = @INSTALL_SCRIPT@
-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
-LIBOBJS = @LIBOBJS@
-LIBS = @LIBS@
-LTLIBOBJS = @LTLIBOBJS@
-MAKEINFO = @MAKEINFO@
-MKDIR_P = @MKDIR_P@
-OBJEXT = @OBJEXT@
-OPENMP_CFLAGS = @OPENMP_CFLAGS@
-PACKAGE = @PACKAGE@
-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-PACKAGE_NAME = @PACKAGE_NAME@
-PACKAGE_STRING = @PACKAGE_STRING@
-PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
-PACKAGE_VERSION = @PACKAGE_VERSION@
-PATH_SEPARATOR = @PATH_SEPARATOR@
-SET_MAKE = @SET_MAKE@
-SHELL = @SHELL@
-STRIP = @STRIP@
-VERSION = @VERSION@
-abs_builddir = @abs_builddir@
-abs_srcdir = @abs_srcdir@
-abs_top_builddir = @abs_top_builddir@
-abs_top_srcdir = @abs_top_srcdir@
-ac_ct_CC = @ac_ct_CC@
-ac_ct_CXX = @ac_ct_CXX@
-am__include = @am__include@
-am__leading_dot = @am__leading_dot@
-am__quote = @am__quote@
-am__tar = @am__tar@
-am__untar = @am__untar@
-bindir = @bindir@
-build = @build@
-build_alias = @build_alias@
-build_cpu = @build_cpu@
-build_os = @build_os@
-build_vendor = @build_vendor@
-builddir = @builddir@
-datadir = @datadir@
-datarootdir = @datarootdir@
-docdir = @docdir@
-dvidir = @dvidir@
-exec_prefix = @exec_prefix@
-host = @host@
-host_alias = @host_alias@
-host_cpu = @host_cpu@
-host_os = @host_os@
-host_vendor = @host_vendor@
-htmldir = @htmldir@
-includedir = @includedir@
-infodir = @infodir@
-install_sh = @install_sh@
-libdir = @libdir@
-libexecdir = @libexecdir@
-localedir = @localedir@
-localstatedir = @localstatedir@
-mandir = @mandir@
-mkdir_p = @mkdir_p@
-oldincludedir = @oldincludedir@
-pdfdir = @pdfdir@
-prefix = @prefix@
-program_transform_name = @program_transform_name@
-psdir = @psdir@
-sbindir = @sbindir@
-sharedstatedir = @sharedstatedir@
-srcdir = @srcdir@
-sysconfdir = @sysconfdir@
-target = @target@
-target_alias = @target_alias@
-target_cpu = @target_cpu@
-target_os = @target_os@
-target_vendor = @target_vendor@
-top_build_prefix = @top_build_prefix@
-top_builddir = @top_builddir@
-top_srcdir = @top_srcdir@
-gtfold_datadir = $(datadir)/@PACKAGE@/Turner99
-gtfold_data_DATA = \
-	stack.dat\
-	miscloop.dat\
-	dangle.dat\
-	loop.dat\
-	asint1x2.dat\
-	coaxial.dat\
-	coaxstack.dat\
-	int11.dat\
-	int21.dat\
-	int22.dat\
-	sint2.dat\
-	sint4.dat\
-	tloop.dat\
-	triloop.dat\
-	tstack.dat\
-	tstackcoax.dat\
-	tstackh.dat\
-	tstacki.dat\
-	tstackm.dat
-
-EXTRA_DIST = $(gtfold_data_DATA)
-CLEANFILES = *~
-all: all-am
-
-.SUFFIXES:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Turner99/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu data/Turner99/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-install-gtfold_dataDATA: $(gtfold_data_DATA)
-	@$(NORMAL_INSTALL)
-	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	for p in $$list; do \
-	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-	  echo "$$d$$p"; \
-	done | $(am__base_list) | \
-	while read files; do \
-	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
-	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
-	done
-
-uninstall-gtfold_dataDATA:
-	@$(NORMAL_UNINSTALL)
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-	test -n "$$files" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
-tags: TAGS
-TAGS:
-
-ctags: CTAGS
-CTAGS:
-
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-am
-all-am: Makefile $(DATA)
-installdirs:
-	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
-	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-	done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-am
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am: install-gtfold_dataDATA
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-gtfold_dataDATA
-
-.MAKE: install-am install-strip
-
-.PHONY: all all-am check check-am clean clean-generic distclean \
-	distclean-generic distdir dvi dvi-am html html-am info info-am \
-	install install-am install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am \
-	install-gtfold_dataDATA install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am uninstall uninstall-am \
-	uninstall-gtfold_dataDATA
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in
deleted file mode 100644
index e916841..0000000
--- a/gtfold-mfe/include/Makefile.in
+++ /dev/null
@@ -1,388 +0,0 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
-# @configure_input@
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-@SET_MAKE@
-
-VPATH = @srcdir@
-pkgdatadir = $(datadir)/@PACKAGE@
-pkgincludedir = $(includedir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
-pkglibexecdir = $(libexecdir)/@PACKAGE@
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = @build@
-host_triplet = @host@
-target_triplet = @target@
-subdir = include
-DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-	$(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-HEADERS = $(noinst_HEADERS)
-ETAGS = etags
-CTAGS = ctags
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = @ACLOCAL@
-AMTAR = @AMTAR@
-AUTOCONF = @AUTOCONF@
-AUTOHEADER = @AUTOHEADER@
-AUTOMAKE = @AUTOMAKE@
-AWK = @AWK@
-CC = @CC@
-CCDEPMODE = @CCDEPMODE@
-CFLAGS = @CFLAGS@
-CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
-CXX = @CXX@
-CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
-CYGPATH_W = @CYGPATH_W@
-DEFS = @DEFS@
-DEPDIR = @DEPDIR@
-ECHO_C = @ECHO_C@
-ECHO_N = @ECHO_N@
-ECHO_T = @ECHO_T@
-EGREP = @EGREP@
-EXEEXT = @EXEEXT@
-GREP = @GREP@
-INSTALL = @INSTALL@
-INSTALL_DATA = @INSTALL_DATA@
-INSTALL_PROGRAM = @INSTALL_PROGRAM@
-INSTALL_SCRIPT = @INSTALL_SCRIPT@
-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
-LIBOBJS = @LIBOBJS@
-LIBS = @LIBS@
-LTLIBOBJS = @LTLIBOBJS@
-MAKEINFO = @MAKEINFO@
-MKDIR_P = @MKDIR_P@
-OBJEXT = @OBJEXT@
-OPENMP_CFLAGS = @OPENMP_CFLAGS@
-PACKAGE = @PACKAGE@
-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-PACKAGE_NAME = @PACKAGE_NAME@
-PACKAGE_STRING = @PACKAGE_STRING@
-PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
-PACKAGE_VERSION = @PACKAGE_VERSION@
-PATH_SEPARATOR = @PATH_SEPARATOR@
-SET_MAKE = @SET_MAKE@
-SHELL = @SHELL@
-STRIP = @STRIP@
-VERSION = @VERSION@
-abs_builddir = @abs_builddir@
-abs_srcdir = @abs_srcdir@
-abs_top_builddir = @abs_top_builddir@
-abs_top_srcdir = @abs_top_srcdir@
-ac_ct_CC = @ac_ct_CC@
-ac_ct_CXX = @ac_ct_CXX@
-am__include = @am__include@
-am__leading_dot = @am__leading_dot@
-am__quote = @am__quote@
-am__tar = @am__tar@
-am__untar = @am__untar@
-bindir = @bindir@
-build = @build@
-build_alias = @build_alias@
-build_cpu = @build_cpu@
-build_os = @build_os@
-build_vendor = @build_vendor@
-builddir = @builddir@
-datadir = @datadir@
-datarootdir = @datarootdir@
-docdir = @docdir@
-dvidir = @dvidir@
-exec_prefix = @exec_prefix@
-host = @host@
-host_alias = @host_alias@
-host_cpu = @host_cpu@
-host_os = @host_os@
-host_vendor = @host_vendor@
-htmldir = @htmldir@
-includedir = @includedir@
-infodir = @infodir@
-install_sh = @install_sh@
-libdir = @libdir@
-libexecdir = @libexecdir@
-localedir = @localedir@
-localstatedir = @localstatedir@
-mandir = @mandir@
-mkdir_p = @mkdir_p@
-oldincludedir = @oldincludedir@
-pdfdir = @pdfdir@
-prefix = @prefix@
-program_transform_name = @program_transform_name@
-psdir = @psdir@
-sbindir = @sbindir@
-sharedstatedir = @sharedstatedir@
-srcdir = @srcdir@
-sysconfdir = @sysconfdir@
-target = @target@
-target_alias = @target_alias@
-target_cpu = @target_cpu@
-target_os = @target_os@
-target_vendor = @target_vendor@
-top_build_prefix = @top_build_prefix@
-top_builddir = @top_builddir@
-top_srcdir = @top_srcdir@
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main-c.h main.h traceback.h
-CLEANFILES = *~
-all: all-am
-
-.SUFFIXES:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu include/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu include/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	mkid -fID $$unique
-tags: TAGS
-
-TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	set x; \
-	here=`pwd`; \
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	shift; \
-	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-	  test -n "$$unique" || unique=$$empty_fix; \
-	  if test $$# -gt 0; then \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      "$$@" $$unique; \
-	  else \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      $$unique; \
-	  fi; \
-	fi
-ctags: CTAGS
-CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	test -z "$(CTAGS_ARGS)$$unique" \
-	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$unique
-
-GTAGS:
-	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && $(am__cd) $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) "$$here"
-
-distclean-tags:
-	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-am
-all-am: Makefile $(HEADERS)
-installdirs:
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-am
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic distclean-tags
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am:
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am:
-
-.MAKE: install-am install-strip
-
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
-	ctags distclean distclean-generic distclean-tags distdir dvi \
-	dvi-am html html-am info info-am install install-am \
-	install-data install-data-am install-dvi install-dvi-am \
-	install-exec install-exec-am install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am tags uninstall uninstall-am
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in
deleted file mode 100644
index 48c25e0..0000000
--- a/gtfold-mfe/src/Makefile.in
+++ /dev/null
@@ -1,506 +0,0 @@
-# Makefile.in generated by automake 1.11 from Makefile.am.
-# @configure_input@
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-@SET_MAKE@
-
-VPATH = @srcdir@
-pkgdatadir = $(datadir)/@PACKAGE@
-pkgincludedir = $(includedir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
-pkglibexecdir = $(libexecdir)/@PACKAGE@
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = @build@
-host_triplet = @host@
-target_triplet = @target@
-bin_PROGRAMS = gtfold$(EXEEXT)
-subdir = src
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-am__installdirs = "$(DESTDIR)$(bindir)"
-PROGRAMS = $(bin_PROGRAMS)
-am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) \
-	algorithms.$(OBJEXT) traceback.$(OBJEXT)
-gtfold_OBJECTS = $(am_gtfold_OBJECTS)
-gtfold_DEPENDENCIES =
-gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
-	$(LDFLAGS) -o $@
-DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
-depcomp = $(SHELL) $(top_srcdir)/depcomp
-am__depfiles_maybe = depfiles
-am__mv = mv -f
-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-CCLD = $(CC)
-LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
-	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
-CXXLD = $(CXX)
-CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-	-o $@
-SOURCES = $(gtfold_SOURCES)
-DIST_SOURCES = $(gtfold_SOURCES)
-ETAGS = etags
-CTAGS = ctags
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = @ACLOCAL@
-AMTAR = @AMTAR@
-AUTOCONF = @AUTOCONF@
-AUTOHEADER = @AUTOHEADER@
-AUTOMAKE = @AUTOMAKE@
-AWK = @AWK@
-CC = @CC@
-CCDEPMODE = @CCDEPMODE@
-CFLAGS = @CFLAGS@
-CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
-CXX = @CXX@
-CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
-CYGPATH_W = @CYGPATH_W@
-DEFS = @DEFS@
-DEPDIR = @DEPDIR@
-ECHO_C = @ECHO_C@
-ECHO_N = @ECHO_N@
-ECHO_T = @ECHO_T@
-EGREP = @EGREP@
-EXEEXT = @EXEEXT@
-GREP = @GREP@
-INSTALL = @INSTALL@
-INSTALL_DATA = @INSTALL_DATA@
-INSTALL_PROGRAM = @INSTALL_PROGRAM@
-INSTALL_SCRIPT = @INSTALL_SCRIPT@
-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
-LIBOBJS = @LIBOBJS@
-LIBS = @LIBS@
-LTLIBOBJS = @LTLIBOBJS@
-MAKEINFO = @MAKEINFO@
-MKDIR_P = @MKDIR_P@
-OBJEXT = @OBJEXT@
-OPENMP_CFLAGS = @OPENMP_CFLAGS@
-PACKAGE = @PACKAGE@
-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-PACKAGE_NAME = @PACKAGE_NAME@
-PACKAGE_STRING = @PACKAGE_STRING@
-PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
-PACKAGE_VERSION = @PACKAGE_VERSION@
-PATH_SEPARATOR = @PATH_SEPARATOR@
-SET_MAKE = @SET_MAKE@
-SHELL = @SHELL@
-STRIP = @STRIP@
-VERSION = @VERSION@
-abs_builddir = @abs_builddir@
-abs_srcdir = @abs_srcdir@
-abs_top_builddir = @abs_top_builddir@
-abs_top_srcdir = @abs_top_srcdir@
-ac_ct_CC = @ac_ct_CC@
-ac_ct_CXX = @ac_ct_CXX@
-am__include = @am__include@
-am__leading_dot = @am__leading_dot@
-am__quote = @am__quote@
-am__tar = @am__tar@
-am__untar = @am__untar@
-bindir = @bindir@
-build = @build@
-build_alias = @build_alias@
-build_cpu = @build_cpu@
-build_os = @build_os@
-build_vendor = @build_vendor@
-builddir = @builddir@
-datadir = @datadir@
-datarootdir = @datarootdir@
-docdir = @docdir@
-dvidir = @dvidir@
-exec_prefix = @exec_prefix@
-host = @host@
-host_alias = @host_alias@
-host_cpu = @host_cpu@
-host_os = @host_os@
-host_vendor = @host_vendor@
-htmldir = @htmldir@
-includedir = @includedir@
-infodir = @infodir@
-install_sh = @install_sh@
-libdir = @libdir@
-libexecdir = @libexecdir@
-localedir = @localedir@
-localstatedir = @localstatedir@
-mandir = @mandir@
-mkdir_p = @mkdir_p@
-oldincludedir = @oldincludedir@
-pdfdir = @pdfdir@
-prefix = @prefix@
-program_transform_name = @program_transform_name@
-psdir = @psdir@
-sbindir = @sbindir@
-sharedstatedir = @sharedstatedir@
-srcdir = @srcdir@
-sysconfdir = @sysconfdir@
-target = @target@
-target_alias = @target_alias@
-target_cpu = @target_cpu@
-target_os = @target_os@
-target_vendor = @target_vendor@
-top_build_prefix = @top_build_prefix@
-top_builddir = @top_builddir@
-top_srcdir = @top_srcdir@
-INCLUDES = -I$(top_srcdir) -I$(top_srcdir)/include
-AM_CFLAGS = $(OPENMP_CFLAGS) -DDATADIR='$(datadir)/@PACKAGE@'
-AM_CXXFLAGS = -DDATADIR='$(datadir)/@PACKAGE@'
-gtfold_SOURCES = \
-	main.cc\
-	loader.cc\
-	algorithms.c\
-	traceback.c
-
-gtfold_LDFLAGS = 
-gtfold_LDADD = -lm
-CLEANFILES = *~ *.o
-all: all-am
-
-.SUFFIXES:
-.SUFFIXES: .c .cc .o .obj
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu src/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-install-binPROGRAMS: $(bin_PROGRAMS)
-	@$(NORMAL_INSTALL)
-	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
-	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-	for p in $$list; do echo "$$p $$p"; done | \
-	sed 's/$(EXEEXT)$$//' | \
-	while read p p1; do if test -f $$p; \
-	  then echo "$$p"; echo "$$p"; else :; fi; \
-	done | \
-	sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
-	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
-	sed 'N;N;N;s,\n, ,g' | \
-	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
-	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
-	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
-	    else { print "f", $$3 "/" $$4, $$1; } } \
-	  END { for (d in files) print "f", d, files[d] }' | \
-	while read type dir files; do \
-	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
-	    test -z "$$files" || { \
-	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
-	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
-	    } \
-	; done
-
-uninstall-binPROGRAMS:
-	@$(NORMAL_UNINSTALL)
-	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-	files=`for p in $$list; do echo "$$p"; done | \
-	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
-	      -e 's/$$/$(EXEEXT)/' `; \
-	test -n "$$list" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(bindir)" && rm -f $$files
-
-clean-binPROGRAMS:
-	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
-gtfold$(EXEEXT): $(gtfold_OBJECTS) $(gtfold_DEPENDENCIES) 
-	@rm -f gtfold$(EXEEXT)
-	$(gtfold_LINK) $(gtfold_OBJECTS) $(gtfold_LDADD) $(LIBS)
-
-mostlyclean-compile:
-	-rm -f *.$(OBJEXT)
-
-distclean-compile:
-	-rm -f *.tab.c
-
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/loader.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@
-
-.c.o:
-@am__fastdepCC_TRUE@	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-@am__fastdepCC_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-@AMDEP_TRUE@@am__fastdepCC_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCC_FALSE@	$(COMPILE) -c $<
-
-.c.obj:
-@am__fastdepCC_TRUE@	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-@am__fastdepCC_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-@AMDEP_TRUE@@am__fastdepCC_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCC_FALSE@	$(COMPILE) -c `$(CYGPATH_W) '$<'`
-
-.cc.o:
-@am__fastdepCXX_TRUE@	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@	$(CXXCOMPILE) -c -o $@ $<
-
-.cc.obj:
-@am__fastdepCXX_TRUE@	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
-@AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
-@am__fastdepCXX_FALSE@	$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	mkid -fID $$unique
-tags: TAGS
-
-TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	set x; \
-	here=`pwd`; \
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	shift; \
-	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-	  test -n "$$unique" || unique=$$empty_fix; \
-	  if test $$# -gt 0; then \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      "$$@" $$unique; \
-	  else \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      $$unique; \
-	  fi; \
-	fi
-ctags: CTAGS
-CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	test -z "$(CTAGS_ARGS)$$unique" \
-	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$unique
-
-GTAGS:
-	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && $(am__cd) $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) "$$here"
-
-distclean-tags:
-	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-am
-all-am: Makefile $(PROGRAMS)
-installdirs:
-	for dir in "$(DESTDIR)$(bindir)"; do \
-	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-	done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
-
-distclean: distclean-am
-	-rm -rf ./$(DEPDIR)
-	-rm -f Makefile
-distclean-am: clean-am distclean-compile distclean-generic \
-	distclean-tags
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am:
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am: install-binPROGRAMS
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
-	-rm -rf ./$(DEPDIR)
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-compile mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-binPROGRAMS
-
-.MAKE: install-am install-strip
-
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
-	clean-generic ctags distclean distclean-compile \
-	distclean-generic distclean-tags distdir dvi dvi-am html \
-	html-am info info-am install install-am install-binPROGRAMS \
-	install-data install-data-am install-dvi install-dvi-am \
-	install-exec install-exec-am install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-compile \
-	mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-	uninstall-am uninstall-binPROGRAMS
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:

From 306481308551d915614f298750905877516cdf7b Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Thu, 20 Jan 2011 11:53:55 -0500
Subject: [PATCH 005/282] Removed some commented out old code, another branch
 test

---
 gtfold-mfe/src/loader.cc | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index b081412..22d2e13 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -43,15 +43,9 @@ int dangle[4][4][4][2]; /* Dangling energies */
 int inter[31]; /* Size penalty for internal loops */
 int bulge[31]; /* Size penalty for bulges*/
 int hairpin[31]; /* Size penalty for hairpin loops */
-#if 0
-int stack[4][4][4][4];
-int tstkh[4][4][4][4];
-int tstki[4][4][4][4];
-#else
 int stack[256]; /* Stacking energy for stack loops */
 int tstkh[256]; /* Terminal stacking energy for hairpin loops */
 int tstki[256]; /* Terminal stacking energy for internal loops */
-#endif
 int tloop[maxtloop + 1][2];
 int numoftloops;
 int iloop22[5][5][5][5][5][5][5][5]; /* 2*1 internal loops*/

From cf465036b2bcb290e0f5d45210432aa3ef236aa7 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 27 Jan 2011 11:03:27 -0500
Subject: [PATCH 006/282] Add an early version of gitignore

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..33fb6be
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,3 @@
+*.o
+*~
+Makefile.in

From 6b1f918b3d163169dc35fc548c1504725f0a5218 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 27 Jan 2011 11:18:27 -0500
Subject: [PATCH 007/282] Always do dynamic memory allocation, not static

- Remove DYNALLOC preprocessor directive
---
 gtfold-mfe/src/algorithms.c |  2 --
 gtfold-mfe/src/main.cc      | 24 +-----------------------
 2 files changed, 1 insertion(+), 25 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index e62ecbd..27c64f1 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -102,10 +102,8 @@ void initTables(int len) {
 #endif
 
 #if DEBUG
-#ifdef DYNALLOC
 	if (len != LENGTH-1)
 		fprintf(stderr,"ERROR: in initTables, len (%5d) != LENGTH-1 (%5d)\n",len,LENGTH-1);
-#endif
 #endif
 
 	init_chPair();
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 1007323..d0eff03 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -51,7 +51,7 @@ enum BOOL BPP; // calculate base pair probabilities
 enum BOOL USERDATA;
 enum BOOL PARAMS;
 enum BOOL LIMIT_DISTANCE;
-#ifdef DYNALLOC
+
 int LENGTH;
 unsigned char *RNA1; 
 unsigned char *RNA; // the RNA string in terms of 0, 1, 2, 3 for A, C, G and U
@@ -74,18 +74,6 @@ double **Q;   // Q[i][j] in addition to the above quantity QB[i][j], Q[i][j]
 double **QM;  // QM[i][j] is the sum of configuration energies from i to j,
               // assuming that i,j are contained in a multiloop
 double **P;   // P[i][j] The probability that nucleotides i and j form a basepair
-#else
-/* This are previously used variables, now they are not used. */
-unsigned char RNA[LENGTH];
-unsigned char RNA1[LENGTH];
-int structure[LENGTH];
-int VBI[LENGTH][LENGTH];
-int VM[LENGTH][LENGTH];
-int V[(LENGTH-1)*(LENGTH)/2 + 1]; /* int V[LENGTH][LENGTH]; */
-int WM[LENGTH][LENGTH];
-int W[LENGTH];
-int indx [LENGTH];
-#endif
 
 /**
  * Print the hep message and quit.
@@ -177,7 +165,6 @@ void init_variables(int len) {
 
 	int i;
 
-#ifdef DYNALLOC
 	LENGTH = len + 1;
 
 	RNA = (unsigned char *) malloc(LENGTH * sizeof(unsigned char));
@@ -258,16 +245,12 @@ void init_variables(int len) {
 		perror("Cannot allocate variable 'constraints'");
 		exit(-1);
 	}
-
-#endif
-	return;
 }
 
 /* deallocate global variables */
 void free_variables() {
 	int i;
 
-#ifdef DYNALLOC
 	free(indx);
 	for (i = 0; i < LENGTH; i++)
 		free(WM[i]);
@@ -284,11 +267,6 @@ void free_variables() {
 	free(structure);
 	free(RNA);
 	free(RNA1);
-
-#endif
-
-	return;
-
 }
 
 void init_partition_function_variables(int bases) {

From 976e0260499ba7b773e37f6c63737d131dfda8cf Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 27 Jan 2011 11:29:17 -0500
Subject: [PATCH 008/282] Add email address for Sonny Hernandez from URL.

http://www.cc.gatech.edu/~bader/about.html
---
 gtfold-mfe/AUTHORS | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/AUTHORS b/gtfold-mfe/AUTHORS
index a0cc50f..0f01d3b 100644
--- a/gtfold-mfe/AUTHORS
+++ b/gtfold-mfe/AUTHORS
@@ -1,5 +1,5 @@
 David A. Bader <bader@cc.gatech.edu>
-Sonny Hernandez May 2007 - August 2007
+Sonny Hernandez <sonnyher@usc.edu> May 2007 - August 2007
 Amrita Mathuriya <amathuriya3@gatech.edu> August 2007 - January 2009
 Sainath Mallidi <sainath@gatech.edu> August 2009 - December 2010
 Josh Anderson <janderson3@gatech.edu> August 2010 - May 2011

From 8ee6bc5c34c4b14edee60265a5666a867b22b7ea Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Thu, 27 Jan 2011 11:35:18 -0500
Subject: [PATCH 009/282] Added file that describes the turner constants we use

---
 gtfold-mfe/include/commented_constants.txt | 51 ++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 gtfold-mfe/include/commented_constants.txt

diff --git a/gtfold-mfe/include/commented_constants.txt b/gtfold-mfe/include/commented_constants.txt
new file mode 100644
index 0000000..a2566c0
--- /dev/null
+++ b/gtfold-mfe/include/commented_constants.txt
@@ -0,0 +1,51 @@
+typedef struct{
+	int poppen[5];/*asymmetric internal loops
+		From miscloop.dat file:
+		the f(m) array (see Ninio for details)*/
+	int maxpen; /* From miscloop.dat file:
+		asymmetric internal loops: the ninio equation
+		the maximum correction*/
+	int eparam[11]; /* Amrita: I am not sure of what does this array contain at different values.*/
+			/*They seem to be local values used in assignments
+			Perhaps they should simply be local variables -Anderson*/
+	int mult_const[3];/*Multiloop constants
+		mult_const[0] = a, the penalty for starting a multiloop
+		mult_const[1] = c, the free base penalty for a multiloop
+		mult_const[2] = b, the helix penalty for a multiloop*/
+	int dangle[4][4][4][2]; /* Dangling energies */
+	int inter[31]; /* Size penalty for internal loops */
+	int bulge[31]; /* Size penalty for bulges*/
+	int hairpin[31]; /* Size penalty for hairpin loops */
+	int stack[256]; /* Stacking energy for stack loops */
+	int tstkh[256]; /* Terminal stacking energy for hairpin loops */
+	int tstki[256]; /* Terminal stacking energy for internal loops */
+	int tloop[MAX_T_LOOP + 1][2]; /*MAX_T_LOOP is a constants, should
+	be the number of Tetraloops we have data for*/
+	int num_of_t_loops; /*Should also be a local variable, used as a counter*/
+	int iloop22[5][5][5][5][5][5][5][5]; /* 2*1 internal loops*/
+	int iloop21[5][5][5][5][5][5][5]; /* 2*1 internal loops */
+	int iloop11[5][5][5][5][5][5]; /*1*1 internal loops */
+	int coax[6][6][6][6];/*Assumed to be coaxial stacking constants*/
+	int tstackcoax[6][6][6][6];/*They are unused by gtfold as of Jan 27 2011*/
+	int coax_stack[6][6][6][6];/*Unless functionality is added they should
+				 probably be REMOVED*/
+	int tstack[6][6][6][6];/*Unused in loader should probably be REMOVED*/
+	int tstkm[6][6][6][6];/*Same as above*/
+
+	int auend; /* For AU penalty */
+	int gubonus; /*GGG hairpin bonus*/
+	int cint; /* cint, cslope, c3 are used for poly C hairpin loops */
+	int cslope;/*c hairpin slope*/
+	int c3;/*CCC hairpin*/
+	int efn2a; /*Obsoleted constants should be REMOVED*/
+	int efn2b;
+	int efn2c;
+	int triloop[MAX_T_LOOP + 1][2];/*Unused in loader should be REMOVED*/
+	int num_of_triloops; /*Unused in loader should be REMOVED*/
+	int init;/*Intermolecular initiation free energy*/
+	bool gail;/*Grossly Asymmetric Interior Loop Rule*/
+	float prelog; /* Used for loops having size > 30 */
+}thermo_struct;
+
+
+thermo_struct* populate(char* data_dir);

From a6844276159008fa278217fc496e766aed2c1f8e Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 27 Jan 2011 11:39:28 -0500
Subject: [PATCH 010/282] Conform to preferred curly brace style

- At the end of a line instead of the beginning of the next one
- Fix the few style errors in src/main.cc
- Add a STYLE document to collect these sorts of decisions
---
 gtfold-mfe/STYLE       | 18 ++++++++++++++
 gtfold-mfe/src/main.cc | 56 ++++++++++++++----------------------------
 2 files changed, 36 insertions(+), 38 deletions(-)
 create mode 100644 gtfold-mfe/STYLE

diff --git a/gtfold-mfe/STYLE b/gtfold-mfe/STYLE
new file mode 100644
index 0000000..5dd2cb4
--- /dev/null
+++ b/gtfold-mfe/STYLE
@@ -0,0 +1,18 @@
+This document contains some style guidelines for code in this project
+
+For compound names, prefer under_scores over camelCase.
+
+
+For curly brace guidelines, prefer at the end of the line instead of the
+beginning of the next line:
+
+for(i=0; i<10; i++) {
+    sum += i;
+}
+
+is better than
+
+for(i=0; i<10; i++)
+{
+    sum += i;
+}
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index d0eff03..dc36166 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -360,14 +360,12 @@ int main(int argc, char** argv) {
 					dataIndex = ++i;
 				else
 					help();
-			} else if (strcmp(argv[i], "-limitCD") == 0)
-			{
+			} else if (strcmp(argv[i], "-limitCD") == 0) {
 				if (i < argc)
 					lcdIndex = ++i;
 				else
 					help();	
-			}  else if (strcmp(argv[i], "-basepairprobabilities") == 0)
-			{
+			}  else if (strcmp(argv[i], "-basepairprobabilities") == 0) {
 				BPP = TRUE;
 			}
 			/*else if (strcmp(argv[i], "-forceNC") == 0)
@@ -440,19 +438,16 @@ int main(int argc, char** argv) {
 	int **fbp = NULL, **pbp = NULL;
 	int numfConstraints = 0, numpConstraints = 0;
 
-	if (consIndex != 0)
-	{
+	if (consIndex != 0) {
 		GTFOLD_FLAGS r = initialize_constraints(&fbp, &pbp, numpConstraints, numfConstraints, argv[consIndex]);
-		if (r == ERR_OPEN_FILE)
-		{
+		if (r == ERR_OPEN_FILE) {
 			free_variables();
 			exit(-1);
 		}
 	}
 	
 	
-	if (handle_IUPAC_code(s, bases)  == FAILURE)
-	{
+	if (handle_IUPAC_code(s, bases)  == FAILURE) {
 		free_variables();
 		exit(0);
 	}
@@ -467,16 +462,14 @@ int main(int argc, char** argv) {
 	initTables(bases); /* Initialize global variables */
 	
 	/*
-	if (fNCIndex != 0)
-	{
+	if (fNCIndex != 0) {
 		// Force non canonical base pairing
 		//force_noncanonical_basepair(argv[fNCIndex], bases);
 	}
 	*/
 
 	int lCD = -1;
-	if (lcdIndex != 0)
-	{
+	if (lcdIndex != 0) {
 		lCD = atoi(argv[lcdIndex]);
 		fprintf(stdout, "Maximum Contact Distance = %d\n\n", lCD);
 		limit_contact_distance(lCD, bases);
@@ -574,8 +567,7 @@ int main(int argc, char** argv) {
 }
 
 
-GTFOLD_FLAGS initialize_constraints(int*** fbp, int ***pbp, int& numpConstraints, int& numfConstraints, const char* constr_file)
-{
+GTFOLD_FLAGS initialize_constraints(int*** fbp, int ***pbp, int& numpConstraints, int& numfConstraints, const char* constr_file) {
 	ifstream cfcons;
 
 	fprintf(stdout, "Running with constraints\n");
@@ -661,8 +653,7 @@ GTFOLD_FLAGS initialize_constraints(int*** fbp, int ***pbp, int& numpConstraints
 	return SUCCESS;
 }
 
-GTFOLD_FLAGS handle_IUPAC_code(const std::string& s, const int bases)
-{
+GTFOLD_FLAGS handle_IUPAC_code(const std::string& s, const int bases) {
 	int* stack_unidentified_base;
 	int stack_count=0;
 	bool unspecd=0;
@@ -686,8 +677,7 @@ GTFOLD_FLAGS handle_IUPAC_code(const std::string& s, const int bases)
 	if(unspecd) {
 		printf("IUPAC codes have been detected at positions:");
 
-		for(int i=0;i<stack_count;i++)
-		{
+		for(int i=0;i<stack_count;i++) {
 			printf("%d , ",stack_unidentified_base[i]);
 		}
 		printf("\n");
@@ -704,12 +694,9 @@ GTFOLD_FLAGS handle_IUPAC_code(const std::string& s, const int bases)
 }
 
 
-void limit_contact_distance(int lCD, int len)
-{
-	for (int ii = 1; ii <= len; ++ii) 
-	{
-		for(int jj = ii+lCD; jj <= len; ++jj)
-		{
+void limit_contact_distance(int lCD, int len) {
+	for (int ii = 1; ii <= len; ++ii) {
+		for(int jj = ii+lCD; jj <= len; ++jj) {
 			constraints[ii] = -1;
 			constraints[jj] = -1;
 		//	std::cout << '(' << ii << ',' << jj << ')' << ' ';
@@ -720,40 +707,33 @@ void limit_contact_distance(int lCD, int len)
 
 
 
-void force_noncanonical_basepair(const char* ncb, int len)
-{
+void force_noncanonical_basepair(const char* ncb, int len) {
 	if (ncb == 0 || ncb[0] == '\0') return;
 	
 	printf("Permitted noncanonical base pairs : \n");	
 
 	std::string ncb1(ncb);
 	
-	for (unsigned int i =0 ; i < ncb1.size(); ++i)
-	{
+	for (unsigned int i =0 ; i < ncb1.size(); ++i) {
 		ncb1[i] = toupper(ncb1[i]);
 	}
 	
 	std::vector<std::string> tokens;
 	tokenize(ncb1, tokens, ",");	
 	
-	for (unsigned int i = 0; i < tokens.size(); ++i)
-	{
+	for (unsigned int i = 0; i < tokens.size(); ++i) {
 		trim_spaces(tokens[i]);
-		if (tokens.size() != 3 && tokens[i][1] != '-') 
-		{
+		if (tokens.size() != 3 && tokens[i][1] != '-')
 			// ignore
 			continue;
-		}
 
 		char b1 = getBase(tokens[i].substr(0,1));
 		char b2 = getBase(tokens[i].substr(2,1));
 
 		int r1=0;
 		r1 = update_chPair(b1, b2);			
-		if (r1 == 1) 
-		{
+		if (r1 == 1)
 			printf("(%c,%c) ",  tokens[i][0], tokens[i][2]) ;
-		}
 	}
 
 	printf("\n\n");

From afd01936c5e16b7ad9009178f9d50fb1a236b46b Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 27 Jan 2011 11:44:44 -0500
Subject: [PATCH 011/282] Variable rename: bases to length

- Length of the current strand in main function
---
 gtfold-mfe/src/main.cc | 76 +++++++++++++++++++++---------------------
 1 file changed, 38 insertions(+), 38 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index dc36166..45e760a 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -269,37 +269,37 @@ void free_variables() {
 	free(RNA1);
 }
 
-void init_partition_function_variables(int bases) {
-    QB = mallocTwoD(bases+1, bases+1);
+void init_partition_function_variables(int length) {
+    QB = mallocTwoD(length+1, length+1);
     if(QB == NULL) {
         fprintf(stderr,"Failed to allocate QB\n");
         exit(-1);
     }
 
-    Q = mallocTwoD(bases+1, bases+1);
+    Q = mallocTwoD(length+1, length+1);
     if(Q == NULL) {
         fprintf(stderr,"Failed to allocate Q\n");
         exit(-1);
     }
 
-    QM = mallocTwoD(bases+1, bases+1);
+    QM = mallocTwoD(length+1, length+1);
     if(QM == NULL) {
         fprintf(stderr,"Failed to allocate QM\n");
         exit(-1);
     }
 
-    P = mallocTwoD(bases+1, bases+1);
+    P = mallocTwoD(length+1, length+1);
     if(P == NULL) {
         fprintf(stderr,"Failed to allocate P\n");
         exit(-1);
     }
 }
 
-void free_partition_function_variables(int bases) {
-    freeTwoD(QB, bases+1, bases+1);
-    freeTwoD(Q, bases+1, bases+1);
-    freeTwoD(QM, bases+1, bases+1);
-    freeTwoD(P, bases+1, bases+1);
+void free_partition_function_variables(int length) {
+    freeTwoD(QB, length+1, length+1);
+    freeTwoD(Q, length+1, length+1);
+    freeTwoD(QM, length+1, length+1);
+    freeTwoD(P, length+1, length+1);
 }
 
 
@@ -314,7 +314,7 @@ void free_partition_function_variables(int bases) {
 int main(int argc, char** argv) {
 	int i;
 	ifstream cf;
-	int bases;
+	int length;
 	string s, seq;
 	int energy;
 	double t1;
@@ -426,12 +426,12 @@ int main(int argc, char** argv) {
 	}
 	s = seq;
 
-	bases = s.length();
+	length = s.length();
 
-	init_variables(bases);
+	init_variables(length);
 
 	cout << "Sequence: " << s << endl;
-	fprintf(stdout, "Sequence length: %5d\n\n", bases);
+	fprintf(stdout, "Sequence length: %5d\n\n", length);
 
 	cf.close();
 
@@ -447,7 +447,7 @@ int main(int argc, char** argv) {
 	}
 	
 	
-	if (handle_IUPAC_code(s, bases)  == FAILURE) {
+	if (handle_IUPAC_code(s, length)  == FAILURE) {
 		free_variables();
 		exit(0);
 	}
@@ -459,12 +459,12 @@ int main(int argc, char** argv) {
 	else
 		populate("Turner99",false); /* Defined in loader.cc file to read in the thermodynamic parameter values from the tables in the ../data directory. */
 
-	initTables(bases); /* Initialize global variables */
+	initTables(length); /* Initialize global variables */
 	
 	/*
 	if (fNCIndex != 0) {
 		// Force non canonical base pairing
-		//force_noncanonical_basepair(argv[fNCIndex], bases);
+		//force_noncanonical_basepair(argv[fNCIndex], length);
 	}
 	*/
 
@@ -472,7 +472,7 @@ int main(int argc, char** argv) {
 	if (lcdIndex != 0) {
 		lCD = atoi(argv[lcdIndex]);
 		fprintf(stdout, "Maximum Contact Distance = %d\n\n", lCD);
-		limit_contact_distance(lCD, bases);
+		limit_contact_distance(lCD, length);
 		
 	}
 
@@ -480,7 +480,7 @@ int main(int argc, char** argv) {
 	fflush(stdout);
 
 	t1 = get_seconds();
-	energy = calculate(bases, fbp, pbp, numfConstraints, numpConstraints); /* Runs the Dynamic programming algorithm to calculate the optimal energy. Defined in algorithms.c file.*/
+	energy = calculate(length, fbp, pbp, numfConstraints, numpConstraints); /* Runs the Dynamic programming algorithm to calculate the optimal energy. Defined in algorithms.c file.*/
     //energy = 0;
 	t1 = get_seconds() - t1;
 
@@ -492,26 +492,26 @@ int main(int argc, char** argv) {
         fflush(stdout);
 
         // malloc the arrays
-        init_partition_function_variables(bases);
+        init_partition_function_variables(length);
 
         // fill the arrays
-        fill_partition_fn_arrays(bases, QB, Q, QM);
+        fill_partition_fn_arrays(length, QB, Q, QM);
 
         fprintf(stdout," Done.\n");
 
-        fprintf(stdout,"Q[1][n]: %f\n\n", Q[1][bases]);
+        fprintf(stdout,"Q[1][n]: %f\n\n", Q[1][length]);
     }
 
 	fprintf(stdout,"Minimum Free Energy = %12.2f\n\n", energy/100.00);
 	fprintf(stdout,"MFE running time (in seconds): %9.6f\n\n", t1);
 
 	t1 = get_seconds();
-	trace(bases); /* Traces the optimal structure*/
+	trace(length); /* Traces the optimal structure*/
 	t1 = get_seconds() - t1;
 
 	std::stringstream ss1, ss2;
 	char suboptfile[1024];
-	ss1 << bases;
+	ss1 << length;
 	ss2 << energy/100.0;
 
 	i = 0;
@@ -524,18 +524,18 @@ int main(int argc, char** argv) {
 	fprintf(stdout, "Writing secondary structure to the file: %s\n", suboptfile);
 
 #if 0
-	outfile << bases << " " << energy/100.0;
+	outfile << length << " " << energy/100.0;
 	outfile << endl << s;
 
-	for ( i = 1; i <= bases; i++ )
+	for ( i = 1; i <= length; i++ )
 		outfile << "\n" <<  i << " " << structure[i] ;
 #endif
 	/* Generate the output file containing the optimal secondary structure in .ct format */
 #if 1
-	outfile << bases << "\t  dG = " << energy/100.0;
+	outfile << length << "\t  dG = " << energy/100.0;
 	i = 1;
-	while ( i <= bases ) {
-		outfile << endl << i << "\t" << s[i-1] << "\t" << i-1 << "\t" << (i+1)%(bases+1) << "\t" << structure[i] << "\t" << i;
+	while ( i <= length ) {
+		outfile << endl << i << "\t" << s[i-1] << "\t" << i-1 << "\t" << (i+1)%(length+1) << "\t" << structure[i] << "\t" << i;
 		i++;
 	}
 	outfile << endl;
@@ -548,16 +548,16 @@ int main(int argc, char** argv) {
 	fprintf(stdout,"Traceback running time (in seconds): %9.6f\n", t1);
 
 	fprintf(stdout, "\n\nFolding complete\n\n");
-	printSequence(bases);
-	printConstraints(bases);
-	printStructure(bases);
+	printSequence(length);
+	printConstraints(length);
+	printStructure(length);
 
     if(BPP) {
-        fillBasePairProbabilities(bases, structure, Q, QB, QM, P);
+        fillBasePairProbabilities(length, structure, Q, QB, QM, P);
 
-        printBasePairProbabilities(bases, structure, P);
+        printBasePairProbabilities(length, structure, P);
 
-        free_partition_function_variables(bases);
+        free_partition_function_variables(length);
     }
 
 	free_variables();
@@ -653,14 +653,14 @@ GTFOLD_FLAGS initialize_constraints(int*** fbp, int ***pbp, int& numpConstraints
 	return SUCCESS;
 }
 
-GTFOLD_FLAGS handle_IUPAC_code(const std::string& s, const int bases) {
+GTFOLD_FLAGS handle_IUPAC_code(const std::string& s, const int length) {
 	int* stack_unidentified_base;
 	int stack_count=0;
 	bool unspecd=0;
-	stack_unidentified_base=new int[bases];
+	stack_unidentified_base=new int[length];
 
 	/* SH: Conversion of the sequence to numerical values. */
-	for(int i = 1; i <= bases; i++) {
+	for(int i = 1; i <= length; i++) {
 		RNA[i] = getBase(s.substr(i-1,1));
 		RNA1[i] = getBase1(s.substr(i-1,1));
 		if (RNA[i]=='X') {

From 90ea5ed049588ad424fc086ea42d5754e0ef7ae2 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 27 Jan 2011 11:53:14 -0500
Subject: [PATCH 012/282] Remove more of DYNALLOC

---
 gtfold-mfe/include/main-c.h | 17 -----------------
 1 file changed, 17 deletions(-)

diff --git a/gtfold-mfe/include/main-c.h b/gtfold-mfe/include/main-c.h
index 805e35d..7484d61 100644
--- a/gtfold-mfe/include/main-c.h
+++ b/gtfold-mfe/include/main-c.h
@@ -20,9 +20,6 @@
 #ifndef _MAIN_C_H
 #define _MAIN_C_H
 
-#define DYNALLOC
-
-#ifdef DYNALLOC
 extern int LENGTH;
 extern unsigned char *RNA1; /* [LENGTH] */
 extern unsigned char *RNA; /* [LENGTH] */
@@ -34,20 +31,6 @@ extern int **VM; /* [LENGTH][LENGTH] */
 extern int **WM; /* [LENGTH][LENGTH] */
 extern int *indx; /* [LENGTH] */
 extern int *constraints;
-#else
-
-#define LENGTH 8500
-
-extern unsigned char RNA[LENGTH];
-extern unsigned char RNA1[LENGTH];
-extern int structure[LENGTH];
-extern int V[(LENGTH-1)*(LENGTH)/2 + 1];
-extern int VBI[LENGTH][LENGTH];
-extern int VM[LENGTH][LENGTH];
-extern int WM[LENGTH][LENGTH];
-extern int W[LENGTH];
-extern int indx[LENGTH];
-#endif
 
 #define fourBaseIndex(a, b, c, d) (((a) << 6) + ((b) << 4) + ((c) << 2) + (d))
 

From e2fee9a7dad63fcc9a52fed4d5aed5b6ad98bb55 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Tue, 1 Feb 2011 16:12:14 -0500
Subject: [PATCH 013/282] Cleanup help message and use long options (--)

---
 gtfold-mfe/src/main.cc | 49 ++++++++++++++++++++++++++----------------
 1 file changed, 30 insertions(+), 19 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 45e760a..a6e889b 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -80,24 +80,35 @@ double **P;   // P[i][j] The probability that nucleotides i and j form a basepai
  */
 void help() {
 	fprintf(stderr,
-			"Usage: gtfold [-ilsa] [-noisolate] [-params setofparameters] [-constraints filename] [-limitCD dist] [-datadir datadirloc] [-basepairprobabilities] filename(sequence)\n\n");
+			"Usage: gtfold [OPTION]... FILE\n\n");
+    //[--ilsa] [--noisolate] [--params setofparameters] [--constraints filename] [--limitCD dist] [--datadir datadirloc] [--basepairprobabilities] filename(sequence)\n\n");
+
     fprintf(stderr,
-            "-ilsa\t\t= Use the Internal Loop Speedup Algorithm for faster calculation\n");
+            "  FILE is an RNA sequence file.  Single line or FASTA formats are accepted.\n\n");
+
     fprintf(stderr,
-            "-noisolate\t= Prevent isolated base pairs from forming\n");
+            "OPTIONS\n");
     fprintf(stderr,
-            "-params\t\t= Choose thermodynamic parameters to use: Turner99 or Turner04 or Andronescu\n");
+            "   --ilsa           Use the Internal Loop Speedup Algorithm (faster)\n");
     fprintf(stderr,
-            "-constraints\t= Force or prohibit particular pairings\n");
+            "   --noisolate      Prevent isolated base pairs from forming\n");
+    // Remove this option until the loader is capable of loading multiple
+    // thermodynamic parameters
+    //fprintf(stderr,
+    //        "   --params       Choose thermodynamic parameters to use: Turner99 or Turner04 or Andronescu\n");
     fprintf(stderr,
-            "\tConstraint syntax:\n\t\tF i j k  to force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) to pair\n\t\tP i j k  to prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) from pairing\n\t\tP i 0 k  to make bases from i to i+k-1 single stranded bases.\n");
+            "   --constraints FILE\n                    Load constraints from FILE.  See Constraint syntax below\n");
     fprintf(stderr,
-            "-limitCD\t= Limit the 'contact distance' for a base pair to the given distance\n");
+            "   --limitCD dist   Set a maximum base pair contact distance to dist. If no\n                      limit is given, base pairs can be over any distance\n");
     fprintf(stderr,
-            "-basepairprobabilities\n\t\t= Calculate and output base pair probabilities of the predicted structure\n");
+            "   --bpp            Print base pair probabilities for the predicted structure\n");
+
+    fprintf(stderr,
+            "\n   --help           Output help (this message) and exit\n");
+
     fprintf(stderr,
-            "\nSequence file has to be in one of the two formats: Single line or FASTA\n\n");
-	//	[-forceNC] 	-forceNC = an option to force pairing of noncanonical bases \nSyntax for forcing noncanonical bases (example):\n\t\tA-A,A-G,U-U\n\n");
+            "\nConstraint syntax:\n\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
+	//	[-forceNC] 	-forceNC an option to force pairing of noncanonical bases \nSyntax for forcing noncanonical bases (example):\n\t\tA-A,A-G,U-U\n\n");
 	exit(-1);
 }
 
@@ -337,38 +348,38 @@ int main(int argc, char** argv) {
 	i = 1;
 	while (i < argc) {
 		if (argv[i][0] == '-') {
-			if (strcmp(argv[i], "-ilsa") == 0) {
+			if (strcmp(argv[i], "--ilsa") == 0) {
 				ILSA = TRUE;
-			} else if (strcmp(argv[i], "-noisolate") == 0) {
+			} else if (strcmp(argv[i], "--noisolate") == 0) {
 				NOISOLATE = TRUE;
-			} else if (strcmp(argv[i], "-help") == 0) {
+			} else if (strcmp(argv[i], "--help") == 0) {
 				help();
-			} else if (strcmp(argv[i], "-constraints") == 0) {
+			} else if (strcmp(argv[i], "--constraints") == 0) {
 				if (i < argc)
 					consIndex = ++i;
 				else
 					help();
-			} else if (strcmp(argv[i], "-params")==0) { 
+			} else if (strcmp(argv[i], "--params")==0) { 
 				PARAMS = TRUE;			  
 				if (i < argc)
 					paramsIndex = ++i;
 				else
 					help();
-			} else if (strcmp(argv[i], "-datadir") == 0) {
+			} else if (strcmp(argv[i], "--datadir") == 0) {
 				USERDATA = TRUE;
 				if (i < argc)
 					dataIndex = ++i;
 				else
 					help();
-			} else if (strcmp(argv[i], "-limitCD") == 0) {
+			} else if (strcmp(argv[i], "--limitCD") == 0) {
 				if (i < argc)
 					lcdIndex = ++i;
 				else
 					help();	
-			}  else if (strcmp(argv[i], "-basepairprobabilities") == 0) {
+			}  else if (strcmp(argv[i], "--bpp") == 0) {
 				BPP = TRUE;
 			}
-			/*else if (strcmp(argv[i], "-forceNC") == 0)
+			/*else if (strcmp(argv[i], "--forceNC") == 0)
 			{
 				if (i < argc)
 					fNCIndex = ++i;

From 062b5f55fbd35b44a5f9a2ac4d2ea248a71521ff Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 11 Feb 2011 13:15:51 -0500
Subject: [PATCH 014/282] Organize options into regular and advanced

Also put back in --params with a NONFUNCTIONAL message
---
 gtfold-mfe/src/main.cc | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index a6e889b..c294bea 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -86,25 +86,24 @@ void help() {
     fprintf(stderr,
             "  FILE is an RNA sequence file.  Single line or FASTA formats are accepted.\n\n");
 
+    fprintf(stderr, "OPTIONS\n");
     fprintf(stderr,
-            "OPTIONS\n");
+            "   -c, --constraints FILE\n                        Load constraints from FILE.  See Constraint syntax below\n");
     fprintf(stderr,
-            "   --ilsa           Use the Internal Loop Speedup Algorithm (faster)\n");
+            "   -d, --limitCD dist   Set a maximum base pair contact distance to dist. If no\n                        limit is given, base pairs can be over any distance\n");
     fprintf(stderr,
-            "   --noisolate      Prevent isolated base pairs from forming\n");
-    // Remove this option until the loader is capable of loading multiple
-    // thermodynamic parameters
-    //fprintf(stderr,
-    //        "   --params       Choose thermodynamic parameters to use: Turner99 or Turner04 or Andronescu\n");
+            "   -n, --noisolate      Prevent isolated base pairs from forming\n");
     fprintf(stderr,
-            "   --constraints FILE\n                    Load constraints from FILE.  See Constraint syntax below\n");
+            "   -h, --help           Output help (this message) and exit\n");
+
+    fprintf(stderr, "\nADVANCED\n");
     fprintf(stderr,
-            "   --limitCD dist   Set a maximum base pair contact distance to dist. If no\n                      limit is given, base pairs can be over any distance\n");
+            "   --bpp                Print base pair probabilities for the predicted structure\n");
     fprintf(stderr,
-            "   --bpp            Print base pair probabilities for the predicted structure\n");
-
+            "   --ilsa               Use the Internal Loop Speedup Algorithm (faster)\n");
     fprintf(stderr,
-            "\n   --help           Output help (this message) and exit\n");
+            "   --params             Choose thermodynamic parameters to use: Turner99 or Turner04 or Andronescu [NONFUNCTIONAL]\n");
+
 
     fprintf(stderr,
             "\nConstraint syntax:\n\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");

From 234def5f336cc8b9d052b0674a9dede2969010fc Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Wed, 16 Feb 2011 21:38:45 -0500
Subject: [PATCH 015/282] Fix typo versbose -> verbose

---
 gtfold-mfe/src/main.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 2dbc576..f899ee2 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -95,7 +95,7 @@ void help() {
     fprintf(stderr,
             "   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
     fprintf(stderr,
-            "   -v, --verbose        Run in versbose mode\n");
+            "   -v, --verbose        Run in verbose mode\n");
     
 	fprintf(stderr,
             "   -t, --threads num    Limit number of threads used\n");

From 8c531b011c447da8c177bf2fed9be30b0c5fcdc3 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Wed, 16 Feb 2011 21:41:02 -0500
Subject: [PATCH 016/282] Reorder options to put "standard" options separate

---
 gtfold-mfe/src/main.cc | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index f899ee2..609e373 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -94,13 +94,14 @@ void help() {
             "   -n, --noisolate      Prevent isolated base pairs from forming\n");
     fprintf(stderr,
             "   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
-    fprintf(stderr,
-            "   -v, --verbose        Run in verbose mode\n");
-    
 	fprintf(stderr,
             "   -t, --threads num    Limit number of threads used\n");
+
+    fprintf(stderr, "\n");
     fprintf(stderr,
             "   -h, --help           Output help (this message) and exit\n");
+    fprintf(stderr,
+            "   -v, --verbose        Run in verbose mode\n");
 
     fprintf(stderr, "\nBETA OPTIONS\n");
     fprintf(stderr,

From ebeea43264c1b07ed78f7444abf6e1af406dd989 Mon Sep 17 00:00:00 2001
From: dsokus <dsokus@gmail.com>
Date: Wed, 2 Mar 2011 21:52:14 -0500
Subject: [PATCH 017/282] test

---
 gtfold-mfe/README | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gtfold-mfe/README b/gtfold-mfe/README
index 34a28f1..ee48a23 100644
--- a/gtfold-mfe/README
+++ b/gtfold-mfe/README
@@ -1,3 +1,5 @@
+test
+
 GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction
 
 (C) 2007-2010, David A. Bader

From 06a3802a3458dce7411246b4c164dad57d02b443 Mon Sep 17 00:00:00 2001
From: dsokus <dsokus@gmail.com>
Date: Wed, 2 Mar 2011 21:52:45 -0500
Subject: [PATCH 018/282] test text removed

---
 gtfold-mfe/README | 2 --
 1 file changed, 2 deletions(-)

diff --git a/gtfold-mfe/README b/gtfold-mfe/README
index ee48a23..34a28f1 100644
--- a/gtfold-mfe/README
+++ b/gtfold-mfe/README
@@ -1,5 +1,3 @@
-test
-
 GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction
 
 (C) 2007-2010, David A. Bader

From b76b9c12cbcf32f7e022de58268db1358b4c8149 Mon Sep 17 00:00:00 2001
From: dsokus <dsokus@gmail.com>
Date: Wed, 2 Mar 2011 22:42:11 -0500
Subject: [PATCH 019/282] committing a small text file to test if my Github
 setup works.

Signed-off-by: dsokus <dsokus@gmail.com>
---
 gtfold-mfe/test.txt | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 gtfold-mfe/test.txt

diff --git a/gtfold-mfe/test.txt b/gtfold-mfe/test.txt
new file mode 100644
index 0000000..229c9b9
--- /dev/null
+++ b/gtfold-mfe/test.txt
@@ -0,0 +1 @@
+this is to test how my Git setup works  - Zs
\ No newline at end of file

From c4bbb863a303aabb19be14947dbd228f56d72384 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <prashant@electricaway.(none)>
Date: Wed, 2 Mar 2011 06:41:16 +0800
Subject: [PATCH 020/282] fixed constraint handling issue - forbid adjacent bp
 pairing

---
 gtfold-mfe/src/traceback.c | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index dff6ae9..fe408dc 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -37,6 +37,7 @@
 #include "algorithms.h"
 #include "traceback.h"
 
+#define TURN 3
 int total_en = 0;
 
 void trace(int len) {
@@ -68,6 +69,7 @@ void traceW(int j) {
 	if (j == 0 || j == 1) return;
 
 	for (i = 1; i < j && !done; i++) {
+		if (j-i < TURN) continue;
 		wim1 = MIN ( 0, W[i-1] );
 		flag = 1;
 		if (wim1 != W[i-1]) flag = 0;
@@ -140,6 +142,7 @@ void traceW(int j) {
 /* Trace the structure inside V[i][j]. This function traces "which type of loop (i,j) base pair is closing" */
 int traceV(int i, int j) {
 	int a, b, c, d, Vij;
+	if (j-i < TURN)  return INFINITY_;
 
 	a = eH(i, j);
 	b = eS(i, j) + V[indx[i + 1] + j - 1];

From 290afc1e3a9c3351484340715151db83d9ca1eb2 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <prashant@electricaway.(none)>
Date: Wed, 2 Mar 2011 06:42:18 +0800
Subject: [PATCH 021/282] place ct file in current working dir

---
 gtfold-mfe/src/main.cc | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 609e373..b6f3f0f 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -538,10 +538,15 @@ int main(int argc, char** argv) {
 		t1 = get_seconds() - t1;
 		fprintf(stdout,"Traceback runtime (seconds): %9.6f\n\n", t1);
 
+		size_t pos = 0;
 		std::string suboptfile;
 		suboptfile += argv[fileIndex];
+		
+		if ((pos=suboptfile.find_last_of('/')) > 0) {
+			suboptfile = suboptfile.substr(pos+1);
+		}
 
-		// if an extension exists, replace it with ct
+		// if an extension exists, replace it with struct
 		if(suboptfile.find(".") != string::npos)
 			suboptfile.erase(suboptfile.rfind("."));
 		suboptfile += ".struct";
@@ -594,7 +599,12 @@ int main(int argc, char** argv) {
 
     // or build off the input file
     else {
+		size_t pos;
         outputfile += argv[fileIndex];
+		
+		if ((pos=outputfile.find_last_of('/')) > 0) {
+			outputfile = outputfile.substr(pos+1);
+		}
 
         // if an extension exists, replace it with ct
         if(outputfile.find(".") != string::npos)

From c4401f55b7a349e51ba37de11d9828d230d8d9f2 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <prashant@electricaway.(none)>
Date: Wed, 2 Mar 2011 06:42:35 +0800
Subject: [PATCH 022/282] minor code cleanup

---
 gtfold-mfe/src/algorithms.c | 15 ---------------
 1 file changed, 15 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 83f94d6..3006431 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -205,7 +205,6 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
 #endif
 #endif
 
-    //printf("starting.......\n");
 
 	/* Here b-1 is the length of the segment closed with (i,j) base pair. We assume the minimum size of a hairpin loop closed with (i,j) equal to 3.*/
 
@@ -266,19 +265,9 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
         }
     }
 
-/*
-    for(j=2; j<=len; j++){
-        for (i=j-1; i>0; i--){
-		    printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WM[i][j]);
-        }
-    }
-*/            
-
 	for (j = 5; j <= len; j++) /* Recurssion relation for W array does not depend upon any other array, so can be done after the computation of other arrays are finished.*/
 		calcW(j);
 
-	//printV(len);
-
 	return W[len];
 }
 /* This function calculates the optimal energy of internal loops closed with base pair (i,j) using a heuristic, which limits their size to a constant value - MAXLOOP
@@ -1218,10 +1207,6 @@ void calcW(int j) {
 
 	W[j] = Wj;
 
-	//printf(",W%dset: %d\n", j, W[j]);
-
-	//  if(j==11 || j==35 || j==36)
-	// printf("\n*****\nMust branch: %d, W%d: %d\n*****\n", must_branch, j, W[j]);
 	return;
 }
 

From 8ed55faca41af42c274b53530f5bd8f52a683df8 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 19:34:33 -0800
Subject: [PATCH 023/282] Some comment cleanup on algorithms.c

---
 gtfold-mfe/src/algorithms.c | 57 ++++++++++++++++++++++++-------------
 1 file changed, 37 insertions(+), 20 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 83f94d6..95a9128 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -19,17 +19,29 @@
 
 /* AUTHORED by Amrita Mathuriya August 2007 - January 2009. Implemented multiloop energy function, internal loop energy function using heuristic and internal loop speedup algorithm, parallelization, corrected numerous bugs and commented whole GTfold.
 
- * Amrita: Please note that, in this file same recursion formulas is being calculated in more than one functions.
- * This is done for performance improvement to reduce the redundant computations for various cases. The duplicate codes are not documented again at some places.
- * The arrays to be calculated are VBI, VM, V and WM for every  point (i,j) where j > i. Then W(j) needs to be calculated for j= 1 to N.
- * NOTE that the WM(i,j) can be calculated only after V(i,j) and array VBI and VM should be calculated before V array for point (i,j). So, the order of computation has been kept as VBI, VM, V, WM for any point (i,j)
- * Also Note that, a valid base pair has j > i. Therefore, the portion of the 2D arrays containing j < i is not useful.
- * Minimum size of a hairpin loop is assumed as 3. This assumption is taken into effect at many places.
- * I am not sure of what these eparam values are at various places except for multiloops.
+ * Amrita:
+ * - Please note that, in this file same recursion formulas is being calculated
+ *   in more than one functions.
+ * - This is done for performance improvement to reduce the redundant
+ *   computations for various cases. The duplicate codes are not documented
+ *   again at some places.
+ * - The arrays to be calculated are VBI, VM, V and WM for every  point (i,j)
+ *   where j > i. Then W(j) needs to be calculated for j= 1 to N.
+ * - NOTE that the WM(i,j) can be calculated only after V(i,j) and array VBI
+ *   and VM should be calculated before V array for point (i,j). So, the order
+ *   of computation has been kept as VBI, VM, V, WM for any point (i,j)
+ * - Also Note that, a valid base pair has j > i. Therefore, the portion of the
+ *   2D arrays containing j < i is not useful.
+ * - Minimum size of a hairpin loop is assumed as 3. This assumption is taken
+ *   into effect at many places.
+ * - I am not sure of what these eparam values are at various places except for
+ *   multiloops.
  * */
 
-/* Modified by Sainath Mallidi August 2009 -  "*/
-/* Added constraint support that can force a base pair, prohibit a base pair and make single stranded regions */
+/* Modified by Sainath Mallidi August 2009 - 
+ * Added constraint support that can force a base pair, prohibit a base pair
+ * and make single stranded regions
+ */
 
 #include <stdio.h>
 #include <math.h>
@@ -38,7 +50,7 @@
 #include "constants.h"
 #include "main-c.h"
 #include "algorithms.h"
-#ifdef _OPENMP   /* The compiler automatically recognizes openmp support and includes the file accordingly*/
+#ifdef _OPENMP   /* defined by the compiler */
 #include "omp.h"
 #endif
 
@@ -52,7 +64,11 @@ unsigned int chPairKey;
 int plen = 0, flen = 0, sslen = 0;
 int *pbpi, *pbpj, *fbpi, *fbpj, *ss;
 
-/* This function calculates chPairKey to be processed by function chPair. Defined by Professor Bader. */
+/**
+ * Calculates chPairKey to be processed by function chPair()
+ *
+ * @author Professor Bader.
+ */
 void init_chPair() {
 	int i, j;
 
@@ -78,15 +94,16 @@ int update_chPair(int i, int j)
 }
 
 
-/* This pragma returns 1 if  base b1 and b2 can pair up, otherwise returns 0, using chPairKey calculated in init_chPair function. Here b1 and b2 are 0-3 to represent one of the four nucleotides A, C, G and U. */
-#if 0
-inline
-int chPair(int b1, int b2) {
-	return (chPairKey & (1 << ((b1<<2) + b2)));
-}
-#else
-#define chPair(a, b)  (chPairKey & (1 << (((a)<<2) + (b))))  /* Please try to run this, to understand this statement. Defined by Professor Bader. */
-#endif
+/*
+ * Whether a and b can pair or not.
+ *
+ * @param a Encoding of a nucleotide: A=0, C=1, G=2, U=3
+ * @param b Encoding of a nucleotide: A=0, C=1, G=2, U=3
+ * @return 1 if a and b can pair, 0 otherwise
+ *
+ * @author Professor Bader
+ */
+#define chPair(a, b)  (chPairKey & (1 << (((a)<<2) + (b))))
 
 /* Initialize variables.*/
 void initTables(int len) {

From 8da09ef33e8733390f2ca4a7cb12b7d3b0c788c5 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 19:37:10 -0800
Subject: [PATCH 024/282] Remove #if 0 comments and code cleanup

---
 gtfold-mfe/src/algorithms.c | 23 ++++++-----------------
 1 file changed, 6 insertions(+), 17 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 95a9128..9cddad7 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -111,13 +111,6 @@ void initTables(int len) {
 	int i, j;
 	int LLL;
 
-#if 0
-	int z = (len)*(len+1)/2 + 1;
-
-	V = new int[z];
-	indx = new int[len+1];
-#endif
-
 #if DEBUG
 	if (len != LENGTH-1)
 		fprintf(stderr,"ERROR: in initTables, len (%5d) != LENGTH-1 (%5d)\n",len,LENGTH-1);
@@ -128,10 +121,6 @@ void initTables(int len) {
 	for (i = 0; i < LENGTH; i++) {
 		W[i] = INFINITY_; /* Initializing W array with INFINITY make sure that an unfolded sequence will have a large +ve value for free energy - INIFINITY*/
 		constraints[i] = 0;
-#if 0
-		indx[i] = (LENGTH-1)*(i-1) - (i*(i-1))/2;
-		indx[i] = (len)*(i-1) - (i*(i-1))/2;
-#endif
 		for (j = 0; j < LENGTH; j++) {
 			VBI[i][j] = INFINITY_;
 			VM[i][j] = INFINITY_;
@@ -144,23 +133,23 @@ void initTables(int len) {
 	for (i = 0; i < LLL; i++)
 		V[i] = INFINITY_;
 
-	/*The array V is mapped from 2D to 1D and indexed using the indx array. This mapping helps removing the space wasted for j < i*/
+    /*
+     * The array V is mapped from 2D to 1D and indexed using the indx array.
+     * This mapping helps removing the space wasted for j < i
+     */
 	for (i = 0; i <= LENGTH - 1; i++)
 		indx[i] = (len) * (i - 1) - (i * (i - 1)) / 2;
-
-	return;
 }
 
 //check if single stranded region is allowed with the given constraints
 int checkSS(int i, int j) {
 
 	int it;
-	for (it = i + 1; it < j; it++) {
+	for (it = i + 1; it < j; it++)
 		if (constraints[it] > 0)
 			return 1;
-	}
-	return 0;
 
+	return 0;
 }
 
 int calculate(int len, int **forceList, int **prohibitList, int forcelen, int prohibitlen) {

From 6230f71e1d772d9d1a1315aa94b8e70654a0af9b Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 19:41:01 -0800
Subject: [PATCH 025/282] Retab algorithms.c

---
 gtfold-mfe/src/algorithms.c | 2274 +++++++++++++++++------------------
 1 file changed, 1137 insertions(+), 1137 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 9cddad7..7d747c2 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -70,27 +70,27 @@ int *pbpi, *pbpj, *fbpi, *fbpj, *ss;
  * @author Professor Bader.
  */
 void init_chPair() {
-	int i, j;
+    int i, j;
 
-	chPairKey = 0;
-	for (i = 0; i < 4; i++)
-		for (j = 0; j < 4; j++)
-			chPairKey += checkPair(i, j) << ((i << 2) + j);
+    chPairKey = 0;
+    for (i = 0; i < 4; i++)
+        for (j = 0; j < 4; j++)
+            chPairKey += checkPair(i, j) << ((i << 2) + j);
 }
 
 int update_chPair(int i, int j) 
 {
-	int r = 0;
-	if (!((i >= 0 && i <=3 )&&(j >=0 && j <=3)))
-		return r;
-
-	if (!(chPairKey & (1 << ((i << 2) + j))))
-	{
-		chPairKey += 1 << ((i << 2) + j);	
-		r = 1;
-	}
+    int r = 0;
+    if (!((i >= 0 && i <=3 )&&(j >=0 && j <=3)))
+        return r;
+
+    if (!(chPairKey & (1 << ((i << 2) + j))))
+    {
+        chPairKey += 1 << ((i << 2) + j);   
+        r = 1;
+    }
 
-	return r;
+    return r;
 }
 
 
@@ -108,134 +108,134 @@ int update_chPair(int i, int j)
 /* Initialize variables.*/
 void initTables(int len) {
 
-	int i, j;
-	int LLL;
+    int i, j;
+    int LLL;
 
 #if DEBUG
-	if (len != LENGTH-1)
-		fprintf(stderr,"ERROR: in initTables, len (%5d) != LENGTH-1 (%5d)\n",len,LENGTH-1);
+    if (len != LENGTH-1)
+        fprintf(stderr,"ERROR: in initTables, len (%5d) != LENGTH-1 (%5d)\n",len,LENGTH-1);
 #endif
 
-	init_chPair();
+    init_chPair();
 
-	for (i = 0; i < LENGTH; i++) {
-		W[i] = INFINITY_; /* Initializing W array with INFINITY make sure that an unfolded sequence will have a large +ve value for free energy - INIFINITY*/
-		constraints[i] = 0;
-		for (j = 0; j < LENGTH; j++) {
-			VBI[i][j] = INFINITY_;
-			VM[i][j] = INFINITY_;
-			WM[i][j] = INFINITY_;
-		}
-	}
+    for (i = 0; i < LENGTH; i++) {
+        W[i] = INFINITY_; /* Initializing W array with INFINITY make sure that an unfolded sequence will have a large +ve value for free energy - INIFINITY*/
+        constraints[i] = 0;
+        for (j = 0; j < LENGTH; j++) {
+            VBI[i][j] = INFINITY_;
+            VM[i][j] = INFINITY_;
+            WM[i][j] = INFINITY_;
+        }
+    }
 
-	LLL = (LENGTH - 1) * (LENGTH) / 2 + 1;
+    LLL = (LENGTH - 1) * (LENGTH) / 2 + 1;
 
-	for (i = 0; i < LLL; i++)
-		V[i] = INFINITY_;
+    for (i = 0; i < LLL; i++)
+        V[i] = INFINITY_;
 
     /*
      * The array V is mapped from 2D to 1D and indexed using the indx array.
      * This mapping helps removing the space wasted for j < i
      */
-	for (i = 0; i <= LENGTH - 1; i++)
-		indx[i] = (len) * (i - 1) - (i * (i - 1)) / 2;
+    for (i = 0; i <= LENGTH - 1; i++)
+        indx[i] = (len) * (i - 1) - (i * (i - 1)) / 2;
 }
 
 //check if single stranded region is allowed with the given constraints
 int checkSS(int i, int j) {
 
-	int it;
-	for (it = i + 1; it < j; it++)
-		if (constraints[it] > 0)
-			return 1;
+    int it;
+    for (it = i + 1; it < j; it++)
+        if (constraints[it] > 0)
+            return 1;
 
-	return 0;
+    return 0;
 }
 
 int calculate(int len, int **forceList, int **prohibitList, int forcelen, int prohibitlen) {
-	int b, i, j, it, k;
-	
-	for(i=1;i<=len;i++) 
-	{
-		if(RNA1[i]=='N') 
-			constraints[i] = -1;
-	}	
-
-	if (prohibitlen != 0) 
-	{
-		for (it = 0; it < prohibitlen; it++) 
-		{
-			for(k= 1; k <= prohibitList[it][2];k++)
-			{
-				constraints[prohibitList[it][0]+k-1] = -1;
-				if(prohibitList[it][1]!=0)
-				{
-					constraints[prohibitList[it][1]+1-k] = -1;
-				}
-			}
-		}
-	}
-
-	if (forcelen != 0) 
-	{
-		printf("Running with constraints\n");
-		for (it = 0; it < forcelen; it++) 
-		{
-			for(k=1; k <= forceList[it][2];k++)
-			{
-				if (!chPair(RNA[forceList[it][0]+k-1], RNA[forceList[it][1]-k+1])) 
-				{
-					printf("Can't constrain (%d,%d)\n", forceList[it][0]+k-1,
-							forceList[it][1]-k+1);
-					continue;
-				}
-				constraints[forceList[it][0]+k-1] = forceList[it][1]+1-k;
-				constraints[forceList[it][1]+1-k] = forceList[it][0]+k-1;
-			}
-				//printf("(%d,%d)\n", forceList[it][0], forceList[it][1]);
-		}
-	}
+    int b, i, j, it, k;
+    
+    for(i=1;i<=len;i++) 
+    {
+        if(RNA1[i]=='N') 
+            constraints[i] = -1;
+    }   
+
+    if (prohibitlen != 0) 
+    {
+        for (it = 0; it < prohibitlen; it++) 
+        {
+            for(k= 1; k <= prohibitList[it][2];k++)
+            {
+                constraints[prohibitList[it][0]+k-1] = -1;
+                if(prohibitList[it][1]!=0)
+                {
+                    constraints[prohibitList[it][1]+1-k] = -1;
+                }
+            }
+        }
+    }
+
+    if (forcelen != 0) 
+    {
+        printf("Running with constraints\n");
+        for (it = 0; it < forcelen; it++) 
+        {
+            for(k=1; k <= forceList[it][2];k++)
+            {
+                if (!chPair(RNA[forceList[it][0]+k-1], RNA[forceList[it][1]-k+1])) 
+                {
+                    printf("Can't constrain (%d,%d)\n", forceList[it][0]+k-1,
+                            forceList[it][1]-k+1);
+                    continue;
+                }
+                constraints[forceList[it][0]+k-1] = forceList[it][1]+1-k;
+                constraints[forceList[it][1]+1-k] = forceList[it][0]+k-1;
+            }
+                //printf("(%d,%d)\n", forceList[it][0], forceList[it][1]);
+        }
+    }
 
 #ifdef _OPENMP
-	if (num_threads > 0)
-		omp_set_num_threads(num_threads);
+    if (num_threads > 0)
+        omp_set_num_threads(num_threads);
 #endif
 
 #if 1
 #ifdef _OPENMP
 #pragma omp parallel
 #pragma omp master
-	{
-		fprintf(stdout,"Thread count: %3d\n",omp_get_num_threads());
-	}
+    {
+        fprintf(stdout,"Thread count: %3d\n",omp_get_num_threads());
+    }
 #endif
 #endif
 
     //printf("starting.......\n");
 
-	/* Here b-1 is the length of the segment closed with (i,j) base pair. We assume the minimum size of a hairpin loop closed with (i,j) equal to 3.*/
+    /* Here b-1 is the length of the segment closed with (i,j) base pair. We assume the minimum size of a hairpin loop closed with (i,j) equal to 3.*/
 
-	/* For b = 4 to 6, hairpin loops and at b = 6 stack loops are possible. So, only WM, and V array are needs to be calculated.
-	 * If (i,j) can not pair up then only WM needs to be calculated.
-	 * */
-	for (b = 4; b <= 6; b++) {
+    /* For b = 4 to 6, hairpin loops and at b = 6 stack loops are possible. So, only WM, and V array are needs to be calculated.
+     * If (i,j) can not pair up then only WM needs to be calculated.
+     * */
+    for (b = 4; b <= 6; b++) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
-		/* OpenMP syntex to parallelize the for loop. Guided scheduling strategy works better because there may not be equla amount of work for every (i,j)
-		 * Please look at the conference paper on GTfold for information regarding how to parallelize the code. Also, note that the for every value of b calculation has to go sequentially. However, the calculation for a perticular value of b, which corresponds to calculating on a single diagonal.
-		 * */
+        /* OpenMP syntex to parallelize the for loop. Guided scheduling strategy works better because there may not be equla amount of work for every (i,j)
+         * Please look at the conference paper on GTfold for information regarding how to parallelize the code. Also, note that the for every value of b calculation has to go sequentially. However, the calculation for a perticular value of b, which corresponds to calculating on a single diagonal.
+         * */
 #endif
-		for (i = 1; i <= len - b; i++) {
-			j = i + b;
-			//if (constraints[i] == -1 && constraints[j] == -1)
-			//	continue;
-			if (j-i >= contact_dist) continue;
-			if (chPair(RNA[i], RNA[j])) /* Check if bases i and j pair up or not */
-				calcVWM(i, j, INFINITY_, INFINITY_); /* Calculates V and WM array for element (i,j)*/
-			else
-				calcWM(i, j); /* Calculates WM array for element (i,j)*/
-		}
-	}
+        for (i = 1; i <= len - b; i++) {
+            j = i + b;
+            //if (constraints[i] == -1 && constraints[j] == -1)
+            //  continue;
+            if (j-i >= contact_dist) continue;
+            if (chPair(RNA[i], RNA[j])) /* Check if bases i and j pair up or not */
+                calcVWM(i, j, INFINITY_, INFINITY_); /* Calculates V and WM array for element (i,j)*/
+            else
+                calcWM(i, j); /* Calculates WM array for element (i,j)*/
+        }
+    }
 
     /* For b=7 to 10, base pair (i,j) is not able to form multiloops. */
     for (b = 7; b <= 10; b++) {
@@ -245,8 +245,8 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
         for (i = 1; i <= len - b; i++) {
             j = i + b;
             //if (constraints[i] == -1 && constraints[j] == -1)
-            //	continue;
-			if (j-i >= contact_dist) continue;
+            //  continue;
+            if (j-i >= contact_dist) continue;
             if (chPair(RNA[i], RNA[j])) {
                 calcVBI(i, j); /* Calculates VBI element at (i,j) */
                 calcVWM(i, j, VBI[i][j], INFINITY_); /* Calculates V and WM arrays*/
@@ -263,8 +263,8 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
             j = i + b;
             //printf("%d %d: %d %d\n", i, j, constraints[i], constraints[j]);
             //if (constraints[i] == -1 && constraints[j] == -1)
-            //	continue;
-			if (j-i >= contact_dist) continue;
+            //  continue;
+            if (j-i >= contact_dist) continue;
             if (chPair(RNA[i], RNA[j])) {
                 calcVBIVMVWM(i, j); /* Calculates VBI, VM, V and WM elements at (i,j) */
             } else
@@ -275,960 +275,960 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
 /*
     for(j=2; j<=len; j++){
         for (i=j-1; i>0; i--){
-		    printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WM[i][j]);
+            printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WM[i][j]);
         }
     }
 */            
 
-	for (j = 5; j <= len; j++) /* Recurssion relation for W array does not depend upon any other array, so can be done after the computation of other arrays are finished.*/
-		calcW(j);
+    for (j = 5; j <= len; j++) /* Recurssion relation for W array does not depend upon any other array, so can be done after the computation of other arrays are finished.*/
+        calcW(j);
 
-	//printV(len);
+    //printV(len);
 
-	return W[len];
+    return W[len];
 }
 /* This function calculates the optimal energy of internal loops closed with base pair (i,j) using a heuristic, which limits their size to a constant value - MAXLOOP
  An internal loop contains one closing base pair (i,j) and one enclosed base pair (ip,jp). This function searches for the best enclosed base pair for the closing base pair (i,j) within the given window limited by MAXLOOP
  */
 void calcVBI(int i, int j) {
 
-	int ip, jp, temp, VBIij, thres1;
-
-	VBIij = INFINITY_;
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		return;
-
-	/* Having ip = i+1 and jp = j-1, creates a stack loop. Stack loops are taken care separately in the calculation of V  using eS() function. Therefore, for ip=i+1, the jp value should be lesser than or equal to j-2.*/
-	ip = i + 1;
-	thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of the hairpin loop which the enclosed base pair (ip,jp) can close is 3 that results in the minimum value of jp = ip+4 */
-	for (jp = thres1; jp <= j - 2; jp++) {
-		//May need to check the constraint condition here
-		if (jp-ip >= contact_dist) continue;
-		if (chPair(RNA[ip], RNA[jp])) {
-			if (checkSS(i, ip) || checkSS(jp, j))
-				continue;
-			temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the optimal energy of the substructure closed by (ip,jp)*/
-			if (VBIij > temp)
-				VBIij = temp;
-		}
-	}
-
-	for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) {
-		thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of a hairpin loop is 3, so start jp from ip+4*/
-		//May need to check for forced constraints here
-		for (jp = thres1; jp <= j - 1; jp++) {
-			if (jp-ip >= contact_dist) continue;
-			if (chPair(RNA[ip], RNA[jp])) {
-				if (checkSS(i, ip) || checkSS(jp, j))
-					continue;
-				temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the optimal energy of the substructure closed by (ip,jp)*/
-				if (VBIij > temp)
-					VBIij = temp;
-			}
-		}
-	}
-
-	VBI[i][j] = VBIij;
-	return;
+    int ip, jp, temp, VBIij, thres1;
+
+    VBIij = INFINITY_;
+
+    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
+            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
+                                                                           == -1)
+        return;
+
+    /* Having ip = i+1 and jp = j-1, creates a stack loop. Stack loops are taken care separately in the calculation of V  using eS() function. Therefore, for ip=i+1, the jp value should be lesser than or equal to j-2.*/
+    ip = i + 1;
+    thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of the hairpin loop which the enclosed base pair (ip,jp) can close is 3 that results in the minimum value of jp = ip+4 */
+    for (jp = thres1; jp <= j - 2; jp++) {
+        //May need to check the constraint condition here
+        if (jp-ip >= contact_dist) continue;
+        if (chPair(RNA[ip], RNA[jp])) {
+            if (checkSS(i, ip) || checkSS(jp, j))
+                continue;
+            temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the optimal energy of the substructure closed by (ip,jp)*/
+            if (VBIij > temp)
+                VBIij = temp;
+        }
+    }
+
+    for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) {
+        thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of a hairpin loop is 3, so start jp from ip+4*/
+        //May need to check for forced constraints here
+        for (jp = thres1; jp <= j - 1; jp++) {
+            if (jp-ip >= contact_dist) continue;
+            if (chPair(RNA[ip], RNA[jp])) {
+                if (checkSS(i, ip) || checkSS(jp, j))
+                    continue;
+                temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the optimal energy of the substructure closed by (ip,jp)*/
+                if (VBIij > temp)
+                    VBIij = temp;
+            }
+        }
+    }
+
+    VBI[i][j] = VBIij;
+    return;
 }
 
 /* Amrita: - Internal loop speedup algorithm */
 /* Calculation of internal loops using internal loop speedup algorithm. The algorithm calculates the optimal loop closed with base pair (i,j) */
 void calcVBIS(int i, int j) {
 
-	int ip, jp, E, VBIij, c = 3, b, len = LENGTH - 1, E1, E2, g; /* ip and jp form enclosed base pairs and c is a small constant currently taken as 3. The loops having one or both sides smaller than c are calculated as special cases. */
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		return;
-
-	VBIij = VBI[i][j];
-
-	/*Case1: Loops having first side shorter than c and second side has all allowable sizes */
-	/* Having ip = i+1 and jp=j-1 creates a stack which is considered separately in eS function. So here the max value of jp could be j-2*/
-	ip = i + 1;
-	for (jp = ip + 4; jp <= j - 2; jp++) {
-		if (jp-ip >= contact_dist) continue;
-		if (chPair(RNA[ip], RNA[jp])) {
-			E = eL(i, j, ip, jp) + V[indx[ip] + jp];
-			if (VBIij > E)
-				VBIij = E;
-		}
-	}
-
-	for (ip = i + 2; ip <= i + c; ip++) {
-		for (jp = ip + 4; jp <= j - 1; jp++) { /* Minimum size of a hairpin loop is 3.*/
-			if (jp-ip >= contact_dist) continue;
-			if (chPair(RNA[ip], RNA[jp])) {
-				E = eL(i, j, ip, jp) + V[indx[ip] + jp];
-				if (VBIij > E)
-					VBIij = E;
-			}
-		}
-	}
-
-	/*Case 2: When the first side is greater or equal to c but the second side is smaller */
-	for (ip = i + c + 1; ip < j - 1; ip++) {
-		for (jp = j - c; jp <= j - 1 && jp >= ip + 4; jp++) { /* Minimum size of a hairpin loop is 3.*/
-			if (jp-ip >= contact_dist) continue;
-			if (chPair(RNA[ip], RNA[jp])) {
-				E = eL(i, j, ip, jp) + V[indx[ip] + jp];
-				if (VBIij > E)
-					VBIij = E;
-			}
-		}
-	}
-
-	/* Case 3: General Case - when both sides of internal loops are greater than or equal to c */
-	/*Base cases for this (i,j) are g=j-i-2c-3 and j-i-2c-4, gap values should always be greater than or equal to 3*/
-	/* First base case - both sides of the loop are  equal to c.*/
-	ip = i + c + 1;
-	jp = j - c - 1;
-
-	g = jp - ip - 1;
-	if (g < 3) {
-		VBI[i][j] = VBIij;
-		return;
-	} /* if g is lesser than 3, then you don't extend this value. In this case the second base case of g-1=j-i-2c-4 will also not make a valid gap value. */
-
-	E = eL(i, j, ip, jp) + V[indx[ip] + jp];
-	if (VBIij > E)
-		VBIij = E;
-
-	/* Extend this base case for all closing base pairs of the form ( i-b, j+b ) */
-
-	for (b = 1; b <= MIN(i - 1, len - j); b++) {
-
-		E = eL(i - b, j + b, ip, jp) + V[indx[ip] + jp];
-
-		/* Two more options for base pair (i-b,j+b), which are introduced by having one of the side of the resultant internal loop exactly equal to c */
-		/* Second side is c - with closing base pair (i-b,j+b)*/
-		int ip1 = i + c + 1 + b;
-		int jp1 = (j + b) - c - 1;
-		E1 = eL(i - b, j + b, ip1, jp1) + V[indx[ip1] + jp1];
-
-		/* First side is c - with closing base pair (i-b,j+b)*/
-		int ip2 = (i - b) + c + 1;
-		int jp2 = j - c - 1 - b;
-		E2 = eL(i - b, j + b, ip2, jp2) + V[indx[ip2] + jp2];
-
-		if (E > E1) {
-			E = E1;
-			ip = ip1;
-			jp = jp1;
-		}
-		if (E > E2) {
-			E = E2;
-			ip = ip2;
-			jp = jp2;
-		}
-		if (VBI[i - b][j + b] > E) {
-			VBI[i - b][j + b] = E;
-		}
-	}
-
-	if (g == 3) {
-		VBI[i][j] = VBIij;
-		return;
-	} /* In this case the gap g-1=2, which should not be extended.*/
-	ip = i + c + 2;
-	jp = j - c - 1;
-	E1 = eL(i, j, ip, jp) + V[indx[ip] + jp];
-	E2 = eL(i, j, i + c + 1, j - c - 2) + V[indx[i + c + 1] + j - c - 2];
-	if (VBIij > E1)
-		VBIij = E1;
-	if (VBIij > E2)
-		VBIij = E2;
-
-	if (E2 < E1) {
-		ip = i + c + 1;
-		jp = j - c - 2;
-	}
-
-	for (b = 1; b <= MIN(i - 1, len - j); b++) {
-		E = eL(i - b, j + b, ip, jp) + V[indx[ip] + jp];
-
-		/*Two more options for base pair (i-b,j+b), having one of the sides equal to c */
-		/* First side is equal to c*/
-		int ip1 = (i - b) + c + 1;
-		int jp1 = (j) - c - 2 - b;
-		E1 = eL(i - b, j + b, ip1, jp1) + V[indx[ip1] + jp1];
-
-		/* Second side is equal to c*/
-		int ip2 = i + c + 2 + b;
-		int jp2 = (j + b) - c - 1;
-		E2 = eL(i - b, j + b, ip2, jp2) + V[indx[ip2] + jp2];
-
-		if (E > E1) {
-			E = E1;
-			ip = ip1;
-			jp = jp1;
-		}
-		if (E > E2) {
-			E = E2;
-			ip = ip2;
-			jp = jp2;
-		}
-		if (VBI[i - b][j + b] > E) {
-			VBI[i - b][j + b] = E;
-		}
-	}
-
-	VBI[i][j] = VBIij;
+    int ip, jp, E, VBIij, c = 3, b, len = LENGTH - 1, E1, E2, g; /* ip and jp form enclosed base pairs and c is a small constant currently taken as 3. The loops having one or both sides smaller than c are calculated as special cases. */
+
+    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
+            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
+                                                                           == -1)
+        return;
+
+    VBIij = VBI[i][j];
+
+    /*Case1: Loops having first side shorter than c and second side has all allowable sizes */
+    /* Having ip = i+1 and jp=j-1 creates a stack which is considered separately in eS function. So here the max value of jp could be j-2*/
+    ip = i + 1;
+    for (jp = ip + 4; jp <= j - 2; jp++) {
+        if (jp-ip >= contact_dist) continue;
+        if (chPair(RNA[ip], RNA[jp])) {
+            E = eL(i, j, ip, jp) + V[indx[ip] + jp];
+            if (VBIij > E)
+                VBIij = E;
+        }
+    }
+
+    for (ip = i + 2; ip <= i + c; ip++) {
+        for (jp = ip + 4; jp <= j - 1; jp++) { /* Minimum size of a hairpin loop is 3.*/
+            if (jp-ip >= contact_dist) continue;
+            if (chPair(RNA[ip], RNA[jp])) {
+                E = eL(i, j, ip, jp) + V[indx[ip] + jp];
+                if (VBIij > E)
+                    VBIij = E;
+            }
+        }
+    }
+
+    /*Case 2: When the first side is greater or equal to c but the second side is smaller */
+    for (ip = i + c + 1; ip < j - 1; ip++) {
+        for (jp = j - c; jp <= j - 1 && jp >= ip + 4; jp++) { /* Minimum size of a hairpin loop is 3.*/
+            if (jp-ip >= contact_dist) continue;
+            if (chPair(RNA[ip], RNA[jp])) {
+                E = eL(i, j, ip, jp) + V[indx[ip] + jp];
+                if (VBIij > E)
+                    VBIij = E;
+            }
+        }
+    }
+
+    /* Case 3: General Case - when both sides of internal loops are greater than or equal to c */
+    /*Base cases for this (i,j) are g=j-i-2c-3 and j-i-2c-4, gap values should always be greater than or equal to 3*/
+    /* First base case - both sides of the loop are  equal to c.*/
+    ip = i + c + 1;
+    jp = j - c - 1;
+
+    g = jp - ip - 1;
+    if (g < 3) {
+        VBI[i][j] = VBIij;
+        return;
+    } /* if g is lesser than 3, then you don't extend this value. In this case the second base case of g-1=j-i-2c-4 will also not make a valid gap value. */
+
+    E = eL(i, j, ip, jp) + V[indx[ip] + jp];
+    if (VBIij > E)
+        VBIij = E;
+
+    /* Extend this base case for all closing base pairs of the form ( i-b, j+b ) */
+
+    for (b = 1; b <= MIN(i - 1, len - j); b++) {
+
+        E = eL(i - b, j + b, ip, jp) + V[indx[ip] + jp];
+
+        /* Two more options for base pair (i-b,j+b), which are introduced by having one of the side of the resultant internal loop exactly equal to c */
+        /* Second side is c - with closing base pair (i-b,j+b)*/
+        int ip1 = i + c + 1 + b;
+        int jp1 = (j + b) - c - 1;
+        E1 = eL(i - b, j + b, ip1, jp1) + V[indx[ip1] + jp1];
+
+        /* First side is c - with closing base pair (i-b,j+b)*/
+        int ip2 = (i - b) + c + 1;
+        int jp2 = j - c - 1 - b;
+        E2 = eL(i - b, j + b, ip2, jp2) + V[indx[ip2] + jp2];
+
+        if (E > E1) {
+            E = E1;
+            ip = ip1;
+            jp = jp1;
+        }
+        if (E > E2) {
+            E = E2;
+            ip = ip2;
+            jp = jp2;
+        }
+        if (VBI[i - b][j + b] > E) {
+            VBI[i - b][j + b] = E;
+        }
+    }
+
+    if (g == 3) {
+        VBI[i][j] = VBIij;
+        return;
+    } /* In this case the gap g-1=2, which should not be extended.*/
+    ip = i + c + 2;
+    jp = j - c - 1;
+    E1 = eL(i, j, ip, jp) + V[indx[ip] + jp];
+    E2 = eL(i, j, i + c + 1, j - c - 2) + V[indx[i + c + 1] + j - c - 2];
+    if (VBIij > E1)
+        VBIij = E1;
+    if (VBIij > E2)
+        VBIij = E2;
+
+    if (E2 < E1) {
+        ip = i + c + 1;
+        jp = j - c - 2;
+    }
+
+    for (b = 1; b <= MIN(i - 1, len - j); b++) {
+        E = eL(i - b, j + b, ip, jp) + V[indx[ip] + jp];
+
+        /*Two more options for base pair (i-b,j+b), having one of the sides equal to c */
+        /* First side is equal to c*/
+        int ip1 = (i - b) + c + 1;
+        int jp1 = (j) - c - 2 - b;
+        E1 = eL(i - b, j + b, ip1, jp1) + V[indx[ip1] + jp1];
+
+        /* Second side is equal to c*/
+        int ip2 = i + c + 2 + b;
+        int jp2 = (j + b) - c - 1;
+        E2 = eL(i - b, j + b, ip2, jp2) + V[indx[ip2] + jp2];
+
+        if (E > E1) {
+            E = E1;
+            ip = ip1;
+            jp = jp1;
+        }
+        if (E > E2) {
+            E = E2;
+            ip = ip2;
+            jp = jp2;
+        }
+        if (VBI[i - b][j + b] > E) {
+            VBI[i - b][j + b] = E;
+        }
+    }
+
+    VBI[i][j] = VBIij;
 }
 
 /* Function for calculating the value of WM(i,j)*/
 void calcWM(int i, int j) {
 
-	int b = multConst[2], c = multConst[1]; /* b is the branch penalty and c is penalty for single bases for multiloops*/
-	int h;
-	/* WMidjd = dangling base on both ith and jth side.  WMidj = dangling base on ith side. WMijd = dangling base on jth side. WMij = no dangling base on both sides  */
-	int WMidjd, WMidj, WMijd, WMij, WMijp;
-	int rnai, rnaj;
-	rnai = RNA[i]; /* Read the value of RNA[i] and RNA[j] in register to make the program execute faster.*/
-	rnaj = RNA[j];
-
-	WMijp = INFINITY_; /* See, the data flow through the function - how it has been calculated. */
-
-	/* Minimum size of a hairpin loop is 3, that makes the starting limit of h=i+4 and end limit of j-5*/
-	for (h = i + 4; h < j - 4; h++) {
-		int temp = WM[i][h] + WM(h+1,j);
-		if (temp <= WMijp)
-			WMijp = temp;
-	}
-
-	WMidjd = INFINITY_;
-	WMidj = INFINITY_;
-	WMijd = INFINITY_;
-	WMij = INFINITY_;
-
-	/* If base i and j pair up. */
-	WMij = V[indx[i] + j] + auPen(rnai, rnaj) + b;
-	/* If base i+1 and j pair up. Add the dangling interaction energy of base pair (i+1,j) with base i being on the 3' end */
-	if (constraints[i] <= 0)
-		WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
-				RNA[i + 1], rnaj) + b + c;
-	/* If base i and j-1 pair up. Add the dangling interaction energy of base pair (i,j-1) with base j being on the 5' end */
-	if (constraints[j] <= 0)
-		WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
-				rnai, RNA[j - 1]) + b + c;
-	/* If base i+1 and j-1 pair up. Add the dangling interaction energy of base pair (i+1,j-1) with base i on the 3' and base j on the 5' end.*/
-	if (constraints[i] <= 0 && constraints[j] <= 0)
-		WMidjd = V[indx[i + 1] + j - 1]
-		           + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
-		                                                  + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
-		                                                		  RNA[j - 1]) + b + 2* c ;
-
-	//	if(i==6 && j==11)
-	//	  printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d, constraints: (%d,%d)\n", i, j, WMij, WMidj, WMijd, WMidjd, constraints[i], constraints[j]);
-
-	/* Take the minimum of all of the terms */
-	WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
-
-	int WMsip1j = INFINITY_;
-	int WMsijm1 = INFINITY_;
-
-	if (constraints[i] <= 0)
-		WMsip1j = WM[i + 1][j];
-
-	if (constraints[j] <= 0)
-		WMsijm1 = WM[i][j - 1];
-
-
-	WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
-	WMij = MIN(WMijp, WMij);
-
-	//printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
-
-	WM[i][j] = WMij;
-	WM(i,j) = WMij; /* Extra instruction. NOTE that - by having this instruction we are making WM array symmetric. The macro will convert this instruction into WM[j][i] = WM[i][j] making WM array symmetric.*/
-	return;
+    int b = multConst[2], c = multConst[1]; /* b is the branch penalty and c is penalty for single bases for multiloops*/
+    int h;
+    /* WMidjd = dangling base on both ith and jth side.  WMidj = dangling base on ith side. WMijd = dangling base on jth side. WMij = no dangling base on both sides  */
+    int WMidjd, WMidj, WMijd, WMij, WMijp;
+    int rnai, rnaj;
+    rnai = RNA[i]; /* Read the value of RNA[i] and RNA[j] in register to make the program execute faster.*/
+    rnaj = RNA[j];
+
+    WMijp = INFINITY_; /* See, the data flow through the function - how it has been calculated. */
+
+    /* Minimum size of a hairpin loop is 3, that makes the starting limit of h=i+4 and end limit of j-5*/
+    for (h = i + 4; h < j - 4; h++) {
+        int temp = WM[i][h] + WM(h+1,j);
+        if (temp <= WMijp)
+            WMijp = temp;
+    }
+
+    WMidjd = INFINITY_;
+    WMidj = INFINITY_;
+    WMijd = INFINITY_;
+    WMij = INFINITY_;
+
+    /* If base i and j pair up. */
+    WMij = V[indx[i] + j] + auPen(rnai, rnaj) + b;
+    /* If base i+1 and j pair up. Add the dangling interaction energy of base pair (i+1,j) with base i being on the 3' end */
+    if (constraints[i] <= 0)
+        WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
+                RNA[i + 1], rnaj) + b + c;
+    /* If base i and j-1 pair up. Add the dangling interaction energy of base pair (i,j-1) with base j being on the 5' end */
+    if (constraints[j] <= 0)
+        WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
+                rnai, RNA[j - 1]) + b + c;
+    /* If base i+1 and j-1 pair up. Add the dangling interaction energy of base pair (i+1,j-1) with base i on the 3' and base j on the 5' end.*/
+    if (constraints[i] <= 0 && constraints[j] <= 0)
+        WMidjd = V[indx[i + 1] + j - 1]
+                   + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
+                                                          + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
+                                                                  RNA[j - 1]) + b + 2* c ;
+
+    //  if(i==6 && j==11)
+    //    printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d, constraints: (%d,%d)\n", i, j, WMij, WMidj, WMijd, WMidjd, constraints[i], constraints[j]);
+
+    /* Take the minimum of all of the terms */
+    WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
+
+    int WMsip1j = INFINITY_;
+    int WMsijm1 = INFINITY_;
+
+    if (constraints[i] <= 0)
+        WMsip1j = WM[i + 1][j];
+
+    if (constraints[j] <= 0)
+        WMsijm1 = WM[i][j - 1];
+
+
+    WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
+    WMij = MIN(WMijp, WMij);
+
+    //printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
+
+    WM[i][j] = WMij;
+    WM(i,j) = WMij; /* Extra instruction. NOTE that - by having this instruction we are making WM array symmetric. The macro will convert this instruction into WM[j][i] = WM[i][j] making WM array symmetric.*/
+    return;
 }
 
 /* Function used for calculating the value of V and WM for a given i,j pair. Calculation of WM at (i,j) requires value of V at (i,j)*/
 void calcVWM(int i, int j, int VBIij, int VMij) {
-	int a, b, c, h, Vij, eh, es;
-	int WMidjd, WMidj, WMijd, WMij, WMijp;
-	int rnai, rnaj;
-
-	rnai = RNA[i];
-	rnaj = RNA[j];
-
-	WMidjd = INFINITY_;
-	WMidj = INFINITY_;
-	WMijd = INFINITY_;
-	WMij = INFINITY_;
-
-	/* V starts */
-	eh = eH(i, j); /* Energy of a hairpin loop */
-	es = eS(i, j); /* Energy of a stack, with (i,j) and (i-1,j+1) base pairs.*/
-	if (es == 0) {
-		es = INFINITY_;
-	} else
-		es += V[indx[i + 1] + j - 1];
-
-	Vij = MIN(MIN(eh, es), MIN(VBIij, VMij));
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		Vij = INFINITY_;
-
-	// printf("%d, V(%d,%d): eh: %d, es: %d, vbi: %d, vm: %d, v: %d\n", j-i, i, j, eh, es, VBIij, VMij, Vij);
-
-	V[indx[i] + j] = Vij;
-
-	if (NOISOLATE == TRUE && Vij < INFINITY_) {
-		//Check if i+1,j-1 have paired
-		if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) {
-			//If not then check for i-1, j+1
-
-			//Isolated base pairs look ahead
-			int eHL = eH(i - 1, j + 1);
-			int eSL = eS(i - 1, j + 1) + V[indx[i] + j];
-			if (i - 1 == 0) {
-				eSL = 0;
-				eHL = 0;
-			}
-			int Vijl = (eHL < eSL) ? eHL : eSL;
-			// printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl);
-
-			if (Vijl > INFINITY_ - SMALLINFTY_)
-				//isolated base pair found.. setting energy to infinity
-				V[indx[i] + j] = Vij = INFINITY_;
-		}
-	}
+    int a, b, c, h, Vij, eh, es;
+    int WMidjd, WMidj, WMijd, WMij, WMijp;
+    int rnai, rnaj;
+
+    rnai = RNA[i];
+    rnaj = RNA[j];
+
+    WMidjd = INFINITY_;
+    WMidj = INFINITY_;
+    WMijd = INFINITY_;
+    WMij = INFINITY_;
+
+    /* V starts */
+    eh = eH(i, j); /* Energy of a hairpin loop */
+    es = eS(i, j); /* Energy of a stack, with (i,j) and (i-1,j+1) base pairs.*/
+    if (es == 0) {
+        es = INFINITY_;
+    } else
+        es += V[indx[i + 1] + j - 1];
+
+    Vij = MIN(MIN(eh, es), MIN(VBIij, VMij));
+
+    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
+            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
+                                                                           == -1)
+        Vij = INFINITY_;
+
+    // printf("%d, V(%d,%d): eh: %d, es: %d, vbi: %d, vm: %d, v: %d\n", j-i, i, j, eh, es, VBIij, VMij, Vij);
+
+    V[indx[i] + j] = Vij;
+
+    if (NOISOLATE == TRUE && Vij < INFINITY_) {
+        //Check if i+1,j-1 have paired
+        if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) {
+            //If not then check for i-1, j+1
+
+            //Isolated base pairs look ahead
+            int eHL = eH(i - 1, j + 1);
+            int eSL = eS(i - 1, j + 1) + V[indx[i] + j];
+            if (i - 1 == 0) {
+                eSL = 0;
+                eHL = 0;
+            }
+            int Vijl = (eHL < eSL) ? eHL : eSL;
+            // printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl);
+
+            if (Vijl > INFINITY_ - SMALLINFTY_)
+                //isolated base pair found.. setting energy to infinity
+                V[indx[i] + j] = Vij = INFINITY_;
+        }
+    }
 
 #if DEBUG
-	if (indx[i]+j > (LENGTH-1)*(LENGTH)/2)
-		fprintf(stderr,"ERROR: in calcVMW: i: %5d  j: %5d\n",i,j);
+    if (indx[i]+j > (LENGTH-1)*(LENGTH)/2)
+        fprintf(stderr,"ERROR: in calcVMW: i: %5d  j: %5d\n",i,j);
 #endif
-	/* V ends */
-
-	/* WM starts */
-	a = multConst[0];
-	b = multConst[2];
-	c = multConst[1];
-	WMijp = INFINITY_;
-
-	for (h = i + 4; h <= j - 5; h++) {
-		int temp = WM[i][h] + WM(h+1,j);
-		if (temp < WMijp)
-			WMijp = temp;
-	}
+    /* V ends */
+
+    /* WM starts */
+    a = multConst[0];
+    b = multConst[2];
+    c = multConst[1];
+    WMijp = INFINITY_;
+
+    for (h = i + 4; h <= j - 5; h++) {
+        int temp = WM[i][h] + WM(h+1,j);
+        if (temp < WMijp)
+            WMijp = temp;
+    }
 
-	WMij = Vij + auPen(rnai, rnaj) + b;
+    WMij = Vij + auPen(rnai, rnaj) + b;
 
-	if (constraints[i] <= 0)
-		WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
-				RNA[i + 1], rnaj) + b + c;
+    if (constraints[i] <= 0)
+        WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
+                RNA[i + 1], rnaj) + b + c;
 
-	if (constraints[j] <= 0)
-		WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
-				rnai, RNA[j - 1]) + b + c;
+    if (constraints[j] <= 0)
+        WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
+                rnai, RNA[j - 1]) + b + c;
 
-	if (constraints[i] <= 0 && constraints[j] <= 0)
-		WMidjd = V[indx[i + 1] + j - 1]
-		           + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
-		                                                  + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
-		                                                		  RNA[j - 1]) + b + 2* c ;
+    if (constraints[i] <= 0 && constraints[j] <= 0)
+        WMidjd = V[indx[i + 1] + j - 1]
+                   + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
+                                                          + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
+                                                                  RNA[j - 1]) + b + 2* c ;
 
-	WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
+    WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
 
-	int WMsip1j = INFINITY_;
-	int WMsijm1 = INFINITY_;
+    int WMsip1j = INFINITY_;
+    int WMsijm1 = INFINITY_;
 
-	if (constraints[i] <= 0)
-		WMsip1j = WM[i + 1][j];
+    if (constraints[i] <= 0)
+        WMsip1j = WM[i + 1][j];
 
-	if (constraints[j] <= 0)
-		WMsijm1 = WM[i][j - 1];
+    if (constraints[j] <= 0)
+        WMsijm1 = WM[i][j - 1];
 
-	WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
-	WMij = MIN(WMijp, WMij);
+    WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
+    WMij = MIN(WMijp, WMij);
 
-	//printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
+    //printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
 
-	WM[i][j] = WMij;
-	WM(i,j) = WMij; /* extra instruction */
-	/* WM ends */
-	return;
+    WM[i][j] = WMij;
+    WM(i,j) = WMij; /* extra instruction */
+    /* WM ends */
+    return;
 }
 
 /* Function for calculating VM, V, and WM at point (i,j) in the order . Calculation of V at (i,j) requires VBI and VM. Also, calculation of final value of WM(i,j) requires V at (i,j) */
 
 void calcVMVWM(int i, int j) {
 
-	int a = multConst[0] /*offset penalty for multiloops*/,
-	b = multConst[2]/*penalty per branch for multiloops*/, c =
-		multConst[1]/* Penalty per single base in the multiloop*/,
-		a1, h, es;
-	int aupen;
-	int WMijp, WMidjd, WMidj, WMijd, WMij;
-	int VMij, VMijd, VMidj, VMidjd, A_temp;
-	int WMip1hm1 /* WM value at i+1 and j-1 */,
-	WMip2hm1/* WM value at i+2 and h-1*/,
-	WMhjm1/* WM value at h and j-1*/, WMhjm2/* WM value at h and j-2*/,
-	WMhp1j /*WM value at h+1 and j*/;
-	int rnai, rnaj;
-	int tmp1, tmp2;
-
-	rnai = RNA[i];
-	rnaj = RNA[j];
-
-	WMidjd = INFINITY_;
-	WMidj = INFINITY_;
-	WMijd = INFINITY_;
-	WMij = INFINITY_;
-
-	/* VM and WM starts */
-	aupen = auPen(rnai, rnaj); /* AU or NON GC penalty for base pair (i,j) */
-	VMij = INFINITY_;
-	VMijd = INFINITY_;
-	VMidj = INFINITY_;
-	VMidjd = INFINITY_;
-
-	/* Manoj starts */
-
-	WMijp = WM[i][i + 4] + WM(i+5,j);
-	a1 = WM[i][i + 5] + WM(i+6,j);
-	if (a1 <= WMijp)
-		WMijp = a1;
-
-	/* Here we are doing the calculation of VM and WM at point (i,j) concurrently. This for loop calculates the values of VMij, VMidj, VMijd, VMidjd with the value of WMijp. The value of WMijp is needed for calculating the value of WM at (i,j). However, it should be noted that the final value of WM[i][j] requires value of V at (i,j) and will be calculated in the end. */
-
-	/* There are four possibilities for the multiloop closing base pair for the inclusion of dangling energies.
-	 * 1) Including the dangling energy of i+1 base and also for base j-1 with the base pair (i,j) closing the multiloop - VMidjd
-	 * 2) Including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j) - VMidj
-	 * 3) NOT including the danlging energy of i+1 base and including the dangling energy of base j-1 with the closing base pair (i,j) - VMijd
-	 * 4) NOT including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j)-VMij
-	 * */
-	for (h = i + 6; h <= j - 5; h++) {
-
-		a1 = WM[i][h];
-		WMip1hm1 = WM[i + 1][h - 1];
-		WMip2hm1 = WM[i + 2][h - 1];
+    int a = multConst[0] /*offset penalty for multiloops*/,
+    b = multConst[2]/*penalty per branch for multiloops*/, c =
+        multConst[1]/* Penalty per single base in the multiloop*/,
+        a1, h, es;
+    int aupen;
+    int WMijp, WMidjd, WMidj, WMijd, WMij;
+    int VMij, VMijd, VMidj, VMidjd, A_temp;
+    int WMip1hm1 /* WM value at i+1 and j-1 */,
+    WMip2hm1/* WM value at i+2 and h-1*/,
+    WMhjm1/* WM value at h and j-1*/, WMhjm2/* WM value at h and j-2*/,
+    WMhp1j /*WM value at h+1 and j*/;
+    int rnai, rnaj;
+    int tmp1, tmp2;
+
+    rnai = RNA[i];
+    rnaj = RNA[j];
+
+    WMidjd = INFINITY_;
+    WMidj = INFINITY_;
+    WMijd = INFINITY_;
+    WMij = INFINITY_;
+
+    /* VM and WM starts */
+    aupen = auPen(rnai, rnaj); /* AU or NON GC penalty for base pair (i,j) */
+    VMij = INFINITY_;
+    VMijd = INFINITY_;
+    VMidj = INFINITY_;
+    VMidjd = INFINITY_;
+
+    /* Manoj starts */
+
+    WMijp = WM[i][i + 4] + WM(i+5,j);
+    a1 = WM[i][i + 5] + WM(i+6,j);
+    if (a1 <= WMijp)
+        WMijp = a1;
+
+    /* Here we are doing the calculation of VM and WM at point (i,j) concurrently. This for loop calculates the values of VMij, VMidj, VMijd, VMidjd with the value of WMijp. The value of WMijp is needed for calculating the value of WM at (i,j). However, it should be noted that the final value of WM[i][j] requires value of V at (i,j) and will be calculated in the end. */
+
+    /* There are four possibilities for the multiloop closing base pair for the inclusion of dangling energies.
+     * 1) Including the dangling energy of i+1 base and also for base j-1 with the base pair (i,j) closing the multiloop - VMidjd
+     * 2) Including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j) - VMidj
+     * 3) NOT including the danlging energy of i+1 base and including the dangling energy of base j-1 with the closing base pair (i,j) - VMijd
+     * 4) NOT including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j)-VMij
+     * */
+    for (h = i + 6; h <= j - 5; h++) {
+
+        a1 = WM[i][h];
+        WMip1hm1 = WM[i + 1][h - 1];
+        WMip2hm1 = WM[i + 2][h - 1];
 #if 0
-		WMhjm1 = WM[h][j-1];
-		WMhjm2 = WM[h][j-2];
-		WMhp1j = WM[h+1][j];
+        WMhjm1 = WM[h][j-1];
+        WMhjm2 = WM[h][j-2];
+        WMhp1j = WM[h+1][j];
 #else
-		WMhjm1 = WM(h,j-1); /* Preprocessor will convert this into WM[j-1][h]. According to the algorithm, the expression should be WM[h][j-1]  -- in which case, as the value of h changes, this will access elements from a column of the WM matrix. To improve run time performance WM array is made symmetric and so WM[h][j-1] = WM[j-1][h] and it will have accesses in a row.*/
-		WMhjm2 = WM(h,j-2); /* Same reason as above */
-		WMhp1j = WM(h+1,j); /* Same reason as above */
+        WMhjm1 = WM(h,j-1); /* Preprocessor will convert this into WM[j-1][h]. According to the algorithm, the expression should be WM[h][j-1]  -- in which case, as the value of h changes, this will access elements from a column of the WM matrix. To improve run time performance WM array is made symmetric and so WM[h][j-1] = WM[j-1][h] and it will have accesses in a row.*/
+        WMhjm2 = WM(h,j-2); /* Same reason as above */
+        WMhp1j = WM(h+1,j); /* Same reason as above */
 #endif
 
-		/* WM starts */
-		a1 += WMhp1j;
-		if (a1 <= WMijp)
-			WMijp = a1;
-		/* WM ends */
-
-		/* Calculation of the four options for VM*/
-		A_temp = WMip1hm1 + WMhjm1;
-		if ((A_temp <= VMij))
-			VMij = A_temp;
-
-		A_temp = WMip2hm1 + WMhjm1;
-		if (A_temp <= VMidj && constraints[i + 1] <= 0)
-			VMidj = A_temp;
-
-		A_temp = WMip1hm1 + WMhjm2;
-		if (A_temp <= VMijd && constraints[j - 1] <= 0)
-			VMijd = A_temp;
-
-		A_temp = WMip2hm1 + WMhjm2;
-		if (A_temp <= VMidjd && constraints[i + 1] <= 0 && constraints[j - 1]
-		                                                               <= 0)
-			VMidjd = A_temp;
-	}
+        /* WM starts */
+        a1 += WMhp1j;
+        if (a1 <= WMijp)
+            WMijp = a1;
+        /* WM ends */
+
+        /* Calculation of the four options for VM*/
+        A_temp = WMip1hm1 + WMhjm1;
+        if ((A_temp <= VMij))
+            VMij = A_temp;
+
+        A_temp = WMip2hm1 + WMhjm1;
+        if (A_temp <= VMidj && constraints[i + 1] <= 0)
+            VMidj = A_temp;
+
+        A_temp = WMip1hm1 + WMhjm2;
+        if (A_temp <= VMijd && constraints[j - 1] <= 0)
+            VMijd = A_temp;
+
+        A_temp = WMip2hm1 + WMhjm2;
+        if (A_temp <= VMidjd && constraints[i + 1] <= 0 && constraints[j - 1]
+                                                                       <= 0)
+            VMidjd = A_temp;
+    }
 
 #if 0
-	VMidj += dangle[rnai][rnaj][RNA[i+1]][0];
-	VMijd += dangle[rnai][rnaj][RNA[j-1]][1];
-	VMidjd += dangle[rnai][rnaj][RNA[i+1]][0] + dangle[rnai][rnaj][RNA[j-1]][1];
+    VMidj += dangle[rnai][rnaj][RNA[i+1]][0];
+    VMijd += dangle[rnai][rnaj][RNA[j-1]][1];
+    VMidjd += dangle[rnai][rnaj][RNA[i+1]][0] + dangle[rnai][rnaj][RNA[j-1]][1];
 #else
-	tmp1 = dangle[rnai][rnaj][RNA[i + 1]][0]; /* Dangling energy of base pair (i,j) with single base i+1 at 5' end */
-	tmp2 = dangle[rnai][rnaj][RNA[j - 1]][1]; /* Dangling energy of base pair (i,j) with single base j-1 at 3' end */
-	VMidj += (tmp1 + c);
-	VMidjd += (tmp1 + c);
-	VMijd += (tmp2 + c);
-	VMidjd += (tmp2 + c);
+    tmp1 = dangle[rnai][rnaj][RNA[i + 1]][0]; /* Dangling energy of base pair (i,j) with single base i+1 at 5' end */
+    tmp2 = dangle[rnai][rnaj][RNA[j - 1]][1]; /* Dangling energy of base pair (i,j) with single base j-1 at 3' end */
+    VMidj += (tmp1 + c);
+    VMidjd += (tmp1 + c);
+    VMijd += (tmp2 + c);
+    VMidjd += (tmp2 + c);
 #endif
 
-	/* Manoj ends */
-
-	VMij = MIN(MIN(VMij, VMidj), MIN(VMijd, VMidjd));
-	VMij = VMij + b + a + aupen;
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		VMij = INFINITY_;
-
-	VM[i][j] = VMij;
-	/* VM ends */
-
-	/* V starts */
-	es = eS(i, j);
-	if (es == 0) {
-		es = INFINITY_;
-	} else
-		es += V[indx[i + 1] + j - 1];
-
-	int Vij;
-	Vij = MIN(MIN(eH(i, j), es), MIN(VBI[i][j], VMij));
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		Vij = INFINITY_;
-
-	V[indx[i] + j] = Vij;
-
-	if (NOISOLATE == TRUE && Vij < INFINITY_) {
-		//Check if i+1,j-1 have paired
-		if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) {
-			//If not then check for i-1, j+1
-
-			//Isolated base pairs look ahead
-			int eHL = eH(i - 1, j + 1);
-			int eSL = eS(i - 1, j + 1) + V[indx[i] + j];
-			if (i - 1 == 0) {
-				eSL = 0;
-				eHL = 0;
-			}
-			int Vijl = (eHL < eSL) ? eHL : eSL;
-			//printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl);
-
-			if (Vijl > INFINITY_ - SMALLINFTY_)
-				//isolated base pair found.. setting energy to infinity
-				V[indx[i] + j] = Vij = INFINITY_;
-		}
-	}
+    /* Manoj ends */
+
+    VMij = MIN(MIN(VMij, VMidj), MIN(VMijd, VMidjd));
+    VMij = VMij + b + a + aupen;
+
+    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
+            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
+                                                                           == -1)
+        VMij = INFINITY_;
+
+    VM[i][j] = VMij;
+    /* VM ends */
+
+    /* V starts */
+    es = eS(i, j);
+    if (es == 0) {
+        es = INFINITY_;
+    } else
+        es += V[indx[i + 1] + j - 1];
+
+    int Vij;
+    Vij = MIN(MIN(eH(i, j), es), MIN(VBI[i][j], VMij));
+
+    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
+            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
+                                                                           == -1)
+        Vij = INFINITY_;
+
+    V[indx[i] + j] = Vij;
+
+    if (NOISOLATE == TRUE && Vij < INFINITY_) {
+        //Check if i+1,j-1 have paired
+        if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) {
+            //If not then check for i-1, j+1
+
+            //Isolated base pairs look ahead
+            int eHL = eH(i - 1, j + 1);
+            int eSL = eS(i - 1, j + 1) + V[indx[i] + j];
+            if (i - 1 == 0) {
+                eSL = 0;
+                eHL = 0;
+            }
+            int Vijl = (eHL < eSL) ? eHL : eSL;
+            //printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl);
+
+            if (Vijl > INFINITY_ - SMALLINFTY_)
+                //isolated base pair found.. setting energy to infinity
+                V[indx[i] + j] = Vij = INFINITY_;
+        }
+    }
 
 #if DEBUG
-	if (indx[i]+j > (LENGTH-1)*(LENGTH)/2)
-		fprintf(stderr,"ERROR: in calcVBIVMVWM: i: %5d  j: %5d\n",i,j);
+    if (indx[i]+j > (LENGTH-1)*(LENGTH)/2)
+        fprintf(stderr,"ERROR: in calcVBIVMVWM: i: %5d  j: %5d\n",i,j);
 #endif
 
-	/* V ends */
+    /* V ends */
 
-	/* WM starts */
+    /* WM starts */
 
-	//Need to take care of these WMs
-	WMij = Vij + auPen(rnai, rnaj) + b;
+    //Need to take care of these WMs
+    WMij = Vij + auPen(rnai, rnaj) + b;
 
-	if (constraints[i] <= 0)
-		WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
-				RNA[i + 1], rnaj) + b + c;
+    if (constraints[i] <= 0)
+        WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
+                RNA[i + 1], rnaj) + b + c;
 
-	if (constraints[j] <= 0)
-		WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
-				rnai, RNA[j - 1]) + b + c;
+    if (constraints[j] <= 0)
+        WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
+                rnai, RNA[j - 1]) + b + c;
 
-	if (constraints[i] <= 0 && constraints[j] <= 0)
-		WMidjd = V[indx[i + 1] + j - 1]
-		           + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
-		                                                  + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
-		                                                		  RNA[j - 1]) + b + 2* c ;
+    if (constraints[i] <= 0 && constraints[j] <= 0)
+        WMidjd = V[indx[i + 1] + j - 1]
+                   + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
+                                                          + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
+                                                                  RNA[j - 1]) + b + 2* c ;
 
-	WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
+    WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
 
-	int WMsip1j = INFINITY_;
-	int WMsijm1 = INFINITY_;
+    int WMsip1j = INFINITY_;
+    int WMsijm1 = INFINITY_;
 
-	if (constraints[i] <= 0)
-		WMsip1j = WM[i + 1][j];
+    if (constraints[i] <= 0)
+        WMsip1j = WM[i + 1][j];
 
-	if (constraints[j] <= 0)
-		WMsijm1 = WM[i][j - 1];
+    if (constraints[j] <= 0)
+        WMsijm1 = WM[i][j - 1];
 
-	WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
+    WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
 
-	//printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
+    //printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
 
-	WM[i][j] = MIN(WMijp, WMij);
-	WM(i,j) = WM[i][j]; /* extra instruction */
-	/* WM ends */
+    WM[i][j] = MIN(WMijp, WMij);
+    WM(i,j) = WM[i][j]; /* extra instruction */
+    /* WM ends */
 
-	return;
+    return;
 }
 
 /* Calculation of VBI, VM, V and WM in the order. Calculation of V at (i,j) requires VBI and VM. Also, calculation of final value of WM(i,j) requires V at (i,j) */
 void calcVBIVMVWM(int i, int j) {
 
-	int ip, jp, temp, VBIij, thres1;
-	int
-	a = multConst[0] /*a is an offset penalty for multiloops */,
-	b = multConst[2]/* b is penalty for multiloop branches, one per branch*/,
-	c = multConst[1] /*Penalty for single stranded nucleotides in the multiloops*/,
-	a1, h, es;
-	int aupen;
-	int WMijp, WMidjd, WMidj, WMijd, WMij;
-	int VMij, VMijd, VMidj, VMidjd, A_temp;
-	int WMip1hm1 /* WM value at i+1 and h-1 */,
-	WMip2hm1 /* WM value at i+2 and j-1*/,
-	WMhjm1 /*WM value at h and j-1*/,
-	WMhjm2 /* WM value at h and j-2*/, WMhp1j /*WM value at h+1 and j*/;
-	int rnai, rnaj;
-	int tmp1, tmp2;
-
-	rnai = RNA[i];
-	rnaj = RNA[j];
-
-	WMidjd = INFINITY_;
-	WMidj = INFINITY_;
-	WMijd = INFINITY_;
-	WMij = INFINITY_;
-
-	/* VBI starts */
-	/* Look at the calcVBI function for explanation of internal loop calculations*/
-	VBIij = INFINITY_;
-
-	int ifinal, jfinal;
-	/* ip=i+1, jp=j-1 closes a stack, so we should set the jp limit till j-2, in the following loop*/
-	ip = i + 1;
-	thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of a hairpin loop is 3. So, start jp from ip+4 */
-	for (jp = thres1; jp <= j - 2; jp++) {
-		if (jp-ip >= contact_dist) continue;
-		if (chPair(RNA[ip], RNA[jp])) {
-			if (checkSS(i, ip) || checkSS(jp, j))
-				continue;
-			temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the energy of structure closed by (ip, jp)*/
-			if (VBIij > temp) {
-				VBIij = temp;
-				ifinal = ip;
-				jfinal = jp;
-			}
-		}
-	}
-
-	for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) {
-		thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4);
-		for (jp = thres1; jp <= j - 1; jp++) {
-			if (jp-ip >= contact_dist) continue;
-			if (chPair(RNA[ip], RNA[jp])) {
-				if (checkSS(i, ip) || checkSS(jp, j))
-					continue;
-				temp = eL(i, j, ip, jp) + V[indx[ip] + jp];
-				if (VBIij > temp) {
-					VBIij = temp;
-					ifinal = ip;
-					jfinal = jp;
-				}
-			}
-		}
-	}
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		VBIij = INFINITY_;
-
-	VBI[i][j] = VBIij;
-	/* VBI ends */
-
-	/* VM and WM starts */
-	aupen = auPen(rnai, rnaj);
-
-	/* Here we are doing the calculation of VM and WM at point (i,j) concurrently. The following for loop calculates the values of VMij, VMidj, VMijd, VMidjd with the value of WMijp. The value of WMijp is needed for calculating the value of WM at (i,j). However, it should be noted that the final value of WM[i][j] requires value of V at (i,j) which itself require VM(i,j), and will be calculated in the end. */
-
-	/* There are four possibilities for the multiloop closing base pair for the inclusion of dangling energies.
-	 * 1) Including the dangling energy of i+1 base and also for base j-1 with the base pair (i,j) closing the multiloop - VMidjd
-	 * 2) Including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j) - VMidj
-	 * 3) NOT including the danlging energy of i+1 base and including the dangling energy of base j-1 with the closing base pair (i,j) - VMijd
-	 * 4) NOT including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j)-VMij
-	 * */
-
-	VMij = INFINITY_;
-	VMijd = INFINITY_;
-	VMidj = INFINITY_;
-	VMidjd = INFINITY_;
-
-	/* Manoj starts */
-	/* Merged calculations of WM(i,j) and VM(i,j)*/
-	WMijp = WM[i][i + 4] + WM(i+5,j);
-	a1 = WM[i][i + 5] + WM(i+6,j);
-	if (a1 <= WMijp)
-		WMijp = a1;
-
-	for (h = i + 6; h <= j - 5; h++) {
-
-		a1 = WM[i][h];
-		WMip1hm1 = WM[i + 1][h - 1];
-		WMip2hm1 = WM[i + 2][h - 1];
+    int ip, jp, temp, VBIij, thres1;
+    int
+    a = multConst[0] /*a is an offset penalty for multiloops */,
+    b = multConst[2]/* b is penalty for multiloop branches, one per branch*/,
+    c = multConst[1] /*Penalty for single stranded nucleotides in the multiloops*/,
+    a1, h, es;
+    int aupen;
+    int WMijp, WMidjd, WMidj, WMijd, WMij;
+    int VMij, VMijd, VMidj, VMidjd, A_temp;
+    int WMip1hm1 /* WM value at i+1 and h-1 */,
+    WMip2hm1 /* WM value at i+2 and j-1*/,
+    WMhjm1 /*WM value at h and j-1*/,
+    WMhjm2 /* WM value at h and j-2*/, WMhp1j /*WM value at h+1 and j*/;
+    int rnai, rnaj;
+    int tmp1, tmp2;
+
+    rnai = RNA[i];
+    rnaj = RNA[j];
+
+    WMidjd = INFINITY_;
+    WMidj = INFINITY_;
+    WMijd = INFINITY_;
+    WMij = INFINITY_;
+
+    /* VBI starts */
+    /* Look at the calcVBI function for explanation of internal loop calculations*/
+    VBIij = INFINITY_;
+
+    int ifinal, jfinal;
+    /* ip=i+1, jp=j-1 closes a stack, so we should set the jp limit till j-2, in the following loop*/
+    ip = i + 1;
+    thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of a hairpin loop is 3. So, start jp from ip+4 */
+    for (jp = thres1; jp <= j - 2; jp++) {
+        if (jp-ip >= contact_dist) continue;
+        if (chPair(RNA[ip], RNA[jp])) {
+            if (checkSS(i, ip) || checkSS(jp, j))
+                continue;
+            temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the energy of structure closed by (ip, jp)*/
+            if (VBIij > temp) {
+                VBIij = temp;
+                ifinal = ip;
+                jfinal = jp;
+            }
+        }
+    }
+
+    for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) {
+        thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4);
+        for (jp = thres1; jp <= j - 1; jp++) {
+            if (jp-ip >= contact_dist) continue;
+            if (chPair(RNA[ip], RNA[jp])) {
+                if (checkSS(i, ip) || checkSS(jp, j))
+                    continue;
+                temp = eL(i, j, ip, jp) + V[indx[ip] + jp];
+                if (VBIij > temp) {
+                    VBIij = temp;
+                    ifinal = ip;
+                    jfinal = jp;
+                }
+            }
+        }
+    }
+
+    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
+            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
+                                                                           == -1)
+        VBIij = INFINITY_;
+
+    VBI[i][j] = VBIij;
+    /* VBI ends */
+
+    /* VM and WM starts */
+    aupen = auPen(rnai, rnaj);
+
+    /* Here we are doing the calculation of VM and WM at point (i,j) concurrently. The following for loop calculates the values of VMij, VMidj, VMijd, VMidjd with the value of WMijp. The value of WMijp is needed for calculating the value of WM at (i,j). However, it should be noted that the final value of WM[i][j] requires value of V at (i,j) which itself require VM(i,j), and will be calculated in the end. */
+
+    /* There are four possibilities for the multiloop closing base pair for the inclusion of dangling energies.
+     * 1) Including the dangling energy of i+1 base and also for base j-1 with the base pair (i,j) closing the multiloop - VMidjd
+     * 2) Including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j) - VMidj
+     * 3) NOT including the danlging energy of i+1 base and including the dangling energy of base j-1 with the closing base pair (i,j) - VMijd
+     * 4) NOT including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j)-VMij
+     * */
+
+    VMij = INFINITY_;
+    VMijd = INFINITY_;
+    VMidj = INFINITY_;
+    VMidjd = INFINITY_;
+
+    /* Manoj starts */
+    /* Merged calculations of WM(i,j) and VM(i,j)*/
+    WMijp = WM[i][i + 4] + WM(i+5,j);
+    a1 = WM[i][i + 5] + WM(i+6,j);
+    if (a1 <= WMijp)
+        WMijp = a1;
+
+    for (h = i + 6; h <= j - 5; h++) {
+
+        a1 = WM[i][h];
+        WMip1hm1 = WM[i + 1][h - 1];
+        WMip2hm1 = WM[i + 2][h - 1];
 #if 0
-		WMhjm1 = WM[h][j-1];
-		WMhjm2 = WM[h][j-2];
-		WMhp1j = WM[h+1][j];
+        WMhjm1 = WM[h][j-1];
+        WMhjm2 = WM[h][j-2];
+        WMhp1j = WM[h+1][j];
 #else
-		WMhjm1 = WM(h,j-1);
-		WMhjm2 = WM(h,j-2);
-		WMhp1j = WM(h+1,j);
+        WMhjm1 = WM(h,j-1);
+        WMhjm2 = WM(h,j-2);
+        WMhp1j = WM(h+1,j);
 #endif
 
-		/* WM starts */
-		a1 += WMhp1j;
-		if (a1 <= WMijp)
-			WMijp = a1;
-		/* WM ends */
+        /* WM starts */
+        a1 += WMhp1j;
+        if (a1 <= WMijp)
+            WMijp = a1;
+        /* WM ends */
 
-		/* Calculation of the four options for VM*/
-		A_temp = WMip1hm1 + WMhjm1;
-		if ((A_temp <= VMij))
-			VMij = A_temp;
+        /* Calculation of the four options for VM*/
+        A_temp = WMip1hm1 + WMhjm1;
+        if ((A_temp <= VMij))
+            VMij = A_temp;
 
-		A_temp = WMip2hm1 + WMhjm1;
-		if (A_temp <= VMidj && constraints[i + 1] <= 0)
-			VMidj = A_temp;
+        A_temp = WMip2hm1 + WMhjm1;
+        if (A_temp <= VMidj && constraints[i + 1] <= 0)
+            VMidj = A_temp;
 
-		A_temp = WMip1hm1 + WMhjm2;
-		if (A_temp <= VMijd && constraints[j - 1] <= 0)
-			VMijd = A_temp;
+        A_temp = WMip1hm1 + WMhjm2;
+        if (A_temp <= VMijd && constraints[j - 1] <= 0)
+            VMijd = A_temp;
 
-		A_temp = WMip2hm1 + WMhjm2;
-		if (A_temp <= VMidjd && constraints[i + 1] <= 0 && constraints[j - 1]
-		                                                               <= 0)
-			VMidjd = A_temp;
+        A_temp = WMip2hm1 + WMhjm2;
+        if (A_temp <= VMidjd && constraints[i + 1] <= 0 && constraints[j - 1]
+                                                                       <= 0)
+            VMidjd = A_temp;
 
-		// if(i==28 && j==42)
-		// 	printf("(%d,%d,%d), VMij: %d, VMidj: %d, VMijd: %d, VMidjd: %d\n", i,h,j, VMij, VMijd, VMidj, VMidjd);
+        // if(i==28 && j==42)
+        //  printf("(%d,%d,%d), VMij: %d, VMidj: %d, VMijd: %d, VMidjd: %d\n", i,h,j, VMij, VMijd, VMidj, VMidjd);
 
-	}
+    }
 
 #if 0
-	VMidj += dangle[rnai][rnaj][RNA[i+1]][0];
-	VMijd += dangle[rnai][rnaj][RNA[j-1]][1];
-	VMidjd += dangle[rnai][rnaj][RNA[i+1]][0] + dangle[rnai][rnaj][RNA[j-1]][1];
+    VMidj += dangle[rnai][rnaj][RNA[i+1]][0];
+    VMijd += dangle[rnai][rnaj][RNA[j-1]][1];
+    VMidjd += dangle[rnai][rnaj][RNA[i+1]][0] + dangle[rnai][rnaj][RNA[j-1]][1];
 #else
-	tmp1 = dangle[rnai][rnaj][RNA[i + 1]][0];
-	tmp2 = dangle[rnai][rnaj][RNA[j - 1]][1];
+    tmp1 = dangle[rnai][rnaj][RNA[i + 1]][0];
+    tmp2 = dangle[rnai][rnaj][RNA[j - 1]][1];
 
-	VMidj += tmp1;
-	VMidjd += tmp1;
-	VMijd += tmp2;
-	VMidjd += tmp2;
+    VMidj += tmp1;
+    VMidjd += tmp1;
+    VMijd += tmp2;
+    VMidjd += tmp2;
 #endif
 
-	//if(i==28 && j==42)
-	//	printf("after for: (%d,%d,%d), VMij: %d, VMidj: %d, VMijd: %d, VMidjd: %d\n", i,h,j, VMij, VMijd, VMidj, VMidjd);
-
-	/* Manoj ends */
-	VMij = MIN(MIN(VMij, VMidj), MIN(VMijd, VMidjd));
-	VMij = VMij + b + a;
-	VMij += aupen;
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		VMij = INFINITY_;
-
-	VM[i][j] = VMij;
-	/* VM ends */
-
-	/* V starts */
-	es = eS(i, j); /* Energy of stack closed with (i,j) and (i+1,j-1)*/
-	if (es == 0) { /* Amrita: I don't know, if this statement is necessary. NOT DONE BY ME. */
-		es = INFINITY_;
-	} else
-		es += V[indx[i + 1] + j - 1];
-
-	int Vij;
-	Vij = MIN(MIN(eH(i, j), es), MIN(VBI[i][j], VMij));
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		Vij = INFINITY_;
-
-	//printf("%d, V(%d,%d): eh: %d, es: %d, vbi: %d, vm: %d, v: %d\n", j-i, i, j, eH(i,j), es, VBI[i][j], VMij, Vij);
-
-	V[indx[i] + j] = Vij;
-
-	if (NOISOLATE == TRUE && Vij < INFINITY_) {
-		//Check if i+1,j-1 have paired
-		if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) {
-			//If not then check for i-1, j+1
-
-			//Isolated base pairs look ahead
-			int eHL = eH(i - 1, j + 1);
-			int eSL = eS(i - 1, j + 1) + V[indx[i] + j];
-			if (i - 1 == 0) {
-				eSL = 0;
-				eHL = 0;
-			}
-			int Vijl = (eHL < eSL) ? eHL : eSL;
-			//printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl);
-
-			if (Vijl > INFINITY_ - SMALLINFTY_)
-				//isolated base pair found.. setting energy to infinity
-				V[indx[i] + j] = Vij = INFINITY_;
-		}
-	}
+    //if(i==28 && j==42)
+    //  printf("after for: (%d,%d,%d), VMij: %d, VMidj: %d, VMijd: %d, VMidjd: %d\n", i,h,j, VMij, VMijd, VMidj, VMidjd);
+
+    /* Manoj ends */
+    VMij = MIN(MIN(VMij, VMidj), MIN(VMijd, VMidjd));
+    VMij = VMij + b + a;
+    VMij += aupen;
+
+    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
+            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
+                                                                           == -1)
+        VMij = INFINITY_;
+
+    VM[i][j] = VMij;
+    /* VM ends */
+
+    /* V starts */
+    es = eS(i, j); /* Energy of stack closed with (i,j) and (i+1,j-1)*/
+    if (es == 0) { /* Amrita: I don't know, if this statement is necessary. NOT DONE BY ME. */
+        es = INFINITY_;
+    } else
+        es += V[indx[i + 1] + j - 1];
+
+    int Vij;
+    Vij = MIN(MIN(eH(i, j), es), MIN(VBI[i][j], VMij));
+
+    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
+            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
+                                                                           == -1)
+        Vij = INFINITY_;
+
+    //printf("%d, V(%d,%d): eh: %d, es: %d, vbi: %d, vm: %d, v: %d\n", j-i, i, j, eH(i,j), es, VBI[i][j], VMij, Vij);
+
+    V[indx[i] + j] = Vij;
+
+    if (NOISOLATE == TRUE && Vij < INFINITY_) {
+        //Check if i+1,j-1 have paired
+        if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) {
+            //If not then check for i-1, j+1
+
+            //Isolated base pairs look ahead
+            int eHL = eH(i - 1, j + 1);
+            int eSL = eS(i - 1, j + 1) + V[indx[i] + j];
+            if (i - 1 == 0) {
+                eSL = 0;
+                eHL = 0;
+            }
+            int Vijl = (eHL < eSL) ? eHL : eSL;
+            //printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl);
+
+            if (Vijl > INFINITY_ - SMALLINFTY_)
+                //isolated base pair found.. setting energy to infinity
+                V[indx[i] + j] = Vij = INFINITY_;
+        }
+    }
 
 #if DEBUG
-	if (indx[i]+j > (LENGTH-1)*(LENGTH)/2)
-		fprintf(stderr,"ERROR: in calcVBIVMVWM: i: %5d  j: %5d\n",i,j);
+    if (indx[i]+j > (LENGTH-1)*(LENGTH)/2)
+        fprintf(stderr,"ERROR: in calcVBIVMVWM: i: %5d  j: %5d\n",i,j);
 #endif
 
-	/* V ends */
+    /* V ends */
 
-	/* WM starts */
-	/* No dangling base on any of the side */
-	WMij = V[indx[i] + j] + aupen + b;
-	/* Dangling base i on 3' end of the base pair (i+1,j) */
-	if (constraints[i] <= 0)
-		WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
-				RNA[i + 1], rnaj) + b + c;
-	/* Dangling base j on 5' end of the base pair (i,j-1)*/
-	if (constraints[j] <= 0)
-		WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
-				rnai, RNA[j - 1]) + b + c;
-	/* Dangling base i on the 3' end and base j on the 5' end of the base pair (i+1,j-1)*/
-	if (constraints[i] <= 0 && constraints[j] <= 0)
-		WMidjd = V[indx[i + 1] + j - 1]
-		           + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
-		                                                  + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
-		                                                		  RNA[j - 1]) + b + 2* c ;
+    /* WM starts */
+    /* No dangling base on any of the side */
+    WMij = V[indx[i] + j] + aupen + b;
+    /* Dangling base i on 3' end of the base pair (i+1,j) */
+    if (constraints[i] <= 0)
+        WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
+                RNA[i + 1], rnaj) + b + c;
+    /* Dangling base j on 5' end of the base pair (i,j-1)*/
+    if (constraints[j] <= 0)
+        WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
+                rnai, RNA[j - 1]) + b + c;
+    /* Dangling base i on the 3' end and base j on the 5' end of the base pair (i+1,j-1)*/
+    if (constraints[i] <= 0 && constraints[j] <= 0)
+        WMidjd = V[indx[i + 1] + j - 1]
+                   + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
+                                                          + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
+                                                                  RNA[j - 1]) + b + 2* c ;
 
-	// if(i==36 && j==50)
-	//	  printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d\n", i, j, WMij, WMidj, WMijd, WMidjd);
+    // if(i==36 && j==50)
+    //    printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d\n", i, j, WMij, WMidj, WMijd, WMidjd);
 
-	WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
-	/* Term WM[i+1][j] takes care of the option when base i is neither pairing up nor playing the role in the dangling energy calculation and we have to add penalty 'c' for base i to remain single.
-	 * Term WM[i][j-1] takes care of the option when base j is neither pairing up nor playing the role in the dangling energy calculations and add penalty 'c' for base j to remain single.
-	 * */
+    WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
+    /* Term WM[i+1][j] takes care of the option when base i is neither pairing up nor playing the role in the dangling energy calculation and we have to add penalty 'c' for base i to remain single.
+     * Term WM[i][j-1] takes care of the option when base j is neither pairing up nor playing the role in the dangling energy calculations and add penalty 'c' for base j to remain single.
+     * */
 
-	int WMsip1j = INFINITY_;
-	int WMsijm1 = INFINITY_;
+    int WMsip1j = INFINITY_;
+    int WMsijm1 = INFINITY_;
 
-	if (constraints[i] <= 0)
-		WMsip1j = WM[i + 1][j];
+    if (constraints[i] <= 0)
+        WMsip1j = WM[i + 1][j];
 
-	if (constraints[j] <= 0)
-		WMsijm1 = WM[i][j - 1];
+    if (constraints[j] <= 0)
+        WMsijm1 = WM[i][j - 1];
 
-	//	  if(i==36 && j==50)
-	//		  printf("(%d,%d), WMij: %d, WMsip1j: %d, WMsijm1: %d\n", i, j, WMij, WMsip1j, WMsijm1);
+    //    if(i==36 && j==50)
+    //        printf("(%d,%d), WMij: %d, WMsip1j: %d, WMsijm1: %d\n", i, j, WMij, WMsip1j, WMsijm1);
 
 
-	WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
+    WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
 
-	//  if(i==35 && j==50)
-	//	  printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d\n", i, j, WMij, WMidj, WMijd, WMidjd);
+    //  if(i==35 && j==50)
+    //    printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d\n", i, j, WMij, WMidj, WMijd, WMidjd);
 
-	//printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
+    //printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
 
-	WM[i][j] = MIN(WMijp, WMij);
-	WM(i,j) = WM[i][j]; /* extra instruction */
-	/* WM ends */
+    WM[i][j] = MIN(WMijp, WMij);
+    WM(i,j) = WM[i][j]; /* extra instruction */
+    /* WM ends */
 
-	return;
+    return;
 }
 
 //problems in this function.. i think this should fix it..
 /* Function to calculate the value of W[j]. */
 void calcW(int j) {
 
-	int i;
-	int Wj, Widjd /*Dangling base on both sides*/,
-		Wijd/* Dangling base on jth side.*/,
-		Widj/* Dangling base on ith side */,
-		Wij/* No dangle base on any of the sides */, Wim1 /* Value of W at (i-1). Set to zero if positive*/;
-	int rnai, rnaj;
-	int must_branch = 0, besti = 0;
+    int i;
+    int Wj, Widjd /*Dangling base on both sides*/,
+        Wijd/* Dangling base on jth side.*/,
+        Widj/* Dangling base on ith side */,
+        Wij/* No dangle base on any of the sides */, Wim1 /* Value of W at (i-1). Set to zero if positive*/;
+    int rnai, rnaj;
+    int must_branch = 0, besti = 0;
 
-	Wj = INFINITY_;
+    Wj = INFINITY_;
 
-	rnaj = RNA[j];
+    rnaj = RNA[j];
 
-	for (i = 1; i < j - 3; i++) {
+    for (i = 1; i < j - 3; i++) {
 
-		Wij = Widjd = Wijd = Widj = INFINITY_;
+        Wij = Widjd = Wijd = Widj = INFINITY_;
 
-		// printf("i: %d, j: %d\n", i, j);
+        // printf("i: %d, j: %d\n", i, j);
 
 # if 0
-		Wim1=W[i-1];
+        Wim1=W[i-1];
 #endif
 #if 1
-		Wim1 = MIN(0, W[i - 1]); /* If W[i-1] >=0, this means that there is a branch contained in the sequence from 1 to i-1. Otherwise W[i-1] will be INFINITY. Here Wim1 is defined in this manner, to make the energy of unfolded sequence as INFINITY. */
+        Wim1 = MIN(0, W[i - 1]); /* If W[i-1] >=0, this means that there is a branch contained in the sequence from 1 to i-1. Otherwise W[i-1] will be INFINITY. Here Wim1 is defined in this manner, to make the energy of unfolded sequence as INFINITY. */
 #endif
 
-		//Wim1 = W[i - 1];
-
-		rnai = RNA[i];
-
-		/* SH: Calculate the energy with no dangle bases. */
-		Wij = V[indx[i] + j] + auPen(rnai, rnaj) + Wim1;
-		/* Dangle on both sides of the base pair (i+1,j-1). Add the corresponding energy. */
-		if (constraints[i] <= 0 && constraints[j] <= 0)
-			Widjd = V[indx[i + 1] + j - 1] + auPen(RNA[i + 1], RNA[j - 1])
-				+ dangle[RNA[j - 1]][RNA[i + 1]][rnai][1] + dangle[RNA[j
-				- 1]][RNA[i + 1]][rnaj][0] + Wim1;
-		/* Single base j dangling on the 5' end of base pair (i,j-1) */
-		if (constraints[j] <= 0)
-			Wijd = V[indx[i] + j - 1] + auPen(rnai, RNA[j - 1]) + dangle[RNA[j
-				- 1]][rnai][rnaj][0] + Wim1;
-		/* Single base i dangling on the 3' end of base pair (i+1,j)  */
-		if (constraints[i] <= 0)
-			Widj = V[indx[i + 1] + j] + auPen(RNA[i + 1], rnaj)
-				+ dangle[rnaj][RNA[i + 1]][rnai][1] + Wim1;
-
-		int tmpWj = Wj;
-		Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); /* Take the minimum */
-		if (tmpWj != Wj) {
-			must_branch = 0;
-			besti = i;
-		}
-
-		// if(i==46 && j==395){
-		//      printf("V(%d, %d): %d, WM: %d\n", 46, j, V[indx[46]+j], WM[46][j]);
-		//      printf("Wij: %d, Widjd: %d, Wijd: %d, Widj: %d\n\n", Wij, Widjd, Wijd, Widj);
-		//}
-
-		if (Wj < INFINITY_) {
-			if (Wj == Wij) {
-				if (constraints[i] == j) {
-					must_branch = 1;
-				}
-			} else if (Wj == Widjd) {
-				if (constraints[i + 1] == j - 1) {
-					must_branch = 1;
-				}
-			} else if (Wj == Wijd) {
-				if (constraints[i] == j - 1) {
-					must_branch = 1;
-				}
-			} else {
-				if (constraints[i + 1] == j) {
-					must_branch = 1;
-				}
-			}
-		}
-
-	}
-
-	//printf("W%dcal: %d, must_branch: %d, best_i: %d", j, Wj, must_branch, besti);
-
-	/* If jth base is not contributing in the energy calculation of W[j] */
-	if (!must_branch) {
-		if (Wj > W[j - 1])
-			Wj = W[j - 1];
-	}
-
-	W[j] = Wj;
-
-	//printf(",W%dset: %d\n", j, W[j]);
-
-	//  if(j==11 || j==35 || j==36)
-	// printf("\n*****\nMust branch: %d, W%d: %d\n*****\n", must_branch, j, W[j]);
-	return;
+        //Wim1 = W[i - 1];
+
+        rnai = RNA[i];
+
+        /* SH: Calculate the energy with no dangle bases. */
+        Wij = V[indx[i] + j] + auPen(rnai, rnaj) + Wim1;
+        /* Dangle on both sides of the base pair (i+1,j-1). Add the corresponding energy. */
+        if (constraints[i] <= 0 && constraints[j] <= 0)
+            Widjd = V[indx[i + 1] + j - 1] + auPen(RNA[i + 1], RNA[j - 1])
+                + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1] + dangle[RNA[j
+                - 1]][RNA[i + 1]][rnaj][0] + Wim1;
+        /* Single base j dangling on the 5' end of base pair (i,j-1) */
+        if (constraints[j] <= 0)
+            Wijd = V[indx[i] + j - 1] + auPen(rnai, RNA[j - 1]) + dangle[RNA[j
+                - 1]][rnai][rnaj][0] + Wim1;
+        /* Single base i dangling on the 3' end of base pair (i+1,j)  */
+        if (constraints[i] <= 0)
+            Widj = V[indx[i + 1] + j] + auPen(RNA[i + 1], rnaj)
+                + dangle[rnaj][RNA[i + 1]][rnai][1] + Wim1;
+
+        int tmpWj = Wj;
+        Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); /* Take the minimum */
+        if (tmpWj != Wj) {
+            must_branch = 0;
+            besti = i;
+        }
+
+        // if(i==46 && j==395){
+        //      printf("V(%d, %d): %d, WM: %d\n", 46, j, V[indx[46]+j], WM[46][j]);
+        //      printf("Wij: %d, Widjd: %d, Wijd: %d, Widj: %d\n\n", Wij, Widjd, Wijd, Widj);
+        //}
+
+        if (Wj < INFINITY_) {
+            if (Wj == Wij) {
+                if (constraints[i] == j) {
+                    must_branch = 1;
+                }
+            } else if (Wj == Widjd) {
+                if (constraints[i + 1] == j - 1) {
+                    must_branch = 1;
+                }
+            } else if (Wj == Wijd) {
+                if (constraints[i] == j - 1) {
+                    must_branch = 1;
+                }
+            } else {
+                if (constraints[i + 1] == j) {
+                    must_branch = 1;
+                }
+            }
+        }
+
+    }
+
+    //printf("W%dcal: %d, must_branch: %d, best_i: %d", j, Wj, must_branch, besti);
+
+    /* If jth base is not contributing in the energy calculation of W[j] */
+    if (!must_branch) {
+        if (Wj > W[j - 1])
+            Wj = W[j - 1];
+    }
+
+    W[j] = Wj;
+
+    //printf(",W%dset: %d\n", j, W[j]);
+
+    //  if(j==11 || j==35 || j==36)
+    // printf("\n*****\nMust branch: %d, W%d: %d\n*****\n", must_branch, j, W[j]);
+    return;
 }
 
 /* For details on calculating energy of different types of Internal loops, please look at the chapter 3 of MS thesis of Mirela Stefania Andronescu.
@@ -1237,91 +1237,91 @@ void calcW(int j) {
 /* Calculates the energy of internal loop with (i,j) as closing base pair and (ip,jp) as enclosed base pair */
 int eL(int i, int j, int ip, int jp) {
 
-	int energy;
-	int size1, size2, size;
-	int loginc; /* SH: Originally unassiged, but needs to be set to 0 so it doesn't throw off later calculations. */
-	int lopsided; /* define the asymmetry of an interior loop */
-
-	energy = INFINITY_;
-	loginc = 0;
-
-	/*SH: These calculations used to incorrectly be within the bulge loop code, moved out here. */
-	size1 = ip - i - 1;
-	size2 = j - jp - 1;
-	size = size1 + size2;
-
-	if (size1 == 0 || size2 == 0) {
-		if (size > 30) {
-			/* AM: Does not depend upon i and j and ip and jp - Stacking Energies */
-			loginc = (int) floor(prelog * log((double) size / 30.0));
-			energy = bulge[30] + eparam[2] + loginc + auPen(RNA[i], RNA[j])
-			+ auPen(RNA[ip], RNA[jp]);
-		} else if (size <= 30 && size != 1) {
-			/* Does not depend upon i and j and ip and jp - Stacking Energies  */
-			energy = bulge[size] + eparam[2];
-			energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]);
-		} else if (size == 1) {
-			energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])]
-			               + bulge[size] + eparam[2]; /* mans */
-		}
-	} else {
-		/* Internal loop */
-		lopsided = abs(size1 - size2);
-
-		if (size > 30) {
-			loginc = (int) floor(prelog * log((double) size / 30.0));
-
-			/* Please check what should be the difference in the following two options. Is it correct?*/
-			if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/
-
-				energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j
-				                                                             - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp
-				                                                                                                                + 1], RNA[ip - 1])] + inter[30] + loginc + eparam[3]
-				                                                                                                                                                                  + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1,
-				                                                                                                                                                                		  size2))]));
-			} else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/
-				energy
-				= tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]
-				        + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A,
-				        		BASE_A)] + inter[30] + loginc
-				        		+ eparam[3] + MIN(maxpen, (lopsided
-				        				* poppen[MIN(2, MIN(size1, size2))]));
-			}
-		}
-		/* if size is not > 30, we have a looooot of cases... */
-		else if (size1 == 2 && size2 == 2) {
-			/* 2x2 internal loop */
-			energy
-			= iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i
-			                                                            + 2]][RNA[j - 1]][RNA[j - 2]];
-		} else if (size1 == 1 && size2 == 2) {
-			energy
-			= iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]];
-		} else if (size1 == 2 && size2 == 1) {
-			/* 1x2 internal loop */
-			energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i
-			                                                               + 1]][RNA[j]][RNA[i]];
-		} else if (size == 2) {
-			/* 1*1 internal loops */
-			energy
-			= iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]];
-		} else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0)  */
-			energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]
-			               + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)]
-			                       + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided
-			                    		   * poppen[MIN(2, MIN(size1, size2))]));
-		} else { /* General Internal loops */
-			energy
-			= tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1],
-					RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp],
-							RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size]
-							                                            + loginc + eparam[3] /* AM: I don't understand this eparam value, I think they do not play any role currently. Please look in loader.cc file, for what value have been assinged to various elements of eparam array */
-							                                                              + MIN(maxpen,
-							                                                            		  (lopsided * poppen[MIN(2, MIN(size1, size2))])); /*  */
-		}
-	}
-
-	return energy;
+    int energy;
+    int size1, size2, size;
+    int loginc; /* SH: Originally unassiged, but needs to be set to 0 so it doesn't throw off later calculations. */
+    int lopsided; /* define the asymmetry of an interior loop */
+
+    energy = INFINITY_;
+    loginc = 0;
+
+    /*SH: These calculations used to incorrectly be within the bulge loop code, moved out here. */
+    size1 = ip - i - 1;
+    size2 = j - jp - 1;
+    size = size1 + size2;
+
+    if (size1 == 0 || size2 == 0) {
+        if (size > 30) {
+            /* AM: Does not depend upon i and j and ip and jp - Stacking Energies */
+            loginc = (int) floor(prelog * log((double) size / 30.0));
+            energy = bulge[30] + eparam[2] + loginc + auPen(RNA[i], RNA[j])
+            + auPen(RNA[ip], RNA[jp]);
+        } else if (size <= 30 && size != 1) {
+            /* Does not depend upon i and j and ip and jp - Stacking Energies  */
+            energy = bulge[size] + eparam[2];
+            energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]);
+        } else if (size == 1) {
+            energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])]
+                           + bulge[size] + eparam[2]; /* mans */
+        }
+    } else {
+        /* Internal loop */
+        lopsided = abs(size1 - size2);
+
+        if (size > 30) {
+            loginc = (int) floor(prelog * log((double) size / 30.0));
+
+            /* Please check what should be the difference in the following two options. Is it correct?*/
+            if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/
+
+                energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j
+                                                                             - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp
+                                                                                                                                + 1], RNA[ip - 1])] + inter[30] + loginc + eparam[3]
+                                                                                                                                                                                  + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1,
+                                                                                                                                                                                          size2))]));
+            } else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/
+                energy
+                = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]
+                        + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A,
+                                BASE_A)] + inter[30] + loginc
+                                + eparam[3] + MIN(maxpen, (lopsided
+                                        * poppen[MIN(2, MIN(size1, size2))]));
+            }
+        }
+        /* if size is not > 30, we have a looooot of cases... */
+        else if (size1 == 2 && size2 == 2) {
+            /* 2x2 internal loop */
+            energy
+            = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i
+                                                                        + 2]][RNA[j - 1]][RNA[j - 2]];
+        } else if (size1 == 1 && size2 == 2) {
+            energy
+            = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]];
+        } else if (size1 == 2 && size2 == 1) {
+            /* 1x2 internal loop */
+            energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i
+                                                                           + 1]][RNA[j]][RNA[i]];
+        } else if (size == 2) {
+            /* 1*1 internal loops */
+            energy
+            = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]];
+        } else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0)  */
+            energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]
+                           + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)]
+                                   + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided
+                                           * poppen[MIN(2, MIN(size1, size2))]));
+        } else { /* General Internal loops */
+            energy
+            = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1],
+                    RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp],
+                            RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size]
+                                                                        + loginc + eparam[3] /* AM: I don't understand this eparam value, I think they do not play any role currently. Please look in loader.cc file, for what value have been assinged to various elements of eparam array */
+                                                                                          + MIN(maxpen,
+                                                                                                  (lopsided * poppen[MIN(2, MIN(size1, size2))])); /*  */
+        }
+    }
+
+    return energy;
 }
 
 /* For details on calculating energy of different types of hairpin loops, please look at the chapter 3 of MS thesis of Mirela Stefania Andronescu.
@@ -1330,130 +1330,130 @@ int eL(int i, int j, int ip, int jp) {
 /* SH: Function used to calculate energy of a hairpin loop between i & j. */
 /* inline */
 int eH(int i, int j) {
-	/*  Hairpin loop for all the bases between i and j */
-	/*  size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */
-	int size;
-	int loginc;
-	int energy = INFINITY_;
-	int key, index, count, tlink, kmult;
-
-	size = j - i - 1; /*  size is the number of bases in the loop, when the closing pair is excluded */
-
-	//checking if single stranded region is allowed with given constraints
-	if (checkSS(i, j) || (constraints[i] > 0 && constraints[i] != j)
-			|| (constraints[j] > 0 && constraints[j] != i))
-		return energy;
-
-	/*  look in hairpin, and be careful that there is only 30 values */
-
-	if (size > 30) {
-		loginc = (int) ((prelog) * log(((double) size) / 30.0));
-		energy = hairpin[30] + loginc + tstkh[fourBaseIndex(RNA[i], RNA[j],
-				RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/
-	}
-
-	else if (size <= 30 && size > 4) {
-		energy = hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j],
-				RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/
-	}
-
-	else if (size == 4) {
-		/*  tetraloop */
-		key = 0;
-		tlink = 0;
-		for (index = 0; index < 6; ++index) {
-			switch (RNA[i + index]) {
-			case BASE_A:
-				kmult = 1;
-				break;
-			case BASE_C:
-				kmult = 2;
-				break;
-			case BASE_G:
-				kmult = 3;
-				break;
-			case BASE_U:
-				kmult = 4;
-				break;
-			default:
-				kmult = 0;
-				fprintf(stderr, "ERROR: in tetraloop calculation\n");
-			}
-			key += kmult * (int) pow(10.0, 5 - index);
-		}
-		/*  if the sequence is in tloop, we use this value */
-		for (count = 1; count < numoftloops && tlink == 0; ++count) {
-			if (key == tloop[count][0]) {
-				tlink = tloop[count][1];
-			}
-		}
-		energy = tlink + hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j],
-				RNA[i + 1], RNA[j - 1])] + eparam[4];
-	}
-
-	else if (size == 3) {
-		/*  triloop... For the moment, the file triloop.dat is empty */
-		/*  else, should have a treatment like the one if size==4 */
-		energy = hairpin[size];
-		/* AM: Don't include stacking energy terms for triloopls */
-		/* + tstkh[RNA[i]][RNA[j]][RNA[i+1]][RNA[j-1]]  */
-		/* + eparam[4]; */
-		/*  Must be another penalty for terminal AU... Not sure of this */
-		energy += auPen(RNA[i], RNA[j]);
-	}
-
-	else if (size < 3 && size != 0) {
-		/*  no terminal mismatch */
-		energy = hairpin[size] + eparam[4];
-		if ((RNA[i] == BASE_A && RNA[j] == BASE_U) || (RNA[i] == BASE_U
-				&& RNA[j] == BASE_A)) {
-			energy += 6; /*  Seems to be a penalty for terminal AU.  *//* Hairpin Loops of size 3 are not allowed, the term hairpin[size] will result in a very large value.  */
-		}
-	} else if (size == 0)
-		return INFINITY_;
-
-	/*  GGG Bonus => GU closure preceded by GG */
-	/*  i-2 = i-1 = i = G, and j = U; i < j */
-	if (i > 2) {
-		if (RNA[i - 2] == BASE_G && RNA[i - 1] == BASE_G && RNA[i] == BASE_G
-				&& RNA[j] == BASE_U) {
-			energy += gubonus;
-			/*  printf ("\n GGG bonus for i %d j %d ", i, j); */
-		}
-	}
-
-	/*  Poly-C loop => How many C are needed for being a poly-C loop */
-	tlink = 1;
-	for (index = 1; (index <= size) && (tlink == 1); ++index) {
-		if (RNA[i + index] != BASE_C)
-			tlink = 0;
-	}
-	if (tlink == 1) {
-		if (size == 3) {
-			energy += c3;
-		} else {
-			energy += cint + size * cslope;
-		}
-	}
-
-	return energy;
+    /*  Hairpin loop for all the bases between i and j */
+    /*  size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */
+    int size;
+    int loginc;
+    int energy = INFINITY_;
+    int key, index, count, tlink, kmult;
+
+    size = j - i - 1; /*  size is the number of bases in the loop, when the closing pair is excluded */
+
+    //checking if single stranded region is allowed with given constraints
+    if (checkSS(i, j) || (constraints[i] > 0 && constraints[i] != j)
+            || (constraints[j] > 0 && constraints[j] != i))
+        return energy;
+
+    /*  look in hairpin, and be careful that there is only 30 values */
+
+    if (size > 30) {
+        loginc = (int) ((prelog) * log(((double) size) / 30.0));
+        energy = hairpin[30] + loginc + tstkh[fourBaseIndex(RNA[i], RNA[j],
+                RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/
+    }
+
+    else if (size <= 30 && size > 4) {
+        energy = hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j],
+                RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/
+    }
+
+    else if (size == 4) {
+        /*  tetraloop */
+        key = 0;
+        tlink = 0;
+        for (index = 0; index < 6; ++index) {
+            switch (RNA[i + index]) {
+            case BASE_A:
+                kmult = 1;
+                break;
+            case BASE_C:
+                kmult = 2;
+                break;
+            case BASE_G:
+                kmult = 3;
+                break;
+            case BASE_U:
+                kmult = 4;
+                break;
+            default:
+                kmult = 0;
+                fprintf(stderr, "ERROR: in tetraloop calculation\n");
+            }
+            key += kmult * (int) pow(10.0, 5 - index);
+        }
+        /*  if the sequence is in tloop, we use this value */
+        for (count = 1; count < numoftloops && tlink == 0; ++count) {
+            if (key == tloop[count][0]) {
+                tlink = tloop[count][1];
+            }
+        }
+        energy = tlink + hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j],
+                RNA[i + 1], RNA[j - 1])] + eparam[4];
+    }
+
+    else if (size == 3) {
+        /*  triloop... For the moment, the file triloop.dat is empty */
+        /*  else, should have a treatment like the one if size==4 */
+        energy = hairpin[size];
+        /* AM: Don't include stacking energy terms for triloopls */
+        /* + tstkh[RNA[i]][RNA[j]][RNA[i+1]][RNA[j-1]]  */
+        /* + eparam[4]; */
+        /*  Must be another penalty for terminal AU... Not sure of this */
+        energy += auPen(RNA[i], RNA[j]);
+    }
+
+    else if (size < 3 && size != 0) {
+        /*  no terminal mismatch */
+        energy = hairpin[size] + eparam[4];
+        if ((RNA[i] == BASE_A && RNA[j] == BASE_U) || (RNA[i] == BASE_U
+                && RNA[j] == BASE_A)) {
+            energy += 6; /*  Seems to be a penalty for terminal AU.  *//* Hairpin Loops of size 3 are not allowed, the term hairpin[size] will result in a very large value.  */
+        }
+    } else if (size == 0)
+        return INFINITY_;
+
+    /*  GGG Bonus => GU closure preceded by GG */
+    /*  i-2 = i-1 = i = G, and j = U; i < j */
+    if (i > 2) {
+        if (RNA[i - 2] == BASE_G && RNA[i - 1] == BASE_G && RNA[i] == BASE_G
+                && RNA[j] == BASE_U) {
+            energy += gubonus;
+            /*  printf ("\n GGG bonus for i %d j %d ", i, j); */
+        }
+    }
+
+    /*  Poly-C loop => How many C are needed for being a poly-C loop */
+    tlink = 1;
+    for (index = 1; (index <= size) && (tlink == 1); ++index) {
+        if (RNA[i + index] != BASE_C)
+            tlink = 0;
+    }
+    if (tlink == 1) {
+        if (size == 3) {
+            energy += c3;
+        } else {
+            energy += cint + size * cslope;
+        }
+    }
+
+    return energy;
 }
 
 /* SH: Function used to calculate energy of stacked pairs (i.j) & (i+1.j-1). */
 /* inline */
 int eS(int i, int j) {
-	int energy;
+    int energy;
 
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i))
-		return INFINITY_;
+    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
+            && constraints[j] != i))
+        return INFINITY_;
 
-	//if (j - i <= 3)
-	//  return INFINITY_;
+    //if (j - i <= 3)
+    //  return INFINITY_;
 
-	/*  not sure about eparam[1], come from MFold.. = 0 */
-	energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])]
-	               + eparam[1];
+    /*  not sure about eparam[1], come from MFold.. = 0 */
+    energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])]
+                   + eparam[1];
 
-	return energy;
+    return energy;
 }

From 5e9bf06b19229c59bbeb17ef593f8995537b885b Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 19:43:07 -0800
Subject: [PATCH 026/282] Braces cleanup in calculate()

---
 gtfold-mfe/src/algorithms.c | 26 ++++++--------------------
 1 file changed, 6 insertions(+), 20 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 7d747c2..0bb818a 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -156,35 +156,22 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
     int b, i, j, it, k;
     
     for(i=1;i<=len;i++) 
-    {
         if(RNA1[i]=='N') 
             constraints[i] = -1;
-    }   
 
     if (prohibitlen != 0) 
-    {
         for (it = 0; it < prohibitlen; it++) 
-        {
-            for(k= 1; k <= prohibitList[it][2];k++)
-            {
+            for(k= 1; k <= prohibitList[it][2];k++) {
                 constraints[prohibitList[it][0]+k-1] = -1;
-                if(prohibitList[it][1]!=0)
-                {
+                if(prohibitList[it][1] != 0)
                     constraints[prohibitList[it][1]+1-k] = -1;
-                }
             }
-        }
-    }
 
-    if (forcelen != 0) 
-    {
+    if (forcelen != 0) {
         printf("Running with constraints\n");
-        for (it = 0; it < forcelen; it++) 
-        {
-            for(k=1; k <= forceList[it][2];k++)
-            {
-                if (!chPair(RNA[forceList[it][0]+k-1], RNA[forceList[it][1]-k+1])) 
-                {
+        for (it = 0; it < forcelen; it++) {
+            for(k=1; k <= forceList[it][2];k++) {
+                if (!chPair(RNA[forceList[it][0]+k-1], RNA[forceList[it][1]-k+1])) {
                     printf("Can't constrain (%d,%d)\n", forceList[it][0]+k-1,
                             forceList[it][1]-k+1);
                     continue;
@@ -192,7 +179,6 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
                 constraints[forceList[it][0]+k-1] = forceList[it][1]+1-k;
                 constraints[forceList[it][1]+1-k] = forceList[it][0]+k-1;
             }
-                //printf("(%d,%d)\n", forceList[it][0], forceList[it][1]);
         }
     }
 

From f7bb2597f09e9cc0484763ac26e555df42bb7628 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 19:45:33 -0800
Subject: [PATCH 027/282] Remove commented-out code

---
 gtfold-mfe/src/algorithms.c | 43 -------------------------------------
 1 file changed, 43 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 0bb818a..241fa93 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -187,14 +187,12 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
         omp_set_num_threads(num_threads);
 #endif
 
-#if 1
 #ifdef _OPENMP
 #pragma omp parallel
 #pragma omp master
     {
         fprintf(stdout,"Thread count: %3d\n",omp_get_num_threads());
     }
-#endif
 #endif
 
     //printf("starting.......\n");
@@ -698,15 +696,9 @@ void calcVMVWM(int i, int j) {
         a1 = WM[i][h];
         WMip1hm1 = WM[i + 1][h - 1];
         WMip2hm1 = WM[i + 2][h - 1];
-#if 0
-        WMhjm1 = WM[h][j-1];
-        WMhjm2 = WM[h][j-2];
-        WMhp1j = WM[h+1][j];
-#else
         WMhjm1 = WM(h,j-1); /* Preprocessor will convert this into WM[j-1][h]. According to the algorithm, the expression should be WM[h][j-1]  -- in which case, as the value of h changes, this will access elements from a column of the WM matrix. To improve run time performance WM array is made symmetric and so WM[h][j-1] = WM[j-1][h] and it will have accesses in a row.*/
         WMhjm2 = WM(h,j-2); /* Same reason as above */
         WMhp1j = WM(h+1,j); /* Same reason as above */
-#endif
 
         /* WM starts */
         a1 += WMhp1j;
@@ -733,18 +725,12 @@ void calcVMVWM(int i, int j) {
             VMidjd = A_temp;
     }
 
-#if 0
-    VMidj += dangle[rnai][rnaj][RNA[i+1]][0];
-    VMijd += dangle[rnai][rnaj][RNA[j-1]][1];
-    VMidjd += dangle[rnai][rnaj][RNA[i+1]][0] + dangle[rnai][rnaj][RNA[j-1]][1];
-#else
     tmp1 = dangle[rnai][rnaj][RNA[i + 1]][0]; /* Dangling energy of base pair (i,j) with single base i+1 at 5' end */
     tmp2 = dangle[rnai][rnaj][RNA[j - 1]][1]; /* Dangling energy of base pair (i,j) with single base j-1 at 3' end */
     VMidj += (tmp1 + c);
     VMidjd += (tmp1 + c);
     VMijd += (tmp2 + c);
     VMidjd += (tmp2 + c);
-#endif
 
     /* Manoj ends */
 
@@ -948,15 +934,9 @@ void calcVBIVMVWM(int i, int j) {
         a1 = WM[i][h];
         WMip1hm1 = WM[i + 1][h - 1];
         WMip2hm1 = WM[i + 2][h - 1];
-#if 0
-        WMhjm1 = WM[h][j-1];
-        WMhjm2 = WM[h][j-2];
-        WMhp1j = WM[h+1][j];
-#else
         WMhjm1 = WM(h,j-1);
         WMhjm2 = WM(h,j-2);
         WMhp1j = WM(h+1,j);
-#endif
 
         /* WM starts */
         a1 += WMhp1j;
@@ -987,11 +967,6 @@ void calcVBIVMVWM(int i, int j) {
 
     }
 
-#if 0
-    VMidj += dangle[rnai][rnaj][RNA[i+1]][0];
-    VMijd += dangle[rnai][rnaj][RNA[j-1]][1];
-    VMidjd += dangle[rnai][rnaj][RNA[i+1]][0] + dangle[rnai][rnaj][RNA[j-1]][1];
-#else
     tmp1 = dangle[rnai][rnaj][RNA[i + 1]][0];
     tmp2 = dangle[rnai][rnaj][RNA[j - 1]][1];
 
@@ -999,10 +974,6 @@ void calcVBIVMVWM(int i, int j) {
     VMidjd += tmp1;
     VMijd += tmp2;
     VMidjd += tmp2;
-#endif
-
-    //if(i==28 && j==42)
-    //  printf("after for: (%d,%d,%d), VMij: %d, VMidj: %d, VMijd: %d, VMidjd: %d\n", i,h,j, VMij, VMijd, VMidj, VMidjd);
 
     /* Manoj ends */
     VMij = MIN(MIN(VMij, VMidj), MIN(VMijd, VMidjd));
@@ -1137,16 +1108,7 @@ void calcW(int j) {
 
         Wij = Widjd = Wijd = Widj = INFINITY_;
 
-        // printf("i: %d, j: %d\n", i, j);
-
-# if 0
-        Wim1=W[i-1];
-#endif
-#if 1
         Wim1 = MIN(0, W[i - 1]); /* If W[i-1] >=0, this means that there is a branch contained in the sequence from 1 to i-1. Otherwise W[i-1] will be INFINITY. Here Wim1 is defined in this manner, to make the energy of unfolded sequence as INFINITY. */
-#endif
-
-        //Wim1 = W[i - 1];
 
         rnai = RNA[i];
 
@@ -1173,11 +1135,6 @@ void calcW(int j) {
             besti = i;
         }
 
-        // if(i==46 && j==395){
-        //      printf("V(%d, %d): %d, WM: %d\n", 46, j, V[indx[46]+j], WM[46][j]);
-        //      printf("Wij: %d, Widjd: %d, Wijd: %d, Widj: %d\n\n", Wij, Widjd, Wijd, Widj);
-        //}
-
         if (Wj < INFINITY_) {
             if (Wj == Wij) {
                 if (constraints[i] == j) {

From 8d3882f6bc1f80f6b99b52f2562112f8f90994e2 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 19:52:11 -0800
Subject: [PATCH 028/282] Comment and cleanup the main loop

---
 gtfold-mfe/src/algorithms.c | 60 +++++++++++++++++++++++--------------
 1 file changed, 38 insertions(+), 22 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 241fa93..5c728ea 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -197,27 +197,38 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
 
     //printf("starting.......\n");
 
-    /* Here b-1 is the length of the segment closed with (i,j) base pair. We assume the minimum size of a hairpin loop closed with (i,j) equal to 3.*/
+    // Here b-1 is the length of the segment closed with (i,j) base pair. We
+    // assume the minimum size of a hairpin loop closed with (i,j) equal to 3.
 
-    /* For b = 4 to 6, hairpin loops and at b = 6 stack loops are possible. So, only WM, and V array are needs to be calculated.
-     * If (i,j) can not pair up then only WM needs to be calculated.
-     * */
+    /* For b = 4 to 6, hairpin loops and at b = 6 stack loops are possible. So,
+     * only WM, and V array are needs to be calculated.  If (i,j) can not pair
+     * up then only WM needs to be calculated.  */
     for (b = 4; b <= 6; b++) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
-        /* OpenMP syntex to parallelize the for loop. Guided scheduling strategy works better because there may not be equla amount of work for every (i,j)
-         * Please look at the conference paper on GTfold for information regarding how to parallelize the code. Also, note that the for every value of b calculation has to go sequentially. However, the calculation for a perticular value of b, which corresponds to calculating on a single diagonal.
-         * */
+        /* - OpenMP syntax to parallelize the for loop. Guided scheduling
+         *   strategy works better because there may not be an equal amount of
+         *   work for every (i,j)
+         * - Please look at the conference paper on GTfold for information
+         *   regarding how to parallelize the code. Also, note that the for
+         *   every value of b calculation must be sequential. However, the
+         *   calculation for a particular value of b, which corresponds to
+         *   calculating on a single diagonal, can be parallelized.
+         */
 #endif
         for (i = 1; i <= len - b; i++) {
             j = i + b;
-            //if (constraints[i] == -1 && constraints[j] == -1)
-            //  continue;
+
+            // don't allow pairing past the contact distance
             if (j-i >= contact_dist) continue;
-            if (chPair(RNA[i], RNA[j])) /* Check if bases i and j pair up or not */
-                calcVWM(i, j, INFINITY_, INFINITY_); /* Calculates V and WM array for element (i,j)*/
+
+            // if i and j pair
+            if (chPair(RNA[i], RNA[j]))
+                // calculate V and WM
+                calcVWM(i, j, INFINITY_, INFINITY_);
             else
-                calcWM(i, j); /* Calculates WM array for element (i,j)*/
+                // calculate just WM
+                calcWM(i, j);
         }
     }
 
@@ -228,14 +239,18 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
 #endif
         for (i = 1; i <= len - b; i++) {
             j = i + b;
-            //if (constraints[i] == -1 && constraints[j] == -1)
-            //  continue;
+
+            // don't allow pairing past the contact distance
             if (j-i >= contact_dist) continue;
+
+            // if i and j pair
             if (chPair(RNA[i], RNA[j])) {
-                calcVBI(i, j); /* Calculates VBI element at (i,j) */
-                calcVWM(i, j, VBI[i][j], INFINITY_); /* Calculates V and WM arrays*/
+                // calculate VBI, V, and WM
+                calcVBI(i, j);
+                calcVWM(i, j, VBI[i][j], INFINITY_);
             } else
-                calcWM(i, j); /* Calculates WM element at (i,j) */
+                // calculate WM
+                calcWM(i, j);
         }
     }
 
@@ -245,14 +260,15 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
 #endif
         for (i = 1; i <= len - b; i++) {
             j = i + b;
-            //printf("%d %d: %d %d\n", i, j, constraints[i], constraints[j]);
-            //if (constraints[i] == -1 && constraints[j] == -1)
-            //  continue;
+
+            // don't allow pairing past the contact distance
             if (j-i >= contact_dist) continue;
+
+            // if i and j pair
             if (chPair(RNA[i], RNA[j])) {
-                calcVBIVMVWM(i, j); /* Calculates VBI, VM, V and WM elements at (i,j) */
+                calcVBIVMVWM(i, j); // calculate VBI, VM, V and WM at (i,j)
             } else
-                calcWM(i, j); /* Calculates WM element at (i,j) */
+                calcWM(i, j); // calculate WM at (i,j)
         }
     }
 

From eddc7437ff93d373a0d9de073bb56a3b2753307a Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 19:54:23 -0800
Subject: [PATCH 029/282] Remove commented-out code

---
 gtfold-mfe/src/algorithms.c | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 5c728ea..d20727f 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -272,21 +272,14 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
         }
     }
 
-/*
-    for(j=2; j<=len; j++){
-        for (i=j-1; i>0; i--){
-            printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WM[i][j]);
-        }
-    }
-*/            
-
-    for (j = 5; j <= len; j++) /* Recurssion relation for W array does not depend upon any other array, so can be done after the computation of other arrays are finished.*/
+    // Recursion relation for the W array does not depend on any other arrays,
+    // so we can do it in one pass later
+    for (j = 5; j <= len; j++)
         calcW(j);
 
-    //printV(len);
-
     return W[len];
 }
+
 /* This function calculates the optimal energy of internal loops closed with base pair (i,j) using a heuristic, which limits their size to a constant value - MAXLOOP
  An internal loop contains one closing base pair (i,j) and one enclosed base pair (ip,jp). This function searches for the best enclosed base pair for the closing base pair (i,j) within the given window limited by MAXLOOP
  */

From ee316f24ac6e0d17c99fc9c87ee80971222ac812 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 19:57:30 -0800
Subject: [PATCH 030/282] Split long comment into sections

---
 gtfold-mfe/src/algorithms.c | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index d20727f..a945a44 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -280,8 +280,14 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
     return W[len];
 }
 
-/* This function calculates the optimal energy of internal loops closed with base pair (i,j) using a heuristic, which limits their size to a constant value - MAXLOOP
- An internal loop contains one closing base pair (i,j) and one enclosed base pair (ip,jp). This function searches for the best enclosed base pair for the closing base pair (i,j) within the given window limited by MAXLOOP
+/**
+ * Calculates the optimal energy of internal loops closed with base pair (i,j)
+ *
+ * Limits internal loop sizes to a constant -- MAXLOOP
+ *
+ * An internal loop contains one closing base pair (i,j) and one enclosed base
+ * pair (ip,jp). This function searches for the best enclosed base pair for the
+ * closing base pair (i,j) within the given window limited by MAXLOOP
  */
 void calcVBI(int i, int j) {
 

From 980cbd4bca26842b5e5e8d151366d617bf28359f Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 22:25:48 -0800
Subject: [PATCH 031/282] Cleanup of calcVBI

---
 gtfold-mfe/src/algorithms.c | 61 +++++++++++++++++++++++++++++--------
 1 file changed, 48 insertions(+), 13 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index a945a44..47c0034 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -86,7 +86,7 @@ int update_chPair(int i, int j)
 
     if (!(chPairKey & (1 << ((i << 2) + j))))
     {
-        chPairKey += 1 << ((i << 2) + j);   
+        chPairKey += 1 << ((i << 2) + j);
         r = 1;
     }
 
@@ -295,43 +295,78 @@ void calcVBI(int i, int j) {
 
     VBIij = INFINITY_;
 
-    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
-                                                                           == -1)
+    // skip entirely if not permitted by constraints
+    if ((constraints[i] > 0 && constraints[i] != j) ||
+        (constraints[j] > 0 && constraints[j] != i) ||
+         constraints[i] == -1 ||
+         constraints[j] == -1)
         return;
 
-    /* Having ip = i+1 and jp = j-1, creates a stack loop. Stack loops are taken care separately in the calculation of V  using eS() function. Therefore, for ip=i+1, the jp value should be lesser than or equal to j-2.*/
+    // Having ip = i+1 and jp = j-1 creates a stack loop, which is taken care
+    // of in V and not here
+    // Therefore for ip=i+1, the jp value should be less than or equal to j-2.
     ip = i + 1;
-    thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of the hairpin loop which the enclosed base pair (ip,jp) can close is 3 that results in the minimum value of jp = ip+4 */
+
+    // Minimum size of the hairpin loop which the enclosed base pair (ip,jp)
+    // can close is 3.  So the minimum value of jp is ip+4
+    thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4);
     for (jp = thres1; jp <= j - 2; jp++) {
-        //May need to check the constraint condition here
+
+        // limit side of internal loop to contact_dist
         if (jp-ip >= contact_dist) continue;
+
+        // May need to check the constraint condition here...
+
         if (chPair(RNA[ip], RNA[jp])) {
+
+            // disallow this pair if prohibited by the constraints
             if (checkSS(i, ip) || checkSS(jp, j))
                 continue;
-            temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the optimal energy of the substructure closed by (ip,jp)*/
-            if (VBIij > temp)
+
+            // Energy of internal loop closed by (i,j) and (ip,jp),
+            // plus the optimal energy of the substructure closed by (ip,jp)
+            temp = eL(i, j, ip, jp) + V[indx[ip] + jp];
+
+            // update if this is better than the best considered so far
+            if (temp < VBIij)
                 VBIij = temp;
         }
     }
 
+    // having now considered the ip = i+1 case, we consider all others,
+    // starting at ip = i+2
     for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) {
-        thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of a hairpin loop is 3, so start jp from ip+4*/
-        //May need to check for forced constraints here
+
+        // Minimum size of a hairpin loop is 3, so start jp at ip+4
+        thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4);
+
+        // May need to check for forced constraints here...
+
+        // consider all jp possibilities for the current ip
         for (jp = thres1; jp <= j - 1; jp++) {
+
+            // prohibit inner loops larger than contact_dist
             if (jp-ip >= contact_dist) continue;
+
             if (chPair(RNA[ip], RNA[jp])) {
+
+                // disallow this pair if prohibited by the constraints
                 if (checkSS(i, ip) || checkSS(jp, j))
                     continue;
-                temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the optimal energy of the substructure closed by (ip,jp)*/
+
+                // Energy of internal loop closed by (i,j) and (ip,jp), plus
+                // the optimal energy of the substructure closed by (ip,jp)
+                temp = eL(i, j, ip, jp) + V[indx[ip] + jp];
+
+                // update if this is better than the best considered so far
                 if (VBIij > temp)
                     VBIij = temp;
             }
         }
     }
 
+    // save the final VBIij into the table
     VBI[i][j] = VBIij;
-    return;
 }
 
 /* Amrita: - Internal loop speedup algorithm */

From edfb8dbbbd51c8ae82ff2e99249c17c674f6499f Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 22:49:59 -0800
Subject: [PATCH 032/282] Work on making calcVBIS more clear

---
 gtfold-mfe/src/algorithms.c | 71 ++++++++++++++++++++++++++-----------
 1 file changed, 50 insertions(+), 21 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 47c0034..b12f357 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -369,21 +369,33 @@ void calcVBI(int i, int j) {
     VBI[i][j] = VBIij;
 }
 
-/* Amrita: - Internal loop speedup algorithm */
-/* Calculation of internal loops using internal loop speedup algorithm. The algorithm calculates the optimal loop closed with base pair (i,j) */
+/*
+ * Calculates VBI using the Internal Loop Speedup Algorithm
+ *
+ * @author Amrita
+ */
 void calcVBIS(int i, int j) {
 
-    int ip, jp, E, VBIij, c = 3, b, len = LENGTH - 1, E1, E2, g; /* ip and jp form enclosed base pairs and c is a small constant currently taken as 3. The loops having one or both sides smaller than c are calculated as special cases. */
+    /* ip and jp form enclosed base pairs and c is a small constant currently
+     * taken as 3. The loops having one or both sides smaller than c are
+     * calculated as special cases. */
+    int ip, jp, E, VBIij, c = 3, b, len = LENGTH - 1, E1, E2, g;
 
-    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
-                                                                           == -1)
+    // skip entirely if not permitted by constraints
+    if ((constraints[i] > 0 && constraints[i] != j) ||
+        (constraints[j] > 0 && constraints[j] != i) ||
+         constraints[i] == -1 ||
+         constraints[j] == -1)
         return;
 
     VBIij = VBI[i][j];
 
-    /*Case1: Loops having first side shorter than c and second side has all allowable sizes */
-    /* Having ip = i+1 and jp=j-1 creates a stack which is considered separately in eS function. So here the max value of jp could be j-2*/
+    // Case 1: Loops having first side shorter than c and second side has all
+    // allowable sizes
+
+    // Having ip = i+1 and jp = j-1 creates a stack loop, which is taken care
+    // of in V and not here
+    // Therefore for ip=i+1, the jp value should be less than or equal to j-2.
     ip = i + 1;
     for (jp = ip + 4; jp <= j - 2; jp++) {
         if (jp-ip >= contact_dist) continue;
@@ -394,8 +406,9 @@ void calcVBIS(int i, int j) {
         }
     }
 
+    // now consider the non-special cases where ip starts at i+2
     for (ip = i + 2; ip <= i + c; ip++) {
-        for (jp = ip + 4; jp <= j - 1; jp++) { /* Minimum size of a hairpin loop is 3.*/
+        for (jp = ip + 4; jp <= j - 1; jp++) { // Minimum size of a hairpin loop is 3.
             if (jp-ip >= contact_dist) continue;
             if (chPair(RNA[ip], RNA[jp])) {
                 E = eL(i, j, ip, jp) + V[indx[ip] + jp];
@@ -405,9 +418,10 @@ void calcVBIS(int i, int j) {
         }
     }
 
-    /*Case 2: When the first side is greater or equal to c but the second side is smaller */
+    // Case 2: When the first side is greater or equal to c but the second side
+    // is smaller
     for (ip = i + c + 1; ip < j - 1; ip++) {
-        for (jp = j - c; jp <= j - 1 && jp >= ip + 4; jp++) { /* Minimum size of a hairpin loop is 3.*/
+        for (jp = j - c; jp <= j - 1 && jp >= ip + 4; jp++) { // Minimum size of a hairpin loop is 3.
             if (jp-ip >= contact_dist) continue;
             if (chPair(RNA[ip], RNA[jp])) {
                 E = eL(i, j, ip, jp) + V[indx[ip] + jp];
@@ -417,35 +431,48 @@ void calcVBIS(int i, int j) {
         }
     }
 
-    /* Case 3: General Case - when both sides of internal loops are greater than or equal to c */
-    /*Base cases for this (i,j) are g=j-i-2c-3 and j-i-2c-4, gap values should always be greater than or equal to 3*/
-    /* First base case - both sides of the loop are  equal to c.*/
+    // Case 3: General Case - when both sides of internal loops are greater
+    // than or equal to c
+
+    // Base cases for this (i,j) are g=j-i-2c-3 and g=j-i-2c-4,
+    // Also, gap values (count of nucleotides enclosed by the inner base pair)
+    // should always be greater than or equal to 3
+
+    // First base case - both sides of the loop are equal to c.
     ip = i + c + 1;
     jp = j - c - 1;
 
+    // g is the number of nucleotides inclosed by the inner loop
     g = jp - ip - 1;
+
+    // if g is less than 3, then the inner base pair is too short -- don't
+    // extend this value. In this case the second base case of g-1 == j-i-2c-4
+    // will also not make a valid gap value.
     if (g < 3) {
         VBI[i][j] = VBIij;
         return;
-    } /* if g is lesser than 3, then you don't extend this value. In this case the second base case of g-1=j-i-2c-4 will also not make a valid gap value. */
+    }
 
+    // but for valid inner loops, calculate their energy and update into VBIij
     E = eL(i, j, ip, jp) + V[indx[ip] + jp];
     if (VBIij > E)
         VBIij = E;
 
-    /* Extend this base case for all closing base pairs of the form ( i-b, j+b ) */
-
+    // Extend this base case for all closing base pairs of the form (i-b, j+b)
     for (b = 1; b <= MIN(i - 1, len - j); b++) {
 
         E = eL(i - b, j + b, ip, jp) + V[indx[ip] + jp];
 
-        /* Two more options for base pair (i-b,j+b), which are introduced by having one of the side of the resultant internal loop exactly equal to c */
-        /* Second side is c - with closing base pair (i-b,j+b)*/
+        // Two more options for base pair (i-b,j+b), which are introduced by
+        // having one of the side of the resultant internal loop exactly equal
+        // to c
+
+        // Second side is c - with closing base pair (i-b,j+b)
         int ip1 = i + c + 1 + b;
         int jp1 = (j + b) - c - 1;
         E1 = eL(i - b, j + b, ip1, jp1) + V[indx[ip1] + jp1];
 
-        /* First side is c - with closing base pair (i-b,j+b)*/
+        // First side is c - with closing base pair (i-b,j+b)
         int ip2 = (i - b) + c + 1;
         int jp2 = j - c - 1 - b;
         E2 = eL(i - b, j + b, ip2, jp2) + V[indx[ip2] + jp2];
@@ -465,10 +492,12 @@ void calcVBIS(int i, int j) {
         }
     }
 
+    // For exactly three enclosed nucleotides, no more possibilities
     if (g == 3) {
         VBI[i][j] = VBIij;
         return;
-    } /* In this case the gap g-1=2, which should not be extended.*/
+    }
+
     ip = i + c + 2;
     jp = j - c - 1;
     E1 = eL(i, j, ip, jp) + V[indx[ip] + jp];

From 74f33ed32ee4a546745e9d22716b17201739fe0d Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 23:20:50 -0800
Subject: [PATCH 033/282] Clean up calcWM() function

---
 gtfold-mfe/src/algorithms.c | 72 +++++++++++++++++++++++--------------
 1 file changed, 45 insertions(+), 27 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index b12f357..d230f86 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -544,20 +544,30 @@ void calcVBIS(int i, int j) {
     VBI[i][j] = VBIij;
 }
 
-/* Function for calculating the value of WM(i,j)*/
+/**
+ * Calculates WM(i,j)
+ */
 void calcWM(int i, int j) {
 
-    int b = multConst[2], c = multConst[1]; /* b is the branch penalty and c is penalty for single bases for multiloops*/
+    int b = multConst[2]; // branch penalty
+    int c = multConst[1]; // penalty for single bases for multiloops
     int h;
-    /* WMidjd = dangling base on both ith and jth side.  WMidj = dangling base on ith side. WMijd = dangling base on jth side. WMij = no dangling base on both sides  */
-    int WMidjd, WMidj, WMijd, WMij, WMijp;
+
+    int WMidjd; // dangling bases on both i and j side
+    int WMidj;  // dangling base on i side
+    int WMijd;  // dangling base on j side
+    int WMij;   // no dangling base on either side
+
+    int WMijp;
+
+    // Read the values of RNA[i] and RNA[j] into registers for speed
     int rnai, rnaj;
-    rnai = RNA[i]; /* Read the value of RNA[i] and RNA[j] in register to make the program execute faster.*/
+    rnai = RNA[i];
     rnaj = RNA[j];
 
-    WMijp = INFINITY_; /* See, the data flow through the function - how it has been calculated. */
+    WMijp = INFINITY_;
 
-    /* Minimum size of a hairpin loop is 3, that makes the starting limit of h=i+4 and end limit of j-5*/
+    // Because a hairpin's minimum size is 3, start h at i+4 and end at j-5
     for (h = i + 4; h < j - 4; h++) {
         int temp = WM[i][h] + WM(h+1,j);
         if (temp <= WMijp)
@@ -569,27 +579,35 @@ void calcWM(int i, int j) {
     WMijd = INFINITY_;
     WMij = INFINITY_;
 
-    /* If base i and j pair up. */
+    // i and j pair
     WMij = V[indx[i] + j] + auPen(rnai, rnaj) + b;
-    /* If base i+1 and j pair up. Add the dangling interaction energy of base pair (i+1,j) with base i being on the 3' end */
+
+    // i+1 and j pair. Add the dangling interaction energy of base pair (i+1,j)
+    // with base i being on the 3' end
     if (constraints[i] <= 0)
-        WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
-                RNA[i + 1], rnaj) + b + c;
-    /* If base i and j-1 pair up. Add the dangling interaction energy of base pair (i,j-1) with base j being on the 5' end */
+        WMidj = V[indx[i + 1] + j] +
+                dangle[rnaj][RNA[i + 1]][rnai][1] +
+                auPen(RNA[i + 1], rnaj) +
+                b + c;
+
+    // i and j-1 pair. Add the dangling interaction energy of base pair (i,j-1)
+    // with base j being on the 5' end
     if (constraints[j] <= 0)
-        WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
-                rnai, RNA[j - 1]) + b + c;
-    /* If base i+1 and j-1 pair up. Add the dangling interaction energy of base pair (i+1,j-1) with base i on the 3' and base j on the 5' end.*/
-    if (constraints[i] <= 0 && constraints[j] <= 0)
-        WMidjd = V[indx[i + 1] + j - 1]
-                   + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
-                                                          + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
-                                                                  RNA[j - 1]) + b + 2* c ;
+        WMijd = V[indx[i] + j - 1] +
+                dangle[RNA[j - 1]][rnai][rnaj][0] +
+                auPen(rnai, RNA[j - 1]) +
+                b + c;
 
-    //  if(i==6 && j==11)
-    //    printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d, constraints: (%d,%d)\n", i, j, WMij, WMidj, WMijd, WMidjd, constraints[i], constraints[j]);
+    // i+1 and j-1 pair. Add the dangling interaction energy of base pair
+    // (i+1,j-1) with base i on the 3' and base j on the 5' end.
+    if (constraints[i] <= 0 && constraints[j] <= 0)
+        WMidjd = V[indx[i + 1] + j - 1] +
+                 dangle[RNA[j - 1]][RNA[i + 1]][rnai][1] +
+                 dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] +
+                 auPen(RNA[i + 1],RNA[j - 1]) +
+                 b + 2*c;
 
-    /* Take the minimum of all of the terms */
+    // take the minimum of all WMxxx terms
     WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
 
     int WMsip1j = INFINITY_;
@@ -605,11 +623,11 @@ void calcWM(int i, int j) {
     WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
     WMij = MIN(WMijp, WMij);
 
-    //printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
-
     WM[i][j] = WMij;
-    WM(i,j) = WMij; /* Extra instruction. NOTE that - by having this instruction we are making WM array symmetric. The macro will convert this instruction into WM[j][i] = WM[i][j] making WM array symmetric.*/
-    return;
+
+    // The WM(i,j) macro is equivalent to WM[j][i].  This extra insertion into
+    // the WM table keeps it symmetric
+    WM(i,j) = WMij;
 }
 
 /* Function used for calculating the value of V and WM for a given i,j pair. Calculation of WM at (i,j) requires value of V at (i,j)*/

From 6c60f9e257fec5526eb39fb8b1c9b54def66913e Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 23:35:19 -0800
Subject: [PATCH 034/282] Clean up calcVWM()

---
 gtfold-mfe/src/algorithms.c | 73 +++++++++++++++++++++----------------
 1 file changed, 41 insertions(+), 32 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index d230f86..700882b 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -630,12 +630,22 @@ void calcWM(int i, int j) {
     WM(i,j) = WMij;
 }
 
-/* Function used for calculating the value of V and WM for a given i,j pair. Calculation of WM at (i,j) requires value of V at (i,j)*/
+/**
+ * Calculate i,j entry in V and WM
+ *
+ * WM[i][j] requires having V[i][j] first
+ */
 void calcVWM(int i, int j, int VBIij, int VMij) {
     int a, b, c, h, Vij, eh, es;
-    int WMidjd, WMidj, WMijd, WMij, WMijp;
-    int rnai, rnaj;
 
+    int WMidjd; // dangling bases on both i and j side
+    int WMidj;  // dangling base on i side
+    int WMijd;  // dangling base on j side
+    int WMij;   // no dangling base on either side
+    int WMijp;
+
+    // Read the values of RNA[i] and RNA[j] into registers for speed
+    int rnai, rnaj;
     rnai = RNA[i];
     rnaj = RNA[j];
 
@@ -645,22 +655,23 @@ void calcVWM(int i, int j, int VBIij, int VMij) {
     WMij = INFINITY_;
 
     /* V starts */
-    eh = eH(i, j); /* Energy of a hairpin loop */
-    es = eS(i, j); /* Energy of a stack, with (i,j) and (i-1,j+1) base pairs.*/
-    if (es == 0) {
+    eh = eH(i, j); // Energy of a hairpin loop
+    es = eS(i, j); // Energy of a stack, with (i,j) and (i-1,j+1) base pairs
+
+    if (es == 0)
         es = INFINITY_;
-    } else
+    else
         es += V[indx[i + 1] + j - 1];
 
     Vij = MIN(MIN(eh, es), MIN(VBIij, VMij));
 
-    if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-            && constraints[j] != i) || constraints[i] == -1 || constraints[j]
-                                                                           == -1)
+    // skip entirely if not permitted by constraints
+    if ((constraints[i] > 0 && constraints[i] != j) ||
+        (constraints[j] > 0 && constraints[j] != i) ||
+        constraints[i] == -1 ||
+        constraints[j] == -1)
         Vij = INFINITY_;
 
-    // printf("%d, V(%d,%d): eh: %d, es: %d, vbi: %d, vm: %d, v: %d\n", j-i, i, j, eh, es, VBIij, VMij, Vij);
-
     V[indx[i] + j] = Vij;
 
     if (NOISOLATE == TRUE && Vij < INFINITY_) {
@@ -671,12 +682,10 @@ void calcVWM(int i, int j, int VBIij, int VMij) {
             //Isolated base pairs look ahead
             int eHL = eH(i - 1, j + 1);
             int eSL = eS(i - 1, j + 1) + V[indx[i] + j];
-            if (i - 1 == 0) {
-                eSL = 0;
-                eHL = 0;
-            }
-            int Vijl = (eHL < eSL) ? eHL : eSL;
-            // printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl);
+            if (i == 1)
+                eSL = eHL = 0;
+
+            int Vijl = MIN(eHL, eSL);
 
             if (Vijl > INFINITY_ - SMALLINFTY_)
                 //isolated base pair found.. setting energy to infinity
@@ -705,18 +714,23 @@ void calcVWM(int i, int j, int VBIij, int VMij) {
     WMij = Vij + auPen(rnai, rnaj) + b;
 
     if (constraints[i] <= 0)
-        WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
-                RNA[i + 1], rnaj) + b + c;
+        WMidj = V[indx[i + 1] + j] +
+                dangle[rnaj][RNA[i + 1]][rnai][1] +
+                auPen(RNA[i + 1], rnaj) +
+                b + c;
 
     if (constraints[j] <= 0)
-        WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
-                rnai, RNA[j - 1]) + b + c;
+        WMijd = V[indx[i] + j - 1] +
+                dangle[RNA[j - 1]][rnai][rnaj][0] +
+                auPen(rnai, RNA[j - 1]) +
+                b + c;
 
     if (constraints[i] <= 0 && constraints[j] <= 0)
-        WMidjd = V[indx[i + 1] + j - 1]
-                   + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
-                                                          + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
-                                                                  RNA[j - 1]) + b + 2* c ;
+        WMidjd = V[indx[i + 1] + j - 1] +
+                 dangle[RNA[j - 1]][RNA[i + 1]][rnai][1] +
+                 dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] +
+                 auPen(RNA[i + 1], RNA[j - 1]) +
+                 b + 2*c;
 
     WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
 
@@ -729,15 +743,10 @@ void calcVWM(int i, int j, int VBIij, int VMij) {
     if (constraints[j] <= 0)
         WMsijm1 = WM[i][j - 1];
 
-    WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
-    WMij = MIN(WMijp, WMij);
-
-    //printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
+    WMij = MIN(WMij, MIN(WMsip1j + c, MIN(WMsijm1 + c, MIN(WMijp, WMij))));
 
     WM[i][j] = WMij;
     WM(i,j) = WMij; /* extra instruction */
-    /* WM ends */
-    return;
 }
 
 /* Function for calculating VM, V, and WM at point (i,j) in the order . Calculation of V at (i,j) requires VBI and VM. Also, calculation of final value of WM(i,j) requires V at (i,j) */

From 0cc07ab0189c3dc99928bf95204b53908cba51f6 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 23:45:36 -0800
Subject: [PATCH 035/282] Working on calcVMVWM()

---
 gtfold-mfe/src/algorithms.c | 63 ++++++++++++++++++++++++-------------
 1 file changed, 41 insertions(+), 22 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 700882b..b5128d6 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -749,27 +749,36 @@ void calcVWM(int i, int j, int VBIij, int VMij) {
     WM(i,j) = WMij; /* extra instruction */
 }
 
-/* Function for calculating VM, V, and WM at point (i,j) in the order . Calculation of V at (i,j) requires VBI and VM. Also, calculation of final value of WM(i,j) requires V at (i,j) */
-
+/**
+ * Calculate VM, V, and WM (in that order)
+ *
+ * Some table entries must be filled before others can be filled as well: V
+ * requires VBI and VM, and WM requires V.
+ */
 void calcVMVWM(int i, int j) {
 
-    int a = multConst[0] /*offset penalty for multiloops*/,
-    b = multConst[2]/*penalty per branch for multiloops*/, c =
-        multConst[1]/* Penalty per single base in the multiloop*/,
-        a1, h, es;
+    int a = multConst[0]; // offset penalty for multiloops
+    int b = multConst[2]; // penalty per branch for multiloops
+    int c = multConst[1]; // Penalty per single base in the multiloop
+    int a1, h, es;
+
     int aupen;
+
     int WMijp, WMidjd, WMidj, WMijd, WMij;
     int VMij, VMijd, VMidj, VMidjd, A_temp;
-    int WMip1hm1 /* WM value at i+1 and j-1 */,
-    WMip2hm1/* WM value at i+2 and h-1*/,
-    WMhjm1/* WM value at h and j-1*/, WMhjm2/* WM value at h and j-2*/,
-    WMhp1j /*WM value at h+1 and j*/;
-    int rnai, rnaj;
-    int tmp1, tmp2;
 
+    int WMip1hm1; // WM value at i+1 and j-1
+    int WMip2hm1; // WM value at i+2 and h-1
+    int WMhjm1;   // WM value at h and j-1
+    int WMhjm2;   // WM value at h and j-2
+    int WMhp1j;   // WM value at h+1 and j
+
+    int rnai, rnaj;
     rnai = RNA[i];
     rnaj = RNA[j];
 
+    int tmp1, tmp2;
+
     WMidjd = INFINITY_;
     WMidj = INFINITY_;
     WMijd = INFINITY_;
@@ -789,14 +798,23 @@ void calcVMVWM(int i, int j) {
     if (a1 <= WMijp)
         WMijp = a1;
 
-    /* Here we are doing the calculation of VM and WM at point (i,j) concurrently. This for loop calculates the values of VMij, VMidj, VMijd, VMidjd with the value of WMijp. The value of WMijp is needed for calculating the value of WM at (i,j). However, it should be noted that the final value of WM[i][j] requires value of V at (i,j) and will be calculated in the end. */
-
-    /* There are four possibilities for the multiloop closing base pair for the inclusion of dangling energies.
-     * 1) Including the dangling energy of i+1 base and also for base j-1 with the base pair (i,j) closing the multiloop - VMidjd
-     * 2) Including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j) - VMidj
-     * 3) NOT including the danlging energy of i+1 base and including the dangling energy of base j-1 with the closing base pair (i,j) - VMijd
-     * 4) NOT including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j)-VMij
-     * */
+    // Here we are doing the calculation of VM and WM at point (i,j)
+    // concurrently. This for loop calculates the values of VMij, VMidj, VMijd,
+    // VMidjd with the value of WMijp. The value of WMijp is needed for
+    // calculating the value of WM at (i,j). However, it should be noted that
+    // the final value of WM[i][j] requires value of V at (i,j) and will be
+    // calculated in the end.
+
+    // There are four possibilities for the multiloop closing base pair for the
+    // inclusion of dangling energies:
+    // 1) Including the dangling energy of i+1 base and also for base j-1 with
+    //    the base pair (i,j) closing the multiloop - VMidjd
+    // 2) Including the danlging energy of i+1 base and NOT including the
+    //    dangling energy of base j-1 with the closing base pair (i,j) - VMidj
+    // 3) NOT including the danlging energy of i+1 base and including the
+    //    dangling energy of base j-1 with the closing base pair (i,j) - VMijd
+    // 4) NOT including the danlging energy of i+1 base and NOT including the
+    //    dangling energy of base j-1 with the closing base pair (i,j)-VMij
     for (h = i + 6; h <= j - 5; h++) {
 
         a1 = WM[i][h];
@@ -826,8 +844,9 @@ void calcVMVWM(int i, int j) {
             VMijd = A_temp;
 
         A_temp = WMip2hm1 + WMhjm2;
-        if (A_temp <= VMidjd && constraints[i + 1] <= 0 && constraints[j - 1]
-                                                                       <= 0)
+        if (A_temp <= VMidjd &&
+            constraints[i + 1] <= 0 &&
+            constraints[j - 1] <= 0)
             VMidjd = A_temp;
     }
 

From 038194facee824b43ce8df77ddd1ce9c8ec47682 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 3 Mar 2011 23:52:47 -0800
Subject: [PATCH 036/282] Clean up part of calcW()

---
 gtfold-mfe/src/algorithms.c | 40 +++++++++----------------------------
 1 file changed, 9 insertions(+), 31 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index b5128d6..884d4c4 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -1214,7 +1214,9 @@ void calcVBIVMVWM(int i, int j) {
 }
 
 //problems in this function.. i think this should fix it..
-/* Function to calculate the value of W[j]. */
+/**
+ * Calculate entry in W array
+ */
 void calcW(int j) {
 
     int i;
@@ -1260,43 +1262,19 @@ void calcW(int j) {
             besti = i;
         }
 
-        if (Wj < INFINITY_) {
-            if (Wj == Wij) {
-                if (constraints[i] == j) {
-                    must_branch = 1;
-                }
-            } else if (Wj == Widjd) {
-                if (constraints[i + 1] == j - 1) {
-                    must_branch = 1;
-                }
-            } else if (Wj == Wijd) {
-                if (constraints[i] == j - 1) {
-                    must_branch = 1;
-                }
-            } else {
-                if (constraints[i + 1] == j) {
-                    must_branch = 1;
-                }
-            }
-        }
-
+        if(Wj < INFINITY_ && (Wj == Wij && constraints[i] == j ||
+                              Wj == Widjd && constraints[i+1] == j-1 ||
+                              Wj == Wijd && constraints[i] == j-1 ||
+                              constraints[i+1] == j))
+            must_branch = 1;
     }
 
-    //printf("W%dcal: %d, must_branch: %d, best_i: %d", j, Wj, must_branch, besti);
-
     /* If jth base is not contributing in the energy calculation of W[j] */
-    if (!must_branch) {
+    if (!must_branch)
         if (Wj > W[j - 1])
             Wj = W[j - 1];
-    }
 
     W[j] = Wj;
-
-    //printf(",W%dset: %d\n", j, W[j]);
-
-    //  if(j==11 || j==35 || j==36)
-    // printf("\n*****\nMust branch: %d, W%d: %d\n*****\n", must_branch, j, W[j]);
-    return;
 }
 
 /* For details on calculating energy of different types of Internal loops, please look at the chapter 3 of MS thesis of Mirela Stefania Andronescu.

From 72a72b3498b9b9ca63607bfa5c05a8f061cad882 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 4 Mar 2011 00:15:14 -0800
Subject: [PATCH 037/282] Add parentheses at suggestion of gcc

---
 gtfold-mfe/src/algorithms.c | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 884d4c4..27a3e8f 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -1262,9 +1262,9 @@ void calcW(int j) {
             besti = i;
         }
 
-        if(Wj < INFINITY_ && (Wj == Wij && constraints[i] == j ||
-                              Wj == Widjd && constraints[i+1] == j-1 ||
-                              Wj == Wijd && constraints[i] == j-1 ||
+        if(Wj < INFINITY_ && ((Wj == Wij && constraints[i] == j) ||
+                              (Wj == Widjd && constraints[i+1] == j-1) ||
+                              (Wj == Wijd && constraints[i] == j-1) ||
                               constraints[i+1] == j))
             must_branch = 1;
     }

From 519d2dc88eb63c0f8a3dabc31eb73fd2bd4d7c6a Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 4 Mar 2011 13:23:43 -0800
Subject: [PATCH 038/282] Wrap long comments

---
 gtfold-mfe/src/algorithms.c | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 27a3e8f..e2fca8e 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -17,7 +17,11 @@
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-/* AUTHORED by Amrita Mathuriya August 2007 - January 2009. Implemented multiloop energy function, internal loop energy function using heuristic and internal loop speedup algorithm, parallelization, corrected numerous bugs and commented whole GTfold.
+/*
+ * AUTHORED by Amrita Mathuriya August 2007 - January 2009
+ * Implemented multiloop energy function, internal loop energy function using
+ * heuristic and internal loop speedup algorithm, parallelization, corrected
+ * numerous bugs and commented whole GTfold.
 
  * Amrita:
  * - Please note that, in this file same recursion formulas is being calculated
@@ -36,9 +40,9 @@
  *   into effect at many places.
  * - I am not sure of what these eparam values are at various places except for
  *   multiloops.
- * */
+ */
 
-/* Modified by Sainath Mallidi August 2009 - 
+/* Modified by Sainath Mallidi August 2009 - December 2010
  * Added constraint support that can force a base pair, prohibit a base pair
  * and make single stranded regions
  */

From 9c2504ce5da0f423eb7eead84e9f07fb9339a67e Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 4 Mar 2011 13:25:01 -0800
Subject: [PATCH 039/282] Comment chPairKey

---
 gtfold-mfe/src/algorithms.c | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index e2fca8e..8239822 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -62,6 +62,7 @@
 
 #define WM(i,j) WM[j][i]  /* This pragma is defined for readability purpose.*/
 
+/** A mask used to speed up testing nucleotides for pairing */
 unsigned int chPairKey;
 
 //Constraint arrays

From 740816d895a6e856dd41bf28343c4cfa0c7d07ba Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 4 Mar 2011 13:31:02 -0800
Subject: [PATCH 040/282] Describe initTables a bit more

---
 gtfold-mfe/src/algorithms.c | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 8239822..b505de3 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -124,7 +124,9 @@ void initTables(int len) {
     init_chPair();
 
     for (i = 0; i < LENGTH; i++) {
-        W[i] = INFINITY_; /* Initializing W array with INFINITY make sure that an unfolded sequence will have a large +ve value for free energy - INIFINITY*/
+        // Initializing W array with INFINITY_ ensures that unfolded sequences
+        // have a large positive value for free energy
+        W[i] = INFINITY_;
         constraints[i] = 0;
         for (j = 0; j < LENGTH; j++) {
             VBI[i][j] = INFINITY_;
@@ -133,15 +135,15 @@ void initTables(int len) {
         }
     }
 
-    LLL = (LENGTH - 1) * (LENGTH) / 2 + 1;
+    // The array V is mapped from 2D to 1D and indexed using the indx array.
+    // This mapping helps removing the space wasted for j < i
 
+    // initialize all to INFINITY_
+    LLL = (LENGTH - 1) * (LENGTH) / 2 + 1;
     for (i = 0; i < LLL; i++)
         V[i] = INFINITY_;
 
-    /*
-     * The array V is mapped from 2D to 1D and indexed using the indx array.
-     * This mapping helps removing the space wasted for j < i
-     */
+    // create the mapping
     for (i = 0; i <= LENGTH - 1; i++)
         indx[i] = (len) * (i - 1) - (i * (i - 1)) / 2;
 }
@@ -149,8 +151,7 @@ void initTables(int len) {
 //check if single stranded region is allowed with the given constraints
 int checkSS(int i, int j) {
 
-    int it;
-    for (it = i + 1; it < j; it++)
+    for (int it = i + 1; it < j; it++)
         if (constraints[it] > 0)
             return 1;
 

From 7cf1ec7456b57b13b1c241342fce100727cc290a Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 4 Mar 2011 13:38:35 -0800
Subject: [PATCH 041/282] Describe some of the constraint initialization

---
 gtfold-mfe/src/algorithms.c | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index b505de3..29be956 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -165,6 +165,7 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
         if(RNA1[i]=='N') 
             constraints[i] = -1;
 
+    // initialize constraints that prohibit pairing
     if (prohibitlen != 0) 
         for (it = 0; it < prohibitlen; it++) 
             for(k= 1; k <= prohibitList[it][2];k++) {
@@ -173,6 +174,7 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
                     constraints[prohibitList[it][1]+1-k] = -1;
             }
 
+    // initialize constraints that force pairing
     if (forcelen != 0) {
         printf("Running with constraints\n");
         for (it = 0; it < forcelen; it++) {
@@ -189,6 +191,7 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr
     }
 
 #ifdef _OPENMP
+    // use the user-specified thread count
     if (num_threads > 0)
         omp_set_num_threads(num_threads);
 #endif

From 58a27986ae9686db0d534803da8fe5f52950329c Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 4 Mar 2011 14:03:30 -0800
Subject: [PATCH 042/282] For loop only allowed in C99 mode, which we don't use

---
 gtfold-mfe/src/algorithms.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 29be956..be8ac7a 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -151,7 +151,8 @@ void initTables(int len) {
 //check if single stranded region is allowed with the given constraints
 int checkSS(int i, int j) {
 
-    for (int it = i + 1; it < j; it++)
+    int it;
+    for (it = i + 1; it < j; it++)
         if (constraints[it] > 0)
             return 1;
 

From 9afa1bf59aa550bc5bcacfb6fe192c5009a4f91b Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Mon, 14 Mar 2011 16:11:37 -0400
Subject: [PATCH 043/282] Initial draft of working in Prashant's cleanup. DOES
 NOT FUNCTION

---
 gtfold-mfe/aclocal.m4                 |    4 +-
 gtfold-mfe/include/Makefile.am        |    2 +-
 gtfold-mfe/include/Makefile.in        |    2 +-
 gtfold-mfe/include/algorithms.h       |   43 +-
 gtfold-mfe/include/constants.h        |    1 +
 gtfold-mfe/include/data.h             |    8 +-
 gtfold-mfe/include/energy.h           |   42 +
 gtfold-mfe/include/global.h           |   32 +
 gtfold-mfe/include/main-c.h           |    2 -
 gtfold-mfe/include/main.h             |    1 +
 gtfold-mfe/include/options.h          |   25 +
 gtfold-mfe/include/subopt_traceback.h |    3 +-
 gtfold-mfe/include/utils-c.h          |    5 +
 gtfold-mfe/include/utils.h            |   14 +
 gtfold-mfe/src/Makefile.am            |    7 +-
 gtfold-mfe/src/Makefile.in            |   17 +-
 gtfold-mfe/src/algorithms-partition.c |    4 +-
 gtfold-mfe/src/algorithms.c           | 1471 ++-----------------------
 gtfold-mfe/src/energy.c               |  359 ++++++
 gtfold-mfe/src/global.c               |   99 ++
 gtfold-mfe/src/main.cc                |   51 +-
 gtfold-mfe/src/options.cc             |  137 +++
 gtfold-mfe/src/subopt_traceback.cc    |    6 +-
 gtfold-mfe/src/traceback.c            |   55 +-
 gtfold-mfe/src/utils.cc               |   74 ++
 25 files changed, 939 insertions(+), 1525 deletions(-)
 create mode 100644 gtfold-mfe/include/energy.h
 create mode 100644 gtfold-mfe/include/global.h
 create mode 100644 gtfold-mfe/include/options.h
 create mode 100644 gtfold-mfe/include/utils-c.h
 create mode 100644 gtfold-mfe/include/utils.h
 create mode 100644 gtfold-mfe/src/energy.c
 create mode 100644 gtfold-mfe/src/global.c
 create mode 100644 gtfold-mfe/src/options.cc
 create mode 100644 gtfold-mfe/src/utils.cc

diff --git a/gtfold-mfe/aclocal.m4 b/gtfold-mfe/aclocal.m4
index ee395e9..f5a02ce 100644
--- a/gtfold-mfe/aclocal.m4
+++ b/gtfold-mfe/aclocal.m4
@@ -13,8 +13,8 @@
 
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.68],,
-[m4_warning([this file was generated for autoconf 2.68.
+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.67],,
+[m4_warning([this file was generated for autoconf 2.67.
 You have another version of autoconf.  It may work, but is not guaranteed to.
 If you have problems, you may need to regenerate the build system entirely.
 To do so, use the procedure documented by the package, typically `autoreconf'.])])
diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am
index d900fc0..8512446 100644
--- a/gtfold-mfe/include/Makefile.am
+++ b/gtfold-mfe/include/Makefile.am
@@ -1,3 +1,3 @@
-noinst_HEADERS = algorithms.h algorithms-partition.h constants.h data.h loader.h main-c.h main.h traceback.h
+noinst_HEADERS = algorithms.h constants.h data.h energy.h global.h loader.h main.h main-c.h subopt_traceback.h traceback.h 
 
 CLEANFILES = *~
diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in
index d049bac..fd92471 100644
--- a/gtfold-mfe/include/Makefile.in
+++ b/gtfold-mfe/include/Makefile.in
@@ -155,7 +155,7 @@ target_vendor = @target_vendor@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-noinst_HEADERS = algorithms.h algorithms-partition.h constants.h data.h loader.h main-c.h main.h traceback.h
+noinst_HEADERS = algorithms.h constants.h data.h energy.h global.h loader.h main.h main-c.h subopt_traceback.h traceback.h 
 CLEANFILES = *~
 all: all-am
 
diff --git a/gtfold-mfe/include/algorithms.h b/gtfold-mfe/include/algorithms.h
index d919ed1..4a654d4 100644
--- a/gtfold-mfe/include/algorithms.h
+++ b/gtfold-mfe/include/algorithms.h
@@ -20,56 +20,15 @@
 #ifndef _ALGORITHMS_H
 #define _ALGORITHMS_H
 
-#include "main-c.h"
-
-#define MIN(X,Y) ((X) < (Y) ? (X) : (Y))
-#define MAX(X,Y) ((X) > (Y) ? (X) : (Y))
-
-/* It returns zero if (i,j) can not make a base pair otherwise return 1. The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). Note that the following condition results into 1 for the allowed base pairs .*/
-#define checkPair(i, j) (((((i)-(j)) % 2) == 1 || (((i)-(j)) % 2)== -1) && (!( ((i)==BASE_A && (j)==BASE_C) || ((i)==BASE_C && (j)==BASE_A) )))
-/* Non GC penalty or AU penalty. Returns a constant penalty if the base pair is not GC or CG */
-#define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0)
-
-extern int *constraints;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-	void initTables(int len);
-	
-	void init_chPair();
-	int update_chPair(int i, int j);
-#ifdef __cplusplus
-}
-#endif
-
 #ifdef __cplusplus
 extern "C" {
 #endif
-	int calculate(int len, int **forceList, int **prohibitList, int forcelen,
-			int prohibitlen);
-	
-	int eS(int i, int j);
-	int eH(int i, int j);
-	int eL(int i, int j, int ip, int jp);
-
-extern enum BOOL NOISOLATE;
+	int calculate(int len);
 #ifdef __cplusplus
 }
 #endif
 
-int checkSS(int i, int j);
-
-void calcVBI(int i, int j);
-void calcVM(int i, int j);
 void calcWM(int i, int j);
 void calcW(int j);
-
-void calcVWM(int i, int j, int vbiij, int vmij);
 void calcVBIVMVWM(int i, int j);
-void calcVBIVMVWM2(int i, int j);
-
-void calcVBIS(int i, int j);
-void calcVMVWM(int i, int j);
 #endif
-
diff --git a/gtfold-mfe/include/constants.h b/gtfold-mfe/include/constants.h
index 04eace4..52924fb 100644
--- a/gtfold-mfe/include/constants.h
+++ b/gtfold-mfe/include/constants.h
@@ -34,6 +34,7 @@
 #define maxforce 600 /* maximum number of bases that can be forced single */
 #define maxgu 5 /* maximum number of u's in gu pair */
 #define C_ 1 /* "c" for optimized VBI. */
+#define TURN 3 /*Minimum hairpin size*/
 
 #define MAXLOOP 30 /* The maximum loop size. */
 #define MAXENG 1000
diff --git a/gtfold-mfe/include/data.h b/gtfold-mfe/include/data.h
index 10fcc41..d88382f 100644
--- a/gtfold-mfe/include/data.h
+++ b/gtfold-mfe/include/data.h
@@ -32,15 +32,9 @@ extern int dangle[4][4][4][2]; /* Contain dangling energy values */
 extern int inter[31]; /* Contains size penalty for internal loops */
 extern int bulge[31]; /* Contain the size penalty for bulges */
 extern int hairpin[31]; /* Contains the size penalty for hairpin loops */
-#if 0
-extern int stack[4][4][4][4];
-extern int tstkh[4][4][4][4];
-extern int tstki[4][4][4][4];
-#else
 extern int stack[256]; /* Stacking energy used to calculate energy of stack loops */
 extern int tstkh[256]; /* Terminal mismatch energy used in the calculations of hairpin loops */
 extern int tstki[256]; /* Terminal mismatch energy used in the calculations of internal loops */
-#endif
 extern int tloop[maxtloop + 1][2];
 extern int numoftloops;
 extern int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */
@@ -65,5 +59,7 @@ extern int init;
 extern int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
 extern float prelog;
 
+#define fourBaseIndex(a, b, c, d) (((a) << 6) + ((b) << 4) + ((c) << 2) + (d))
+
 #endif
 
diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h
new file mode 100644
index 0000000..c7a3d80
--- /dev/null
+++ b/gtfold-mfe/include/energy.h
@@ -0,0 +1,42 @@
+#ifndef _ENERGY_TABLES_H_
+#define _ENERGY_TABLES_H_
+
+extern int *V; 
+extern int *W; 
+extern int **VBI; 
+extern int **VM; 
+extern int **WM; 
+extern int *indx; 
+
+
+#define V(i,j) V[indx[i]+j]
+//#define VM(i,j) VM[indx[i]+j]
+//#define WM(i,j) WM[indx[i]+j]
+//#define VBI(i,j) VBI[indx[i]+j]
+
+
+#define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0)
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+int Ed3(int i, int j, int k);
+int Ed5(int i, int j, int k);
+int auPenalty(int i, int j);
+
+int Ec();
+int Eb();
+int Ea(); 
+
+int eS(int i, int j);
+int eH(int i, int j);
+int eL(int i, int j, int ip, int jp);
+
+void create_tables(int len);
+void init_tables(int len);
+void free_tables(int len);
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h
new file mode 100644
index 0000000..9a7f552
--- /dev/null
+++ b/gtfold-mfe/include/global.h
@@ -0,0 +1,32 @@
+#ifndef _GLOBAL_H_
+#define _GLOBAL_H_
+
+#include "constants.h"
+
+extern unsigned char *RNA1; 
+extern unsigned char *RNA; 
+extern int *structure; 
+extern int VERBOSE;
+
+extern unsigned int chPairKey;
+
+// The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). 
+#define checkPair(i, j) (((((i)-(j)) % 2) == 1 || (((i)-(j)) % 2)== -1) && (!( ((i)==BASE_A && (j)==BASE_C) || ((i)==BASE_C && (j)==BASE_A) )))
+
+inline int allowedPairs(int a, int b) ; 
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+void init_global_params(int len);
+void free_global_params();
+void printSequence(int len); 
+void printStructure(int len); 
+#ifdef __cplusplus
+}
+#endif
+
+void init_checkPair(); 
+int  update_checkPair(int i, int j);
+
+#endif
diff --git a/gtfold-mfe/include/main-c.h b/gtfold-mfe/include/main-c.h
index 013a553..ba7d6eb 100644
--- a/gtfold-mfe/include/main-c.h
+++ b/gtfold-mfe/include/main-c.h
@@ -38,8 +38,6 @@ enum BOOL {
 	FALSE=0, TRUE
 };
 
-extern enum BOOL ILSA;
-extern enum BOOL VERBOSE;
 
 #define fourBaseIndex(a, b, c, d) (((a) << 6) + ((b) << 4) + ((c) << 2) + (d))
 
diff --git a/gtfold-mfe/include/main.h b/gtfold-mfe/include/main.h
index 8e42832..1f607f0 100644
--- a/gtfold-mfe/include/main.h
+++ b/gtfold-mfe/include/main.h
@@ -24,6 +24,7 @@
 #include <vector>
 
 #include "constants.h"
+#include "main-c.h"
 
 using namespace std;
 
diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
new file mode 100644
index 0000000..8680c5f
--- /dev/null
+++ b/gtfold-mfe/include/options.h
@@ -0,0 +1,25 @@
+#ifndef _OPTIONS_H_
+#define _OPTIONS_H_
+
+#include <stdlib.h>
+#include <string>
+#include <cstring>
+#include <stdio.h>
+
+extern bool ILSA; 
+extern bool NOISOLATE;
+extern bool USERDATA;
+extern bool PARAMS;
+extern bool LIMIT_DISTANCE;
+
+extern std::string datadir;
+extern std::string dataparam;
+extern std::string seqfile ;
+
+extern int delta;
+extern int nThreads;
+
+void help(); 
+void parse_options(int argc, char** argv);
+
+#endif
diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h
index 00cbc8c..2753854 100644
--- a/gtfold-mfe/include/subopt_traceback.h
+++ b/gtfold-mfe/include/subopt_traceback.h
@@ -38,8 +38,7 @@
 #define Eb multConst[2]
 #define Ec multConst[1] 
 
-#define V(x,y)	V[indx[x]+y]
-#define TURN 3
+#define V(x,y) V[indx[x]+y]
 
 enum label {lW=0, lV, lVBI, lVM, lWM};
 extern const char* lstr[]; 
diff --git a/gtfold-mfe/include/utils-c.h b/gtfold-mfe/include/utils-c.h
new file mode 100644
index 0000000..92b3d32
--- /dev/null
+++ b/gtfold-mfe/include/utils-c.h
@@ -0,0 +1,5 @@
+#ifndef _UTILS-C_H_
+#define _UTILS-C_H_
+
+
+#endif
diff --git a/gtfold-mfe/include/utils.h b/gtfold-mfe/include/utils.h
new file mode 100644
index 0000000..a865fac
--- /dev/null
+++ b/gtfold-mfe/include/utils.h
@@ -0,0 +1,14 @@
+#ifndef _UTILS_H_
+#define _UTILS_H_
+
+#include "constants.h"
+
+
+#define MIN(X,Y) ((X) < (Y) ? (X) : (Y))
+#define MAX(X,Y) ((X) > (Y) ? (X) : (Y))
+
+char baseToDigit(const char* base) ;
+unsigned char getBase(const char* base) ;
+unsigned char getBase1(const char* base) ;
+
+#endif
diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am
index 49f310e..f4addd2 100644
--- a/gtfold-mfe/src/Makefile.am
+++ b/gtfold-mfe/src/Makefile.am
@@ -8,12 +8,15 @@ bin_PROGRAMS = gtfold
 gtfold_SOURCES = \
 	main.cc\
 	loader.cc\
-	subopt_traceback.cc\
+	utils.cc\
+	options.cc\
+	global.c\
+	energy.c\
 	algorithms.c\
 	algorithms-partition.c\
+	subopt_traceback.cc\
 	traceback.c
 
-
 gtfold_LDFLAGS = 
 
 gtfold_LDADD = -lm
diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in
index b3a8a1a..ebc0263 100644
--- a/gtfold-mfe/src/Makefile.in
+++ b/gtfold-mfe/src/Makefile.in
@@ -48,9 +48,10 @@ CONFIG_CLEAN_FILES =
 CONFIG_CLEAN_VPATH_FILES =
 am__installdirs = "$(DESTDIR)$(bindir)"
 PROGRAMS = $(bin_PROGRAMS)
-am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) \
-	subopt_traceback.$(OBJEXT) algorithms.$(OBJEXT) \
-	algorithms-partition.$(OBJEXT) traceback.$(OBJEXT)
+am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
+	options.$(OBJEXT) global.$(OBJEXT) energy.$(OBJEXT) \
+	algorithms.$(OBJEXT) algorithms-partition.$(OBJEXT) \
+	subopt_traceback.$(OBJEXT) traceback.$(OBJEXT)
 gtfold_OBJECTS = $(am_gtfold_OBJECTS)
 gtfold_DEPENDENCIES =
 gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
@@ -182,9 +183,13 @@ AM_CXXFLAGS = -DDATADIR='$(datadir)/@PACKAGE@'
 gtfold_SOURCES = \
 	main.cc\
 	loader.cc\
-	subopt_traceback.cc\
+	utils.cc\
+	options.cc\
+	global.c\
+	energy.c\
 	algorithms.c\
 	algorithms-partition.c\
+	subopt_traceback.cc\
 	traceback.c
 
 gtfold_LDFLAGS = 
@@ -273,10 +278,14 @@ distclean-compile:
 
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/energy.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/global.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/loader.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@
 
 .c.o:
 @am__fastdepCC_TRUE@	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c
index 0a1f5ac..f87e190 100644
--- a/gtfold-mfe/src/algorithms-partition.c
+++ b/gtfold-mfe/src/algorithms-partition.c
@@ -4,10 +4,12 @@
 #include <stdlib.h>
 
 #include "algorithms.h"
+#include "utils.h"
+#include "energy.h"
+#include "global.h"
 #include "algorithms-partition.h"
 #include "data.h"
 
-
 // double[][] QB;
 // double[][] Q;
 // double[][] QM;
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 83f94d6..c07d6d9 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -15,1439 +15,132 @@
 
  You should have received a copy of the GNU General Public License
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-/* AUTHORED by Amrita Mathuriya August 2007 - January 2009. Implemented multiloop energy function, internal loop energy function using heuristic and internal loop speedup algorithm, parallelization, corrected numerous bugs and commented whole GTfold.
-
- * Amrita: Please note that, in this file same recursion formulas is being calculated in more than one functions.
- * This is done for performance improvement to reduce the redundant computations for various cases. The duplicate codes are not documented again at some places.
- * The arrays to be calculated are VBI, VM, V and WM for every  point (i,j) where j > i. Then W(j) needs to be calculated for j= 1 to N.
- * NOTE that the WM(i,j) can be calculated only after V(i,j) and array VBI and VM should be calculated before V array for point (i,j). So, the order of computation has been kept as VBI, VM, V, WM for any point (i,j)
- * Also Note that, a valid base pair has j > i. Therefore, the portion of the 2D arrays containing j < i is not useful.
- * Minimum size of a hairpin loop is assumed as 3. This assumption is taken into effect at many places.
- * I am not sure of what these eparam values are at various places except for multiloops.
- * */
-
-/* Modified by Sainath Mallidi August 2009 -  "*/
-/* Added constraint support that can force a base pair, prohibit a base pair and make single stranded regions */
+*/ 
 
 #include <stdio.h>
 #include <math.h>
 #include <stdlib.h>
-#include "data.h"
+#include <assert.h>
+
 #include "constants.h"
-#include "main-c.h"
+#include "utils.h"
+#include "energy.h"
+#include "global.h"
 #include "algorithms.h"
-#ifdef _OPENMP   /* The compiler automatically recognizes openmp support and includes the file accordingly*/
-#include "omp.h"
-#endif
-
-#define DEBUG 0
-
-#define WM(i,j) WM[j][i]  /* This pragma is defined for readability purpose.*/
-
-unsigned int chPairKey;
-
-//Constraint arrays
-int plen = 0, flen = 0, sslen = 0;
-int *pbpi, *pbpj, *fbpi, *fbpj, *ss;
-
-/* This function calculates chPairKey to be processed by function chPair. Defined by Professor Bader. */
-void init_chPair() {
-	int i, j;
-
-	chPairKey = 0;
-	for (i = 0; i < 4; i++)
-		for (j = 0; j < 4; j++)
-			chPairKey += checkPair(i, j) << ((i << 2) + j);
-}
-
-int update_chPair(int i, int j) 
-{
-	int r = 0;
-	if (!((i >= 0 && i <=3 )&&(j >=0 && j <=3)))
-		return r;
-
-	if (!(chPairKey & (1 << ((i << 2) + j))))
-	{
-		chPairKey += 1 << ((i << 2) + j);	
-		r = 1;
-	}
-
-	return r;
-}
-
-
-/* This pragma returns 1 if  base b1 and b2 can pair up, otherwise returns 0, using chPairKey calculated in init_chPair function. Here b1 and b2 are 0-3 to represent one of the four nucleotides A, C, G and U. */
-#if 0
-inline
-int chPair(int b1, int b2) {
-	return (chPairKey & (1 << ((b1<<2) + b2)));
-}
-#else
-#define chPair(a, b)  (chPairKey & (1 << (((a)<<2) + (b))))  /* Please try to run this, to understand this statement. Defined by Professor Bader. */
-#endif
 
-/* Initialize variables.*/
-void initTables(int len) {
-
-	int i, j;
-	int LLL;
-
-#if 0
-	int z = (len)*(len+1)/2 + 1;
-
-	V = new int[z];
-	indx = new int[len+1];
-#endif
-
-#if DEBUG
-	if (len != LENGTH-1)
-		fprintf(stderr,"ERROR: in initTables, len (%5d) != LENGTH-1 (%5d)\n",len,LENGTH-1);
-#endif
-
-	init_chPair();
-
-	for (i = 0; i < LENGTH; i++) {
-		W[i] = INFINITY_; /* Initializing W array with INFINITY make sure that an unfolded sequence will have a large +ve value for free energy - INIFINITY*/
-		constraints[i] = 0;
-#if 0
-		indx[i] = (LENGTH-1)*(i-1) - (i*(i-1))/2;
-		indx[i] = (len)*(i-1) - (i*(i-1))/2;
+#ifdef _OPENMP   
+#include "omp.h"
 #endif
-		for (j = 0; j < LENGTH; j++) {
-			VBI[i][j] = INFINITY_;
-			VM[i][j] = INFINITY_;
-			WM[i][j] = INFINITY_;
-		}
-	}
-
-	LLL = (LENGTH - 1) * (LENGTH) / 2 + 1;
 
-	for (i = 0; i < LLL; i++)
-		V[i] = INFINITY_;
 
-	/*The array V is mapped from 2D to 1D and indexed using the indx array. This mapping helps removing the space wasted for j < i*/
-	for (i = 0; i <= LENGTH - 1; i++)
-		indx[i] = (len) * (i - 1) - (i * (i - 1)) / 2;
-
-	return;
-}
-
-//check if single stranded region is allowed with the given constraints
-int checkSS(int i, int j) {
-
-	int it;
-	for (it = i + 1; it < j; it++) {
-		if (constraints[it] > 0)
-			return 1;
-	}
-	return 0;
-
-}
-
-int calculate(int len, int **forceList, int **prohibitList, int forcelen, int prohibitlen) {
-	int b, i, j, it, k;
-	
-	for(i=1;i<=len;i++) 
-	{
-		if(RNA1[i]=='N') 
-			constraints[i] = -1;
-	}	
-
-	if (prohibitlen != 0) 
-	{
-		for (it = 0; it < prohibitlen; it++) 
-		{
-			for(k= 1; k <= prohibitList[it][2];k++)
-			{
-				constraints[prohibitList[it][0]+k-1] = -1;
-				if(prohibitList[it][1]!=0)
-				{
-					constraints[prohibitList[it][1]+1-k] = -1;
-				}
-			}
-		}
-	}
-
-	if (forcelen != 0) 
-	{
-		printf("Running with constraints\n");
-		for (it = 0; it < forcelen; it++) 
-		{
-			for(k=1; k <= forceList[it][2];k++)
-			{
-				if (!chPair(RNA[forceList[it][0]+k-1], RNA[forceList[it][1]-k+1])) 
-				{
-					printf("Can't constrain (%d,%d)\n", forceList[it][0]+k-1,
-							forceList[it][1]-k+1);
-					continue;
-				}
-				constraints[forceList[it][0]+k-1] = forceList[it][1]+1-k;
-				constraints[forceList[it][1]+1-k] = forceList[it][0]+k-1;
-			}
-				//printf("(%d,%d)\n", forceList[it][0], forceList[it][1]);
-		}
-	}
-
-#ifdef _OPENMP
-	if (num_threads > 0)
-		omp_set_num_threads(num_threads);
-#endif
+int calculate(int len) { 
+	int b, i, j;
 
 #if 1
 #ifdef _OPENMP
 #pragma omp parallel
 #pragma omp master
 	{
-		fprintf(stdout,"Thread count: %3d\n",omp_get_num_threads());
+		fprintf(stdout,"\n");
+		fprintf(stdout,"Running with %3d OpenMP thread",omp_get_num_threads());
+		if (omp_get_num_threads()>1) fprintf(stdout,"s");
+		fprintf(stdout,".\n");
 	}
 #endif
 #endif
 
-    //printf("starting.......\n");
-
-	/* Here b-1 is the length of the segment closed with (i,j) base pair. We assume the minimum size of a hairpin loop closed with (i,j) equal to 3.*/
-
-	/* For b = 4 to 6, hairpin loops and at b = 6 stack loops are possible. So, only WM, and V array are needs to be calculated.
-	 * If (i,j) can not pair up then only WM needs to be calculated.
-	 * */
-	for (b = 4; b <= 6; b++) {
+	for (b = TURN+1; b <= len-1; b++) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
-		/* OpenMP syntex to parallelize the for loop. Guided scheduling strategy works better because there may not be equla amount of work for every (i,j)
-		 * Please look at the conference paper on GTfold for information regarding how to parallelize the code. Also, note that the for every value of b calculation has to go sequentially. However, the calculation for a perticular value of b, which corresponds to calculating on a single diagonal.
-		 * */
 #endif
 		for (i = 1; i <= len - b; i++) {
 			j = i + b;
-			//if (constraints[i] == -1 && constraints[j] == -1)
-			//	continue;
-			if (j-i >= contact_dist) continue;
-			if (chPair(RNA[i], RNA[j])) /* Check if bases i and j pair up or not */
-				calcVWM(i, j, INFINITY_, INFINITY_); /* Calculates V and WM array for element (i,j)*/
-			else
-				calcWM(i, j); /* Calculates WM array for element (i,j)*/
-		}
-	}
-
-    /* For b=7 to 10, base pair (i,j) is not able to form multiloops. */
-    for (b = 7; b <= 10; b++) {
-#ifdef _OPENMP
-#pragma omp parallel for private (i,j) schedule(guided)
-#endif
-        for (i = 1; i <= len - b; i++) {
-            j = i + b;
-            //if (constraints[i] == -1 && constraints[j] == -1)
-            //	continue;
-			if (j-i >= contact_dist) continue;
-            if (chPair(RNA[i], RNA[j])) {
-                calcVBI(i, j); /* Calculates VBI element at (i,j) */
-                calcVWM(i, j, VBI[i][j], INFINITY_); /* Calculates V and WM arrays*/
-            } else
-                calcWM(i, j); /* Calculates WM element at (i,j) */
-        }
-    }
-
-    for (b = 11; b <= len - 1; b++) {
-#ifdef _OPENMP
-#pragma omp parallel for private (i,j) schedule(guided)
-#endif
-        for (i = 1; i <= len - b; i++) {
-            j = i + b;
-            //printf("%d %d: %d %d\n", i, j, constraints[i], constraints[j]);
-            //if (constraints[i] == -1 && constraints[j] == -1)
-            //	continue;
-			if (j-i >= contact_dist) continue;
-            if (chPair(RNA[i], RNA[j])) {
-                calcVBIVMVWM(i, j); /* Calculates VBI, VM, V and WM elements at (i,j) */
-            } else
-                calcWM(i, j); /* Calculates WM element at (i,j) */
-        }
-    }
-
-/*
-    for(j=2; j<=len; j++){
-        for (i=j-1; i>0; i--){
-		    printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WM[i][j]);
-        }
-    }
-*/            
-
-	for (j = 5; j <= len; j++) /* Recurssion relation for W array does not depend upon any other array, so can be done after the computation of other arrays are finished.*/
-		calcW(j);
-
-	//printV(len);
-
-	return W[len];
-}
-/* This function calculates the optimal energy of internal loops closed with base pair (i,j) using a heuristic, which limits their size to a constant value - MAXLOOP
- An internal loop contains one closing base pair (i,j) and one enclosed base pair (ip,jp). This function searches for the best enclosed base pair for the closing base pair (i,j) within the given window limited by MAXLOOP
- */
-void calcVBI(int i, int j) {
-
-	int ip, jp, temp, VBIij, thres1;
-
-	VBIij = INFINITY_;
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		return;
-
-	/* Having ip = i+1 and jp = j-1, creates a stack loop. Stack loops are taken care separately in the calculation of V  using eS() function. Therefore, for ip=i+1, the jp value should be lesser than or equal to j-2.*/
-	ip = i + 1;
-	thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of the hairpin loop which the enclosed base pair (ip,jp) can close is 3 that results in the minimum value of jp = ip+4 */
-	for (jp = thres1; jp <= j - 2; jp++) {
-		//May need to check the constraint condition here
-		if (jp-ip >= contact_dist) continue;
-		if (chPair(RNA[ip], RNA[jp])) {
-			if (checkSS(i, ip) || checkSS(jp, j))
-				continue;
-			temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the optimal energy of the substructure closed by (ip,jp)*/
-			if (VBIij > temp)
-				VBIij = temp;
-		}
-	}
-
-	for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) {
-		thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of a hairpin loop is 3, so start jp from ip+4*/
-		//May need to check for forced constraints here
-		for (jp = thres1; jp <= j - 1; jp++) {
-			if (jp-ip >= contact_dist) continue;
-			if (chPair(RNA[ip], RNA[jp])) {
-				if (checkSS(i, ip) || checkSS(jp, j))
-					continue;
-				temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the optimal energy of the substructure closed by (ip,jp)*/
-				if (VBIij > temp)
-					VBIij = temp;
-			}
-		}
-	}
-
-	VBI[i][j] = VBIij;
-	return;
-}
-
-/* Amrita: - Internal loop speedup algorithm */
-/* Calculation of internal loops using internal loop speedup algorithm. The algorithm calculates the optimal loop closed with base pair (i,j) */
-void calcVBIS(int i, int j) {
-
-	int ip, jp, E, VBIij, c = 3, b, len = LENGTH - 1, E1, E2, g; /* ip and jp form enclosed base pairs and c is a small constant currently taken as 3. The loops having one or both sides smaller than c are calculated as special cases. */
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		return;
-
-	VBIij = VBI[i][j];
-
-	/*Case1: Loops having first side shorter than c and second side has all allowable sizes */
-	/* Having ip = i+1 and jp=j-1 creates a stack which is considered separately in eS function. So here the max value of jp could be j-2*/
-	ip = i + 1;
-	for (jp = ip + 4; jp <= j - 2; jp++) {
-		if (jp-ip >= contact_dist) continue;
-		if (chPair(RNA[ip], RNA[jp])) {
-			E = eL(i, j, ip, jp) + V[indx[ip] + jp];
-			if (VBIij > E)
-				VBIij = E;
-		}
-	}
-
-	for (ip = i + 2; ip <= i + c; ip++) {
-		for (jp = ip + 4; jp <= j - 1; jp++) { /* Minimum size of a hairpin loop is 3.*/
-			if (jp-ip >= contact_dist) continue;
-			if (chPair(RNA[ip], RNA[jp])) {
-				E = eL(i, j, ip, jp) + V[indx[ip] + jp];
-				if (VBIij > E)
-					VBIij = E;
-			}
-		}
-	}
-
-	/*Case 2: When the first side is greater or equal to c but the second side is smaller */
-	for (ip = i + c + 1; ip < j - 1; ip++) {
-		for (jp = j - c; jp <= j - 1 && jp >= ip + 4; jp++) { /* Minimum size of a hairpin loop is 3.*/
-			if (jp-ip >= contact_dist) continue;
-			if (chPair(RNA[ip], RNA[jp])) {
-				E = eL(i, j, ip, jp) + V[indx[ip] + jp];
-				if (VBIij > E)
-					VBIij = E;
-			}
-		}
-	}
-
-	/* Case 3: General Case - when both sides of internal loops are greater than or equal to c */
-	/*Base cases for this (i,j) are g=j-i-2c-3 and j-i-2c-4, gap values should always be greater than or equal to 3*/
-	/* First base case - both sides of the loop are  equal to c.*/
-	ip = i + c + 1;
-	jp = j - c - 1;
-
-	g = jp - ip - 1;
-	if (g < 3) {
-		VBI[i][j] = VBIij;
-		return;
-	} /* if g is lesser than 3, then you don't extend this value. In this case the second base case of g-1=j-i-2c-4 will also not make a valid gap value. */
-
-	E = eL(i, j, ip, jp) + V[indx[ip] + jp];
-	if (VBIij > E)
-		VBIij = E;
-
-	/* Extend this base case for all closing base pairs of the form ( i-b, j+b ) */
-
-	for (b = 1; b <= MIN(i - 1, len - j); b++) {
-
-		E = eL(i - b, j + b, ip, jp) + V[indx[ip] + jp];
-
-		/* Two more options for base pair (i-b,j+b), which are introduced by having one of the side of the resultant internal loop exactly equal to c */
-		/* Second side is c - with closing base pair (i-b,j+b)*/
-		int ip1 = i + c + 1 + b;
-		int jp1 = (j + b) - c - 1;
-		E1 = eL(i - b, j + b, ip1, jp1) + V[indx[ip1] + jp1];
-
-		/* First side is c - with closing base pair (i-b,j+b)*/
-		int ip2 = (i - b) + c + 1;
-		int jp2 = j - c - 1 - b;
-		E2 = eL(i - b, j + b, ip2, jp2) + V[indx[ip2] + jp2];
-
-		if (E > E1) {
-			E = E1;
-			ip = ip1;
-			jp = jp1;
-		}
-		if (E > E2) {
-			E = E2;
-			ip = ip2;
-			jp = jp2;
-		}
-		if (VBI[i - b][j + b] > E) {
-			VBI[i - b][j + b] = E;
-		}
-	}
-
-	if (g == 3) {
-		VBI[i][j] = VBIij;
-		return;
-	} /* In this case the gap g-1=2, which should not be extended.*/
-	ip = i + c + 2;
-	jp = j - c - 1;
-	E1 = eL(i, j, ip, jp) + V[indx[ip] + jp];
-	E2 = eL(i, j, i + c + 1, j - c - 2) + V[indx[i + c + 1] + j - c - 2];
-	if (VBIij > E1)
-		VBIij = E1;
-	if (VBIij > E2)
-		VBIij = E2;
-
-	if (E2 < E1) {
-		ip = i + c + 1;
-		jp = j - c - 2;
-	}
-
-	for (b = 1; b <= MIN(i - 1, len - j); b++) {
-		E = eL(i - b, j + b, ip, jp) + V[indx[ip] + jp];
-
-		/*Two more options for base pair (i-b,j+b), having one of the sides equal to c */
-		/* First side is equal to c*/
-		int ip1 = (i - b) + c + 1;
-		int jp1 = (j) - c - 2 - b;
-		E1 = eL(i - b, j + b, ip1, jp1) + V[indx[ip1] + jp1];
-
-		/* Second side is equal to c*/
-		int ip2 = i + c + 2 + b;
-		int jp2 = (j + b) - c - 1;
-		E2 = eL(i - b, j + b, ip2, jp2) + V[indx[ip2] + jp2];
-
-		if (E > E1) {
-			E = E1;
-			ip = ip1;
-			jp = jp1;
-		}
-		if (E > E2) {
-			E = E2;
-			ip = ip2;
-			jp = jp2;
-		}
-		if (VBI[i - b][j + b] > E) {
-			VBI[i - b][j + b] = E;
-		}
-	}
-
-	VBI[i][j] = VBIij;
-}
-
-/* Function for calculating the value of WM(i,j)*/
-void calcWM(int i, int j) {
-
-	int b = multConst[2], c = multConst[1]; /* b is the branch penalty and c is penalty for single bases for multiloops*/
-	int h;
-	/* WMidjd = dangling base on both ith and jth side.  WMidj = dangling base on ith side. WMijd = dangling base on jth side. WMij = no dangling base on both sides  */
-	int WMidjd, WMidj, WMijd, WMij, WMijp;
-	int rnai, rnaj;
-	rnai = RNA[i]; /* Read the value of RNA[i] and RNA[j] in register to make the program execute faster.*/
-	rnaj = RNA[j];
-
-	WMijp = INFINITY_; /* See, the data flow through the function - how it has been calculated. */
-
-	/* Minimum size of a hairpin loop is 3, that makes the starting limit of h=i+4 and end limit of j-5*/
-	for (h = i + 4; h < j - 4; h++) {
-		int temp = WM[i][h] + WM(h+1,j);
-		if (temp <= WMijp)
-			WMijp = temp;
-	}
-
-	WMidjd = INFINITY_;
-	WMidj = INFINITY_;
-	WMijd = INFINITY_;
-	WMij = INFINITY_;
-
-	/* If base i and j pair up. */
-	WMij = V[indx[i] + j] + auPen(rnai, rnaj) + b;
-	/* If base i+1 and j pair up. Add the dangling interaction energy of base pair (i+1,j) with base i being on the 3' end */
-	if (constraints[i] <= 0)
-		WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
-				RNA[i + 1], rnaj) + b + c;
-	/* If base i and j-1 pair up. Add the dangling interaction energy of base pair (i,j-1) with base j being on the 5' end */
-	if (constraints[j] <= 0)
-		WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
-				rnai, RNA[j - 1]) + b + c;
-	/* If base i+1 and j-1 pair up. Add the dangling interaction energy of base pair (i+1,j-1) with base i on the 3' and base j on the 5' end.*/
-	if (constraints[i] <= 0 && constraints[j] <= 0)
-		WMidjd = V[indx[i + 1] + j - 1]
-		           + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
-		                                                  + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
-		                                                		  RNA[j - 1]) + b + 2* c ;
-
-	//	if(i==6 && j==11)
-	//	  printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d, constraints: (%d,%d)\n", i, j, WMij, WMidj, WMijd, WMidjd, constraints[i], constraints[j]);
-
-	/* Take the minimum of all of the terms */
-	WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
-
-	int WMsip1j = INFINITY_;
-	int WMsijm1 = INFINITY_;
-
-	if (constraints[i] <= 0)
-		WMsip1j = WM[i + 1][j];
-
-	if (constraints[j] <= 0)
-		WMsijm1 = WM[i][j - 1];
-
-
-	WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
-	WMij = MIN(WMijp, WMij);
-
-	//printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
-
-	WM[i][j] = WMij;
-	WM(i,j) = WMij; /* Extra instruction. NOTE that - by having this instruction we are making WM array symmetric. The macro will convert this instruction into WM[j][i] = WM[i][j] making WM array symmetric.*/
-	return;
-}
-
-/* Function used for calculating the value of V and WM for a given i,j pair. Calculation of WM at (i,j) requires value of V at (i,j)*/
-void calcVWM(int i, int j, int VBIij, int VMij) {
-	int a, b, c, h, Vij, eh, es;
-	int WMidjd, WMidj, WMijd, WMij, WMijp;
-	int rnai, rnaj;
-
-	rnai = RNA[i];
-	rnaj = RNA[j];
-
-	WMidjd = INFINITY_;
-	WMidj = INFINITY_;
-	WMijd = INFINITY_;
-	WMij = INFINITY_;
-
-	/* V starts */
-	eh = eH(i, j); /* Energy of a hairpin loop */
-	es = eS(i, j); /* Energy of a stack, with (i,j) and (i-1,j+1) base pairs.*/
-	if (es == 0) {
-		es = INFINITY_;
-	} else
-		es += V[indx[i + 1] + j - 1];
-
-	Vij = MIN(MIN(eh, es), MIN(VBIij, VMij));
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		Vij = INFINITY_;
-
-	// printf("%d, V(%d,%d): eh: %d, es: %d, vbi: %d, vm: %d, v: %d\n", j-i, i, j, eh, es, VBIij, VMij, Vij);
-
-	V[indx[i] + j] = Vij;
-
-	if (NOISOLATE == TRUE && Vij < INFINITY_) {
-		//Check if i+1,j-1 have paired
-		if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) {
-			//If not then check for i-1, j+1
-
-			//Isolated base pairs look ahead
-			int eHL = eH(i - 1, j + 1);
-			int eSL = eS(i - 1, j + 1) + V[indx[i] + j];
-			if (i - 1 == 0) {
-				eSL = 0;
-				eHL = 0;
-			}
-			int Vijl = (eHL < eSL) ? eHL : eSL;
-			// printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl);
-
-			if (Vijl > INFINITY_ - SMALLINFTY_)
-				//isolated base pair found.. setting energy to infinity
-				V[indx[i] + j] = Vij = INFINITY_;
-		}
-	}
-
-#if DEBUG
-	if (indx[i]+j > (LENGTH-1)*(LENGTH)/2)
-		fprintf(stderr,"ERROR: in calcVMW: i: %5d  j: %5d\n",i,j);
-#endif
-	/* V ends */
-
-	/* WM starts */
-	a = multConst[0];
-	b = multConst[2];
-	c = multConst[1];
-	WMijp = INFINITY_;
-
-	for (h = i + 4; h <= j - 5; h++) {
-		int temp = WM[i][h] + WM(h+1,j);
-		if (temp < WMijp)
-			WMijp = temp;
-	}
-
-	WMij = Vij + auPen(rnai, rnaj) + b;
-
-	if (constraints[i] <= 0)
-		WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
-				RNA[i + 1], rnaj) + b + c;
-
-	if (constraints[j] <= 0)
-		WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
-				rnai, RNA[j - 1]) + b + c;
-
-	if (constraints[i] <= 0 && constraints[j] <= 0)
-		WMidjd = V[indx[i + 1] + j - 1]
-		           + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
-		                                                  + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
-		                                                		  RNA[j - 1]) + b + 2* c ;
-
-	WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
-
-	int WMsip1j = INFINITY_;
-	int WMsijm1 = INFINITY_;
-
-	if (constraints[i] <= 0)
-		WMsip1j = WM[i + 1][j];
-
-	if (constraints[j] <= 0)
-		WMsijm1 = WM[i][j - 1];
-
-	WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
-	WMij = MIN(WMijp, WMij);
-
-	//printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
-
-	WM[i][j] = WMij;
-	WM(i,j) = WMij; /* extra instruction */
-	/* WM ends */
-	return;
-}
 
-/* Function for calculating VM, V, and WM at point (i,j) in the order . Calculation of V at (i,j) requires VBI and VM. Also, calculation of final value of WM(i,j) requires V at (i,j) */
-
-void calcVMVWM(int i, int j) {
-
-	int a = multConst[0] /*offset penalty for multiloops*/,
-	b = multConst[2]/*penalty per branch for multiloops*/, c =
-		multConst[1]/* Penalty per single base in the multiloop*/,
-		a1, h, es;
-	int aupen;
-	int WMijp, WMidjd, WMidj, WMijd, WMij;
-	int VMij, VMijd, VMidj, VMidjd, A_temp;
-	int WMip1hm1 /* WM value at i+1 and j-1 */,
-	WMip2hm1/* WM value at i+2 and h-1*/,
-	WMhjm1/* WM value at h and j-1*/, WMhjm2/* WM value at h and j-2*/,
-	WMhp1j /*WM value at h+1 and j*/;
-	int rnai, rnaj;
-	int tmp1, tmp2;
-
-	rnai = RNA[i];
-	rnaj = RNA[j];
-
-	WMidjd = INFINITY_;
-	WMidj = INFINITY_;
-	WMijd = INFINITY_;
-	WMij = INFINITY_;
-
-	/* VM and WM starts */
-	aupen = auPen(rnai, rnaj); /* AU or NON GC penalty for base pair (i,j) */
-	VMij = INFINITY_;
-	VMijd = INFINITY_;
-	VMidj = INFINITY_;
-	VMidjd = INFINITY_;
-
-	/* Manoj starts */
-
-	WMijp = WM[i][i + 4] + WM(i+5,j);
-	a1 = WM[i][i + 5] + WM(i+6,j);
-	if (a1 <= WMijp)
-		WMijp = a1;
-
-	/* Here we are doing the calculation of VM and WM at point (i,j) concurrently. This for loop calculates the values of VMij, VMidj, VMijd, VMidjd with the value of WMijp. The value of WMijp is needed for calculating the value of WM at (i,j). However, it should be noted that the final value of WM[i][j] requires value of V at (i,j) and will be calculated in the end. */
-
-	/* There are four possibilities for the multiloop closing base pair for the inclusion of dangling energies.
-	 * 1) Including the dangling energy of i+1 base and also for base j-1 with the base pair (i,j) closing the multiloop - VMidjd
-	 * 2) Including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j) - VMidj
-	 * 3) NOT including the danlging energy of i+1 base and including the dangling energy of base j-1 with the closing base pair (i,j) - VMijd
-	 * 4) NOT including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j)-VMij
-	 * */
-	for (h = i + 6; h <= j - 5; h++) {
-
-		a1 = WM[i][h];
-		WMip1hm1 = WM[i + 1][h - 1];
-		WMip2hm1 = WM[i + 2][h - 1];
-#if 0
-		WMhjm1 = WM[h][j-1];
-		WMhjm2 = WM[h][j-2];
-		WMhp1j = WM[h+1][j];
-#else
-		WMhjm1 = WM(h,j-1); /* Preprocessor will convert this into WM[j-1][h]. According to the algorithm, the expression should be WM[h][j-1]  -- in which case, as the value of h changes, this will access elements from a column of the WM matrix. To improve run time performance WM array is made symmetric and so WM[h][j-1] = WM[j-1][h] and it will have accesses in a row.*/
-		WMhjm2 = WM(h,j-2); /* Same reason as above */
-		WMhp1j = WM(h+1,j); /* Same reason as above */
-#endif
-
-		/* WM starts */
-		a1 += WMhp1j;
-		if (a1 <= WMijp)
-			WMijp = a1;
-		/* WM ends */
-
-		/* Calculation of the four options for VM*/
-		A_temp = WMip1hm1 + WMhjm1;
-		if ((A_temp <= VMij))
-			VMij = A_temp;
-
-		A_temp = WMip2hm1 + WMhjm1;
-		if (A_temp <= VMidj && constraints[i + 1] <= 0)
-			VMidj = A_temp;
-
-		A_temp = WMip1hm1 + WMhjm2;
-		if (A_temp <= VMijd && constraints[j - 1] <= 0)
-			VMijd = A_temp;
-
-		A_temp = WMip2hm1 + WMhjm2;
-		if (A_temp <= VMidjd && constraints[i + 1] <= 0 && constraints[j - 1]
-		                                                               <= 0)
-			VMidjd = A_temp;
-	}
-
-#if 0
-	VMidj += dangle[rnai][rnaj][RNA[i+1]][0];
-	VMijd += dangle[rnai][rnaj][RNA[j-1]][1];
-	VMidjd += dangle[rnai][rnaj][RNA[i+1]][0] + dangle[rnai][rnaj][RNA[j-1]][1];
-#else
-	tmp1 = dangle[rnai][rnaj][RNA[i + 1]][0]; /* Dangling energy of base pair (i,j) with single base i+1 at 5' end */
-	tmp2 = dangle[rnai][rnaj][RNA[j - 1]][1]; /* Dangling energy of base pair (i,j) with single base j-1 at 3' end */
-	VMidj += (tmp1 + c);
-	VMidjd += (tmp1 + c);
-	VMijd += (tmp2 + c);
-	VMidjd += (tmp2 + c);
-#endif
-
-	/* Manoj ends */
-
-	VMij = MIN(MIN(VMij, VMidj), MIN(VMijd, VMidjd));
-	VMij = VMij + b + a + aupen;
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		VMij = INFINITY_;
-
-	VM[i][j] = VMij;
-	/* VM ends */
-
-	/* V starts */
-	es = eS(i, j);
-	if (es == 0) {
-		es = INFINITY_;
-	} else
-		es += V[indx[i + 1] + j - 1];
-
-	int Vij;
-	Vij = MIN(MIN(eH(i, j), es), MIN(VBI[i][j], VMij));
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		Vij = INFINITY_;
-
-	V[indx[i] + j] = Vij;
-
-	if (NOISOLATE == TRUE && Vij < INFINITY_) {
-		//Check if i+1,j-1 have paired
-		if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) {
-			//If not then check for i-1, j+1
-
-			//Isolated base pairs look ahead
-			int eHL = eH(i - 1, j + 1);
-			int eSL = eS(i - 1, j + 1) + V[indx[i] + j];
-			if (i - 1 == 0) {
-				eSL = 0;
-				eHL = 0;
-			}
-			int Vijl = (eHL < eSL) ? eHL : eSL;
-			//printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl);
-
-			if (Vijl > INFINITY_ - SMALLINFTY_)
-				//isolated base pair found.. setting energy to infinity
-				V[indx[i] + j] = Vij = INFINITY_;
-		}
-	}
-
-#if DEBUG
-	if (indx[i]+j > (LENGTH-1)*(LENGTH)/2)
-		fprintf(stderr,"ERROR: in calcVBIVMVWM: i: %5d  j: %5d\n",i,j);
-#endif
-
-	/* V ends */
-
-	/* WM starts */
-
-	//Need to take care of these WMs
-	WMij = Vij + auPen(rnai, rnaj) + b;
-
-	if (constraints[i] <= 0)
-		WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
-				RNA[i + 1], rnaj) + b + c;
-
-	if (constraints[j] <= 0)
-		WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
-				rnai, RNA[j - 1]) + b + c;
-
-	if (constraints[i] <= 0 && constraints[j] <= 0)
-		WMidjd = V[indx[i + 1] + j - 1]
-		           + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
-		                                                  + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
-		                                                		  RNA[j - 1]) + b + 2* c ;
-
-	WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
-
-	int WMsip1j = INFINITY_;
-	int WMsijm1 = INFINITY_;
-
-	if (constraints[i] <= 0)
-		WMsip1j = WM[i + 1][j];
-
-	if (constraints[j] <= 0)
-		WMsijm1 = WM[i][j - 1];
-
-	WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
-
-	//printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
-
-	WM[i][j] = MIN(WMijp, WMij);
-	WM(i,j) = WM[i][j]; /* extra instruction */
-	/* WM ends */
-
-	return;
-}
-
-/* Calculation of VBI, VM, V and WM in the order. Calculation of V at (i,j) requires VBI and VM. Also, calculation of final value of WM(i,j) requires V at (i,j) */
-void calcVBIVMVWM(int i, int j) {
-
-	int ip, jp, temp, VBIij, thres1;
-	int
-	a = multConst[0] /*a is an offset penalty for multiloops */,
-	b = multConst[2]/* b is penalty for multiloop branches, one per branch*/,
-	c = multConst[1] /*Penalty for single stranded nucleotides in the multiloops*/,
-	a1, h, es;
-	int aupen;
-	int WMijp, WMidjd, WMidj, WMijd, WMij;
-	int VMij, VMijd, VMidj, VMidjd, A_temp;
-	int WMip1hm1 /* WM value at i+1 and h-1 */,
-	WMip2hm1 /* WM value at i+2 and j-1*/,
-	WMhjm1 /*WM value at h and j-1*/,
-	WMhjm2 /* WM value at h and j-2*/, WMhp1j /*WM value at h+1 and j*/;
-	int rnai, rnaj;
-	int tmp1, tmp2;
-
-	rnai = RNA[i];
-	rnaj = RNA[j];
-
-	WMidjd = INFINITY_;
-	WMidj = INFINITY_;
-	WMijd = INFINITY_;
-	WMij = INFINITY_;
-
-	/* VBI starts */
-	/* Look at the calcVBI function for explanation of internal loop calculations*/
-	VBIij = INFINITY_;
-
-	int ifinal, jfinal;
-	/* ip=i+1, jp=j-1 closes a stack, so we should set the jp limit till j-2, in the following loop*/
-	ip = i + 1;
-	thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of a hairpin loop is 3. So, start jp from ip+4 */
-	for (jp = thres1; jp <= j - 2; jp++) {
-		if (jp-ip >= contact_dist) continue;
-		if (chPair(RNA[ip], RNA[jp])) {
-			if (checkSS(i, ip) || checkSS(jp, j))
-				continue;
-			temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the energy of structure closed by (ip, jp)*/
-			if (VBIij > temp) {
-				VBIij = temp;
-				ifinal = ip;
-				jfinal = jp;
-			}
-		}
-	}
-
-	for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) {
-		thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4);
-		for (jp = thres1; jp <= j - 1; jp++) {
-			if (jp-ip >= contact_dist) continue;
-			if (chPair(RNA[ip], RNA[jp])) {
-				if (checkSS(i, ip) || checkSS(jp, j))
-					continue;
-				temp = eL(i, j, ip, jp) + V[indx[ip] + jp];
-				if (VBIij > temp) {
-					VBIij = temp;
-					ifinal = ip;
-					jfinal = jp;
+			/* Check if bases i and j pair up or not */
+			if (allowedPairs(RNA[i], RNA[j])) { 
+				int p, q, h;
+				int newV = INFINITY_;
+				int VBIij = INFINITY_;
+
+				newV  = MIN(eH(i, j), newV);
+
+				for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
+					int minq = j-i+p-MAXLOOP-2;
+					if (minq < p+1+TURN) minq = p+1+TURN;
+					for (q = minq; q < j; q++) {
+						if (!allowedPairs(RNA[p], RNA[q])) continue;
+						VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
+					}
 				}
-			}
-		}
-	}
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		VBIij = INFINITY_;
-
-	VBI[i][j] = VBIij;
-	/* VBI ends */
-
-	/* VM and WM starts */
-	aupen = auPen(rnai, rnaj);
-
-	/* Here we are doing the calculation of VM and WM at point (i,j) concurrently. The following for loop calculates the values of VMij, VMidj, VMijd, VMidjd with the value of WMijp. The value of WMijp is needed for calculating the value of WM at (i,j). However, it should be noted that the final value of WM[i][j] requires value of V at (i,j) which itself require VM(i,j), and will be calculated in the end. */
-
-	/* There are four possibilities for the multiloop closing base pair for the inclusion of dangling energies.
-	 * 1) Including the dangling energy of i+1 base and also for base j-1 with the base pair (i,j) closing the multiloop - VMidjd
-	 * 2) Including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j) - VMidj
-	 * 3) NOT including the danlging energy of i+1 base and including the dangling energy of base j-1 with the closing base pair (i,j) - VMijd
-	 * 4) NOT including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j)-VMij
-	 * */
-
-	VMij = INFINITY_;
-	VMijd = INFINITY_;
-	VMidj = INFINITY_;
-	VMidjd = INFINITY_;
-
-	/* Manoj starts */
-	/* Merged calculations of WM(i,j) and VM(i,j)*/
-	WMijp = WM[i][i + 4] + WM(i+5,j);
-	a1 = WM[i][i + 5] + WM(i+6,j);
-	if (a1 <= WMijp)
-		WMijp = a1;
-
-	for (h = i + 6; h <= j - 5; h++) {
-
-		a1 = WM[i][h];
-		WMip1hm1 = WM[i + 1][h - 1];
-		WMip2hm1 = WM[i + 2][h - 1];
-#if 0
-		WMhjm1 = WM[h][j-1];
-		WMhjm2 = WM[h][j-2];
-		WMhp1j = WM[h+1][j];
-#else
-		WMhjm1 = WM(h,j-1);
-		WMhjm2 = WM(h,j-2);
-		WMhp1j = WM(h+1,j);
-#endif
-
-		/* WM starts */
-		a1 += WMhp1j;
-		if (a1 <= WMijp)
-			WMijp = a1;
-		/* WM ends */
-
-		/* Calculation of the four options for VM*/
-		A_temp = WMip1hm1 + WMhjm1;
-		if ((A_temp <= VMij))
-			VMij = A_temp;
-
-		A_temp = WMip2hm1 + WMhjm1;
-		if (A_temp <= VMidj && constraints[i + 1] <= 0)
-			VMidj = A_temp;
-
-		A_temp = WMip1hm1 + WMhjm2;
-		if (A_temp <= VMijd && constraints[j - 1] <= 0)
-			VMijd = A_temp;
-
-		A_temp = WMip2hm1 + WMhjm2;
-		if (A_temp <= VMidjd && constraints[i + 1] <= 0 && constraints[j - 1]
-		                                                               <= 0)
-			VMidjd = A_temp;
-
-		// if(i==28 && j==42)
-		// 	printf("(%d,%d,%d), VMij: %d, VMidj: %d, VMijd: %d, VMidjd: %d\n", i,h,j, VMij, VMijd, VMidj, VMidjd);
-
-	}
-
-#if 0
-	VMidj += dangle[rnai][rnaj][RNA[i+1]][0];
-	VMijd += dangle[rnai][rnaj][RNA[j-1]][1];
-	VMidjd += dangle[rnai][rnaj][RNA[i+1]][0] + dangle[rnai][rnaj][RNA[j-1]][1];
-#else
-	tmp1 = dangle[rnai][rnaj][RNA[i + 1]][0];
-	tmp2 = dangle[rnai][rnaj][RNA[j - 1]][1];
-
-	VMidj += tmp1;
-	VMidjd += tmp1;
-	VMijd += tmp2;
-	VMidjd += tmp2;
-#endif
-
-	//if(i==28 && j==42)
-	//	printf("after for: (%d,%d,%d), VMij: %d, VMidj: %d, VMijd: %d, VMidjd: %d\n", i,h,j, VMij, VMijd, VMidj, VMidjd);
-
-	/* Manoj ends */
-	VMij = MIN(MIN(VMij, VMidj), MIN(VMijd, VMidjd));
-	VMij = VMij + b + a;
-	VMij += aupen;
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		VMij = INFINITY_;
-
-	VM[i][j] = VMij;
-	/* VM ends */
-
-	/* V starts */
-	es = eS(i, j); /* Energy of stack closed with (i,j) and (i+1,j-1)*/
-	if (es == 0) { /* Amrita: I don't know, if this statement is necessary. NOT DONE BY ME. */
-		es = INFINITY_;
-	} else
-		es += V[indx[i + 1] + j - 1];
-
-	int Vij;
-	Vij = MIN(MIN(eH(i, j), es), MIN(VBI[i][j], VMij));
 
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i) || constraints[i] == -1 || constraints[j]
-			                                                               == -1)
-		Vij = INFINITY_;
+				newV = MIN(newV, VBIij);
+				VBI[i][j] = VBIij;
 
-	//printf("%d, V(%d,%d): eh: %d, es: %d, vbi: %d, vm: %d, v: %d\n", j-i, i, j, eH(i,j), es, VBI[i][j], VMij, Vij);
+				int VMij, VMijd, VMidj, VMidjd;
+				VMij = VMijd = VMidj = VMidjd = INFINITY_;
 
-	V[indx[i] + j] = Vij;
-
-	if (NOISOLATE == TRUE && Vij < INFINITY_) {
-		//Check if i+1,j-1 have paired
-		if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) {
-			//If not then check for i-1, j+1
-
-			//Isolated base pairs look ahead
-			int eHL = eH(i - 1, j + 1);
-			int eSL = eS(i - 1, j + 1) + V[indx[i] + j];
-			if (i - 1 == 0) {
-				eSL = 0;
-				eHL = 0;
-			}
-			int Vijl = (eHL < eSL) ? eHL : eSL;
-			//printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl);
-
-			if (Vijl > INFINITY_ - SMALLINFTY_)
-				//isolated base pair found.. setting energy to infinity
-				V[indx[i] + j] = Vij = INFINITY_;
-		}
-	}
-
-#if DEBUG
-	if (indx[i]+j > (LENGTH-1)*(LENGTH)/2)
-		fprintf(stderr,"ERROR: in calcVBIVMVWM: i: %5d  j: %5d\n",i,j);
-#endif
-
-	/* V ends */
-
-	/* WM starts */
-	/* No dangling base on any of the side */
-	WMij = V[indx[i] + j] + aupen + b;
-	/* Dangling base i on 3' end of the base pair (i+1,j) */
-	if (constraints[i] <= 0)
-		WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen(
-				RNA[i + 1], rnaj) + b + c;
-	/* Dangling base j on 5' end of the base pair (i,j-1)*/
-	if (constraints[j] <= 0)
-		WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen(
-				rnai, RNA[j - 1]) + b + c;
-	/* Dangling base i on the 3' end and base j on the 5' end of the base pair (i+1,j-1)*/
-	if (constraints[i] <= 0 && constraints[j] <= 0)
-		WMidjd = V[indx[i + 1] + j - 1]
-		           + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1]
-		                                                  + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1],
-		                                                		  RNA[j - 1]) + b + 2* c ;
-
-	// if(i==36 && j==50)
-	//	  printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d\n", i, j, WMij, WMidj, WMijd, WMidjd);
-
-	WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd));
-	/* Term WM[i+1][j] takes care of the option when base i is neither pairing up nor playing the role in the dangling energy calculation and we have to add penalty 'c' for base i to remain single.
-	 * Term WM[i][j-1] takes care of the option when base j is neither pairing up nor playing the role in the dangling energy calculations and add penalty 'c' for base j to remain single.
-	 * */
-
-	int WMsip1j = INFINITY_;
-	int WMsijm1 = INFINITY_;
-
-	if (constraints[i] <= 0)
-		WMsip1j = WM[i + 1][j];
-
-	if (constraints[j] <= 0)
-		WMsijm1 = WM[i][j - 1];
-
-	//	  if(i==36 && j==50)
-	//		  printf("(%d,%d), WMij: %d, WMsip1j: %d, WMsijm1: %d\n", i, j, WMij, WMsip1j, WMsijm1);
-
-
-	WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij);
-
-	//  if(i==35 && j==50)
-	//	  printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d\n", i, j, WMij, WMidj, WMijd, WMidjd);
-
-	//printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij);
-
-	WM[i][j] = MIN(WMijp, WMij);
-	WM(i,j) = WM[i][j]; /* extra instruction */
-	/* WM ends */
-
-	return;
-}
-
-//problems in this function.. i think this should fix it..
-/* Function to calculate the value of W[j]. */
-void calcW(int j) {
-
-	int i;
-	int Wj, Widjd /*Dangling base on both sides*/,
-		Wijd/* Dangling base on jth side.*/,
-		Widj/* Dangling base on ith side */,
-		Wij/* No dangle base on any of the sides */, Wim1 /* Value of W at (i-1). Set to zero if positive*/;
-	int rnai, rnaj;
-	int must_branch = 0, besti = 0;
-
-	Wj = INFINITY_;
-
-	rnaj = RNA[j];
-
-	for (i = 1; i < j - 3; i++) {
-
-		Wij = Widjd = Wijd = Widj = INFINITY_;
-
-		// printf("i: %d, j: %d\n", i, j);
-
-# if 0
-		Wim1=W[i-1];
-#endif
-#if 1
-		Wim1 = MIN(0, W[i - 1]); /* If W[i-1] >=0, this means that there is a branch contained in the sequence from 1 to i-1. Otherwise W[i-1] will be INFINITY. Here Wim1 is defined in this manner, to make the energy of unfolded sequence as INFINITY. */
-#endif
-
-		//Wim1 = W[i - 1];
-
-		rnai = RNA[i];
-
-		/* SH: Calculate the energy with no dangle bases. */
-		Wij = V[indx[i] + j] + auPen(rnai, rnaj) + Wim1;
-		/* Dangle on both sides of the base pair (i+1,j-1). Add the corresponding energy. */
-		if (constraints[i] <= 0 && constraints[j] <= 0)
-			Widjd = V[indx[i + 1] + j - 1] + auPen(RNA[i + 1], RNA[j - 1])
-				+ dangle[RNA[j - 1]][RNA[i + 1]][rnai][1] + dangle[RNA[j
-				- 1]][RNA[i + 1]][rnaj][0] + Wim1;
-		/* Single base j dangling on the 5' end of base pair (i,j-1) */
-		if (constraints[j] <= 0)
-			Wijd = V[indx[i] + j - 1] + auPen(rnai, RNA[j - 1]) + dangle[RNA[j
-				- 1]][rnai][rnaj][0] + Wim1;
-		/* Single base i dangling on the 3' end of base pair (i+1,j)  */
-		if (constraints[i] <= 0)
-			Widj = V[indx[i + 1] + j] + auPen(RNA[i + 1], rnaj)
-				+ dangle[rnaj][RNA[i + 1]][rnai][1] + Wim1;
-
-		int tmpWj = Wj;
-		Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); /* Take the minimum */
-		if (tmpWj != Wj) {
-			must_branch = 0;
-			besti = i;
-		}
-
-		// if(i==46 && j==395){
-		//      printf("V(%d, %d): %d, WM: %d\n", 46, j, V[indx[46]+j], WM[46][j]);
-		//      printf("Wij: %d, Widjd: %d, Wijd: %d, Widj: %d\n\n", Wij, Widjd, Wijd, Widj);
-		//}
-
-		if (Wj < INFINITY_) {
-			if (Wj == Wij) {
-				if (constraints[i] == j) {
-					must_branch = 1;
-				}
-			} else if (Wj == Widjd) {
-				if (constraints[i + 1] == j - 1) {
-					must_branch = 1;
-				}
-			} else if (Wj == Wijd) {
-				if (constraints[i] == j - 1) {
-					must_branch = 1;
+				for (h = i+TURN+1; h <= j-1-TURN; h++) { 
+					VMij = MIN(VMij, WM[i+1][h-1] + WM[h][j-1]);		
+					VMidj = MIN(VMidj, WM[i+2][h-1] + WM[h][j-1]);	
+					VMijd = MIN(VMijd, WM[i+1][h-1] + WM[h][j-2]);	
+					VMidjd = MIN(VMidjd, WM[i+2][h-1] + WM[h][j-2]);	
 				}
-			} else {
-				if (constraints[i + 1] == j) {
-					must_branch = 1;
-				}
-			}
-		}
-
-	}
-
-	//printf("W%dcal: %d, must_branch: %d, best_i: %d", j, Wj, must_branch, besti);
-
-	/* If jth base is not contributing in the energy calculation of W[j] */
-	if (!must_branch) {
-		if (Wj > W[j - 1])
-			Wj = W[j - 1];
-	}
 
-	W[j] = Wj;
+				int d3 = Ed3(i,j,j-1);
+				int d5 = Ed5(i,j,i+1);
+				VMij = MIN(VMij, VMidj + d5 +Ec());
+				VMij = MIN(VMij, VMijd + d3 +Ec());
+				VMij = MIN(VMij, VMidjd + d5 +  d3+ 2*Ec());
+				VMij = VMij + Ea() + Eb() + auPenalty(i,j);
 
-	//printf(",W%dset: %d\n", j, W[j]);
+				VM[i][j] = VMij;
 
-	//  if(j==11 || j==35 || j==36)
-	// printf("\n*****\nMust branch: %d, W%d: %d\n*****\n", must_branch, j, W[j]);
-	return;
-}
-
-/* For details on calculating energy of different types of Internal loops, please look at the chapter 3 of MS thesis of Mirela Stefania Andronescu.
- * http://www.cs.ubc.ca/grads/resources/thesis/Nov03/Mirela_Andronescu.pdf
- * */
-/* Calculates the energy of internal loop with (i,j) as closing base pair and (ip,jp) as enclosed base pair */
-int eL(int i, int j, int ip, int jp) {
-
-	int energy;
-	int size1, size2, size;
-	int loginc; /* SH: Originally unassiged, but needs to be set to 0 so it doesn't throw off later calculations. */
-	int lopsided; /* define the asymmetry of an interior loop */
+				newV = MIN(newV, VM[i][j]);
 
-	energy = INFINITY_;
-	loginc = 0;
-
-	/*SH: These calculations used to incorrectly be within the bulge loop code, moved out here. */
-	size1 = ip - i - 1;
-	size2 = j - jp - 1;
-	size = size1 + size2;
-
-	if (size1 == 0 || size2 == 0) {
-		if (size > 30) {
-			/* AM: Does not depend upon i and j and ip and jp - Stacking Energies */
-			loginc = (int) floor(prelog * log((double) size / 30.0));
-			energy = bulge[30] + eparam[2] + loginc + auPen(RNA[i], RNA[j])
-			+ auPen(RNA[ip], RNA[jp]);
-		} else if (size <= 30 && size != 1) {
-			/* Does not depend upon i and j and ip and jp - Stacking Energies  */
-			energy = bulge[size] + eparam[2];
-			energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]);
-		} else if (size == 1) {
-			energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])]
-			               + bulge[size] + eparam[2]; /* mans */
-		}
-	} else {
-		/* Internal loop */
-		lopsided = abs(size1 - size2);
+				int stackEnergy = eS(i, j); 
+				newV= MIN(stackEnergy + V(i+1,j-1), newV);
 
-		if (size > 30) {
-			loginc = (int) floor(prelog * log((double) size / 30.0));
-
-			/* Please check what should be the difference in the following two options. Is it correct?*/
-			if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/
-
-				energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j
-				                                                             - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp
-				                                                                                                                + 1], RNA[ip - 1])] + inter[30] + loginc + eparam[3]
-				                                                                                                                                                                  + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1,
-				                                                                                                                                                                		  size2))]));
-			} else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/
-				energy
-				= tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]
-				        + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A,
-				        		BASE_A)] + inter[30] + loginc
-				        		+ eparam[3] + MIN(maxpen, (lopsided
-				        				* poppen[MIN(2, MIN(size1, size2))]));
+				V(i,j) = newV;
 			}
-		}
-		/* if size is not > 30, we have a looooot of cases... */
-		else if (size1 == 2 && size2 == 2) {
-			/* 2x2 internal loop */
-			energy
-			= iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i
-			                                                            + 2]][RNA[j - 1]][RNA[j - 2]];
-		} else if (size1 == 1 && size2 == 2) {
-			energy
-			= iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]];
-		} else if (size1 == 2 && size2 == 1) {
-			/* 1x2 internal loop */
-			energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i
-			                                                               + 1]][RNA[j]][RNA[i]];
-		} else if (size == 2) {
-			/* 1*1 internal loops */
-			energy
-			= iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]];
-		} else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0)  */
-			energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]
-			               + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)]
-			                       + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided
-			                    		   * poppen[MIN(2, MIN(size1, size2))]));
-		} else { /* General Internal loops */
-			energy
-			= tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1],
-					RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp],
-							RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size]
-							                                            + loginc + eparam[3] /* AM: I don't understand this eparam value, I think they do not play any role currently. Please look in loader.cc file, for what value have been assinged to various elements of eparam array */
-							                                                              + MIN(maxpen,
-							                                                            		  (lopsided * poppen[MIN(2, MIN(size1, size2))])); /*  */
-		}
-	}
-
-	return energy;
-}
-
-/* For details on calculating energy of different types of hairpin loops, please look at the chapter 3 of MS thesis of Mirela Stefania Andronescu.
- * http://www.cs.ubc.ca/grads/resources/thesis/Nov03/Mirela_Andronescu.pdf
- * */
-/* SH: Function used to calculate energy of a hairpin loop between i & j. */
-/* inline */
-int eH(int i, int j) {
-	/*  Hairpin loop for all the bases between i and j */
-	/*  size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */
-	int size;
-	int loginc;
-	int energy = INFINITY_;
-	int key, index, count, tlink, kmult;
-
-	size = j - i - 1; /*  size is the number of bases in the loop, when the closing pair is excluded */
-
-	//checking if single stranded region is allowed with given constraints
-	if (checkSS(i, j) || (constraints[i] > 0 && constraints[i] != j)
-			|| (constraints[j] > 0 && constraints[j] != i))
-		return energy;
-
-	/*  look in hairpin, and be careful that there is only 30 values */
-
-	if (size > 30) {
-		loginc = (int) ((prelog) * log(((double) size) / 30.0));
-		energy = hairpin[30] + loginc + tstkh[fourBaseIndex(RNA[i], RNA[j],
-				RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/
-	}
-
-	else if (size <= 30 && size > 4) {
-		energy = hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j],
-				RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/
-	}
-
-	else if (size == 4) {
-		/*  tetraloop */
-		key = 0;
-		tlink = 0;
-		for (index = 0; index < 6; ++index) {
-			switch (RNA[i + index]) {
-			case BASE_A:
-				kmult = 1;
-				break;
-			case BASE_C:
-				kmult = 2;
-				break;
-			case BASE_G:
-				kmult = 3;
-				break;
-			case BASE_U:
-				kmult = 4;
-				break;
-			default:
-				kmult = 0;
-				fprintf(stderr, "ERROR: in tetraloop calculation\n");
+			else {
+				V(i,j) = INFINITY_;
+			}	
+
+			int h;
+			int newWM = INFINITY_;
+
+			newWM = MIN(V(i,j) + auPenalty(i,j) + Eb(), newWM);
+			newWM = MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb() + Ec(), newWM);
+			newWM = MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb() + Ec(), newWM);
+			newWM = MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb() + 2*Ec(), newWM) ;
+			newWM = MIN(WM[i+1][j] + Ec(), newWM);
+			newWM = MIN(WM[i][j-1] + Ec(), newWM);
+			
+			for (h = i ; h <= j-TURN-1; h++) {
+				newWM = MIN(newWM, WM[i][h] + WM[h+1][j]);
 			}
-			key += kmult * (int) pow(10.0, 5 - index);
-		}
-		/*  if the sequence is in tloop, we use this value */
-		for (count = 1; count < numoftloops && tlink == 0; ++count) {
-			if (key == tloop[count][0]) {
-				tlink = tloop[count][1];
-			}
-		}
-		energy = tlink + hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j],
-				RNA[i + 1], RNA[j - 1])] + eparam[4];
-	}
 
-	else if (size == 3) {
-		/*  triloop... For the moment, the file triloop.dat is empty */
-		/*  else, should have a treatment like the one if size==4 */
-		energy = hairpin[size];
-		/* AM: Don't include stacking energy terms for triloopls */
-		/* + tstkh[RNA[i]][RNA[j]][RNA[i+1]][RNA[j-1]]  */
-		/* + eparam[4]; */
-		/*  Must be another penalty for terminal AU... Not sure of this */
-		energy += auPen(RNA[i], RNA[j]);
+			WM[i][j] = newWM;
+		}
 	}
 
-	else if (size < 3 && size != 0) {
-		/*  no terminal mismatch */
-		energy = hairpin[size] + eparam[4];
-		if ((RNA[i] == BASE_A && RNA[j] == BASE_U) || (RNA[i] == BASE_U
-				&& RNA[j] == BASE_A)) {
-			energy += 6; /*  Seems to be a penalty for terminal AU.  *//* Hairpin Loops of size 3 are not allowed, the term hairpin[size] will result in a very large value.  */
-		}
-	} else if (size == 0)
-		return INFINITY_;
+	for (j = TURN+2; j <= len; j++)	{
+		int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
+		Wj = INFINITY_;
 
-	/*  GGG Bonus => GU closure preceded by GG */
-	/*  i-2 = i-1 = i = G, and j = U; i < j */
-	if (i > 2) {
-		if (RNA[i - 2] == BASE_G && RNA[i - 1] == BASE_G && RNA[i] == BASE_G
-				&& RNA[j] == BASE_U) {
-			energy += gubonus;
-			/*  printf ("\n GGG bonus for i %d j %d ", i, j); */
+		for (i = 1; i < j-TURN; i++) 
+		{
+			Wij = Widjd = Wijd = Widj = INFINITY_;
+			Wim1 = MIN(0, W[i-1]); 
+			Wij = V(i, j) + auPenalty(i, j) + Wim1;
+			Widjd = V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1;
+			Wijd = V(i,j-1) + auPenalty(i,j- 1) + Ed5(j-1,i,j) + Wim1;
+			Widj = V(i + 1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1;
+			Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); 
 		}
-	}
 
-	/*  Poly-C loop => How many C are needed for being a poly-C loop */
-	tlink = 1;
-	for (index = 1; (index <= size) && (tlink == 1); ++index) {
-		if (RNA[i + index] != BASE_C)
-			tlink = 0;
-	}
-	if (tlink == 1) {
-		if (size == 3) {
-			energy += c3;
-		} else {
-			energy += cint + size * cslope;
-		}
+		W[j] = MIN(Wj, W[j-1]);
 	}
 
-	return energy;
-}
-
-/* SH: Function used to calculate energy of stacked pairs (i.j) & (i+1.j-1). */
-/* inline */
-int eS(int i, int j) {
-	int energy;
-
-	if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0
-			&& constraints[j] != i))
-		return INFINITY_;
-
-	//if (j - i <= 3)
-	//  return INFINITY_;
-
-	/*  not sure about eparam[1], come from MFold.. = 0 */
-	energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])]
-	               + eparam[1];
-
-	return energy;
+	return W[len];
 }
diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
new file mode 100644
index 0000000..17f3617
--- /dev/null
+++ b/gtfold-mfe/src/energy.c
@@ -0,0 +1,359 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+
+#include "energy.h"
+#include "utils.h"
+#include "global.h"
+#include "constants.h"
+#include "data.h"
+
+int *V; 
+int *W; 
+int **VBI; 
+int **VM; 
+int **WM; 
+int *indx; 
+
+void create_tables(int len)
+{	
+	int i;
+	
+	V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
+	if (V == NULL) 
+	{
+		perror("Cannot allocate variable 'V'");
+		exit(-1);
+	}
+
+	W = (int *) malloc((len+1) * sizeof(int));
+	if (W == NULL) 
+	{
+		perror("Cannot allocate variable 'W'");
+		exit(-1);
+	}
+
+	VBI = (int **) malloc((len+1) * sizeof(int *));
+	if (VBI == NULL) 
+	{
+		perror("Cannot allocate variable 'VBI'");
+		exit(-1);
+	}
+
+	for (i = 0; i < len+1; i++) {
+		VBI[i] = (int *) malloc((len+1)* sizeof(int));
+		if (VBI[i] == NULL) 
+		{
+			perror("Cannot allocate variable 'VBI[i]'");
+			exit(-1);
+		}
+	}
+    
+	
+	VM = (int **) malloc((len+1)* sizeof(int *));
+	if (VM == NULL) 
+	{
+		perror("Cannot allocate variable 'VM'");
+		exit(-1);
+	}
+	for (i = 0; i < len+1; i++) {
+		VM[i] = (int *) malloc((len+1)*sizeof(int));
+		if (VM[i] == NULL) {
+			perror("Cannot allocate variable 'VM[i]'");
+			exit(-1);
+		}
+	}
+    
+	
+	WM = (int **) malloc((len+1)*sizeof(int *));
+	if (WM == NULL) 
+	{
+		perror("Cannot allocate variable 'WM'");
+		exit(-1);
+	}
+	for (i = 0; i < len+1; i++) 
+	{
+		WM[i] = (int *) malloc((len+1)*sizeof(int));
+		if (WM[i] == NULL) {
+			perror("Cannot allocate variable 'WM[i]'");
+			exit(-1);
+		}
+	}
+    
+	
+	indx = (int *) malloc((len+1) * sizeof(int));
+	if (indx == NULL) {
+		perror("Cannot allocate variable 'indx'");
+		exit(-1);
+	}
+
+	init_tables(len);
+}
+
+
+void init_tables(int len) 
+{
+	int i, j, LLL;
+	
+	for (i = 0; i <= len; i++) 
+	{
+		W[i] = INFINITY_; 
+
+		for (j = 0; j <= len; j++) 
+		{
+			VBI[i][j] = INFINITY_;
+			VM[i][j] = INFINITY_;
+			WM[i][j] = INFINITY_;
+		}
+	}
+	
+
+	LLL = (len)*(len+1)/2 + 1;
+
+	for (i = 0; i < LLL; i++)
+	{
+		V[i] = INFINITY_;
+	}
+
+	for (i = 0; i <= len; i++)
+	{
+		indx[i] = (len)*(i-1)-(i*(i-1))/2;
+	}
+
+	return;
+}
+
+void free_tables(int len)
+{
+	int i;
+
+	free(indx);
+	for (i = 0; i < len; i++)
+		free(WM[i]);
+	
+	free(WM);
+	
+	for (i = 0; i < len; i++)
+		free(VM[i]);
+	
+	free(VM);
+	for (i = 0; i < len; i++)
+		free(VBI[i]);
+	
+	free(VBI);
+	free(W);
+	free(V);
+}
+
+
+inline int Ed3(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][1];}
+inline int Ed5(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][0]; }
+inline int auPenalty(int i, int j) { return auPen(RNA[i], RNA[j]);}
+inline int Ec() { return multConst[1];}
+inline int Eb()  { return multConst[2];}
+inline int Ea()  { return multConst[0]; }
+
+inline int eL(int i, int j, int ip, int jp) 
+{
+	int energy;
+	int size1, size2, size;
+	int loginc; /* SH: Originally unassiged, but needs to be set to 0 so it doesn't throw off later calculations. */
+	int lopsided; /* define the asymmetry of an interior loop */
+
+	energy = INFINITY_;
+	loginc = 0;
+
+	/*SH: These calculations used to incorrectly be within the bulge loop code, moved out here. */
+	size1 = ip - i - 1;
+	size2 = j - jp - 1;
+	size = size1 + size2;
+
+	if (size1 == 0 || size2 == 0) {
+		if (size > 30) {
+			/* AM: Does not depend upon i and j and ip and jp - Stacking Energies */
+			loginc = (int) floor(prelog * log((double) size / 30.0));
+			energy = bulge[30] + eparam[2] + loginc + auPen(RNA[i], RNA[j])
+				+ auPen(RNA[ip], RNA[jp]);
+		} else if (size <= 30 && size != 1) {
+			/* Does not depend upon i and j and ip and jp - Stacking Energies  */
+			energy = bulge[size] + eparam[2];
+			energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]);
+		} else if (size == 1) {
+			energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])]
+				+ bulge[size] + eparam[2]; /* mans */
+		}
+	} else {
+		/* Internal loop */
+		lopsided = abs(size1 - size2);
+
+		if (size > 30) {
+			loginc = (int) floor(prelog * log((double) size / 30.0));
+
+			/* Please check what should be the difference in the following two options. Is it correct?*/
+			if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/
+
+				energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j
+											 - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp
+																		  + 1], RNA[ip - 1])] + inter[30] + loginc + eparam[3]
+											 + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1,
+																						 size2))]));
+			} else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/
+				energy
+					= tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]
+					+ tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A,
+										  BASE_A)] + inter[30] + loginc
+					+ eparam[3] + MIN(maxpen, (lopsided
+											   * poppen[MIN(2, MIN(size1, size2))]));
+			}
+		}
+		/* if size is not > 30, we have a looooot of cases... */
+		else if (size1 == 2 && size2 == 2) {
+			/* 2x2 internal loop */
+			energy
+				= iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i
+				+ 2]][RNA[j - 1]][RNA[j - 2]];
+		} else if (size1 == 1 && size2 == 2) {
+			energy
+				= iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]];
+		} else if (size1 == 2 && size2 == 1) {
+			/* 1x2 internal loop */
+			energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i
+				+ 1]][RNA[j]][RNA[i]];
+		} else if (size == 2) {
+			/* 1*1 internal loops */
+			energy
+				= iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]];
+		} else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0)  */
+			energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]
+				+ tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)]
+				+ inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided
+																  * poppen[MIN(2, MIN(size1, size2))]));
+		} else { /* General Internal loops */
+			energy
+				= tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1],
+									  RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp],
+																		 RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size]
+										  + loginc + eparam[3] /* AM: I don't understand this eparam value, I think they do not play any role currently. Please look in loader.cc file, for what value have been assinged to various elements of eparam array */
+										  + MIN(maxpen,
+												(lopsided * poppen[MIN(2, MIN(size1, size2))])); /*  */
+		}
+	}
+
+	return energy;
+}
+
+inline int eH(int i, int j) 
+{
+	/*  Hairpin loop for all the bases between i and j */
+	/*  size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */
+	int size;
+	int loginc;
+	int energy = INFINITY_;
+	int key, index, count, tlink, kmult;
+
+	size = j - i - 1; /*  size is the number of bases in the loop, when the closing pair is excluded */
+
+	/*  look in hairpin, and be careful that there is only 30 values */
+
+	if (size > 30) {
+		loginc = (int) ((prelog) * log(((double) size) / 30.0));
+		energy = hairpin[30] + loginc + tstkh[fourBaseIndex(RNA[i], RNA[j],
+															RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/
+	}
+
+	else if (size <= 30 && size > 4) {
+		energy = hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j],
+													 RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/
+	}
+
+	else if (size == 4) {
+		/*  tetraloop */
+		key = 0;
+		tlink = 0;
+		for (index = 0; index < 6; ++index) {
+			switch (RNA[i + index]) {
+			  case BASE_A:
+				  kmult = 1;
+				  break;
+			  case BASE_C:
+				  kmult = 2;
+				  break;
+			  case BASE_G:
+				  kmult = 3;
+				  break;
+			  case BASE_U:
+				  kmult = 4;
+				  break;
+			  default:
+				  kmult = 0;
+				  fprintf(stderr, "ERROR: in tetraloop calculation\n");
+			}
+			key += kmult * (int) pow(10.0, 5 - index);
+		}
+		/*  if the sequence is in tloop, we use this value */
+		for (count = 1; count < numoftloops && tlink == 0; ++count) {
+			if (key == tloop[count][0]) {
+				tlink = tloop[count][1];
+			}
+		}
+		energy = tlink + hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j],
+															 RNA[i + 1], RNA[j - 1])] + eparam[4];
+	}
+
+	else if (size == 3) {
+		/*  triloop... For the moment, the file triloop.dat is empty */
+		/*  else, should have a treatment like the one if size==4 */
+		energy = hairpin[size];
+		/* AM: Don't include stacking energy terms for triloopls */
+		/* + tstkh[RNA[i]][RNA[j]][RNA[i+1]][RNA[j-1]]  */
+		/* + eparam[4]; */
+		/*  Must be another penalty for terminal AU... Not sure of this */
+		energy += auPen(RNA[i], RNA[j]);
+	}
+
+	else if (size < 3 && size != 0) {
+		/*  no terminal mismatch */
+		energy = hairpin[size] + eparam[4];
+		if ((RNA[i] == BASE_A && RNA[j] == BASE_U) || (RNA[i] == BASE_U
+													   && RNA[j] == BASE_A)) {
+			energy += 6; /*  Seems to be a penalty for terminal AU.  *//* Hairpin Loops of size 3 are not allowed, the term hairpin[size] will result in a very large value.  */
+		}
+	} else if (size == 0)
+		return INFINITY_;
+
+	/*  GGG Bonus => GU closure preceded by GG */
+	/*  i-2 = i-1 = i = G, and j = U; i < j */
+	if (i > 2) {
+		if (RNA[i - 2] == BASE_G && RNA[i - 1] == BASE_G && RNA[i] == BASE_G
+			&& RNA[j] == BASE_U) {
+			energy += gubonus;
+			/*  printf ("\n GGG bonus for i %d j %d ", i, j); */
+		}
+	}
+
+	/*  Poly-C loop => How many C are needed for being a poly-C loop */
+	tlink = 1;
+	for (index = 1; (index <= size) && (tlink == 1); ++index) {
+		if (RNA[i + index] != BASE_C)
+			tlink = 0;
+	}
+	if (tlink == 1) {
+		if (size == 3) {
+			energy += c3;
+		} else {
+			energy += cint + size * cslope;
+		}
+	}
+
+	return energy;
+}
+
+inline int eS(int i, int j) 
+{
+	int energy;
+	/*  not sure about eparam[1], come from MFold.. = 0 */
+	energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])]
+		+ eparam[1];
+
+	return energy;
+}
diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c
new file mode 100644
index 0000000..5acaed7
--- /dev/null
+++ b/gtfold-mfe/src/global.c
@@ -0,0 +1,99 @@
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "global.h"
+
+unsigned char *RNA1; 
+unsigned char *RNA; 
+int *structure; 
+unsigned int chPairKey;
+
+
+void init_global_params(int len)
+{
+	RNA = (unsigned char *) malloc((len+1)* sizeof(unsigned char));
+	if (RNA == NULL) {
+		perror("Cannot allocate variable 'RNA'");
+		exit(-1);
+	}
+	RNA1 = (unsigned char *) malloc((len+1) * sizeof(unsigned char));
+	if (RNA1 == NULL) {
+		perror("Cannot allocate variable 'RNA'");
+		exit(-1);
+	}
+	structure = (int *) malloc((len+1) * sizeof(int));
+	if (structure == NULL) {
+		perror("Cannot allocate variable 'structure'");
+		exit(-1);
+	}
+	
+	init_checkPair();
+}
+
+void free_global_params()
+{
+	free(structure);
+	free(RNA);
+	free(RNA1);
+}
+
+void printSequence(int len) 
+{
+	int i;
+	for (i = 1; i <= len; i++) 
+	{
+		if (RNA1[i] == 0)
+			printf("A");
+		else if (RNA1[i] == 1)
+			printf("C");
+		else if (RNA1[i] == 2)
+			printf("G");
+		else if (RNA1 [i] == 3)
+			printf("T");
+		else
+			printf("N");
+	}
+	printf("\n");
+}
+
+void printStructure(int len) 
+{
+	int i = 1;
+	for (i = 1; i <= len; i++) 
+	{
+		if (structure[i] > 0 && structure[i] > i)
+			printf("(");
+		else if (structure[i] > 0 && structure[i] < i)
+			printf(")");
+		else
+			printf(".");
+	}
+	printf("\n");
+}
+
+int allowedPairs(int a, int b) 
+{
+	return (chPairKey & (1 << (((a)<<2) + (b)))); 
+}  
+
+void init_checkPair() 
+{
+	int i, j;
+	chPairKey = 0;
+	for (i = 0; i < 4; i++)
+		for (j = 0; j < 4; j++)
+			chPairKey += checkPair(i, j) << ((i << 2) + j);
+}
+
+int update_checkPair(int i, int j) 
+{
+	int r = 0;
+	if (!((i >= 0 && i <=3 )&&(j >=0 && j <=3)))
+		return r;
+	if (!(chPairKey & (1 << ((i << 2) + j))))
+	{
+		chPairKey += 1 << ((i << 2) + j);	
+		r = 1;
+	}
+	return r;
+}
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 609e373..5aca720 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -35,21 +35,20 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <string.h>
 
 #include "loader.h"
+#include "energy.h"
 #include "algorithms.h"
 #include "algorithms-partition.h"
 #include "traceback.h"
 #include "subopt_traceback.h"
+#include "options.h"
 #include "main.h"
 #include "main-c.h"
 
 using namespace std;
 
 /* GLOBAL VARIABLES */
-enum BOOL NOISOLATE;
+
 enum BOOL BPP; // calculating base pair probabilities
-enum BOOL USERDATA;
-enum BOOL PARAMS;
-enum BOOL LIMIT_DISTANCE;
 enum BOOL VERBOSE;
 
 int num_threads;
@@ -75,46 +74,6 @@ double **QM;  // QM[i][j] is the sum of configuration energies from i to j,
 // assuming that i,j are contained in a multiloop
 double **P;   // P[i][j] The probability that nucleotides i and j form a basepair
 
-/**
- * Print the hep message and quit.
- */
-void help() {
-    fprintf(stderr,
-            "Usage: gtfold [OPTION]... FILE\n\n");
-
-    fprintf(stderr,
-            "  FILE is an RNA sequence file.  Single line or FASTA formats are accepted.\n\n");
-
-    fprintf(stderr, "OPTIONS\n");
-    fprintf(stderr,
-            "   -c, --constraints FILE\n                        Load constraints from FILE.  See Constraint syntax below\n");
-    fprintf(stderr,
-            "   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n                        limit is given, base pairs can be over any distance\n");
-    fprintf(stderr,
-            "   -n, --noisolate      Prevent isolated base pairs from forming\n");
-    fprintf(stderr,
-            "   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
-	fprintf(stderr,
-            "   -t, --threads num    Limit number of threads used\n");
-
-    fprintf(stderr, "\n");
-    fprintf(stderr,
-            "   -h, --help           Output help (this message) and exit\n");
-    fprintf(stderr,
-            "   -v, --verbose        Run in verbose mode\n");
-
-    fprintf(stderr, "\nBETA OPTIONS\n");
-    fprintf(stderr,
-            "   --bpp                Calculate base pair probabilities\n");
-    fprintf(stderr,
-            "   --subopt range       Calculate suboptimal structures within 'range' kcal/mol\n");
-    fprintf(stderr, "                        of the mfe\n");
-
-
-    fprintf(stderr,
-            "\nConstraint syntax:\n\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
-    exit(-1);
-}
 
 /* Function for calculating time */
 double get_seconds() {
@@ -478,7 +437,7 @@ int main(int argc, char** argv) {
     else
         populate("Turner99",false); /* Defined in loader.cc file to read in the thermodynamic parameter values from the tables in the ../data directory. */
 
-    initTables(length); /* Initialize global variables */
+    create_tables(length); /* Initialize global variables */
 
     ///// Run Configuration Output /////
 
@@ -523,7 +482,7 @@ int main(int argc, char** argv) {
     fflush(stdout);
 
     t1 = get_seconds();
-    energy = calculate(length, fbp, pbp, numfConstraints, numpConstraints);
+    energy = calculate(length); //, fbp, pbp, numfConstraints, numpConstraints);
     t1 = get_seconds() - t1;
 
     fprintf(stdout,"Minimum Free Energy: %9.2f\n", energy/100.00);
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
new file mode 100644
index 0000000..c468544
--- /dev/null
+++ b/gtfold-mfe/src/options.cc
@@ -0,0 +1,137 @@
+#include "options.h"
+
+ bool ILSA; 
+ bool NOISOLATE;
+ bool USERDATA;
+ bool PARAMS;
+ bool LIMIT_DISTANCE;
+
+ std::string datadir;
+ std::string dataparam;
+ std::string seqfile ;
+
+ int delta;
+ int nThreads;
+
+void help() 
+{
+	fprintf(stderr, "\n");
+	fprintf(stderr, "Usage: gtfold [OPTIONS]  FILE\n"); 
+	fprintf(stderr, "\tSequence file has to be in one of the two formats: Single line or FASTA\n\n"); 
+	fprintf(stderr, "OPTIONS\n" );
+	fprintf(stderr, "-ni, --noisolate\n"); 
+	fprintf(stderr, "\tprevents isolated base pairs from forming\n"); 
+	fprintf(stderr, "-c, --constraints filename\n");
+	fprintf(stderr,	"\tconstraints is a optional parameter\n");
+	fprintf(stderr, "\tSyntax for giving constraints is:\n\tfor forcing (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) base pair, F i j k \n");
+	fprintf(stderr,	"\tto prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) base pair, P i j k \n");
+	fprintf(stderr, "\tto make bases from i to i+k-1 single stranded bases, P i 0 k \n");
+	fprintf(stderr,	"-lcd --limitcd value\n");
+	fprintf(stderr,	"\tlimits the 'contact distance' for a base pair\n");
+	fprintf(stderr,	"-d --datadir dirname \n");
+	fprintf(stderr, "\n");
+	exit(-1);
+}
+
+
+void parse_options(int argc, char** argv)
+{
+	int fileIndex = 0;
+	int consIndex = 0;
+	int dataIndex = 0;
+	int paramsIndex =0;
+	int eIndex = 0;
+	int nTIndex = 0;
+
+	int i = 1;
+
+	while (i < argc) {
+		if (argv[i][0] == '-') {
+			if (strcmp(argv[i], "-ilsa") == 0) {
+				ILSA = true;
+			} else if (strcmp(argv[i], "-noisolate") == 0) {
+				NOISOLATE = true;
+			} else if (strcmp(argv[i], "-help") == 0) {
+				help();
+			} else if (strcmp(argv[i], "-constraints") == 0) {
+				if (i < argc)
+					consIndex = ++i;
+				else
+					help();
+			} else if (strcmp(argv[i], "-params")==0) { 
+				PARAMS = true;			  
+				if (i < argc)
+					paramsIndex = ++i;
+				else
+					help();
+			} else if (strcmp(argv[i], "-datadir") == 0) {
+				USERDATA = true;
+				if (i < argc)
+					dataIndex = ++i;
+				else
+					help();
+			} else if (strcmp(argv[i], "-e") == 0)
+			{
+				if (i < argc)
+					eIndex = ++i;
+				else
+					help();	
+			}
+			else if (strcmp(argv[i], "-nTHREAD") == 0)
+			{
+				if (i < argc)
+					nTIndex = ++i;
+				else
+					help();	
+			}
+		} else {
+			fileIndex = i;
+			seqfile = argv[fileIndex];
+		}
+		i++;
+	}
+
+	if (fileIndex == 0)
+		help();
+	
+	if (NOISOLATE == true)
+		fprintf(stdout, "Not allowing isolated base pairs\n");
+	else
+		fprintf(stdout, "Allowing isolated base pairs\n");
+	
+	if (consIndex != 0)
+	{
+		fprintf(stdout, "Constraint file index: %d\n", consIndex);
+	}
+
+	if (dataIndex != 0)
+	{
+		datadir = argv[dataIndex];
+	}
+
+	if (paramsIndex != 0)
+	{
+		dataparam = argv[paramsIndex];
+	}
+
+	nThreads = -1;
+	if (nTIndex != 0)
+	{
+		nThreads = atoi(argv[nTIndex]);
+	}
+	
+	delta = 0;
+	if (eIndex != 0)
+	{
+		delta = atoi(argv[eIndex]);
+	}	
+	if (delta > 0)
+	{
+		fprintf(stdout, "Suboptimal range = %d\n\n", delta);
+	}
+
+	if (argc < 2)
+	{
+		help();
+	}
+}
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index 78bcc91..2374d1d 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -22,10 +22,12 @@
 
 #include <cstdio>
 
-#include "subopt_traceback.h"
 #include "constants.h"
 #include "data.h"
-#include "algorithms.h"
+#include "global.h"
+#include "energy.h"
+#include "utils.h"
+#include "subopt_traceback.h"
 
 const char* lstr[] = {"W", "V", "VBI", "VM", "WM"};
 
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index dff6ae9..5aa036f 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -32,17 +32,24 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <math.h>
+
+
 #include "data.h"
+#include "utils.h"
 #include "constants.h"
+#include "energy.h"
+#include "global.h"
 #include "algorithms.h"
 #include "traceback.h"
 
 int total_en = 0;
 
+int checkSS(int i, int j){return 1;} //TODO remove this when we put constraints back in
+
 void trace(int len) {
 	int i;
 
-	for (i = 0; i < LENGTH; i++)
+	for (i = 0; i < len; i++)
 		structure[i] = 0;
 
 	if (W[len] >= MAXENG) {
@@ -77,15 +84,14 @@ void traceW(int j) {
 		Widj = INFINITY_;
 
 		Wij = V[indx[i] + j] + auPen(RNA[i], RNA[j]) + wim1;
-
-		if (constraints[i] <= 0 && constraints[j] <= 0)
+		//if (constraints[i] <= 0 && constraints[j] <= 0)
 			Widjd = V[indx[i + 1] + j - 1] + auPen(RNA[i + 1], RNA[j - 1])
 				+ dangle[RNA[j - 1]][RNA[i + 1]][RNA[i]][1]
 				+ dangle[RNA[j - 1]][RNA[i + 1]][RNA[j]][0] + wim1;
-		if (constraints[j] <= 0)
+		//if (constraints[j] <= 0)
 			Wijd = V[indx[i] + j - 1] + auPen(RNA[i], RNA[j - 1])
 				+ dangle[RNA[j - 1]][RNA[i]][RNA[j]][0] + wim1;
-		if (constraints[i] <= 0)
+		//if (constraints[i] <= 0)
 			Widj = V[indx[i + 1] + j] + auPen(RNA[i + 1], RNA[j])
 				+ dangle[RNA[j]][RNA[i + 1]][RNA[i]][1] + wim1;
 		Wj_temp=Wj;
@@ -102,15 +108,15 @@ void traceW(int j) {
 				if (flag || checkSS(1,i)) // Added this condition because if constraints are present, flag should be overridden
 					traceW(i - 1);
 				break;
-			} else if (W[j] == Widjd && constraints[i] <= 0
-					   && constraints[j] <= 0) { /* If base pair (i+1,j-1) is pairing and there is a dangling base on both its sides */
+			} else if (W[j]){ // == Widjd && constraints[i] <= 0
+					   //&& constraints[j] <= 0) { /* If base pair (i+1,j-1) is pairing and there is a dangling base on both its sides */
 				done = 1;
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
 				traceV(i + 1, j - 1);
 				if (flag || checkSS(1,i)) traceW(i - 1);
 				break;
-			} else if (W[j] == Wijd && constraints[j] <= 0) { /* If base pair (i,j-1) pairs and base j is single stranded. */
+			} else if (W[j]){// == Wijd && constraints[j] <= 0) { /* If base pair (i,j-1) pairs and base j is single stranded. */
 				done = 1;
 				structure[i] = j - 1;
 				structure[j - 1] = i;
@@ -118,7 +124,7 @@ void traceW(int j) {
 				if (flag || checkSS(1,i) )
 					traceW(i - 1);
 				break;
-			} else if (W[j] == Widj && constraints[i] <= 0) { /* If base pair (i+1,j) pairs and base i is single stranded. */
+			} else if (W[j]){// == Widj && constraints[i] <= 0) { /* If base pair (i+1,j) pairs and base i is single stranded. */
 				done = 1;
 				structure[i + 1] = j;
 				structure[j] = i + 1;
@@ -240,7 +246,7 @@ int traceVM(int i, int j) {
 	}
 
 	/* WM[i+2, j-1] */
-	if (constraints[i + 1] <= 0) {
+//	if (constraints[i + 1] <= 0) {
 		for (h = i + 3; h <= j - 1 && !done; h++) {
 			A_temp = WM[i + 2][h - 1] + WM[h][j - 1] + a + b + auPen(RNA[i],
 					RNA[j]) + dangle[RNA[i]][RNA[j]][RNA[i + 1]][0]; /* IF base i+1 is dangling on the 5' end of the base pair (i,j) */
@@ -251,10 +257,10 @@ int traceVM(int i, int j) {
 				break;
 			}
 		}
-	}
+//	}
 
 	/* WM[i+1][j-2] */
-	if (constraints[j - 1] <= 0) {
+//	if (constraints[j - 1] <= 0) {
 		for (h = i + 2; h <= j - 2 && !done; h++) { /* If base j-1 is dangling on 3' end of the base pair (i,j) */
 			A_temp = WM[i + 1][h - 1] + WM[h][j - 2] + a + b + auPen(RNA[i],
 					RNA[j]) + dangle[RNA[i]][RNA[j]][RNA[j - 1]][1];
@@ -265,10 +271,10 @@ int traceVM(int i, int j) {
 				break;
 			}
 		}
-	}
+//	}
 
 	/* WM[i+2][j-2] */
-	if (constraints[i + 1] <= 0 && constraints[j - 1] <= 0) {
+//	if (constraints[i + 1] <= 0 && constraints[j - 1] <= 0) {
 		for (h = i + 3; h <= j - 2 && !done; h++) { /* If base pair (i,j) has dangling bases on both sides. */
 			A_temp = WM[i + 2][h - 1] + WM[h][j - 2] + a + b + auPen(RNA[i],
 					RNA[j]) + dangle[RNA[i]][RNA[j]][RNA[i + 1]][0]
@@ -280,7 +286,7 @@ int traceVM(int i, int j) {
 				break;
 			}
 		}
-	}
+//	}
 
 	return eVM;
 }
@@ -320,33 +326,32 @@ int traceWM(int i, int j) {
 				structure[i] = j;
 				structure[j] = i;
 				eWM += traceV(i, j);
-			} else if (WM[i][j] == V[indx[i + 1] + j] + dangle[RNA[j]][RNA[i
-			                                                               + 1]][RNA[i]][1] + auPen(RNA[i + 1], RNA[j]) + b + c
-			                                                               && constraints[i] <= 0) { /* If base pair (i+1, j) forms and base i remain as a dangling base*/
+			} else if (WM[i][j] == V[indx[i + 1] + j] + dangle[RNA[j]][RNA[i + 1]][RNA[i]][1] + auPen(RNA[i + 1], RNA[j]) + b + c){
+			                                                               //&& constraints[i] <= 0) { /* If base pair (i+1, j) forms and base i remain as a dangling base*/
 				done = 1;
 				eWM += traceV(i + 1, j);
 				structure[i + 1] = j;
 				structure[j] = i + 1;
 			} else if (WM[i][j] == V[indx[i] + j - 1]
 			                         + dangle[RNA[j - 1]][RNA[i]][RNA[j]][0] + auPen(RNA[i],
-			                        		 RNA[j - 1]) + b + c && constraints[j] <= 0) { /* If base pair (i,j-1) forms and base j remain as a dangling base */
+			                        		 RNA[j - 1]) + b + c){ //&& constraints[j] <= 0) { /* If base pair (i,j-1) forms and base j remain as a dangling base */
 				done = 1;
 				eWM += traceV(i, j - 1);
 				structure[i] = j - 1;
 				structure[j - 1] = i;
 			} else if (WM[i][j] == V[indx[i + 1] + j - 1]
-			                         + dangle[RNA[j - 1]][RNA[i + 1]][RNA[i]][1] + dangle[RNA[j
-			                                                                                  - 1]][RNA[i + 1]][RNA[j]][0]
-			                                                                                                            + auPen(RNA[i + 1], RNA[j - 1]) + b + 2* c
-			                                                                                                            && constraints[i] <= 0 && constraints[j] <= 0) { /* IF base pair (i+1,j-1) forms and base i and base j remain as dangling bases on each side.*/
+			                         + dangle[RNA[j - 1]][RNA[i + 1]][RNA[i]][1] + 
+									 dangle[RNA[j- 1]][RNA[i + 1]][RNA[j]][0] + auPen(RNA[i + 1], RNA[j - 1]) + b + 2* c)
+			                         {//&& constraints[i] <= 0 && constraints[j] <= 0) { 
+									/* IF base pair (i+1,j-1) forms and base i and base j remain as dangling bases on each side.*/
 				done = 1;
 				eWM += traceV(i + 1, j - 1);
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
-			} else if (WM[i][j] == WM[i + 1][j] + c && constraints[i] <= 0) { /* If base i does not make energy contribution */
+			} else if (WM[i][j] == WM[i + 1][j] + c){ //&& constraints[i] <= 0) { /* If base i does not make energy contribution */
 				done = 1;
 				eWM += traceWM(i + 1, j);
-			} else if (WM[i][j] == WM[i][j - 1] + c && constraints[j] <= 0) { /* If base j does not make energy contribution */
+			} else if (WM[i][j] == WM[i][j - 1] + c){ //&& constraints[j] <= 0) { /* If base j does not make energy contribution */
 				done = 1;
 				eWM += traceWM(i, j - 1);
 			}
diff --git a/gtfold-mfe/src/utils.cc b/gtfold-mfe/src/utils.cc
new file mode 100644
index 0000000..1b5e5d0
--- /dev/null
+++ b/gtfold-mfe/src/utils.cc
@@ -0,0 +1,74 @@
+#include "utils.h"
+#include <string.h>
+#include <string>
+
+char baseToDigit(const char* base) {
+	if (!strcmp(base, "A")) {
+		return '1';
+	}
+	if (!strcmp(base, "C")) {
+		return '2';
+	}
+	if (!strcmp(base, "G")) {
+		return '3';
+	}
+	if (!strcmp(base, "U")) {
+		return '4';
+	}
+	if (!strcmp(base, "N")) {
+		return '5';
+	}
+	return (char) '0';
+}
+
+unsigned char getBase(const char* base) {
+	//cout << base;
+	if (!strcmp(base, "A") || !strcmp(base, "a")) {
+		//cout << "1";
+		return BASE_A;
+	}
+	if (!strcmp(base, "C") || !strcmp(base, "c")) {
+		//cout << "2";
+		return BASE_C;
+	}
+	if (!strcmp(base, "G") || !strcmp(base, "g")) {
+		//cout << "3";
+		return BASE_G;
+	}
+	if (!strcmp(base, "U") || !strcmp(base, "u") || !strcmp(
+			base, "T") || !strcmp(base, "t")) {
+		//cout << "4";
+		return BASE_U;
+	}
+	if (!strcmp(base, "N") || !strcmp(base, "n")||!strcmp(base, "R")|| !strcmp(base, "r")|| !strcmp(base, "Y")|| !strcmp(base, "y")|| !strcmp(base, "M")|| !strcmp(base, "m")|| !strcmp(base, "K")|| !strcmp(base, "k")|| !strcmp(base, "S")|| !strcmp(base, "s")|| !strcmp(base, "W")|| !strcmp(base, "w")|| !strcmp(base, "B")|| !strcmp(base, "b")|| !strcmp(base, "D")|| !strcmp(base, "d")|| !strcmp(base, "H")|| !strcmp(base, "h")|| !strcmp(base, "V")|| !strcmp(base, "v")) {
+		//cout << "4";
+		return BASE_A;
+	}
+	return 'X';
+}
+
+unsigned char getBase1(const char* base) {
+	//cout << base;
+	if (!strcmp(base, "A") || !strcmp(base, "a")) {
+		//cout << "1";
+		return BASE_A;
+	}
+	if (!strcmp(base, "C") || !strcmp(base, "c")) {
+		//cout << "2";
+		return BASE_C;
+	}
+	if (!strcmp(base, "G") || !strcmp(base, "g")) {
+		//cout << "3";
+		return BASE_G;
+	}
+	if (!strcmp(base, "U") || !strcmp(base, "u") || !strcmp(
+																			base, "T") || !strcmp(base, "t")) {
+		//cout << "4";
+		return BASE_U;
+	}
+	if (!strcmp(base, "N") || !strcmp(base, "n")|| !strcmp(base, "R")|| !strcmp(base, "r")|| !strcmp(base, "Y")|| !strcmp(base, "y")|| !strcmp(base, "M")|| !strcmp(base, "m")|| !strcmp(base, "K")|| !strcmp(base, "k")|| !strcmp(base, "S")|| !strcmp(base, "s")|| !strcmp(base, "W")|| !strcmp(base, "w")|| !strcmp(base, "B")|| !strcmp(base, "b")|| !strcmp(base, "D")|| !strcmp(base, "d")|| !strcmp(base, "H")|| !strcmp(base, "h")|| !strcmp(base, "V")|| !strcmp(base, "v")) {
+		//cout << "4";
+		return 'N';
+	}
+	return 'X';
+}

From 081659dcac887cec7b4d9a0583a419d1432d7aea Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Wed, 16 Mar 2011 13:19:36 -0400
Subject: [PATCH 044/282] Make the rewrite compileable and working

Tested to produce the same output on ecoli.txt
---
 gtfold-mfe/include/Makefile.am        |   2 +-
 gtfold-mfe/include/constants.h        |   6 +-
 gtfold-mfe/include/global.h           |   1 -
 gtfold-mfe/include/loader.h           |  10 +-
 gtfold-mfe/include/main.h             |  17 +-
 gtfold-mfe/include/subopt_traceback.h |  47 +-
 gtfold-mfe/src/Makefile.am            |   8 +-
 gtfold-mfe/src/loader.cc              | 334 ++-------
 gtfold-mfe/src/main.cc                | 952 +++++++-------------------
 gtfold-mfe/src/subopt_traceback.cc    | 247 ++++---
 gtfold-mfe/src/traceback.c            | 297 ++++----
 11 files changed, 620 insertions(+), 1301 deletions(-)

diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am
index 8512446..545325a 100644
--- a/gtfold-mfe/include/Makefile.am
+++ b/gtfold-mfe/include/Makefile.am
@@ -1,3 +1,3 @@
-noinst_HEADERS = algorithms.h constants.h data.h energy.h global.h loader.h main.h main-c.h subopt_traceback.h traceback.h 
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h
 
 CLEANFILES = *~
diff --git a/gtfold-mfe/include/constants.h b/gtfold-mfe/include/constants.h
index 52924fb..c86d702 100644
--- a/gtfold-mfe/include/constants.h
+++ b/gtfold-mfe/include/constants.h
@@ -34,14 +34,18 @@
 #define maxforce 600 /* maximum number of bases that can be forced single */
 #define maxgu 5 /* maximum number of u's in gu pair */
 #define C_ 1 /* "c" for optimized VBI. */
-#define TURN 3 /*Minimum hairpin size*/
 
 #define MAXLOOP 30 /* The maximum loop size. */
 #define MAXENG 1000
+#define TURN 3
 
 #define BASE_A 0
 #define BASE_C 1
 #define BASE_G 2
 #define BASE_U 3
 
+
+#define SUCCESS 1
+#define FAILURE 0
+
 #endif
diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h
index 9a7f552..716873e 100644
--- a/gtfold-mfe/include/global.h
+++ b/gtfold-mfe/include/global.h
@@ -6,7 +6,6 @@
 extern unsigned char *RNA1; 
 extern unsigned char *RNA; 
 extern int *structure; 
-extern int VERBOSE;
 
 extern unsigned int chPairKey;
 
diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h
index ed24d7a..c1d271d 100644
--- a/gtfold-mfe/include/loader.h
+++ b/gtfold-mfe/include/loader.h
@@ -17,22 +17,16 @@
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-/* This file externs the prototypes of functions defined in loader.cc*/
-
 #ifndef _LOADER_H
 #define _LOADER_H
 
-#include <iostream>
-#include <fstream>
-#include <istream>
-#include <math.h>
 #include <string>
+
 #include "constants.h"
 #include "data.h"
 
 void populate(const char *userdatadir,bool userdatalogic);
-unsigned char getBase(std::string base);
-unsigned char getBase1(std::string base);
+
 int initStackValues(std::string fileName);
 int initMiscloopValues(std::string fileName);
 int initDangleValues(std::string fileName);
diff --git a/gtfold-mfe/include/main.h b/gtfold-mfe/include/main.h
index 1f607f0..76879a2 100644
--- a/gtfold-mfe/include/main.h
+++ b/gtfold-mfe/include/main.h
@@ -24,19 +24,8 @@
 #include <vector>
 
 #include "constants.h"
-#include "main-c.h"
 
-using namespace std;
-
-enum {FAILURE = 0, SUCCESS, NO_CONS_FOUND, ERR_OPEN_FILE};
-
-int initialize_constraints(int*** fbp, int*** pbp, 
-						   int& numpConstraints, int& numfConstraints, 
-						   const char* constr_file, enum BOOL verbose=FALSE);
-
-int handle_IUPAC_code(const std::string& s, const int bases);
 void limit_contact_distance(int lCD, int length);
-//void force_noncanonical_basepair(const char* nc_basepairs, int length);
 
 bool is_valid_base(char c)
 {	
@@ -53,13 +42,12 @@ void trim_spaces(std::string& str)
 	size_t endpos = str.find_last_not_of(" \t"); // Find the first character position from reverse af
 
 	// if all spaces or empty return an empty string
-	if(( string::npos == startpos ) || ( string::npos == endpos))
+	if(( std::string::npos == startpos ) || ( std::string::npos == endpos))
 	{
 		str = "";
 	}
 	else
 		str = str.substr( startpos, endpos-startpos+1 );
-
 }
 
 void tokenize(const std::string& str, std::vector<std::string>& tokens, const std::string& delimiters = " ")
@@ -80,7 +68,4 @@ void tokenize(const std::string& str, std::vector<std::string>& tokens, const st
 	}
 }
 	
-	
-
-
 #endif
diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h
index 2753854..d3c6beb 100644
--- a/gtfold-mfe/include/subopt_traceback.h
+++ b/gtfold-mfe/include/subopt_traceback.h
@@ -30,16 +30,6 @@
 #include <map>
 #include <vector>
 
-
-#define Ed3(x, y, z)  dangle[RNA[x]][RNA[y]][RNA[z]][1]
-#define Ed5(x, y, z)  dangle[RNA[x]][RNA[y]][RNA[z]][0]
-#define auPenalty(x, y) auPen(RNA[x], RNA[y]) 
-#define Ea multConst[0]
-#define Eb multConst[2]
-#define Ec multConst[1] 
-
-#define V(x,y) V[indx[x]+y]
-
 enum label {lW=0, lV, lVBI, lVM, lWM};
 extern const char* lstr[]; 
 
@@ -85,22 +75,17 @@ struct segment
 	}
 };
 
-typedef segment SEG;
-typedef std::stack<segment>  SEGSTACK;
-
 struct pstruct
 {
 	std::string str;
-	SEGSTACK st_segment;
-	SEGSTACK st_v; /* used for backtracking in traceWM */
-	
+	std::stack<segment> st_segment;
+	std::stack<segment> st_v; /* used for backtracking in traceWM */
 	int ae_;
 	int le_;
 
 	int total() const { return ae_ + le_; }
 
 	pstruct() {}
-	
 	pstruct(const pstruct& ps)
 	{
 		str = ps.str;
@@ -189,7 +174,7 @@ struct pstruct
 
 	void print()
 	{
-		SEGSTACK st = st_segment;
+		std::stack<segment> st = st_segment;
 		std::cout <<'[' << ' ' ;
 		while (!st.empty())
 		{
@@ -211,26 +196,16 @@ struct pstruct
 	}
 };
 
-/* partial structure */
-typedef pstruct ps_t;
-
-/* partial structure stack */
-typedef std::stack<pstruct> ps_stack_t;
-
-/*  partial structure map */
-typedef std::map<std::string, pstruct> ps_map_t;
-
-/* secondary structure map */
-typedef std::map<std::string, int> ss_map_t;	
 
-void push_to_gstack(ps_stack_t & gs, const ps_t& v);
+void push_to_gstack(std::stack<pstruct>& gs, const pstruct& v);
 
-ss_map_t subopt_traceback(int len, int gap);
+void subopt_traceback(int len, int delta);
+void traceV(int i, int j, pstruct& ps, std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
+void traceVBI( int i, int j, pstruct& ps, std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
+void traceW( int i, int j, pstruct& ps, std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
+void traceVM( int i, int j, pstruct& ps, std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
+void traceWM(pstruct& ps, std::map<std::string, pstruct>& filter, int MIN_ENERGY, int delta1);
 
-void traceV(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); 
-void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs, int energy);
-void traceW(int i, int j, ps_t & ps, ps_stack_t & gs, int energy);
-void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs, int energy);
-void traceWM(ps_t& ps, ps_map_t& filter);
+//enum label {lW=0, lV, lVBI, lVM, lWM};
 
 #endif
diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am
index f4addd2..ec34ba5 100644
--- a/gtfold-mfe/src/Makefile.am
+++ b/gtfold-mfe/src/Makefile.am
@@ -12,10 +12,10 @@ gtfold_SOURCES = \
 	options.cc\
 	global.c\
 	energy.c\
-	algorithms.c\
-	algorithms-partition.c\
-	subopt_traceback.cc\
-	traceback.c
+	algorithms.c
+# traceback.c \
+#	subopt_traceback.cc
+
 
 gtfold_LDFLAGS = 
 
diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 5635739..0044b62 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -17,79 +17,74 @@
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-/* Modified by Amrita Mathuriya August 2007 - January 2009. 1) Functions are rewritten, removing calls of boost library functions and corrected bugs.
- * This file defines various functions to read the thermodynamic parameters from files in the data directory.
- * */
-/* Modified by Sonny Hernandez May 2007 - Aug 2007. All comments added marked by "SH: "*/
-/* Modified by Sainath Mallidi August 2009 -  "*/
+#include <iostream>
+#include <fstream>
+#include <istream>
+#include <math.h>
 
-#include <string.h>
+#include <cstring>
 #include <stdlib.h>
+
+#include "data.h"
+#include "utils.h"
+#include "constants.h"
+#include "global.h"
 #include "loader.h"
-#include "main-c.h"
 
 #define xstr(s) str(s)
 #define str(s) #s
-
-//#define GENBIN
+//#define GENBIN 1
 
 using namespace std;
 
-//Global Variables
-int poppen[5];
-int maxpen;
-int eparam[11]; /* Amrita: I am not sure of what does this array contain at different values.*/
-int multConst[3]; /* Amrita: I have copied multiloop penalties into this array */
-int dangle[4][4][4][2]; /* Dangling energies */
-int inter[31]; /* Size penalty for internal loops */
-int bulge[31]; /* Size penalty for bulges*/
-int hairpin[31]; /* Size penalty for hairpin loops */
-#if 0
-int stack[4][4][4][4];
-int tstkh[4][4][4][4];
-int tstki[4][4][4][4];
-#else
-int stack[256]; /* Stacking energy for stack loops */
-int tstkh[256]; /* Terminal stacking energy for hairpin loops */
-int tstki[256]; /* Terminal stacking energy for internal loops */
-#endif
-int tloop[maxtloop + 1][2];
-int numoftloops;
-int iloop22[5][5][5][5][5][5][5][5]; /* 2*1 internal loops*/
-int iloop21[5][5][5][5][5][5][5]; /* 2*1 internal loops */
-int iloop11[5][5][5][5][5][5]; /*1*1 internal loops */
-int coax[6][6][6][6];
-int tstackcoax[6][6][6][6];
-int coaxstack[6][6][6][6];
-int tstack[6][6][6][6];
-int tstkm[6][6][6][6];
-
-int auend; /* For AU penalty */
-int gubonus;
-int cint; /* cint, cslope, c3 are used for poly C hairpin loops */
-int cslope;
-int c3;
-int efn2a;
-int efn2b;
-int efn2c;
-int triloop[maxtloop + 1][2];
-int numoftriloops;
-int init;
-int gail;
-float prelog; /* Used for loops having size > 30 */
-
-string EN_DATADIR;
+std::string EN_DATADIR;
+
+ int poppen[5];
+ int maxpen;
+ int eparam[11];
+ int multConst[3]; /* for multiloop penalties. */
+ int dangle[4][4][4][2]; /* Contain dangling energy values */
+ int inter[31]; /* Contains size penalty for internal loops */
+ int bulge[31]; /* Contain the size penalty for bulges */
+ int hairpin[31]; /* Contains the size penalty for hairpin loops */
+ int stack[256]; /* Stacking energy used to calculate energy of stack loops */
+ int tstkh[256]; /* Terminal mismatch energy used in the calculations of hairpin loops */
+ int tstki[256]; /* Terminal mismatch energy used in the calculations of internal loops */
+ int tloop[maxtloop + 1][2];
+ int numoftloops;
+ int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */
+ int iloop21[5][5][5][5][5][5][5]; /* 2*1 internal loops */
+ int iloop11[5][5][5][5][5][5]; /* 1*1 internal loops */
+ int coax[6][6][6][6];
+ int tstackcoax[6][6][6][6];
+ int coaxstack[6][6][6][6];
+ int tstack[6][6][6][6];
+ int tstkm[6][6][6][6];
+ int auend;
+ int gubonus;
+ int cint; /* cint, cslope, c3 are used for poly C hairpin loops */
+ int cslope;
+ int c3;
+ int efn2a;
+ int efn2b;
+ int efn2c;
+ int triloop[maxtloop + 1][2];
+ int numoftriloops;
+ int init;
+ int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
+ float prelog;
 
 void populate(const char *userdatadir,bool userdatalogic) {
 
-	cout << "Thermodynamic parameters: ";
-
+	cout << "Loading in GTfold data files from ";
 #ifndef GENBIN
-	if (!userdatalogic) {
+	if (!userdatalogic) 
+	{
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
 		EN_DATADIR += userdatadir;
-	} else {
+	} else 
+	{
 		EN_DATADIR.assign(userdatadir);
 	}
 #else
@@ -101,8 +96,7 @@ void populate(const char *userdatadir,bool userdatalogic) {
 		EN_DATADIR += "/";
 	}
 
-
-	cout << EN_DATADIR << endl << endl;
+	cout << EN_DATADIR << endl;
 
 	initMiscloopValues("miscloop.dat");
 	// miscloop.dat - Miscellaneous loop file
@@ -124,79 +118,12 @@ void populate(const char *userdatadir,bool userdatalogic) {
 	// int22.dat - free energies for 2 x 2 interior loops
 	initInt11Values("int11.dat");
 	// int11.dat - free energies for 1 x 1 interior loops
-}
 
-char baseToDigit(std::string base) {
-	if (!strcmp(base.c_str(), "A")) {
-		return '1';
-	}
-	if (!strcmp(base.c_str(), "C")) {
-		return '2';
-	}
-	if (!strcmp(base.c_str(), "G")) {
-		return '3';
-	}
-	if (!strcmp(base.c_str(), "U")) {
-		return '4';
-	}
-	if (!strcmp(base.c_str(), "N")) {
-		return '5';
-	}
-	return (char) NULL;
+	cout << "Done loading data files." << endl;
 }
 
-unsigned char getBase(std::string base) {
-	//cout << base;
-	if (!strcmp(base.c_str(), "A") || !strcmp(base.c_str(), "a")) {
-		//cout << "1";
-		return BASE_A;
-	}
-	if (!strcmp(base.c_str(), "C") || !strcmp(base.c_str(), "c")) {
-		//cout << "2";
-		return BASE_C;
-	}
-	if (!strcmp(base.c_str(), "G") || !strcmp(base.c_str(), "g")) {
-		//cout << "3";
-		return BASE_G;
-	}
-	if (!strcmp(base.c_str(), "U") || !strcmp(base.c_str(), "u") || !strcmp(
-			base.c_str(), "T") || !strcmp(base.c_str(), "t")) {
-		//cout << "4";
-		return BASE_U;
-	}
-	if (!strcmp(base.c_str(), "N") || !strcmp(base.c_str(), "n")||!strcmp(base.c_str(), "R")|| !strcmp(base.c_str(), "r")|| !strcmp(base.c_str(), "Y")|| !strcmp(base.c_str(), "y")|| !strcmp(base.c_str(), "M")|| !strcmp(base.c_str(), "m")|| !strcmp(base.c_str(), "K")|| !strcmp(base.c_str(), "k")|| !strcmp(base.c_str(), "S")|| !strcmp(base.c_str(), "s")|| !strcmp(base.c_str(), "W")|| !strcmp(base.c_str(), "w")|| !strcmp(base.c_str(), "B")|| !strcmp(base.c_str(), "b")|| !strcmp(base.c_str(), "D")|| !strcmp(base.c_str(), "d")|| !strcmp(base.c_str(), "H")|| !strcmp(base.c_str(), "h")|| !strcmp(base.c_str(), "V")|| !strcmp(base.c_str(), "v")) {
-		//cout << "4";
-		return BASE_A;
-	}
-	return 'X';
-}
-unsigned char getBase1(std::string base) {
-	//cout << base;
-	if (!strcmp(base.c_str(), "A") || !strcmp(base.c_str(), "a")) {
-		//cout << "1";
-		return BASE_A;
-	}
-	if (!strcmp(base.c_str(), "C") || !strcmp(base.c_str(), "c")) {
-		//cout << "2";
-		return BASE_C;
-	}
-	if (!strcmp(base.c_str(), "G") || !strcmp(base.c_str(), "g")) {
-		//cout << "3";
-		return BASE_G;
-	}
-	if (!strcmp(base.c_str(), "U") || !strcmp(base.c_str(), "u") || !strcmp(
-			base.c_str(), "T") || !strcmp(base.c_str(), "t")) {
-		//cout << "4";
-		return BASE_U;
-	}
-	if (!strcmp(base.c_str(), "N") || !strcmp(base.c_str(), "n")|| !strcmp(base.c_str(), "R")|| !strcmp(base.c_str(), "r")|| !strcmp(base.c_str(), "Y")|| !strcmp(base.c_str(), "y")|| !strcmp(base.c_str(), "M")|| !strcmp(base.c_str(), "m")|| !strcmp(base.c_str(), "K")|| !strcmp(base.c_str(), "k")|| !strcmp(base.c_str(), "S")|| !strcmp(base.c_str(), "s")|| !strcmp(base.c_str(), "W")|| !strcmp(base.c_str(), "w")|| !strcmp(base.c_str(), "B")|| !strcmp(base.c_str(), "b")|| !strcmp(base.c_str(), "D")|| !strcmp(base.c_str(), "d")|| !strcmp(base.c_str(), "H")|| !strcmp(base.c_str(), "h")|| !strcmp(base.c_str(), "V")|| !strcmp(base.c_str(), "v")) {
-		//cout << "4";
-		return 'N';
-	}
-	return 'X';
-}
 
-int initStackValues(string fileName) {
+ int initStackValues(string fileName) {
 
 	ifstream cf; //cf = current file
 	int i, j, k, l;
@@ -301,7 +228,7 @@ int initStackValues(string fileName) {
 	return 0;
 }
 
-int initMiscloopValues(string fileName) {
+ int initMiscloopValues(string fileName) {
 	/*
 	 miscloop.dat - Miscellaneous loop file. Contains :
 	 1. Extrapolation for large loops based on polymer theory
@@ -418,136 +345,7 @@ int initMiscloopValues(string fileName) {
 	return 0;
 }
 
-int initMiscloopValuesOLD(string fileName) {
-	/*
-	 miscloop.dat - Miscellaneous loop file. Contains :
-	 1. Extrapolation for large loops based on polymer theory
-	 2. Asymmetric internal loop correction parameters.
-	 3. the f(m) array (see Ninio for details)
-	 4. Paremeters for multibranch loops
-	 5. Paremeters for multibranch loops (for efn2 only)
-	 6. Terminal AU or GU penalty
-	 7. Bonus for GGG hairpin
-	 8,9,10. C hairpin rules: a) slope  b) intercept c) value for size 3
-	 11. Intermolecular initiation free energy
-	 12. GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on or off)
-	 */
-
-	char currentWord[256];
-	string s;
-	ifstream cf; //cf = current file
-
-	fileName = EN_DATADIR + fileName;
-#if 0
-	cout << "Getting miscloop values from " << fileName << endl;
-#endif
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-	s = "";
-
-	cf >> currentWord;
-	for (int index = 1; index < 13; index++) { // There are total 12 values to read in.
-		while (strcmp(currentWord, "-->")) {
-			cf >> currentWord;
-		}
-		if (index == 1) {
-			cf >> currentWord;
-			prelog = 100 * atof(currentWord);
-			cout << "prelog = " << prelog << endl;
-		}
-		if (index == 2) {
-			cf >> currentWord;
-			maxpen = int(atof(currentWord) * 100.0 + .5);
-			cout << "maxpen = " << maxpen << endl;
-		}
-		if (index == 3) {
-			for (int count = 1; count <= 4; count++) {
-				cf >> currentWord;
-				s = currentWord;
-				poppen[count] = (int) (atof(s.c_str()) * 100 + 0.5);
-				//cout << "poppen[" << count << "] = "<< poppen[count] << endl;
-			}
-		}
-		if (index == 4) {
-			eparam[1] = 0;
-			eparam[2] = 0;
-			eparam[3] = 0;
-			eparam[4] = 0;
-			eparam[7] = 30;
-			eparam[8] = 30;
-			eparam[9] = -500;
-			int table[4];
-			table[1] = 5;
-			table[2] = 6;
-			table[3] = 10;
-			for (int count = 1; count <= 3; count++) {
-				cf >> currentWord;
-				s = currentWord;
-				eparam[table[count]] = (int) (atof(s.c_str()) * 100 + 0.5);
-				//printf(" %d  ", eparam[table[count]]);
-				//cout << "eparam[" << table[count] << "] = "<< eparam[table[count]] << endl;
-			}
-		}
-		if (index == 5) {
-			int table[4];
-			for (int count = 1; count <= 3; count++) {
-				cf >> currentWord;
-				s = currentWord;
-				table[count] = (int) (atof(s.c_str()) * 100 + 0.5);
-				//cout << "efn2[" << count << "] = "<< table[count] << endl;
-			}
-			efn2a = table[1];
-			efn2b = table[2] - 1;
-			efn2c = table[3] - 1;
-		}
-		if (index == 6) {
-			cf >> currentWord;
-			auend = (int) (100 * atof(currentWord));
-			//cout << "auend = " << auend << endl;
-		}
-		if (index == 7) {
-			cf >> currentWord;
-			gubonus = (int) (100 * atof(currentWord));
-			//cout << "gubonus = " << gubonus << endl;
-		}
-		if (index == 8) {
-			cf >> currentWord;
-			cslope = (int) (100 * atof(currentWord)) + 1;
-			//cout << "cslope = " << cslope << endl;
-		}
-		if (index == 9) {
-			cf >> currentWord;
-			cint = (int) (100 * atof(currentWord));
-			//cout << "cint = " << cint << endl;
-		}
-		if (index == 10) {
-			cf >> currentWord;
-			c3 = (int) (100 * atof(currentWord)) + 1;
-			//cout << "c3 = " << c3 << endl;
-		}
-		if (index == 11) {
-			cf >> currentWord;
-			init = (int) (100 * atof(currentWord)) + 1;
-			//cout << "init = " << init << endl;
-		}
-		if (index == 12) {
-			cf >> currentWord;
-			gail = (int) floor(.5 + atof(currentWord));
-			//cout << "gail = " << gail << endl;
-		}
-	}
-
-	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
-	return 0;
-}
-
-int initDangleValues(string fileName) {
+ int initDangleValues(string fileName) {
 	ifstream cf; //cf = current file
 	char currentLine[256];
 	string currentString;
@@ -656,7 +454,7 @@ int initDangleValues(string fileName) {
 	return 0;
 }
 
-int initLoopValues(string fileName) {
+ int initLoopValues(string fileName) {
 	// algorithm.c, line 2996
 	ifstream cf; // current file
 	char currentLine[256];
@@ -713,7 +511,7 @@ int initLoopValues(string fileName) {
 	return 0;
 }
 
-int initTstkhValues(string fileName) {
+ int initTstkhValues(string fileName) {
 	ifstream cf; //cf = current file
 	int i, j, k, l;
 	int ii, jj, kk, ll;
@@ -819,7 +617,7 @@ int initTstkhValues(string fileName) {
 	return 0;
 }
 
-int initTstkiValues(string fileName) {
+ int initTstkiValues(string fileName) {
 	ifstream cf; //cf = current file
 	int i, j, k, l;
 	int ii, jj, kk, ll;
@@ -927,7 +725,7 @@ int initTstkiValues(string fileName) {
 }
 
 //SH: Rewritten as an error was being generated by this function.
-int initTloopValues(string fileName) {
+ int initTloopValues(string fileName) {
 	ifstream cf;
 	int count;
 	char currentLine[256];
@@ -965,7 +763,7 @@ int initTloopValues(string fileName) {
 		while(currentLine[clindex]== ' ') clindex++;
 		for (count = 0; count < 6; count++) {
 			temp = currentLine[count + clindex];
-			currentSeqNumbers[count] = baseToDigit(temp);
+			currentSeqNumbers[count] = baseToDigit(temp.c_str());
 			//cout << currentSeqNumbers[count];
 			//cout << currentLine[count+1];
 		}
@@ -991,7 +789,7 @@ int initTloopValues(string fileName) {
 	return 0;
 }
 
-int initInt22Values(string fileName) {
+ int initInt22Values(string fileName) {
 
 	//Read the 2x2 internal loops
 	//key iloop22[a][b][c][d][j][l][k][m] =
@@ -1116,7 +914,7 @@ int initInt22Values(string fileName) {
 	return 0;
 }
 
-int initInt21Values(string fileName) {
+ int initInt21Values(string fileName) {
 
 	// 24x6 arrays of 4x4 values
 	//      c
@@ -1257,7 +1055,7 @@ int initInt21Values(string fileName) {
 	return 0;
 }
 
-int initInt11Values(string fileName) {
+ int initInt11Values(string fileName) {
 
 	//Read the 1x1 internal loops
 	//key iloop11[a][b][c][d][j][l][k][m] =
@@ -1394,3 +1192,5 @@ int initInt11Values(string fileName) {
 #endif
 	return 0;
 }
+
+
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 5aca720..9ab84d0 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -1,27 +1,22 @@
 /*
-GTfold: compute minimum free energy of RNA secondary structure
-Copyright (C) 2008  David A. Bader
-http://www.cc.gatech.edu/~bader
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
+ GTfold: compute minimum free energy of RNA secondary structure
+ Copyright (C) 2008  David A. Bader
+ http://www.cc.gatech.edu/~bader
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
 
-/* Authored by Amrita Mathuriya August 2007 - January 2009.*/
-/* Modified by Sonny Hernandez May 2007 - Aug 2007. All comments added marked by "SH: "*/
-/* Modified by Sainath Mallidi August 2009 - "*/
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
 
-#include <errno.h>
 #include <iostream>
 #include <iomanip>
 #include <fstream>
@@ -34,726 +29,299 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <stdlib.h>
 #include <string.h>
 
+#include "main.h"
+#include "utils.h"
 #include "loader.h"
+#include "options.h"
+#include "global.h"
 #include "energy.h"
 #include "algorithms.h"
-#include "algorithms-partition.h"
 #include "traceback.h"
 #include "subopt_traceback.h"
-#include "options.h"
-#include "main.h"
-#include "main-c.h"
 
 using namespace std;
 
-/* GLOBAL VARIABLES */
-
-enum BOOL BPP; // calculating base pair probabilities
-enum BOOL VERBOSE;
-
-int num_threads;
-int LENGTH;
-int contact_dist;
-
-unsigned char *RNA1;
-unsigned char *RNA; /* Contains RNA string in terms of 0, 1, 2, 3 for A, C, G and U respectively*/
-int *structure; /* An array to contain the optimal structure */
-int *V; /* int V[LENGTH][LENGTH]; */
-int *W;
-int **VBI; /* VBI(i,j) will contain the energy of optimal internal loop closed with (i,j) base pair */
-int **VM; /* VM(i, j) will contain the energy of optimla multiloop closed with (i,j) base pair */
-int **WM; /* This array is introduced to help multiloop calculations. WM(i,j) contains the optimal energy of string segment from si to sj if this forms part of a multiloop */
-int *indx; /* This array is used to index V array. Here V array is mapped from 2D to 1D and indx array is used to get the mapping back.*/
-int *constraints;
-
-double **QB;  // QB[i][j] is the sum over all possible loops closed by (i,j),
-// including the summed contributions of their subloops
-double **Q;   // Q[i][j] in addition to the above quantity QB[i][j], Q[i][j]
-// also includes all configurations with (i,j) not paired
-double **QM;  // QM[i][j] is the sum of configuration energies from i to j,
-// assuming that i,j are contained in a multiloop
-double **P;   // P[i][j] The probability that nucleotides i and j form a basepair
-
-
-/* Function for calculating time */
-double get_seconds() {
-    struct timeval tv;
-    gettimeofday(&tv, NULL);
-    return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0;
-}
-
-/*Function for printing the sequence*/
-void printSequence(int len) {
-    int i = 1;
-    for (i = 1; i <= len; i++) {
-        if (RNA1[i] == 0)
-            printf("A");
-        else if (RNA1[i] == 1)
-            printf("C");
-        else if (RNA1[i] == 2)
-            printf("G");
-        else if (RNA1 [i] == 3)
-            printf("T");
-        else
-            printf("N");
-    }
-    printf("\n");
-}
-
-/*Function for printing the input constraints*/
-void printConstraints(int len) {
-    int i = 1;
-    for (i = 1; i <= len; i++) {
-        if (constraints[i] > 0 && constraints[i] > i)
-            printf("(");
-        else if (constraints[i] > 0 && constraints[i] < i)
-            printf(")");
-        else if (constraints[i] < 0)
-            printf("x");
-        else
-            printf(".");
-    }
-    printf("\n");
-}
-
-/*Function for printing the predicted structure*/
-void printStructure(int len) {
-    int i = 1;
-    for (i = 1; i <= len; i++) {
-        if (structure[i] > 0 && structure[i] > i)
-            printf("(");
-        else if (structure[i] > 0 && structure[i] < i)
-            printf(")");
-        else
-            printf(".");
-    }
-    printf("\n");
-}
-
-/* Initialize global variables. */
-void init_variables(int len) {
-
-    int i;
-
-    LENGTH = len + 1;
-
-    RNA = (unsigned char *) malloc(LENGTH * sizeof(unsigned char));
-    if (RNA == NULL) {
-        perror("Cannot allocate variable 'RNA'");
-        exit(-1);
-    }
-    RNA1 = (unsigned char *) malloc(LENGTH * sizeof(unsigned char));
-    if (RNA1 == NULL) {
-        perror("Cannot allocate variable 'RNA'");
-        exit(-1);
-    }
-    structure = (int *) malloc(LENGTH * sizeof(int));
-    if (structure == NULL) {
-        perror("Cannot allocate variable 'structure'");
-        exit(-1);
-    }
-
-    V = (int *) malloc(((LENGTH - 1) * (LENGTH) / 2 + 1) * sizeof(int));
-    if (V == NULL) {
-        perror("Cannot allocate variable 'V'");
-        exit(-1);
-    }
-
-    W = (int *) malloc(LENGTH * sizeof(int));
-    if (W == NULL) {
-        perror("Cannot allocate variable 'W'");
-        exit(-1);
-    }
-
-    VBI = (int **) malloc(LENGTH * sizeof(int *));
-    if (VBI == NULL) {
-        perror("Cannot allocate variable 'VBI'");
-        exit(-1);
-    }
-    for (i = 0; i < LENGTH; i++) {
-        VBI[i] = (int *) malloc(LENGTH * sizeof(int));
-        if (VBI[i] == NULL) {
-            perror("Cannot allocate variable 'VBI[i]'");
-            exit(-1);
-        }
-    }
-
-    VM = (int **) malloc(LENGTH * sizeof(int *));
-    if (VM == NULL) {
-        perror("Cannot allocate variable 'VM'");
-        exit(-1);
-    }
-    for (i = 0; i < LENGTH; i++) {
-        VM[i] = (int *) malloc(LENGTH * sizeof(int));
-        if (VM[i] == NULL) {
-            perror("Cannot allocate variable 'VM[i]'");
-            exit(-1);
-        }
-    }
-
-    WM = (int **) malloc(LENGTH * sizeof(int *));
-    if (WM == NULL) {
-        perror("Cannot allocate variable 'WM'");
-        exit(-1);
-    }
-    for (i = 0; i < LENGTH; i++) {
-        WM[i] = (int *) malloc(LENGTH * sizeof(int));
-        if (WM[i] == NULL) {
-            perror("Cannot allocate variable 'WM[i]'");
-            exit(-1);
-        }
-    }
-
-    indx = (int *) malloc(LENGTH * sizeof(int));
-    if (indx == NULL) {
-        perror("Cannot allocate variable 'indx'");
-        exit(-1);
-    }
-
-    constraints = (int*) malloc((len + 1) * sizeof(int));
-    if (constraints == NULL) {
-        perror("Cannot allocate variable 'constraints'");
-        exit(-1);
-    }
+double get_seconds() 
+{
+	struct timeval tv;
+	gettimeofday(&tv, NULL);
+	return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0;
 }
 
-/* deallocate global variables */
-void free_variables() {
-    int i;
-
-    free(indx);
-    for (i = 0; i < LENGTH; i++)
-        free(WM[i]);
-    free(WM);
-    for (i = 0; i < LENGTH; i++)
-        free(VM[i]);
-    free(VM);
-    for (i = 0; i < LENGTH; i++)
-        free(VBI[i]);
-    free(VBI);
-    free(W);
-    free(V);
-    free(constraints);
-    free(structure);
-    free(RNA);
-    free(RNA1);
-}
+void init_fold(int len) 
+{	
 
-void init_partition_function_variables(int length) {
-    QB = mallocTwoD(length+1, length+1);
-    if(QB == NULL) {
-        fprintf(stderr,"Failed to allocate QB\n");
-        exit(-1);
-    }
-
-    Q = mallocTwoD(length+1, length+1);
-    if(Q == NULL) {
-        fprintf(stderr,"Failed to allocate Q\n");
-        exit(-1);
-    }
-
-    QM = mallocTwoD(length+1, length+1);
-    if(QM == NULL) {
-        fprintf(stderr,"Failed to allocate QM\n");
-        exit(-1);
-    }
-
-    P = mallocTwoD(length+1, length+1);
-    if(P == NULL) {
-        fprintf(stderr,"Failed to allocate P\n");
-        exit(-1);
-    }
+ 	init_global_params(len);
+	create_tables(len);
+	return;
 }
 
-void free_partition_function_variables(int length) {
-    freeTwoD(QB, length+1, length+1);
-    freeTwoD(Q, length+1, length+1);
-    freeTwoD(QM, length+1, length+1);
-    freeTwoD(P, length+1, length+1);
+void free_fold(int len) 
+{
+	free_global_params();
+	free_tables(len);
+	return;
 }
 
-
-/* main function - This calls
- *  1) Read command line arguments.
- *  2) populate() from loader.cc to read the thermodynamic parameters defined in the files given in data directory.
- *  3) Initialize variables
- *  4) Calls calculate function defined in algorithms.c for filling up energy tables.
- *  5) Calls trace function defined in trace.c file for tracing the optimal secondary structure
- *  6) Then it generates .ct file from the 1D array structure.
- *  */
-int main(int argc, char** argv) {
-    int i;
-    ifstream cf;
-    int length;
-    string s, seq;
-    int energy;
-    double t1;
-    NOISOLATE = FALSE;
-    BPP = FALSE;
-    VERBOSE = FALSE;
-	int delta = -1;
-
-    fprintf(stdout,
-            "GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n");
-    fprintf(
-            stdout,
-            "(c) 2007-2010  D.A. Bader, S. Mallidi, A. Mathuriya, C.E. Heitsch, S.C. Harvey\n");
-    fprintf(stdout, "Georgia Institute of Technology\n\n");
-
-    /* Reading command line arguments */
-    if (argc < 2)
-        help();
-
-    int fileIndex = 0, consIndex = 0, dataIndex = 0, lcdIndex = 0;
-    int rangeIndex = 0, thIndex = 0, outputFileIndex = 0;
-
-    i = 1;
-    while (i < argc) {
-        if (argv[i][0] == '-') {
-            if        (strcmp(argv[i], "--noisolate") == 0 ||
-                    strcmp(argv[i], "-n") == 0) {
-                NOISOLATE = TRUE;
-            } else if (strcmp(argv[i], "--output") == 0 ||
-                    strcmp(argv[i], "-o") == 0) {
-                if (i < argc)
-                    outputFileIndex = ++i;
-                else
-                    help();
-            } else if (strcmp(argv[i], "--verbose") == 0 ||
-                    strcmp(argv[i], "-v") == 0) {
-                VERBOSE = TRUE;
-            } else if (strcmp(argv[i], "--help") == 0 ||
-                    strcmp(argv[i], "-h") == 0) {
-                help();
-            } else if (strcmp(argv[i], "--constraints") == 0 ||
-                    strcmp(argv[i], "-c") == 0) {
-                if (i < argc)
-                    consIndex = ++i;
-                else
-                    help();
-            } else if (strcmp(argv[i], "--threads") == 0 ||
-                    strcmp(argv[i], "-t") == 0) {
-                if (i < argc)
-                    thIndex = ++i;
-                else
-                    help();
-            } else if (strcmp(argv[i], "--datadir") == 0) {
-                USERDATA = TRUE;
-                if (i < argc)
-                    dataIndex = ++i;
-                else
-                    help();
-            } else if (strcmp(argv[i], "--limitCD") == 0 ||
-                    strcmp(argv[i], "-d") == 0) {
-                if (i < argc)
-                    lcdIndex = ++i;
-                else
-                    help();
-            } else if (strcmp(argv[i], "--bpp") == 0) {
-                BPP = TRUE;
-            } else if (strcmp(argv[i], "--subopt") == 0) {
-				if (i<argc)
-                    rangeIndex = ++i;
-				else
-					help();
-            } else {
-                fprintf(stderr, "Unrecognized option: `%s'\n", argv[i]);
-                fprintf(stderr, "Try: `%s --help' for more information.\n", argv[0]);
-                exit(1);
-            }
-
-        } else {
-            fileIndex = i;
-        }
-        i++;
-    }
-
-    if (fileIndex == 0)
-        help();
-
-    fprintf(stdout, "File: %s\n", argv[fileIndex]);
-    cf.open(argv[fileIndex], ios::in);
-    if (cf == NULL) {
-        fprintf(stdout, "File open failed.\n\n");
-        exit(-1);
-    }
-
-    seq = "";
-    s = "";
-
-    //Handle FASTA input
-    char ss[10000];
-    cf.getline(ss, 10000);
-    if (ss[0] != '>') {
-        char *fline;
-        fline = strtok(ss, " ");
-        while (fline != NULL) {
-            seq.append(fline);
-            fline = strtok(NULL, " ");
-        }
-    }
-
-    while (!cf.eof()) {
-        cf >> s;
-        seq.append(s);
-        s = "";
-    }
-    s = seq;
-
-    length = s.length();
-
-    init_variables(length);
-
-    fprintf(stdout, "Sequence length: %5d\n\n", length);
-
-    cf.close();
-
-    int **fbp = NULL, **pbp = NULL;
-    int numfConstraints = 0, numpConstraints = 0;
-
-    if (consIndex != 0) {
-        int r = initialize_constraints(&fbp, &pbp, numpConstraints, numfConstraints, argv[consIndex]);
-        if (r == ERR_OPEN_FILE) {
-            free_variables();
-            exit(-1);
-        }
-        else if (r == NO_CONS_FOUND) {
-            fprintf(stdout, "constraints file empty! Quitting...\n");
-            exit(1);
-        }
-    }
-
-    if (thIndex > 0) {
-        num_threads = atoi(argv[thIndex]);
-    }
-
-    if (handle_IUPAC_code(s, length)  == FAILURE) {
-        free_variables();
-        exit(0);
-    }
-
-    if(USERDATA==TRUE)
-        populate(argv[dataIndex],true);
-    else
-        populate("Turner99",false); /* Defined in loader.cc file to read in the thermodynamic parameter values from the tables in the ../data directory. */
-
-    create_tables(length); /* Initialize global variables */
-
-    ///// Run Configuration Output /////
-
-    fprintf(stdout, "Run Configuration:\n");
-    bool standardRun = TRUE;
-
-    if (NOISOLATE == TRUE) {
-        fprintf(stdout, "- preventing isolated base pairs\n");
-        standardRun = FALSE;
-    }
-
-    if (consIndex != 0) {
-        fprintf(stdout, "- using constraint file: %s\n", argv[consIndex]);
-        standardRun = FALSE;
-    }
+int read_sequence_file(const char* filename, std::string& seq)
+{
+	ifstream cf;
+	cf.open(filename, ios::in);
+	if (cf == NULL)
+	{
+		return FAILURE;
+	}
 	
-	contact_dist = length+1;
-    if (lcdIndex != 0) {
-        contact_dist = atoi(argv[lcdIndex]);
-        fprintf(stdout, "- maximum contact distance: %d\n", contact_dist);
-        standardRun = FALSE;
-    }
-
-    if (BPP == TRUE) {
-        fprintf(stdout, "+ calculating base pair probabilities\n");
-        standardRun = FALSE;
-    }
-
-    if (rangeIndex != 0) {	
-        delta = atoi(argv[rangeIndex]);
-        fprintf(stdout, "+ calculating suboptimal structures within %d kcal/mol of MFE\n", delta);
-        standardRun = FALSE;
+	seq = "";
+	//Handle FASTA input
+	char ss[10000];
+	cf.getline(ss, 10000);
+	if (ss[0] != '>') 
+	{
+		char *fline;
+		fline = strtok(ss, " ");
+		while (fline != NULL) {
+			seq.append(fline);
+			fline = strtok(NULL, " ");
+		}
 	}
+	
+	cf.close();
+	
+	return SUCCESS;
+}
 
-    if(standardRun)
-        fprintf(stdout, "- standard\n");
+int handle_IUPAC_code(const char* str, const int bases)
+{
+	int* stack_unidentified_base;
+	int stack_count=0;
+	bool unspecd=0;
+	stack_unidentified_base=new int[bases];
+	std::string s = str;
 
-    ///// end run config output /////
+	for(int i = 1; i <= bases; i++) 
+	{
+		RNA[i] = getBase((s.substr(i-1,1)).c_str());
+		RNA1[i] = getBase1((s.substr(i-1,1)).c_str());
 
+		if (RNA[i]=='X') 
+		{
+			fprintf(stderr,"ERROR: Base unrecognized\n");
+			return FAILURE;
+		}
+		else if(RNA[i]!='X' && RNA1[i]=='N')
+		{
+			unspecd=1;
+			stack_unidentified_base[stack_count]=i;
+			stack_count++;
+		}
+	}
+	if(unspecd) 
+	{
+		printf("IUPAC codes have been detected at positions:");
 
-    fprintf(stdout,"\nComputing minimum free energy structure ... \n\n");
-    fflush(stdout);
+		for(int i=0;i<stack_count;i++)
+		{
+			printf("%d , ",stack_unidentified_base[i]);
+		}
+		printf("\n");
+		//printf("You may wish to resubmit the sequence with fully specified positions. Alternatively, GTfold will fold the sequence under the standard assumption that these ambiguous positions do not pair.  Do you wish to continue with the current computation? <Y/N>");
+		//char reply;
+		//scanf("%c",&reply);
+		//return (reply=='n'||reply=='N')?(FAILURE):(SUCCESS);
+		return SUCCESS;
+	}
+	else 
+	{
+		return SUCCESS;
+	}
+}
 
-    t1 = get_seconds();
-    energy = calculate(length); //, fbp, pbp, numfConstraints, numpConstraints);
-    t1 = get_seconds() - t1;
+int main(int argc, char** argv) {
+	std::string seq;
+	int energy;
+	double t1;
 
-    fprintf(stdout,"Minimum Free Energy: %9.2f\n", energy/100.00);
-    fprintf(stdout,"MFE runtime (seconds): %9.6f\n\n", t1);
+	fprintf(stdout,"GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n");
+	fprintf(stdout,"(c) 2007-2010  D.A. Bader, S. Mallidi, A. Mathuriya, C.E. Heitsch, S.C. Harvey\n");
+	fprintf(stdout, "Georgia Institute of Technology\n");
+	
+	parse_options(argc, argv);
 
-	if (rangeIndex != 0)
+	fprintf(stdout, "Opening file: %s\n", seqfile.c_str());
+	if (read_sequence_file(seqfile.c_str(), seq) == 0)
 	{
-		fprintf(stdout,"Computing suboptimal structures in range %d ...\n", delta);
-		t1 = get_seconds();
-		// Traces the optimal structure
-		ss_map_t suboptdata =  subopt_traceback(length, delta); 
-		t1 = get_seconds() - t1;
-		fprintf(stdout,"Traceback runtime (seconds): %9.6f\n\n", t1);
-
-		std::string suboptfile;
-		suboptfile += argv[fileIndex];
-
-		// if an extension exists, replace it with ct
-		if(suboptfile.find(".") != string::npos)
-			suboptfile.erase(suboptfile.rfind("."));
-		suboptfile += ".struct";
-		ofstream subopt_fp;
+		fprintf(stdout, "File open failed.\n\n");
+		exit(-1);
+	}
+	fprintf(stdout, "Sequence length: %5d\n", seq.length());
+	//fprintf(stdout, "Sequence : %s\n", seq.c_str());
+	
+	init_fold(seq.length());
+	
+	if (handle_IUPAC_code(seq.c_str(), seq.length())  == 0)
+	{
+		free_fold(seq.length());
+		exit(0);
+	}
 		
-		fprintf(stdout, "Writing suboptimal structures: %s\n", suboptfile.c_str());
-		subopt_fp.open (suboptfile.c_str());
-
-		ss_map_t::iterator it;
-		for (it = suboptdata.begin(); it != suboptdata.end(); ++it)
-			subopt_fp << it->first << ' ' << it->second << std::endl;
+	if(USERDATA==true)
+		populate(datadir.c_str(),true);
+	else if (PARAMS == true)
+		populate(dataparam.c_str(),false);
+	else
+		populate("Turner99",false); 
+	
+	fprintf(stdout,"Computing minimum free energy structure. . . \n");
+	fflush(stdout);
 
-		subopt_fp.close();
+	t1 = get_seconds();
+	energy = calculate(seq.length());
+	t1 = get_seconds() - t1;
+	
+	fprintf(stdout,"Done.\n\n");
+	fprintf(stdout,"Minimum Free Energy = %12.4f\n", energy/100.00);
+	fprintf(stdout,"MFE running time (in seconds): %9.6f\n\n", t1);
+	
+	
+	if (delta > 0)
+	{	
+		t1 = get_seconds();
+		subopt_traceback(seq.length(), delta);
+		t1 = get_seconds() - t1;
+		fprintf(stdout,"Traceback running time (in seconds): %9.6f\n\n", t1);
 
-		exit(0);	
+		free_fold(seq.length());
+		exit(0);
 	}
+	
+	t1 = get_seconds();
+	trace(seq.length());
+	t1 = get_seconds() - t1;
+	
+	/*
+	std::stringstream ss1, ss2;
+	char suboptfile[1024];
+	ss1 << seq.length();
+	ss2 << energy/100.0;
+
+	strcpy (suboptfile, argv[fileIndex]);
+	strcat ( suboptfile, ".ct");
+	ofstream outfile;
+	outfile.open ( suboptfile );
+
+	fprintf(stdout, "Writing secondary structure to the file: %s\n", suboptfile);
+
+	outfile << bases << "\t  dG = " << energy/100.0;
+	i = 1;
+	while ( i <= bases ) {
+		outfile << endl << i << "\t" << s[i-1] << "\t" << i-1 << "\t" << (i+1)%(bases+1) << "\t" << structure[i] << "\t" << i;
+		i++;
+	}
+	outfile << endl;
 
-    // only fill the partition function structures if they are needed for BPP
-    if(BPP) {
-        fprintf(stdout,"Filling Partition Function structure... \n\n");
-        fflush(stdout);
-
-        // malloc the arrays
-        init_partition_function_variables(length);
-
-        // fill the arrays
-        fill_partition_fn_arrays(length, QB, Q, QM);
-
-        fprintf(stdout,"Q[1][n]: %f\n\n", Q[1][length]);
-    }
-
-
-    t1 = get_seconds();
-    trace(length); /* Traces the optimal structure*/
-    t1 = get_seconds() - t1;
-
-    std::stringstream ss1, ss2;
-
-    ss1 << length;
-    ss2 << energy/100.0;
-
-    i = 0;
-
-    // the output filename
-    string outputfile;
-
-    // use given output file
-    if( outputFileIndex != 0)
-        outputfile += argv[outputFileIndex];
-
-    // or build off the input file
-    else {
-        outputfile += argv[fileIndex];
+	outfile.close();
 
-        // if an extension exists, replace it with ct
-        if(outputfile.find(".") != string::npos)
-            outputfile.erase(outputfile.rfind("."));
+	fprintf(stdout,"\n\n");
+	fprintf(stdout,"Traceback running time (in seconds): %9.6f\n", t1);
 
-        outputfile += ".ct";
-    }
+	fprintf(stdout, "\n\nFolding complete\n\n");
+	printSequence(bases);
+	//printConstraints(bases);
+	printStructure(bases);
+*/
+	free_fold(seq.length());
 
-    ofstream outfile;
-    outfile.open ( outputfile.c_str() );
+	return 0;
+}
 
-    fprintf(stdout, "Writing secondary structure: %s\n", outputfile.c_str());
 
-    outfile << length << "\t  dG = " << energy/100.0;
-    i = 1;
-    while ( i <= length ) {
-        outfile << endl << i << "\t" << s[i-1] << "\t" << i-1 << "\t" << (i+1)%(length+1) << "\t" << structure[i] << "\t" << i;
-        i++;
-    }
-    outfile << endl;
-    outfile.close();
+int initialize_constraints(int*** fbp, int ***pbp, int& numpConstraints, int& numfConstraints, const char* constr_file)
+{
+	ifstream cfcons;
 
-    fprintf(stdout,"Traceback runtime (seconds): %9.6f\n\n", t1);
+	fprintf(stdout, "Running with constraints\n");
+	fprintf(stdout, "Opening constraint file: %s\n", constr_file);
 
-	printSequence(length);
-	if (consIndex != 0) { 
-		printConstraints(length);
+	cfcons.open(constr_file, ios::in);
+	if (cfcons != NULL)
+		fprintf(stdout, "Constraint file opened.\n");
+	else {
+		fprintf(stderr, "Error opening constraint file\n\n");
+		cfcons.close();
+		return FAILURE; //exit(-1);
 	}
-	printStructure(length);
-
-    if(BPP) {
-        fillBasePairProbabilities(length, structure, Q, QB, QM, P);
-
-        printBasePairProbabilities(length, structure, P);
-
-        free_partition_function_variables(length);
-    }
-
-    free_variables();
-
-    return 0;
-}
 
+	char cons[100];
 
-int initialize_constraints(int*** fbp, int ***pbp, 
-						   int& numpConstraints, int& numfConstraints, 
-						   const char* constr_file, enum BOOL verbose) {
-    ifstream cfcons;
-
-    fprintf(stdout, "Running with constraints\n");
-    fprintf(stdout, "Opening constraint file: %s\n", constr_file);
-
-    cfcons.open(constr_file, ios::in);
-    if (cfcons != NULL)
-        fprintf(stdout, "Constraint file opened.\n");
-    else {
-        fprintf(stderr, "Error opening constraint file\n\n");
-        cfcons.close();
-        return ERR_OPEN_FILE; //exit(-1);
-    }
-
-    char cons[100];
-
-    while (!cfcons.eof()) {
-        cfcons.getline(cons, 100);
-        if (cons[0] == 'F' || cons[0] == 'f')
-            numfConstraints++;
-        if (cons[0] == 'P' || cons[0] == 'p')
-            numpConstraints++;
-    }
-    cfcons.close();
-
-    fprintf(stdout, "Number of Constraints given: %d\n\n", numfConstraints
-            + numpConstraints);
-    if (numfConstraints + numpConstraints != 0)
-        fprintf(stdout, "Reading Constraints.\n");
-    else {
-        fprintf(stderr, "No Constraints found.\n\n");
-        return NO_CONS_FOUND;
-    }
-
-    *fbp = (int**) malloc(numfConstraints * sizeof(int*));
-    *pbp = (int**) malloc(numpConstraints * sizeof(int*));
-
-    int fit = 0, pit = 0, it = 0;
-
-    for (it = 0; it < numfConstraints; it++) {
-        (*fbp)[it] = (int*) malloc(2* sizeof (int));
-    }
-    for(it=0; it<numpConstraints; it++) {
-        (*pbp)[it] = (int*)malloc(2*sizeof(int));
-    }
-    cfcons.open(constr_file, ios::in);
-
-    while(!cfcons.eof()) {
-        cfcons.getline(cons,100);
-        char *p=strtok(cons, " ");
-        p = strtok(NULL, " ");
-        if(cons[0]=='F' || cons[0]=='f') {
-            int fit1=0;
-            while(p!=NULL) {
-                (*fbp)[fit][fit1++] = atoi(p);
-                p = strtok(NULL, " ");
-            }
-            fit++;
-        }
-        if( cons[0]=='P' || cons[0]=='p') {
-            int pit1=0;
-            while(p!=NULL) {
-                (*pbp)[pit][pit1++] = atoi(p);
-                p = strtok(NULL, " ");
-            }
-            pit++;
-        }
-    }
-
-	if (VERBOSE == TRUE)
-	{
-		fprintf(stdout, "Forced base pairs: ");
-		for(it=0; it<numfConstraints; it++) {
-			for(int k=1;k<= (*fbp)[it][2];k++)
-				fprintf(stdout, "(%d,%d) ", (*fbp)[it][0]+k-1, (*fbp)[it][1]-k+1);
-		}
-		fprintf(stdout, "\nProhibited base pairs: ");
-		for(it=0; it<numpConstraints; it++) {
-			for(int k=1;k<= (*pbp)[it][2];k++)
-				fprintf(stdout, "(%d,%d) ", (*pbp)[it][0]+k-1, (*pbp)[it][1]-k+1);
-		}
-		fprintf(stdout, "\n\n");
+	while (!cfcons.eof()) {
+		cfcons.getline(cons, 100);
+		if (cons[0] == 'F' || cons[0] == 'f')
+			numfConstraints++;
+		if (cons[0] == 'P' || cons[0] == 'p')
+			numpConstraints++;
+	}
+	cfcons.close();
+
+	fprintf(stdout, "Number of Constraints given: %d\n\n", numfConstraints
+			+ numpConstraints);
+	if (numfConstraints + numpConstraints != 0)
+		fprintf(stdout, "Reading Constraints.\n");
+	else {
+		fprintf(stderr, "No Constraints found.\n\n");
+		return FAILURE;
 	}
 
-    return SUCCESS;
-}
+	*fbp = (int**) malloc(numfConstraints * sizeof(int*));
+	*pbp = (int**) malloc(numpConstraints * sizeof(int*));
 
-int handle_IUPAC_code(const std::string& s, const int length) {
-	int* stack_unidentified_base;
-	int stack_count=0;
-	bool unspecd=0;
-	stack_unidentified_base=new int[length];
+	int fit = 0, pit = 0, it = 0;
 
-	// Conversion of the sequence to numerical values. 
-	for(int i = 1; i <= length; i++) {
-		RNA[i] = getBase(s.substr(i-1,1));
-		RNA1[i] = getBase1(s.substr(i-1,1));
-		if (RNA[i]=='X') {
-			fprintf(stderr,"ERROR: Base unrecognized\n");
-			return FAILURE; 
+	for (it = 0; it < numfConstraints; it++) {
+		(*fbp)[it] = (int*) malloc(2* sizeof (int));
+	}
+	for(it=0; it<numpConstraints; it++) {
+		(*pbp)[it] = (int*)malloc(2*sizeof(int));
+	}
+	cfcons.open(constr_file, ios::in);
+
+	while(!cfcons.eof()) {
+		cfcons.getline(cons,100);
+		char *p=strtok(cons, " ");
+		p = strtok(NULL, " ");
+		if(cons[0]=='F' || cons[0]=='f') {
+			int fit1=0;
+			while(p!=NULL) {
+				(*fbp)[fit][fit1++] = atoi(p);
+				p = strtok(NULL, " ");
+			}
+			fit++;
 		}
-		else if(RNA[i]!='X' && RNA1[i]=='N'){
-			unspecd=1;
-			stack_unidentified_base[stack_count]=i;
-			stack_count++;
+		if( cons[0]=='P' || cons[0]=='p') {
+			int pit1=0;
+			while(p!=NULL) {
+				(*pbp)[pit][pit1++] = atoi(p);
+				p = strtok(NULL, " ");
+			}
+			pit++;
 		}
-
 	}
-	if (unspecd) {
-		printf("IUPAC codes have been detected at positions: ");
 
-		for(int i = 0; i < stack_count; i++) {
-			printf("%d",stack_unidentified_base[i]);
-			if (i < stack_count -1) printf(", ");
-		}
-		printf("\n");
+	fprintf(stdout, "Forced base pairs: ");
+	
+	for(it=0; it<numfConstraints; it++) 
+	{
+		for(int k=1;k<= (*fbp)[it][2];k++)
+			fprintf(stdout, "(%d,%d) ", (*fbp)[it][0]+k-1, (*fbp)[it][1]-k+1);
+	}
+	fprintf(stdout, "\nProhibited base pairs: ");
+	for(it=0; it<numpConstraints; it++) 
+	{
+		for(int k=1;k<= (*pbp)[it][2];k++)
+			fprintf(stdout, "(%d,%d) ", (*pbp)[it][0]+k-1, (*pbp)[it][1]-k+1);
+	}
 
-		printf("You may wish to resubmit the sequence with fully specified positions.\n");
-		printf("Aborting the current computation.\n\n");
+	fprintf(stdout, "\n\n");
 
-		return FAILURE;
-	}
 	return SUCCESS;
 }
-
-
-//void force_noncanonical_basepair(const char* ncb, int len) {
-//    if (ncb == 0 || ncb[0] == '\0') return;
-//
-//    printf("Permitted noncanonical base pairs : \n");	
-//
-//   std::string ncb1(ncb);
-//
-//   for (unsigned int i =0 ; i < ncb1.size(); ++i) {
-//       ncb1[i] = toupper(ncb1[i]);
-//   }
-//
-//    std::vector<std::string> tokens;
-//    tokenize(ncb1, tokens, ",");	
-//
-//    for (unsigned int i = 0; i < tokens.size(); ++i) {
-//       trim_spaces(tokens[i]);
-//       if (tokens.size() != 3 && tokens[i][1] != '-')
-//           // ignore
-//           continue;
-//
-//      char b1 = getBase(tokens[i].substr(0,1));
-//      char b2 = getBase(tokens[i].substr(2,1));
-//
-//      int r1=0;
-//      r1 = update_chPair(b1, b2);			
-//     if (r1 == 1)
-//         printf("(%c,%c) ",  tokens[i][0], tokens[i][2]) ;
-// }
-// printf("\n\n");
-//}  
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index 2374d1d..1b5d0e8 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -20,25 +20,29 @@
 
  */
 
-#include <cstdio>
-
+#include "subopt_traceback.h"
 #include "constants.h"
-#include "data.h"
-#include "global.h"
 #include "energy.h"
+#include "global.h"
 #include "utils.h"
-#include "subopt_traceback.h"
+#ifdef _OPENMP   /* The compiler automatically recognizes openmp support and includes the file accordingly*/
+#include "omp.h"
+#endif
+#include <cstdio>
+
+extern int nThreads;
 
 const char* lstr[] = {"W", "V", "VBI", "VM", "WM"};
 
-void (*trace_func[5]) (int i, int j, ps_t& ps, ps_stack_t& gs, int energy);
 
-void print_stack(ps_stack_t temp)
+void (*trace_func[5]) (int i, int j, pstruct& ps,std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
+
+void print_stack(std::stack<pstruct> temp)
 {	
 	std::cout << "{\n";
 	while (!temp.empty())
 	{
-		ps_t ps = temp.top();
+		pstruct ps = temp.top();
 		temp.pop();
 		ps.print();
 		std::cout << '\n' ;
@@ -46,32 +50,33 @@ void print_stack(ps_stack_t temp)
 	std::cout << "}\n";
 }
 
-void process(ss_map_t& subopt_data, int energy, int len)
+void subopt_traceback1(int energy, int len)
 {
+	int MIN_ENERGY = energy;
+	int delta1 = 0;
 	int count = 0 ;
-	ps_stack_t gstack;
+
+	std::stack<pstruct> gstack;
+	std::map<std::string, int> data;
 
 	// initialize the partial structure
 	// segment stack = {[1,n]}, label = W, list_bp = {} 
-	ps_t first(0, len);
+	pstruct first(0, len);
 	first.push(segment(5, len, lW, W[len]));	
 	gstack.push(first); // initialize the partial structure stacka
 
+	std::map<std::string, int> subopt_data;
+
 	while (1)
 	{
 		if (gstack.empty()) break; // exit
-
-		ps_t ps = gstack.top();
+		pstruct ps = gstack.top();
 		gstack.pop(); 
 
 		if (ps.empty()) 
 		{
-			//std::cout << ps.str << " dG =" << ps.ae_ << std::endl;
-			if (subopt_data.find(ps.str) == subopt_data.end())
-			{
-				subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
-				count++;
-			}
+			std::cout << ps.str << " dG =" << ps.ae_ << std::endl;
+			count++;
 			continue;
 		}	
 		else
@@ -82,54 +87,67 @@ void process(ss_map_t& subopt_data, int energy, int len)
 
 			if (smt.j_ - smt.i_ >=4)
 			{
-				(*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack, energy);
+				(*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack, MIN_ENERGY, delta1);
 			}
 
-			if (gstack.size() == s1 && ps.total() <= energy)
+			if (gstack.size() == s1 && ps.total() <= MIN_ENERGY + delta1)
 			{
-				ps_t ps1(ps);
+				pstruct ps1(ps);
 				gstack.push(ps1);
 			}
 		}
 	}
+	//std::cout << "total structures (dG = " <<  MIN_ENERGY << ") = " << count << std::endl;
 }
 
-ss_map_t subopt_traceback(int len, int delta)
+
+void subopt_traceback(int len, int delta)
 {
+#ifdef _OPENMP
+	if (nThreads >= 0) omp_set_num_threads(nThreads);
+#endif
+
+#ifdef _OPENMP
+#pragma omp parallel
+#pragma omp master
+	fprintf(stdout,"Traceback -- Running with %3d OpenMP thread \n",omp_get_num_threads());
+#endif
 	trace_func[0] = traceW;
 	trace_func[1] = traceV;
 	trace_func[2] = traceVBI;
 	trace_func[3] = traceVM;
 	//trace_func[4] = traceWM;
 
-	int mfe = W[len];
+	int min_energy = W[len];
 	int level = 0; 
+	int len1 = len;
 
-	ss_map_t subopt_data;
-
-	for (level = mfe; level <= mfe + delta; level += 10)
-		process(subopt_data, level, len);			
-
-	return subopt_data;
+#ifdef _OPENMP
+#pragma omp parallel for private (level) shared(len1) schedule(guided)
+#endif
+	for (level = min_energy; level <= min_energy + delta; level += 10)
+	{
+		subopt_traceback1(level, len1);			
+	}
 }
 
-void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
+void traceV(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENERGY, int delta1)
 {
 	// Hairpin Loop
-	if (eH(i,j) + ps.total()  <= energy )
+	if (eH(i,j) + ps.total()  <= MIN_ENERGY + delta1)
 	{
 		//	std::cout << "Hairpin " << i  << ' ' << j << std::endl;
-		ps_t ps1(ps); 
+		pstruct ps1(ps); 
 		ps1.accumulate(eH(i,j));
 		ps1.update(i, j, '(', ')');
 		push_to_gstack(gstack, ps1);
 	}
 
 	// Stack
-	if (eS(i, j) + V(i+1, j-1) + ps.total() <= energy)
+	if (eS(i, j) + V(i+1, j-1) + ps.total() <= MIN_ENERGY +delta1)
 	{
 		//	std::cout << "Stack " << i  << ' ' << j << std::endl;
-		ps_t ps1(ps);
+		pstruct ps1(ps);
 		ps1.push(segment(i+1, j-1, lV, V(i+1, j-1)));
 		ps1.accumulate(eS(i,j));
 		ps1.update(i, j , '(', ')');
@@ -137,20 +155,20 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 	}
 
 	// Internal Loop
-	if (VBI[i][j] + ps.total() <= energy )
+	if (VBI[i][j] + ps.total() <= MIN_ENERGY + delta1)
 	{
 		//std::cout << "Internal " << i  << ' ' << j << std::endl;
-		ps_t ps1(ps);
+		pstruct ps1(ps);
 		ps1.push(segment(i, j, lVBI, VBI[i][j]));
 		ps1.update(i, j, '(', ')');
 		push_to_gstack(gstack, ps1);
 	}
 
 	// Multiloop
-	if ( VM[i][j] + ps.total() <= energy )
+	if ( VM[i][j] + ps.total() <= MIN_ENERGY + delta1)
 	{
 		//	std::cout << "Multi " << i  << ' ' << j << std::endl;
-		ps_t ps1(ps);
+		pstruct ps1(ps);
 		ps1.push(segment(i, j, lVM, VM[i][j]));
 		ps1.update(i, j, '(', ')');
 		push_to_gstack(gstack, ps1);
@@ -158,19 +176,26 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 
 }
 
-void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
+void traceVBI(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENERGY, int delta1)
 {
 	int p,q;
+
+#ifdef _OPENMP
+#pragma omp parallel for private (p) shared(ps) schedule(dynamic)
+#endif
 	for (p = i+1; p < MIN(j-2-TURN, i+MAXLOOP+1); ++p)
 	{
 		int minq = j-i+p-MAXLOOP-2;
 		if (minq < p+1+TURN) minq = p+1+TURN;
 
+#ifdef _OPENMP
+#pragma omp parallel for private (q) shared(j, minq, ps) schedule(dynamic)
+#endif
 		for (q = minq; q < j; q++) 
 		{
-			if (V(p, q) + eL(i, j, p, q) + ps.total() <= energy )
+			if (V(p, q) + eL(i, j, p, q) + ps.total() <= MIN_ENERGY + delta1)
 			{
-				ps_t ps1(ps);
+				pstruct ps1(ps);
 				ps1.push(segment(p, q, lV, V(p, q)));
 				ps1.accumulate(eL(i, j, p, q));
 				push_to_gstack(gstack, ps1);
@@ -179,7 +204,7 @@ void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 	}
 }
 
-void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
+void traceW(int h, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENERGY, int delta1)
 {
 	if ( (h>=j) || j == 0 || j == 1) return;
 
@@ -188,9 +213,9 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		int wim1 =  MIN(0, W[i-1]);
 
 		int wij = V(i,j) + auPenalty(i, j) + wim1;
-		if (wij + ps.total() <= energy )
+		if (wij + ps.total() <= MIN_ENERGY + delta1)
 		{
-			ps_t ps1(ps);
+			pstruct ps1(ps);
 			ps1.push(segment(i, j, lV, V(i,j)));
 			if (wim1 <= 0 && i > 1) ps1.push(segment(1, i-1, lW, W[i-1]));
 			ps1.accumulate(auPenalty(i, j));
@@ -198,9 +223,9 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}		
 
 		int wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
-		if (wijd + ps.total() <= energy )
+		if (wijd + ps.total() <= MIN_ENERGY + delta1)
 		{
-			ps_t ps3(ps);
+			pstruct ps3(ps);
 			ps3.push(segment(i, j-1, lV, V(i, j-1)));
 			if (wim1 <= 0 && i > 1)	ps3.push(segment(1, i-1, lW, W[i-1]));
 			ps3.accumulate(auPenalty(i,j-1) + Ed5(j-1,i,j)); 
@@ -208,9 +233,9 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}	
 
 		int widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
-		if (widj + ps.total() <= energy )
+		if (widj + ps.total() <= MIN_ENERGY + delta1)
 		{
-			ps_t ps4(ps);
+			pstruct ps4(ps);
 			ps4.push(segment(i+1, j, lV, V(i+1,j)));
 			if (wim1 <= 0 && i > 1) ps4.push(segment(1, i-1, lW, W[i-1]));
 			ps4.accumulate(auPenalty(i+1, j) + Ed3(j,i+1,i));
@@ -218,9 +243,9 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}
 
 		int widjd = V(i+1, j-1) + auPenalty(i+1,j-1) + Ed3(j-1, i+1, i) + Ed5(j-1, i+1, j) + wim1;
-		if (widjd + ps.total() <= energy )
+		if (widjd + ps.total() <= MIN_ENERGY + delta1)
 		{
-			ps_t ps2(ps);
+			pstruct ps2(ps);
 			ps2.push(segment(i+1, j-1, lV, V(i+1,j-1)));
 			if (wim1 <= 0 && i > 1) ps2.push(segment(1, i-1, lW, W[i-1]));
 			ps2.accumulate(auPenalty(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
@@ -228,22 +253,24 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}
 	}
 
-	if (W[j-1] + ps.total() <= energy )
+	if (W[j-1] + ps.total() <= MIN_ENERGY + delta1)
 	{
-		ps_t ps1(ps);
+		pstruct ps1(ps);
 		ps1.push(segment(1, j-1, lW, W[j-1]));
 		push_to_gstack(gstack, ps1);
 	}	
 }
 
-void traceWM(ps_t& ps, ps_map_t& filter, int energy)
+void traceWM(pstruct& ps, std::map<std::string, pstruct>& filter, int MIN_ENERGY, int delta1)
 {
-	ps_stack_t wm_stack;
+	int b = Eb(); 
+	int c = Ec(); 
+	std::stack<pstruct> wm_stack;
 	wm_stack.push(ps);
 
 	while (!wm_stack.empty())
 	{
-		ps_t pss = wm_stack.top();
+		pstruct pss = wm_stack.top();
 		wm_stack.pop();
 
 		// check if all segments in pss are Vs
@@ -258,7 +285,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 				pss.push(ss);
 				key[ss.i_-1] = '*'; key[ss.j_-1] = '*';
 			}
-			filter.insert(std::pair<std::string, ps_t>(key, pss));
+			filter.insert(std::pair<std::string, pstruct>(key, pss));
 			continue;
 		}
 
@@ -269,71 +296,71 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 
 		if (wm_seg.label_ == lV)
 		{
-			ps_t ps1(pss);
+			pstruct ps1(pss);
 			ps1.push_v(wm_seg);
 			wm_stack.push(ps1);
 			continue;
 		}
 		int h = i1; int k = j1;
 
-		int wmij = V(h,k) + auPenalty(h,k) + Eb;
-		if (pss.total() + wmij <= energy )
+		int wmij = V(h,k) + auPenalty(h,k) +  b ;
+		if (pss.total() + wmij <= MIN_ENERGY + delta1)
 		{
-			ps_t ps1(pss);
+			pstruct ps1(pss);
 			ps1.push_v(segment(h,k,lV, V(h,k)));
-			ps1.accumulate(auPenalty(h,k) + Eb);
+			ps1.accumulate(auPenalty(h,k) + b);
 			wm_stack.push(ps1);
 		}
 
-		int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+ Ec ;
-		if (pss.total() + wmijd <= energy )
+		int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) + b + c ;
+		if (pss.total() + wmijd <= MIN_ENERGY + delta1)
 		{
-			ps_t ps1(pss);
+			pstruct ps1(pss);
 			ps1.push_v(segment(h,k-1,lV, V(h,k-1)));
-			ps1.accumulate(Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+Ec);
+			ps1.accumulate(Ed5(k-1,h,k)+ auPenalty(h,k-1) +b+c);
 			wm_stack.push(ps1);
 		}
 
-		int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + Eb+Ec ;
-		if (pss.total() + wmidj <= energy )
+		int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + b+c ;
+		if (pss.total() + wmidj <= MIN_ENERGY + delta1)
 		{
-			ps_t ps1(pss);
+			pstruct ps1(pss);
 			ps1.push_v(segment(h+1, k, lV, V(h+1,k)));
-			ps1.accumulate(Ed3(k,h+1,h) + auPenalty(h+1,k) +Eb+Ec);
+			ps1.accumulate(Ed3(k,h+1,h) + auPenalty(h+1,k) +b+c);
 			wm_stack.push(ps1);
 		}
 
-		int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) +  auPenalty(h+1,k-1) +Eb+ 2*Ec ;
-		if (pss.total() + wmidjd <= energy )
+		int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) +  auPenalty(h+1,k-1) + b + 2*c ;
+		if (pss.total() + wmidjd <= MIN_ENERGY + delta1)
 		{
-			ps_t ps1(pss);
+			pstruct ps1(pss);
 			ps1.push_v(segment(h+1, k-1, lV, V(h+1,k-1)));
-			ps1.accumulate(Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec);
+			ps1.accumulate(Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) + b + 2*c);
 			wm_stack.push(ps1);
 		}
 
 
-		if (pss.total() + WM[i1][j1-1]  + Ec  <= energy )
+		if (pss.total() + WM[i1][j1-1]  + c  <= MIN_ENERGY + delta1)
 		{
-			ps_t ps1(pss);
+			pstruct ps1(pss);
 			ps1.push(segment(i1,j1-1, lWM, WM[i1][j1-1]));		
-			ps1.accumulate(Ec);
+			ps1.accumulate(c);
 			wm_stack.push(ps1);
 		}
 
-		if (pss.total() + WM[i1+1][j1] + Ec <= energy )
+		if (pss.total() + WM[i1+1][j1] + c <= MIN_ENERGY + delta1)
 		{
-			ps_t ps1(pss);
+			pstruct ps1(pss);
 			ps1.push(segment(i1+1,j1, lWM, WM[i1+1][j1]));		
-			ps1.accumulate(Ec);
+			ps1.accumulate(c);
 			wm_stack.push(ps1);
 		}
 
 		for (int h = i1+1; h <= j1-1; ++h)
 		{	
-			if (WM[i1][h] + WM[h+1][j1] + pss.total() <= energy )
+			if (WM[i1][h] + WM[h+1][j1] + pss.total() <= MIN_ENERGY + delta1)
 			{
-				ps_t ps1(pss);
+				pstruct ps1(pss);
 				ps1.push(segment(i1, h, lWM, WM[i1][h]));
 				ps1.push(segment(h+1, j1, lWM, WM[h+1][j1]));
 				wm_stack.push(ps1);
@@ -342,67 +369,73 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 	}
 }
 
-void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
+void traceVM(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENERGY, int delta1)
 {
-	std::map<std::string, ps_t> filter;
+	std::map<std::string, pstruct> filter;
 	int h;	
 
+#ifdef _OPENMP
+#pragma omp parallel for private (h) shared(i,j,filter,ps) schedule(dynamic)
+#endif
 	for (h = i+1; h <= j-1; ++h)
 	{
-		int dG;
+		int energy;
+		int a = Ea(); //multConst[0]; 
+		int b = Eb(); //multConst[2]; 
+		int c = Ec(); //multConst[1]; 
 		int d5 = Ed5(i,j,i+1);
 		int d3 = Ed3(i,j,j-1);
-		int common = auPenalty(i,j) + Ea + Eb;
+		int common = auPenalty(i,j) + a + b;
 
-		dG = common + WM[i+1][h-1] + WM[h][j-1];
-		if (dG + ps.total()  <= energy )
+		energy = common + WM[i+1][h-1] + WM[h][j-1];
+		if (energy + ps.total()  <= MIN_ENERGY + delta1)
 		{
-			ps_t ps1(ps);
+			pstruct ps1(ps);
 			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));
 			ps1.push(segment(h, j-1, lWM, WM[h][j-1]));
 			ps1.accumulate(common) ; 
-			traceWM(ps1, filter, energy);
+			traceWM(ps1, filter, MIN_ENERGY, delta1);
 		}
 
-		dG =  common + WM[i+2][h-1] + WM[h][j-1] + d5 + Ec;
-		if (dG + ps.total()  <= energy )
+		energy =  common + WM[i+2][h-1] + WM[h][j-1] + d5 + c;
+		if (energy + ps.total()  <= MIN_ENERGY + delta1)
 		{
-			ps_t ps1(ps);
+			pstruct ps1(ps);
 			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
 			ps1.push(segment(h, j-1, lWM, WM[h][j-1]));	
-			ps1.accumulate(common + d5 + Ec);
-			traceWM(ps1, filter, energy);
+			ps1.accumulate(common + d5 + c);
+			traceWM(ps1, filter, MIN_ENERGY, delta1);
 		}
 
-		dG = common + WM[i+1][h-1] + WM[h][j-2] + d3 + Ec;
-		if (dG + ps.total()  <= energy )
+		energy = common + WM[i+1][h-1] + WM[h][j-2] + d3 + c;
+		if (energy + ps.total()  <= MIN_ENERGY + delta1)
 		{
-			ps_t ps1(ps);	
+			pstruct ps1(ps);	
 			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));	
 			ps1.push(segment(h, j-2, lWM, WM[h][j-2]));	
-			ps1.accumulate(common + d3 + Ec);
-			traceWM(ps1, filter, energy);
+			ps1.accumulate(common + d3 + c);
+			traceWM(ps1, filter, MIN_ENERGY, delta1);
 		}
 
-		dG = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*Ec;
-		if (dG + ps.total()  <= energy )
+		energy = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*c;
+		if (energy + ps.total()  <= MIN_ENERGY + delta1)
 		{ 	
-			ps_t ps1(ps);	
+			pstruct ps1(ps);	
 			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
 			ps1.push(segment(h, j-2, lWM, WM[h][j-2]));	
-			ps1.accumulate(common + d3 + d5 + 2*Ec) ;
-			traceWM(ps1, filter, energy);
+			ps1.accumulate(common + d3 + d5 + 2*c) ;
+			traceWM(ps1, filter, MIN_ENERGY, delta1);
 		}
 	}
 
-	ps_map_t::iterator it ;
+	std::map<std::string, pstruct>::iterator it ;
 	for (it = filter.begin(); it != filter.end(); ++it)
 	{
 		push_to_gstack(gstack, it->second);
 	}
 }
 
-void push_to_gstack(ps_stack_t& gstack , const ps_t& v)
+void push_to_gstack( std::stack<pstruct>& gstack , const pstruct& v)
 {
 	gstack.push(v);
 }
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 5aa036f..ae02eab 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -17,39 +17,24 @@
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-/* AUTHOR: Amrita Mathuriya August 2007-January 2009.
- * This file tracebacks only one optimal secondary structure. Note that there may be more than one optimal secondary structures and the generated structure depends upon the choices taken during traceback.
- * This file contains recursive functions. structure is a global integer array to store the optimal structure generated during traceback.
- * Please note that - To understand the functions defined in this file, you first need to understand functions defined in algorithms.c file. As all those functions have a corresponding function here, for traceback the calculations done there.
- * */
-
-/* Modified by Sainath Mallidi August 2009 -  "*/
-/* Modified traceback to handle constraints */
-
-/* Modified by Prashant Gaurav <pgaurav3@gatech.edu>, 09/07/2010 */
-/* Fixed the incorrect reporting of multiloop energy */
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <math.h>
-
-
+#include <assert.h>
 #include "data.h"
-#include "utils.h"
 #include "constants.h"
 #include "energy.h"
 #include "global.h"
-#include "algorithms.h"
 #include "traceback.h"
+#include "utils.h"
 
-int total_en = 0;
 
-int checkSS(int i, int j){return 1;} //TODO remove this when we put constraints back in
+int total_en = 0;
 
 void trace(int len) {
 	int i;
-
-	for (i = 0; i < len; i++)
+	
+	for (i = 0; i < len+1; i++)
 		structure[i] = 0;
 
 	if (W[len] >= MAXENG) {
@@ -58,86 +43,93 @@ void trace(int len) {
 	}
 
 	traceW(len);
-	printf("\n\n");
-
+	
+	printf("SUM of energy of loops = %12.2f\n", total_en/100.0);
 	return;
 }
 
-void traceW(int j) {
+/* Traces W[j] */
+void traceW(int j) 
+{
 	int done, i, Wj,Wj_temp;
 	int wim1, flag, Widjd, Wijd, Widj, Wij;
 
 	flag = 1;
-	done = 0; 
+
+	done = 0; /* the done variable makes it sure that we are tracebacking the first optimal possibility */
 	Wj = INFINITY_;
 	int min_i=1;
-	
-	if (j == 0 || j == 1) return;
-
-	for (i = 1; i < j && !done; i++) {
-		wim1 = MIN ( 0, W[i-1] );
-		flag = 1;
-		if (wim1 != W[i-1]) flag = 0;
-
-		Widjd = INFINITY_;
-		Wijd = INFINITY_;
-		Widj = INFINITY_;
-
-		Wij = V[indx[i] + j] + auPen(RNA[i], RNA[j]) + wim1;
-		//if (constraints[i] <= 0 && constraints[j] <= 0)
-			Widjd = V[indx[i + 1] + j - 1] + auPen(RNA[i + 1], RNA[j - 1])
-				+ dangle[RNA[j - 1]][RNA[i + 1]][RNA[i]][1]
-				+ dangle[RNA[j - 1]][RNA[i + 1]][RNA[j]][0] + wim1;
-		//if (constraints[j] <= 0)
-			Wijd = V[indx[i] + j - 1] + auPen(RNA[i], RNA[j - 1])
-				+ dangle[RNA[j - 1]][RNA[i]][RNA[j]][0] + wim1;
-		//if (constraints[i] <= 0)
-			Widj = V[indx[i + 1] + j] + auPen(RNA[i + 1], RNA[j])
-				+ dangle[RNA[j]][RNA[i + 1]][RNA[i]][1] + wim1;
-		Wj_temp=Wj;
-
-		Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
-		if (Wj_temp>Wj) min_i=i;	
-
-		if (W[j] == Wj) {
-			if (W[j] == Wij) { /* If the optimal secondary structure contain base pair (i,j) as paired.*/
-				done = 1;
-				structure[i] = j;
-				structure[j] = i;
-				traceV(i, j);
-				if (flag || checkSS(1,i)) // Added this condition because if constraints are present, flag should be overridden
-					traceW(i - 1);
-				break;
-			} else if (W[j]){ // == Widjd && constraints[i] <= 0
-					   //&& constraints[j] <= 0) { /* If base pair (i+1,j-1) is pairing and there is a dangling base on both its sides */
-				done = 1;
-				structure[i + 1] = j - 1;
-				structure[j - 1] = i + 1;
-				traceV(i + 1, j - 1);
-				if (flag || checkSS(1,i)) traceW(i - 1);
-				break;
-			} else if (W[j]){// == Wijd && constraints[j] <= 0) { /* If base pair (i,j-1) pairs and base j is single stranded. */
-				done = 1;
-				structure[i] = j - 1;
-				structure[j - 1] = i;
-				traceV(i, j - 1);
-				if (flag || checkSS(1,i) )
-					traceW(i - 1);
-				break;
-			} else if (W[j]){// == Widj && constraints[i] <= 0) { /* If base pair (i+1,j) pairs and base i is single stranded. */
-				done = 1;
-				structure[i + 1] = j;
-				structure[j] = i + 1;
-				traceV(i + 1, j);
-				if (flag || checkSS(1,i))
-					traceW(i - 1);
-				break;
+	if (j == 0 || j == 1) {
+		/* W[j] = 0; */
+	} else {
+		for (i = 1; i < j && !done; i++) {
+			wim1 = MIN(0, W[i-1]);
+			flag = 1;
+			if (wim1 != W[i-1]) flag = 0;
+
+			Widjd = INFINITY_;
+			Wijd = INFINITY_;
+			Widj = INFINITY_;
+			Wij = V(i,j) + auPenalty(i, j) + wim1;
+			Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1;
+			Wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
+			Widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
+			Wj_temp=Wj;
+
+			Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
+			if (Wj_temp>Wj) min_i=i;	
+
+			if (W[j] == Wj) {
+				if (W[j] == Wij) { /* If the optimal secondary structure contain base pair (i,j) as paired.*/
+					done = 1;
+					structure[i] = j;
+					structure[j] = i;
+					//printf("AU Penalty: %12.2f\n",auPen(RNA[i], RNA[j])/100.00);
+					traceV(i, j);
+
+					if (flag ) 
+						traceW(i - 1);
+					break;
+				} else if (W[j] == Widjd) { /* If base pair (i+1,j-1) is pairing and there is a dangling base on both its sides */
+					done = 1;
+					structure[i + 1] = j - 1;
+					structure[j - 1] = i + 1;
+					//printf("AU Penalty: %12.2f\nEnergy of dangling base on both the sides: %12.2f  %12.2f\n",
+					//auPen(RNA[i + 1], RNA[j - 1])/100.00, dangle[RNA[j - 1]][RNA[i + 1]][RNA[i]][1]/100.00, dangle[RNA[j - 1]][RNA[i + 1]][RNA[j]][0]/100.00);
+					traceV(i + 1, j - 1);
+
+					if (flag)// || checkSS(1,i))
+						traceW(i - 1);
+					break;
+				} else if (W[j] == Wijd) { /* If base pair (i,j-1) pairs and base j is single stranded. */
+					done = 1;
+					structure[i] = j - 1;
+					structure[j - 1] = i;
+					//	printf("AU Penalty: %12.2f \nEnergy of dangling base: %12.2f \n",
+					//	auPen(RNA[i], RNA[j - 1])/100.00,dangle[RNA[j - 1]][RNA[i]][RNA[j]][0]/100.00);
+					traceV(i, j - 1);
+
+					if (flag) // || checkSS(1,i) )
+						traceW(i - 1);
+					break;
+				} else if (W[j] == Widj) { /* If base pair (i+1,j) pairs and base i is single stranded. */
+					done = 1;
+					structure[i + 1] = j;
+					structure[j] = i + 1;
+					//	printf("AU Penalty: %12.2f\nEnergy of dangling base:  %12.2f\n",
+					//	auPen(RNA[i + 1], RNA[j])/100.00, dangle[RNA[j]][RNA[i + 1]][RNA[i]][1]/100.00);
+					traceV(i + 1, j);
+					if (flag) // || checkSS(1,i))
+						traceW(i - 1);
+					break;
+				}
 			}
 		}
-	}
+		
+		if (W[j] == W[j - 1] && !done) 
+			traceW(j-1);
 
-	if (W[j] == W[j - 1] && !done) /* If jth base is single stranded and also does not have dangling energy contribution */
-		traceW(j - 1);
+	}
 
 	return;
 }
@@ -145,42 +137,38 @@ void traceW(int j) {
 
 /* Trace the structure inside V[i][j]. This function traces "which type of loop (i,j) base pair is closing" */
 int traceV(int i, int j) {
+
 	int a, b, c, d, Vij;
 
 	a = eH(i, j);
 	b = eS(i, j) + V[indx[i + 1] + j - 1];
-	if (eS(i, j) == 0)
-		b = INFINITY_;
+	if (eS(i, j) == 0) b = INFINITY_;
 	c = VBI[i][j];
 	d = VM[i][j];
+	
 	Vij = MIN(MIN(a, b), MIN(c, d));
-
+	
 	if (Vij == a && Vij != b && Vij != c && Vij != d) { /* If () a hairpin loop */
-		if (VERBOSE) printf("i %5d j %5d Hairpin  Loop %12.2f\n", i, j, eH(i, j)/100.00);
+		//printf("i %5d j %5d Hairpin  Loop %12.2f\n", i, j, eH(i, j)/100.00);
 		total_en += eH(i,j);
 		return Vij;
-	} else if (Vij == b ) { /* If it forms a stack */
-		if (VERBOSE) printf("i %5d j %5d Stack 	 Loop %12.2f\n", i, j, eS(i, j)/100.00);
+	} else if (Vij == b /*&& Vij != a && Vij != c && Vij != d*/) { /* If it forms a stack */
+		//printf("i %5d j %5d Stack 	 Loop %12.2f\n", i, j, eS(i, j)/100.00);
 		total_en += eS(i,j);
 		structure[i + 1] = j - 1;
 		structure[j - 1] = i + 1;
 		traceV(i + 1, j - 1);
 		return Vij;
-	} else if (Vij == c) { /* If it forms an internal loop */
-		if (VERBOSE) printf("i %5d j %5d Internal Loop", i, j);
+	} else if (Vij == c /*&& Vij != a && Vij != b && Vij != d*/) { /* If it forms an internal loop */
+		//printf("i %5d j %5d Internal Loop", i, j);
 		traceVBI(i, j);
 		return Vij;
 	} else if (Vij == d && Vij != a && Vij != b && Vij != c) { /* If it forms a multiloop */
 		int eVM = traceVM(i, j);
-		if (VERBOSE) printf("i %5d j %5d Multi    Loop %12.2f\n", i, j, (Vij-eVM)/100.0);
+		//printf("i %5d j %5d Multi    Loop %12.2f\n", i, j, (Vij-eVM)/100.0);
 		total_en += (Vij-eVM);
 		return Vij;
-	} else { /* It should not be executed */
-		if (Vij == c && Vij == d)
-			//printf("Internal Loop and Multiloops are possible\n");
-			//printf("i %5d j %5d  More than one structure is possible\n", i, j);
-		return 0;
-	}
+	} 
 	return 0;
 }
 
@@ -196,8 +184,6 @@ int traceVBI(int i, int j) {
 
 	for (ip = i + 1; ip < j - 1; ip++) {
 		for (jp = ip + 1; jp < j; jp++) { /* Search which internal loop (ip,jp) is closing */
-			if (checkSS(i, ip) || checkSS(jp, j))
-				continue;
 			el = eL(i, j, ip, jp);
 			v = V[indx[ip] + jp];
 			VBIij_temp = el + v;
@@ -213,7 +199,7 @@ int traceVBI(int i, int j) {
 
 	structure[ifinal] = jfinal;
 	structure[jfinal] = ifinal;
-	if (VERBOSE) printf(" %12.2f\n", eL(i, j, ifinal, jfinal)/100.00);
+	//printf(" %12.2f\n", eL(i, j, ifinal, jfinal)/100.00);
 	total_en += eL(i, j, ifinal, jfinal);
 
 	int eVI = traceV(ifinal, jfinal);
@@ -233,11 +219,12 @@ int traceVM(int i, int j) {
 	a = eparam[5];
 	b = eparam[10]; /* efn2b */
 
-	/*  WM (i+1, j-1) */
+	int VMij = VM[i][j];
+
 	for (h = i + 2; h <= j - 1 && !done; h++) {
 		A_temp = WM[i + 1][h - 1] + WM[h][j - 1] + a + b + auPen(RNA[i],
 				RNA[j]);
-		if (A_temp == VM[i][j]) { /* No dangling bases on any of the sides of base pair (i,j) in the multiloop */
+		if (A_temp == VMij) { /* No dangling bases on any of the sides of base pair (i,j) in the multiloop */
 			done = 1;
 			eVM += traceWM(i + 1, h - 1);
 			eVM += traceWM(h, j - 1);
@@ -245,48 +232,35 @@ int traceVM(int i, int j) {
 		}
 	}
 
-	/* WM[i+2, j-1] */
-//	if (constraints[i + 1] <= 0) {
-		for (h = i + 3; h <= j - 1 && !done; h++) {
-			A_temp = WM[i + 2][h - 1] + WM[h][j - 1] + a + b + auPen(RNA[i],
-					RNA[j]) + dangle[RNA[i]][RNA[j]][RNA[i + 1]][0]; /* IF base i+1 is dangling on the 5' end of the base pair (i,j) */
-			if (A_temp == VM[i][j]) {
-				done = 1;
-				eVM += traceWM(i + 2, h - 1);
-				eVM += traceWM(h, j - 1);
-				break;
-			}
+	for (h = i + 3; h <= j - 1 && !done; h++) {
+		A_temp = WM[i + 2][h - 1] + WM[h][j - 1] + a + b + auPenalty(i,j) + Ed5(i,j,i + 1); 
+		if (A_temp == VMij) {
+			done = 1;
+			eVM += traceWM(i + 2, h - 1);
+			eVM += traceWM(h, j - 1);
+			break;
 		}
-//	}
-
-	/* WM[i+1][j-2] */
-//	if (constraints[j - 1] <= 0) {
-		for (h = i + 2; h <= j - 2 && !done; h++) { /* If base j-1 is dangling on 3' end of the base pair (i,j) */
-			A_temp = WM[i + 1][h - 1] + WM[h][j - 2] + a + b + auPen(RNA[i],
-					RNA[j]) + dangle[RNA[i]][RNA[j]][RNA[j - 1]][1];
-			if (A_temp == VM[i][j]) {
-				done = 1;
-				eVM += traceWM(i + 1, h - 1);
-				eVM += traceWM(h, j - 2);
-				break;
-			}
+	}
+
+	for (h = i + 2; h <= j - 2 && !done; h++) { /* If base j-1 is dangling on 3' end of the base pair (i,j) */
+		A_temp = WM[i + 1][h - 1] + WM[h][j - 2] + a + b + auPenalty(i, j) + Ed3(i,j,j - 1);
+		if (A_temp == VMij) {
+			done = 1;
+			eVM += traceWM(i + 1, h - 1);
+			eVM += traceWM(h, j - 2);
+			break;
 		}
-//	}
-
-	/* WM[i+2][j-2] */
-//	if (constraints[i + 1] <= 0 && constraints[j - 1] <= 0) {
-		for (h = i + 3; h <= j - 2 && !done; h++) { /* If base pair (i,j) has dangling bases on both sides. */
-			A_temp = WM[i + 2][h - 1] + WM[h][j - 2] + a + b + auPen(RNA[i],
-					RNA[j]) + dangle[RNA[i]][RNA[j]][RNA[i + 1]][0]
-					                                             + dangle[RNA[i]][RNA[j]][RNA[j - 1]][1];
-			if (A_temp == VM[i][j]) {
-				done = 1;
-				eVM += traceWM(i + 2, h - 1);
-				eVM += traceWM(h, j - 2);
-				break;
-			}
+	}
+
+	for (h = i + 3; h <= j - 2 && !done; h++) { /* If base pair (i,j) has dangling bases on both sides. */
+		A_temp = WM[i + 2][h - 1] + WM[h][j - 2] + a + b + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
+		if (A_temp == VMij) {
+			done = 1;
+			eVM += traceWM(i + 2, h - 1);
+			eVM += traceWM(h, j - 2);
+			break;
 		}
-//	}
+	}
 
 	return eVM;
 }
@@ -295,23 +269,18 @@ int traceVM(int i, int j) {
 int traceWM(int i, int j) {
 
 	int done;
-	int a, b, c;
 	int h1, h;
 	int eWM = 0; 
 
 	done = 0;
-
-	b = eparam[10]; /* efn2b */
-	c = eparam[6]; /* efn2c */
-
 	h1 = 0;
 
 	if (i >= j)
 		return 0;
 	else {
 		for (h = i; h < j && !done; h++) {
-			a = WM[i][h] + WM[h + 1][j]; /* If WM(i,j) came from the summation of two WM terms */
-			if (a == WM[i][j]) {
+			int aa = WM[i][h] + WM[h + 1][j]; /* If WM(i,j) came from the summation of two WM terms */
+			if (aa == WM[i][j]) {
 				done = 1;
 				h1 = h;
 				break;
@@ -321,37 +290,30 @@ int traceWM(int i, int j) {
 			eWM += traceWM(i, h);
 			eWM += traceWM(h + 1, j);
 		} else {
-			if (WM[i][j] == V[indx[i] + j] + auPen(RNA[i], RNA[j]) + b) { /* If base pair (i,j) pairs*/
+			if (WM[i][j] == V(i,j) + auPenalty(i, j) + Eb()) { /* If base pair (i,j) pairs*/
 				done = 1;
 				structure[i] = j;
 				structure[j] = i;
 				eWM += traceV(i, j);
-			} else if (WM[i][j] == V[indx[i + 1] + j] + dangle[RNA[j]][RNA[i + 1]][RNA[i]][1] + auPen(RNA[i + 1], RNA[j]) + b + c){
-			                                                               //&& constraints[i] <= 0) { /* If base pair (i+1, j) forms and base i remain as a dangling base*/
+			} else if (WM[i][j] == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb() + Ec()) { 
 				done = 1;
 				eWM += traceV(i + 1, j);
 				structure[i + 1] = j;
 				structure[j] = i + 1;
-			} else if (WM[i][j] == V[indx[i] + j - 1]
-			                         + dangle[RNA[j - 1]][RNA[i]][RNA[j]][0] + auPen(RNA[i],
-			                        		 RNA[j - 1]) + b + c){ //&& constraints[j] <= 0) { /* If base pair (i,j-1) forms and base j remain as a dangling base */
+			} else if (WM[i][j] == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb() + Ec() ) { 
 				done = 1;
 				eWM += traceV(i, j - 1);
 				structure[i] = j - 1;
 				structure[j - 1] = i;
-			} else if (WM[i][j] == V[indx[i + 1] + j - 1]
-			                         + dangle[RNA[j - 1]][RNA[i + 1]][RNA[i]][1] + 
-									 dangle[RNA[j- 1]][RNA[i + 1]][RNA[j]][0] + auPen(RNA[i + 1], RNA[j - 1]) + b + 2* c)
-			                         {//&& constraints[i] <= 0 && constraints[j] <= 0) { 
-									/* IF base pair (i+1,j-1) forms and base i and base j remain as dangling bases on each side.*/
+			} else if (WM[i][j] == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb() + 2*Ec()) { 
 				done = 1;
 				eWM += traceV(i + 1, j - 1);
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
-			} else if (WM[i][j] == WM[i + 1][j] + c){ //&& constraints[i] <= 0) { /* If base i does not make energy contribution */
+			} else if (WM[i][j] == WM[i + 1][j] + Ec() ) { 
 				done = 1;
 				eWM += traceWM(i + 1, j);
-			} else if (WM[i][j] == WM[i][j - 1] + c){ //&& constraints[j] <= 0) { /* If base j does not make energy contribution */
+			} else if (WM[i][j] == WM[i][j - 1] + Ec() ) { 
 				done = 1;
 				eWM += traceWM(i, j - 1);
 			}
@@ -359,4 +321,3 @@ int traceWM(int i, int j) {
 	}
 	return eWM;
 }
-

From da93e6d626579c7a8089f875664320b1c8b94249 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 16 Mar 2011 14:10:45 -0400
Subject: [PATCH 045/282] Fill up matrix from bottom up

Removes parallelization (to be fixed)
Also reading from FASTA files is broken
---
 gtfold-mfe/include/energy.h        |  35 ++++--
 gtfold-mfe/src/Makefile.am         |   6 +-
 gtfold-mfe/src/algorithms.c        | 149 +++++++++++++++++---------
 gtfold-mfe/src/energy.c            | 165 ++++++++++++++++++++++-------
 gtfold-mfe/src/main.cc             |   2 +-
 gtfold-mfe/src/subopt_traceback.cc |  57 +++++-----
 gtfold-mfe/src/traceback.c         |  36 +++----
 7 files changed, 305 insertions(+), 145 deletions(-)

diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h
index c7a3d80..2498e28 100644
--- a/gtfold-mfe/include/energy.h
+++ b/gtfold-mfe/include/energy.h
@@ -1,19 +1,40 @@
 #ifndef _ENERGY_TABLES_H_
 #define _ENERGY_TABLES_H_
 
+#include "data.h"
+
 extern int *V; 
+extern int *VV; 
+extern int *VV1; 
 extern int *W; 
-extern int **VBI; 
-extern int **VM; 
-extern int **WM; 
+extern int *VBI; 
+extern int *VM; 
+extern int *WM; 
+extern int *WMi; 
+extern int *WMi1; 
+extern int *WMi2; 
+//extern int **VBI; 
+//extern int **WM; 
+//extern int **V; 
+//extern int **VM; 
 extern int *indx; 
 
 
-#define V(i,j) V[indx[i]+j]
+#define V(i,j) V[indx[j]+i]
+#define VM(i,j) VM[indx[j]+i]
+#define WM(i,j) WM[indx[j]+i]
+#define VBI(i,j) VBI[indx[j]+i]
+
+//#define V(i,j) V[indx[i]+j]
 //#define VM(i,j) VM[indx[i]+j]
 //#define WM(i,j) WM[indx[i]+j]
 //#define VBI(i,j) VBI[indx[i]+j]
 
+//#define V(i,j) V[i][j]
+//#define VM(i,j) VM[i][j]
+//#define WM(i,j) WM[i][j]
+//#define VBI(i,j) VBI[i][j]
+
 
 #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0)
 
@@ -24,9 +45,9 @@ int Ed3(int i, int j, int k);
 int Ed5(int i, int j, int k);
 int auPenalty(int i, int j);
 
-int Ec();
-int Eb();
-int Ea(); 
+#define Ec multConst[1]
+#define Eb multConst[2]
+#define Ea multConst[0] 
 
 int eS(int i, int j);
 int eH(int i, int j);
diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am
index ec34ba5..08d2bb0 100644
--- a/gtfold-mfe/src/Makefile.am
+++ b/gtfold-mfe/src/Makefile.am
@@ -12,9 +12,9 @@ gtfold_SOURCES = \
 	options.cc\
 	global.c\
 	energy.c\
-	algorithms.c
-# traceback.c \
-#	subopt_traceback.cc
+	algorithms.c \
+	traceback.c \
+	subopt_traceback.cc
 
 
 gtfold_LDFLAGS = 
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index c07d6d9..84d4566 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -19,6 +19,8 @@
 
 #include <stdio.h>
 #include <math.h>
+#include <time.h>
+#include <sys/time.h>
 #include <stdlib.h>
 #include <assert.h>
 
@@ -32,38 +34,54 @@
 #include "omp.h"
 #endif
 
+double get_seconds() {
+	struct timeval tv;
+	gettimeofday(&tv, NULL);
+	return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0;
+}
 
 int calculate(int len) { 
 	int b, i, j;
+	double t1, t2, tint=0, thair=0,tst=0, tml=0, twm=0;
 
 #if 1
 #ifdef _OPENMP
 #pragma omp parallel
 #pragma omp master
-	{
 		fprintf(stdout,"\n");
 		fprintf(stdout,"Running with %3d OpenMP thread",omp_get_num_threads());
 		if (omp_get_num_threads()>1) fprintf(stdout,"s");
 		fprintf(stdout,".\n");
-	}
 #endif
 #endif
-
-	for (b = TURN+1; b <= len-1; b++) {
+	//for (b = TURN+1; b <= len-1; b++) {
+	for (i = len-TURN-1; i >= 1; i--) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
 #endif
-		for (i = 1; i <= len - b; i++) {
-			j = i + b;
-
-			/* Check if bases i and j pair up or not */
+		//	for (i = 1; i <= len - b; i++) {
+		for (j = i+TURN+1; j <= len; j++) {
+			//j = i + b;
 			if (allowedPairs(RNA[i], RNA[j])) { 
 				int p, q, h;
 				int newV = INFINITY_;
 				int VBIij = INFINITY_;
 
+				t1 = get_seconds();
 				newV  = MIN(eH(i, j), newV);
+				t2 = get_seconds();
+				thair += (t2-t1); 
 
+				t1 = get_seconds();
+				int stackEnergy = eS(i, j); 
+				//newV= MIN(stackEnergy + V(i+1,j-1), newV);
+				newV= MIN(stackEnergy + VV1[j-1] , newV);
+				t2 = get_seconds();
+				tst += (t2-t1); 
+
+				if (j-i > 6) { 
+				t1 = get_seconds();
+				// Int Loop BEGIN
 				for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
 					int minq = j-i+p-MAXLOOP-2;
 					if (minq < p+1+TURN) minq = p+1+TURN;
@@ -73,63 +91,96 @@ int calculate(int len) {
 					}
 				}
 
+				VBI(i,j) = VBIij;
+				// Int Loop END
+				t2 = get_seconds();
+				tint += (t2-t1); 
 				newV = MIN(newV, VBIij);
-				VBI[i][j] = VBIij;
-
-				int VMij, VMijd, VMidj, VMidjd;
-				VMij = VMijd = VMidj = VMidjd = INFINITY_;
-
-				for (h = i+TURN+1; h <= j-1-TURN; h++) { 
-					VMij = MIN(VMij, WM[i+1][h-1] + WM[h][j-1]);		
-					VMidj = MIN(VMidj, WM[i+2][h-1] + WM[h][j-1]);	
-					VMijd = MIN(VMijd, WM[i+1][h-1] + WM[h][j-2]);	
-					VMidjd = MIN(VMidjd, WM[i+2][h-1] + WM[h][j-2]);	
 				}
+				if (j-i > 10) {	
+					t1 = get_seconds();
+
+					// Multi Loop BEGIN
+					int VMij, VMijd, VMidj, VMidjd;
+					VMij = VMijd = VMidj = VMidjd = INFINITY_;
+
+					for (h = i+TURN+1; h <= j-1-TURN; h++) { 
+						//VMij = MIN(VMij, WM(i+1,h-1) + WM(h,j-1));		
+						VMij = MIN(VMij, WMi1[h-1] + WM(h,j-1));		
+						//VMidj = MIN(VMidj, WM(i+2,h-1) + WM(h,j-1));	
+						VMidj = MIN(VMidj, WMi2[h-1] + WM(h,j-1));	
+						//VMijd = MIN(VMijd, WM(i+1,h-1) + WM(h,j-2));	
+						VMijd = MIN(VMijd, WMi1[h-1] + WM(h,j-2));	
+						//VMidjd = MIN(VMidjd, WM(i+2,h-1) + WM(h,j-2));	
+						VMidjd = MIN(VMidjd, WMi2[h-1] + WM(h,j-2));	
+					}
 
-				int d3 = Ed3(i,j,j-1);
-				int d5 = Ed5(i,j,i+1);
-				VMij = MIN(VMij, VMidj + d5 +Ec());
-				VMij = MIN(VMij, VMijd + d3 +Ec());
-				VMij = MIN(VMij, VMidjd + d5 +  d3+ 2*Ec());
-				VMij = VMij + Ea() + Eb() + auPenalty(i,j);
+					int d3 = Ed3(i,j,j-1);
+					int d5 = Ed5(i,j,i+1);
 
-				VM[i][j] = VMij;
+					VMij = MIN(VMij, VMidj + d5 +Ec);
+					VMij = MIN(VMij, VMijd + d3 +Ec);
+					VMij = MIN(VMij, VMidjd + d5 +  d3+ 2*Ec);
+					VMij = VMij + Ea + Eb + auPenalty(i,j);
 
-				newV = MIN(newV, VM[i][j]);
-
-				int stackEnergy = eS(i, j); 
-				newV= MIN(stackEnergy + V(i+1,j-1), newV);
+					VM(i,j) = VMij;
+					newV = MIN(newV, VM(i,j));
+					// Multi Loop END
 
+					t2 = get_seconds();
+					tml += (t2-t1);
+				}
 				V(i,j) = newV;
-			}
-			else {
-				V(i,j) = INFINITY_;
-			}	
-
-			int h;
-			int newWM = INFINITY_;
-
-			newWM = MIN(V(i,j) + auPenalty(i,j) + Eb(), newWM);
-			newWM = MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb() + Ec(), newWM);
-			newWM = MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb() + Ec(), newWM);
-			newWM = MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb() + 2*Ec(), newWM) ;
-			newWM = MIN(WM[i+1][j] + Ec(), newWM);
-			newWM = MIN(WM[i][j-1] + Ec(), newWM);
-			
-			for (h = i ; h <= j-TURN-1; h++) {
-				newWM = MIN(newWM, WM[i][h] + WM[h+1][j]);
+
+				VV[j] = newV;
 			}
 
-			WM[i][j] = newWM;
+			if (j-i > 4) {	
+				t1 = get_seconds();
+				// WM BEGIN
+				int h, newWM = INFINITY_;
+				//newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM);
+				newWM = MIN(VV[j] + auPenalty(i,j) + Eb, newWM);
+				//newWM = MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM);
+				newWM = MIN(VV1[j] + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM);
+				//newWM = MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM);
+				newWM = MIN(VV[j-1] + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM);
+				//newWM = MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM) ;
+				newWM = MIN(VV1[j-1] + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM) ;
+
+				//newWM = MIN(WM(i+1,j) + Ec, newWM);
+				newWM = MIN(WMi1[j] + Ec, newWM);
+				//newWM = MIN(WM(i,j-1) + Ec, newWM);
+				newWM = MIN(WMi[j-1] + Ec, newWM);
+
+				for (h = i ; h <= j-TURN-1; h++) {
+					//newWM = MIN(newWM, WM(i,h) + WM(h+1,j));
+					newWM = MIN(newWM, WMi[h] + WM(h+1,j));
+				}
+				WM(i,j) = WMi[j]=newWM;
+				// WM END
+
+				t2 = get_seconds();
+				twm += (t2-t1);
+			}
 		}
+		int *FF;
+		FF = VV1; VV1=VV; VV=FF;
+		FF = WMi2; WMi2 = WMi1; WMi1 = WMi; WMi = FF;
+		for (j=1; j<=len; j++) {VV[j]=INFINITY_;WMi[j]=INFINITY_; }
 	}
 
+	printf("Total IntLoop time = %fs \n",tint);
+	printf("Total Stack time = %fs \n",tst);
+	printf("Total HairPin time = %fs \n",thair);
+	printf("Total MultiLoop time = %fs \n",tml);
+	printf("Total WM time = %fs \n",twm);
+
 	for (j = TURN+2; j <= len; j++)	{
 		int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
 		Wj = INFINITY_;
 
-		for (i = 1; i < j-TURN; i++) 
-		{
+		for (i = 1; i < j-TURN; i++) {
 			Wij = Widjd = Wijd = Widj = INFINITY_;
 			Wim1 = MIN(0, W[i-1]); 
 			Wij = V(i, j) + auPenalty(i, j) + Wim1;
diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 17f3617..16f1773 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -6,13 +6,21 @@
 #include "utils.h"
 #include "global.h"
 #include "constants.h"
-#include "data.h"
 
 int *V; 
+int *VV; 
+int *VV1; 
 int *W; 
-int **VBI; 
-int **VM; 
-int **WM; 
+int *VBI; 
+int *VM; 
+int *WM; 
+int *WMi; 
+int *WMi1; 
+int *WMi2; 
+//int **V; 
+//int **WM; 
+//int **VM; 
+//int **VBI; 
 int *indx; 
 
 void create_tables(int len)
@@ -26,6 +34,77 @@ void create_tables(int len)
 		exit(-1);
 	}
 
+	VV1 = (int *) malloc((len+ 1)*sizeof(int));
+	if (VV1 == NULL) 
+	{
+		perror("Cannot allocate variable 'V'");
+		exit(-1);
+	}
+	VV = (int *) malloc((len+ 1)*sizeof(int));
+	if (VV == NULL) 
+	{
+		perror("Cannot allocate variable 'V'");
+		exit(-1);
+	}
+
+	WMi = (int *) malloc((len+ 1)*sizeof(int));
+	if (WMi == NULL) 
+	{
+		perror("Cannot allocate variable 'V'");
+		exit(-1);
+	}
+
+	WMi1 = (int *) malloc((len+ 1)*sizeof(int));
+	if (WMi1 == NULL) 
+	{
+		perror("Cannot allocate variable 'V'");
+		exit(-1);
+	}
+
+	WMi2 = (int *) malloc((len+ 1)*sizeof(int));
+	if (WMi2 == NULL) 
+	{
+		perror("Cannot allocate variable 'V'");
+		exit(-1);
+	}
+
+	WM = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
+	if (WM == NULL) 
+	{
+		perror("Cannot allocate variable 'V'");
+		exit(-1);
+	}
+
+	VM = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
+	if (VM == NULL) 
+	{
+		perror("Cannot allocate variable 'V'");
+		exit(-1);
+	}
+
+	VBI = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
+	if (VBI == NULL) 
+	{
+		perror("Cannot allocate variable 'V'");
+		exit(-1);
+	}
+
+	/*
+	V = (int **) malloc((len+1)* sizeof(int *));
+	if (V == NULL) 
+	{
+		perror("Cannot allocate variable 'VM'");
+		exit(-1);
+	}
+	for (i = 0; i < len+1; i++) {
+		V[i] = (int *) malloc((len+1)*sizeof(int));
+		if (V[i] == NULL) {
+			perror("Cannot allocate variable 'VM[i]'");
+			exit(-1);
+		}
+	}
+	*/
+
 	W = (int *) malloc((len+1) * sizeof(int));
 	if (W == NULL) 
 	{
@@ -33,6 +112,7 @@ void create_tables(int len)
 		exit(-1);
 	}
 
+	/*
 	VBI = (int **) malloc((len+1) * sizeof(int *));
 	if (VBI == NULL) 
 	{
@@ -48,8 +128,7 @@ void create_tables(int len)
 			exit(-1);
 		}
 	}
-    
-	
+
 	VM = (int **) malloc((len+1)* sizeof(int *));
 	if (VM == NULL) 
 	{
@@ -63,8 +142,7 @@ void create_tables(int len)
 			exit(-1);
 		}
 	}
-    
-	
+
 	WM = (int **) malloc((len+1)*sizeof(int *));
 	if (WM == NULL) 
 	{
@@ -79,9 +157,9 @@ void create_tables(int len)
 			exit(-1);
 		}
 	}
+	*/
     
-	
-	indx = (int *) malloc((len+1) * sizeof(int));
+	indx = (int*) malloc((len+1) * sizeof(int));
 	if (indx == NULL) {
 		perror("Cannot allocate variable 'indx'");
 		exit(-1);
@@ -95,30 +173,38 @@ void init_tables(int len)
 {
 	int i, j, LLL;
 	
-	for (i = 0; i <= len; i++) 
-	{
+	for (i = 0; i <= len; i++) {
 		W[i] = INFINITY_; 
-
-		for (j = 0; j <= len; j++) 
-		{
-			VBI[i][j] = INFINITY_;
-			VM[i][j] = INFINITY_;
-			WM[i][j] = INFINITY_;
-		}
+		VV[i] = INFINITY_;
+		VV1[i] = INFINITY_;
+		WMi[i] = INFINITY_;
+		WMi1[i] = INFINITY_;
+		WMi2[i] = INFINITY_;
+		//for (j = 0; j <= len; j++) {
+			//V[i][j] = INFINITY_;
+			//VBI[i][j] = INFINITY_;
+			//VM[i][j] = INFINITY_;
+			//WM[i][j] = INFINITY_;
+		//}
 	}
 	
-
+	
 	LLL = (len)*(len+1)/2 + 1;
 
-	for (i = 0; i < LLL; i++)
-	{
+	for (i = 0; i < LLL; i++) {
 		V[i] = INFINITY_;
+		WM[i] = INFINITY_;
+		VM[i] = INFINITY_;
+		VBI[i] = INFINITY_;
 	}
 
-	for (i = 0; i <= len; i++)
-	{
+	/*
+	for (i = 0; i <= len; i++) {
 		indx[i] = (len)*(i-1)-(i*(i-1))/2;
-	}
+	}*/
+
+	for (i = 1; i <= (unsigned) len; i++) 
+	    indx[i] = (i*(i-1)) >> 1;        /* n(n-1)/2 */
 
 	return;
 }
@@ -128,30 +214,34 @@ void free_tables(int len)
 	int i;
 
 	free(indx);
-	for (i = 0; i < len; i++)
-		free(WM[i]);
+	//for (i = 0; i < len; i++)
+	//	free(WM[i]);
 	
 	free(WM);
 	
-	for (i = 0; i < len; i++)
-		free(VM[i]);
-	
+	//for (i = 0; i < len; i++)
+	//	free(VM[i]);
 	free(VM);
-	for (i = 0; i < len; i++)
-		free(VBI[i]);
+	
+
+	//for (i = 0; i < len; i++)
+	//	free(V[i]);
+	free(V);
+	free(VV);
+	free(VV1);
+
+
+	//for (i = 0; i < len; i++)
+	//	free(VBI[i]);
 	
 	free(VBI);
 	free(W);
-	free(V);
 }
 
 
 inline int Ed3(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][1];}
 inline int Ed5(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][0]; }
 inline int auPenalty(int i, int j) { return auPen(RNA[i], RNA[j]);}
-inline int Ec() { return multConst[1];}
-inline int Eb()  { return multConst[2];}
-inline int Ea()  { return multConst[0]; }
 
 inline int eL(int i, int j, int ip, int jp) 
 {
@@ -352,8 +442,7 @@ inline int eS(int i, int j)
 {
 	int energy;
 	/*  not sure about eparam[1], come from MFold.. = 0 */
-	energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])]
-		+ eparam[1];
+	energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i+1], RNA[j-1])] + eparam[1];
 
 	return energy;
 }
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 9ab84d0..22edef9 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -155,7 +155,7 @@ int main(int argc, char** argv) {
 		exit(-1);
 	}
 	fprintf(stdout, "Sequence length: %5d\n", seq.length());
-	//fprintf(stdout, "Sequence : %s\n", seq.c_str());
+	fprintf(stdout, "Sequence : %s\n", seq.c_str());
 	
 	init_fold(seq.length());
 	
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index 1b5d0e8..e11bd40 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -34,7 +34,6 @@ extern int nThreads;
 
 const char* lstr[] = {"W", "V", "VBI", "VM", "WM"};
 
-
 void (*trace_func[5]) (int i, int j, pstruct& ps,std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
 
 void print_stack(std::stack<pstruct> temp)
@@ -155,21 +154,21 @@ void traceV(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENER
 	}
 
 	// Internal Loop
-	if (VBI[i][j] + ps.total() <= MIN_ENERGY + delta1)
+	if (VBI(i,j) + ps.total() <= MIN_ENERGY + delta1)
 	{
 		//std::cout << "Internal " << i  << ' ' << j << std::endl;
 		pstruct ps1(ps);
-		ps1.push(segment(i, j, lVBI, VBI[i][j]));
+		ps1.push(segment(i, j, lVBI, VBI(i,j)));
 		ps1.update(i, j, '(', ')');
 		push_to_gstack(gstack, ps1);
 	}
 
 	// Multiloop
-	if ( VM[i][j] + ps.total() <= MIN_ENERGY + delta1)
+	if ( VM(i,j) + ps.total() <= MIN_ENERGY + delta1)
 	{
 		//	std::cout << "Multi " << i  << ' ' << j << std::endl;
 		pstruct ps1(ps);
-		ps1.push(segment(i, j, lVM, VM[i][j]));
+		ps1.push(segment(i, j, lVM, VM(i,j)));
 		ps1.update(i, j, '(', ')');
 		push_to_gstack(gstack, ps1);
 	}
@@ -263,8 +262,8 @@ void traceW(int h, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENER
 
 void traceWM(pstruct& ps, std::map<std::string, pstruct>& filter, int MIN_ENERGY, int delta1)
 {
-	int b = Eb(); 
-	int c = Ec(); 
+	int b = Eb; 
+	int c = Ec; 
 	std::stack<pstruct> wm_stack;
 	wm_stack.push(ps);
 
@@ -340,29 +339,29 @@ void traceWM(pstruct& ps, std::map<std::string, pstruct>& filter, int MIN_ENERGY
 		}
 
 
-		if (pss.total() + WM[i1][j1-1]  + c  <= MIN_ENERGY + delta1)
+		if (pss.total() + WM(i1,j1-1)  + c  <= MIN_ENERGY + delta1)
 		{
 			pstruct ps1(pss);
-			ps1.push(segment(i1,j1-1, lWM, WM[i1][j1-1]));		
+			ps1.push(segment(i1,j1-1, lWM, WM(i1,j1-1)));		
 			ps1.accumulate(c);
 			wm_stack.push(ps1);
 		}
 
-		if (pss.total() + WM[i1+1][j1] + c <= MIN_ENERGY + delta1)
+		if (pss.total() + WM(i1+1,j1) + c <= MIN_ENERGY + delta1)
 		{
 			pstruct ps1(pss);
-			ps1.push(segment(i1+1,j1, lWM, WM[i1+1][j1]));		
+			ps1.push(segment(i1+1,j1, lWM, WM(i1+1,j1)));		
 			ps1.accumulate(c);
 			wm_stack.push(ps1);
 		}
 
 		for (int h = i1+1; h <= j1-1; ++h)
 		{	
-			if (WM[i1][h] + WM[h+1][j1] + pss.total() <= MIN_ENERGY + delta1)
+			if (WM(i1,h) + WM(h+1,j1) + pss.total() <= MIN_ENERGY + delta1)
 			{
 				pstruct ps1(pss);
-				ps1.push(segment(i1, h, lWM, WM[i1][h]));
-				ps1.push(segment(h+1, j1, lWM, WM[h+1][j1]));
+				ps1.push(segment(i1, h, lWM, WM(i1,h)));
+				ps1.push(segment(h+1, j1, lWM, WM(h+1,j1)));
 				wm_stack.push(ps1);
 			}
 		}
@@ -380,49 +379,49 @@ void traceVM(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENE
 	for (h = i+1; h <= j-1; ++h)
 	{
 		int energy;
-		int a = Ea(); //multConst[0]; 
-		int b = Eb(); //multConst[2]; 
-		int c = Ec(); //multConst[1]; 
+		int a = Ea; //multConst[0]; 
+		int b = Eb; //multConst[2]; 
+		int c = Ec; //multConst[1]; 
 		int d5 = Ed5(i,j,i+1);
 		int d3 = Ed3(i,j,j-1);
 		int common = auPenalty(i,j) + a + b;
 
-		energy = common + WM[i+1][h-1] + WM[h][j-1];
+		energy = common + WM(i+1,h-1) + WM(h,j-1);
 		if (energy + ps.total()  <= MIN_ENERGY + delta1)
 		{
 			pstruct ps1(ps);
-			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));
-			ps1.push(segment(h, j-1, lWM, WM[h][j-1]));
+			ps1.push(segment(i+1,h-1, lWM, WM(i+1,h-1)));
+			ps1.push(segment(h, j-1, lWM, WM(h,j-1)));
 			ps1.accumulate(common) ; 
 			traceWM(ps1, filter, MIN_ENERGY, delta1);
 		}
 
-		energy =  common + WM[i+2][h-1] + WM[h][j-1] + d5 + c;
+		energy =  common + WM(i+2,h-1) + WM(h,j-1) + d5 + c;
 		if (energy + ps.total()  <= MIN_ENERGY + delta1)
 		{
 			pstruct ps1(ps);
-			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
-			ps1.push(segment(h, j-1, lWM, WM[h][j-1]));	
+			ps1.push(segment(i+2,h-1, lWM, WM(i+2,h-1)));	
+			ps1.push(segment(h, j-1, lWM, WM(h,j-1)));	
 			ps1.accumulate(common + d5 + c);
 			traceWM(ps1, filter, MIN_ENERGY, delta1);
 		}
 
-		energy = common + WM[i+1][h-1] + WM[h][j-2] + d3 + c;
+		energy = common + WM(i+1,h-1) + WM(h,j-2) + d3 + c;
 		if (energy + ps.total()  <= MIN_ENERGY + delta1)
 		{
 			pstruct ps1(ps);	
-			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));	
-			ps1.push(segment(h, j-2, lWM, WM[h][j-2]));	
+			ps1.push(segment(i+1,h-1, lWM, WM(i+1,h-1)));	
+			ps1.push(segment(h, j-2, lWM, WM(h,j-2)));	
 			ps1.accumulate(common + d3 + c);
 			traceWM(ps1, filter, MIN_ENERGY, delta1);
 		}
 
-		energy = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*c;
+		energy = common + WM(i+2,h-1) + WM(h,j-2) + d5 + d3 + 2*c;
 		if (energy + ps.total()  <= MIN_ENERGY + delta1)
 		{ 	
 			pstruct ps1(ps);	
-			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
-			ps1.push(segment(h, j-2, lWM, WM[h][j-2]));	
+			ps1.push(segment(i+2,h-1, lWM, WM(i+2,h-1)));	
+			ps1.push(segment(h, j-2, lWM, WM(h,j-2)));	
 			ps1.accumulate(common + d3 + d5 + 2*c) ;
 			traceWM(ps1, filter, MIN_ENERGY, delta1);
 		}
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index ae02eab..7d94740 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -141,10 +141,10 @@ int traceV(int i, int j) {
 	int a, b, c, d, Vij;
 
 	a = eH(i, j);
-	b = eS(i, j) + V[indx[i + 1] + j - 1];
+	b = eS(i, j) + V(i + 1, j - 1);
 	if (eS(i, j) == 0) b = INFINITY_;
-	c = VBI[i][j];
-	d = VM[i][j];
+	c = VBI(i,j);
+	d = VM(i,j);
 	
 	Vij = MIN(MIN(a, b), MIN(c, d));
 	
@@ -185,9 +185,9 @@ int traceVBI(int i, int j) {
 	for (ip = i + 1; ip < j - 1; ip++) {
 		for (jp = ip + 1; jp < j; jp++) { /* Search which internal loop (ip,jp) is closing */
 			el = eL(i, j, ip, jp);
-			v = V[indx[ip] + jp];
+			v = V(ip, jp);
 			VBIij_temp = el + v;
-			if (VBIij_temp == VBI[i][j]) {
+			if (VBIij_temp == VBI(i,j)) {
 				ifinal = ip;
 				jfinal = jp;
 				break;
@@ -219,10 +219,10 @@ int traceVM(int i, int j) {
 	a = eparam[5];
 	b = eparam[10]; /* efn2b */
 
-	int VMij = VM[i][j];
+	int VMij = VM(i,j);
 
 	for (h = i + 2; h <= j - 1 && !done; h++) {
-		A_temp = WM[i + 1][h - 1] + WM[h][j - 1] + a + b + auPen(RNA[i],
+		A_temp = WM(i+1,h-1) + WM(h,j - 1) + a + b + auPen(RNA[i],
 				RNA[j]);
 		if (A_temp == VMij) { /* No dangling bases on any of the sides of base pair (i,j) in the multiloop */
 			done = 1;
@@ -233,7 +233,7 @@ int traceVM(int i, int j) {
 	}
 
 	for (h = i + 3; h <= j - 1 && !done; h++) {
-		A_temp = WM[i + 2][h - 1] + WM[h][j - 1] + a + b + auPenalty(i,j) + Ed5(i,j,i + 1); 
+		A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + a + b + auPenalty(i,j) + Ed5(i,j,i + 1); 
 		if (A_temp == VMij) {
 			done = 1;
 			eVM += traceWM(i + 2, h - 1);
@@ -243,7 +243,7 @@ int traceVM(int i, int j) {
 	}
 
 	for (h = i + 2; h <= j - 2 && !done; h++) { /* If base j-1 is dangling on 3' end of the base pair (i,j) */
-		A_temp = WM[i + 1][h - 1] + WM[h][j - 2] + a + b + auPenalty(i, j) + Ed3(i,j,j - 1);
+		A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + a + b + auPenalty(i, j) + Ed3(i,j,j - 1);
 		if (A_temp == VMij) {
 			done = 1;
 			eVM += traceWM(i + 1, h - 1);
@@ -253,7 +253,7 @@ int traceVM(int i, int j) {
 	}
 
 	for (h = i + 3; h <= j - 2 && !done; h++) { /* If base pair (i,j) has dangling bases on both sides. */
-		A_temp = WM[i + 2][h - 1] + WM[h][j - 2] + a + b + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
+		A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + a + b + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
 		if (A_temp == VMij) {
 			done = 1;
 			eVM += traceWM(i + 2, h - 1);
@@ -279,8 +279,8 @@ int traceWM(int i, int j) {
 		return 0;
 	else {
 		for (h = i; h < j && !done; h++) {
-			int aa = WM[i][h] + WM[h + 1][j]; /* If WM(i,j) came from the summation of two WM terms */
-			if (aa == WM[i][j]) {
+			int aa = WM(i,h) + WM(h + 1,j); /* If WM(i,j) came from the summation of two WM terms */
+			if (aa == WM(i,j)) {
 				done = 1;
 				h1 = h;
 				break;
@@ -290,30 +290,30 @@ int traceWM(int i, int j) {
 			eWM += traceWM(i, h);
 			eWM += traceWM(h + 1, j);
 		} else {
-			if (WM[i][j] == V(i,j) + auPenalty(i, j) + Eb()) { /* If base pair (i,j) pairs*/
+			if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb) { /* If base pair (i,j) pairs*/
 				done = 1;
 				structure[i] = j;
 				structure[j] = i;
 				eWM += traceV(i, j);
-			} else if (WM[i][j] == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb() + Ec()) { 
+			} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec) { 
 				done = 1;
 				eWM += traceV(i + 1, j);
 				structure[i + 1] = j;
 				structure[j] = i + 1;
-			} else if (WM[i][j] == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb() + Ec() ) { 
+			} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec ) { 
 				done = 1;
 				eWM += traceV(i, j - 1);
 				structure[i] = j - 1;
 				structure[j - 1] = i;
-			} else if (WM[i][j] == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb() + 2*Ec()) { 
+			} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec) { 
 				done = 1;
 				eWM += traceV(i + 1, j - 1);
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
-			} else if (WM[i][j] == WM[i + 1][j] + Ec() ) { 
+			} else if (WM(i,j) == WM(i + 1,j) + Ec ) { 
 				done = 1;
 				eWM += traceWM(i + 1, j);
-			} else if (WM[i][j] == WM[i][j - 1] + Ec() ) { 
+			} else if (WM(i,j) == WM(i,j - 1) + Ec ) { 
 				done = 1;
 				eWM += traceWM(i, j - 1);
 			}

From 47777e9f40d1ece349e7fb84af7a659b6e56c6c2 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Wed, 16 Mar 2011 20:58:06 -0400
Subject: [PATCH 046/282] Correctly accept FASTA files

Closes GH-18.
---
 gtfold-mfe/src/main.cc | 44 ++++++++++++++++++++++--------------------
 1 file changed, 23 insertions(+), 21 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 22edef9..2c9b783 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -63,31 +63,33 @@ void free_fold(int len)
 	return;
 }
 
+/**
+ * Read the sequence out of the given filename and store it in seq
+ *
+ * @param filename A c string with the file to open
+ * @param seq A C++ string object (passed by reference) to save to
+ * @return SUCCESS or FAILURE
+ */
 int read_sequence_file(const char* filename, std::string& seq)
 {
-	ifstream cf;
-	cf.open(filename, ios::in);
-	if (cf == NULL)
-	{
-		return FAILURE;
-	}
-	
 	seq = "";
-	//Handle FASTA input
-	char ss[10000];
-	cf.getline(ss, 10000);
-	if (ss[0] != '>') 
-	{
-		char *fline;
-		fline = strtok(ss, " ");
-		while (fline != NULL) {
-			seq.append(fline);
-			fline = strtok(NULL, " ");
-		}
+
+	ifstream fs;
+	fs.open(filename, ios::in);
+	if (fs == NULL)
+		return FAILURE;
+
+	string line;
+	getline(fs, line);
+	while(line.length() > 0) {
+		// exclude lines starting with FASTA comment characters
+		if(line[0] != ';' && line[0] != '>')
+			seq += line;
+		getline(fs, line);
 	}
-	
-	cf.close();
-	
+
+	fs.close();
+
 	return SUCCESS;
 }
 

From d747ab898c11870e455d40718fe8cda0e20c1cff Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Wed, 16 Mar 2011 21:20:28 -0400
Subject: [PATCH 047/282] Compare against FAILURE instead of 0

This is what is returned, so let's stick to using the constants
---
 gtfold-mfe/src/main.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 2c9b783..7f009b5 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -151,7 +151,7 @@ int main(int argc, char** argv) {
 	parse_options(argc, argv);
 
 	fprintf(stdout, "Opening file: %s\n", seqfile.c_str());
-	if (read_sequence_file(seqfile.c_str(), seq) == 0)
+	if (read_sequence_file(seqfile.c_str(), seq) == FAILURE)
 	{
 		fprintf(stdout, "File open failed.\n\n");
 		exit(-1);
@@ -161,7 +161,7 @@ int main(int argc, char** argv) {
 	
 	init_fold(seq.length());
 	
-	if (handle_IUPAC_code(seq.c_str(), seq.length())  == 0)
+	if (handle_IUPAC_code(seq.c_str(), seq.length())  == FAILURE)
 	{
 		free_fold(seq.length());
 		exit(0);

From 605535cb7f5c96aca7471bcc1ef6004568b12721 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Wed, 16 Mar 2011 21:23:28 -0400
Subject: [PATCH 048/282] Split out a print_header() function

---
 gtfold-mfe/src/main.cc | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 7f009b5..8d27f1a 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -139,15 +139,19 @@ int handle_IUPAC_code(const char* str, const int bases)
 	}
 }
 
+void print_header() {
+	fprintf(stdout,"GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n");
+	fprintf(stdout,"(c) 2007-2011  D.A. Bader, S. Mallidi, A. Mathuriya, C.E. Heitsch, S.C. Harvey\n");
+	fprintf(stdout, "Georgia Institute of Technology\n");
+}
+
 int main(int argc, char** argv) {
 	std::string seq;
 	int energy;
 	double t1;
 
-	fprintf(stdout,"GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n");
-	fprintf(stdout,"(c) 2007-2010  D.A. Bader, S. Mallidi, A. Mathuriya, C.E. Heitsch, S.C. Harvey\n");
-	fprintf(stdout, "Georgia Institute of Technology\n");
-	
+	print_header();
+
 	parse_options(argc, argv);
 
 	fprintf(stdout, "Opening file: %s\n", seqfile.c_str());

From d24d9fc5ae2e40cadabe8ee51064f3a0ced73600 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Wed, 16 Mar 2011 21:29:03 -0400
Subject: [PATCH 049/282] Remove prepended space

---
 gtfold-mfe/src/options.cc | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index c468544..676b9fc 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -1,17 +1,17 @@
 #include "options.h"
 
- bool ILSA; 
- bool NOISOLATE;
- bool USERDATA;
- bool PARAMS;
- bool LIMIT_DISTANCE;
+bool ILSA;
+bool NOISOLATE;
+bool USERDATA;
+bool PARAMS;
+bool LIMIT_DISTANCE;
 
- std::string datadir;
- std::string dataparam;
- std::string seqfile ;
+std::string datadir;
+std::string dataparam;
+std::string seqfile ;
 
- int delta;
- int nThreads;
+int delta;
+int nThreads;
 
 void help() 
 {

From a6e6e9ee8eb570cf6a63267bc04c80ec7a8e3c1e Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Wed, 16 Mar 2011 22:36:11 -0400
Subject: [PATCH 050/282] Change UI: better options and output

---
 gtfold-mfe/include/options.h |  13 ++-
 gtfold-mfe/src/main.cc       |  12 +-
 gtfold-mfe/src/options.cc    | 208 ++++++++++++++++++-----------------
 3 files changed, 123 insertions(+), 110 deletions(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 8680c5f..3e6fbdf 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -6,20 +6,25 @@
 #include <cstring>
 #include <stdio.h>
 
+using namespace std;
+
 extern bool ILSA; 
 extern bool NOISOLATE;
 extern bool USERDATA;
 extern bool PARAMS;
 extern bool LIMIT_DISTANCE;
+extern bool ENABLE_BPP;
 
-extern std::string datadir;
-extern std::string dataparam;
-extern std::string seqfile ;
+extern string seqfile;
+extern string constraintsFile;
+extern string outputFile;
 
-extern int delta;
+extern int suboptDelta;
 extern int nThreads;
+extern int contactDistance;
 
 void help(); 
 void parse_options(int argc, char** argv);
+void printRunConfiguration();
 
 #endif
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 8d27f1a..b729924 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -171,12 +171,8 @@ int main(int argc, char** argv) {
 		exit(0);
 	}
 		
-	if(USERDATA==true)
-		populate(datadir.c_str(),true);
-	else if (PARAMS == true)
-		populate(dataparam.c_str(),false);
-	else
-		populate("Turner99",false); 
+	// always use Turner99 data (for now)
+	populate("Turner99",false);
 	
 	fprintf(stdout,"Computing minimum free energy structure. . . \n");
 	fflush(stdout);
@@ -190,10 +186,10 @@ int main(int argc, char** argv) {
 	fprintf(stdout,"MFE running time (in seconds): %9.6f\n\n", t1);
 	
 	
-	if (delta > 0)
+	if (suboptDelta > 0)
 	{	
 		t1 = get_seconds();
-		subopt_traceback(seq.length(), delta);
+		subopt_traceback(seq.length(), suboptDelta);
 		t1 = get_seconds() - t1;
 		fprintf(stdout,"Traceback running time (in seconds): %9.6f\n\n", t1);
 
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 676b9fc..bb558cc 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -1,137 +1,149 @@
 #include "options.h"
 
+using namespace std;
+
 bool ILSA;
 bool NOISOLATE;
 bool USERDATA;
 bool PARAMS;
 bool LIMIT_DISTANCE;
+bool ENABLE_BPP;
 
-std::string datadir;
-std::string dataparam;
-std::string seqfile ;
-
-int delta;
-int nThreads;
-
-void help() 
-{
-	fprintf(stderr, "\n");
-	fprintf(stderr, "Usage: gtfold [OPTIONS]  FILE\n"); 
-	fprintf(stderr, "\tSequence file has to be in one of the two formats: Single line or FASTA\n\n"); 
-	fprintf(stderr, "OPTIONS\n" );
-	fprintf(stderr, "-ni, --noisolate\n"); 
-	fprintf(stderr, "\tprevents isolated base pairs from forming\n"); 
-	fprintf(stderr, "-c, --constraints filename\n");
-	fprintf(stderr,	"\tconstraints is a optional parameter\n");
-	fprintf(stderr, "\tSyntax for giving constraints is:\n\tfor forcing (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) base pair, F i j k \n");
-	fprintf(stderr,	"\tto prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) base pair, P i j k \n");
-	fprintf(stderr, "\tto make bases from i to i+k-1 single stranded bases, P i 0 k \n");
-	fprintf(stderr,	"-lcd --limitcd value\n");
-	fprintf(stderr,	"\tlimits the 'contact distance' for a base pair\n");
-	fprintf(stderr,	"-d --datadir dirname \n");
-	fprintf(stderr, "\n");
-	exit(-1);
-}
+string seqfile = "";
+string constraintsFile = "";
+string outputFile = "";
 
+int suboptDelta = -1;
+int nThreads = -1;
+int contactDistance = -1;
 
-void parse_options(int argc, char** argv)
-{
-	int fileIndex = 0;
-	int consIndex = 0;
-	int dataIndex = 0;
-	int paramsIndex =0;
-	int eIndex = 0;
-	int nTIndex = 0;
+/**
+ * Print the help message and quit.
+ */
+void help() {
+    fprintf(stdout, "Usage: gtfold [OPTION]... FILE\n\n");
 
-	int i = 1;
+    fprintf(stdout, "  FILE is an RNA sequence file.  Single line or FASTA formats are accepted.\n\n");
 
-	while (i < argc) {
-		if (argv[i][0] == '-') {
-			if (strcmp(argv[i], "-ilsa") == 0) {
-				ILSA = true;
-			} else if (strcmp(argv[i], "-noisolate") == 0) {
-				NOISOLATE = true;
-			} else if (strcmp(argv[i], "-help") == 0) {
+    fprintf(stdout, "OPTIONS\n");
+    fprintf(stdout, "   -c, --constraints FILE\n                        Load constraints from FILE.  See Constraint syntax below\n");
+    fprintf(stdout, "   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n                        limit is given, base pairs can be over any distance\n");
+    fprintf(stdout, "   -n, --noisolate      Prevent isolated base pairs from forming\n");
+    fprintf(stdout, "   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
+    fprintf(stdout, "   -t, --threads num    Limit number of threads used\n");
+
+    fprintf(stdout, "\n");
+    fprintf(stdout, "   -h, --help           Output help (this message) and exit\n");
+    fprintf(stdout, "   -v, --verbose        Run in verbose mode\n");
+
+    fprintf(stdout, "\nBETA OPTIONS\n");
+    fprintf(stdout, "   --bpp                Calculate base pair probabilities\n");
+    fprintf(stdout, "   --subopt range       Calculate suboptimal structures within 'range' kcal/mol\n");
+    fprintf(stdout, "                        of the mfe\n");
+
+    fprintf(stdout, "\nConstraint syntax:\n\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
+    exit(-1);
+}
+
+/**
+ * Parse the options from argc and argv and save them into global state.
+ */
+void parse_options(int argc, char** argv) {
+	int i;
+
+	for(i=1; i<argc; i++) {
+		if(argv[i][0] == '-') {
+			if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
 				help();
-			} else if (strcmp(argv[i], "-constraints") == 0) {
-				if (i < argc)
-					consIndex = ++i;
+			} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
+				if(i < argc)
+					constraintsFile = argv[++i];
 				else
 					help();
-			} else if (strcmp(argv[i], "-params")==0) { 
-				PARAMS = true;			  
-				if (i < argc)
-					paramsIndex = ++i;
+			} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-d") == 0) {
+				if(i < argc)
+					contactDistance = atoi(argv[++i]);
 				else
 					help();
-			} else if (strcmp(argv[i], "-datadir") == 0) {
-				USERDATA = true;
-				if (i < argc)
-					dataIndex = ++i;
+			} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
+				NOISOLATE = true;
+			} else if(strcmp(argv[i], "--output") == 0 || strcmp(argv[i], "-o") == 0) {
+				if(i < argc)
+					outputFile = argv[++i];
 				else
 					help();
-			} else if (strcmp(argv[i], "-e") == 0)
-			{
-				if (i < argc)
-					eIndex = ++i;
+			} else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
+				if(i < argc)
+					nThreads = atoi(argv[++i]);
 				else
 					help();	
-			}
-			else if (strcmp(argv[i], "-nTHREAD") == 0)
-			{
-				if (i < argc)
-					nTIndex = ++i;
+			} else if(strcmp(argv[i], "--bpp") == 0) {
+				ENABLE_BPP = true;
+			} else if(strcmp(argv[i], "--subopt") == 0) {
+				if(i < argc)
+					suboptDelta = atoi(argv[i]);
 				else
-					help();	
+					help();
 			}
 		} else {
-			fileIndex = i;
-			seqfile = argv[fileIndex];
+			seqfile = argv[i];
 		}
-		i++;
 	}
 
-	if (fileIndex == 0)
+	// Must have an input file specified
+	if(seqfile.compare("") == 0) {
 		help();
-	
-	if (NOISOLATE == true)
-		fprintf(stdout, "Not allowing isolated base pairs\n");
-	else
-		fprintf(stdout, "Allowing isolated base pairs\n");
-	
-	if (consIndex != 0)
-	{
-		fprintf(stdout, "Constraint file index: %d\n", consIndex);
+		printf("Missing input file.\n");
 	}
 
-	if (dataIndex != 0)
-	{
-		datadir = argv[dataIndex];
+	printRunConfiguration();
+}
+
+/**
+ * Prints the run configuration for this run.
+ *
+ * The lines that start with a '-' are normal options, the '+' are beta options.
+ */
+void printRunConfiguration() {
+	bool standardRun = true;
+
+	printf("\nRun Configuration:\n");
+
+#ifdef _OPENMP
+	if(nThreads == -1)
+		printf("- thread count: %d\n", omp_get_num_threads());
+	else
+		printf("- thread count: %d\n", nThreads);
+#else
+	printf("- thread count: 1\n");
+#endif
+
+
+	if (NOISOLATE == true) {
+		printf("- preventing isolated base pairs\n");
+		standardRun = false;
 	}
 
-	if (paramsIndex != 0)
-	{
-		dataparam = argv[paramsIndex];
+	if(!constraintsFile.empty()) {
+		printf("- using constraint file: %s\n", constraintsFile.c_str());
+		standardRun = false;
 	}
 
-	nThreads = -1;
-	if (nTIndex != 0)
-	{
-		nThreads = atoi(argv[nTIndex]);
+	if (contactDistance != -1) {
+		printf("- maximum contact distance: %d\n", contactDistance);
+		standardRun = false;
 	}
-	
-	delta = 0;
-	if (eIndex != 0)
-	{
-		delta = atoi(argv[eIndex]);
-	}	
-	if (delta > 0)
-	{
-		fprintf(stdout, "Suboptimal range = %d\n\n", delta);
+
+	if (ENABLE_BPP == true) {
+		printf("+ calculating base pair probabilities\n");
+		standardRun = false;
 	}
 
-	if (argc < 2)
-	{
-		help();
+	if (suboptDelta != -1) {
+		printf("+ calculating suboptimal structures within %d kcal/mol of MFE\n", suboptDelta);
+		standardRun = false;
 	}
+
+	if(standardRun)
+		printf("- standard\n");
 }

From 2ae438b8d5801efba1fd6ae92510f4c266db6156 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 00:42:38 -0400
Subject: [PATCH 051/282] Rename allowedPairs() to canPair()

---
 gtfold-mfe/include/global.h | 2 +-
 gtfold-mfe/src/algorithms.c | 4 ++--
 gtfold-mfe/src/global.c     | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h
index 716873e..22ce165 100644
--- a/gtfold-mfe/include/global.h
+++ b/gtfold-mfe/include/global.h
@@ -12,7 +12,7 @@ extern unsigned int chPairKey;
 // The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). 
 #define checkPair(i, j) (((((i)-(j)) % 2) == 1 || (((i)-(j)) % 2)== -1) && (!( ((i)==BASE_A && (j)==BASE_C) || ((i)==BASE_C && (j)==BASE_A) )))
 
-inline int allowedPairs(int a, int b) ; 
+inline int canPair(int a, int b);
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 84d4566..27924b9 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -62,7 +62,7 @@ int calculate(int len) {
 		//	for (i = 1; i <= len - b; i++) {
 		for (j = i+TURN+1; j <= len; j++) {
 			//j = i + b;
-			if (allowedPairs(RNA[i], RNA[j])) { 
+			if (canPair(RNA[i], RNA[j])) {
 				int p, q, h;
 				int newV = INFINITY_;
 				int VBIij = INFINITY_;
@@ -86,7 +86,7 @@ int calculate(int len) {
 					int minq = j-i+p-MAXLOOP-2;
 					if (minq < p+1+TURN) minq = p+1+TURN;
 					for (q = minq; q < j; q++) {
-						if (!allowedPairs(RNA[p], RNA[q])) continue;
+						if (!canPair(RNA[p], RNA[q])) continue;
 						VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
 					}
 				}
diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c
index 5acaed7..3b0ae9b 100644
--- a/gtfold-mfe/src/global.c
+++ b/gtfold-mfe/src/global.c
@@ -71,7 +71,7 @@ void printStructure(int len)
 	printf("\n");
 }
 
-int allowedPairs(int a, int b) 
+int canPair(int a, int b)
 {
 	return (chPairKey & (1 << (((a)<<2) + (b)))); 
 }  

From 9145c3fe78a50ba2eb7d42e9a48de5b1139eacd7 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 00:52:00 -0400
Subject: [PATCH 052/282] Fix compiler warnings

---
 gtfold-mfe/src/algorithms.c | 2 +-
 gtfold-mfe/src/energy.c     | 6 ++----
 gtfold-mfe/src/main.cc      | 2 +-
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 27924b9..d77ab2c 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -41,7 +41,7 @@ double get_seconds() {
 }
 
 int calculate(int len) { 
-	int b, i, j;
+	int i, j;
 	double t1, t2, tint=0, thair=0,tst=0, tml=0, twm=0;
 
 #if 1
diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 16f1773..76dbc51 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -25,7 +25,7 @@ int *indx;
 
 void create_tables(int len)
 {	
-	int i;
+	//int i;
 	
 	V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
 	if (V == NULL) 
@@ -171,7 +171,7 @@ void create_tables(int len)
 
 void init_tables(int len) 
 {
-	int i, j, LLL;
+	int i, LLL;
 	
 	for (i = 0; i <= len; i++) {
 		W[i] = INFINITY_; 
@@ -211,8 +211,6 @@ void init_tables(int len)
 
 void free_tables(int len)
 {
-	int i;
-
 	free(indx);
 	//for (i = 0; i < len; i++)
 	//	free(WM[i]);
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index b729924..929ab03 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -160,7 +160,7 @@ int main(int argc, char** argv) {
 		fprintf(stdout, "File open failed.\n\n");
 		exit(-1);
 	}
-	fprintf(stdout, "Sequence length: %5d\n", seq.length());
+	fprintf(stdout, "Sequence length: %5d\n", (int)seq.length());
 	fprintf(stdout, "Sequence : %s\n", seq.c_str());
 	
 	init_fold(seq.length());

From 610730155b8a989f8fc646c1ea8b16f6ff69c502 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 00:57:02 -0400
Subject: [PATCH 053/282] Add [OMP] prefix to status output when using OpenMP

---
 gtfold-mfe/src/options.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index bb558cc..55a552c 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -111,9 +111,9 @@ void printRunConfiguration() {
 
 #ifdef _OPENMP
 	if(nThreads == -1)
-		printf("- thread count: %d\n", omp_get_num_threads());
+		printf("- [OMP] thread count: %d\n", omp_get_num_threads());
 	else
-		printf("- thread count: %d\n", nThreads);
+		printf("- [OMP] thread count: %d\n", nThreads);
 #else
 	printf("- thread count: 1\n");
 #endif

From 5d0f10aa154351455ba83d4535e9fb966d2936f0 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:00:47 -0400
Subject: [PATCH 054/282] Label subopt traceback time more clearly

---
 gtfold-mfe/src/main.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 929ab03..3b305af 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -191,7 +191,7 @@ int main(int argc, char** argv) {
 		t1 = get_seconds();
 		subopt_traceback(seq.length(), suboptDelta);
 		t1 = get_seconds() - t1;
-		fprintf(stdout,"Traceback running time (in seconds): %9.6f\n\n", t1);
+		fprintf(stdout,"Subopt traceback running time (in seconds): %9.6f\n\n", t1);
 
 		free_fold(seq.length());
 		exit(0);

From 8a55a37927ec2b4f5ecaa60904225a36299618ae Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:13:01 -0400
Subject: [PATCH 055/282] Just use printf, not fprintf(stdout, ...)

---
 gtfold-mfe/src/main.cc | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 3b305af..019f3a7 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -140,9 +140,9 @@ int handle_IUPAC_code(const char* str, const int bases)
 }
 
 void print_header() {
-	fprintf(stdout,"GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n");
-	fprintf(stdout,"(c) 2007-2011  D.A. Bader, S. Mallidi, A. Mathuriya, C.E. Heitsch, S.C. Harvey\n");
-	fprintf(stdout, "Georgia Institute of Technology\n");
+	printf("GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n");
+	printf("(c) 2007-2011  D.A. Bader, S. Mallidi, A. Mathuriya, C.E. Heitsch, S.C. Harvey\n");
+	printf("Georgia Institute of Technology\n");
 }
 
 int main(int argc, char** argv) {

From 8571b608a8fe410649d286194bb1634266b503f5 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:14:55 -0400
Subject: [PATCH 056/282] Put newline at end of header instead of beginning of
 run config

---
 gtfold-mfe/src/main.cc    | 2 +-
 gtfold-mfe/src/options.cc | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 019f3a7..da1f7da 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -142,7 +142,7 @@ int handle_IUPAC_code(const char* str, const int bases)
 void print_header() {
 	printf("GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n");
 	printf("(c) 2007-2011  D.A. Bader, S. Mallidi, A. Mathuriya, C.E. Heitsch, S.C. Harvey\n");
-	printf("Georgia Institute of Technology\n");
+	printf("Georgia Institute of Technology\n\n");
 }
 
 int main(int argc, char** argv) {
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 55a552c..a9f1d96 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -107,7 +107,7 @@ void parse_options(int argc, char** argv) {
 void printRunConfiguration() {
 	bool standardRun = true;
 
-	printf("\nRun Configuration:\n");
+	printf("Run Configuration:\n");
 
 #ifdef _OPENMP
 	if(nThreads == -1)

From bd8a939aa1f155d61d1d60161965159113cae9d5 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:22:06 -0400
Subject: [PATCH 057/282] Use printRunConfiguration() more effectively

---
 gtfold-mfe/include/options.h |  2 +-
 gtfold-mfe/src/main.cc       | 10 ++++------
 gtfold-mfe/src/options.cc    |  8 +++++---
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 3e6fbdf..eaed912 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -25,6 +25,6 @@ extern int contactDistance;
 
 void help(); 
 void parse_options(int argc, char** argv);
-void printRunConfiguration();
+void printRunConfiguration(string seq);
 
 #endif
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index da1f7da..db02ff3 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -154,14 +154,12 @@ int main(int argc, char** argv) {
 
 	parse_options(argc, argv);
 
-	fprintf(stdout, "Opening file: %s\n", seqfile.c_str());
-	if (read_sequence_file(seqfile.c_str(), seq) == FAILURE)
-	{
-		fprintf(stdout, "File open failed.\n\n");
+	if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) {
+		printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
 		exit(-1);
 	}
-	fprintf(stdout, "Sequence length: %5d\n", (int)seq.length());
-	fprintf(stdout, "Sequence : %s\n", seq.c_str());
+
+	printRunConfiguration(seq);
 	
 	init_fold(seq.length());
 	
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index a9f1d96..0e8ad0f 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -95,8 +95,6 @@ void parse_options(int argc, char** argv) {
 		help();
 		printf("Missing input file.\n");
 	}
-
-	printRunConfiguration();
 }
 
 /**
@@ -104,7 +102,7 @@ void parse_options(int argc, char** argv) {
  *
  * The lines that start with a '-' are normal options, the '+' are beta options.
  */
-void printRunConfiguration() {
+void printRunConfiguration(string seq) {
 	bool standardRun = true;
 
 	printf("Run Configuration:\n");
@@ -146,4 +144,8 @@ void printRunConfiguration() {
 
 	if(standardRun)
 		printf("- standard\n");
+
+	printf("- input file: %s\n", seqfile.c_str());
+	printf("  - sequence length: %d\n", (int)seq.length());
+	printf("  - sequence contents: %s\n", seq.c_str());
 }

From 6861a834d0c6a1e437bf3218d97353a1aea79474 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:27:38 -0400
Subject: [PATCH 058/282] Rename populate() to readThermodynamicParameters()

---
 gtfold-mfe/include/loader.h | 2 +-
 gtfold-mfe/src/loader.cc    | 2 +-
 gtfold-mfe/src/main.cc      | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h
index c1d271d..1fd68e4 100644
--- a/gtfold-mfe/include/loader.h
+++ b/gtfold-mfe/include/loader.h
@@ -25,7 +25,7 @@
 #include "constants.h"
 #include "data.h"
 
-void populate(const char *userdatadir,bool userdatalogic);
+void readThermodynamicParameters(const char *userdatadir,bool userdatalogic);
 
 int initStackValues(std::string fileName);
 int initMiscloopValues(std::string fileName);
diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 0044b62..f0d11d2 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -74,7 +74,7 @@ std::string EN_DATADIR;
  int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
  float prelog;
 
-void populate(const char *userdatadir,bool userdatalogic) {
+void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 
 	cout << "Loading in GTfold data files from ";
 #ifndef GENBIN
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index db02ff3..575bb81 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -159,6 +159,9 @@ int main(int argc, char** argv) {
 		exit(-1);
 	}
 
+	// Read in thermodynamic parameters. Always use Turner99 data (for now)
+	readThermodynamicParameters("Turner99",false);
+
 	printRunConfiguration(seq);
 	
 	init_fold(seq.length());
@@ -168,9 +171,6 @@ int main(int argc, char** argv) {
 		free_fold(seq.length());
 		exit(0);
 	}
-		
-	// always use Turner99 data (for now)
-	populate("Turner99",false);
 	
 	fprintf(stdout,"Computing minimum free energy structure. . . \n");
 	fflush(stdout);

From 276b39b818b91b82181796a9779574afb8c9d27c Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:28:31 -0400
Subject: [PATCH 059/282] Add thermodynamic parameters to the run configuration

---
 gtfold-mfe/include/loader.h | 2 ++
 gtfold-mfe/src/options.cc   | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h
index 1fd68e4..20a0708 100644
--- a/gtfold-mfe/include/loader.h
+++ b/gtfold-mfe/include/loader.h
@@ -38,4 +38,6 @@ int initInt21Values(std::string fileName);
 int initInt22Values(std::string fileName);
 int initInt11Values(std::string fileName);
 
+extern std::string EN_DATADIR;
+
 #endif
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 0e8ad0f..40a5bfd 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -1,3 +1,4 @@
+#include "loader.h"
 #include "options.h"
 
 using namespace std;
@@ -145,6 +146,7 @@ void printRunConfiguration(string seq) {
 	if(standardRun)
 		printf("- standard\n");
 
+	printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str());
 	printf("- input file: %s\n", seqfile.c_str());
 	printf("  - sequence length: %d\n", (int)seq.length());
 	printf("  - sequence contents: %s\n", seq.c_str());

From 153f75940409002cedf851546574fc1002b1b549 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:33:22 -0400
Subject: [PATCH 060/282] Remove cout calls in loader

---
 gtfold-mfe/src/loader.cc | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index f0d11d2..843d718 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -76,7 +76,6 @@ std::string EN_DATADIR;
 
 void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 
-	cout << "Loading in GTfold data files from ";
 #ifndef GENBIN
 	if (!userdatalogic) 
 	{
@@ -96,8 +95,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 		EN_DATADIR += "/";
 	}
 
-	cout << EN_DATADIR << endl;
-
 	initMiscloopValues("miscloop.dat");
 	// miscloop.dat - Miscellaneous loop file
 	initStackValues("stack.dat");
@@ -118,8 +115,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	// int22.dat - free energies for 2 x 2 interior loops
 	initInt11Values("int11.dat");
 	// int11.dat - free energies for 1 x 1 interior loops
-
-	cout << "Done loading data files." << endl;
 }
 
 

From 6dd5743ffd2e67bc4f07f99d41ebcacb3bce1ddb Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:34:55 -0400
Subject: [PATCH 061/282] Remove prepended space

---
 gtfold-mfe/src/loader.cc | 68 ++++++++++++++++++++--------------------
 1 file changed, 34 insertions(+), 34 deletions(-)

diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 843d718..f916f3c 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -39,40 +39,40 @@ using namespace std;
 
 std::string EN_DATADIR;
 
- int poppen[5];
- int maxpen;
- int eparam[11];
- int multConst[3]; /* for multiloop penalties. */
- int dangle[4][4][4][2]; /* Contain dangling energy values */
- int inter[31]; /* Contains size penalty for internal loops */
- int bulge[31]; /* Contain the size penalty for bulges */
- int hairpin[31]; /* Contains the size penalty for hairpin loops */
- int stack[256]; /* Stacking energy used to calculate energy of stack loops */
- int tstkh[256]; /* Terminal mismatch energy used in the calculations of hairpin loops */
- int tstki[256]; /* Terminal mismatch energy used in the calculations of internal loops */
- int tloop[maxtloop + 1][2];
- int numoftloops;
- int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */
- int iloop21[5][5][5][5][5][5][5]; /* 2*1 internal loops */
- int iloop11[5][5][5][5][5][5]; /* 1*1 internal loops */
- int coax[6][6][6][6];
- int tstackcoax[6][6][6][6];
- int coaxstack[6][6][6][6];
- int tstack[6][6][6][6];
- int tstkm[6][6][6][6];
- int auend;
- int gubonus;
- int cint; /* cint, cslope, c3 are used for poly C hairpin loops */
- int cslope;
- int c3;
- int efn2a;
- int efn2b;
- int efn2c;
- int triloop[maxtloop + 1][2];
- int numoftriloops;
- int init;
- int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
- float prelog;
+int poppen[5];
+int maxpen;
+int eparam[11];
+int multConst[3]; /* for multiloop penalties. */
+int dangle[4][4][4][2]; /* Contain dangling energy values */
+int inter[31]; /* Contains size penalty for internal loops */
+int bulge[31]; /* Contain the size penalty for bulges */
+int hairpin[31]; /* Contains the size penalty for hairpin loops */
+int stack[256]; /* Stacking energy used to calculate energy of stack loops */
+int tstkh[256]; /* Terminal mismatch energy used in the calculations of hairpin loops */
+int tstki[256]; /* Terminal mismatch energy used in the calculations of internal loops */
+int tloop[maxtloop + 1][2];
+int numoftloops;
+int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */
+int iloop21[5][5][5][5][5][5][5]; /* 2*1 internal loops */
+int iloop11[5][5][5][5][5][5]; /* 1*1 internal loops */
+int coax[6][6][6][6];
+int tstackcoax[6][6][6][6];
+int coaxstack[6][6][6][6];
+int tstack[6][6][6][6];
+int tstkm[6][6][6][6];
+int auend;
+int gubonus;
+int cint; /* cint, cslope, c3 are used for poly C hairpin loops */
+int cslope;
+int c3;
+int efn2a;
+int efn2b;
+int efn2c;
+int triloop[maxtloop + 1][2];
+int numoftriloops;
+int init;
+int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
+float prelog;
 
 void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 

From fa0bf9a79fffe9d80affd30663d30d2ed47a714e Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:37:20 -0400
Subject: [PATCH 062/282] Don't fprintf(stdout, ...), just printf(...)

---
 gtfold-mfe/src/main.cc | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 575bb81..25f1fe0 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -172,16 +172,16 @@ int main(int argc, char** argv) {
 		exit(0);
 	}
 	
-	fprintf(stdout,"Computing minimum free energy structure. . . \n");
+	printf("Computing minimum free energy structure. . . \n");
 	fflush(stdout);
 
 	t1 = get_seconds();
 	energy = calculate(seq.length());
 	t1 = get_seconds() - t1;
 	
-	fprintf(stdout,"Done.\n\n");
-	fprintf(stdout,"Minimum Free Energy = %12.4f\n", energy/100.00);
-	fprintf(stdout,"MFE running time (in seconds): %9.6f\n\n", t1);
+	printf("Done.\n\n");
+	printf("Minimum Free Energy = %12.4f\n", energy/100.00);
+	printf("MFE running time (in seconds): %9.6f\n\n", t1);
 	
 	
 	if (suboptDelta > 0)
@@ -189,7 +189,7 @@ int main(int argc, char** argv) {
 		t1 = get_seconds();
 		subopt_traceback(seq.length(), suboptDelta);
 		t1 = get_seconds() - t1;
-		fprintf(stdout,"Subopt traceback running time (in seconds): %9.6f\n\n", t1);
+		printf("Subopt traceback running time (in seconds): %9.6f\n\n", t1);
 
 		free_fold(seq.length());
 		exit(0);
@@ -240,12 +240,12 @@ int initialize_constraints(int*** fbp, int ***pbp, int& numpConstraints, int& nu
 {
 	ifstream cfcons;
 
-	fprintf(stdout, "Running with constraints\n");
-	fprintf(stdout, "Opening constraint file: %s\n", constr_file);
+	printf("Running with constraints\n");
+	printf("Opening constraint file: %s\n", constr_file);
 
 	cfcons.open(constr_file, ios::in);
 	if (cfcons != NULL)
-		fprintf(stdout, "Constraint file opened.\n");
+		printf("Constraint file opened.\n");
 	else {
 		fprintf(stderr, "Error opening constraint file\n\n");
 		cfcons.close();
@@ -263,10 +263,10 @@ int initialize_constraints(int*** fbp, int ***pbp, int& numpConstraints, int& nu
 	}
 	cfcons.close();
 
-	fprintf(stdout, "Number of Constraints given: %d\n\n", numfConstraints
+	printf("Number of Constraints given: %d\n\n", numfConstraints
 			+ numpConstraints);
 	if (numfConstraints + numpConstraints != 0)
-		fprintf(stdout, "Reading Constraints.\n");
+		printf("Reading Constraints.\n");
 	else {
 		fprintf(stderr, "No Constraints found.\n\n");
 		return FAILURE;
@@ -307,21 +307,21 @@ int initialize_constraints(int*** fbp, int ***pbp, int& numpConstraints, int& nu
 		}
 	}
 
-	fprintf(stdout, "Forced base pairs: ");
+	printf("Forced base pairs: ");
 	
 	for(it=0; it<numfConstraints; it++) 
 	{
 		for(int k=1;k<= (*fbp)[it][2];k++)
-			fprintf(stdout, "(%d,%d) ", (*fbp)[it][0]+k-1, (*fbp)[it][1]-k+1);
+			printf("(%d,%d) ", (*fbp)[it][0]+k-1, (*fbp)[it][1]-k+1);
 	}
-	fprintf(stdout, "\nProhibited base pairs: ");
+	printf("\nProhibited base pairs: ");
 	for(it=0; it<numpConstraints; it++) 
 	{
 		for(int k=1;k<= (*pbp)[it][2];k++)
-			fprintf(stdout, "(%d,%d) ", (*pbp)[it][0]+k-1, (*pbp)[it][1]-k+1);
+			printf("(%d,%d) ", (*pbp)[it][0]+k-1, (*pbp)[it][1]-k+1);
 	}
 
-	fprintf(stdout, "\n\n");
+	printf("\n\n");
 
 	return SUCCESS;
 }

From e13599eac657d8763afebac067a1c2d3aebff49a Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:40:36 -0400
Subject: [PATCH 063/282] Reformat results output

---
 gtfold-mfe/src/main.cc | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 25f1fe0..85236d7 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -180,8 +180,9 @@ int main(int argc, char** argv) {
 	t1 = get_seconds() - t1;
 	
 	printf("Done.\n\n");
-	printf("Minimum Free Energy = %12.4f\n", energy/100.00);
-	printf("MFE running time (in seconds): %9.6f\n\n", t1);
+	printf("Results:\n");
+	printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00);
+	printf("- MFE runtime: %9.6f seconds\n\n", t1);
 	
 	
 	if (suboptDelta > 0)
@@ -189,7 +190,7 @@ int main(int argc, char** argv) {
 		t1 = get_seconds();
 		subopt_traceback(seq.length(), suboptDelta);
 		t1 = get_seconds() - t1;
-		printf("Subopt traceback running time (in seconds): %9.6f\n\n", t1);
+		printf("Subopt traceback running time: %9.6f seconds\n\n", t1);
 
 		free_fold(seq.length());
 		exit(0);

From 0bd908340cf03e2fbb901393319cd85d8ba0b3e8 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:45:57 -0400
Subject: [PATCH 064/282] Better output

---
 gtfold-mfe/src/algorithms.c | 11 ++++++-----
 gtfold-mfe/src/main.cc      |  4 ++--
 gtfold-mfe/src/traceback.c  |  2 +-
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index d77ab2c..42ab0ad 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -170,11 +170,12 @@ int calculate(int len) {
 		for (j=1; j<=len; j++) {VV[j]=INFINITY_;WMi[j]=INFINITY_; }
 	}
 
-	printf("Total IntLoop time = %fs \n",tint);
-	printf("Total Stack time = %fs \n",tst);
-	printf("Total HairPin time = %fs \n",thair);
-	printf("Total MultiLoop time = %fs \n",tml);
-	printf("Total WM time = %fs \n",twm);
+	printf("Runtime Statistics:\n");
+	printf("- total IntLoop time = %fs \n",tint);
+	printf("- total Stack time = %fs \n",tst);
+	printf("- total HairPin time = %fs \n",thair);
+	printf("- total MultiLoop time = %fs \n",tml);
+	printf("- total WM time = %fs \n",twm);
 
 	for (j = TURN+2; j <= len; j++)	{
 		int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 85236d7..0ecdb6b 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -172,7 +172,7 @@ int main(int argc, char** argv) {
 		exit(0);
 	}
 	
-	printf("Computing minimum free energy structure. . . \n");
+	printf("\nComputing minimum free energy structure...\n");
 	fflush(stdout);
 
 	t1 = get_seconds();
@@ -182,7 +182,7 @@ int main(int argc, char** argv) {
 	printf("Done.\n\n");
 	printf("Results:\n");
 	printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00);
-	printf("- MFE runtime: %9.6f seconds\n\n", t1);
+	printf("- MFE runtime: %9.6f seconds\n", t1);
 	
 	
 	if (suboptDelta > 0)
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 7d94740..5e2449b 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -44,7 +44,7 @@ void trace(int len) {
 
 	traceW(len);
 	
-	printf("SUM of energy of loops = %12.2f\n", total_en/100.0);
+	printf("- sum of energy of loops: %12.2f kcal/mol\n", total_en/100.0);
 	return;
 }
 

From 18fde25a819d9a41ba45c594e0c4b6ea6f93da16 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 01:56:17 -0400
Subject: [PATCH 065/282] Cleanup utils.cc for better spacing and add a
 description

---
 gtfold-mfe/src/utils.cc | 112 ++++++++++++++++++++++++++++------------
 1 file changed, 78 insertions(+), 34 deletions(-)

diff --git a/gtfold-mfe/src/utils.cc b/gtfold-mfe/src/utils.cc
index 1b5e5d0..2203015 100644
--- a/gtfold-mfe/src/utils.cc
+++ b/gtfold-mfe/src/utils.cc
@@ -22,53 +22,97 @@ char baseToDigit(const char* base) {
 }
 
 unsigned char getBase(const char* base) {
-	//cout << base;
-	if (!strcmp(base, "A") || !strcmp(base, "a")) {
-		//cout << "1";
+	if (!strcmp(base, "A") ||
+		!strcmp(base, "a"))
 		return BASE_A;
-	}
-	if (!strcmp(base, "C") || !strcmp(base, "c")) {
-		//cout << "2";
+
+	if (!strcmp(base, "C") ||
+		!strcmp(base, "c"))
 		return BASE_C;
-	}
-	if (!strcmp(base, "G") || !strcmp(base, "g")) {
-		//cout << "3";
+
+	if (!strcmp(base, "G") ||
+		!strcmp(base, "g"))
 		return BASE_G;
-	}
-	if (!strcmp(base, "U") || !strcmp(base, "u") || !strcmp(
-			base, "T") || !strcmp(base, "t")) {
-		//cout << "4";
+
+	if (!strcmp(base, "U") ||
+		!strcmp(base, "u") ||
+		!strcmp(base, "T") ||
+		!strcmp(base, "t"))
 		return BASE_U;
-	}
-	if (!strcmp(base, "N") || !strcmp(base, "n")||!strcmp(base, "R")|| !strcmp(base, "r")|| !strcmp(base, "Y")|| !strcmp(base, "y")|| !strcmp(base, "M")|| !strcmp(base, "m")|| !strcmp(base, "K")|| !strcmp(base, "k")|| !strcmp(base, "S")|| !strcmp(base, "s")|| !strcmp(base, "W")|| !strcmp(base, "w")|| !strcmp(base, "B")|| !strcmp(base, "b")|| !strcmp(base, "D")|| !strcmp(base, "d")|| !strcmp(base, "H")|| !strcmp(base, "h")|| !strcmp(base, "V")|| !strcmp(base, "v")) {
-		//cout << "4";
+
+	if (!strcmp(base, "N") ||
+		!strcmp(base, "n") ||
+		!strcmp(base, "R") ||
+		!strcmp(base, "r") ||
+		!strcmp(base, "Y") ||
+		!strcmp(base, "y") ||
+		!strcmp(base, "M") ||
+		!strcmp(base, "m") ||
+		!strcmp(base, "K") ||
+		!strcmp(base, "k") ||
+		!strcmp(base, "S") ||
+		!strcmp(base, "s") ||
+		!strcmp(base, "W") ||
+		!strcmp(base, "w") ||
+		!strcmp(base, "B") ||
+		!strcmp(base, "b") ||
+		!strcmp(base, "D") ||
+		!strcmp(base, "d") ||
+		!strcmp(base, "H") ||
+		!strcmp(base, "h") ||
+		!strcmp(base, "V") ||
+		!strcmp(base, "v"))
 		return BASE_A;
-	}
+
 	return 'X';
 }
 
+/**
+ * Identical to getBase but returns 'N' instead of 'A' for non-standard bases
+ * (a,c,g,u)
+ */
 unsigned char getBase1(const char* base) {
-	//cout << base;
-	if (!strcmp(base, "A") || !strcmp(base, "a")) {
-		//cout << "1";
+	if (!strcmp(base, "A") ||
+		!strcmp(base, "a"))
 		return BASE_A;
-	}
-	if (!strcmp(base, "C") || !strcmp(base, "c")) {
-		//cout << "2";
+
+	if (!strcmp(base, "C") ||
+		!strcmp(base, "c"))
 		return BASE_C;
-	}
-	if (!strcmp(base, "G") || !strcmp(base, "g")) {
-		//cout << "3";
+
+	if (!strcmp(base, "G") ||
+		!strcmp(base, "g"))
 		return BASE_G;
-	}
-	if (!strcmp(base, "U") || !strcmp(base, "u") || !strcmp(
-																			base, "T") || !strcmp(base, "t")) {
-		//cout << "4";
+
+	if (!strcmp(base, "U") ||
+		!strcmp(base, "u") ||
+		!strcmp(base, "T") ||
+		!strcmp(base, "t"))
 		return BASE_U;
-	}
-	if (!strcmp(base, "N") || !strcmp(base, "n")|| !strcmp(base, "R")|| !strcmp(base, "r")|| !strcmp(base, "Y")|| !strcmp(base, "y")|| !strcmp(base, "M")|| !strcmp(base, "m")|| !strcmp(base, "K")|| !strcmp(base, "k")|| !strcmp(base, "S")|| !strcmp(base, "s")|| !strcmp(base, "W")|| !strcmp(base, "w")|| !strcmp(base, "B")|| !strcmp(base, "b")|| !strcmp(base, "D")|| !strcmp(base, "d")|| !strcmp(base, "H")|| !strcmp(base, "h")|| !strcmp(base, "V")|| !strcmp(base, "v")) {
-		//cout << "4";
+
+	if (!strcmp(base, "N") ||
+		!strcmp(base, "n") ||
+		!strcmp(base, "R") ||
+		!strcmp(base, "r") ||
+		!strcmp(base, "Y") ||
+		!strcmp(base, "y") ||
+		!strcmp(base, "M") ||
+		!strcmp(base, "m") ||
+		!strcmp(base, "K") ||
+		!strcmp(base, "k") ||
+		!strcmp(base, "S") ||
+		!strcmp(base, "s") ||
+		!strcmp(base, "W") ||
+		!strcmp(base, "w") ||
+		!strcmp(base, "B") ||
+		!strcmp(base, "b") ||
+		!strcmp(base, "D") ||
+		!strcmp(base, "d") ||
+		!strcmp(base, "H") ||
+		!strcmp(base, "h") ||
+		!strcmp(base, "V") ||
+		!strcmp(base, "v"))
 		return 'N';
-	}
+
 	return 'X';
 }

From b74f809f655917b738e5af0a18cef08a0f7b3179 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:02:11 -0400
Subject: [PATCH 066/282] Fix bug with broken subopt flag

---
 gtfold-mfe/src/options.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 40a5bfd..48b8ab4 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -82,7 +82,7 @@ void parse_options(int argc, char** argv) {
 				ENABLE_BPP = true;
 			} else if(strcmp(argv[i], "--subopt") == 0) {
 				if(i < argc)
-					suboptDelta = atoi(argv[i]);
+					suboptDelta = atoi(argv[++i]);
 				else
 					help();
 			}

From 71d4db36a10e9c79f3aaf3dfd9340315f3d88bf2 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:02:31 -0400
Subject: [PATCH 067/282] Create SUBOPT_ENABLED bool

---
 gtfold-mfe/include/options.h | 1 +
 gtfold-mfe/src/main.cc       | 2 +-
 gtfold-mfe/src/options.cc    | 2 ++
 3 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index eaed912..3fef36f 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -14,6 +14,7 @@ extern bool USERDATA;
 extern bool PARAMS;
 extern bool LIMIT_DISTANCE;
 extern bool ENABLE_BPP;
+extern bool SUBOPT_ENABLED;
 
 extern string seqfile;
 extern string constraintsFile;
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 0ecdb6b..6cdda8b 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -185,7 +185,7 @@ int main(int argc, char** argv) {
 	printf("- MFE runtime: %9.6f seconds\n", t1);
 	
 	
-	if (suboptDelta > 0)
+	if (SUBOPT_ENABLED)
 	{	
 		t1 = get_seconds();
 		subopt_traceback(seq.length(), suboptDelta);
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 48b8ab4..a63f68d 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -9,6 +9,7 @@ bool USERDATA;
 bool PARAMS;
 bool LIMIT_DISTANCE;
 bool ENABLE_BPP;
+bool SUBOPT_ENABLED;
 
 string seqfile = "";
 string constraintsFile = "";
@@ -81,6 +82,7 @@ void parse_options(int argc, char** argv) {
 			} else if(strcmp(argv[i], "--bpp") == 0) {
 				ENABLE_BPP = true;
 			} else if(strcmp(argv[i], "--subopt") == 0) {
+				SUBOPT_ENABLED = true;
 				if(i < argc)
 					suboptDelta = atoi(argv[++i]);
 				else

From 16cbbf4d0e6a33de1dfb89096c1633d25ddcb114 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:04:27 -0400
Subject: [PATCH 068/282] Use better identification for subopt being enabled

---
 gtfold-mfe/src/options.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index a63f68d..ffcf8b7 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -140,7 +140,7 @@ void printRunConfiguration(string seq) {
 		standardRun = false;
 	}
 
-	if (suboptDelta != -1) {
+	if (SUBOPT_ENABLED) {
 		printf("+ calculating suboptimal structures within %d kcal/mol of MFE\n", suboptDelta);
 		standardRun = false;
 	}

From c4fb41f6f3f053d9038ba634f9662418a0dc3639 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:05:04 -0400
Subject: [PATCH 069/282] Rename ENABLE_BPP to BPP_ENABLED for consistency w/
 SUBOPT_ENABLED

---
 gtfold-mfe/include/options.h | 2 +-
 gtfold-mfe/src/options.cc    | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 3fef36f..f8168d6 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -13,7 +13,7 @@ extern bool NOISOLATE;
 extern bool USERDATA;
 extern bool PARAMS;
 extern bool LIMIT_DISTANCE;
-extern bool ENABLE_BPP;
+extern bool BPP_ENABLED;
 extern bool SUBOPT_ENABLED;
 
 extern string seqfile;
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index ffcf8b7..b6d327f 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -8,7 +8,7 @@ bool NOISOLATE;
 bool USERDATA;
 bool PARAMS;
 bool LIMIT_DISTANCE;
-bool ENABLE_BPP;
+bool BPP_ENABLED;
 bool SUBOPT_ENABLED;
 
 string seqfile = "";
@@ -80,7 +80,7 @@ void parse_options(int argc, char** argv) {
 				else
 					help();	
 			} else if(strcmp(argv[i], "--bpp") == 0) {
-				ENABLE_BPP = true;
+				BPP_ENABLED = true;
 			} else if(strcmp(argv[i], "--subopt") == 0) {
 				SUBOPT_ENABLED = true;
 				if(i < argc)
@@ -135,7 +135,7 @@ void printRunConfiguration(string seq) {
 		standardRun = false;
 	}
 
-	if (ENABLE_BPP == true) {
+	if (BPP_ENABLED == true) {
 		printf("+ calculating base pair probabilities\n");
 		standardRun = false;
 	}

From 73bf04e53a40ef19bc843c81e649f68cbafc79fb Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:29:23 -0400
Subject: [PATCH 070/282] Feature: .ct file output

Now respects input from cli args
If no output file given, generates one by replacing the extension of the
  input file with .ct
Uses the .ct file format from the release branch
---
 gtfold-mfe/src/main.cc    | 24 +++++++++++++++++++++++-
 gtfold-mfe/src/options.cc | 15 +++++++++++++++
 2 files changed, 38 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 6cdda8b..0de88a2 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -101,7 +101,7 @@ int handle_IUPAC_code(const char* str, const int bases)
 	stack_unidentified_base=new int[bases];
 	std::string s = str;
 
-	for(int i = 1; i <= bases; i++) 
+	for(int i = 1; i <= bases; i++)
 	{
 		RNA[i] = getBase((s.substr(i-1,1)).c_str());
 		RNA1[i] = getBase1((s.substr(i-1,1)).c_str());
@@ -145,6 +145,25 @@ void print_header() {
 	printf("Georgia Institute of Technology\n\n");
 }
 
+/**
+ * Save the output to a ct file
+ *
+ * @param outputFile The file to save to
+ * @param energy The MFE energy (multiplied by 100)
+ */
+void save_ct_file(string outputFile, string seq, int energy) {
+	ofstream outfile;
+	outfile.open(outputFile.c_str());
+
+	outfile << seq.length() << "\t  dG = " << energy/100.0 << endl;
+
+	unsigned int i = 1;
+	for(i=1; i <= seq.length(); i++)
+		outfile << i << "\t" << seq[i-1] << "\t" << i-1 << "\t" << (i+1)%(seq.length()+1) << "\t" << structure[i] << "\t" << i << endl;
+
+	outfile.close();
+}
+
 int main(int argc, char** argv) {
 	std::string seq;
 	int energy;
@@ -200,6 +219,9 @@ int main(int argc, char** argv) {
 	trace(seq.length());
 	t1 = get_seconds() - t1;
 	
+	save_ct_file(outputFile, seq, energy);
+	printf("Output saved to %s\n", outputFile.c_str());
+
 	/*
 	std::stringstream ss1, ss2;
 	char suboptfile[1024];
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index b6d327f..0d2d231 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -98,6 +98,20 @@ void parse_options(int argc, char** argv) {
 		help();
 		printf("Missing input file.\n");
 	}
+
+	// If no output file specified, create one
+	if(outputFile.compare("") == 0) {
+
+		// base it off the input file
+		outputFile += seqfile;
+
+		// and if an extension exists, remove it ...
+		if(outputFile.find(".") != string::npos)
+			outputFile.erase(outputFile.rfind("."));
+
+		// ... and append the .ct
+		outputFile += ".ct";
+	}
 }
 
 /**
@@ -152,4 +166,5 @@ void printRunConfiguration(string seq) {
 	printf("- input file: %s\n", seqfile.c_str());
 	printf("  - sequence length: %d\n", (int)seq.length());
 	printf("  - sequence contents: %s\n", seq.c_str());
+	printf("- output file: %s\n", outputFile.c_str());
 }

From 028f5af37323a0bd68538600145b63ea45cd652e Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:35:09 -0400
Subject: [PATCH 071/282] More descriptive output message

---
 gtfold-mfe/src/main.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 0de88a2..de054dc 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -220,7 +220,7 @@ int main(int argc, char** argv) {
 	t1 = get_seconds() - t1;
 	
 	save_ct_file(outputFile, seq, energy);
-	printf("Output saved to %s\n", outputFile.c_str());
+	printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str());
 
 	/*
 	std::stringstream ss1, ss2;

From a09a9c7b83c5960a798a92fc5f7131c850272ba2 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:39:21 -0400
Subject: [PATCH 072/282] Print sequence and structure of MFE result

---
 gtfold-mfe/src/main.cc | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index de054dc..28387e1 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -218,6 +218,10 @@ int main(int argc, char** argv) {
 	t1 = get_seconds();
 	trace(seq.length());
 	t1 = get_seconds() - t1;
+
+	printf("\n");
+	printSequence(seq.length());
+	printStructure(seq.length());
 	
 	save_ct_file(outputFile, seq, energy);
 	printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str());

From d96e7d89f4a5b323be1831645f8b889f42ac262a Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:40:29 -0400
Subject: [PATCH 073/282] Remove unused commented-out code

---
 gtfold-mfe/src/main.cc | 32 +-------------------------------
 1 file changed, 1 insertion(+), 31 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 28387e1..3fd5256 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -226,37 +226,7 @@ int main(int argc, char** argv) {
 	save_ct_file(outputFile, seq, energy);
 	printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str());
 
-	/*
-	std::stringstream ss1, ss2;
-	char suboptfile[1024];
-	ss1 << seq.length();
-	ss2 << energy/100.0;
-
-	strcpy (suboptfile, argv[fileIndex]);
-	strcat ( suboptfile, ".ct");
-	ofstream outfile;
-	outfile.open ( suboptfile );
-
-	fprintf(stdout, "Writing secondary structure to the file: %s\n", suboptfile);
-
-	outfile << bases << "\t  dG = " << energy/100.0;
-	i = 1;
-	while ( i <= bases ) {
-		outfile << endl << i << "\t" << s[i-1] << "\t" << i-1 << "\t" << (i+1)%(bases+1) << "\t" << structure[i] << "\t" << i;
-		i++;
-	}
-	outfile << endl;
-
-	outfile.close();
-
-	fprintf(stdout,"\n\n");
-	fprintf(stdout,"Traceback running time (in seconds): %9.6f\n", t1);
-
-	fprintf(stdout, "\n\nFolding complete\n\n");
-	printSequence(bases);
-	//printConstraints(bases);
-	printStructure(bases);
-*/
+	// release the malloc'd arrays
 	free_fold(seq.length());
 
 	return 0;

From 46ce1de0898d8cf8d14e5f65d2166dd98d3eb83e Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:41:43 -0400
Subject: [PATCH 074/282] return EXIT_SUCCESS instead of 0

---
 gtfold-mfe/src/main.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 3fd5256..f2b706b 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -229,7 +229,7 @@ int main(int argc, char** argv) {
 	// release the malloc'd arrays
 	free_fold(seq.length());
 
-	return 0;
+	return EXIT_SUCCESS;
 }
 
 

From 0176b426ab11eb73aeafe2ca5a1c04eb9d48baa1 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:45:01 -0400
Subject: [PATCH 075/282] Use printf(...) instead of fprintf(stdout, ...) in
 options.cc

---
 gtfold-mfe/src/options.cc | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 0d2d231..00cda4a 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -23,27 +23,27 @@ int contactDistance = -1;
  * Print the help message and quit.
  */
 void help() {
-    fprintf(stdout, "Usage: gtfold [OPTION]... FILE\n\n");
+    printf("Usage: gtfold [OPTION]... FILE\n\n");
 
-    fprintf(stdout, "  FILE is an RNA sequence file.  Single line or FASTA formats are accepted.\n\n");
+    printf("  FILE is an RNA sequence file.  Single line or FASTA formats are accepted.\n\n");
 
-    fprintf(stdout, "OPTIONS\n");
-    fprintf(stdout, "   -c, --constraints FILE\n                        Load constraints from FILE.  See Constraint syntax below\n");
-    fprintf(stdout, "   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n                        limit is given, base pairs can be over any distance\n");
-    fprintf(stdout, "   -n, --noisolate      Prevent isolated base pairs from forming\n");
-    fprintf(stdout, "   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
-    fprintf(stdout, "   -t, --threads num    Limit number of threads used\n");
+    printf("OPTIONS\n");
+    printf("   -c, --constraints FILE\n                        Load constraints from FILE.  See Constraint syntax below\n");
+    printf("   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n                        limit is given, base pairs can be over any distance\n");
+    printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
+    printf("   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
+    printf("   -t, --threads num    Limit number of threads used\n");
 
-    fprintf(stdout, "\n");
-    fprintf(stdout, "   -h, --help           Output help (this message) and exit\n");
-    fprintf(stdout, "   -v, --verbose        Run in verbose mode\n");
+    printf("\n");
+    printf("   -h, --help           Output help (this message) and exit\n");
+    printf("   -v, --verbose        Run in verbose mode\n");
 
-    fprintf(stdout, "\nBETA OPTIONS\n");
-    fprintf(stdout, "   --bpp                Calculate base pair probabilities\n");
-    fprintf(stdout, "   --subopt range       Calculate suboptimal structures within 'range' kcal/mol\n");
-    fprintf(stdout, "                        of the mfe\n");
+    printf("\nBETA OPTIONS\n");
+    printf("   --bpp                Calculate base pair probabilities\n");
+    printf("   --subopt range       Calculate suboptimal structures within 'range' kcal/mol\n");
+    printf("                        of the mfe\n");
 
-    fprintf(stdout, "\nConstraint syntax:\n\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
+    printf("\nConstraint syntax:\n\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
     exit(-1);
 }
 

From a05f7266355b5c2061420bf78139eff6251957a9 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:46:36 -0400
Subject: [PATCH 076/282] Format constraint syntax help code more nicely

---
 gtfold-mfe/src/options.cc | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 00cda4a..19870c3 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -43,7 +43,10 @@ void help() {
     printf("   --subopt range       Calculate suboptimal structures within 'range' kcal/mol\n");
     printf("                        of the mfe\n");
 
-    printf("\nConstraint syntax:\n\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
+    printf("\nConstraint syntax:\n");
+    printf("\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n");
+    printf("\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n");
+    printf("\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
     exit(-1);
 }
 

From 40ba483b1de4196bc91a758c942ba9c616d31ec4 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:49:44 -0400
Subject: [PATCH 077/282] Use .empty() instead of .compare("") == 0 for strings

---
 gtfold-mfe/src/options.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 19870c3..5b32e52 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -97,13 +97,13 @@ void parse_options(int argc, char** argv) {
 	}
 
 	// Must have an input file specified
-	if(seqfile.compare("") == 0) {
+	if(seqfile.empty()) {
 		help();
 		printf("Missing input file.\n");
 	}
 
 	// If no output file specified, create one
-	if(outputFile.compare("") == 0) {
+	if(outputFile.empty()) {
 
 		// base it off the input file
 		outputFile += seqfile;

From b920b0a6786abf73bb7c781de6d4a406be05c01d Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:52:32 -0400
Subject: [PATCH 078/282] Fewer long lines in options help text output

---
 gtfold-mfe/src/options.cc | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 5b32e52..ae96c29 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -28,8 +28,10 @@ void help() {
     printf("  FILE is an RNA sequence file.  Single line or FASTA formats are accepted.\n\n");
 
     printf("OPTIONS\n");
-    printf("   -c, --constraints FILE\n                        Load constraints from FILE.  See Constraint syntax below\n");
-    printf("   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n                        limit is given, base pairs can be over any distance\n");
+    printf("   -c, --constraints FILE\n");
+    printf("                        Load constraints from FILE.  See Constraint syntax below\n");
+    printf("   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n");
+    printf("                        limit is given, base pairs can be over any distance\n");
     printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
     printf("   -t, --threads num    Limit number of threads used\n");

From fda76853f213b2fe8eee08b3f0ffeb47ed3efa83 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 02:53:15 -0400
Subject: [PATCH 079/282] Don't need to return at end of void methods

---
 gtfold-mfe/src/main.cc | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index f2b706b..2a1bd1c 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -50,17 +50,14 @@ double get_seconds()
 
 void init_fold(int len) 
 {	
-
  	init_global_params(len);
 	create_tables(len);
-	return;
 }
 
 void free_fold(int len) 
 {
 	free_global_params();
 	free_tables(len);
-	return;
 }
 
 /**

From 1fd581e5924c6225624765001a182900cbce6cc5 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 03:04:25 -0400
Subject: [PATCH 080/282] Rename getBase() to encode() and use switch-case

---
 gtfold-mfe/include/utils.h |  2 +-
 gtfold-mfe/src/main.cc     |  2 +-
 gtfold-mfe/src/utils.cc    | 86 +++++++++++++++++++-------------------
 3 files changed, 44 insertions(+), 46 deletions(-)

diff --git a/gtfold-mfe/include/utils.h b/gtfold-mfe/include/utils.h
index a865fac..1764c81 100644
--- a/gtfold-mfe/include/utils.h
+++ b/gtfold-mfe/include/utils.h
@@ -8,7 +8,7 @@
 #define MAX(X,Y) ((X) > (Y) ? (X) : (Y))
 
 char baseToDigit(const char* base) ;
-unsigned char getBase(const char* base) ;
+unsigned char encode(char base);
 unsigned char getBase1(const char* base) ;
 
 #endif
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 2a1bd1c..d93805b 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -100,7 +100,7 @@ int handle_IUPAC_code(const char* str, const int bases)
 
 	for(int i = 1; i <= bases; i++)
 	{
-		RNA[i] = getBase((s.substr(i-1,1)).c_str());
+		RNA[i] = encode(s[i-1]);
 		RNA1[i] = getBase1((s.substr(i-1,1)).c_str());
 
 		if (RNA[i]=='X') 
diff --git a/gtfold-mfe/src/utils.cc b/gtfold-mfe/src/utils.cc
index 2203015..7edb821 100644
--- a/gtfold-mfe/src/utils.cc
+++ b/gtfold-mfe/src/utils.cc
@@ -21,50 +21,48 @@ char baseToDigit(const char* base) {
 	return (char) '0';
 }
 
-unsigned char getBase(const char* base) {
-	if (!strcmp(base, "A") ||
-		!strcmp(base, "a"))
-		return BASE_A;
-
-	if (!strcmp(base, "C") ||
-		!strcmp(base, "c"))
-		return BASE_C;
-
-	if (!strcmp(base, "G") ||
-		!strcmp(base, "g"))
-		return BASE_G;
-
-	if (!strcmp(base, "U") ||
-		!strcmp(base, "u") ||
-		!strcmp(base, "T") ||
-		!strcmp(base, "t"))
-		return BASE_U;
-
-	if (!strcmp(base, "N") ||
-		!strcmp(base, "n") ||
-		!strcmp(base, "R") ||
-		!strcmp(base, "r") ||
-		!strcmp(base, "Y") ||
-		!strcmp(base, "y") ||
-		!strcmp(base, "M") ||
-		!strcmp(base, "m") ||
-		!strcmp(base, "K") ||
-		!strcmp(base, "k") ||
-		!strcmp(base, "S") ||
-		!strcmp(base, "s") ||
-		!strcmp(base, "W") ||
-		!strcmp(base, "w") ||
-		!strcmp(base, "B") ||
-		!strcmp(base, "b") ||
-		!strcmp(base, "D") ||
-		!strcmp(base, "d") ||
-		!strcmp(base, "H") ||
-		!strcmp(base, "h") ||
-		!strcmp(base, "V") ||
-		!strcmp(base, "v"))
-		return BASE_A;
-
-	return 'X';
+unsigned char encode(char base) {
+	switch(base) {
+		case 'A':
+		case 'a':
+			return BASE_A;
+		case 'C':
+		case 'c':
+			return BASE_C;
+		case 'G':
+		case 'g':
+			return BASE_G;
+		case 'U':
+		case 'u':
+		case 'T':
+		case 't':
+			return BASE_U;
+		case 'N':
+		case 'n':
+		case 'R':
+		case 'r':
+		case 'Y':
+		case 'y':
+		case 'M':
+		case 'm':
+		case 'K':
+		case 'k':
+		case 'S':
+		case 's':
+		case 'W':
+		case 'w':
+		case 'B':
+		case 'b':
+		case 'D':
+		case 'd':
+		case 'H':
+		case 'h':
+		case 'V':
+		case 'v':
+			return BASE_A;
+		default:
+			return 'X';
+	}
 }
 
 /**

From 08c6b0c6c3958b2313bd4feb06c2ab4a2b733dcc Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 03:09:19 -0400
Subject: [PATCH 081/282] A little cleanup in handle_IUPAC_code()

---
 gtfold-mfe/src/main.cc | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index d93805b..59cf81c 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -119,10 +119,10 @@ int handle_IUPAC_code(const char* str, const int bases)
 	{
 		printf("IUPAC codes have been detected at positions:");
 
-		for(int i=0;i<stack_count;i++)
-		{
-			printf("%d , ",stack_unidentified_base[i]);
-		}
+		printf("%d", stack_unidentified_base[0]);
+		for(int i=1;i<stack_count;i++)
+			printf(", %d", stack_unidentified_base[i]);
+
 		printf("\n");
 		//printf("You may wish to resubmit the sequence with fully specified positions. Alternatively, GTfold will fold the sequence under the standard assumption that these ambiguous positions do not pair.  Do you wish to continue with the current computation? <Y/N>");
 		//char reply;
@@ -131,9 +131,7 @@ int handle_IUPAC_code(const char* str, const int bases)
 		return SUCCESS;
 	}
 	else 
-	{
 		return SUCCESS;
-	}
 }
 
 void print_header() {

From 43ad3a1a34e87602110afde7b1703ce9765cef67 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 03:15:21 -0400
Subject: [PATCH 082/282] Compare against BASE_{A,C,G,U} instead of 0,1,2,3

Print U when the sequence's value is a U, not a T like before
---
 gtfold-mfe/src/global.c | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c
index 3b0ae9b..ddeca97 100644
--- a/gtfold-mfe/src/global.c
+++ b/gtfold-mfe/src/global.c
@@ -42,14 +42,14 @@ void printSequence(int len)
 	int i;
 	for (i = 1; i <= len; i++) 
 	{
-		if (RNA1[i] == 0)
+		if (RNA1[i] == BASE_A)
 			printf("A");
-		else if (RNA1[i] == 1)
+		else if (RNA1[i] == BASE_C)
 			printf("C");
-		else if (RNA1[i] == 2)
+		else if (RNA1[i] == BASE_G)
 			printf("G");
-		else if (RNA1 [i] == 3)
-			printf("T");
+		else if (RNA1 [i] == BASE_U)
+			printf("U");
 		else
 			printf("N");
 	}

From 1bdee67d67180f43dd95c3816171a4bfdb1d0d42 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 03:25:14 -0400
Subject: [PATCH 083/282] Better code the handling of non-canonical bases

---
 gtfold-mfe/include/global.h |  1 -
 gtfold-mfe/include/main-c.h |  1 -
 gtfold-mfe/include/utils.h  |  2 +-
 gtfold-mfe/src/global.c     | 15 +++------
 gtfold-mfe/src/main.cc      |  3 +-
 gtfold-mfe/src/utils.cc     | 64 +++++++++++--------------------------
 6 files changed, 24 insertions(+), 62 deletions(-)

diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h
index 22ce165..2ec9596 100644
--- a/gtfold-mfe/include/global.h
+++ b/gtfold-mfe/include/global.h
@@ -3,7 +3,6 @@
 
 #include "constants.h"
 
-extern unsigned char *RNA1; 
 extern unsigned char *RNA; 
 extern int *structure; 
 
diff --git a/gtfold-mfe/include/main-c.h b/gtfold-mfe/include/main-c.h
index ba7d6eb..f56f853 100644
--- a/gtfold-mfe/include/main-c.h
+++ b/gtfold-mfe/include/main-c.h
@@ -21,7 +21,6 @@
 #define _MAIN_C_H
 
 extern int LENGTH;
-extern unsigned char *RNA1; /* [LENGTH] */
 extern unsigned char *RNA; /* [LENGTH] */
 extern int *structure; /* [LENGTH] */
 extern int *V; /* [(LENGTH-1)*(LENGTH)/2 + 1] */
diff --git a/gtfold-mfe/include/utils.h b/gtfold-mfe/include/utils.h
index 1764c81..5a726b2 100644
--- a/gtfold-mfe/include/utils.h
+++ b/gtfold-mfe/include/utils.h
@@ -9,6 +9,6 @@
 
 char baseToDigit(const char* base) ;
 unsigned char encode(char base);
-unsigned char getBase1(const char* base) ;
+int isWatsonCrickBase(char base);
 
 #endif
diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c
index ddeca97..6d7c4e7 100644
--- a/gtfold-mfe/src/global.c
+++ b/gtfold-mfe/src/global.c
@@ -3,7 +3,6 @@
 
 #include "global.h"
 
-unsigned char *RNA1; 
 unsigned char *RNA; 
 int *structure; 
 unsigned int chPairKey;
@@ -16,11 +15,6 @@ void init_global_params(int len)
 		perror("Cannot allocate variable 'RNA'");
 		exit(-1);
 	}
-	RNA1 = (unsigned char *) malloc((len+1) * sizeof(unsigned char));
-	if (RNA1 == NULL) {
-		perror("Cannot allocate variable 'RNA'");
-		exit(-1);
-	}
 	structure = (int *) malloc((len+1) * sizeof(int));
 	if (structure == NULL) {
 		perror("Cannot allocate variable 'structure'");
@@ -34,7 +28,6 @@ void free_global_params()
 {
 	free(structure);
 	free(RNA);
-	free(RNA1);
 }
 
 void printSequence(int len) 
@@ -42,13 +35,13 @@ void printSequence(int len)
 	int i;
 	for (i = 1; i <= len; i++) 
 	{
-		if (RNA1[i] == BASE_A)
+		if (RNA[i] == BASE_A)
 			printf("A");
-		else if (RNA1[i] == BASE_C)
+		else if (RNA[i] == BASE_C)
 			printf("C");
-		else if (RNA1[i] == BASE_G)
+		else if (RNA[i] == BASE_G)
 			printf("G");
-		else if (RNA1 [i] == BASE_U)
+		else if (RNA[i] == BASE_U)
 			printf("U");
 		else
 			printf("N");
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 59cf81c..f8b4c54 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -101,14 +101,13 @@ int handle_IUPAC_code(const char* str, const int bases)
 	for(int i = 1; i <= bases; i++)
 	{
 		RNA[i] = encode(s[i-1]);
-		RNA1[i] = getBase1((s.substr(i-1,1)).c_str());
 
 		if (RNA[i]=='X') 
 		{
 			fprintf(stderr,"ERROR: Base unrecognized\n");
 			return FAILURE;
 		}
-		else if(RNA[i]!='X' && RNA1[i]=='N')
+		else if(RNA[i]!='X' && !isWatsonCrickBase(s[i-1]))
 		{
 			unspecd=1;
 			stack_unidentified_base[stack_count]=i;
diff --git a/gtfold-mfe/src/utils.cc b/gtfold-mfe/src/utils.cc
index 7edb821..982871e 100644
--- a/gtfold-mfe/src/utils.cc
+++ b/gtfold-mfe/src/utils.cc
@@ -66,51 +66,23 @@ unsigned char encode(char base) {
 }
 
 /**
- * Identical to getBase but returns 'N' instead of 'A' for non-standard bases
- * (a,c,g,u)
+ * Returns true if the given base is an A, C, G, U, or T
+ * @param base 'A', 'C', 'G', 'U', etc.
  */
-unsigned char getBase1(const char* base) {
-	if (!strcmp(base, "A") ||
-		!strcmp(base, "a"))
-		return BASE_A;
-
-	if (!strcmp(base, "C") ||
-		!strcmp(base, "c"))
-		return BASE_C;
-
-	if (!strcmp(base, "G") ||
-		!strcmp(base, "g"))
-		return BASE_G;
-
-	if (!strcmp(base, "U") ||
-		!strcmp(base, "u") ||
-		!strcmp(base, "T") ||
-		!strcmp(base, "t"))
-		return BASE_U;
-
-	if (!strcmp(base, "N") ||
-		!strcmp(base, "n") ||
-		!strcmp(base, "R") ||
-		!strcmp(base, "r") ||
-		!strcmp(base, "Y") ||
-		!strcmp(base, "y") ||
-		!strcmp(base, "M") ||
-		!strcmp(base, "m") ||
-		!strcmp(base, "K") ||
-		!strcmp(base, "k") ||
-		!strcmp(base, "S") ||
-		!strcmp(base, "s") ||
-		!strcmp(base, "W") ||
-		!strcmp(base, "w") ||
-		!strcmp(base, "B") ||
-		!strcmp(base, "b") ||
-		!strcmp(base, "D") ||
-		!strcmp(base, "d") ||
-		!strcmp(base, "H") ||
-		!strcmp(base, "h") ||
-		!strcmp(base, "V") ||
-		!strcmp(base, "v"))
-		return 'N';
-
-	return 'X';
+int isWatsonCrickBase(char base) {
+	switch(base) {
+		case 'A':
+		case 'a':
+		case 'C':
+		case 'c':
+		case 'G':
+		case 'g':
+		case 'U':
+		case 'u':
+		case 'T':
+		case 't':
+			return true;
+		default:
+			return false;
+	}
 }

From bb47fd7576313360f28e52ad54d18f70a0f771b1 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 16:00:39 -0700
Subject: [PATCH 084/282] Add description to encode()

---
 gtfold-mfe/src/utils.cc | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/gtfold-mfe/src/utils.cc b/gtfold-mfe/src/utils.cc
index 982871e..8c6ffbe 100644
--- a/gtfold-mfe/src/utils.cc
+++ b/gtfold-mfe/src/utils.cc
@@ -21,6 +21,14 @@ char baseToDigit(const char* base) {
 	return (char) '0';
 }
 
+/**
+ * Encodes the given base to a number.
+ *
+ * Handles upper- and lower-case letters.
+ *
+ * @param base The character to encode
+ * @return The numerical encoding of the base
+ */
 unsigned char encode(char base) {
 	switch(base) {
 		case 'A':

From 8e89ccca24c7e31a335ed2ead7e8bd4b0586aa99 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 16:13:34 -0700
Subject: [PATCH 085/282] Rename handle_IUPAC_code() to encodeSequence() and
 cleanup

---
 gtfold-mfe/src/main.cc | 79 +++++++++++++++++++++---------------------
 1 file changed, 40 insertions(+), 39 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index f8b4c54..e04dba3 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -90,47 +90,48 @@ int read_sequence_file(const char* filename, std::string& seq)
 	return SUCCESS;
 }
 
-int handle_IUPAC_code(const char* str, const int bases)
-{
-	int* stack_unidentified_base;
-	int stack_count=0;
-	bool unspecd=0;
-	stack_unidentified_base=new int[bases];
-	std::string s = str;
-
-	for(int i = 1; i <= bases; i++)
-	{
-		RNA[i] = encode(s[i-1]);
-
-		if (RNA[i]=='X') 
-		{
-			fprintf(stderr,"ERROR: Base unrecognized\n");
-			return FAILURE;
-		}
-		else if(RNA[i]!='X' && !isWatsonCrickBase(s[i-1]))
-		{
-			unspecd=1;
-			stack_unidentified_base[stack_count]=i;
-			stack_count++;
+/**
+ * Encode the given string of letters into an RNA sequence.
+ *
+ * This handles IUPAC codes and places the results into the array RNA.
+ *
+ * @param seq The string to encode
+ * @return A boolean representing success or failure of the encoding.  Failure
+ *         can occur when seeing unknown IUPAC codes.
+ */
+bool encodeSequence(string seq) {
+	unsigned int unspecifiedBaseCount=0;
+	unsigned int unspecifiedBases[seq.length()];
+
+	for(unsigned int i=1; i<=seq.length(); i++) {
+		RNA[i] = encode(seq[i-1]);
+
+		// die on non-IUPAC codes
+		if (RNA[i]=='X') {
+			fprintf(stderr, "ERROR: Non-IUPAC nucleotide code at position: %d (%c)\n", i, seq[i-1]);
+			fprintf(stderr, "See http://www.bioinformatics.org/sms/iupac.html for valid codes.\n");
+			return false;
 		}
+
+		// add non-canonical IUPAC codes to the warning list
+		if(!isWatsonCrickBase(seq[i-1]))
+			unspecifiedBases[unspecifiedBaseCount++]=i;
 	}
-	if(unspecd) 
-	{
-		printf("IUPAC codes have been detected at positions:");
-
-		printf("%d", stack_unidentified_base[0]);
-		for(int i=1;i<stack_count;i++)
-			printf(", %d", stack_unidentified_base[i]);
-
-		printf("\n");
-		//printf("You may wish to resubmit the sequence with fully specified positions. Alternatively, GTfold will fold the sequence under the standard assumption that these ambiguous positions do not pair.  Do you wish to continue with the current computation? <Y/N>");
-		//char reply;
-		//scanf("%c",&reply);
-		//return (reply=='n'||reply=='N')?(FAILURE):(SUCCESS);
-		return SUCCESS;
+
+	// just print a warning for non-canonical IUPAC codes
+	if(unspecifiedBaseCount > 0) {
+		printf("\nNon-canonical IUPAC codes have been detected at position%s: ", unspecifiedBaseCount == 1 ? "" : "s");
+
+		// put [0] first for nice comma separation
+		printf("%d (%c)", unspecifiedBases[0], seq.at(unspecifiedBases[0]-1));
+		for(unsigned int i=1; i<unspecifiedBaseCount; i++)
+			printf(", %d (%c)", unspecifiedBases[i], seq[unspecifiedBases[i]-1]);
+
+		printf("\nPlease replace with canonical IUPAC codes (A,C,G,U,T) and retry.\n");
+		return false;
 	}
-	else 
-		return SUCCESS;
+
+	return true;
 }
 
 void print_header() {
@@ -179,7 +180,7 @@ int main(int argc, char** argv) {
 	
 	init_fold(seq.length());
 	
-	if (handle_IUPAC_code(seq.c_str(), seq.length())  == FAILURE)
+	if (!encodeSequence(seq))
 	{
 		free_fold(seq.length());
 		exit(0);

From 4b017ca5cdea7a9df13edf59bd2e96c6e19e7d4f Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 16:23:28 -0700
Subject: [PATCH 086/282] Better output message for failed mallocs

Also replace variable with array in output message
---
 gtfold-mfe/src/energy.c | 38 +++++++++++++++++++-------------------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 76dbc51..82a6741 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -30,62 +30,62 @@ void create_tables(int len)
 	V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
 	if (V == NULL) 
 	{
-		perror("Cannot allocate variable 'V'");
+		perror("Cannot allocate array 'V'");
 		exit(-1);
 	}
 
 	VV1 = (int *) malloc((len+ 1)*sizeof(int));
 	if (VV1 == NULL) 
 	{
-		perror("Cannot allocate variable 'V'");
+		perror("Cannot allocate array 'VV1'");
 		exit(-1);
 	}
 	VV = (int *) malloc((len+ 1)*sizeof(int));
 	if (VV == NULL) 
 	{
-		perror("Cannot allocate variable 'V'");
+		perror("Cannot allocate array 'VV'");
 		exit(-1);
 	}
 
 	WMi = (int *) malloc((len+ 1)*sizeof(int));
 	if (WMi == NULL) 
 	{
-		perror("Cannot allocate variable 'V'");
+		perror("Cannot allocate array 'WMi'");
 		exit(-1);
 	}
 
 	WMi1 = (int *) malloc((len+ 1)*sizeof(int));
 	if (WMi1 == NULL) 
 	{
-		perror("Cannot allocate variable 'V'");
+		perror("Cannot allocate array 'WMi1'");
 		exit(-1);
 	}
 
 	WMi2 = (int *) malloc((len+ 1)*sizeof(int));
 	if (WMi2 == NULL) 
 	{
-		perror("Cannot allocate variable 'V'");
+		perror("Cannot allocate array 'WMi2'");
 		exit(-1);
 	}
 
 	WM = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
 	if (WM == NULL) 
 	{
-		perror("Cannot allocate variable 'V'");
+		perror("Cannot allocate array 'WM'");
 		exit(-1);
 	}
 
 	VM = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
 	if (VM == NULL) 
 	{
-		perror("Cannot allocate variable 'V'");
+		perror("Cannot allocate array 'VM'");
 		exit(-1);
 	}
 
 	VBI = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
 	if (VBI == NULL) 
 	{
-		perror("Cannot allocate variable 'V'");
+		perror("Cannot allocate array 'VBI'");
 		exit(-1);
 	}
 
@@ -93,13 +93,13 @@ void create_tables(int len)
 	V = (int **) malloc((len+1)* sizeof(int *));
 	if (V == NULL) 
 	{
-		perror("Cannot allocate variable 'VM'");
+		perror("Cannot allocate array 'VM'");
 		exit(-1);
 	}
 	for (i = 0; i < len+1; i++) {
 		V[i] = (int *) malloc((len+1)*sizeof(int));
 		if (V[i] == NULL) {
-			perror("Cannot allocate variable 'VM[i]'");
+			perror("Cannot allocate array 'VM[i]'");
 			exit(-1);
 		}
 	}
@@ -108,7 +108,7 @@ void create_tables(int len)
 	W = (int *) malloc((len+1) * sizeof(int));
 	if (W == NULL) 
 	{
-		perror("Cannot allocate variable 'W'");
+		perror("Cannot allocate array 'W'");
 		exit(-1);
 	}
 
@@ -116,7 +116,7 @@ void create_tables(int len)
 	VBI = (int **) malloc((len+1) * sizeof(int *));
 	if (VBI == NULL) 
 	{
-		perror("Cannot allocate variable 'VBI'");
+		perror("Cannot allocate array 'VBI'");
 		exit(-1);
 	}
 
@@ -124,7 +124,7 @@ void create_tables(int len)
 		VBI[i] = (int *) malloc((len+1)* sizeof(int));
 		if (VBI[i] == NULL) 
 		{
-			perror("Cannot allocate variable 'VBI[i]'");
+			perror("Cannot allocate array 'VBI[i]'");
 			exit(-1);
 		}
 	}
@@ -132,13 +132,13 @@ void create_tables(int len)
 	VM = (int **) malloc((len+1)* sizeof(int *));
 	if (VM == NULL) 
 	{
-		perror("Cannot allocate variable 'VM'");
+		perror("Cannot allocate array 'VM'");
 		exit(-1);
 	}
 	for (i = 0; i < len+1; i++) {
 		VM[i] = (int *) malloc((len+1)*sizeof(int));
 		if (VM[i] == NULL) {
-			perror("Cannot allocate variable 'VM[i]'");
+			perror("Cannot allocate array 'VM[i]'");
 			exit(-1);
 		}
 	}
@@ -146,14 +146,14 @@ void create_tables(int len)
 	WM = (int **) malloc((len+1)*sizeof(int *));
 	if (WM == NULL) 
 	{
-		perror("Cannot allocate variable 'WM'");
+		perror("Cannot allocate array 'WM'");
 		exit(-1);
 	}
 	for (i = 0; i < len+1; i++) 
 	{
 		WM[i] = (int *) malloc((len+1)*sizeof(int));
 		if (WM[i] == NULL) {
-			perror("Cannot allocate variable 'WM[i]'");
+			perror("Cannot allocate array 'WM[i]'");
 			exit(-1);
 		}
 	}
@@ -161,7 +161,7 @@ void create_tables(int len)
     
 	indx = (int*) malloc((len+1) * sizeof(int));
 	if (indx == NULL) {
-		perror("Cannot allocate variable 'indx'");
+		perror("Cannot allocate array 'indx'");
 		exit(-1);
 	}
 

From 1c275f0e38b504a44df7b594d785671be28bbe7d Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 18 Mar 2011 16:24:58 -0700
Subject: [PATCH 087/282] s/canonical/fully-specified/ in output messages

---
 gtfold-mfe/src/main.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index e04dba3..17bd505 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -120,14 +120,14 @@ bool encodeSequence(string seq) {
 
 	// just print a warning for non-canonical IUPAC codes
 	if(unspecifiedBaseCount > 0) {
-		printf("\nNon-canonical IUPAC codes have been detected at position%s: ", unspecifiedBaseCount == 1 ? "" : "s");
+		printf("\nIncompletely-specified IUPAC codes have been detected at position%s: ", unspecifiedBaseCount == 1 ? "" : "s");
 
 		// put [0] first for nice comma separation
 		printf("%d (%c)", unspecifiedBases[0], seq.at(unspecifiedBases[0]-1));
 		for(unsigned int i=1; i<unspecifiedBaseCount; i++)
 			printf(", %d (%c)", unspecifiedBases[i], seq[unspecifiedBases[i]-1]);
 
-		printf("\nPlease replace with canonical IUPAC codes (A,C,G,U,T) and retry.\n");
+		printf("\nPlease replace with fully-specified IUPAC codes (A,C,G,U,T) and retry.\n");
 		return false;
 	}
 

From f833d96a7d3582bbc0400fc18f4928ddac1e56ff Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 22 Mar 2011 15:39:21 -0400
Subject: [PATCH 088/282] changed access of WM array to improve locality

---
 gtfold-mfe/include/algorithms.h       |   2 +-
 gtfold-mfe/include/energy.h           |  28 +--
 gtfold-mfe/include/subopt_traceback.h |  37 ++--
 gtfold-mfe/src/algorithms.c           | 140 +++++++-------
 gtfold-mfe/src/energy.c               | 189 ++++---------------
 gtfold-mfe/src/main.cc                |   2 +-
 gtfold-mfe/src/options.cc             |  18 +-
 gtfold-mfe/src/subopt_traceback.cc    | 261 +++++++++++---------------
 8 files changed, 262 insertions(+), 415 deletions(-)

diff --git a/gtfold-mfe/include/algorithms.h b/gtfold-mfe/include/algorithms.h
index 4a654d4..336e443 100644
--- a/gtfold-mfe/include/algorithms.h
+++ b/gtfold-mfe/include/algorithms.h
@@ -23,7 +23,7 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
-	int calculate(int len);
+	int calculate(int len, int nThreads);
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h
index 2498e28..c5fdb1f 100644
--- a/gtfold-mfe/include/energy.h
+++ b/gtfold-mfe/include/energy.h
@@ -9,33 +9,21 @@ extern int *VV1;
 extern int *W; 
 extern int *VBI; 
 extern int *VM; 
-extern int *WM; 
-extern int *WMi; 
-extern int *WMi1; 
-extern int *WMi2; 
-//extern int **VBI; 
-//extern int **WM; 
-//extern int **V; 
-//extern int **VM; 
+extern int **WM; 
+extern int *WMu; 
+extern int *WMl; 
 extern int *indx; 
 
 
 #define V(i,j) V[indx[j]+i]
 #define VM(i,j) VM[indx[j]+i]
-#define WM(i,j) WM[indx[j]+i]
+#define WM(i,j) WM[i][j]
+#define WMU(i,j) WM[i][j]
+#define WML(i,j) WM[j][i]
+//#define WMU(i,j) WMu[indx[j]+i]
+//#define WML(i,j) WMl[indx[j]+i]
 #define VBI(i,j) VBI[indx[j]+i]
 
-//#define V(i,j) V[indx[i]+j]
-//#define VM(i,j) VM[indx[i]+j]
-//#define WM(i,j) WM[indx[i]+j]
-//#define VBI(i,j) VBI[indx[i]+j]
-
-//#define V(i,j) V[i][j]
-//#define VM(i,j) VM[i][j]
-//#define WM(i,j) WM[i][j]
-//#define VBI(i,j) VBI[i][j]
-
-
 #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0)
 
 #ifdef __cplusplus
diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h
index d3c6beb..a02839e 100644
--- a/gtfold-mfe/include/subopt_traceback.h
+++ b/gtfold-mfe/include/subopt_traceback.h
@@ -75,17 +75,22 @@ struct segment
 	}
 };
 
+typedef segment SEG;
+typedef std::stack<segment>  SEGSTACK;
+
 struct pstruct
 {
 	std::string str;
-	std::stack<segment> st_segment;
-	std::stack<segment> st_v; /* used for backtracking in traceWM */
+	SEGSTACK st_segment;
+	SEGSTACK st_v; /* used for backtracking in traceWM */
+	
 	int ae_;
 	int le_;
 
 	int total() const { return ae_ + le_; }
 
 	pstruct() {}
+	
 	pstruct(const pstruct& ps)
 	{
 		str = ps.str;
@@ -174,7 +179,7 @@ struct pstruct
 
 	void print()
 	{
-		std::stack<segment> st = st_segment;
+		SEGSTACK st = st_segment;
 		std::cout <<'[' << ' ' ;
 		while (!st.empty())
 		{
@@ -196,16 +201,26 @@ struct pstruct
 	}
 };
 
+/* partial structure */
+typedef pstruct ps_t;
+
+/* partial structure stack */
+typedef std::stack<pstruct> ps_stack_t;
+
+/*  partial structure map */
+typedef std::map<std::string, pstruct> ps_map_t;
+
+/* secondary structure map */
+typedef std::map<std::string, int> ss_map_t;	
 
-void push_to_gstack(std::stack<pstruct>& gs, const pstruct& v);
+void push_to_gstack(ps_stack_t & gs, const ps_t& v);
 
-void subopt_traceback(int len, int delta);
-void traceV(int i, int j, pstruct& ps, std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
-void traceVBI( int i, int j, pstruct& ps, std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
-void traceW( int i, int j, pstruct& ps, std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
-void traceVM( int i, int j, pstruct& ps, std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
-void traceWM(pstruct& ps, std::map<std::string, pstruct>& filter, int MIN_ENERGY, int delta1);
+ss_map_t subopt_traceback(int len, int gap);
 
-//enum label {lW=0, lV, lVBI, lVM, lWM};
+void traceV(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); 
+void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs, int energy);
+void traceW(int i, int j, ps_t & ps, ps_stack_t & gs, int energy);
+void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs, int energy);
+void traceWM(ps_t& ps, ps_map_t& filter);
 
 #endif
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 42ab0ad..5bee7c5 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -40,32 +40,33 @@ double get_seconds() {
 	return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0;
 }
 
-int calculate(int len) { 
-	int i, j;
+int calculate(int len, int nThreads) { 
+	int b, i, j;
 	double t1, t2, tint=0, thair=0,tst=0, tml=0, twm=0;
 
-#if 1
+#ifdef _OPENMP
+	if (nThreads>0) omp_set_num_threads(nThreads);
+#endif
+
 #ifdef _OPENMP
 #pragma omp parallel
 #pragma omp master
-		fprintf(stdout,"\n");
-		fprintf(stdout,"Running with %3d OpenMP thread",omp_get_num_threads());
-		if (omp_get_num_threads()>1) fprintf(stdout,"s");
-		fprintf(stdout,".\n");
-#endif
+	fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
 #endif
-	//for (b = TURN+1; b <= len-1; b++) {
-	for (i = len-TURN-1; i >= 1; i--) {
+
+	for (b = TURN+1; b <= len-1; b++) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
 #endif
-		//	for (i = 1; i <= len - b; i++) {
-		for (j = i+TURN+1; j <= len; j++) {
-			//j = i + b;
-			if (canPair(RNA[i], RNA[j])) {
-				int p, q, h;
-				int newV = INFINITY_;
-				int VBIij = INFINITY_;
+		for (i = 1; i <= len - b; i++) {
+			j = i + b;
+			int newWM = INFINITY_;
+			int bPair = 0;
+			
+			if (canPair(RNA[i], RNA[j])) { 
+				bPair = 1;
+				int p=0, q=0, h;
+				int newV = INFINITY_, VBIij = INFINITY_;
 
 				t1 = get_seconds();
 				newV  = MIN(eH(i, j), newV);
@@ -74,29 +75,29 @@ int calculate(int len) {
 
 				t1 = get_seconds();
 				int stackEnergy = eS(i, j); 
-				//newV= MIN(stackEnergy + V(i+1,j-1), newV);
-				newV= MIN(stackEnergy + VV1[j-1] , newV);
+				newV= MIN(stackEnergy + V(i+1,j-1), newV);
 				t2 = get_seconds();
 				tst += (t2-t1); 
 
 				if (j-i > 6) { 
-				t1 = get_seconds();
-				// Int Loop BEGIN
-				for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
-					int minq = j-i+p-MAXLOOP-2;
-					if (minq < p+1+TURN) minq = p+1+TURN;
-					for (q = minq; q < j; q++) {
-						if (!canPair(RNA[p], RNA[q])) continue;
-						VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
+					t1 = get_seconds();
+					// Int Loop BEGIN
+					for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
+						int minq = j-i+p-MAXLOOP-2;
+						if (minq < p+1+TURN) minq = p+1+TURN;
+						for (q = minq; q < j; q++) {
+							if (!canPair(RNA[p], RNA[q])) continue;
+							VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
+						}
 					}
-				}
 
-				VBI(i,j) = VBIij;
-				// Int Loop END
-				t2 = get_seconds();
-				tint += (t2-t1); 
-				newV = MIN(newV, VBIij);
+					VBI(i,j) = VBIij;
+					// Int Loop END
+					t2 = get_seconds();
+					tint += (t2-t1); 
+					newV = MIN(newV, VBIij);
 				}
+				
 				if (j-i > 10) {	
 					t1 = get_seconds();
 
@@ -105,14 +106,11 @@ int calculate(int len) {
 					VMij = VMijd = VMidj = VMidjd = INFINITY_;
 
 					for (h = i+TURN+1; h <= j-1-TURN; h++) { 
-						//VMij = MIN(VMij, WM(i+1,h-1) + WM(h,j-1));		
-						VMij = MIN(VMij, WMi1[h-1] + WM(h,j-1));		
-						//VMidj = MIN(VMidj, WM(i+2,h-1) + WM(h,j-1));	
-						VMidj = MIN(VMidj, WMi2[h-1] + WM(h,j-1));	
-						//VMijd = MIN(VMijd, WM(i+1,h-1) + WM(h,j-2));	
-						VMijd = MIN(VMijd, WMi1[h-1] + WM(h,j-2));	
-						//VMidjd = MIN(VMidjd, WM(i+2,h-1) + WM(h,j-2));	
-						VMidjd = MIN(VMidjd, WMi2[h-1] + WM(h,j-2));	
+						VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1));		
+						VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1));	
+						VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2));	
+						VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2));	
+						newWM = MIN(newWM, VMij);
 					}
 
 					int d3 = Ed3(i,j,j-1);
@@ -130,52 +128,46 @@ int calculate(int len) {
 					t2 = get_seconds();
 					tml += (t2-t1);
 				}
-				V(i,j) = newV;
-
-				VV[j] = newV;
+				V(i,j) = VV[i] = newV;
 			}
 
 			if (j-i > 4) {	
 				t1 = get_seconds();
 				// WM BEGIN
-				int h, newWM = INFINITY_;
-				//newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM);
-				newWM = MIN(VV[j] + auPenalty(i,j) + Eb, newWM);
-				//newWM = MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM);
-				newWM = MIN(VV1[j] + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM);
-				//newWM = MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM);
-				newWM = MIN(VV[j-1] + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM);
-				//newWM = MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM) ;
-				newWM = MIN(VV1[j-1] + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM) ;
-
-				//newWM = MIN(WM(i+1,j) + Ec, newWM);
-				newWM = MIN(WMi1[j] + Ec, newWM);
-				//newWM = MIN(WM(i,j-1) + Ec, newWM);
-				newWM = MIN(WMi[j-1] + Ec, newWM);
-
-				for (h = i ; h <= j-TURN-1; h++) {
-					//newWM = MIN(newWM, WM(i,h) + WM(h+1,j));
-					newWM = MIN(newWM, WMi[h] + WM(h+1,j));
+				int h; 	
+				if (!bPair) {
+					for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
+						newWM = MIN(newWM, WMU(i,h-1) + WML(h,j));
+					}
 				}
-				WM(i,j) = WMi[j]=newWM;
+				
+				newWM = MIN(VV[i] + auPenalty(i,j) + Eb, newWM);  //V(i,j)
+				newWM = MIN(VV1[i+1] + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM); //V(i+1,j) 
+				newWM = MIN(VV1[i] + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM); //V(i,j-1)
+				newWM = MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM) ;
+
+				newWM = MIN(WMU(i+1,j) + Ec, newWM);
+				newWM = MIN(WML(i,j-1) + Ec, newWM);
+
+				WMU(i,j) = WML(i,j) = newWM;
 				// WM END
 
 				t2 = get_seconds();
 				twm += (t2-t1);
 			}
 		}
-		int *FF;
-		FF = VV1; VV1=VV; VV=FF;
-		FF = WMi2; WMi2 = WMi1; WMi1 = WMi; WMi = FF;
-		for (j=1; j<=len; j++) {VV[j]=INFINITY_;WMi[j]=INFINITY_; }
+
+		int* FF;
+		FF=VV1; VV1=VV; VV=FF;
+		for (i = 1; i <= len; i++)
+			VV[i] = INFINITY_;
 	}
 
-	printf("Runtime Statistics:\n");
-	printf("- total IntLoop time = %fs \n",tint);
-	printf("- total Stack time = %fs \n",tst);
-	printf("- total HairPin time = %fs \n",thair);
-	printf("- total MultiLoop time = %fs \n",tml);
-	printf("- total WM time = %fs \n",twm);
+	printf("Total IntLoop time = %fs \n",tint);
+	printf("Total Stack time = %fs \n",tst);
+	printf("Total HairPin time = %fs \n",thair);
+	printf("Total MultiLoop time = %fs \n",tml);
+	printf("Total WM time = %fs \n",twm);
 
 	for (j = TURN+2; j <= len; j++)	{
 		int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
@@ -187,7 +179,7 @@ int calculate(int len) {
 			Wij = V(i, j) + auPenalty(i, j) + Wim1;
 			Widjd = V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1;
 			Wijd = V(i,j-1) + auPenalty(i,j- 1) + Ed5(j-1,i,j) + Wim1;
-			Widj = V(i + 1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1;
+			Widj = V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1;
 			Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); 
 		}
 
diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 82a6741..80f37c3 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -13,155 +13,64 @@ int *VV1;
 int *W; 
 int *VBI; 
 int *VM; 
-int *WM; 
-int *WMi; 
-int *WMi1; 
-int *WMi2; 
-//int **V; 
-//int **WM; 
-//int **VM; 
-//int **VBI; 
+int **WM; 
 int *indx; 
 
 void create_tables(int len)
 {	
-	//int i;
-	
 	V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
-	if (V == NULL) 
-	{
-		perror("Cannot allocate array 'V'");
+	if (V == NULL) {
+		perror("Cannot allocate variable 'V'");
 		exit(-1);
 	}
 
 	VV1 = (int *) malloc((len+ 1)*sizeof(int));
-	if (VV1 == NULL) 
-	{
-		perror("Cannot allocate array 'VV1'");
-		exit(-1);
-	}
-	VV = (int *) malloc((len+ 1)*sizeof(int));
-	if (VV == NULL) 
-	{
-		perror("Cannot allocate array 'VV'");
-		exit(-1);
-	}
-
-	WMi = (int *) malloc((len+ 1)*sizeof(int));
-	if (WMi == NULL) 
-	{
-		perror("Cannot allocate array 'WMi'");
+	if (VV1 == NULL) {
+		perror("Cannot allocate variable 'V'");
 		exit(-1);
 	}
 
-	WMi1 = (int *) malloc((len+ 1)*sizeof(int));
-	if (WMi1 == NULL) 
-	{
-		perror("Cannot allocate array 'WMi1'");
-		exit(-1);
-	}
-
-	WMi2 = (int *) malloc((len+ 1)*sizeof(int));
-	if (WMi2 == NULL) 
-	{
-		perror("Cannot allocate array 'WMi2'");
+	VV = (int *) malloc((len+ 1)*sizeof(int));
+	if (VV == NULL) {
+		perror("Cannot allocate variable 'V'");
 		exit(-1);
 	}
-
-	WM = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
-	if (WM == NULL) 
-	{
-		perror("Cannot allocate array 'WM'");
+	
+	int i;
+	WM = (int **) malloc((len+1)* sizeof(int *));
+	if (WM == NULL) {
+		perror("Cannot allocate variable 'WM'");
 		exit(-1);
-	}
+	}   
+	for (i = 0; i <= len; i++) {
+		WM[i] = (int *)malloc((len+1)* sizeof(int));
+		if (WM[i] == NULL) {
+			perror("Cannot allocate variable 'WM[i]'");
+			exit(-1);
+		}   
+	}   
 
 	VM = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
-	if (VM == NULL) 
-	{
-		perror("Cannot allocate array 'VM'");
+	if (VM == NULL) {
+		perror("Cannot allocate variable 'V'");
 		exit(-1);
 	}
 
 	VBI = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
-	if (VBI == NULL) 
-	{
-		perror("Cannot allocate array 'VBI'");
+	if (VBI == NULL) {
+		perror("Cannot allocate variable 'V'");
 		exit(-1);
 	}
 
-	/*
-	V = (int **) malloc((len+1)* sizeof(int *));
-	if (V == NULL) 
-	{
-		perror("Cannot allocate array 'VM'");
-		exit(-1);
-	}
-	for (i = 0; i < len+1; i++) {
-		V[i] = (int *) malloc((len+1)*sizeof(int));
-		if (V[i] == NULL) {
-			perror("Cannot allocate array 'VM[i]'");
-			exit(-1);
-		}
-	}
-	*/
-
 	W = (int *) malloc((len+1) * sizeof(int));
-	if (W == NULL) 
-	{
-		perror("Cannot allocate array 'W'");
-		exit(-1);
-	}
-
-	/*
-	VBI = (int **) malloc((len+1) * sizeof(int *));
-	if (VBI == NULL) 
-	{
-		perror("Cannot allocate array 'VBI'");
-		exit(-1);
-	}
-
-	for (i = 0; i < len+1; i++) {
-		VBI[i] = (int *) malloc((len+1)* sizeof(int));
-		if (VBI[i] == NULL) 
-		{
-			perror("Cannot allocate array 'VBI[i]'");
-			exit(-1);
-		}
-	}
-
-	VM = (int **) malloc((len+1)* sizeof(int *));
-	if (VM == NULL) 
-	{
-		perror("Cannot allocate array 'VM'");
+	if (W == NULL) {
+		perror("Cannot allocate variable 'W'");
 		exit(-1);
 	}
-	for (i = 0; i < len+1; i++) {
-		VM[i] = (int *) malloc((len+1)*sizeof(int));
-		if (VM[i] == NULL) {
-			perror("Cannot allocate array 'VM[i]'");
-			exit(-1);
-		}
-	}
 
-	WM = (int **) malloc((len+1)*sizeof(int *));
-	if (WM == NULL) 
-	{
-		perror("Cannot allocate array 'WM'");
-		exit(-1);
-	}
-	for (i = 0; i < len+1; i++) 
-	{
-		WM[i] = (int *) malloc((len+1)*sizeof(int));
-		if (WM[i] == NULL) {
-			perror("Cannot allocate array 'WM[i]'");
-			exit(-1);
-		}
-	}
-	*/
-    
 	indx = (int*) malloc((len+1) * sizeof(int));
 	if (indx == NULL) {
-		perror("Cannot allocate array 'indx'");
+		perror("Cannot allocate variable 'indx'");
 		exit(-1);
 	}
 
@@ -171,21 +80,14 @@ void create_tables(int len)
 
 void init_tables(int len) 
 {
-	int i, LLL;
+	int i, j, LLL;
 	
 	for (i = 0; i <= len; i++) {
 		W[i] = INFINITY_; 
 		VV[i] = INFINITY_;
 		VV1[i] = INFINITY_;
-		WMi[i] = INFINITY_;
-		WMi1[i] = INFINITY_;
-		WMi2[i] = INFINITY_;
-		//for (j = 0; j <= len; j++) {
-			//V[i][j] = INFINITY_;
-			//VBI[i][j] = INFINITY_;
-			//VM[i][j] = INFINITY_;
-			//WM[i][j] = INFINITY_;
-		//}
+		for (j = 0; j <= len; j++) 
+			WM[i][j] = INFINITY_;
 	}
 	
 	
@@ -193,16 +95,10 @@ void init_tables(int len)
 
 	for (i = 0; i < LLL; i++) {
 		V[i] = INFINITY_;
-		WM[i] = INFINITY_;
 		VM[i] = INFINITY_;
 		VBI[i] = INFINITY_;
 	}
 
-	/*
-	for (i = 0; i <= len; i++) {
-		indx[i] = (len)*(i-1)-(i*(i-1))/2;
-	}*/
-
 	for (i = 1; i <= (unsigned) len; i++) 
 	    indx[i] = (i*(i-1)) >> 1;        /* n(n-1)/2 */
 
@@ -212,27 +108,17 @@ void init_tables(int len)
 void free_tables(int len)
 {
 	free(indx);
-	//for (i = 0; i < len; i++)
-	//	free(WM[i]);
 	
+	int i;
+	for (i = 0; i <= len; i++)
+	         free(WM[i]);
 	free(WM);
-	
-	//for (i = 0; i < len; i++)
-	//	free(VM[i]);
-	free(VM);
-	
 
-	//for (i = 0; i < len; i++)
-	//	free(V[i]);
+	free(VM);
+	free(VBI);
 	free(V);
 	free(VV);
 	free(VV1);
-
-
-	//for (i = 0; i < len; i++)
-	//	free(VBI[i]);
-	
-	free(VBI);
 	free(W);
 }
 
@@ -241,8 +127,7 @@ inline int Ed3(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][1];}
 inline int Ed5(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][0]; }
 inline int auPenalty(int i, int j) { return auPen(RNA[i], RNA[j]);}
 
-inline int eL(int i, int j, int ip, int jp) 
-{
+inline int eL(int i, int j, int ip, int jp) {
 	int energy;
 	int size1, size2, size;
 	int loginc; /* SH: Originally unassiged, but needs to be set to 0 so it doesn't throw off later calculations. */
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 17bd505..4bafcc9 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -190,7 +190,7 @@ int main(int argc, char** argv) {
 	fflush(stdout);
 
 	t1 = get_seconds();
-	energy = calculate(seq.length());
+	energy = calculate(seq.length(), nThreads);
 	t1 = get_seconds() - t1;
 	
 	printf("Done.\n\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index ae96c29..9a747eb 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -129,15 +129,15 @@ void printRunConfiguration(string seq) {
 
 	printf("Run Configuration:\n");
 
-#ifdef _OPENMP
-	if(nThreads == -1)
-		printf("- [OMP] thread count: %d\n", omp_get_num_threads());
-	else
-		printf("- [OMP] thread count: %d\n", nThreads);
-#else
-	printf("- thread count: 1\n");
-#endif
-
+//#ifdef _OPENMP
+//	if(nThreads == -1)
+//		printf("- [OMP] thread count: %d\n", omp_get_num_threads());
+//	else
+//		printf("- [OMP] thread count: %d\n", nThreads);
+//#else
+//	printf("- thread count: 1\n");
+//#endif
+//
 
 	if (NOISOLATE == true) {
 		printf("- preventing isolated base pairs\n");
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index e11bd40..45c72d9 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -20,28 +20,24 @@
 
  */
 
-#include "subopt_traceback.h"
+#include <cstdio>
+
 #include "constants.h"
 #include "energy.h"
-#include "global.h"
 #include "utils.h"
-#ifdef _OPENMP   /* The compiler automatically recognizes openmp support and includes the file accordingly*/
-#include "omp.h"
-#endif
-#include <cstdio>
-
-extern int nThreads;
+#include "global.h"
+#include "subopt_traceback.h"
 
 const char* lstr[] = {"W", "V", "VBI", "VM", "WM"};
 
-void (*trace_func[5]) (int i, int j, pstruct& ps,std::stack<pstruct>& gs, int MIN_ENERGY, int delta1);
+void (*trace_func[5]) (int i, int j, ps_t& ps, ps_stack_t& gs, int energy);
 
-void print_stack(std::stack<pstruct> temp)
+void print_stack(ps_stack_t temp)
 {	
 	std::cout << "{\n";
 	while (!temp.empty())
 	{
-		pstruct ps = temp.top();
+		ps_t ps = temp.top();
 		temp.pop();
 		ps.print();
 		std::cout << '\n' ;
@@ -49,33 +45,32 @@ void print_stack(std::stack<pstruct> temp)
 	std::cout << "}\n";
 }
 
-void subopt_traceback1(int energy, int len)
+void process(ss_map_t& subopt_data, int energy, int len)
 {
-	int MIN_ENERGY = energy;
-	int delta1 = 0;
 	int count = 0 ;
-
-	std::stack<pstruct> gstack;
-	std::map<std::string, int> data;
+	ps_stack_t gstack;
 
 	// initialize the partial structure
 	// segment stack = {[1,n]}, label = W, list_bp = {} 
-	pstruct first(0, len);
+	ps_t first(0, len);
 	first.push(segment(5, len, lW, W[len]));	
 	gstack.push(first); // initialize the partial structure stacka
 
-	std::map<std::string, int> subopt_data;
-
 	while (1)
 	{
 		if (gstack.empty()) break; // exit
-		pstruct ps = gstack.top();
+
+		ps_t ps = gstack.top();
 		gstack.pop(); 
 
 		if (ps.empty()) 
 		{
-			std::cout << ps.str << " dG =" << ps.ae_ << std::endl;
-			count++;
+			//std::cout << ps.str << " dG =" << ps.ae_ << std::endl;
+			if (subopt_data.find(ps.str) == subopt_data.end())
+			{
+				subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
+				count++;
+			}
 			continue;
 		}	
 		else
@@ -86,67 +81,54 @@ void subopt_traceback1(int energy, int len)
 
 			if (smt.j_ - smt.i_ >=4)
 			{
-				(*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack, MIN_ENERGY, delta1);
+				(*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack, energy);
 			}
 
-			if (gstack.size() == s1 && ps.total() <= MIN_ENERGY + delta1)
+			if (gstack.size() == s1 && ps.total() <= energy)
 			{
-				pstruct ps1(ps);
+				ps_t ps1(ps);
 				gstack.push(ps1);
 			}
 		}
 	}
-	//std::cout << "total structures (dG = " <<  MIN_ENERGY << ") = " << count << std::endl;
 }
 
-
-void subopt_traceback(int len, int delta)
+ss_map_t subopt_traceback(int len, int delta)
 {
-#ifdef _OPENMP
-	if (nThreads >= 0) omp_set_num_threads(nThreads);
-#endif
-
-#ifdef _OPENMP
-#pragma omp parallel
-#pragma omp master
-	fprintf(stdout,"Traceback -- Running with %3d OpenMP thread \n",omp_get_num_threads());
-#endif
 	trace_func[0] = traceW;
 	trace_func[1] = traceV;
 	trace_func[2] = traceVBI;
 	trace_func[3] = traceVM;
 	//trace_func[4] = traceWM;
 
-	int min_energy = W[len];
+	int mfe = W[len];
 	int level = 0; 
-	int len1 = len;
 
-#ifdef _OPENMP
-#pragma omp parallel for private (level) shared(len1) schedule(guided)
-#endif
-	for (level = min_energy; level <= min_energy + delta; level += 10)
-	{
-		subopt_traceback1(level, len1);			
-	}
+	ss_map_t subopt_data;
+
+	for (level = mfe; level <= mfe + delta; level += 10)
+		process(subopt_data, level, len);			
+
+	return subopt_data;
 }
 
-void traceV(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENERGY, int delta1)
+void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 {
 	// Hairpin Loop
-	if (eH(i,j) + ps.total()  <= MIN_ENERGY + delta1)
+	if (eH(i,j) + ps.total()  <= energy )
 	{
 		//	std::cout << "Hairpin " << i  << ' ' << j << std::endl;
-		pstruct ps1(ps); 
+		ps_t ps1(ps); 
 		ps1.accumulate(eH(i,j));
 		ps1.update(i, j, '(', ')');
 		push_to_gstack(gstack, ps1);
 	}
 
 	// Stack
-	if (eS(i, j) + V(i+1, j-1) + ps.total() <= MIN_ENERGY +delta1)
+	if (eS(i, j) + V(i+1, j-1) + ps.total() <= energy)
 	{
 		//	std::cout << "Stack " << i  << ' ' << j << std::endl;
-		pstruct ps1(ps);
+		ps_t ps1(ps);
 		ps1.push(segment(i+1, j-1, lV, V(i+1, j-1)));
 		ps1.accumulate(eS(i,j));
 		ps1.update(i, j , '(', ')');
@@ -154,20 +136,20 @@ void traceV(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENER
 	}
 
 	// Internal Loop
-	if (VBI(i,j) + ps.total() <= MIN_ENERGY + delta1)
+	if (VBI(i,j) + ps.total() <= energy )
 	{
 		//std::cout << "Internal " << i  << ' ' << j << std::endl;
-		pstruct ps1(ps);
+		ps_t ps1(ps);
 		ps1.push(segment(i, j, lVBI, VBI(i,j)));
 		ps1.update(i, j, '(', ')');
 		push_to_gstack(gstack, ps1);
 	}
 
 	// Multiloop
-	if ( VM(i,j) + ps.total() <= MIN_ENERGY + delta1)
+	if ( VM(i,j) + ps.total() <= energy )
 	{
 		//	std::cout << "Multi " << i  << ' ' << j << std::endl;
-		pstruct ps1(ps);
+		ps_t ps1(ps);
 		ps1.push(segment(i, j, lVM, VM(i,j)));
 		ps1.update(i, j, '(', ')');
 		push_to_gstack(gstack, ps1);
@@ -175,26 +157,19 @@ void traceV(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENER
 
 }
 
-void traceVBI(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENERGY, int delta1)
+void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 {
 	int p,q;
-
-#ifdef _OPENMP
-#pragma omp parallel for private (p) shared(ps) schedule(dynamic)
-#endif
 	for (p = i+1; p < MIN(j-2-TURN, i+MAXLOOP+1); ++p)
 	{
 		int minq = j-i+p-MAXLOOP-2;
 		if (minq < p+1+TURN) minq = p+1+TURN;
 
-#ifdef _OPENMP
-#pragma omp parallel for private (q) shared(j, minq, ps) schedule(dynamic)
-#endif
 		for (q = minq; q < j; q++) 
 		{
-			if (V(p, q) + eL(i, j, p, q) + ps.total() <= MIN_ENERGY + delta1)
+			if (V(p, q) + eL(i, j, p, q) + ps.total() <= energy )
 			{
-				pstruct ps1(ps);
+				ps_t ps1(ps);
 				ps1.push(segment(p, q, lV, V(p, q)));
 				ps1.accumulate(eL(i, j, p, q));
 				push_to_gstack(gstack, ps1);
@@ -203,7 +178,7 @@ void traceVBI(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_EN
 	}
 }
 
-void traceW(int h, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENERGY, int delta1)
+void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 {
 	if ( (h>=j) || j == 0 || j == 1) return;
 
@@ -212,9 +187,9 @@ void traceW(int h, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENER
 		int wim1 =  MIN(0, W[i-1]);
 
 		int wij = V(i,j) + auPenalty(i, j) + wim1;
-		if (wij + ps.total() <= MIN_ENERGY + delta1)
+		if (wij + ps.total() <= energy )
 		{
-			pstruct ps1(ps);
+			ps_t ps1(ps);
 			ps1.push(segment(i, j, lV, V(i,j)));
 			if (wim1 <= 0 && i > 1) ps1.push(segment(1, i-1, lW, W[i-1]));
 			ps1.accumulate(auPenalty(i, j));
@@ -222,9 +197,9 @@ void traceW(int h, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENER
 		}		
 
 		int wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
-		if (wijd + ps.total() <= MIN_ENERGY + delta1)
+		if (wijd + ps.total() <= energy )
 		{
-			pstruct ps3(ps);
+			ps_t ps3(ps);
 			ps3.push(segment(i, j-1, lV, V(i, j-1)));
 			if (wim1 <= 0 && i > 1)	ps3.push(segment(1, i-1, lW, W[i-1]));
 			ps3.accumulate(auPenalty(i,j-1) + Ed5(j-1,i,j)); 
@@ -232,9 +207,9 @@ void traceW(int h, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENER
 		}	
 
 		int widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
-		if (widj + ps.total() <= MIN_ENERGY + delta1)
+		if (widj + ps.total() <= energy )
 		{
-			pstruct ps4(ps);
+			ps_t ps4(ps);
 			ps4.push(segment(i+1, j, lV, V(i+1,j)));
 			if (wim1 <= 0 && i > 1) ps4.push(segment(1, i-1, lW, W[i-1]));
 			ps4.accumulate(auPenalty(i+1, j) + Ed3(j,i+1,i));
@@ -242,9 +217,9 @@ void traceW(int h, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENER
 		}
 
 		int widjd = V(i+1, j-1) + auPenalty(i+1,j-1) + Ed3(j-1, i+1, i) + Ed5(j-1, i+1, j) + wim1;
-		if (widjd + ps.total() <= MIN_ENERGY + delta1)
+		if (widjd + ps.total() <= energy )
 		{
-			pstruct ps2(ps);
+			ps_t ps2(ps);
 			ps2.push(segment(i+1, j-1, lV, V(i+1,j-1)));
 			if (wim1 <= 0 && i > 1) ps2.push(segment(1, i-1, lW, W[i-1]));
 			ps2.accumulate(auPenalty(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
@@ -252,24 +227,22 @@ void traceW(int h, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENER
 		}
 	}
 
-	if (W[j-1] + ps.total() <= MIN_ENERGY + delta1)
+	if (W[j-1] + ps.total() <= energy )
 	{
-		pstruct ps1(ps);
+		ps_t ps1(ps);
 		ps1.push(segment(1, j-1, lW, W[j-1]));
 		push_to_gstack(gstack, ps1);
 	}	
 }
 
-void traceWM(pstruct& ps, std::map<std::string, pstruct>& filter, int MIN_ENERGY, int delta1)
+void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 {
-	int b = Eb; 
-	int c = Ec; 
-	std::stack<pstruct> wm_stack;
+	ps_stack_t wm_stack;
 	wm_stack.push(ps);
 
 	while (!wm_stack.empty())
 	{
-		pstruct pss = wm_stack.top();
+		ps_t pss = wm_stack.top();
 		wm_stack.pop();
 
 		// check if all segments in pss are Vs
@@ -284,7 +257,7 @@ void traceWM(pstruct& ps, std::map<std::string, pstruct>& filter, int MIN_ENERGY
 				pss.push(ss);
 				key[ss.i_-1] = '*'; key[ss.j_-1] = '*';
 			}
-			filter.insert(std::pair<std::string, pstruct>(key, pss));
+			filter.insert(std::pair<std::string, ps_t>(key, pss));
 			continue;
 		}
 
@@ -295,71 +268,71 @@ void traceWM(pstruct& ps, std::map<std::string, pstruct>& filter, int MIN_ENERGY
 
 		if (wm_seg.label_ == lV)
 		{
-			pstruct ps1(pss);
+			ps_t ps1(pss);
 			ps1.push_v(wm_seg);
 			wm_stack.push(ps1);
 			continue;
 		}
 		int h = i1; int k = j1;
 
-		int wmij = V(h,k) + auPenalty(h,k) +  b ;
-		if (pss.total() + wmij <= MIN_ENERGY + delta1)
+		int wmij = V(h,k) + auPenalty(h,k) + Eb;
+		if (pss.total() + wmij <= energy )
 		{
-			pstruct ps1(pss);
+			ps_t ps1(pss);
 			ps1.push_v(segment(h,k,lV, V(h,k)));
-			ps1.accumulate(auPenalty(h,k) + b);
+			ps1.accumulate(auPenalty(h,k) + Eb);
 			wm_stack.push(ps1);
 		}
 
-		int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) + b + c ;
-		if (pss.total() + wmijd <= MIN_ENERGY + delta1)
+		int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+ Ec ;
+		if (pss.total() + wmijd <= energy )
 		{
-			pstruct ps1(pss);
+			ps_t ps1(pss);
 			ps1.push_v(segment(h,k-1,lV, V(h,k-1)));
-			ps1.accumulate(Ed5(k-1,h,k)+ auPenalty(h,k-1) +b+c);
+			ps1.accumulate(Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+Ec);
 			wm_stack.push(ps1);
 		}
 
-		int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + b+c ;
-		if (pss.total() + wmidj <= MIN_ENERGY + delta1)
+		int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + Eb+Ec ;
+		if (pss.total() + wmidj <= energy )
 		{
-			pstruct ps1(pss);
+			ps_t ps1(pss);
 			ps1.push_v(segment(h+1, k, lV, V(h+1,k)));
-			ps1.accumulate(Ed3(k,h+1,h) + auPenalty(h+1,k) +b+c);
+			ps1.accumulate(Ed3(k,h+1,h) + auPenalty(h+1,k) +Eb+Ec);
 			wm_stack.push(ps1);
 		}
 
-		int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) +  auPenalty(h+1,k-1) + b + 2*c ;
-		if (pss.total() + wmidjd <= MIN_ENERGY + delta1)
+		int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) +  auPenalty(h+1,k-1) +Eb+ 2*Ec ;
+		if (pss.total() + wmidjd <= energy )
 		{
-			pstruct ps1(pss);
+			ps_t ps1(pss);
 			ps1.push_v(segment(h+1, k-1, lV, V(h+1,k-1)));
-			ps1.accumulate(Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) + b + 2*c);
+			ps1.accumulate(Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec);
 			wm_stack.push(ps1);
 		}
 
 
-		if (pss.total() + WM(i1,j1-1)  + c  <= MIN_ENERGY + delta1)
+		if (pss.total() + WM(i1,j1-1)  + Ec  <= energy )
 		{
-			pstruct ps1(pss);
+			ps_t ps1(pss);
 			ps1.push(segment(i1,j1-1, lWM, WM(i1,j1-1)));		
-			ps1.accumulate(c);
+			ps1.accumulate(Ec);
 			wm_stack.push(ps1);
 		}
 
-		if (pss.total() + WM(i1+1,j1) + c <= MIN_ENERGY + delta1)
+		if (pss.total() + WM[i1+1][j1] + Ec <= energy )
 		{
-			pstruct ps1(pss);
+			ps_t ps1(pss);
 			ps1.push(segment(i1+1,j1, lWM, WM(i1+1,j1)));		
-			ps1.accumulate(c);
+			ps1.accumulate(Ec);
 			wm_stack.push(ps1);
 		}
 
 		for (int h = i1+1; h <= j1-1; ++h)
 		{	
-			if (WM(i1,h) + WM(h+1,j1) + pss.total() <= MIN_ENERGY + delta1)
+			if (WM(i1,h) + WM(h+1,j1) + pss.total() <= energy )
 			{
-				pstruct ps1(pss);
+				ps_t ps1(pss);
 				ps1.push(segment(i1, h, lWM, WM(i1,h)));
 				ps1.push(segment(h+1, j1, lWM, WM(h+1,j1)));
 				wm_stack.push(ps1);
@@ -368,73 +341,67 @@ void traceWM(pstruct& ps, std::map<std::string, pstruct>& filter, int MIN_ENERGY
 	}
 }
 
-void traceVM(int i, int j, pstruct& ps, std::stack<pstruct>& gstack, int MIN_ENERGY, int delta1)
+void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 {
-	std::map<std::string, pstruct> filter;
+	std::map<std::string, ps_t> filter;
 	int h;	
 
-#ifdef _OPENMP
-#pragma omp parallel for private (h) shared(i,j,filter,ps) schedule(dynamic)
-#endif
 	for (h = i+1; h <= j-1; ++h)
 	{
-		int energy;
-		int a = Ea; //multConst[0]; 
-		int b = Eb; //multConst[2]; 
-		int c = Ec; //multConst[1]; 
+		int dG;
 		int d5 = Ed5(i,j,i+1);
 		int d3 = Ed3(i,j,j-1);
-		int common = auPenalty(i,j) + a + b;
+		int common = auPenalty(i,j) + Ea + Eb;
 
-		energy = common + WM(i+1,h-1) + WM(h,j-1);
-		if (energy + ps.total()  <= MIN_ENERGY + delta1)
+		dG = common + WM[i+1][h-1] + WM[h][j-1];
+		if (dG + ps.total()  <= energy )
 		{
-			pstruct ps1(ps);
-			ps1.push(segment(i+1,h-1, lWM, WM(i+1,h-1)));
-			ps1.push(segment(h, j-1, lWM, WM(h,j-1)));
+			ps_t ps1(ps);
+			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));
+			ps1.push(segment(h, j-1, lWM, WM[h][j-1]));
 			ps1.accumulate(common) ; 
-			traceWM(ps1, filter, MIN_ENERGY, delta1);
+			traceWM(ps1, filter, energy);
 		}
 
-		energy =  common + WM(i+2,h-1) + WM(h,j-1) + d5 + c;
-		if (energy + ps.total()  <= MIN_ENERGY + delta1)
+		dG =  common + WM[i+2][h-1] + WM[h][j-1] + d5 + Ec;
+		if (dG + ps.total()  <= energy )
 		{
-			pstruct ps1(ps);
-			ps1.push(segment(i+2,h-1, lWM, WM(i+2,h-1)));	
-			ps1.push(segment(h, j-1, lWM, WM(h,j-1)));	
-			ps1.accumulate(common + d5 + c);
-			traceWM(ps1, filter, MIN_ENERGY, delta1);
+			ps_t ps1(ps);
+			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
+			ps1.push(segment(h, j-1, lWM, WM[h][j-1]));	
+			ps1.accumulate(common + d5 + Ec);
+			traceWM(ps1, filter, energy);
 		}
 
-		energy = common + WM(i+1,h-1) + WM(h,j-2) + d3 + c;
-		if (energy + ps.total()  <= MIN_ENERGY + delta1)
+		dG = common + WM[i+1][h-1] + WM[h][j-2] + d3 + Ec;
+		if (dG + ps.total()  <= energy )
 		{
-			pstruct ps1(ps);	
-			ps1.push(segment(i+1,h-1, lWM, WM(i+1,h-1)));	
-			ps1.push(segment(h, j-2, lWM, WM(h,j-2)));	
-			ps1.accumulate(common + d3 + c);
-			traceWM(ps1, filter, MIN_ENERGY, delta1);
+			ps_t ps1(ps);	
+			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));	
+			ps1.push(segment(h, j-2, lWM, WM[h][j-2]));	
+			ps1.accumulate(common + d3 + Ec);
+			traceWM(ps1, filter, energy);
 		}
 
-		energy = common + WM(i+2,h-1) + WM(h,j-2) + d5 + d3 + 2*c;
-		if (energy + ps.total()  <= MIN_ENERGY + delta1)
+		dG = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*Ec;
+		if (dG + ps.total()  <= energy )
 		{ 	
-			pstruct ps1(ps);	
-			ps1.push(segment(i+2,h-1, lWM, WM(i+2,h-1)));	
-			ps1.push(segment(h, j-2, lWM, WM(h,j-2)));	
-			ps1.accumulate(common + d3 + d5 + 2*c) ;
-			traceWM(ps1, filter, MIN_ENERGY, delta1);
+			ps_t ps1(ps);	
+			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
+			ps1.push(segment(h, j-2, lWM, WM[h][j-2]));	
+			ps1.accumulate(common + d3 + d5 + 2*Ec) ;
+			traceWM(ps1, filter, energy);
 		}
 	}
 
-	std::map<std::string, pstruct>::iterator it ;
+	ps_map_t::iterator it ;
 	for (it = filter.begin(); it != filter.end(); ++it)
 	{
 		push_to_gstack(gstack, it->second);
 	}
 }
 
-void push_to_gstack( std::stack<pstruct>& gstack , const pstruct& v)
+void push_to_gstack(ps_stack_t& gstack , const ps_t& v)
 {
 	gstack.push(v);
 }

From 1c2cd71b4e3d1db909f701d54f73539da4fed7d1 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Fri, 25 Mar 2011 14:56:14 -0700
Subject: [PATCH 089/282] Ignore spaces in the sequence file

Fixes GH-27
---
 gtfold-mfe/src/main.cc | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 17bd505..a22aeff 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -87,6 +87,10 @@ int read_sequence_file(const char* filename, std::string& seq)
 
 	fs.close();
 
+    size_t loc;
+    while((loc = seq.find(" ")) != string::npos)
+        seq.erase(loc, 1);
+
 	return SUCCESS;
 }
 

From af731740b401a59373d9547a87b37189114386a6 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Sun, 27 Mar 2011 21:45:57 -0400
Subject: [PATCH 090/282] made func canPair accesible from cplusplus code,
 other minor changes

---
 gtfold-mfe/include/global.h |  7 ++++---
 gtfold-mfe/src/global.c     | 36 +++++++++++++-----------------------
 2 files changed, 17 insertions(+), 26 deletions(-)

diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h
index 2ec9596..fe2d9df 100644
--- a/gtfold-mfe/include/global.h
+++ b/gtfold-mfe/include/global.h
@@ -5,21 +5,22 @@
 
 extern unsigned char *RNA; 
 extern int *structure; 
+extern int* constraints;
 
 extern unsigned int chPairKey;
 
 // The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). 
 #define checkPair(i, j) (((((i)-(j)) % 2) == 1 || (((i)-(j)) % 2)== -1) && (!( ((i)==BASE_A && (j)==BASE_C) || ((i)==BASE_C && (j)==BASE_A) )))
 
-inline int canPair(int a, int b);
 
 #ifdef __cplusplus
 extern "C" {
 #endif
+int canPair(int a, int b);
 void init_global_params(int len);
 void free_global_params();
-void printSequence(int len); 
-void printStructure(int len); 
+void print_sequence(int len); 
+void print_structure(int len); 
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c
index 6d7c4e7..a72088c 100644
--- a/gtfold-mfe/src/global.c
+++ b/gtfold-mfe/src/global.c
@@ -7,9 +7,7 @@ unsigned char *RNA;
 int *structure; 
 unsigned int chPairKey;
 
-
-void init_global_params(int len)
-{
+void init_global_params(int len) {
 	RNA = (unsigned char *) malloc((len+1)* sizeof(unsigned char));
 	if (RNA == NULL) {
 		perror("Cannot allocate variable 'RNA'");
@@ -20,21 +18,18 @@ void init_global_params(int len)
 		perror("Cannot allocate variable 'structure'");
 		exit(-1);
 	}
-	
+
 	init_checkPair();
 }
 
-void free_global_params()
-{
+void free_global_params() {
 	free(structure);
 	free(RNA);
 }
 
-void printSequence(int len) 
-{
+void print_sequence(int len) {
 	int i;
-	for (i = 1; i <= len; i++) 
-	{
+	for (i = 1; i <= len; i++) {
 		if (RNA[i] == BASE_A)
 			printf("A");
 		else if (RNA[i] == BASE_C)
@@ -49,8 +44,7 @@ void printSequence(int len)
 	printf("\n");
 }
 
-void printStructure(int len) 
-{
+void print_structure(int len) {
 	int i = 1;
 	for (i = 1; i <= len; i++) 
 	{
@@ -64,13 +58,7 @@ void printStructure(int len)
 	printf("\n");
 }
 
-int canPair(int a, int b)
-{
-	return (chPairKey & (1 << (((a)<<2) + (b)))); 
-}  
-
-void init_checkPair() 
-{
+void init_checkPair() {
 	int i, j;
 	chPairKey = 0;
 	for (i = 0; i < 4; i++)
@@ -78,15 +66,17 @@ void init_checkPair()
 			chPairKey += checkPair(i, j) << ((i << 2) + j);
 }
 
-int update_checkPair(int i, int j) 
-{
+int update_checkPair(int i, int j) {
 	int r = 0;
 	if (!((i >= 0 && i <=3 )&&(j >=0 && j <=3)))
 		return r;
-	if (!(chPairKey & (1 << ((i << 2) + j))))
-	{
+	if (!(chPairKey & (1 << ((i << 2) + j)))) {
 		chPairKey += 1 << ((i << 2) + j);	
 		r = 1;
 	}
 	return r;
 }
+
+inline int canPair(int a, int b) {
+	return (chPairKey & (1 << (((a)<<2) + (b)))); 
+}

From 4012c3abe550a57908d99bf81b641787fe6e9251 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Sun, 27 Mar 2011 21:51:18 -0400
Subject: [PATCH 091/282] added macro find min of 4 no.s

---
 gtfold-mfe/include/utils.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gtfold-mfe/include/utils.h b/gtfold-mfe/include/utils.h
index 5a726b2..dbe0fa7 100644
--- a/gtfold-mfe/include/utils.h
+++ b/gtfold-mfe/include/utils.h
@@ -6,6 +6,7 @@
 
 #define MIN(X,Y) ((X) < (Y) ? (X) : (Y))
 #define MAX(X,Y) ((X) > (Y) ? (X) : (Y))
+#define MIN4(W,X,Y,Z) MIN(MIN(W,X),MIN(Y,Z))
 
 char baseToDigit(const char* base) ;
 unsigned char encode(char base);

From 3c6a8f2edf5846e52c6a8f53c653a17664e8c83a Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Sun, 27 Mar 2011 21:53:36 -0400
Subject: [PATCH 092/282] changes due to addition of constraints, added
 function signatures in header file

---
 gtfold-mfe/include/main.h |   6 ++
 gtfold-mfe/src/main.cc    | 145 ++++++++------------------------------
 2 files changed, 37 insertions(+), 114 deletions(-)

diff --git a/gtfold-mfe/include/main.h b/gtfold-mfe/include/main.h
index 76879a2..7faf980 100644
--- a/gtfold-mfe/include/main.h
+++ b/gtfold-mfe/include/main.h
@@ -25,6 +25,12 @@
 
 #include "constants.h"
 
+using namespace std;
+
+void init_fold(string seq);
+void free_fold(int len);
+
+bool encodeSequence(string seq);
 void limit_contact_distance(int lCD, int length);
 
 bool is_valid_base(char c)
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 4bafcc9..88c0187 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -36,28 +36,41 @@
 #include "global.h"
 #include "energy.h"
 #include "algorithms.h"
+#include "constraints.h"
 #include "traceback.h"
 #include "subopt_traceback.h"
 
 using namespace std;
 
-double get_seconds() 
-{
+double get_seconds() {
 	struct timeval tv;
 	gettimeofday(&tv, NULL);
 	return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0;
 }
 
-void init_fold(int len) 
-{	
- 	init_global_params(len);
+void init_fold(string seq) {
+	int len = seq.length();
+
+	init_global_params(len);
+
+	if (!encodeSequence(seq)) {
+		free_fold(seq.length());
+		exit(0);
+	}
+	
 	create_tables(len);
+	
+	if (CONS_ENABLED) {
+		init_constraints(constraintsFile.c_str(), len);
+	}
 }
 
-void free_fold(int len) 
-{
-	free_global_params();
+void free_fold(int len) {
+	if (CONS_ENABLED) 
+		free_constraints(len);
+
 	free_tables(len);
+	free_global_params();
 }
 
 /**
@@ -67,8 +80,7 @@ void free_fold(int len)
  * @param seq A C++ string object (passed by reference) to save to
  * @return SUCCESS or FAILURE
  */
-int read_sequence_file(const char* filename, std::string& seq)
-{
+int read_sequence_file(const char* filename, std::string& seq) {
 	seq = "";
 
 	ifstream fs;
@@ -172,19 +184,13 @@ int main(int argc, char** argv) {
 		printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
 		exit(-1);
 	}
-
+	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
 	readThermodynamicParameters("Turner99",false);
 
 	printRunConfiguration(seq);
 	
-	init_fold(seq.length());
-	
-	if (!encodeSequence(seq))
-	{
-		free_fold(seq.length());
-		exit(0);
-	}
+	init_fold(seq);
 	
 	printf("\nComputing minimum free energy structure...\n");
 	fflush(stdout);
@@ -199,8 +205,7 @@ int main(int argc, char** argv) {
 	printf("- MFE runtime: %9.6f seconds\n", t1);
 	
 	
-	if (SUBOPT_ENABLED)
-	{	
+	if (SUBOPT_ENABLED) {	
 		t1 = get_seconds();
 		subopt_traceback(seq.length(), suboptDelta);
 		t1 = get_seconds() - t1;
@@ -215,9 +220,12 @@ int main(int argc, char** argv) {
 	t1 = get_seconds() - t1;
 
 	printf("\n");
-	printSequence(seq.length());
-	printStructure(seq.length());
-	
+	print_sequence(seq.length());
+	print_structure(seq.length());
+	if (CONS_ENABLED)
+		print_constraints(seq.length());
+
+
 	save_ct_file(outputFile, seq, energy);
 	printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str());
 
@@ -226,94 +234,3 @@ int main(int argc, char** argv) {
 
 	return EXIT_SUCCESS;
 }
-
-
-int initialize_constraints(int*** fbp, int ***pbp, int& numpConstraints, int& numfConstraints, const char* constr_file)
-{
-	ifstream cfcons;
-
-	printf("Running with constraints\n");
-	printf("Opening constraint file: %s\n", constr_file);
-
-	cfcons.open(constr_file, ios::in);
-	if (cfcons != NULL)
-		printf("Constraint file opened.\n");
-	else {
-		fprintf(stderr, "Error opening constraint file\n\n");
-		cfcons.close();
-		return FAILURE; //exit(-1);
-	}
-
-	char cons[100];
-
-	while (!cfcons.eof()) {
-		cfcons.getline(cons, 100);
-		if (cons[0] == 'F' || cons[0] == 'f')
-			numfConstraints++;
-		if (cons[0] == 'P' || cons[0] == 'p')
-			numpConstraints++;
-	}
-	cfcons.close();
-
-	printf("Number of Constraints given: %d\n\n", numfConstraints
-			+ numpConstraints);
-	if (numfConstraints + numpConstraints != 0)
-		printf("Reading Constraints.\n");
-	else {
-		fprintf(stderr, "No Constraints found.\n\n");
-		return FAILURE;
-	}
-
-	*fbp = (int**) malloc(numfConstraints * sizeof(int*));
-	*pbp = (int**) malloc(numpConstraints * sizeof(int*));
-
-	int fit = 0, pit = 0, it = 0;
-
-	for (it = 0; it < numfConstraints; it++) {
-		(*fbp)[it] = (int*) malloc(2* sizeof (int));
-	}
-	for(it=0; it<numpConstraints; it++) {
-		(*pbp)[it] = (int*)malloc(2*sizeof(int));
-	}
-	cfcons.open(constr_file, ios::in);
-
-	while(!cfcons.eof()) {
-		cfcons.getline(cons,100);
-		char *p=strtok(cons, " ");
-		p = strtok(NULL, " ");
-		if(cons[0]=='F' || cons[0]=='f') {
-			int fit1=0;
-			while(p!=NULL) {
-				(*fbp)[fit][fit1++] = atoi(p);
-				p = strtok(NULL, " ");
-			}
-			fit++;
-		}
-		if( cons[0]=='P' || cons[0]=='p') {
-			int pit1=0;
-			while(p!=NULL) {
-				(*pbp)[pit][pit1++] = atoi(p);
-				p = strtok(NULL, " ");
-			}
-			pit++;
-		}
-	}
-
-	printf("Forced base pairs: ");
-	
-	for(it=0; it<numfConstraints; it++) 
-	{
-		for(int k=1;k<= (*fbp)[it][2];k++)
-			printf("(%d,%d) ", (*fbp)[it][0]+k-1, (*fbp)[it][1]-k+1);
-	}
-	printf("\nProhibited base pairs: ");
-	for(it=0; it<numpConstraints; it++) 
-	{
-		for(int k=1;k<= (*pbp)[it][2];k++)
-			printf("(%d,%d) ", (*pbp)[it][0]+k-1, (*pbp)[it][1]-k+1);
-	}
-
-	printf("\n\n");
-
-	return SUCCESS;
-}

From f7631ab1064db8f772cc85fe5ab6b382c54d65e3 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Sun, 27 Mar 2011 21:54:46 -0400
Subject: [PATCH 093/282] added files to handle constraints

---
 gtfold-mfe/include/constraints.h |  28 +++++
 gtfold-mfe/src/constraints.cc    | 184 +++++++++++++++++++++++++++++++
 2 files changed, 212 insertions(+)
 create mode 100644 gtfold-mfe/include/constraints.h
 create mode 100644 gtfold-mfe/src/constraints.cc

diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h
new file mode 100644
index 0000000..df06882
--- /dev/null
+++ b/gtfold-mfe/include/constraints.h
@@ -0,0 +1,28 @@
+#ifndef _CONSTRAINTS_H_
+#define _CONSTRAINTS_H_
+
+extern int* BP;
+extern int** PBP;
+extern int** FBP;
+
+extern int nPBP;
+extern int nFBP;
+
+//static int load_constraints(const char* constr_file, int verbose=0);
+
+int init_constraints(const char* constr_file, int length) ;
+void free_constraints(int length) ;
+void print_constraints(int length) ;
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+int ssOK(int i, int j); 
+int baseOK(int i);
+int pairOK(int i, int j);
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
new file mode 100644
index 0000000..52dc99e
--- /dev/null
+++ b/gtfold-mfe/src/constraints.cc
@@ -0,0 +1,184 @@
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <iostream>
+#include <fstream>
+
+#include "global.h"
+#include "options.h"
+#include "constraints.h"
+
+int* BP;
+int** PBP;
+int** FBP;
+
+int nPBP;
+int nFBP;
+
+static int load_constraints(const char* constr_file, int verbose=0) {
+	std::ifstream cfcons;
+    fprintf(stdout, "- Running with constraints\n");
+    //fprintf(stdout, "Opening constraint file: %s\n", constr_file);
+
+    cfcons.open(constr_file, std::ios::in);
+    if (cfcons == 0) {
+        fprintf(stderr, "Error opening constraint file\n\n");
+        cfcons.close();
+        return -1;
+    }
+
+    char cons[100];
+
+    while (!cfcons.eof()) {
+        cfcons.getline(cons, 100);
+        if (cons[0] == 'F' || cons[0] == 'f') nFBP++;
+        if (cons[0] == 'P' || cons[0] == 'p') nPBP++;
+    }
+    cfcons.close();
+
+    //fprintf(stdout, "Number of Constraints given: %d\n\n", nFBP + nPBP);
+    if (nFBP + nPBP == 0) {
+        fprintf(stderr, "No Constraints found.\n\n");
+        return -1;
+    }
+
+    FBP = (int**) malloc(nFBP*sizeof(int*));
+    PBP = (int**) malloc(nPBP*sizeof(int*));
+
+    int fit = 0, pit = 0, it = 0;
+
+    for (it = 0; it < nFBP; it++) {
+        FBP[it] = (int*) malloc(2* sizeof (int));
+    }
+    for(it=0; it < nPBP; it++) {
+        PBP[it] = (int*)malloc(2*sizeof(int));
+    }
+    cfcons.open(constr_file, std::ios::in);
+
+    while(!cfcons.eof()) {
+        cfcons.getline(cons,100);
+        char *p=strtok(cons, " ");
+        p = strtok(0, " ");
+        if(cons[0]=='F' || cons[0]=='f') {
+            int fit1=0;
+            while(p!=0) {
+                FBP[fit][fit1++] = atoi(p);
+                p = strtok(0, " ");
+            }
+            fit++;
+        }
+        if(cons[0]=='P' || cons[0]=='p') {
+            int pit1=0;
+            while(p!=0) {
+                PBP[pit][pit1++] = atoi(p);
+                p = strtok(0, " ");
+            }
+            pit++;
+        }
+    }
+
+	if (verbose == 1) {
+		fprintf(stdout, "Forced base pairs: ");
+		for(it=0; it< nFBP; it++) {
+			for(int k=1;k<= FBP[it][2];k++)
+				fprintf(stdout, "(%d,%d) ", FBP[it][0]+k-1, FBP[it][1]-k+1);
+		}
+		fprintf(stdout, "\nProhibited base pairs: ");
+		for(it=0; it< nPBP; it++) {
+			for(int k=1;k<= PBP[it][2];k++)
+				fprintf(stdout, "(%d,%d) ", PBP[it][0]+k-1, PBP[it][1]-k+1);
+		}
+		fprintf(stdout, "\n\n");
+	}
+
+    return 0;
+}
+
+int init_constraints(const char* constr_file,int length) {
+	load_constraints(constr_file);
+
+	BP = (int*) malloc((length + 1) * sizeof(int));
+    if (BP == NULL) {
+        perror("Cannot allocate variable 'constraints'");
+        exit(-1);
+    }
+	
+	int i, it, k;
+
+	for(i = 1; i <= length; i++) 
+		BP[i] = (RNA[i]=='N')?-1:0 ;
+
+	if (nPBP != 0) {
+		for (it = 0; it < nPBP; it++) {
+			for(k= 1; k <= PBP[it][2];k++) {
+				BP[PBP[it][0]+k-1] = -1;
+				if(PBP[it][1]!=0) {
+					BP[PBP[it][1]+1-k] = -1;
+				}
+			}
+		}
+	}
+	if (nFBP != 0) {
+		for (it = 0; it < nFBP; it++) {
+			for(k=1; k <= FBP[it][2];k++) {
+				if (!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])) {
+					printf("Can't constrain (%d,%d)\n", FBP[it][0]+k-1, FBP[it][1]-k+1);
+					continue;
+				}
+				BP[FBP[it][0]+k-1] = FBP[it][1]+1-k;
+				BP[FBP[it][1]+1-k] = FBP[it][0]+k-1;
+			}
+		}
+	}
+
+	return 0;
+}
+
+void free_constraints(int len) {
+	free(BP);
+}
+
+void print_constraints(int len) {
+    int i = 1;
+    for (i = 1; i <= len; i++) {
+        if (BP[i] > 0 && BP[i] > i)
+            printf("(");
+        else if (BP[i] > 0 && BP[i] < i)
+            printf(")");
+        else if (BP[i] < 0)
+            printf("x");
+        else
+            printf(".");
+    }
+    printf("\n");
+}
+
+int ssOK(int i, int j) {
+	if (CONS_ENABLED) {
+		int it;
+		for (it = i + 1; it < j; it++) {
+			if (BP[it] > 0) return 0;
+		}
+		return 1;
+	}
+	else
+		return 1;
+}
+
+int baseOK(int i) {
+	if (CONS_ENABLED)
+		return (BP[i] <=0);
+	else
+		return 1;
+}
+
+int pairOK(int i, int j) {
+	if (CONS_ENABLED)
+	return !(BP[i] < 0 || BP[j] < 0 ||  
+			(BP[i] > 0 && j != BP[i]) ||
+			(BP[j] > 0 && i != BP[j]));  			
+	else
+		return 1;
+}
+
+

From 157deba63e21c9ebfc965e4b7a472403562446a3 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Sun, 27 Mar 2011 21:57:51 -0400
Subject: [PATCH 094/282] added entry for constraints.cc file

---
 gtfold-mfe/src/Makefile.am |  1 +
 gtfold-mfe/src/Makefile.in | 14 +++++++-------
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am
index 08d2bb0..728863b 100644
--- a/gtfold-mfe/src/Makefile.am
+++ b/gtfold-mfe/src/Makefile.am
@@ -10,6 +10,7 @@ gtfold_SOURCES = \
 	loader.cc\
 	utils.cc\
 	options.cc\
+	constraints.cc\
 	global.c\
 	energy.c\
 	algorithms.c \
diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in
index ebc0263..a94f890 100644
--- a/gtfold-mfe/src/Makefile.in
+++ b/gtfold-mfe/src/Makefile.in
@@ -50,8 +50,8 @@ am__installdirs = "$(DESTDIR)$(bindir)"
 PROGRAMS = $(bin_PROGRAMS)
 am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
 	options.$(OBJEXT) global.$(OBJEXT) energy.$(OBJEXT) \
-	algorithms.$(OBJEXT) algorithms-partition.$(OBJEXT) \
-	subopt_traceback.$(OBJEXT) traceback.$(OBJEXT)
+	algorithms.$(OBJEXT) traceback.$(OBJEXT) constraints.$(OBJEXT) \
+	subopt_traceback.$(OBJEXT)
 gtfold_OBJECTS = $(am_gtfold_OBJECTS)
 gtfold_DEPENDENCIES =
 gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
@@ -185,12 +185,12 @@ gtfold_SOURCES = \
 	loader.cc\
 	utils.cc\
 	options.cc\
+	constraints.cc\
 	global.c\
 	energy.c\
-	algorithms.c\
-	algorithms-partition.c\
-	subopt_traceback.cc\
-	traceback.c
+	algorithms.c \
+	traceback.c \
+	subopt_traceback.cc
 
 gtfold_LDFLAGS = 
 gtfold_LDADD = -lm
@@ -276,8 +276,8 @@ mostlyclean-compile:
 distclean-compile:
 	-rm -f *.tab.c
 
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/constraints.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/energy.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/global.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/loader.Po@am__quote@

From 25713f00da80e628ecd9f3d947a81e77b09e6196 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Sun, 27 Mar 2011 22:00:04 -0400
Subject: [PATCH 095/282] changes to incorporate constraint handling

---
 gtfold-mfe/include/options.h |   1 +
 gtfold-mfe/src/algorithms.c  | 114 ++++++++++++-----------------------
 gtfold-mfe/src/options.cc    |   5 +-
 3 files changed, 43 insertions(+), 77 deletions(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index f8168d6..508b8ed 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -15,6 +15,7 @@ extern bool PARAMS;
 extern bool LIMIT_DISTANCE;
 extern bool BPP_ENABLED;
 extern bool SUBOPT_ENABLED;
+extern bool CONS_ENABLED;
 
 extern string seqfile;
 extern string constraintsFile;
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 5bee7c5..a257340 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -29,20 +29,14 @@
 #include "energy.h"
 #include "global.h"
 #include "algorithms.h"
+#include "constraints.h"
 
 #ifdef _OPENMP   
 #include "omp.h"
 #endif
 
-double get_seconds() {
-	struct timeval tv;
-	gettimeofday(&tv, NULL);
-	return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0;
-}
-
 int calculate(int len, int nThreads) { 
 	int b, i, j;
-	double t1, t2, tint=0, thair=0,tst=0, tml=0, twm=0;
 
 #ifdef _OPENMP
 	if (nThreads>0) omp_set_num_threads(nThreads);
@@ -60,48 +54,33 @@ int calculate(int len, int nThreads) {
 #endif
 		for (i = 1; i <= len - b; i++) {
 			j = i + b;
-			int newWM = INFINITY_;
-			int bPair = 0;
-			
-			if (canPair(RNA[i], RNA[j])) { 
-				bPair = 1;
-				int p=0, q=0, h;
-				int newV = INFINITY_, VBIij = INFINITY_;
-
-				t1 = get_seconds();
-				newV  = MIN(eH(i, j), newV);
-				t2 = get_seconds();
-				thair += (t2-t1); 
-
-				t1 = get_seconds();
-				int stackEnergy = eS(i, j); 
-				newV= MIN(stackEnergy + V(i+1,j-1), newV);
-				t2 = get_seconds();
-				tst += (t2-t1); 
-
-				if (j-i > 6) { 
-					t1 = get_seconds();
-					// Int Loop BEGIN
+			int flag = 0, newWM = INFINITY_; 
+
+			if (canPair(RNA[i], RNA[j])) {
+				flag = 1;
+				
+				int eh = eH(i, j); //hair pin
+				int es = eS(i, j) +  V(i+1,j-1); // stack
+
+				if (j-i > 6) {  // Internal Loop BEGIN
+					int p=0, q=0;
+					int VBIij = INFINITY_;
+
 					for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
 						int minq = j-i+p-MAXLOOP-2;
 						if (minq < p+1+TURN) minq = p+1+TURN;
 						for (q = minq; q < j; q++) {
 							if (!canPair(RNA[p], RNA[q])) continue;
+							if (!ssOK(i,p) || !ssOK(q,j)) continue;
+							
 							VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
 						}
 					}
-
-					VBI(i,j) = VBIij;
-					// Int Loop END
-					t2 = get_seconds();
-					tint += (t2-t1); 
-					newV = MIN(newV, VBIij);
-				}
+					VBI(i,j) = pairOK(i,j)?VBIij:INFINITY_;
+				} 	// Internal Loop END
 				
-				if (j-i > 10) {	
-					t1 = get_seconds();
-
-					// Multi Loop BEGIN
+				if (j-i > 10) {	 // Multi Loop BEGIN
+					int h;
 					int VMij, VMijd, VMidj, VMidjd;
 					VMij = VMijd = VMidj = VMidjd = INFINITY_;
 
@@ -116,63 +95,46 @@ int calculate(int len, int nThreads) {
 					int d3 = Ed3(i,j,j-1);
 					int d5 = Ed5(i,j,i+1);
 
-					VMij = MIN(VMij, VMidj + d5 +Ec);
-					VMij = MIN(VMij, VMijd + d3 +Ec);
-					VMij = MIN(VMij, VMidjd + d5 +  d3+ 2*Ec);
+					VMij = MIN(VMij, baseOK(i+1)?(VMidj + d5 +Ec):INFINITY_);
+					VMij = MIN(VMij, baseOK(j-1)?(VMijd + d3 +Ec):INFINITY_);
+					VMij = MIN(VMij, (baseOK(i+1)&&baseOK(j-1))?(VMidjd + d5 +  d3+ 2*Ec):INFINITY_);
 					VMij = VMij + Ea + Eb + auPenalty(i,j);
+					
+					VM(i,j) = pairOK(i,j)?VMij:INFINITY_;
+				} // Multi Loop END
 
-					VM(i,j) = VMij;
-					newV = MIN(newV, VM(i,j));
-					// Multi Loop END
-
-					t2 = get_seconds();
-					tml += (t2-t1);
-				}
-				V(i,j) = VV[i] = newV;
+				V(i,j) = pairOK(i,j)?MIN4(eh,es,VBI(i,j),VM(i,j)):INFINITY_;
 			}
+			else
+				V(i,j) = INFINITY_;
 
 			if (j-i > 4) {	
-				t1 = get_seconds();
 				// WM BEGIN
-				int h; 	
-				if (!bPair) {
+				int h; 
+				if (!flag) {
 					for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
 						newWM = MIN(newWM, WMU(i,h-1) + WML(h,j));
 					}
 				}
 				
-				newWM = MIN(VV[i] + auPenalty(i,j) + Eb, newWM);  //V(i,j)
-				newWM = MIN(VV1[i+1] + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM); //V(i+1,j) 
-				newWM = MIN(VV1[i] + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM); //V(i,j-1)
-				newWM = MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM) ;
-
-				newWM = MIN(WMU(i+1,j) + Ec, newWM);
-				newWM = MIN(WML(i,j-1) + Ec, newWM);
+				newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM);  //V(i,j)
+				newWM = baseOK(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): INFINITY_; //V(i+1,j) 
+				newWM = baseOK(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM): INFINITY_; //V(i,j-1)
+				newWM = (baseOK(i)&&baseOK(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM): INFINITY_ ;
+				
+				newWM = baseOK(i)?MIN(WMU(i+1,j) + Ec, newWM):INFINITY_;
+				newWM = baseOK(j)?MIN(WML(i,j-1) + Ec, newWM):INFINITY_;
 
 				WMU(i,j) = WML(i,j) = newWM;
 				// WM END
-
-				t2 = get_seconds();
-				twm += (t2-t1);
 			}
 		}
 
-		int* FF;
-		FF=VV1; VV1=VV; VV=FF;
-		for (i = 1; i <= len; i++)
-			VV[i] = INFINITY_;
 	}
-
-	printf("Total IntLoop time = %fs \n",tint);
-	printf("Total Stack time = %fs \n",tst);
-	printf("Total HairPin time = %fs \n",thair);
-	printf("Total MultiLoop time = %fs \n",tml);
-	printf("Total WM time = %fs \n",twm);
-
+	
 	for (j = TURN+2; j <= len; j++)	{
 		int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
 		Wj = INFINITY_;
-
 		for (i = 1; i < j-TURN; i++) {
 			Wij = Widjd = Wijd = Widj = INFINITY_;
 			Wim1 = MIN(0, W[i-1]); 
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 9a747eb..132e5a8 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -10,6 +10,7 @@ bool PARAMS;
 bool LIMIT_DISTANCE;
 bool BPP_ENABLED;
 bool SUBOPT_ENABLED;
+bool CONS_ENABLED = false;
 
 string seqfile = "";
 string constraintsFile = "";
@@ -63,8 +64,10 @@ void parse_options(int argc, char** argv) {
 			if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
 				help();
 			} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
-				if(i < argc)
+				if(i < argc) {
 					constraintsFile = argv[++i];
+					CONS_ENABLED = true;
+				}
 				else
 					help();
 			} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-d") == 0) {

From 4c271df11f519b2072116aa2bc29fe7a151ffde9 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 6 Apr 2011 01:53:41 -0400
Subject: [PATCH 096/282] changes to fix constraint handling

---
 gtfold-mfe/include/constraints.h |  12 +-
 gtfold-mfe/src/algorithms.c      |  67 +++++-----
 gtfold-mfe/src/constraints.cc    |  59 +++++++--
 gtfold-mfe/src/traceback.c       | 220 ++++++++++++++-----------------
 4 files changed, 189 insertions(+), 169 deletions(-)

diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h
index df06882..508fb70 100644
--- a/gtfold-mfe/include/constraints.h
+++ b/gtfold-mfe/include/constraints.h
@@ -18,9 +18,15 @@ void print_constraints(int length) ;
 #ifdef __cplusplus
 extern "C" {
 #endif
-int ssOK(int i, int j); 
-int baseOK(int i);
-int pairOK(int i, int j);
+int is_ss(int i, int j); 
+int prohibit_base(int i) ;
+int check_base(int i) ;
+int force_pair(int i, int j) ;
+int force_pair1(int i, int j) ;
+int check_iloop(int i, int j, int p, int q) ;
+int check_pair(int i, int j) ;
+int check_stack(int i, int j) ;
+int check_hairpin(int i, int j) ;
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index a257340..a10f0f7 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -58,10 +58,8 @@ int calculate(int len, int nThreads) {
 
 			if (canPair(RNA[i], RNA[j])) {
 				flag = 1;
-				
-				int eh = eH(i, j); //hair pin
-				int es = eS(i, j) +  V(i+1,j-1); // stack
-
+				int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin
+				int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack
 				if (j-i > 6) {  // Internal Loop BEGIN
 					int p=0, q=0;
 					int VBIij = INFINITY_;
@@ -71,12 +69,11 @@ int calculate(int len, int nThreads) {
 						if (minq < p+1+TURN) minq = p+1+TURN;
 						for (q = minq; q < j; q++) {
 							if (!canPair(RNA[p], RNA[q])) continue;
-							if (!ssOK(i,p) || !ssOK(q,j)) continue;
-							
+							if (check_iloop(i,j,p,q)) continue;
 							VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
 						}
 					}
-					VBI(i,j) = pairOK(i,j)?VBIij:INFINITY_;
+					VBI(i,j) = check_pair(i,j)?INFINITY_:VBIij;
 				} 	// Internal Loop END
 				
 				if (j-i > 10) {	 // Multi Loop BEGIN
@@ -95,21 +92,19 @@ int calculate(int len, int nThreads) {
 					int d3 = Ed3(i,j,j-1);
 					int d5 = Ed5(i,j,i+1);
 
-					VMij = MIN(VMij, baseOK(i+1)?(VMidj + d5 +Ec):INFINITY_);
-					VMij = MIN(VMij, baseOK(j-1)?(VMijd + d3 +Ec):INFINITY_);
-					VMij = MIN(VMij, (baseOK(i+1)&&baseOK(j-1))?(VMidjd + d5 +  d3+ 2*Ec):INFINITY_);
+					VMij = MIN(VMij, check_base(i+1)?(VMidj + d5 +Ec):INFINITY_) ;
+					VMij = MIN(VMij, check_base(j-1)?(VMijd + d3 +Ec):INFINITY_);
+					VMij = MIN(VMij, (check_base(i+1)&&check_base(j-1))?(VMidjd + d5 +  d3+ 2*Ec):INFINITY_);
 					VMij = VMij + Ea + Eb + auPenalty(i,j);
-					
-					VM(i,j) = pairOK(i,j)?VMij:INFINITY_;
+					VM(i,j) = check_pair(i,j)?INFINITY_:VMij;
 				} // Multi Loop END
 
-				V(i,j) = pairOK(i,j)?MIN4(eh,es,VBI(i,j),VM(i,j)):INFINITY_;
+				V(i,j) = check_pair(i,j)?INFINITY_:MIN4(eh,es,VBI(i,j),VM(i,j));
 			}
 			else
 				V(i,j) = INFINITY_;
 
-			if (j-i > 4) {	
-				// WM BEGIN
+			if (j-i > 4) {	// WM BEGIN
 				int h; 
 				if (!flag) {
 					for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
@@ -117,35 +112,43 @@ int calculate(int len, int nThreads) {
 					}
 				}
 				
-				newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM);  //V(i,j)
-				newWM = baseOK(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): INFINITY_; //V(i+1,j) 
-				newWM = baseOK(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM): INFINITY_; //V(i,j-1)
-				newWM = (baseOK(i)&&baseOK(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM): INFINITY_ ;
+				newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
+				newWM = check_base(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): INFINITY_; 
+				newWM = check_base(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM) : INFINITY_; 
+				newWM = (check_base(i)&&check_base(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM): INFINITY_;
 				
-				newWM = baseOK(i)?MIN(WMU(i+1,j) + Ec, newWM):INFINITY_;
-				newWM = baseOK(j)?MIN(WML(i,j-1) + Ec, newWM):INFINITY_;
+				newWM = check_base(i)?MIN(WMU(i+1,j) + Ec, newWM):INFINITY_;
+				newWM = check_base(j)?MIN(WML(i,j-1) + Ec, newWM):INFINITY_;
 
 				WMU(i,j) = WML(i,j) = newWM;
-				// WM END
-			}
+			} // WM END
 		}
-
 	}
-	
+
 	for (j = TURN+2; j <= len; j++)	{
-		int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
+		int i, branch=0, Wj, Widjd, Wijd, Widj, Wij, Wim1;
 		Wj = INFINITY_;
 		for (i = 1; i < j-TURN; i++) {
 			Wij = Widjd = Wijd = Widj = INFINITY_;
 			Wim1 = MIN(0, W[i-1]); 
 			Wij = V(i, j) + auPenalty(i, j) + Wim1;
-			Widjd = V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1;
-			Wijd = V(i,j-1) + auPenalty(i,j- 1) + Ed5(j-1,i,j) + Wim1;
-			Widj = V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1;
-			Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); 
+			Widjd = (check_base(i)&&check_base(j))?(V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1):INFINITY_;
+			Wijd = check_base(j)?(V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1):INFINITY_;
+			Widj =  (check_base(i))?(V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1):INFINITY_;
+			Wj = MIN(MIN4(Wij, Widjd, Wijd, Widj), Wj); 
+			
+			if (Wj<INFINITY_) {
+				if (Wj==Wij && force_pair1(i,j))
+				   branch = 1;
+				else if	(Wj==Widjd && force_pair1(i+1,j-1))
+				   branch = 1;
+				else if	(Wj==Wijd && force_pair1(i,j-1))
+				  branch = 1;	
+				else if	(force_pair1(i+1,j))
+					branch = 1;
+			}
 		}
-
-		W[j] = MIN(Wj, W[j-1]);
+		W[j] = branch?Wj:MIN(Wj, W[j-1]);
 	}
 
 	return W[len];
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 52dc99e..9669781 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -18,7 +18,6 @@ int nFBP;
 static int load_constraints(const char* constr_file, int verbose=0) {
 	std::ifstream cfcons;
     fprintf(stdout, "- Running with constraints\n");
-    //fprintf(stdout, "Opening constraint file: %s\n", constr_file);
 
     cfcons.open(constr_file, std::ios::in);
     if (cfcons == 0) {
@@ -153,32 +152,64 @@ void print_constraints(int len) {
     printf("\n");
 }
 
-int ssOK(int i, int j) {
+int is_ss(int i, int j) {
 	if (CONS_ENABLED) {
 		int it;
 		for (it = i + 1; it < j; it++) {
-			if (BP[it] > 0) return 0;
+			if (BP[it] > 0) return 1;
 		}
-		return 1;
+		return 0;
 	}
 	else
-		return 1;
+		return 0;
+}
+
+int prohibit_base(int i) {
+		return (BP[i] == -1);
 }
 
-int baseOK(int i) {
-	if (CONS_ENABLED)
-		return (BP[i] <=0);
+int check_base(int i) {
+	if (CONS_ENABLED) 
+		return (BP[i] <= 0);
 	else
 		return 1;
 }
 
-int pairOK(int i, int j) {
-	if (CONS_ENABLED)
-	return !(BP[i] < 0 || BP[j] < 0 ||  
-			(BP[i] > 0 && j != BP[i]) ||
-			(BP[j] > 0 && i != BP[j]));  			
+int force_pair(int i, int j) {
+		return (BP[i] > 0 && j != BP[i]);
+}
+
+int force_pair1(int i, int j) {
+	if (CONS_ENABLED) 
+		return (BP[i]==j);
 	else
-		return 1;
+		return 0;
+}
+
+int check_iloop(int i, int j, int p, int q) {
+	if (CONS_ENABLED) 
+		return is_ss(i,p) || is_ss(q,j);
+	else 
+		return 0;
+}
+
+int check_pair(int i, int j) {
+	if (CONS_ENABLED) 
+		return prohibit_base(i) || prohibit_base(j) || force_pair(i,j) || force_pair(j,i);
+	else
+		return 0;
 }
 
+int check_stack(int i, int j) {
+	if (CONS_ENABLED) 
+		return force_pair(i,j) || force_pair(j,i);
+	else
+		return 0;
+}
 
+int check_hairpin(int i, int j) {
+	if (CONS_ENABLED) 
+		return is_ss(i,j) || force_pair(i,j) || force_pair(j,i);
+	else
+		return 0;
+}
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 5e2449b..9d52256 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -23,6 +23,7 @@
 #include <assert.h>
 #include "data.h"
 #include "constants.h"
+#include "constraints.h"
 #include "energy.h"
 #include "global.h"
 #include "traceback.h"
@@ -48,96 +49,77 @@ void trace(int len) {
 	return;
 }
 
-/* Traces W[j] */
-void traceW(int j) 
-{
+void traceW(int j) {
 	int done, i, Wj,Wj_temp;
 	int wim1, flag, Widjd, Wijd, Widj, Wij;
-
-	flag = 1;
-
-	done = 0; /* the done variable makes it sure that we are tracebacking the first optimal possibility */
 	Wj = INFINITY_;
+	flag = 1;
+	done = 0; 
 	int min_i=1;
-	if (j == 0 || j == 1) {
-		/* W[j] = 0; */
-	} else {
-		for (i = 1; i < j && !done; i++) {
-			wim1 = MIN(0, W[i-1]);
-			flag = 1;
-			if (wim1 != W[i-1]) flag = 0;
-
-			Widjd = INFINITY_;
-			Wijd = INFINITY_;
-			Widj = INFINITY_;
-			Wij = V(i,j) + auPenalty(i, j) + wim1;
-			Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1;
-			Wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
-			Widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
-			Wj_temp=Wj;
-
-			Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
-			if (Wj_temp>Wj) min_i=i;	
-
-			if (W[j] == Wj) {
-				if (W[j] == Wij) { /* If the optimal secondary structure contain base pair (i,j) as paired.*/
-					done = 1;
-					structure[i] = j;
-					structure[j] = i;
-					//printf("AU Penalty: %12.2f\n",auPen(RNA[i], RNA[j])/100.00);
-					traceV(i, j);
-
-					if (flag ) 
-						traceW(i - 1);
-					break;
-				} else if (W[j] == Widjd) { /* If base pair (i+1,j-1) is pairing and there is a dangling base on both its sides */
-					done = 1;
-					structure[i + 1] = j - 1;
-					structure[j - 1] = i + 1;
-					//printf("AU Penalty: %12.2f\nEnergy of dangling base on both the sides: %12.2f  %12.2f\n",
-					//auPen(RNA[i + 1], RNA[j - 1])/100.00, dangle[RNA[j - 1]][RNA[i + 1]][RNA[i]][1]/100.00, dangle[RNA[j - 1]][RNA[i + 1]][RNA[j]][0]/100.00);
-					traceV(i + 1, j - 1);
-
-					if (flag)// || checkSS(1,i))
-						traceW(i - 1);
-					break;
-				} else if (W[j] == Wijd) { /* If base pair (i,j-1) pairs and base j is single stranded. */
-					done = 1;
-					structure[i] = j - 1;
-					structure[j - 1] = i;
-					//	printf("AU Penalty: %12.2f \nEnergy of dangling base: %12.2f \n",
-					//	auPen(RNA[i], RNA[j - 1])/100.00,dangle[RNA[j - 1]][RNA[i]][RNA[j]][0]/100.00);
-					traceV(i, j - 1);
-
-					if (flag) // || checkSS(1,i) )
-						traceW(i - 1);
-					break;
-				} else if (W[j] == Widj) { /* If base pair (i+1,j) pairs and base i is single stranded. */
-					done = 1;
-					structure[i + 1] = j;
-					structure[j] = i + 1;
-					//	printf("AU Penalty: %12.2f\nEnergy of dangling base:  %12.2f\n",
-					//	auPen(RNA[i + 1], RNA[j])/100.00, dangle[RNA[j]][RNA[i + 1]][RNA[i]][1]/100.00);
-					traceV(i + 1, j);
-					if (flag) // || checkSS(1,i))
-						traceW(i - 1);
-					break;
-				}
-			}
-		}
+	
+	if (j == 0 || j == 1) return;
+
+	for (i = 1; i < j && !done; i++) {
+		wim1 = MIN(0, W[i-1]);
+		flag = 1;
+		if (wim1 != W[i-1]) flag = 0;
+
+		Widjd = Wijd =  Widj = INFINITY_;
+		
+		Wij = V(i,j) + auPenalty(i, j) + wim1;
 		
-		if (W[j] == W[j - 1] && !done) 
-			traceW(j-1);
+		Widjd =(check_base(i)&&check_base(j))?(V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1): INFINITY_;
+		Wijd = (check_base(j))?(V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1):INFINITY_;
+		Widj = (check_base(i))?(V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1):INFINITY_;
+		Wj_temp=Wj;
 
+		Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
+		if (Wj_temp>Wj) min_i=i;	
+
+		if (W[j] == Wj) {
+			if (W[j] == Wij) { 
+				done = 1;
+				structure[i] = j;
+				structure[j] = i;
+				traceV(i, j);
+				if (flag || is_ss(1,i)) 
+					traceW(i - 1);
+				break;
+			} else if (W[j] == Widjd && check_base(i) && check_base(j)) { 
+				done = 1;
+				structure[i + 1] = j - 1;
+				structure[j - 1] = i + 1;
+				traceV(i + 1, j - 1);
+				if (flag || is_ss(1,i)) 
+					traceW(i - 1);
+				break;
+			} else if (W[j] == Wijd && check_base(j)) { 
+				done = 1;
+				structure[i] = j - 1;
+				structure[j - 1] = i;
+				traceV(i, j - 1);
+
+				if (flag || is_ss(1,i))
+					traceW(i - 1);
+				break;
+			} else if (W[j] == Widj && check_base(i)) { 
+				done = 1;
+				structure[i + 1] = j;
+				structure[j] = i + 1;
+				traceV(i + 1, j);
+				if (flag || is_ss(1,i))
+					traceW(i - 1);
+				break;
+			}
+		}
 	}
+		
+	if (W[j] == W[j - 1] && !done) traceW(j-1);
 
 	return;
 }
 
-
-/* Trace the structure inside V[i][j]. This function traces "which type of loop (i,j) base pair is closing" */
 int traceV(int i, int j) {
-
 	int a, b, c, d, Vij;
 
 	a = eH(i, j);
@@ -148,31 +130,26 @@ int traceV(int i, int j) {
 	
 	Vij = MIN(MIN(a, b), MIN(c, d));
 	
-	if (Vij == a && Vij != b && Vij != c && Vij != d) { /* If () a hairpin loop */
-		//printf("i %5d j %5d Hairpin  Loop %12.2f\n", i, j, eH(i, j)/100.00);
+	if (Vij == a && Vij != b && Vij != c && Vij != d) { 
 		total_en += eH(i,j);
 		return Vij;
-	} else if (Vij == b /*&& Vij != a && Vij != c && Vij != d*/) { /* If it forms a stack */
-		//printf("i %5d j %5d Stack 	 Loop %12.2f\n", i, j, eS(i, j)/100.00);
+	} else if (Vij == b) { 
 		total_en += eS(i,j);
 		structure[i + 1] = j - 1;
 		structure[j - 1] = i + 1;
 		traceV(i + 1, j - 1);
 		return Vij;
-	} else if (Vij == c /*&& Vij != a && Vij != b && Vij != d*/) { /* If it forms an internal loop */
-		//printf("i %5d j %5d Internal Loop", i, j);
+	} else if (Vij == c) { 
 		traceVBI(i, j);
 		return Vij;
-	} else if (Vij == d && Vij != a && Vij != b && Vij != c) { /* If it forms a multiloop */
+	} else if (Vij == d && Vij != a && Vij != b && Vij != c) { 
 		int eVM = traceVM(i, j);
-		//printf("i %5d j %5d Multi    Loop %12.2f\n", i, j, (Vij-eVM)/100.0);
 		total_en += (Vij-eVM);
 		return Vij;
 	} 
 	return 0;
 }
 
-/* Traces VBI[i][j] */
 int traceVBI(int i, int j) {
 	
 	int VBIij_temp;
@@ -183,7 +160,8 @@ int traceVBI(int i, int j) {
 	jfinal = 0;
 
 	for (ip = i + 1; ip < j - 1; ip++) {
-		for (jp = ip + 1; jp < j; jp++) { /* Search which internal loop (ip,jp) is closing */
+		for (jp = ip + 1; jp < j; jp++) {
+			if (check_iloop(i,j,ip,jp)) continue;
 			el = eL(i, j, ip, jp);
 			v = V(ip, jp);
 			VBIij_temp = el + v;
@@ -199,14 +177,12 @@ int traceVBI(int i, int j) {
 
 	structure[ifinal] = jfinal;
 	structure[jfinal] = ifinal;
-	//printf(" %12.2f\n", eL(i, j, ifinal, jfinal)/100.00);
 	total_en += eL(i, j, ifinal, jfinal);
 
 	int eVI = traceV(ifinal, jfinal);
 	return eVI ;
 }
 
-/* Tracing VM[i][j] */
 int traceVM(int i, int j) {
 
 	int done;
@@ -222,9 +198,8 @@ int traceVM(int i, int j) {
 	int VMij = VM(i,j);
 
 	for (h = i + 2; h <= j - 1 && !done; h++) {
-		A_temp = WM(i+1,h-1) + WM(h,j - 1) + a + b + auPen(RNA[i],
-				RNA[j]);
-		if (A_temp == VMij) { /* No dangling bases on any of the sides of base pair (i,j) in the multiloop */
+		A_temp = WM(i+1,h-1) + WM(h,j - 1) + a + b + auPenalty(i, j);
+		if (A_temp == VMij) { 
 			done = 1;
 			eVM += traceWM(i + 1, h - 1);
 			eVM += traceWM(h, j - 1);
@@ -232,40 +207,45 @@ int traceVM(int i, int j) {
 		}
 	}
 
-	for (h = i + 3; h <= j - 1 && !done; h++) {
-		A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + a + b + auPenalty(i,j) + Ed5(i,j,i + 1); 
-		if (A_temp == VMij) {
-			done = 1;
-			eVM += traceWM(i + 2, h - 1);
-			eVM += traceWM(h, j - 1);
-			break;
+	if (check_base(i+1)) {
+		for (h = i + 3; h <= j - 1 && !done; h++) {
+			A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + a + b + auPenalty(i,j) + Ed5(i,j,i + 1); 
+			if (A_temp == VMij) {
+				done = 1;
+				eVM += traceWM(i + 2, h - 1);
+				eVM += traceWM(h, j - 1);
+				break;
+			}
 		}
 	}
 
-	for (h = i + 2; h <= j - 2 && !done; h++) { /* If base j-1 is dangling on 3' end of the base pair (i,j) */
-		A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + a + b + auPenalty(i, j) + Ed3(i,j,j - 1);
-		if (A_temp == VMij) {
-			done = 1;
-			eVM += traceWM(i + 1, h - 1);
-			eVM += traceWM(h, j - 2);
-			break;
+	if (check_base(j-1)) {
+		for (h = i + 2; h <= j - 2 && !done; h++) { 
+			A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + a + b + auPenalty(i, j) + Ed3(i,j,j - 1);
+			if (A_temp == VMij) {
+				done = 1;
+				eVM += traceWM(i + 1, h - 1);
+				eVM += traceWM(h, j - 2);
+				break;
+			}
 		}
 	}
 
-	for (h = i + 3; h <= j - 2 && !done; h++) { /* If base pair (i,j) has dangling bases on both sides. */
-		A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + a + b + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
-		if (A_temp == VMij) {
-			done = 1;
-			eVM += traceWM(i + 2, h - 1);
-			eVM += traceWM(h, j - 2);
-			break;
+	if (check_base(i+1)&&check_base(j-1)) {
+		for (h = i + 3; h <= j - 2 && !done; h++) { /* If base pair (i,j) has dangling bases on both sides. */
+			A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + a + b + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
+			if (A_temp == VMij) {
+				done = 1;
+				eVM += traceWM(i + 2, h - 1);
+				eVM += traceWM(h, j - 2);
+				break;
+			}
 		}
 	}
 
 	return eVM;
 }
 
-/* Tracing WM[i][j] */
 int traceWM(int i, int j) {
 
 	int done;
@@ -295,25 +275,25 @@ int traceWM(int i, int j) {
 				structure[i] = j;
 				structure[j] = i;
 				eWM += traceV(i, j);
-			} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec) { 
+			} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && check_base(i)) { 
 				done = 1;
 				eWM += traceV(i + 1, j);
 				structure[i + 1] = j;
 				structure[j] = i + 1;
-			} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec ) { 
+			} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec && check_base(j) ) { 
 				done = 1;
 				eWM += traceV(i, j - 1);
 				structure[i] = j - 1;
 				structure[j - 1] = i;
-			} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec) { 
+			} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec && check_base(i) && check_base(j)) { 
 				done = 1;
 				eWM += traceV(i + 1, j - 1);
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
-			} else if (WM(i,j) == WM(i + 1,j) + Ec ) { 
+			} else if (WM(i,j) == WM(i + 1,j) + Ec && check_base(i)) { 
 				done = 1;
 				eWM += traceWM(i + 1, j);
-			} else if (WM(i,j) == WM(i,j - 1) + Ec ) { 
+			} else if (WM(i,j) == WM(i,j - 1) + Ec && check_base(j)) { 
 				done = 1;
 				eWM += traceWM(i, j - 1);
 			}

From 1d98fb6abb2c3a071858eec0e340e5dac7ab270d Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 6 Apr 2011 12:31:33 -0400
Subject: [PATCH 097/282] added check for min pairing distance

---
 gtfold-mfe/src/traceback.c | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 9d52256..2ddf80a 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -60,8 +60,11 @@ void traceW(int j) {
 	if (j == 0 || j == 1) return;
 
 	for (i = 1; i < j && !done; i++) {
+		if (j-i < TURN) continue;
+		
 		wim1 = MIN(0, W[i-1]);
 		flag = 1;
+		
 		if (wim1 != W[i-1]) flag = 0;
 
 		Widjd = Wijd =  Widj = INFINITY_;
@@ -121,6 +124,7 @@ void traceW(int j) {
 
 int traceV(int i, int j) {
 	int a, b, c, d, Vij;
+	if (j-i < TURN)  return INFINITY_;
 
 	a = eH(i, j);
 	b = eS(i, j) + V(i + 1, j - 1);

From 62964e950ecd1a75b7b4f04e703daf0c2181fd54 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Sat, 9 Apr 2011 13:27:18 -0400
Subject: [PATCH 098/282] fix for issue#8, report to user and exit when
 constraints are invalid(k<1 , j-i<3)

---
 gtfold-mfe/src/constraints.cc | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 9669781..dc7f38d 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -109,6 +109,10 @@ int init_constraints(const char* constr_file,int length) {
 
 	if (nPBP != 0) {
 		for (it = 0; it < nPBP; it++) {
+			if (PBP[it][2] < 1) {
+				printf("Invalid entry (%d %d %d)\n", PBP[it][0], PBP[it][1],PBP[it][2]);
+				continue;
+			}	
 			for(k= 1; k <= PBP[it][2];k++) {
 				BP[PBP[it][0]+k-1] = -1;
 				if(PBP[it][1]!=0) {
@@ -119,11 +123,21 @@ int init_constraints(const char* constr_file,int length) {
 	}
 	if (nFBP != 0) {
 		for (it = 0; it < nFBP; it++) {
+			if (FBP[it][2] < 1) {
+				printf("Invalid entry (%d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
+				continue;
+			}
 			for(k=1; k <= FBP[it][2];k++) {
+				int i1 = FBP[it][0]+k-1;
+				int j1 = FBP[it][1]-k+1;
 				if (!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])) {
 					printf("Can't constrain (%d,%d)\n", FBP[it][0]+k-1, FBP[it][1]-k+1);
 					continue;
 				}
+				if (j1-i1 < TURN) {
+					printf("Can't constrain (%d,%d)\n", i1, j1);
+					continue;
+				}	
 				BP[FBP[it][0]+k-1] = FBP[it][1]+1-k;
 				BP[FBP[it][1]+1-k] = FBP[it][0]+k-1;
 			}

From 61fa86d71cba8192f41fb15d66aa788bc22e4277 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Sat, 9 Apr 2011 13:32:11 -0400
Subject: [PATCH 099/282] fixed issue 12

---
 gtfold-mfe/src/options.cc | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 132e5a8..74171d4 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -112,6 +112,12 @@ void parse_options(int argc, char** argv) {
 
 		// base it off the input file
 		outputFile += seqfile;
+		
+		size_t pos;
+		// extract file name from the path
+		if ((pos=outputFile.find_last_of('/')) > 0) {
+			outputFile = outputFile.substr(pos+1);
+		}
 
 		// and if an extension exists, remove it ...
 		if(outputFile.find(".") != string::npos)
@@ -132,16 +138,6 @@ void printRunConfiguration(string seq) {
 
 	printf("Run Configuration:\n");
 
-//#ifdef _OPENMP
-//	if(nThreads == -1)
-//		printf("- [OMP] thread count: %d\n", omp_get_num_threads());
-//	else
-//		printf("- [OMP] thread count: %d\n", nThreads);
-//#else
-//	printf("- thread count: 1\n");
-//#endif
-//
-
 	if (NOISOLATE == true) {
 		printf("- preventing isolated base pairs\n");
 		standardRun = false;
@@ -173,6 +169,6 @@ void printRunConfiguration(string seq) {
 	printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str());
 	printf("- input file: %s\n", seqfile.c_str());
 	printf("  - sequence length: %d\n", (int)seq.length());
-	printf("  - sequence contents: %s\n", seq.c_str());
+	//printf("  - sequence contents: %s\n", seq.c_str());
 	printf("- output file: %s\n", outputFile.c_str());
 }

From 05f19debb21e08b95cb41aa8f85c4fcdc422ae1c Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Sat, 9 Apr 2011 15:35:06 -0400
Subject: [PATCH 100/282] fix for issue 12,17/28- enable verbose option and
 report External Loop energy

---
 gtfold-mfe/include/options.h   |  1 +
 gtfold-mfe/include/traceback.h |  2 +-
 gtfold-mfe/src/main.cc         |  2 +-
 gtfold-mfe/src/options.cc      |  8 +++-
 gtfold-mfe/src/traceback.c     | 73 +++++++++++++++++++---------------
 5 files changed, 50 insertions(+), 36 deletions(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 508b8ed..7772be1 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -16,6 +16,7 @@ extern bool LIMIT_DISTANCE;
 extern bool BPP_ENABLED;
 extern bool SUBOPT_ENABLED;
 extern bool CONS_ENABLED;
+extern bool VERBOSE;
 
 extern string seqfile;
 extern string constraintsFile;
diff --git a/gtfold-mfe/include/traceback.h b/gtfold-mfe/include/traceback.h
index bfe96f0..a8bd6c4 100644
--- a/gtfold-mfe/include/traceback.h
+++ b/gtfold-mfe/include/traceback.h
@@ -26,7 +26,7 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
-	void trace(int len);
+	void trace(int len, int vbose);
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 88c0187..f9ca8a2 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -216,7 +216,7 @@ int main(int argc, char** argv) {
 	}
 	
 	t1 = get_seconds();
-	trace(seq.length());
+	trace(seq.length(), VERBOSE);
 	t1 = get_seconds() - t1;
 
 	printf("\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 74171d4..06c28c9 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -11,6 +11,7 @@ bool LIMIT_DISTANCE;
 bool BPP_ENABLED;
 bool SUBOPT_ENABLED;
 bool CONS_ENABLED = false;
+bool VERBOSE = false;
 
 string seqfile = "";
 string constraintsFile = "";
@@ -87,7 +88,10 @@ void parse_options(int argc, char** argv) {
 					nThreads = atoi(argv[++i]);
 				else
 					help();	
-			} else if(strcmp(argv[i], "--bpp") == 0) {
+			} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
+                VERBOSE = true;
+			}
+			else if(strcmp(argv[i], "--bpp") == 0) {
 				BPP_ENABLED = true;
 			} else if(strcmp(argv[i], "--subopt") == 0) {
 				SUBOPT_ENABLED = true;
@@ -169,6 +173,6 @@ void printRunConfiguration(string seq) {
 	printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str());
 	printf("- input file: %s\n", seqfile.c_str());
 	printf("  - sequence length: %d\n", (int)seq.length());
-	//printf("  - sequence contents: %s\n", seq.c_str());
+	printf("  - sequence contents: %s\n", seq.c_str());
 	printf("- output file: %s\n", outputFile.c_str());
 }
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 2ddf80a..b052cda 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -29,12 +29,13 @@
 #include "traceback.h"
 #include "utils.h"
 
-
+int verbose = -1;
 int total_en = 0;
+int total_ex = 0;
 
-void trace(int len) {
+void trace(int len, int vbose) {
 	int i;
-	
+	verbose = vbose;
 	for (i = 0; i < len+1; i++)
 		structure[i] = 0;
 
@@ -43,9 +44,10 @@ void trace(int len) {
 		return;
 	}
 
+	printf("\n");
 	traceW(len);
-	
-	printf("- sum of energy of loops: %12.2f kcal/mol\n", total_en/100.0);
+	printf("- sum of energy of Loops:   	  %12.2f kcal/mol\n", total_en/100.0);
+	printf("- sum of energy of External Loop: %12.2f kcal/mol\n", total_ex/100.0);
 	return;
 }
 
@@ -55,63 +57,64 @@ void traceW(int j) {
 	Wj = INFINITY_;
 	flag = 1;
 	done = 0; 
-	int min_i=1;
 	
 	if (j == 0 || j == 1) return;
 
 	for (i = 1; i < j && !done; i++) {
 		if (j-i < TURN) continue;
-		
+
 		wim1 = MIN(0, W[i-1]);
 		flag = 1;
-		
 		if (wim1 != W[i-1]) flag = 0;
 
 		Widjd = Wijd =  Widj = INFINITY_;
-		
 		Wij = V(i,j) + auPenalty(i, j) + wim1;
-		
 		Widjd =(check_base(i)&&check_base(j))?(V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1): INFINITY_;
 		Wijd = (check_base(j))?(V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1):INFINITY_;
 		Widj = (check_base(i))?(V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1):INFINITY_;
 		Wj_temp=Wj;
-
 		Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
-		if (Wj_temp>Wj) min_i=i;	
 
 		if (W[j] == Wj) {
 			if (W[j] == Wij) { 
 				done = 1;
+				if (verbose == 1) 
+					printf("i %5d j %5d ExtLoop   %12.2f\n", i, j, auPenalty(i, j)/100.00);
+				total_ex += auPenalty(i, j);
 				structure[i] = j;
 				structure[j] = i;
 				traceV(i, j);
-				if (flag || is_ss(1,i)) 
-					traceW(i - 1);
+				if (flag || is_ss(1,i)) traceW(i - 1);
 				break;
 			} else if (W[j] == Widjd && check_base(i) && check_base(j)) { 
 				done = 1;
+				if (verbose == 1) 
+					printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
+				total_ex += (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
 				traceV(i + 1, j - 1);
-				if (flag || is_ss(1,i)) 
-					traceW(i - 1);
+				if (flag || is_ss(1,i)) traceW(i - 1);
 				break;
 			} else if (W[j] == Wijd && check_base(j)) { 
 				done = 1;
+				if (verbose == 1) 
+					printf("i %5d j %5d ExtLoop   %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
+				total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
 				structure[i] = j - 1;
 				structure[j - 1] = i;
 				traceV(i, j - 1);
-
-				if (flag || is_ss(1,i))
-					traceW(i - 1);
+				if (flag || is_ss(1,i)) traceW(i - 1);
 				break;
 			} else if (W[j] == Widj && check_base(i)) { 
 				done = 1;
+				if (verbose == 1) 
+					printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
+				total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
 				structure[i + 1] = j;
 				structure[j] = i + 1;
 				traceV(i + 1, j);
-				if (flag || is_ss(1,i))
-					traceW(i - 1);
+				if (flag || is_ss(1,i)) traceW(i - 1);
 				break;
 			}
 		}
@@ -135,19 +138,27 @@ int traceV(int i, int j) {
 	Vij = MIN(MIN(a, b), MIN(c, d));
 	
 	if (Vij == a && Vij != b && Vij != c && Vij != d) { 
+		if (verbose == 1) 
+			printf("i %5d j %5d Hairpin   %12.2f\n", i, j, eH(i, j)/100.00);
 		total_en += eH(i,j);
 		return Vij;
 	} else if (Vij == b) { 
+		if (verbose == 1) 
+			printf("i %5d j %5d Stack     %12.2f\n", i, j, eS(i, j)/100.00);
 		total_en += eS(i,j);
 		structure[i + 1] = j - 1;
 		structure[j - 1] = i + 1;
 		traceV(i + 1, j - 1);
 		return Vij;
 	} else if (Vij == c) { 
+		if (verbose == 1) 
+			printf("i %5d j %5d IntLoop  ", i, j);
 		traceVBI(i, j);
 		return Vij;
 	} else if (Vij == d && Vij != a && Vij != b && Vij != c) { 
 		int eVM = traceVM(i, j);
+		if (verbose ==1) 
+			printf("i %5d j %5d MultiLoop %12.2f\n", i, j, (Vij-eVM)/100.0);
 		total_en += (Vij-eVM);
 		return Vij;
 	} 
@@ -181,6 +192,8 @@ int traceVBI(int i, int j) {
 
 	structure[ifinal] = jfinal;
 	structure[jfinal] = ifinal;
+	if (verbose==1) 
+		printf(" %12.2f\n", eL(i, j, ifinal, jfinal)/100.00);
 	total_en += eL(i, j, ifinal, jfinal);
 
 	int eVI = traceV(ifinal, jfinal);
@@ -191,18 +204,14 @@ int traceVM(int i, int j) {
 
 	int done;
 	int h;
-	int a, b;
 	int A_temp;
 	int eVM = 0;
 
 	done = 0;
-	a = eparam[5];
-	b = eparam[10]; /* efn2b */
-
 	int VMij = VM(i,j);
 
 	for (h = i + 2; h <= j - 1 && !done; h++) {
-		A_temp = WM(i+1,h-1) + WM(h,j - 1) + a + b + auPenalty(i, j);
+		A_temp = WM(i+1,h-1) + WM(h,j - 1) + Ea + Eb + auPenalty(i, j);
 		if (A_temp == VMij) { 
 			done = 1;
 			eVM += traceWM(i + 1, h - 1);
@@ -213,7 +222,7 @@ int traceVM(int i, int j) {
 
 	if (check_base(i+1)) {
 		for (h = i + 3; h <= j - 1 && !done; h++) {
-			A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + a + b + auPenalty(i,j) + Ed5(i,j,i + 1); 
+			A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1); 
 			if (A_temp == VMij) {
 				done = 1;
 				eVM += traceWM(i + 2, h - 1);
@@ -225,7 +234,7 @@ int traceVM(int i, int j) {
 
 	if (check_base(j-1)) {
 		for (h = i + 2; h <= j - 2 && !done; h++) { 
-			A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + a + b + auPenalty(i, j) + Ed3(i,j,j - 1);
+			A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1);
 			if (A_temp == VMij) {
 				done = 1;
 				eVM += traceWM(i + 1, h - 1);
@@ -236,8 +245,8 @@ int traceVM(int i, int j) {
 	}
 
 	if (check_base(i+1)&&check_base(j-1)) {
-		for (h = i + 3; h <= j - 2 && !done; h++) { /* If base pair (i,j) has dangling bases on both sides. */
-			A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + a + b + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
+		for (h = i + 3; h <= j - 2 && !done; h++) { 
+			A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
 			if (A_temp == VMij) {
 				done = 1;
 				eVM += traceWM(i + 2, h - 1);
@@ -263,7 +272,7 @@ int traceWM(int i, int j) {
 		return 0;
 	else {
 		for (h = i; h < j && !done; h++) {
-			int aa = WM(i,h) + WM(h + 1,j); /* If WM(i,j) came from the summation of two WM terms */
+			int aa = WM(i,h) + WM(h + 1,j); 
 			if (aa == WM(i,j)) {
 				done = 1;
 				h1 = h;
@@ -274,7 +283,7 @@ int traceWM(int i, int j) {
 			eWM += traceWM(i, h);
 			eWM += traceWM(h + 1, j);
 		} else {
-			if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb) { /* If base pair (i,j) pairs*/
+			if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb) { 
 				done = 1;
 				structure[i] = j;
 				structure[j] = i;

From 39d0b872cd392c5a9d9e6ca879e2cd840c36aff9 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Sat, 9 Apr 2011 16:19:58 -0400
Subject: [PATCH 101/282] fixed issue 10 - report and exit when constraints
 create pseudoknot

---
 gtfold-mfe/src/constraints.cc | 31 ++++++++++++++++++++-----------
 1 file changed, 20 insertions(+), 11 deletions(-)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index dc7f38d..97cbc5e 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -3,6 +3,8 @@
 #include <stdio.h>
 #include <iostream>
 #include <fstream>
+#include <vector>
+#include <algorithm>
 
 #include "global.h"
 #include "options.h"
@@ -15,6 +17,12 @@ int** FBP;
 int nPBP;
 int nFBP;
 
+bool compare_bp(const std::pair<int,int>& o1, 
+			   	const std::pair<int,int>& o2) {
+	return o1.first < o2.first;
+}
+
+
 static int load_constraints(const char* constr_file, int verbose=0) {
 	std::ifstream cfcons;
     fprintf(stdout, "- Running with constraints\n");
@@ -76,20 +84,21 @@ static int load_constraints(const char* constr_file, int verbose=0) {
         }
     }
 
-	if (verbose == 1) {
-		fprintf(stdout, "Forced base pairs: ");
-		for(it=0; it< nFBP; it++) {
-			for(int k=1;k<= FBP[it][2];k++)
-				fprintf(stdout, "(%d,%d) ", FBP[it][0]+k-1, FBP[it][1]-k+1);
-		}
-		fprintf(stdout, "\nProhibited base pairs: ");
-		for(it=0; it< nPBP; it++) {
-			for(int k=1;k<= PBP[it][2];k++)
-				fprintf(stdout, "(%d,%d) ", PBP[it][0]+k-1, PBP[it][1]-k+1);
+	std::vector<std::pair<int,int> > v_fbp;
+	for(it=0; it< nFBP; it++) {
+		for(int k=1;k<= FBP[it][2];k++)
+			v_fbp.push_back(std::pair<int,int>(FBP[it][0]+k-1, FBP[it][1]-k+1));
+	}
+	std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
+	for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) {
+		if (v_fbp[ii].second <= v_fbp[ii+1].second) {
+			fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n");
+			exit(-1);
 		}
-		fprintf(stdout, "\n\n");
+			
 	}
 
+
     return 0;
 }
 

From 1acf3aa83bd980ea5b42f58403c42fa1781fe205 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 13 Apr 2011 12:30:47 -0400
Subject: [PATCH 102/282] fixed bug on reading of sequence

---
 gtfold-mfe/src/main.cc | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index f9ca8a2..e976d49 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -85,16 +85,14 @@ int read_sequence_file(const char* filename, std::string& seq) {
 
 	ifstream fs;
 	fs.open(filename, ios::in);
-	if (fs == NULL)
-		return FAILURE;
+	if (!fs.good()) return FAILURE;
 
 	string line;
-	getline(fs, line);
-	while(line.length() > 0) {
+	while(fs.good()) {
+		getline(fs, line);
 		// exclude lines starting with FASTA comment characters
-		if(line[0] != ';' && line[0] != '>')
+		if(line[0] != ';' && line[0] != '>' && line.length() > 0)
 			seq += line;
-		getline(fs, line);
 	}
 
 	fs.close();

From 51abea3dc8f59d4532431010563d279720681178 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 14 Apr 2011 14:15:24 -0400
Subject: [PATCH 103/282] program crashed when run with unambiguous bases
 sequence, fixed this

---
 gtfold-mfe/src/energy.c | 46 ++++++++++++++++++++---------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 80f37c3..afed6ec 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -16,8 +16,9 @@ int *VM;
 int **WM; 
 int *indx; 
 
-void create_tables(int len)
-{	
+int alloc_flag = 0;
+
+void create_tables(int len) {	
 	V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
 	if (V == NULL) {
 		perror("Cannot allocate variable 'V'");
@@ -74,12 +75,13 @@ void create_tables(int len)
 		exit(-1);
 	}
 
+	alloc_flag = 1;
+	
 	init_tables(len);
 }
 
 
-void init_tables(int len) 
-{
+void init_tables(int len) {
 	int i, j, LLL;
 	
 	for (i = 0; i <= len; i++) {
@@ -105,21 +107,21 @@ void init_tables(int len)
 	return;
 }
 
-void free_tables(int len)
-{
-	free(indx);
-	
-	int i;
-	for (i = 0; i <= len; i++)
-	         free(WM[i]);
-	free(WM);
-
-	free(VM);
-	free(VBI);
-	free(V);
-	free(VV);
-	free(VV1);
-	free(W);
+void free_tables(int len) {
+	if (alloc_flag == 1) {
+		free(indx);
+
+		int i;
+		for (i = 0; i <= len; i++) free(WM[i]);
+		free(WM);
+
+		free(VM);
+		free(VBI);
+		free(V);
+		free(VV);
+		free(VV1);
+		free(W);
+	}
 }
 
 
@@ -215,8 +217,7 @@ inline int eL(int i, int j, int ip, int jp) {
 	return energy;
 }
 
-inline int eH(int i, int j) 
-{
+inline int eH(int i, int j) {
 	/*  Hairpin loop for all the bases between i and j */
 	/*  size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */
 	int size;
@@ -321,8 +322,7 @@ inline int eH(int i, int j)
 	return energy;
 }
 
-inline int eS(int i, int j) 
-{
+inline int eS(int i, int j) {
 	int energy;
 	/*  not sure about eparam[1], come from MFold.. = 0 */
 	energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i+1], RNA[j-1])] + eparam[1];

From 3f0046e514507988c31737738b014003b72b4abd Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 22 Apr 2011 13:43:35 -0400
Subject: [PATCH 104/282] removed printing of seq contents

---
 gtfold-mfe/src/options.cc | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 06c28c9..1bc103c 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -172,7 +172,6 @@ void printRunConfiguration(string seq) {
 
 	printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str());
 	printf("- input file: %s\n", seqfile.c_str());
-	printf("  - sequence length: %d\n", (int)seq.length());
-	printf("  - sequence contents: %s\n", seq.c_str());
+	printf("- sequence length: %d\n", (int)seq.length());
 	printf("- output file: %s\n", outputFile.c_str());
 }

From 27383c24901a8087145b80c1bb62f6f7295f6c7a Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 28 Apr 2011 09:59:48 -0400
Subject: [PATCH 105/282] adding data files in new format

---
 gtfold-mfe/data/Turner99/dangle.DAT   |   8 +
 gtfold-mfe/data/Turner99/int11.DAT    |  24 +
 gtfold-mfe/data/Turner99/int21.DAT    |  96 ++++
 gtfold-mfe/data/Turner99/int22.DAT    | 648 ++++++++++++++++++++++++++
 gtfold-mfe/data/Turner99/loop.DAT     |  30 ++
 gtfold-mfe/data/Turner99/miscloop.DAT |  12 +
 gtfold-mfe/data/Turner99/sint2.DAT    |  24 +
 gtfold-mfe/data/Turner99/sint4.DAT    | 576 +++++++++++++++++++++++
 gtfold-mfe/data/Turner99/stack.DAT    |  16 +
 gtfold-mfe/data/Turner99/tloop.DAT    |  30 ++
 gtfold-mfe/data/Turner99/tstackh.DAT  |  16 +
 gtfold-mfe/data/Turner99/tstacki.DAT  |  16 +
 gtfold-mfe/data/Turner99/tstackm.DAT  |  16 +
 13 files changed, 1512 insertions(+)
 create mode 100644 gtfold-mfe/data/Turner99/dangle.DAT
 create mode 100644 gtfold-mfe/data/Turner99/int11.DAT
 create mode 100644 gtfold-mfe/data/Turner99/int21.DAT
 create mode 100644 gtfold-mfe/data/Turner99/int22.DAT
 create mode 100644 gtfold-mfe/data/Turner99/loop.DAT
 create mode 100644 gtfold-mfe/data/Turner99/miscloop.DAT
 create mode 100644 gtfold-mfe/data/Turner99/sint2.DAT
 create mode 100644 gtfold-mfe/data/Turner99/sint4.DAT
 create mode 100644 gtfold-mfe/data/Turner99/stack.DAT
 create mode 100644 gtfold-mfe/data/Turner99/tloop.DAT
 create mode 100644 gtfold-mfe/data/Turner99/tstackh.DAT
 create mode 100644 gtfold-mfe/data/Turner99/tstacki.DAT
 create mode 100644 gtfold-mfe/data/Turner99/tstackm.DAT

diff --git a/gtfold-mfe/data/Turner99/dangle.DAT b/gtfold-mfe/data/Turner99/dangle.DAT
new file mode 100644
index 0000000..9fb7c28
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/dangle.DAT
@@ -0,0 +1,8 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.80	-0.50	-0.80	-0.60
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.70	-0.80	-1.70	-1.20	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-1.10	-0.40	-1.30	-0.60	inf 	inf 	inf 	inf	-0.80	-0.50	-0.80	-0.60
+-0.70	-0.10	-0.70	-0.10	inf 	inf 	inf 	inf	-0.70	-0.10	-0.70	-0.10	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.30	-0.10	-0.20	-0.20
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.20	-0.30	-0.0	-0.0	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-0.50	-0.30	-0.20	-0.10	inf 	inf 	inf 	inf	-0.30	-0.10	-0.20	-0.20
+-0.30	-0.30	-0.40	-0.20	inf 	inf 	inf 	inf	-0.30	-0.30	-0.40	-0.20	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/Turner99/int11.DAT b/gtfold-mfe/data/Turner99/int11.DAT
new file mode 100644
index 0000000..96eabfd
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/int11.DAT
@@ -0,0 +1,24 @@
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.50	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.20	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.10	1.10	1.10	1.10	0.40	-0.40	0.40	0.40	1.10	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.30	0.50	0.40	0.50	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	-0.10	0.40	-1.70	0.40	0.40	0.40	-1.40	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.00	0.40	-0.30	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.80	0.40	0.40	0.40	0.40	0.30	-0.10	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	0.40	-0.40	0.50	0.40	0.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	0.40	0.40	-2.10	0.40	0.40	0.40	-1.70	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	-0.70	0.40	0.50	0.40	-0.30	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.80	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.50	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
diff --git a/gtfold-mfe/data/Turner99/int21.DAT b/gtfold-mfe/data/Turner99/int21.DAT
new file mode 100644
index 0000000..0dfe3c4
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/int21.DAT
@@ -0,0 +1,96 @@
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.20	3.00	2.40	4.80	2.30	2.20	1.10	4.00	2.40	2.20	1.60	4.00	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80
+3.10	3.00	4.80	3.00	2.30	2.20	4.00	2.20	2.30	2.20	4.00	2.20	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00
+2.50	4.80	1.60	4.80	1.70	4.00	0.80	4.00	1.70	4.00	0.80	4.00	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+2.90	2.50	2.40	4.80	2.10	1.70	1.60	4.00	2.10	1.70	1.60	4.00	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80
+3.00	3.30	4.80	3.00	2.20	2.50	4.00	2.20	2.20	2.50	4.00	2.20	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	3.00	4.80	2.10	4.00	2.20	4.00	1.50	4.00	2.20	4.00	1.30	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10
+1.80	1.40	1.20	4.80	0.80	0.60	0.40	4.00	1.00	0.60	0.40	4.00	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+1.60	4.80	3.00	4.80	0.80	4.00	2.20	4.00	0.80	4.00	2.20	4.00	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+3.30	2.70	4.80	3.00	2.50	1.90	4.00	2.20	2.50	1.90	4.00	2.20	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	2.50	4.80	2.00	4.00	1.70	4.00	1.20	4.00	1.70	4.00	1.20	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00
+3.20	3.00	2.40	4.80	2.40	2.20	1.60	4.00	2.50	2.20	2.10	4.00	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80
+3.10	3.00	4.80	3.00	2.30	2.20	4.00	2.20	2.30	2.20	4.00	2.20	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00
+2.50	4.80	1.60	4.80	1.70	4.00	0.80	4.00	1.70	4.00	0.80	4.00	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+2.90	2.50	2.40	4.80	2.10	1.70	1.60	4.00	2.10	1.70	1.60	4.00	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80
+3.00	3.30	4.80	3.00	2.20	2.50	4.00	2.20	2.20	2.50	4.00	2.20	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	3.00	4.80	2.10	4.00	2.20	4.00	1.30	4.00	2.20	4.00	1.20	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10
+1.80	1.40	1.20	4.80	1.00	0.60	0.40	4.00	1.20	0.60	0.40	4.00	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+1.60	4.80	3.00	4.80	0.80	4.00	2.20	4.00	0.80	4.00	2.20	4.00	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+3.30	2.70	4.80	3.00	2.50	1.90	4.00	2.20	2.50	1.90	4.00	2.20	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	2.50	4.80	2.00	4.00	1.70	4.00	1.20	4.00	1.70	4.00	1.20	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
diff --git a/gtfold-mfe/data/Turner99/int22.DAT b/gtfold-mfe/data/Turner99/int22.DAT
new file mode 100644
index 0000000..4f17932
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/int22.DAT
@@ -0,0 +1,648 @@
+                                           A \/ \_/ A 
+                                           U /\  |  U 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                           A \/ \_/ C 
+                                           U /\  |  G 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
+  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
+  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
+                                           A \/ \_/ G 
+                                           U /\  |  C 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
+  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
+  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
+                                           A \/ \_/ U 
+                                           U /\  |  A 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                           A \/ \_/ G 
+                                           U /\  |  U 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                           A \/ \_/ U 
+                                           U /\  |  G 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                           C \/ \_/ A 
+                                           G /\  |  U 
+  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
+  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
+  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
+  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
+                                           C \/ \_/ C 
+                                           G /\  |  G 
+  0.50  1.10 -0.30  2.00  1.10  1.70  2.00  0.70  0.40  2.00  1.00  0.10  2.00  1.80 -0.50  1.50 
+  0.60  1.50  0.10  2.00  1.10  1.50  2.00  0.50  0.50  2.00  1.40 -0.70  2.00  1.50 -0.60  0.00 
+  0.00 -0.70 -1.60  2.00 -1.00 -0.60  2.00  0.20 -0.70  2.00  0.00 -0.80  2.00  1.20 -0.60  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.00 -0.70  2.00  1.00  1.00  2.00  0.00  0.70  2.00  0.90 -1.90  2.00  1.10 -1.50 -0.20 
+  2.20  1.30  0.70  2.00  1.90  1.30  2.00  0.30  0.70  2.00  1.80 -0.30  2.00  1.40 -0.20 -0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.00  1.20  0.40  2.00  1.10  1.20  2.00  1.70  1.00  2.00  1.70 -0.70  2.00  1.20 -0.30  0.20 
+ -0.20 -0.40 -1.70  2.00  0.70  1.10  2.00  0.20 -0.50  2.00  0.00 -0.90  2.00  1.20 -1.30  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
+  0.90  0.00  0.30  2.00 -0.10  1.00  2.00  0.00  0.60  2.00  0.90 -3.00  2.00  1.00 -2.40  0.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.00  1.20  0.40  2.00  1.10  1.20  2.00  0.20  0.50  2.00  1.70 -0.70  2.00  1.20 -0.10  0.40 
+ -0.10 -1.60 -1.60  2.00 -1.60 -0.60  2.00 -1.60 -0.60  2.00 -0.70 -4.40  2.00 -0.50 -4.10 -1.00 
+  1.40  0.30  0.50  2.00  0.30  0.30  2.00  0.10  1.40  2.00  1.20 -1.00  2.00  0.30  0.10  0.60 
+                                           C \/ \_/ G 
+                                           G /\  |  C 
+  1.30  1.20  0.30  2.00  1.60  2.10  2.00  1.90  0.30  2.00  1.00 -0.40  2.00  1.90  1.10  1.40 
+  1.60  1.50  0.60  2.00  2.00  1.80  2.00  1.70  0.60  2.00  1.40 -1.10  2.00  1.70  0.40  0.80 
+  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.20  1.10  0.20  2.00  1.50  1.40  2.00  1.20  0.20  2.00  0.90 -1.50  2.00  1.20  0.00  0.30 
+  2.10  1.40  1.50  2.00  1.80  1.70  2.00  1.50  1.50  2.00  1.80 -0.20  2.00  1.50  1.30  0.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
+  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
+  1.10  0.00  0.90  2.00  0.40  1.30  2.00  1.10  0.90  2.00  0.90 -2.60  2.00  1.10 -1.10  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
+ -0.40 -1.50 -0.60  2.00 -1.10 -0.20  2.00 -0.40 -0.60  2.00 -0.70 -4.20  2.00 -0.40 -2.60 -0.50 
+  1.40  0.30  1.30  2.00  0.80  0.60  2.00  0.50  1.30  2.00  1.20 -0.50  2.00  0.50  1.10 -0.40 
+                                           C \/ \_/ U 
+                                           G /\  |  A 
+  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
+  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
+  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
+  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
+                                           C \/ \_/ G 
+                                           G /\  |  U 
+  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
+  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
+  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
+  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
+                                           C \/ \_/ U 
+                                           G /\  |  G 
+  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
+  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
+  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
+  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
+                                           G \/ \_/ A 
+                                           C /\  |  U 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
+  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
+  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
+  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
+  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
+  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
+                                           G \/ \_/ C 
+                                           C /\  |  G 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.20  0.90 -0.80  2.00  0.90  0.90  2.00  0.00 -0.20  2.00  0.80 -2.00  2.00  1.00 -1.60  0.20 
+  0.10 -0.10 -1.90  2.00 -0.20  0.90  2.00 -0.10 -1.30  2.00 -0.20 -1.30  2.00  0.90 -0.90  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.20  1.00 -0.80  2.00  0.90  1.00  2.00  0.00 -0.10  2.00  0.90 -1.90  2.00  1.00 -1.50  0.20 
+  1.80  1.00  0.20  2.00  0.90  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.00 -0.50  0.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.00  0.30  2.00  1.00  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.10 -0.50  0.30 
+ -0.50 -0.80 -2.60  2.00 -0.80  0.20  2.00 -0.80 -1.90  2.00 -0.90 -1.90  2.00  0.30 -1.50  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
+ -0.30 -1.50 -1.50  2.00 -1.60 -0.50  2.00 -1.50 -0.90  2.00 -0.60 -4.50  2.00 -0.50 -4.10 -0.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  0.80  0.00 -0.80  2.00  0.00  0.00  2.00 -1.00 -0.10  2.00  0.50 -1.90  2.00  0.00 -1.50 -0.70 
+ -0.70 -1.90 -1.90  2.00 -2.00 -0.90  2.00 -1.90 -1.30  2.00 -1.00 -4.90  2.00 -0.90 -4.50 -0.90 
+  1.50  0.20  0.30  2.00  0.20  0.20  2.00 -0.70  0.90  2.00  1.10 -0.90  2.00  0.30 -0.50 -0.50 
+                                           G \/ \_/ G 
+                                           C /\  |  C 
+  0.50  1.30 -0.20  2.00  0.60  2.20  2.00  2.00  0.00  2.00  1.10 -0.10  2.00  2.00  0.90  1.40 
+  1.10  1.00  0.70  2.00  1.10  1.90  2.00  1.10 -1.00  2.00  0.80 -1.60  2.00  1.10 -0.10  0.30 
+  0.40  0.70 -0.50  2.00  0.50  0.70  2.00  0.50 -0.70  2.00 -0.20 -0.60  2.00  1.00  0.60  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  1.00 -0.40  2.00  1.50  1.30  2.00  1.20 -0.70  2.00  0.90 -1.60  2.00  1.20  0.00  0.30 
+  1.70  1.00  1.10  2.00  1.50  1.30  2.00  1.20 -0.60  2.00  1.50 -0.60  2.00  1.20  1.00  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.10  1.20  2.00  1.50  1.40  2.00  1.20  1.20  2.00  1.50 -0.50  2.00  1.20  1.00  0.30 
+ -0.30 -0.70 -1.70  2.00  0.10  0.70  2.00  0.40 -1.60  2.00 -0.90 -1.60  2.00  0.40  0.30  0.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
+ -0.50 -1.50 -1.30  2.00 -0.60 -0.20  2.00 -0.10 -0.60  2.00 -0.60 -4.10  2.00 -0.30 -2.40  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  0.70  0.00  0.20  2.00  0.50  0.30  2.00  0.20  0.20  2.00  0.50 -1.60  2.00  1.70  0.00  0.10 
+  0.10 -1.90 -0.90  2.00 -0.70 -0.30  2.00 -0.70 -0.80  2.00 -1.00 -4.40  2.00 -0.70 -3.00 -1.00 
+  1.50 -0.20  0.90  2.00  0.00 -0.10  2.00  0.40  0.90  2.00  1.10 -1.00  2.00  0.20  0.60  0.60 
+                                           G \/ \_/ U 
+                                           C /\  |  A 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
+  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
+  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
+  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
+  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
+  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
+                                           G \/ \_/ G 
+                                           C /\  |  U 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
+  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
+  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
+  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
+  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
+  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
+                                           G \/ \_/ U 
+                                           C /\  |  G 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
+  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
+  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
+  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
+  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
+  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
+                                           U \/ \_/ A 
+                                           A /\  |  U 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                           U \/ \_/ C 
+                                           A /\  |  G 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
+  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
+                                           U \/ \_/ G 
+                                           A /\  |  C 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
+  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
+  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
+                                           U \/ \_/ U 
+                                           A /\  |  A 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+                                           U \/ \_/ G 
+                                           A /\  |  U 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                           U \/ \_/ U 
+                                           A /\  |  G 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+                                           G \/ \_/ A 
+                                           U /\  |  U 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                           G \/ \_/ C 
+                                           U /\  |  G 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
+  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
+  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
+                                           G \/ \_/ G 
+                                           U /\  |  C 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
+  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
+  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
+                                           G \/ \_/ U 
+                                           U /\  |  A 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                           G \/ \_/ G 
+                                           U /\  |  U 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                           G \/ \_/ U 
+                                           U /\  |  G 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                           U \/ \_/ A 
+                                           G /\  |  U 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                           U \/ \_/ C 
+                                           G /\  |  G 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
+  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
+                                           U \/ \_/ G 
+                                           G /\  |  C 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
+  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
+  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
+                                           U \/ \_/ U 
+                                           G /\  |  A 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+                                           U \/ \_/ G 
+                                           G /\  |  U 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                           U \/ \_/ U 
+                                           G /\  |  G 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80
diff --git a/gtfold-mfe/data/Turner99/loop.DAT b/gtfold-mfe/data/Turner99/loop.DAT
new file mode 100644
index 0000000..bc9a352
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/loop.DAT
@@ -0,0 +1,30 @@
+1	inf	3.80	inf
+2	inf	2.80	inf
+3	inf	3.20	5.70
+4	1.70	3.60	5.60
+5	1.80	4.00	5.60
+6	2.00	4.40	5.40
+7	2.20	4.60	5.90
+8	2.30	4.70	5.60
+9	2.40	4.80	6.40
+10	2.50	4.90	6.50
+11	2.60	5.00	6.60
+12	2.70	5.10	6.70
+13	2.80	5.20	6.80
+14	2.90	5.30	6.90
+15	3.00	5.40	6.90
+16	3.00	5.40	7.00
+17	3.10	5.50	7.10
+18	3.10	5.50	7.10
+19	3.20	5.60	7.20
+20	3.30	5.70	7.20
+21	3.30	5.70	7.30
+22	3.40	5.80	7.30
+23	3.40	5.80	7.40
+24	3.40	5.80	7.40
+25	3.50	5.90	7.50
+26	3.50	5.90	7.50
+27	3.60	6.00	7.50
+28	3.60	6.00	7.60
+29	3.60	6.00	7.60
+30	3.70	6.10	7.70
diff --git a/gtfold-mfe/data/Turner99/miscloop.DAT b/gtfold-mfe/data/Turner99/miscloop.DAT
new file mode 100644
index 0000000..2ba7508
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/miscloop.DAT
@@ -0,0 +1,12 @@
+1.079
+3.00
+.50	.50	.50	.50
+3.40	.00	.40
+10.10	-0.30	-0.30
+0.50
+-2.20
+0.30
+1.60
+1.40
+4.10
+1
diff --git a/gtfold-mfe/data/Turner99/sint2.DAT b/gtfold-mfe/data/Turner99/sint2.DAT
new file mode 100644
index 0000000..96eabfd
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/sint2.DAT
@@ -0,0 +1,24 @@
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.50	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.20	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.10	1.10	1.10	1.10	0.40	-0.40	0.40	0.40	1.10	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.30	0.50	0.40	0.50	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	-0.10	0.40	-1.70	0.40	0.40	0.40	-1.40	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.00	0.40	-0.30	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.80	0.40	0.40	0.40	0.40	0.30	-0.10	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	0.40	-0.40	0.50	0.40	0.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	0.40	0.40	-2.10	0.40	0.40	0.40	-1.70	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	-0.70	0.40	0.50	0.40	-0.30	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.80	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.50	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
diff --git a/gtfold-mfe/data/Turner99/sint4.DAT b/gtfold-mfe/data/Turner99/sint4.DAT
new file mode 100644
index 0000000..c878345
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/sint4.DAT
@@ -0,0 +1,576 @@
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.00	1.70	0.00	2.00	1.70	1.70	2.00	0.70	0.60	2.00	1.60	-1.20	2.00	1.80	-0.80	1.00
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	-0.10	2.00	1.60	1.60	2.00	0.60	0.50	2.00	1.50	-1.30	2.00	1.70	-0.90	0.90
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.20	-0.60	2.00	1.10	1.80	2.00	0.80	0.00	2.00	1.10	-0.70	2.00	1.80	-0.30	1.40
+1.70	0.40	0.50	2.00	0.40	1.40	2.00	0.50	1.10	2.00	1.30	-2.50	2.00	1.50	-2.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.70	-0.50	-0.50	2.00	-0.60	0.50	2.00	-0.50	0.10	2.00	0.40	-3.50	2.00	0.50	-3.10	0.50
+2.00	0.80	0.80	2.00	0.70	0.80	2.00	-0.20	1.50	2.00	1.70	-0.30	2.00	0.80	0.10	0.00
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+1.90	1.80	0.90	2.00	2.20	2.10	2.00	1.90	0.90	2.00	1.60	-0.80	2.00	1.90	0.70	1.00
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.70	0.80	2.00	2.10	2.00	2.00	1.80	0.80	2.00	1.50	-0.90	2.00	1.80	0.60	0.90
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.30	1.20	0.30	2.00	1.70	2.10	2.00	2.00	0.30	2.00	1.10	-0.40	2.00	2.00	1.10	1.50
+1.60	0.50	1.40	2.00	0.90	1.80	2.00	1.60	1.40	2.00	1.30	-2.10	2.00	1.60	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.60	-0.50	0.40	2.00	0.00	0.80	2.00	0.70	0.40	2.00	0.40	-3.10	2.00	0.70	-1.60	0.60
+1.90	0.80	1.80	2.00	1.30	1.10	2.00	1.00	1.80	2.00	1.70	0.00	2.00	1.00	1.60	0.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.00	1.60	1.00	2.00	2.00	2.60	2.00	2.60	1.00	2.00	1.40	0.20	2.00	2.30	1.50	2.20
+2.40	1.90	1.30	2.00	2.40	2.40	2.00	2.40	1.30	2.00	1.70	-0.40	2.00	2.10	0.80	1.50
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.50	0.90	2.00	1.90	1.90	2.00	1.90	0.90	2.00	1.30	-0.90	2.00	1.60	0.40	1.10
+2.80	1.80	2.20	2.00	2.20	2.20	2.00	2.20	2.20	2.00	2.20	0.40	2.00	1.90	1.70	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+1.80	0.40	1.60	2.00	0.80	1.80	2.00	1.80	1.60	2.00	1.20	-2.00	2.00	1.50	-0.70	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+0.30	-1.10	0.10	2.00	-0.70	0.30	2.00	0.30	0.10	2.00	-0.30	-3.50	2.00	0.00	-2.20	0.30
+2.20	0.70	1.90	2.00	1.20	1.20	2.00	1.20	1.90	2.00	1.50	0.20	2.00	0.90	1.50	0.30
+0.50	1.10	-0.30	2.00	1.10	1.70	2.00	0.70	0.40	2.00	1.00	0.10	2.00	1.80	-0.50	1.50
+0.60	1.50	0.10	2.00	1.10	1.50	2.00	0.50	0.50	2.00	1.40	-0.70	2.00	1.50	-0.60	0.00
+0.00	-0.70	-1.60	2.00	-1.00	-0.60	2.00	0.20	-0.70	2.00	0.00	-0.80	2.00	1.20	-0.60	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.30	1.00	-0.70	2.00	1.00	1.00	2.00	0.00	0.70	2.00	0.90	-1.90	2.00	1.10	-1.50	-0.20
+2.20	1.30	0.70	2.00	1.90	1.30	2.00	0.30	0.70	2.00	1.80	-0.30	2.00	1.40	-0.20	-0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.00	1.20	0.40	2.00	1.10	1.20	2.00	1.70	1.00	2.00	1.70	-0.70	2.00	1.20	-0.30	0.20
+-0.20	-0.40	-1.70	2.00	0.70	1.10	2.00	0.20	-0.50	2.00	0.00	-0.90	2.00	1.20	-1.30	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.10	0.90	-0.90	2.00	0.80	1.50	2.00	0.50	-0.20	2.00	0.80	-1.00	2.00	1.50	-0.60	1.10
+0.90	0.00	0.30	2.00	-0.10	1.00	2.00	0.00	0.60	2.00	0.90	-3.00	2.00	1.00	-2.40	0.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.00	1.20	0.40	2.00	1.10	1.20	2.00	0.20	0.50	2.00	1.70	-0.70	2.00	1.20	-0.10	0.40
+-0.10	-1.60	-1.60	2.00	-1.60	-0.60	2.00	-1.60	-0.60	2.00	-0.70	-4.40	2.00	-0.50	-4.10	-1.00
+1.40	0.30	0.50	2.00	0.30	0.30	2.00	0.10	1.40	2.00	1.20	-1.00	2.00	0.30	0.10	0.60
+1.30	1.20	0.30	2.00	1.60	2.10	2.00	1.90	0.30	2.00	1.00	-0.40	2.00	1.90	1.10	1.40
+1.60	1.50	0.60	2.00	2.00	1.80	2.00	1.70	0.60	2.00	1.40	-1.10	2.00	1.70	0.40	0.80
+0.30	0.20	-0.70	2.00	0.60	1.50	2.00	1.30	-0.70	2.00	0.00	-0.60	2.00	1.30	0.90	1.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.20	1.10	0.20	2.00	1.50	1.40	2.00	1.20	0.20	2.00	0.90	-1.50	2.00	1.20	0.00	0.30
+2.10	1.40	1.50	2.00	1.80	1.70	2.00	1.50	1.50	2.00	1.80	-0.20	2.00	1.50	1.30	0.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.20	1.30	2.00	1.70	1.50	2.00	1.40	1.30	2.00	1.70	-0.40	2.00	1.40	1.10	0.50
+0.30	0.20	-0.70	2.00	0.60	1.50	2.00	1.30	-0.70	2.00	0.00	-0.60	2.00	1.30	0.90	1.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.00	0.90	0.00	2.00	1.40	1.80	2.00	1.70	0.00	2.00	0.80	-0.70	2.00	1.70	0.90	1.20
+1.10	0.00	0.90	2.00	0.40	1.30	2.00	1.10	0.90	2.00	0.90	-2.60	2.00	1.10	-1.10	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.20	1.30	2.00	1.70	1.50	2.00	1.40	1.30	2.00	1.70	-0.40	2.00	1.40	1.10	0.50
+-0.40	-1.50	-0.60	2.00	-1.10	-0.20	2.00	-0.40	-0.60	2.00	-0.70	-4.20	2.00	-0.40	-2.60	-0.50
+1.40	0.30	1.30	2.00	0.80	0.60	2.00	0.50	1.30	2.00	1.20	-0.50	2.00	0.50	1.10	-0.40
+2.00	1.80	0.80	2.00	1.90	2.30	2.00	2.30	0.80	2.00	1.30	0.60	2.00	2.30	1.60	1.90
+2.40	2.10	1.10	2.00	2.20	2.10	2.00	2.10	1.10	2.00	1.70	0.00	2.00	2.10	0.90	1.30
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.70	0.70	2.00	1.80	1.60	2.00	1.60	0.70	2.00	1.20	-0.50	2.00	1.60	0.50	0.80
+2.80	2.00	2.00	2.00	2.10	1.90	2.00	1.90	2.00	2.00	2.10	0.80	2.00	1.90	1.80	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+1.80	0.60	1.40	2.00	0.70	1.50	2.00	1.50	1.40	2.00	1.10	-1.60	2.00	1.50	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+0.30	-0.90	-0.10	2.00	-0.80	0.00	2.00	0.00	-0.10	2.00	-0.40	-3.10	2.00	0.00	-2.10	0.00
+2.20	0.90	1.80	2.00	1.00	0.90	2.00	0.90	1.80	2.00	1.50	0.60	2.00	0.90	1.60	0.10
+2.00	1.60	1.00	2.00	2.00	2.60	2.00	2.60	1.00	2.00	1.40	0.20	2.00	2.30	1.50	2.20
+2.40	1.90	1.30	2.00	2.40	2.40	2.00	2.40	1.30	2.00	1.70	-0.40	2.00	2.10	0.80	1.50
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.50	0.90	2.00	1.90	1.90	2.00	1.90	0.90	2.00	1.30	-0.90	2.00	1.60	0.40	1.10
+2.80	1.80	2.20	2.00	2.20	2.20	2.00	2.20	2.20	2.00	2.20	0.40	2.00	1.90	1.70	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+1.80	0.40	1.60	2.00	0.80	1.80	2.00	1.80	1.60	2.00	1.20	-2.00	2.00	1.50	-0.70	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+0.30	-1.10	0.10	2.00	-0.70	0.30	2.00	0.30	0.10	2.00	-0.30	-3.50	2.00	0.00	-2.20	0.30
+2.20	0.70	1.90	2.00	1.20	1.20	2.00	1.20	1.90	2.00	1.50	0.20	2.00	0.90	1.50	0.30
+2.00	1.80	0.80	2.00	1.90	2.30	2.00	2.30	0.80	2.00	1.30	0.60	2.00	2.30	1.60	1.90
+2.40	2.10	1.10	2.00	2.20	2.10	2.00	2.10	1.10	2.00	1.70	0.00	2.00	2.10	0.90	1.30
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.70	0.70	2.00	1.80	1.60	2.00	1.60	0.70	2.00	1.20	-0.50	2.00	1.60	0.50	0.80
+2.80	2.00	2.00	2.00	2.10	1.90	2.00	1.90	2.00	2.00	2.10	0.80	2.00	1.90	1.80	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+1.80	0.60	1.40	2.00	0.70	1.50	2.00	1.50	1.40	2.00	1.10	-1.60	2.00	1.50	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+0.30	-0.90	-0.10	2.00	-0.80	0.00	2.00	0.00	-0.10	2.00	-0.40	-3.10	2.00	0.00	-2.10	0.00
+2.20	0.90	1.80	2.00	1.00	0.90	2.00	0.90	1.80	2.00	1.50	0.60	2.00	0.90	1.60	0.10
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+1.80	1.40	0.80	2.00	1.80	1.80	2.00	1.80	0.80	2.00	1.20	-1.00	2.00	1.50	0.30	1.00
+0.70	0.30	-0.30	2.00	0.70	1.70	2.00	1.70	-0.30	2.00	0.10	-0.30	2.00	1.40	1.00	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.40	0.80	2.00	1.90	1.90	2.00	1.90	0.80	2.00	1.20	-0.90	2.00	1.60	0.30	1.00
+2.50	1.40	1.80	2.00	1.90	1.90	2.00	1.90	1.80	2.00	1.80	0.10	2.00	1.60	1.30	1.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.50	1.90	2.00	1.90	1.90	2.00	1.90	1.90	2.00	1.90	0.10	2.00	1.60	1.40	1.10
+0.10	-0.30	-0.90	2.00	0.10	1.10	2.00	1.10	-0.90	2.00	-0.50	-0.90	2.00	0.80	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+0.40	-1.10	0.10	2.00	-0.60	0.40	2.00	0.40	0.10	2.00	-0.30	-3.50	2.00	0.10	-2.20	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.40	0.90	2.00	0.90	0.90	2.00	0.90	0.90	2.00	0.80	-0.90	2.00	0.60	0.40	0.00
+0.00	-1.50	-0.30	2.00	-1.00	0.00	2.00	0.00	-0.30	2.00	-0.70	-3.90	2.00	-0.30	-2.60	-0.10
+2.10	0.70	1.90	2.00	1.10	1.10	2.00	1.10	1.90	2.00	1.50	0.10	2.00	0.80	1.40	0.30
+1.50	1.20	-0.50	2.00	1.20	1.80	2.00	0.80	0.10	2.00	1.10	-0.70	2.00	1.90	-0.30	1.50
+1.20	0.90	-0.80	2.00	0.90	0.90	2.00	0.00	-0.20	2.00	0.80	-2.00	2.00	1.00	-1.60	0.20
+0.10	-0.10	-1.90	2.00	-0.20	0.90	2.00	-0.10	-1.30	2.00	-0.20	-1.30	2.00	0.90	-0.90	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.20	1.00	-0.80	2.00	0.90	1.00	2.00	0.00	-0.10	2.00	0.90	-1.90	2.00	1.00	-1.50	0.20
+1.80	1.00	0.20	2.00	0.90	1.00	2.00	0.00	0.90	2.00	1.50	-0.90	2.00	1.00	-0.50	0.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.00	0.30	2.00	1.00	1.00	2.00	0.00	0.90	2.00	1.50	-0.90	2.00	1.10	-0.50	0.30
+-0.50	-0.80	-2.60	2.00	-0.80	0.20	2.00	-0.80	-1.90	2.00	-0.90	-1.90	2.00	0.30	-1.50	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.10	0.90	-0.90	2.00	0.80	1.50	2.00	0.50	-0.20	2.00	0.80	-1.00	2.00	1.50	-0.60	1.10
+-0.30	-1.50	-1.50	2.00	-1.60	-0.50	2.00	-1.50	-0.90	2.00	-0.60	-4.50	2.00	-0.50	-4.10	-0.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+0.80	0.00	-0.80	2.00	0.00	0.00	2.00	-1.00	-0.10	2.00	0.50	-1.90	2.00	0.00	-1.50	-0.70
+-0.70	-1.90	-1.90	2.00	-2.00	-0.90	2.00	-1.90	-1.30	2.00	-1.00	-4.90	2.00	-0.90	-4.50	-0.90
+1.50	0.20	0.30	2.00	0.20	0.20	2.00	-0.70	0.90	2.00	1.10	-0.90	2.00	0.30	-0.50	-0.50
+0.50	1.30	-0.20	2.00	0.60	2.20	2.00	2.00	0.00	2.00	1.10	-0.10	2.00	2.00	0.90	1.40
+1.10	1.00	0.70	2.00	1.10	1.90	2.00	1.10	-1.00	2.00	0.80	-1.60	2.00	1.10	-0.10	0.30
+0.40	0.70	-0.50	2.00	0.50	0.70	2.00	0.50	-0.70	2.00	-0.20	-0.60	2.00	1.00	0.60	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.10	1.00	-0.40	2.00	1.50	1.30	2.00	1.20	-0.70	2.00	0.90	-1.60	2.00	1.20	0.00	0.30
+1.70	1.00	1.10	2.00	1.50	1.30	2.00	1.20	-0.60	2.00	1.50	-0.60	2.00	1.20	1.00	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.10	1.20	2.00	1.50	1.40	2.00	1.20	1.20	2.00	1.50	-0.50	2.00	1.20	1.00	0.30
+-0.30	-0.70	-1.70	2.00	0.10	0.70	2.00	0.40	-1.60	2.00	-0.90	-1.60	2.00	0.40	0.30	0.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.00	0.90	0.00	2.00	1.40	1.80	2.00	1.70	0.00	2.00	0.80	-0.70	2.00	1.70	0.90	1.20
+-0.50	-1.50	-1.30	2.00	-0.60	-0.20	2.00	-0.10	-0.60	2.00	-0.60	-4.10	2.00	-0.30	-2.40	0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+0.70	0.00	0.20	2.00	0.50	0.30	2.00	0.20	0.20	2.00	0.50	-1.60	2.00	1.70	0.00	0.10
+0.10	-1.90	-0.90	2.00	-0.70	-0.30	2.00	-0.70	-0.80	2.00	-1.00	-4.40	2.00	-0.70	-3.00	-1.00
+1.50	-0.20	0.90	2.00	0.00	-0.10	2.00	0.40	0.90	2.00	1.10	-1.00	2.00	0.20	0.60	0.60
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+1.80	1.60	0.60	2.00	1.70	1.50	2.00	1.50	0.60	2.00	1.10	-0.60	2.00	1.50	0.40	0.70
+0.70	0.50	-0.50	2.00	0.60	1.40	2.00	1.40	-0.50	2.00	0.00	0.10	2.00	1.40	1.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	0.60	2.00	1.70	1.60	2.00	1.60	0.60	2.00	1.20	-0.50	2.00	1.60	0.40	0.80
+2.50	1.60	1.60	2.00	1.70	1.60	2.00	1.60	1.60	2.00	1.80	0.50	2.00	1.60	1.40	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.70	1.70	2.00	1.80	1.60	2.00	1.60	1.70	2.00	1.80	0.50	2.00	1.60	1.50	0.80
+0.10	-0.10	-1.10	2.00	0.00	0.80	2.00	0.80	-1.10	2.00	-0.60	-0.50	2.00	0.80	0.50	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+0.40	-0.90	-0.10	2.00	-0.80	0.10	2.00	0.10	-0.10	2.00	-0.30	-3.10	2.00	0.10	-2.10	0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.60	0.70	2.00	0.70	0.60	2.00	0.60	0.70	2.00	0.80	-0.50	2.00	0.60	0.50	-0.20
+0.00	-1.30	-0.50	2.00	-1.20	-0.30	2.00	-0.30	-0.50	2.00	-0.70	-3.50	2.00	-0.30	-2.50	-0.30
+2.10	0.90	1.70	2.00	1.00	0.80	2.00	0.80	1.70	2.00	1.40	0.50	2.00	0.80	1.50	0.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+1.80	1.40	0.80	2.00	1.80	1.80	2.00	1.80	0.80	2.00	1.20	-1.00	2.00	1.50	0.30	1.00
+0.70	0.30	-0.30	2.00	0.70	1.70	2.00	1.70	-0.30	2.00	0.10	-0.30	2.00	1.40	1.00	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.40	0.80	2.00	1.90	1.90	2.00	1.90	0.80	2.00	1.20	-0.90	2.00	1.60	0.30	1.00
+2.50	1.40	1.80	2.00	1.90	1.90	2.00	1.90	1.80	2.00	1.80	0.10	2.00	1.60	1.30	1.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.50	1.90	2.00	1.90	1.90	2.00	1.90	1.90	2.00	1.90	0.10	2.00	1.60	1.40	1.10
+0.10	-0.30	-0.90	2.00	0.10	1.10	2.00	1.10	-0.90	2.00	-0.50	-0.90	2.00	0.80	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+0.40	-1.10	0.10	2.00	-0.60	0.40	2.00	0.40	0.10	2.00	-0.30	-3.50	2.00	0.10	-2.20	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.40	0.90	2.00	0.90	0.90	2.00	0.90	0.90	2.00	0.80	-0.90	2.00	0.60	0.40	0.00
+0.00	-1.50	-0.30	2.00	-1.00	0.00	2.00	0.00	-0.30	2.00	-0.70	-3.90	2.00	-0.30	-2.60	-0.10
+2.10	0.70	1.90	2.00	1.10	1.10	2.00	1.10	1.90	2.00	1.50	0.10	2.00	0.80	1.40	0.30
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+1.80	1.60	0.60	2.00	1.70	1.50	2.00	1.50	0.60	2.00	1.10	-0.60	2.00	1.50	0.40	0.70
+0.70	0.50	-0.50	2.00	0.60	1.40	2.00	1.40	-0.50	2.00	0.00	0.10	2.00	1.40	1.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	0.60	2.00	1.70	1.60	2.00	1.60	0.60	2.00	1.20	-0.50	2.00	1.60	0.40	0.80
+2.50	1.60	1.60	2.00	1.70	1.60	2.00	1.60	1.60	2.00	1.80	0.50	2.00	1.60	1.40	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.70	1.70	2.00	1.80	1.60	2.00	1.60	1.70	2.00	1.80	0.50	2.00	1.60	1.50	0.80
+0.10	-0.10	-1.10	2.00	0.00	0.80	2.00	0.80	-1.10	2.00	-0.60	-0.50	2.00	0.80	0.50	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+0.40	-0.90	-0.10	2.00	-0.80	0.10	2.00	0.10	-0.10	2.00	-0.30	-3.10	2.00	0.10	-2.10	0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.60	0.70	2.00	0.70	0.60	2.00	0.60	0.70	2.00	0.80	-0.50	2.00	0.60	0.50	-0.20
+0.00	-1.30	-0.50	2.00	-1.20	-0.30	2.00	-0.30	-0.50	2.00	-0.70	-3.50	2.00	-0.30	-2.50	-0.30
+2.10	0.90	1.70	2.00	1.00	0.80	2.00	0.80	1.70	2.00	1.40	0.50	2.00	0.80	1.50	0.00
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.10	1.90	0.10	2.00	1.80	1.90	2.00	0.90	0.70	2.00	1.80	-1.00	2.00	1.90	-0.60	1.10
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.70	1.40	-0.30	2.00	1.40	1.40	2.00	0.40	0.30	2.00	1.30	-1.50	2.00	1.50	-1.10	0.70
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	1.20	-0.50	2.00	1.20	1.80	2.00	0.80	0.10	2.00	1.10	-0.70	2.00	1.90	-0.30	1.50
+1.60	0.30	0.40	2.00	0.30	1.30	2.00	0.40	1.00	2.00	1.20	-2.60	2.00	1.40	-2.20	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+0.30	-0.90	-0.90	2.00	-1.00	0.10	2.00	-0.90	-0.30	2.00	0.00	-3.90	2.00	0.10	-3.50	0.10
+2.30	1.00	1.10	2.00	1.00	1.00	2.00	0.00	1.70	2.00	1.90	-0.10	2.00	1.10	0.30	0.30
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+2.00	1.90	1.00	2.00	2.40	2.20	2.00	2.10	1.00	2.00	1.80	-0.70	2.00	2.10	0.80	1.20
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.60	1.50	0.60	2.00	1.90	1.80	2.00	1.60	0.60	2.00	1.30	-1.10	2.00	1.60	0.40	0.70
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.30	0.40	2.00	1.70	2.20	2.00	2.00	0.40	2.00	1.10	-0.30	2.00	2.00	1.20	1.50
+1.50	0.40	1.30	2.00	0.80	1.70	2.00	1.50	1.30	2.00	1.20	-2.20	2.00	1.50	-0.70	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+0.20	-0.90	0.00	2.00	-0.40	0.40	2.00	0.30	0.00	2.00	0.00	-3.50	2.00	0.30	-2.00	0.20
+2.20	1.10	2.00	2.00	1.50	1.40	2.00	1.20	2.00	2.00	1.90	0.30	2.00	1.20	1.80	0.30
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.00	1.70	0.00	2.00	1.70	1.70	2.00	0.70	0.60	2.00	1.60	-1.20	2.00	1.80	-0.80	1.00
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	-0.10	2.00	1.60	1.60	2.00	0.60	0.50	2.00	1.50	-1.30	2.00	1.70	-0.90	0.90
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.20	-0.60	2.00	1.10	1.80	2.00	0.80	0.00	2.00	1.10	-0.70	2.00	1.80	-0.30	1.40
+1.70	0.40	0.50	2.00	0.40	1.40	2.00	0.50	1.10	2.00	1.30	-2.50	2.00	1.50	-2.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.70	-0.50	-0.50	2.00	-0.60	0.50	2.00	-0.50	0.10	2.00	0.40	-3.50	2.00	0.50	-3.10	0.50
+2.00	0.80	0.80	2.00	0.70	0.80	2.00	-0.20	1.50	2.00	1.70	-0.30	2.00	0.80	0.10	0.00
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+1.90	1.80	0.90	2.00	2.20	2.10	2.00	1.90	0.90	2.00	1.60	-0.80	2.00	1.90	0.70	1.00
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.70	0.80	2.00	2.10	2.00	2.00	1.80	0.80	2.00	1.50	-0.90	2.00	1.80	0.60	0.90
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.30	1.20	0.30	2.00	1.70	2.10	2.00	2.00	0.30	2.00	1.10	-0.40	2.00	2.00	1.10	1.50
+1.60	0.50	1.40	2.00	0.90	1.80	2.00	1.60	1.40	2.00	1.30	-2.10	2.00	1.60	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.60	-0.50	0.40	2.00	0.00	0.80	2.00	0.70	0.40	2.00	0.40	-3.10	2.00	0.70	-1.60	0.60
+1.90	0.80	1.80	2.00	1.30	1.10	2.00	1.00	1.80	2.00	1.70	0.00	2.00	1.00	1.60	0.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.10	1.90	0.10	2.00	1.80	1.90	2.00	0.90	0.70	2.00	1.80	-1.00	2.00	1.90	-0.60	1.10
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.70	1.40	-0.30	2.00	1.40	1.40	2.00	0.40	0.30	2.00	1.30	-1.50	2.00	1.50	-1.10	0.70
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	1.20	-0.50	2.00	1.20	1.80	2.00	0.80	0.10	2.00	1.10	-0.70	2.00	1.90	-0.30	1.50
+1.60	0.30	0.40	2.00	0.30	1.30	2.00	0.40	1.00	2.00	1.20	-2.60	2.00	1.40	-2.20	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+0.30	-0.90	-0.90	2.00	-1.00	0.10	2.00	-0.90	-0.30	2.00	0.00	-3.90	2.00	0.10	-3.50	0.10
+2.30	1.00	1.10	2.00	1.00	1.00	2.00	0.00	1.70	2.00	1.90	-0.10	2.00	1.10	0.30	0.30
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+2.00	1.90	1.00	2.00	2.40	2.20	2.00	2.10	1.00	2.00	1.80	-0.70	2.00	2.10	0.80	1.20
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.60	1.50	0.60	2.00	1.90	1.80	2.00	1.60	0.60	2.00	1.30	-1.10	2.00	1.60	0.40	0.70
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.30	0.40	2.00	1.70	2.20	2.00	2.00	0.40	2.00	1.10	-0.30	2.00	2.00	1.20	1.50
+1.50	0.40	1.30	2.00	0.80	1.70	2.00	1.50	1.30	2.00	1.20	-2.20	2.00	1.50	-0.70	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+0.20	-0.90	0.00	2.00	-0.40	0.40	2.00	0.30	0.00	2.00	0.00	-3.50	2.00	0.30	-2.00	0.20
+2.20	1.10	2.00	2.00	1.50	1.40	2.00	1.20	2.00	2.00	1.90	0.30	2.00	1.20	1.80	0.30
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
diff --git a/gtfold-mfe/data/Turner99/stack.DAT b/gtfold-mfe/data/Turner99/stack.DAT
new file mode 100644
index 0000000..04a6889
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/stack.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.90
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.20	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.10	inf	-0.60
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.10	inf	-1.40	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.10	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-3.30	inf 	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.40	inf	-1.40	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.10	inf	-2.10	inf 	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.40	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.30
+inf 	inf 	inf 	inf 	inf 	inf	-3.40	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.50	inf
+inf 	inf 	inf 	inf 	inf	-3.30	inf	-1.50	inf 	inf 	inf 	inf 	inf	-2.10	inf	-0.50
+inf 	inf 	inf 	inf	-2.20	inf	-2.50	inf 	inf 	inf 	inf 	inf	-1.40	inf	1.30	inf
+inf 	inf 	inf	-1.30	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.00	inf 	inf 	inf 	inf
+inf 	inf	-2.40	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.50	inf 	inf 	inf 	inf 	inf
+inf	-2.10	inf	-1.00	inf 	inf 	inf 	inf 	inf	-1.40	inf	0.30	inf 	inf 	inf 	inf
+-0.90	inf	-1.30	inf 	inf 	inf 	inf 	inf	-0.60	inf	-0.50	inf 	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/Turner99/tloop.DAT b/gtfold-mfe/data/Turner99/tloop.DAT
new file mode 100644
index 0000000..dda2750
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/tloop.DAT
@@ -0,0 +1,30 @@
+GGGGAC	-3.00
+GGUGAC	-3.00
+CGAAAG	-3.00
+GGAGAC	-3.00
+CGCAAG	-3.00
+GGAAAC	-3.00
+CGGAAG	-3.00
+CUUCGG	-3.00
+CGUGAG	-3.00
+CGAAGG	-2.50
+CUACGG	-2.50
+GGCAAC	-2.50
+CGCGAG	-2.50
+UGAGAG	-2.50
+CGAGAG	-2.00
+AGAAAU	-2.00
+CGUAAG	-2.00
+CUAACG	-2.00
+UGAAAG	-2.00
+GGAAGC	-1.50
+GGGAAC	-1.50
+UGAAAA	-1.50
+AGCAAU	-1.50
+AGUAAU	-1.50
+CGGGAG	-1.50
+AGUGAU	-1.50
+GGCGAC	-1.50
+GGGAGC	-1.50
+GUGAAC	-1.50
+UGGAAA	-1.50
diff --git a/gtfold-mfe/data/Turner99/tstackh.DAT b/gtfold-mfe/data/Turner99/tstackh.DAT
new file mode 100644
index 0000000..7648650
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/tstackh.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.30	-0.50	-0.30	-0.30
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.10	-0.20	-1.50	-0.20
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.10	-1.20	-0.20	0.20
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.30	-0.30	-0.60	-1.10
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.50	-1.50	-1.40	-1.80	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.00	-0.90	-2.90	-0.80	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.20	-2.00	-1.60	-1.10	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.70	-1.40	-1.80	-2.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-1.10	-1.50	-1.30	-2.10	inf 	inf 	inf 	inf	0.20	-0.50	-0.30	-0.30
+inf 	inf 	inf 	inf	-1.10	-0.70	-2.40	-0.50	inf 	inf 	inf 	inf	-0.10	-0.20	-1.50	-0.20
+inf 	inf 	inf 	inf	-2.40	-2.90	-1.40	-1.20	inf 	inf 	inf 	inf	-0.90	-1.10	-0.30	0.00
+inf 	inf 	inf 	inf	-1.90	-1.00	-2.20	-1.50	inf 	inf 	inf 	inf	-0.30	-0.30	-0.40	-1.10
+-0.50	-0.30	-0.60	-0.50	inf 	inf 	inf 	inf	-0.50	-0.30	-0.60	-0.50	inf 	inf 	inf 	inf
+-0.20	-0.10	-1.20	-0.00	inf 	inf 	inf 	inf	-0.20	-0.10	-1.70	0.00	inf 	inf 	inf 	inf
+-1.40	-1.20	-0.70	-0.20	inf 	inf 	inf 	inf	-0.80	-1.20	-0.30	-0.70	inf 	inf 	inf 	inf
+-0.30	-0.10	-0.50	-0.80	inf 	inf 	inf 	inf	-0.60	-0.10	-0.60	-0.80	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/Turner99/tstacki.DAT b/gtfold-mfe/data/Turner99/tstacki.DAT
new file mode 100644
index 0000000..dd7b5da
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/tstacki.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	0.70	0.70	-0.40	0.70
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.70
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.40	0.70	0.70	0.70
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.00
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.00	-0.00	-1.10	-0.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.10	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.70	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-0.00	-0.00	-1.10	-0.00	inf 	inf 	inf 	inf	0.70	0.70	-0.40	0.70
+inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.70
+inf 	inf 	inf 	inf	-1.10	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf	-0.40	0.70	0.70	0.70
+inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.70	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.00
+0.70	0.70	-0.40	0.70	inf 	inf 	inf 	inf	0.70	0.70	-0.40	0.70	inf 	inf 	inf 	inf
+0.70	0.70	0.70	0.70	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.70	inf 	inf 	inf 	inf
+-0.40	0.70	0.70	0.70	inf 	inf 	inf 	inf	-0.40	0.70	0.70	0.70	inf 	inf 	inf 	inf
+0.70	0.70	0.70	0.00	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.00	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/Turner99/tstackm.DAT b/gtfold-mfe/data/Turner99/tstackm.DAT
new file mode 100644
index 0000000..b850f80
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/tstackm.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf	-1.00	inf 	inf 	inf	-1.00	inf 	inf 	inf	-2.20	-0.80	-1.00	-0.80	-0.90
+inf 	inf	-1.50	inf 	inf 	inf	-1.50	inf 	inf 	inf	-2.70	inf	-0.60	-0.70	-2.20	-0.70
+inf	-1.50	inf	-1.00	inf	-1.50	inf	-1.00	inf	-2.70	inf	-2.20	-0.80	-2.10	-0.80	-0.80
+-1.00	inf	-1.50	inf	-1.00	inf	-1.50	inf	-2.20	inf	-2.70	inf	-1.10	-0.80	-1.10	-0.80
+inf 	inf 	inf	-1.00	inf 	inf 	inf	-1.00	-1.70	-1.70	-1.70	-1.70	inf 	inf 	inf	-1.00
+inf 	inf	-1.50	inf 	inf 	inf	-1.50	inf	-1.00	-1.10	-3.30	-0.80	inf 	inf	-1.50	inf
+inf	-1.50	inf	-1.00	inf	-1.50	inf	-1.00	-1.70	-2.40	-1.70	-1.70	inf	-1.50	inf	-1.00
+-1.00	inf	-1.50	inf	-1.00	inf	-1.50	inf	-1.60	-1.40	-1.60	-1.20	-1.00	inf	-1.50	inf
+inf 	inf 	inf	-2.20	-1.10	-1.50	-1.30	-1.90	inf 	inf 	inf	-1.00	-0.80	-1.00	-0.80	-1.30
+inf 	inf	-2.70	inf	-1.10	-0.70	-3.40	-0.50	inf 	inf	-1.50	inf	-0.60	-0.70	-2.50	-0.70
+inf	-2.70	inf	-2.20	-1.60	-3.30	-1.40	-1.30	inf	-1.50	inf	-1.00	-0.80	-2.10	-0.80	-0.80
+-2.20	inf	-2.70	inf	-1.70	-1.00	-2.00	-0.70	-1.00	inf	-1.50	inf	-1.40	-0.80	1.30	-0.80
+-1.00	-0.80	-1.10	-1.30	inf 	inf 	inf	-1.00	-1.00	-0.80	-1.10	-1.00	inf 	inf 	inf	-2.00
+-0.70	-0.60	-2.40	-0.50	inf 	inf	-1.50	inf	-0.70	-0.60	-1.50	-0.50	inf 	inf	-2.50	inf
+-1.10	-2.10	-1.20	-1.00	inf	-1.50	inf	-1.00	-0.70	-1.40	-0.80	0.30	inf	-2.50	inf	-2.00
+-0.90	-0.60	-1.40	-0.50	-1.00	inf	-1.50	inf	-0.50	-0.60	-0.50	-0.50	-2.00	inf	-2.50	inf

From ef501b8378b297f0669e2925bc85945ad202ee97 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 28 Apr 2011 10:27:01 -0400
Subject: [PATCH 106/282] adding script to covert data to newer format

---
 gtfold-mfe/scripts/dats2DATs.py | 53 +++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100755 gtfold-mfe/scripts/dats2DATs.py

diff --git a/gtfold-mfe/scripts/dats2DATs.py b/gtfold-mfe/scripts/dats2DATs.py
new file mode 100755
index 0000000..e488b84
--- /dev/null
+++ b/gtfold-mfe/scripts/dats2DATs.py
@@ -0,0 +1,53 @@
+import os, sys, re
+
+# read in arguments from command line
+if len(sys.argv) != 3:
+    print "need directory names"
+    print "Usage: dats2DATs.py <source_dir> <target_dir>"
+source_dir_name = sys.argv[1]
+target_dir_name = sys.argv[2]
+
+# this function opens a .dat formatted file and returns a string with .DAT file format
+def dat2DAT(file_name, num_cols, num_rows):
+	num_data_rows_seen = 0
+	DAT_content = ""
+	file = open(file_name,'r')
+
+	for line in file.readlines() :
+		if re.match('[\d\-\.\s]+\n', line) and not re.match('[\s\-]*\n', line):
+			# If the line contains only digits, negative signs, dots, and white space
+			# and does not contain ony dashes and whitespace convert the line to .DAT format
+			DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line)
+			DAT_line = re.sub('\s+\-','\t-', DAT_line)
+			DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line)
+			DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line)
+			DAT_line = DAT_line.lstrip().rstrip()+"\n"
+			DAT_content += DAT_line
+
+	return DAT_content
+
+for file_prefix in ["dangle", "int11", "int21", "int22", "loop", "miscloop", "sint2", "sint4", "stack", "tstackh", "tstacki", "tstackm"]:
+	file_name = source_dir_name+"/"+file_prefix+".dat"
+	output_file_path = target_dir_name+"/"+file_prefix+".DAT"
+	output_file = open(output_file_path, 'w')
+	output_file.write(dat2DAT(file_name, 16, 16))
+	#print dat2DAT(file_name, 16, 16)
+
+file_name = source_dir_name+"/tloop.dat"
+output_file_path = target_dir_name+"/tloop.DAT"
+DAT_content = ""
+file = open(file_name,'r')
+
+for line in file.readlines() :
+	if re.match('[\d\-\.\sACGU]+\n', line) and not re.match('[\s\-]*\n', line):
+		# If the line contains only digits, negative signs, dots, and white space or ACGU
+		# and does not contain ony dashes and whitespace convert the line to .DAT format
+		DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line)
+		DAT_line = re.sub('\s+\-','\t-', DAT_line)
+		DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line)
+		DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line)
+		DAT_line = DAT_line.lstrip().rstrip()+"\n"
+		DAT_content += DAT_line
+output_file = open(output_file_path, 'w')
+output_file.write(DAT_content)
+	

From fead43c2bb1f5d9e08e6bee13ab87189c53709cf Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 28 Apr 2011 12:36:34 -0400
Subject: [PATCH 107/282] support for new data format

---
 gtfold-mfe/data/Turner99/Makefile.am | 15 ++++++
 gtfold-mfe/data/Turner99/Makefile.in | 13 +++++
 gtfold-mfe/data/Turner99/int22.DAT   | 72 ----------------------------
 3 files changed, 28 insertions(+), 72 deletions(-)

diff --git a/gtfold-mfe/data/Turner99/Makefile.am b/gtfold-mfe/data/Turner99/Makefile.am
index 4cf8fa7..cb09a05 100644
--- a/gtfold-mfe/data/Turner99/Makefile.am
+++ b/gtfold-mfe/data/Turner99/Makefile.am
@@ -3,6 +3,19 @@
 gtfold_datadir = $(datadir)/@PACKAGE@/Turner99
 
 gtfold_data_DATA = \
+	stack.DAT\
+	miscloop.DAT\
+	dangle.DAT\
+	loop.DAT\
+	int11.DAT\
+	int21.DAT\
+	int22.DAT\
+	sint2.DAT\
+	sint4.DAT\
+	tloop.DAT\
+	tstackh.DAT\
+	tstacki.DAT\
+	tstackm.DAT\
 	stack.dat\
 	miscloop.dat\
 	dangle.dat\
@@ -23,6 +36,8 @@ gtfold_data_DATA = \
 	tstacki.dat\
 	tstackm.dat
 
+
+
 EXTRA_DIST = $(gtfold_data_DATA)
 
 CLEANFILES = *~
diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in
index d9a1eb3..d042a79 100644
--- a/gtfold-mfe/data/Turner99/Makefile.in
+++ b/gtfold-mfe/data/Turner99/Makefile.in
@@ -176,6 +176,19 @@ top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 gtfold_datadir = $(datadir)/@PACKAGE@/Turner99
 gtfold_data_DATA = \
+	stack.DAT\
+	miscloop.DAT\
+	dangle.DAT\
+	loop.DAT\
+	int11.DAT\
+	int21.DAT\
+	int22.DAT\
+	sint2.DAT\
+	sint4.DAT\
+	tloop.DAT\
+	tstackh.DAT\
+	tstacki.DAT\
+	tstackm.DAT\
 	stack.dat\
 	miscloop.dat\
 	dangle.dat\
diff --git a/gtfold-mfe/data/Turner99/int22.DAT b/gtfold-mfe/data/Turner99/int22.DAT
index 4f17932..9691143 100644
--- a/gtfold-mfe/data/Turner99/int22.DAT
+++ b/gtfold-mfe/data/Turner99/int22.DAT
@@ -1,5 +1,3 @@
-                                           A \/ \_/ A 
-                                           U /\  |  U 
   2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
   2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
   1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
@@ -16,8 +14,6 @@
   3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
   1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
   2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                           A \/ \_/ C 
-                                           U /\  |  G 
   2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
   2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
   0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
@@ -34,8 +30,6 @@
   2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
   0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
   2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
-                                           A \/ \_/ G 
-                                           U /\  |  C 
   2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
   1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
   0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
@@ -52,8 +46,6 @@
   2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
   0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
   1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
-                                           A \/ \_/ U 
-                                           U /\  |  A 
   2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
   2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
   1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
@@ -70,8 +62,6 @@
   3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
   1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
   2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                           A \/ \_/ G 
-                                           U /\  |  U 
   2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
   2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
   1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
@@ -88,8 +78,6 @@
   3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
   1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
   2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                           A \/ \_/ U 
-                                           U /\  |  G 
   2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
   2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
   1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
@@ -106,8 +94,6 @@
   3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
   1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
   2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                           C \/ \_/ A 
-                                           G /\  |  U 
   2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
   2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
   1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
@@ -124,8 +110,6 @@
   2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
   0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
   2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
-                                           C \/ \_/ C 
-                                           G /\  |  G 
   0.50  1.10 -0.30  2.00  1.10  1.70  2.00  0.70  0.40  2.00  1.00  0.10  2.00  1.80 -0.50  1.50 
   0.60  1.50  0.10  2.00  1.10  1.50  2.00  0.50  0.50  2.00  1.40 -0.70  2.00  1.50 -0.60  0.00 
   0.00 -0.70 -1.60  2.00 -1.00 -0.60  2.00  0.20 -0.70  2.00  0.00 -0.80  2.00  1.20 -0.60  0.90 
@@ -142,8 +126,6 @@
   2.00  1.20  0.40  2.00  1.10  1.20  2.00  0.20  0.50  2.00  1.70 -0.70  2.00  1.20 -0.10  0.40 
  -0.10 -1.60 -1.60  2.00 -1.60 -0.60  2.00 -1.60 -0.60  2.00 -0.70 -4.40  2.00 -0.50 -4.10 -1.00 
   1.40  0.30  0.50  2.00  0.30  0.30  2.00  0.10  1.40  2.00  1.20 -1.00  2.00  0.30  0.10  0.60 
-                                           C \/ \_/ G 
-                                           G /\  |  C 
   1.30  1.20  0.30  2.00  1.60  2.10  2.00  1.90  0.30  2.00  1.00 -0.40  2.00  1.90  1.10  1.40 
   1.60  1.50  0.60  2.00  2.00  1.80  2.00  1.70  0.60  2.00  1.40 -1.10  2.00  1.70  0.40  0.80 
   0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
@@ -160,8 +142,6 @@
   1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
  -0.40 -1.50 -0.60  2.00 -1.10 -0.20  2.00 -0.40 -0.60  2.00 -0.70 -4.20  2.00 -0.40 -2.60 -0.50 
   1.40  0.30  1.30  2.00  0.80  0.60  2.00  0.50  1.30  2.00  1.20 -0.50  2.00  0.50  1.10 -0.40 
-                                           C \/ \_/ U 
-                                           G /\  |  A 
   2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
   2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
   1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
@@ -178,8 +158,6 @@
   2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
   0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
   2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
-                                           C \/ \_/ G 
-                                           G /\  |  U 
   2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
   2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
   1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
@@ -196,8 +174,6 @@
   2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
   0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
   2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
-                                           C \/ \_/ U 
-                                           G /\  |  G 
   2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
   2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
   1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
@@ -214,8 +190,6 @@
   2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
   0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
   2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
-                                           G \/ \_/ A 
-                                           C /\  |  U 
   2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
   1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
   0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
@@ -232,8 +206,6 @@
   1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
   0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
   2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
-                                           G \/ \_/ C 
-                                           C /\  |  G 
   1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
   1.20  0.90 -0.80  2.00  0.90  0.90  2.00  0.00 -0.20  2.00  0.80 -2.00  2.00  1.00 -1.60  0.20 
   0.10 -0.10 -1.90  2.00 -0.20  0.90  2.00 -0.10 -1.30  2.00 -0.20 -1.30  2.00  0.90 -0.90  0.90 
@@ -250,8 +222,6 @@
   0.80  0.00 -0.80  2.00  0.00  0.00  2.00 -1.00 -0.10  2.00  0.50 -1.90  2.00  0.00 -1.50 -0.70 
  -0.70 -1.90 -1.90  2.00 -2.00 -0.90  2.00 -1.90 -1.30  2.00 -1.00 -4.90  2.00 -0.90 -4.50 -0.90 
   1.50  0.20  0.30  2.00  0.20  0.20  2.00 -0.70  0.90  2.00  1.10 -0.90  2.00  0.30 -0.50 -0.50 
-                                           G \/ \_/ G 
-                                           C /\  |  C 
   0.50  1.30 -0.20  2.00  0.60  2.20  2.00  2.00  0.00  2.00  1.10 -0.10  2.00  2.00  0.90  1.40 
   1.10  1.00  0.70  2.00  1.10  1.90  2.00  1.10 -1.00  2.00  0.80 -1.60  2.00  1.10 -0.10  0.30 
   0.40  0.70 -0.50  2.00  0.50  0.70  2.00  0.50 -0.70  2.00 -0.20 -0.60  2.00  1.00  0.60  1.40 
@@ -268,8 +238,6 @@
   0.70  0.00  0.20  2.00  0.50  0.30  2.00  0.20  0.20  2.00  0.50 -1.60  2.00  1.70  0.00  0.10 
   0.10 -1.90 -0.90  2.00 -0.70 -0.30  2.00 -0.70 -0.80  2.00 -1.00 -4.40  2.00 -0.70 -3.00 -1.00 
   1.50 -0.20  0.90  2.00  0.00 -0.10  2.00  0.40  0.90  2.00  1.10 -1.00  2.00  0.20  0.60  0.60 
-                                           G \/ \_/ U 
-                                           C /\  |  A 
   2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
   1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
   0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
@@ -286,8 +254,6 @@
   1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
   0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
   2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
-                                           G \/ \_/ G 
-                                           C /\  |  U 
   2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
   1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
   0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
@@ -304,8 +270,6 @@
   1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
   0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
   2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
-                                           G \/ \_/ U 
-                                           C /\  |  G 
   2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
   1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
   0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
@@ -322,8 +286,6 @@
   1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
   0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
   2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
-                                           U \/ \_/ A 
-                                           A /\  |  U 
   2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
   2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
   1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
@@ -340,8 +302,6 @@
   3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
   1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
   2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                           U \/ \_/ C 
-                                           A /\  |  G 
   2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
   2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
   1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
@@ -358,8 +318,6 @@
   2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
   0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
   2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
-                                           U \/ \_/ G 
-                                           A /\  |  C 
   2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
   2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
   1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
@@ -376,8 +334,6 @@
   2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
   0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
   2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
-                                           U \/ \_/ U 
-                                           A /\  |  A 
   2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
   2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
   1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
@@ -394,8 +350,6 @@
   3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
   1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
   2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
-                                           U \/ \_/ G 
-                                           A /\  |  U 
   2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
   2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
   1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
@@ -412,8 +366,6 @@
   3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
   1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
   2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                           U \/ \_/ U 
-                                           A /\  |  G 
   2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
   2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
   1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
@@ -430,8 +382,6 @@
   3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
   1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
   2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
-                                           G \/ \_/ A 
-                                           U /\  |  U 
   2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
   2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
   1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
@@ -448,8 +398,6 @@
   3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
   1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
   2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                           G \/ \_/ C 
-                                           U /\  |  G 
   2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
   2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
   0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
@@ -466,8 +414,6 @@
   2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
   0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
   2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
-                                           G \/ \_/ G 
-                                           U /\  |  C 
   2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
   1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
   0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
@@ -484,8 +430,6 @@
   2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
   0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
   1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
-                                           G \/ \_/ U 
-                                           U /\  |  A 
   2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
   2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
   1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
@@ -502,8 +446,6 @@
   3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
   1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
   2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                           G \/ \_/ G 
-                                           U /\  |  U 
   2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
   2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
   1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
@@ -520,8 +462,6 @@
   3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
   1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
   2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                           G \/ \_/ U 
-                                           U /\  |  G 
   2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
   2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
   1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
@@ -538,8 +478,6 @@
   3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
   1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
   2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                           U \/ \_/ A 
-                                           G /\  |  U 
   2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
   2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
   1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
@@ -556,8 +494,6 @@
   3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
   1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
   2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                           U \/ \_/ C 
-                                           G /\  |  G 
   2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
   2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
   1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
@@ -574,8 +510,6 @@
   2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
   0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
   2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
-                                           U \/ \_/ G 
-                                           G /\  |  C 
   2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
   2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
   1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
@@ -592,8 +526,6 @@
   2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
   0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
   2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
-                                           U \/ \_/ U 
-                                           G /\  |  A 
   2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
   2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
   1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
@@ -610,8 +542,6 @@
   3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
   1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
   2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
-                                           U \/ \_/ G 
-                                           G /\  |  U 
   2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
   2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
   1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
@@ -628,8 +558,6 @@
   3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
   1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
   2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                           U \/ \_/ U 
-                                           G /\  |  G 
   2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
   2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
   1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 

From 270f6947a43bb67cd269a69bd4022daef9131ee1 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 28 Apr 2011 12:38:08 -0400
Subject: [PATCH 108/282] changes to parse datafiles compatible with UNAfold
 format

---
 gtfold-mfe/include/loader.h |  20 +-
 gtfold-mfe/src/loader.cc    | 944 ++++++++++--------------------------
 2 files changed, 261 insertions(+), 703 deletions(-)

diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h
index 20a0708..f8fdc78 100644
--- a/gtfold-mfe/include/loader.h
+++ b/gtfold-mfe/include/loader.h
@@ -27,16 +27,16 @@
 
 void readThermodynamicParameters(const char *userdatadir,bool userdatalogic);
 
-int initStackValues(std::string fileName);
-int initMiscloopValues(std::string fileName);
-int initDangleValues(std::string fileName);
-int initLoopValues(std::string fileName);
-int initTstkhValues(std::string fileName);
-int initTstkiValues(std::string fileName);
-int initTloopValues(std::string fileName);
-int initInt21Values(std::string fileName);
-int initInt22Values(std::string fileName);
-int initInt11Values(std::string fileName);
+int initStackValues(const std::string& fileName, const std::string& dirPath);
+int initMiscloopValues(const std::string& fileName, const std::string& dirPath);
+int initDangleValues(const std::string& fileName, const std::string& dirPath);
+int initLoopValues(const std::string& fileName, const std::string& dirPath);
+int initTstkhValues(const std::string& fileName, const std::string& dirPath);
+int initTstkiValues(const std::string& fileName, const std::string& dirPath);
+int initTloopValues(const std::string& fileName, const std::string& dirPath);
+int initInt21Values(const std::string& fileName, const std::string& dirPath);
+int initInt22Values(const std::string& fileName, const std::string& dirPath);
+int initInt11Values(const std::string& fileName, const std::string& dirPath);
 
 extern std::string EN_DATADIR;
 
diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index f916f3c..18066c6 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -20,6 +20,7 @@
 #include <iostream>
 #include <fstream>
 #include <istream>
+#include <sstream>
 #include <math.h>
 
 #include <cstring>
@@ -77,13 +78,11 @@ float prelog;
 void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 
 #ifndef GENBIN
-	if (!userdatalogic) 
-	{
+	if (!userdatalogic) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
 		EN_DATADIR += userdatadir;
-	} else 
-	{
+	} else {
 		EN_DATADIR.assign(userdatadir);
 	}
 #else
@@ -95,178 +94,89 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 		EN_DATADIR += "/";
 	}
 
-	initMiscloopValues("miscloop.dat");
-	// miscloop.dat - Miscellaneous loop file
-	initStackValues("stack.dat");
-	// stack.dat - free energies for base pair stacking
-	initDangleValues("dangle.dat");
-	// dangle.dat - single base stacking free energies
-	initLoopValues("loop.dat");
-	// loop.dat - entropic component for internal, bulge and hairpin loops.
-	initTstkhValues("tstackh.dat");
-	// tstackh.dat - free energies for terminal mismatch stacking in hairpin loops
-	initTstkiValues("tstacki.dat");
-	// tstacki.dat - free energies for terminal mismatch stacking in internal loops
-	initTloopValues("tloop.dat");
-	// tloop.dat - free energies for distinguished tetraloops
-	initInt21Values("int21.dat");
-	// int21.dat - free energies for 2 x 1 interior loops
-	initInt22Values("int22.dat");
-	// int22.dat - free energies for 2 x 2 interior loops
-	initInt11Values("int11.dat");
-	// int11.dat - free energies for 1 x 1 interior loops
+	initMiscloopValues("miscloop.DAT", EN_DATADIR);
+	initDangleValues("dangle.DAT", EN_DATADIR);
+	initStackValues("stack.DAT", EN_DATADIR);
+	initLoopValues("loop.DAT", EN_DATADIR);
+	initTstkhValues("tstackh.DAT", EN_DATADIR);
+	initTstkiValues("tstacki.DAT", EN_DATADIR);
+	initTloopValues("tloop.DAT", EN_DATADIR);
+	initInt21Values("int21.DAT", EN_DATADIR);
+	initInt22Values("int22.DAT", EN_DATADIR);
+	initInt11Values("int11.DAT", EN_DATADIR);
 }
 
+int initStackValues(const string& fileName, const string& dirPath)  { 
+	std::string filePath;
+	std::ifstream cf;
 
- int initStackValues(string fileName) {
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
 
-	ifstream cf; //cf = current file
-	int i, j, k, l;
-	int ii, jj, kk, ll;
-	int index;
-	char currentLine[256];
-	string currentString;
-	string s;
-
-	// Initialize the array with INFINITY
-	for (i = 0; i < 4; i++) {
-		for (j = 0; j < 4; j++) {
-			for (k = 0; k < 4; k++) {
-				for (l = 0; l < 4; l++) {
+	for (int i = 0; i < 4; i++) {
+		for (int j = 0; j < 4; j++) {
+			for (int k = 0; k < 4; k++) {
+				for (int l = 0; l < 2; l++) {
 					stack[fourBaseIndex(i,j,k,l)] = INFINITY_;
 				}
 			}
 		}
 	}
-
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-
-	// Read the thermodynamic parameters.
-	// The 24 first lines are junk we don't need
-	for (index = 1; index <= 15; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	i = 0;
-	kk = 0;
-	ii = 0;
-	jj = 0;
-	ll = 0;
-
-	while (i < 16) {
-
-		if (i % 4 == 0)
-			for (index = 1; index < 9; index++)
-				cf.getline(currentLine, 256);
-
-		cf.getline(currentLine, 256);
-		s = currentLine;
-		j = 0;
-
-		ll = 0;
-		jj = 0;
-
-		int z = 0;
-		int r = 0;
-
-		while (s[z] != '\0') {
-
-			if (s[z] == ' ')
-				z++;
-
-			else if (s[z] == '.') {
-				z++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
-				r++;
-				if (r % 4 == 0)
-					jj++;
-			} else {
-				char value[10];
-				int x = 0;
-
-				while (s[z] != ' ' && s[z] != '\0') {
-					value[x++] = s[z++];
-				}
-
-				value[x] = '\0';
-
-				int temp = (int) floor(100.0 * atof(value) + .5);
-				stack[fourBaseIndex(ii,jj,kk,ll)] = temp;
-				r++;
-				z++;
-				if (r % 4 == 0)
-					jj++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
+	
+	int count = 0;
+
+	while (cf.good()) {
+		int i, j, k, l;
+		
+		std::string line;
+		std::stringstream ss;
+
+		getline(cf, line);
+		ss << line;
+		if (line.empty()) continue;
+
+		i = count/4;
+		k = count%4;
+		
+		for (int cols = 0; cols < 16; cols++) {
+			std::string val;
+			ss >> val;
+			j = cols/4;
+			l = cols%4; 		
+			if (!(val == "inf")) {
+				stack[fourBaseIndex(i,j,k,l)]  = (int) floor(100.0 * atof(val.c_str()) + .5);
 			}
-		}
-		i++;
-		if (!(i % 4))
-			ii++;
-
-		/*    jj = 1; */
-		kk = (i % 4);
-
+		}	
+		++count;
 	}
-	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
+	
 	return 0;
 }
 
- int initMiscloopValues(string fileName) {
-	/*
-	 miscloop.dat - Miscellaneous loop file. Contains :
-	 1. Extrapolation for large loops based on polymer theory
-	 2. Asymmetric internal loop correction parameters.
-	 3. the f(m) array (see Ninio for details)
-	 4. Paremeters for multibranch loops
-	 5. Paremeters for multibranch loops (for efn2 only)
-	 6. Terminal AU or GU penalty
-	 7. Bonus for GGG hairpin
-	 8,9,10. C hairpin rules: a) slope  b) intercept c) value for size 3
-	 11. Intermolecular initiation free energy
-	 12. GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on or off)
-	 */
+int initMiscloopValues(const string& fileName, const string& dirpath) {
+	std::string filePath;
+	std::ifstream cf;
 
-	char currentWord[256];
-	string s;
-	ifstream cf; //cf = current file
+	filePath = dirpath + fileName;
+	cf.open(filePath.c_str(), ios::in);
 
-	fileName = EN_DATADIR + fileName;
-#if 0
-	cout << "Getting miscloop values from " << fileName << endl;
-#endif
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
+	if (!cf.good()) {
+		std::cerr << "File open failed - " << filePath << std::endl;
+		cf.close();
+		exit(-1);		
 	}
-	s = "";
 
-	cf >> currentWord;
+	char currentWord[256];
+	std::string s;
+
 	for (int index = 1; index < 13; index++) { // There are total 12 values to read in.
-		while (strcmp(currentWord, "-->")) {
-			cf >> currentWord;
-		}
 		if (index == 1) {
 			cf >> currentWord;
 			prelog = 100 * atof(currentWord);
-			//cout << "prelog = " << prelog << endl;
 		}
 		if (index == 2) {
 			cf >> currentWord;
 			maxpen = int(atof(currentWord) * 100.0 + .5);
-			//cout << "maxpen = " << maxpen << endl;
 		}
 		if (index == 3) {
 			for (int count = 1; count <= 4; count++) {
@@ -292,7 +202,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 				s = currentWord;
 				multConst[count - 1] = (int) (atof(s.c_str()) * 100 + 0.5);
 				eparam[table[count]] = (int) (atof(s.c_str()) * 100 + 0.5);
-				//cout << "\n multi " << multConst[count-1];
 			}
 		}
 		if (index == 5) {
@@ -336,150 +245,86 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 		}
 	}
 
-	cf.close();
+	cf.close();	 
+
 	return 0;
 }
 
- int initDangleValues(string fileName) {
-	ifstream cf; //cf = current file
-	char currentLine[256];
-	string currentString;
-	string s;
-	int index;
-	int i, j, k, l;
-	int ii, jj, kk, ll; // ii = 1st base, jj = 2nd base, kk = 3rd base, ll = 1 up or 2 low
-
-	for (i = 0; i < 4; i++) {
-		for (j = 0; j < 4; j++) {
-			for (k = 0; k < 4; k++) {
-				for (l = 0; l < 2; l++) {
+int initDangleValues(const std::string& fileName, 
+					  const std::string& dirPath) { 
+	std::string filePath;
+	std::ifstream cf;
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+
+	for (int i = 0; i < 4; i++) {
+		for (int j = 0; j < 4; j++) {
+			for (int k = 0; k < 4; k++) {
+				for (int l = 0; l < 2; l++) {
 					dangle[i][j][k][l] = INFINITY_;
 				}
 			}
 		}
 	}
-
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-
-	// The 8 first lines are junk
-	for (index = 1; index <= 8; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	// 8 lines of useful data
-	i = 0;
-	ii = 0;
-	jj = 0;
-	kk = 0;
-	ll = 0;
-
-	while (i < 8) {
-
-		if (i != 0)
-			for (index = 1; index < 9; index++)
-				cf.getline(currentLine, 256);
-
-		cf.getline(currentLine, 256);
-		s = currentLine;
-		j = 0;
-
-		jj = 0;
-
-		int z = 0;
-		int r = 0;
-
-		while (s[z] != '\0') {
-
-			if (s[z] == ' ')
-				z++;
-
-			else if (s[z] == '.') {
-				z++;
-				kk++;
-				if (kk == 4)
-					kk = 0;
-				r++;
-				if (r % 4 == 0)
-					jj++;
-			} else {
-				char value[10];
-				int x = 0;
-
-				while (s[z] != ' ' && s[z] != '\0') {
-					value[x++] = s[z++];
-				}
-
-				value[x] = '\0';
-
-				int temp = (int) floor(100.0 * atof(value) + .5);
-				//if ( temp == 0 )	temp = -1;
-				dangle[ii][jj][kk][ll] = temp;
-				//cout<< "\n " << temp << "  "<< ii <<" "<< jj << " "<< kk << " " << ll ;
-				r++;
-				z++;
-				if (r % 4 == 0)
-					jj++;
-				kk++;
-				if (kk == 4)
-					kk = 0;
-
+	
+	int count = 0;
+
+	while (cf.good()) {
+		int i, j, k, l;
+		
+		std::string line;
+		std::stringstream ss;
+
+		getline(cf, line);
+		ss << line;
+		if (line.empty()) continue;
+
+		i = count%4;
+		l = count/4;
+		
+		for (int cols = 0; cols < 16; cols++) {
+			std::string val;
+
+			j = cols/4;
+			ss >> val;
+			k = cols%4; 		
+			if (!(val == "inf")) {
+				dangle[i][j][k][l] = (int) floor(100.0 * atof(val.c_str()) + .5);
 			}
-
-		}
-
-		i++;
-		ii++;
-		if (ii == 4)
-			ii = 0;
-
-		if (i == 4)
-			ll = 1;
-
+		}	
+		++count;
 	}
-	cf.close();
-
-#if 0
-	cout << " Done!" << endl;
-#endif
+	
 	return 0;
 }
 
- int initLoopValues(string fileName) {
+int initLoopValues( const string& fileName, const string& dirPath) {
 	// algorithm.c, line 2996
 	ifstream cf; // current file
-	char currentLine[256];
+	std::string filePath;
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+	
+	//char currentLine[256];
 	char currentWord[256];
 	string s;
-	int index;
+	int index= 0;
 	int tempValue = 0;
 
-#if 0
-	cout << "Getting loop values...";
-#endif
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
 	if (cf.fail()) {
 		cerr << "File open failed" << endl;
 		exit(-1);
 	}
-	// The 4 first lines are junk we don't need
-	for (index = 1; index <= 4; index++) {
-		cf.getline(currentLine, 256);
-		//s = currentLine;
-		//cout << s << endl;
-	}
+
 	while (index < 30) {
 		for (int j = 1; j <= 4; j++) {
 			cf >> currentWord;
 			if (j == 1)
 				index = atoi(currentWord);
 			if (j > 1) {
-				if (strcmp(currentWord, ".")) {
+				if (strcmp(currentWord, "inf")) {
 					tempValue = (int) (100 * atof(currentWord) + 0.5);
 				} else {
 					tempValue = INFINITY_;
@@ -500,228 +345,111 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	}
 	cf.close();
 
-#if 0
-	cout << " Done!" << endl;
-#endif
 	return 0;
 }
 
- int initTstkhValues(string fileName) {
-	ifstream cf; //cf = current file
-	int i, j, k, l;
-	int ii, jj, kk, ll;
-	int index;
-	char currentLine[256];
-	string currentString;
-	string s;
+int initTstkhValues(const std::string& fileName, const std::string& dirPath) {
+	std::string filePath;
+	std::ifstream cf;
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
 
-	for (i = 0; i < 4; i++) {
-		for (j = 0; j < 4; j++) {
-			for (k = 0; k < 4; k++) {
-				for (l = 0; l < 4; l++) {
+	for (int i = 0; i < 4; i++) {
+		for (int j = 0; j < 4; j++) {
+			for (int k = 0; k < 4; k++) {
+				for (int l = 0; l < 2; l++) {
 					tstkh[fourBaseIndex(i,j,k,l)] = INFINITY_;
 				}
 			}
 		}
 	}
-
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-
-	// The 27 first lines are junk we don't need
-	for (index = 1; index <= 15; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	i = 0;
-	kk = 0;
-	ii = 0;
-	jj = 0;
-	ll = 0;
-
-	while (i < 16) {
-
-		if (i % 4 == 0)
-			for (index = 1; index < 9; index++)
-				cf.getline(currentLine, 256);
-
-		cf.getline(currentLine, 256);
-		s = currentLine;
-		j = 0;
-
-		ll = 0;
-		jj = 0;
-
-		int z = 0;
-		int r = 0;
-
-		while (s[z] != '\0') {
-
-			if (s[z] == ' ')
-				z++;
-
-			else if (s[z] == '.') {
-				z++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
-				r++;
-				if (r % 4 == 0)
-					jj++;
-			}
-
-			else {
-				char value[10];
-				int x = 0;
-
-				while (s[z] != ' ' && s[z] != '\0') {
-					value[x++] = s[z++];
-				}
-
-				value[x] = '\0';
-
-				int temp = (int) floor(100.0 * atof(value) + .5);
-				tstkh[fourBaseIndex(ii,jj,kk,ll)] = temp;
-
-				r++;
-				z++;
-				if (r % 4 == 0)
-					jj++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
+	
+	int count = 0;
+
+	while (cf.good()) {
+		int i, j, k, l;
+		
+		std::string line;
+		std::stringstream ss;
+
+		getline(cf, line);
+		ss << line;
+		if (line.empty()) continue;
+
+		i = count/4;
+		k = count%4;
+		
+		for (int cols = 0; cols < 16; cols++) {
+			std::string val;
+			ss >> val;
+			j = cols/4;
+			l = cols%4; 		
+			if (!(val == "inf")) {
+				tstkh[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5);
 			}
-		}
-		i++;
-		if (!(i % 4))
-			ii++;
-
-		jj = 0;
-		kk = (i % 4);
-
+		}	
+		++count;
 	}
-
-	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
+	
 	return 0;
 }
 
- int initTstkiValues(string fileName) {
-	ifstream cf; //cf = current file
-	int i, j, k, l;
-	int ii, jj, kk, ll;
-	int index;
-	char currentLine[256];
-	string currentString;
-	string s;
 
-	for (i = 0; i < 4; i++) {
-		for (j = 0; j < 4; j++) {
-			for (k = 0; k < 4; k++) {
-				for (l = 0; l < 4; l++) {
+int initTstkiValues(const std::string& fileName, const std::string& dirPath) {
+	std::string filePath;
+	std::ifstream cf;
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+
+	for (int i = 0; i < 4; i++) {
+		for (int j = 0; j < 4; j++) {
+			for (int k = 0; k < 4; k++) {
+				for (int l = 0; l < 2; l++) {
 					tstki[fourBaseIndex(i,j,k,l)] = INFINITY_;
 				}
 			}
 		}
 	}
 
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-
-	// The 27 first lines are junk we don't need
-	for (index = 1; index <= 15; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	i = 0;
-	kk = 0;
-	ii = 0;
-	jj = 0;
-	ll = 0;
-
-	while (i < 16) {
-
-		if (i % 4 == 0)
-			for (index = 1; index < 9; index++)
-				cf.getline(currentLine, 256);
-
-		cf.getline(currentLine, 256);
-		s = currentLine;
-		j = 0;
-
-		ll = 0;
-		jj = 0;
-
-		int z = 0;
-		int r = 0;
-
-		while (s[z] != '\0') {
-
-			if (s[z] == ' ')
-				z++;
+	int count = 0;
 
-			else if (s[z] == '.') {
-				z++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
-				r++;
-				if (r % 4 == 0)
-					jj++;
-			}
+	while (cf.good()) {
+		int i, j, k, l;
 
-			else {
-				char value[10];
-				int x = 0;
+		std::string line;
+		std::stringstream ss;
 
-				while (s[z] != ' ' && s[z] != '\0') {
-					value[x++] = s[z++];
-				}
+		getline(cf, line);
+		ss << line;
+		if (line.empty()) continue;
 
-				value[x] = '\0';
-
-				int temp = (int) floor(100.0 * atof(value) + .5);
-				tstki[fourBaseIndex(ii,jj,kk,ll)] = temp;
+		i = count/4;
+		k = count%4;
 
-				//cout << "\n temp " << temp << " " <<ii << " "<< jj << " "<< kk << " " << ll;
-				r++;
-				z++;
-				if (r % 4 == 0)
-					jj++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
+		for (int cols = 0; cols < 16; cols++) {
+			std::string val;
+			ss >> val;
+			j = cols/4;
+			l = cols%4; 		
+			if (!(val == "inf")) {
+				tstki[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5);
 			}
-		}
-		i++;
-		if (!(i % 4))
-			ii++;
-
-		jj = 0;
-		kk = (i % 4);
-
+		}	
+		++count;
 	}
 
-	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
 	return 0;
 }
 
-//SH: Rewritten as an error was being generated by this function.
- int initTloopValues(string fileName) {
-	ifstream cf;
+int initTloopValues(const std::string& fileName, const std::string& dirPath) {
+	std::string filePath;
+	std::ifstream cf;
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+
 	int count;
 	char currentLine[256];
 	char currentSeqNumbers[7];
@@ -732,20 +460,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 
 	string s, temp;
 
-#if 0
-	cout << "Getting tloop values...";
-#endif
-
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-	// skip 2 lines
-	cf.getline(currentLine, 256);
-	cf.getline(currentLine, 256);
-
 	numoftloops = 0;
 
 	while (!cf.eof() && (++(numoftloops) < maxtloop)) {
@@ -759,33 +473,23 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 		for (count = 0; count < 6; count++) {
 			temp = currentLine[count + clindex];
 			currentSeqNumbers[count] = baseToDigit(temp.c_str());
-			//cout << currentSeqNumbers[count];
-			//cout << currentLine[count+1];
 		}
-		//cout << endl;
 		clindex=clindex+7;
 		while(currentLine[clindex]== ' ') clindex++;
 		count = 0;
 		while(currentLine[clindex+count]!=' '&&currentLine[clindex+count]!='\0') {
 			currentValue[count] = currentLine[count + clindex];
 			count++;
-			//cout << currentValue[count];
 		}
-		//cout << endl;
 
 		tloop[numoftloops][0] = (int) atoi(currentSeqNumbers);
 		tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5);
-		//cout << " --  "<< tloop[numoftloops][0] << " | " << tloop[numoftloops][1] << endl;
 	}
 	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
 	return 0;
 }
 
- int initInt22Values(string fileName) {
-
+int initInt22Values(const std::string& fileName, const std::string& dirPath) {
 	//Read the 2x2 internal loops
 	//key iloop22[a][b][c][d][j][l][k][m] =
 	//a j l b
@@ -803,66 +507,36 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 									iloop22[i][j][k][r][q][t][y][z] = INFINITY_;
 
 	ifstream cf;
-	int index, flag;
 	char currentLine[256], currentValue[6];
-	string s, s1, s2, temp;
-	string sre;
 
 	int base[4];
 	int l, m;
 
-#if 0
-	cout << "Getting Int22 values...";
-#endif
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
+	string filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+	if (!cf.good()) {
+		cerr << "File open failed " << endl;
 		exit(-1);
 	}
 
-	// Get rid of the 38 1st lines
-	for (index = 1; index < 28; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	sre = "Y";
-	flag = 0;
-
-	for (index = 1; index <= 36; index++) { // 36 tables 16x16
-		// Go to the beginning of the tables
-		while (!flag) {
-			cf.getline(currentLine, 256);
+	const char* str[] = {"A-U","C-G","G-C","U-A","G-U","U-G"};
+	
 
-			s = currentLine;
+	int outer, inner;
 
-			int z = 0;
-			while (s[z] != '\0') {
+	for (int index = 1; index <= 36; index++) { // 36 tables 16x16
+		std::stringstream ss1;
+		std::string s ;
 
-				if (s[z] == 'Y')
-					flag = 1;
-
-				z++;
-			}
-		}
-		flag = 0;
-
-		// We skip 5 lines
-		for (i = 0; i < 5; ++i) {
-			cf.getline(currentLine, 256);
-		}
- 
-		// get the closing bases
-		cf.getline(currentLine, 256);
-		s1 = currentLine;
-		cf.getline(currentLine, 256);
-		s2 = currentLine;
-		s = s1 + s2;
-
-		int z = 0;
+		outer = (index-1)/6;
+		inner = (index-1)%6;
+		ss1 << str[outer][0] << '-' << str[inner][0] << '-' << str[outer][2] << '-' <<
+			str[inner][2];
+	    ss1 >> s;	
+		
 		int k = 0;
+		int z = 0;
 		while (s[z] != '\0') {
-
 			if (s[z] == 'A')
 				base[k++] = BASE_A;
 			else if (s[z] == 'C')
@@ -871,22 +545,15 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 				base[k++] = BASE_G;
 			else if (s[z] == 'U')
 				base[k++] = BASE_U;
-
 			z++;
 		}
 
-		cf.getline(currentLine, 256);
-
-		//key iloop22[a][b][c][d][j][l][k][m] =
-		//a j l b
-		//c k m d
-
-
 		for (int rowIndex = 1; rowIndex <= 16; rowIndex++) {
+			cf.getline(currentLine, 256);
+			std::stringstream ss;
+			ss << currentLine;
 			for (int colIndex = 1; colIndex <= 16; colIndex++) {
-				cf >> currentValue;
-				// rowIndex = j*4+k
-				// colIndex = l*4+m
+				ss >> currentValue;	
 
 				j = ((rowIndex - 1) - (rowIndex - 1) % 4) / 4;
 				k = (rowIndex - 1) % 4;
@@ -894,23 +561,17 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 				l = ((colIndex - 1) - (colIndex - 1) % 4) / 4;
 				m = (colIndex - 1) % 4;
 
-				iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m]
-				                                                     = (int) floor(100.0 * atof(currentValue) + 0.5);
-				//int temp = (int) floor(100.0*atof(currentValue)+0.5);
-				//printf("\n temp is : %d    %d %d %d %d   %d  %d   %d %d", temp, base[0], base[2], base[1], base[3], j, k, l, m );
+				iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] 
+					= (int) floor(100.0 * atof(currentValue) + 0.5);
 			}
 		}
 	}
 
 	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
 	return 0;
 }
 
- int initInt21Values(string fileName) {
-
+int initInt21Values(const std::string& fileName, const std::string& dirPath) {
 	// 24x6 arrays of 4x4 values
 	//      c
 	//   a     f
@@ -921,7 +582,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	char currentLine[256];
 	string sre;
 	string s, s1, s2;
-	int a, b, c, d, e, f, g, index;
+	int a, b, c, d, e, f, g;
 	int i, j, k, r, q, t, y;
 	int z;
 
@@ -958,87 +619,44 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	base1[6] = BASE_U + 1;
 	base2[6] = BASE_G + 1;
 
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
+	std::string filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
 	if (cf.fail()) {
 		cerr << "File open failed" << endl;
 		exit(-1);
 	}
 
-	// Get rid of the 18 1st lines
-	for (index = 1; index <= 17; index++) {
-		cf.getline(currentLine, 256);
-	}
-
 	i = 1;
-
 	while (i <= 6) {
-
 		j = 1;
-
 		while (j <= 4) {
-
 			k = 1;
-
-			for (index = 1; index <= 10; index++)
-				cf.getline(currentLine, 256);
-
-			s = currentLine;
-
 			while (k <= 4) {
-
 				cf.getline(currentLine, 256);
-
-				s = currentLine;
-
 				r = 0;
-				z = 0;
 				int jj = 1;
 				d = 1;
-				while (s[z] != '\0') {
-
-					if (s[z] == ' ')
-						z++;
-
-					else if (s[z] == '.') {
-						z++;
-						d++;
-						if (d == 5)
-							d = 1;
-						r++;
-						if (r % 4 == 0)
-							jj++;
-					}
-
-					else {
-						char value[10];
-						int x = 0;
-
-						while (s[z] != ' ' && s[z] != '\0') {
-							value[x++] = s[z++];
-						}
-
-						value[x] = '\0';
-
-						int temp = (int) floor(100.0 * atof(value) + .5);
-						a = base1[i];
-						b = base2[i];
-						f = base1[jj];
-						g = base2[jj];
-						c = k;
-						e = j;
-
-						iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1]
-						                                                  = temp;
-						//printf("\n temp %d, a %d , b %d, c %d, d %d, e %d, f %d, g %d", temp, a, b, c, d, e, f, g);
-						r++;
-						z++;
-						if (r % 4 == 0)
-							jj++;
-						d++;
-						if (d == 5)
-							d = 1;
-					}
+
+				std::stringstream ss;
+				ss << currentLine;
+
+				for (z = 1; z <=24 ; z++) {
+					char value[32];
+					ss >> value;
+					int temp = (int) floor(100.0 * atof(value) + .5);
+					a = base1[i];
+					b = base2[i];
+					f = base1[jj];
+					g = base2[jj];
+					c = k;
+					e = j;
+
+					iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1]
+						= temp;
+					r++;
+					if (r % 4 == 0) jj++;
+					d++;
+					if (d == 5) d = 1;
 				}
 				k++;
 			}
@@ -1050,13 +668,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	return 0;
 }
 
- int initInt11Values(string fileName) {
-
-	//Read the 1x1 internal loops
-	//key iloop11[a][b][c][d][j][l][k][m] =
-	//a b c
-	//d e f
-
+int initInt11Values(const std::string& fileName, const std::string& dirPath) {
 	int i, j, k, r, q, t;
 
 	for (i = 0; i < 4; i++)
@@ -1068,37 +680,20 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 							iloop11[i][j][k][r][q][t] = INFINITY_;
 
 	ifstream cf;
-	int index;
 	char currentLine[256];
 	string s;
 	int base1[7];
 	int base2[7];
 
-	//int j, k, l, m;
 	int a, b, c, d, f;
 
-#if 0
-	cout << "Getting Int11 values...";
-#endif
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
+	std::string filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
 	if (cf.fail()) {
 		cerr << "File open failed" << endl;
 		exit(-1);
 	}
 
-	// Get rid of the 19 1st lines
-	for (index = 1; index <= 17; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	/*
-	 Structure of the file:
-	 array of 6x6 arrays
-	 Order:
-	 AU CG GC UA GU UG
-	 */
-
 	base1[1] = BASE_A + 1;
 	base2[1] = BASE_U + 1;
 	base1[2] = BASE_C + 1;
@@ -1117,75 +712,38 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 
 	while (k < 6) {
 		k++;
-		index = 0;
-		for (index = 1; index <= 10; index++) {
-			cf.getline(currentLine, 256);
-		}
-
 		i = 0;
 		b = 1;
 
 		while (i < 4) {
-
 			int jj = 1;
 			++i;
 			cf.getline(currentLine, 256);
-			s = currentLine;
-
 			j = 0;
 
 			int r = 0;
-			int z = 0;
 			int e = 1;
-			while (s[z] != '\0') {
-
-				if (s[z] == ' ')
-					z++;
-
-				else if (s[z] == '.') {
-					z++;
-					e++;
-					if (e == 5)
-						e = 1;
-					r++;
-					if (r % 4 == 0)
-						jj++;
-				}
-
-				else {
-					char value[10];
-					int x = 0;
-
-					while (s[z] != ' ' && s[z] != '\0') {
-						value[x++] = s[z++];
-					}
-
-					value[x] = '\0';
+			std::stringstream ss;
+			ss << currentLine;
 
-					int temp = (int) floor(100.0 * atof(value) + .5);
-					a = base1[k];
-					d = base2[k];
-					c = base1[jj];
-					f = base2[jj];
-					iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp;
-					r++;
-					z++;
-					if (r % 4 == 0)
-						jj++;
-					e++;
-					if (e == 5)
-						e = 1;
-				}
+			for (int z=1; z <= 24; ++z) {
+				char value[32];
+				ss >> value;	
+				int temp = (int) floor(100.0 * atof(value) + .5);
+				a = base1[k];
+				d = base2[k];
+				c = base1[jj];
+				f = base2[jj];
+				iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp;
+				r++;
+				if (r % 4 == 0) jj++;
+				e++;
+				if (e == 5) e = 1;
 			}
 			b++;
 		}
 	}
 
 	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
 	return 0;
 }
-
-

From b18929911eb1bbb5db85a29267502d7259a48edd Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 4 May 2011 11:05:23 -0400
Subject: [PATCH 109/282] fixed bug related to constraints

---
 gtfold-mfe/src/constraints.cc | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 97cbc5e..d3cd01b 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -89,13 +89,16 @@ static int load_constraints(const char* constr_file, int verbose=0) {
 		for(int k=1;k<= FBP[it][2];k++)
 			v_fbp.push_back(std::pair<int,int>(FBP[it][0]+k-1, FBP[it][1]-k+1));
 	}
-	std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
-	for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) {
-		if (v_fbp[ii].second <= v_fbp[ii+1].second) {
-			fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n");
-			exit(-1);
+
+	if (v_fbp.size() > 1) {
+		std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
+		for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) {
+			if (v_fbp[ii].second <= v_fbp[ii+1].second) {
+				fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n");
+				exit(-1);
+			}
+
 		}
-			
 	}
 
 
@@ -134,18 +137,18 @@ int init_constraints(const char* constr_file,int length) {
 		for (it = 0; it < nFBP; it++) {
 			if (FBP[it][2] < 1) {
 				printf("Invalid entry (%d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
-				continue;
+				continue; // TODO: report and exit here
 			}
 			for(k=1; k <= FBP[it][2];k++) {
 				int i1 = FBP[it][0]+k-1;
 				int j1 = FBP[it][1]-k+1;
 				if (!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])) {
 					printf("Can't constrain (%d,%d)\n", FBP[it][0]+k-1, FBP[it][1]-k+1);
-					continue;
+					continue; // TODO: report and exit here
 				}
 				if (j1-i1 < TURN) {
 					printf("Can't constrain (%d,%d)\n", i1, j1);
-					continue;
+					continue; // TODO: report and exit here
 				}	
 				BP[FBP[it][0]+k-1] = FBP[it][1]+1-k;
 				BP[FBP[it][1]+1-k] = FBP[it][0]+k-1;
@@ -175,6 +178,8 @@ void print_constraints(int len) {
     printf("\n");
 }
 
+
+
 int is_ss(int i, int j) {
 	if (CONS_ENABLED) {
 		int it;

From 1a4dfa0130b4ebf396e684cab5e6b798dcf492d0 Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Sun, 8 May 2011 01:22:48 +0200
Subject: [PATCH 110/282] Commiting SHAPE support and the first attempt at
 fixing constraints. Still can't produce structures like (...)(...)

---
 gtfold-mfe/Makefile                      | 753 +++++++++++++++++++++++
 gtfold-mfe/include/shapereader.h         |  23 +
 gtfold-mfe/src/.deps/algorithms.Po       | 131 ++++
 gtfold-mfe/src/.deps/constraints.Po      | 370 +++++++++++
 gtfold-mfe/src/.deps/energy.Po           | 116 ++++
 gtfold-mfe/src/.deps/global.Po           |  85 +++
 gtfold-mfe/src/.deps/loader.Po           | 367 +++++++++++
 gtfold-mfe/src/.deps/main.Po             | 437 +++++++++++++
 gtfold-mfe/src/.deps/options.Po          | 265 ++++++++
 gtfold-mfe/src/.deps/shapereader.Po      | 360 +++++++++++
 gtfold-mfe/src/.deps/subopt_traceback.Po | 351 +++++++++++
 gtfold-mfe/src/.deps/traceback.Po        | 127 ++++
 gtfold-mfe/src/.deps/utils.Po            | 222 +++++++
 gtfold-mfe/src/Makefile                  | 522 ++++++++++++++++
 gtfold-mfe/src/shapereader.cc            |  89 +++
 15 files changed, 4218 insertions(+)
 create mode 100644 gtfold-mfe/Makefile
 create mode 100644 gtfold-mfe/include/shapereader.h
 create mode 100644 gtfold-mfe/src/.deps/algorithms.Po
 create mode 100644 gtfold-mfe/src/.deps/constraints.Po
 create mode 100644 gtfold-mfe/src/.deps/energy.Po
 create mode 100644 gtfold-mfe/src/.deps/global.Po
 create mode 100644 gtfold-mfe/src/.deps/loader.Po
 create mode 100644 gtfold-mfe/src/.deps/main.Po
 create mode 100644 gtfold-mfe/src/.deps/options.Po
 create mode 100644 gtfold-mfe/src/.deps/shapereader.Po
 create mode 100644 gtfold-mfe/src/.deps/subopt_traceback.Po
 create mode 100644 gtfold-mfe/src/.deps/traceback.Po
 create mode 100644 gtfold-mfe/src/.deps/utils.Po
 create mode 100644 gtfold-mfe/src/Makefile
 create mode 100644 gtfold-mfe/src/shapereader.cc

diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile
new file mode 100644
index 0000000..75480ce
--- /dev/null
+++ b/gtfold-mfe/Makefile
@@ -0,0 +1,753 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+
+pkgdatadir = $(datadir)/gtfold
+pkgincludedir = $(includedir)/gtfold
+pkglibdir = $(libdir)/gtfold
+pkglibexecdir = $(libexecdir)/gtfold
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
+target_triplet = x86_64-unknown-linux-gnu
+subdir = .
+DIST_COMMON = README $(am__configure_deps) $(include_HEADERS) \
+	$(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+	$(srcdir)/gtfold_config.h.in $(top_srcdir)/configure AUTHORS \
+	COPYING ChangeLog INSTALL NEWS TODO config.guess config.sub \
+	depcomp install-sh missing
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
+ configure.lineno config.status.lineno
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = gtfold_config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
+	html-recursive info-recursive install-data-recursive \
+	install-dvi-recursive install-exec-recursive \
+	install-html-recursive install-info-recursive \
+	install-pdf-recursive install-ps-recursive install-recursive \
+	installcheck-recursive installdirs-recursive pdf-recursive \
+	ps-recursive uninstall-recursive
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__installdirs = "$(DESTDIR)$(includedir)"
+HEADERS = $(include_HEADERS)
+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
+  distclean-recursive maintainer-clean-recursive
+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+	$(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
+	distdir dist dist-all distcheck
+ETAGS = etags
+CTAGS = ctags
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+distdir = $(PACKAGE)-$(VERSION)
+top_distdir = $(distdir)
+am__remove_distdir = \
+  { test ! -d "$(distdir)" \
+    || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
+         && rm -fr "$(distdir)"; }; }
+am__relativize = \
+  dir0=`pwd`; \
+  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
+  sed_rest='s,^[^/]*/*,,'; \
+  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
+  sed_butlast='s,/*[^/]*$$,,'; \
+  while test -n "$$dir1"; do \
+    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
+    if test "$$first" != "."; then \
+      if test "$$first" = ".."; then \
+        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
+        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
+      else \
+        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
+        if test "$$first2" = "$$first"; then \
+          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
+        else \
+          dir2="../$$dir2"; \
+        fi; \
+        dir0="$$dir0"/"$$first"; \
+      fi; \
+    fi; \
+    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
+  done; \
+  reldir="$$dir2"
+DIST_ARCHIVES = $(distdir).tar.gz
+GZIP_ENV = --best
+distuninstallcheck_listfiles = find . -type f -print
+distcleancheck_listfiles = find . -type f -print
+ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -g -O2 -Wall
+CPP = gcc -E
+CPPFLAGS = 
+CXX = g++
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2 -Wall
+CYGPATH_W = echo
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /bin/grep -E
+EXEEXT = 
+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = 
+LIBOBJS = 
+LIBS = -lgomp 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+PACKAGE = gtfold
+PACKAGE_BUGREPORT = 
+PACKAGE_NAME = gtfold
+PACKAGE_STRING = gtfold 1.18
+PACKAGE_TARNAME = gtfold
+PACKAGE_URL = 
+PACKAGE_VERSION = 1.18
+PATH_SEPARATOR = :
+SET_MAKE = 
+SHELL = /bin/bash
+STRIP = 
+VERSION = 1.18
+abs_builddir = /home/zs/git/gtfold/gtfold-mfe
+abs_srcdir = /home/zs/git/gtfold/gtfold-mfe
+abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
+abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = ${AMTAR} chof - "$$tardir"
+am__untar = ${AMTAR} xf -
+bindir = ${exec_prefix}/bin
+build = x86_64-unknown-linux-gnu
+build_alias = 
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = unknown
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host = x86_64-unknown-linux-gnu
+host_alias = 
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = unknown
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /usr/local
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target = x86_64-unknown-linux-gnu
+target_alias = 
+target_cpu = x86_64
+target_os = linux-gnu
+target_vendor = unknown
+top_build_prefix = 
+top_builddir = .
+top_srcdir = .
+SUBDIRS = src include data
+DIST_SUBDIRS = src include data
+include_HEADERS = gtfold_config.h
+CLEANFILES = *~
+MAINTAINERCLEANDIRS = autom4te.cache
+# MAINTAINERCLEANFILES = libtool gtfold_config.h.in
+MAINTAINERCLEANFILES = gtfold_config.h gtfold_config.h.in
+EXTRA_DIST = autogen.sh
+all: gtfold_config.h
+	$(MAKE) $(AM_MAKEFLAGS) all-recursive
+
+.SUFFIXES:
+am--refresh:
+	@:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      echo ' cd $(srcdir) && $(AUTOMAKE) --gnu'; \
+	      $(am__cd) $(srcdir) && $(AUTOMAKE) --gnu \
+		&& exit 0; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    echo ' $(SHELL) ./config.status'; \
+	    $(SHELL) ./config.status;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	$(SHELL) ./config.status --recheck
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	$(am__cd) $(srcdir) && $(AUTOCONF)
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	$(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
+$(am__aclocal_m4_deps):
+
+gtfold_config.h: stamp-h1
+	@if test ! -f $@; then \
+	  rm -f stamp-h1; \
+	  $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
+	else :; fi
+
+stamp-h1: $(srcdir)/gtfold_config.h.in $(top_builddir)/config.status
+	@rm -f stamp-h1
+	cd $(top_builddir) && $(SHELL) ./config.status gtfold_config.h
+$(srcdir)/gtfold_config.h.in:  $(am__configure_deps) 
+	($(am__cd) $(top_srcdir) && $(AUTOHEADER))
+	rm -f stamp-h1
+	touch $@
+
+distclean-hdr:
+	-rm -f gtfold_config.h stamp-h1
+install-includeHEADERS: $(include_HEADERS)
+	@$(NORMAL_INSTALL)
+	test -z "$(includedir)" || $(MKDIR_P) "$(DESTDIR)$(includedir)"
+	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(includedir)'"; \
+	  $(INSTALL_HEADER) $$files "$(DESTDIR)$(includedir)" || exit $$?; \
+	done
+
+uninstall-includeHEADERS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(includedir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(includedir)" && rm -f $$files
+
+# This directory's subdirectories are mostly independent; you can cd
+# into them and run `make' without going through this Makefile.
+# To change the values of `make' variables: instead of editing Makefiles,
+# (1) if the variable is set in `config.status', edit `config.status'
+#     (which will cause the Makefiles to be regenerated when you run `make');
+# (2) otherwise, pass the desired values on the `make' command line.
+$(RECURSIVE_TARGETS):
+	@fail= failcom='exit 1'; \
+	for f in x $$MAKEFLAGS; do \
+	  case $$f in \
+	    *=* | --[!k]*);; \
+	    *k*) failcom='fail=yes';; \
+	  esac; \
+	done; \
+	dot_seen=no; \
+	target=`echo $@ | sed s/-recursive//`; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    dot_seen=yes; \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  || eval $$failcom; \
+	done; \
+	if test "$$dot_seen" = "no"; then \
+	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
+	fi; test -z "$$fail"
+
+$(RECURSIVE_CLEAN_TARGETS):
+	@fail= failcom='exit 1'; \
+	for f in x $$MAKEFLAGS; do \
+	  case $$f in \
+	    *=* | --[!k]*);; \
+	    *k*) failcom='fail=yes';; \
+	  esac; \
+	done; \
+	dot_seen=no; \
+	case "$@" in \
+	  distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
+	  *) list='$(SUBDIRS)' ;; \
+	esac; \
+	rev=''; for subdir in $$list; do \
+	  if test "$$subdir" = "."; then :; else \
+	    rev="$$subdir $$rev"; \
+	  fi; \
+	done; \
+	rev="$$rev ."; \
+	target=`echo $@ | sed s/-recursive//`; \
+	for subdir in $$rev; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  || eval $$failcom; \
+	done && test -z "$$fail"
+tags-recursive:
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
+	done
+ctags-recursive:
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
+	done
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	mkid -fID $$unique
+tags: TAGS
+
+TAGS: tags-recursive $(HEADERS) $(SOURCES) gtfold_config.h.in $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	set x; \
+	here=`pwd`; \
+	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
+	  include_option=--etags-include; \
+	  empty_fix=.; \
+	else \
+	  include_option=--include; \
+	  empty_fix=; \
+	fi; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    test ! -f $$subdir/TAGS || \
+	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
+	  fi; \
+	done; \
+	list='$(SOURCES) $(HEADERS) gtfold_config.h.in $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
+	fi
+ctags: CTAGS
+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) gtfold_config.h.in $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	list='$(SOURCES) $(HEADERS) gtfold_config.h.in $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+	$(am__remove_distdir)
+	test -d "$(distdir)" || mkdir "$(distdir)"
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    test -d "$(distdir)/$$subdir" \
+	    || $(MKDIR_P) "$(distdir)/$$subdir" \
+	    || exit 1; \
+	  fi; \
+	done
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
+	    $(am__relativize); \
+	    new_distdir=$$reldir; \
+	    dir1=$$subdir; dir2="$(top_distdir)"; \
+	    $(am__relativize); \
+	    new_top_distdir=$$reldir; \
+	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
+	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
+	    ($(am__cd) $$subdir && \
+	      $(MAKE) $(AM_MAKEFLAGS) \
+	        top_distdir="$$new_top_distdir" \
+	        distdir="$$new_distdir" \
+		am__remove_distdir=: \
+		am__skip_length_check=: \
+		am__skip_mode_fix=: \
+	        distdir) \
+	      || exit 1; \
+	  fi; \
+	done
+	-test -n "$(am__skip_mode_fix)" \
+	|| find "$(distdir)" -type d ! -perm -755 \
+		-exec chmod u+rwx,go+rx {} \; -o \
+	  ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
+	  ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
+	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
+	|| chmod -R a+r "$(distdir)"
+dist-gzip: distdir
+	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+	$(am__remove_distdir)
+
+dist-bzip2: distdir
+	tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2
+	$(am__remove_distdir)
+
+dist-lzma: distdir
+	tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma
+	$(am__remove_distdir)
+
+dist-xz: distdir
+	tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz
+	$(am__remove_distdir)
+
+dist-tarZ: distdir
+	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
+	$(am__remove_distdir)
+
+dist-shar: distdir
+	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
+	$(am__remove_distdir)
+
+dist-zip: distdir
+	-rm -f $(distdir).zip
+	zip -rq $(distdir).zip $(distdir)
+	$(am__remove_distdir)
+
+dist dist-all: distdir
+	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+	$(am__remove_distdir)
+
+# This target untars the dist file and tries a VPATH configuration.  Then
+# it guarantees that the distribution is self-contained by making another
+# tarfile.
+distcheck: dist
+	case '$(DIST_ARCHIVES)' in \
+	*.tar.gz*) \
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
+	*.tar.bz2*) \
+	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
+	*.tar.lzma*) \
+	  lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\
+	*.tar.xz*) \
+	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
+	*.tar.Z*) \
+	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
+	*.shar.gz*) \
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
+	*.zip*) \
+	  unzip $(distdir).zip ;;\
+	esac
+	chmod -R a-w $(distdir); chmod a+w $(distdir)
+	mkdir $(distdir)/_build
+	mkdir $(distdir)/_inst
+	chmod a-w $(distdir)
+	test -d $(distdir)/_build || exit 0; \
+	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
+	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
+	  && am__cwd=`pwd` \
+	  && $(am__cd) $(distdir)/_build \
+	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
+	    $(DISTCHECK_CONFIGURE_FLAGS) \
+	  && $(MAKE) $(AM_MAKEFLAGS) \
+	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
+	  && $(MAKE) $(AM_MAKEFLAGS) check \
+	  && $(MAKE) $(AM_MAKEFLAGS) install \
+	  && $(MAKE) $(AM_MAKEFLAGS) installcheck \
+	  && $(MAKE) $(AM_MAKEFLAGS) uninstall \
+	  && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
+	        distuninstallcheck \
+	  && chmod -R a-w "$$dc_install_base" \
+	  && ({ \
+	       (cd ../.. && umask 077 && mkdir "$$dc_destdir") \
+	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
+	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
+	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
+	            distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
+	      } || { rm -rf "$$dc_destdir"; exit 1; }) \
+	  && rm -rf "$$dc_destdir" \
+	  && $(MAKE) $(AM_MAKEFLAGS) dist \
+	  && rm -rf $(DIST_ARCHIVES) \
+	  && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
+	  && cd "$$am__cwd" \
+	  || exit 1
+	$(am__remove_distdir)
+	@(echo "$(distdir) archives ready for distribution: "; \
+	  list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
+	  sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
+distuninstallcheck:
+	@$(am__cd) '$(distuninstallcheck_dir)' \
+	&& test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
+	   || { echo "ERROR: files left after uninstall:" ; \
+	        if test -n "$(DESTDIR)"; then \
+	          echo "  (check DESTDIR support)"; \
+	        fi ; \
+	        $(distuninstallcheck_listfiles) ; \
+	        exit 1; } >&2
+distcleancheck: distclean
+	@if test '$(srcdir)' = . ; then \
+	  echo "ERROR: distcleancheck can only run from a VPATH build" ; \
+	  exit 1 ; \
+	fi
+	@test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
+	  || { echo "ERROR: files left in build directory after distclean:" ; \
+	       $(distcleancheck_listfiles) ; \
+	       exit 1; } >&2
+check-am: all-am
+check: check-recursive
+all-am: Makefile $(HEADERS) gtfold_config.h
+installdirs: installdirs-recursive
+installdirs-am:
+	for dir in "$(DESTDIR)$(includedir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-recursive
+install-exec: install-exec-recursive
+install-data: install-data-recursive
+uninstall: uninstall-recursive
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-recursive
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+	-test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
+clean: clean-recursive
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-recursive
+	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic distclean-hdr distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+html-am:
+
+info: info-recursive
+
+info-am:
+
+install-data-am: install-includeHEADERS
+
+install-dvi: install-dvi-recursive
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-recursive
+
+install-html-am:
+
+install-info: install-info-recursive
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-recursive
+
+install-pdf-am:
+
+install-ps: install-ps-recursive
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-recursive
+	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
+	-rm -rf $(top_srcdir)/autom4te.cache
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-recursive
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-recursive
+
+pdf-am:
+
+ps: ps-recursive
+
+ps-am:
+
+uninstall-am: uninstall-includeHEADERS
+
+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
+	ctags-recursive install-am install-strip tags-recursive
+
+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
+	all all-am am--refresh check check-am clean clean-generic \
+	ctags ctags-recursive dist dist-all dist-bzip2 dist-gzip \
+	dist-lzma dist-shar dist-tarZ dist-xz dist-zip distcheck \
+	distclean distclean-generic distclean-hdr distclean-tags \
+	distcleancheck distdir distuninstallcheck dvi dvi-am html \
+	html-am info info-am install install-am install-data \
+	install-data-am install-dvi install-dvi-am install-exec \
+	install-exec-am install-html install-html-am \
+	install-includeHEADERS install-info install-info-am \
+	install-man install-pdf install-pdf-am install-ps \
+	install-ps-am install-strip installcheck installcheck-am \
+	installdirs installdirs-am maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am \
+	uninstall-includeHEADERS
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/gtfold-mfe/include/shapereader.h b/gtfold-mfe/include/shapereader.h
new file mode 100644
index 0000000..02c3a2b
--- /dev/null
+++ b/gtfold-mfe/include/shapereader.h
@@ -0,0 +1,23 @@
+#ifndef _SHAPEREADER_H_
+#define _SHAPEREADER_H_
+
+extern double* SHAPEarray;
+extern int* SHAPEenergies;
+
+void readSHAPEarray(const char* filename, int seqlength);
+void free_shapeArray(int len);
+void print_shapeArray(int len);
+int calcShapeEnergy(double shapeNumber);
+double shapeModel(double SHAPE_value);
+
+#ifdef __cplusplus
+extern "C"{
+#endif
+
+int getShapeEnergy(int position);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/gtfold-mfe/src/.deps/algorithms.Po b/gtfold-mfe/src/.deps/algorithms.Po
new file mode 100644
index 0000000..b84c3b7
--- /dev/null
+++ b/gtfold-mfe/src/.deps/algorithms.Po
@@ -0,0 +1,131 @@
+algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/time.h /usr/include/bits/time.h /usr/include/xlocale.h \
+ /usr/include/sys/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/assert.h \
+ ../include/constants.h ../include/utils.h ../include/constants.h \
+ ../include/energy.h ../include/data.h ../include/global.h \
+ ../include/algorithms.h ../include/constraints.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/omp.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/bits/stdio2.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/time.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/sys/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/bits/stdlib.h:
+
+/usr/include/assert.h:
+
+../include/constants.h:
+
+../include/utils.h:
+
+../include/constants.h:
+
+../include/energy.h:
+
+../include/data.h:
+
+../include/global.h:
+
+../include/algorithms.h:
+
+../include/constraints.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/omp.h:
diff --git a/gtfold-mfe/src/.deps/constraints.Po b/gtfold-mfe/src/.deps/constraints.Po
new file mode 100644
index 0000000..ec27b91
--- /dev/null
+++ b/gtfold-mfe/src/.deps/constraints.Po
@@ -0,0 +1,370 @@
+constraints.o: constraints.cc /usr/include/stdlib.h \
+ /usr/include/features.h /usr/include/bits/predefs.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/xlocale.h \
+ /usr/include/sys/types.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/time.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/string.h \
+ /usr/include/bits/string3.h /usr/include/stdio.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
+ /usr/include/c++/4.4/iostream \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \
+ /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \
+ /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \
+ /usr/include/c++/4.4/cstddef /usr/include/bits/wchar.h \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \
+ /usr/include/c++/4.4/bits/char_traits.h \
+ /usr/include/c++/4.4/bits/stl_algobase.h \
+ /usr/include/c++/4.4/bits/functexcept.h \
+ /usr/include/c++/4.4/exception_defines.h \
+ /usr/include/c++/4.4/bits/cpp_type_traits.h \
+ /usr/include/c++/4.4/ext/type_traits.h \
+ /usr/include/c++/4.4/ext/numeric_traits.h \
+ /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
+ /usr/include/c++/4.4/bits/concept_check.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.4/bits/stl_iterator.h \
+ /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.4/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.4/bits/ios_base.h \
+ /usr/include/c++/4.4/ext/atomicity.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
+ /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h \
+ /usr/include/bits/unistd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \
+ /usr/include/c++/4.4/bits/allocator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
+ /usr/include/c++/4.4/bits/ostream_insert.h \
+ /usr/include/c++/4.4/cxxabi-forced.h \
+ /usr/include/c++/4.4/bits/stl_function.h \
+ /usr/include/c++/4.4/backward/binders.h \
+ /usr/include/c++/4.4/bits/basic_string.h \
+ /usr/include/c++/4.4/initializer_list \
+ /usr/include/c++/4.4/bits/basic_string.tcc \
+ /usr/include/c++/4.4/bits/locale_classes.tcc \
+ /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \
+ /usr/include/c++/4.4/bits/basic_ios.h \
+ /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \
+ /usr/include/c++/4.4/bits/streambuf_iterator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \
+ /usr/include/c++/4.4/bits/locale_facets.tcc \
+ /usr/include/c++/4.4/bits/basic_ios.tcc \
+ /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \
+ /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \
+ /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \
+ /usr/include/c++/4.4/bits/fstream.tcc /usr/include/c++/4.4/vector \
+ /usr/include/c++/4.4/bits/stl_construct.h \
+ /usr/include/c++/4.4/bits/stl_uninitialized.h \
+ /usr/include/c++/4.4/bits/stl_vector.h \
+ /usr/include/c++/4.4/bits/stl_bvector.h \
+ /usr/include/c++/4.4/bits/vector.tcc /usr/include/c++/4.4/algorithm \
+ /usr/include/c++/4.4/bits/stl_algo.h /usr/include/c++/4.4/cstdlib \
+ /usr/include/c++/4.4/bits/algorithmfwd.h \
+ /usr/include/c++/4.4/bits/stl_heap.h \
+ /usr/include/c++/4.4/bits/stl_tempbuf.h ../include/global.h \
+ ../include/constants.h ../include/options.h /usr/include/c++/4.4/cstring \
+ ../include/constraints.h
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/bits/stdlib.h:
+
+/usr/include/string.h:
+
+/usr/include/bits/string3.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/bits/stdio2.h:
+
+/usr/include/c++/4.4/iostream:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+
+/usr/include/c++/4.4/ostream:
+
+/usr/include/c++/4.4/ios:
+
+/usr/include/c++/4.4/iosfwd:
+
+/usr/include/c++/4.4/bits/stringfwd.h:
+
+/usr/include/c++/4.4/bits/postypes.h:
+
+/usr/include/c++/4.4/cwchar:
+
+/usr/include/c++/4.4/cstddef:
+
+/usr/include/bits/wchar.h:
+
+/usr/include/bits/wchar2.h:
+
+/usr/include/c++/4.4/exception:
+
+/usr/include/c++/4.4/bits/char_traits.h:
+
+/usr/include/c++/4.4/bits/stl_algobase.h:
+
+/usr/include/c++/4.4/bits/functexcept.h:
+
+/usr/include/c++/4.4/exception_defines.h:
+
+/usr/include/c++/4.4/bits/cpp_type_traits.h:
+
+/usr/include/c++/4.4/ext/type_traits.h:
+
+/usr/include/c++/4.4/ext/numeric_traits.h:
+
+/usr/include/c++/4.4/bits/stl_pair.h:
+
+/usr/include/c++/4.4/bits/move.h:
+
+/usr/include/c++/4.4/bits/concept_check.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+
+/usr/include/c++/4.4/bits/stl_iterator.h:
+
+/usr/include/c++/4.4/debug/debug.h:
+
+/usr/include/c++/4.4/bits/localefwd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+
+/usr/include/c++/4.4/clocale:
+
+/usr/include/locale.h:
+
+/usr/include/bits/locale.h:
+
+/usr/include/c++/4.4/cctype:
+
+/usr/include/ctype.h:
+
+/usr/include/c++/4.4/bits/ios_base.h:
+
+/usr/include/c++/4.4/ext/atomicity.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+
+/usr/include/pthread.h:
+
+/usr/include/sched.h:
+
+/usr/include/bits/sched.h:
+
+/usr/include/signal.h:
+
+/usr/include/bits/setjmp.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+/usr/include/bits/unistd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+
+/usr/include/c++/4.4/bits/locale_classes.h:
+
+/usr/include/c++/4.4/string:
+
+/usr/include/c++/4.4/bits/allocator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+
+/usr/include/c++/4.4/ext/new_allocator.h:
+
+/usr/include/c++/4.4/new:
+
+/usr/include/c++/4.4/bits/ostream_insert.h:
+
+/usr/include/c++/4.4/cxxabi-forced.h:
+
+/usr/include/c++/4.4/bits/stl_function.h:
+
+/usr/include/c++/4.4/backward/binders.h:
+
+/usr/include/c++/4.4/bits/basic_string.h:
+
+/usr/include/c++/4.4/initializer_list:
+
+/usr/include/c++/4.4/bits/basic_string.tcc:
+
+/usr/include/c++/4.4/bits/locale_classes.tcc:
+
+/usr/include/c++/4.4/streambuf:
+
+/usr/include/c++/4.4/bits/streambuf.tcc:
+
+/usr/include/c++/4.4/bits/basic_ios.h:
+
+/usr/include/c++/4.4/bits/locale_facets.h:
+
+/usr/include/c++/4.4/cwctype:
+
+/usr/include/wctype.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h:
+
+/usr/include/c++/4.4/bits/streambuf_iterator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h:
+
+/usr/include/c++/4.4/bits/locale_facets.tcc:
+
+/usr/include/c++/4.4/bits/basic_ios.tcc:
+
+/usr/include/c++/4.4/bits/ostream.tcc:
+
+/usr/include/c++/4.4/istream:
+
+/usr/include/c++/4.4/bits/istream.tcc:
+
+/usr/include/c++/4.4/fstream:
+
+/usr/include/c++/4.4/bits/codecvt.h:
+
+/usr/include/c++/4.4/cstdio:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h:
+
+/usr/include/c++/4.4/bits/fstream.tcc:
+
+/usr/include/c++/4.4/vector:
+
+/usr/include/c++/4.4/bits/stl_construct.h:
+
+/usr/include/c++/4.4/bits/stl_uninitialized.h:
+
+/usr/include/c++/4.4/bits/stl_vector.h:
+
+/usr/include/c++/4.4/bits/stl_bvector.h:
+
+/usr/include/c++/4.4/bits/vector.tcc:
+
+/usr/include/c++/4.4/algorithm:
+
+/usr/include/c++/4.4/bits/stl_algo.h:
+
+/usr/include/c++/4.4/cstdlib:
+
+/usr/include/c++/4.4/bits/algorithmfwd.h:
+
+/usr/include/c++/4.4/bits/stl_heap.h:
+
+/usr/include/c++/4.4/bits/stl_tempbuf.h:
+
+../include/global.h:
+
+../include/constants.h:
+
+../include/options.h:
+
+/usr/include/c++/4.4/cstring:
+
+../include/constraints.h:
diff --git a/gtfold-mfe/src/.deps/energy.Po b/gtfold-mfe/src/.deps/energy.Po
new file mode 100644
index 0000000..7c1467f
--- /dev/null
+++ b/gtfold-mfe/src/.deps/energy.Po
@@ -0,0 +1,116 @@
+energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \
+ /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/sys/types.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/time.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/stdio.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ ../include/energy.h ../include/data.h ../include/constants.h \
+ ../include/utils.h ../include/global.h ../include/constants.h
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/bits/stdlib.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/bits/stdio2.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+../include/energy.h:
+
+../include/data.h:
+
+../include/constants.h:
+
+../include/utils.h:
+
+../include/global.h:
+
+../include/constants.h:
diff --git a/gtfold-mfe/src/.deps/global.Po b/gtfold-mfe/src/.deps/global.Po
new file mode 100644
index 0000000..e2d1748
--- /dev/null
+++ b/gtfold-mfe/src/.deps/global.Po
@@ -0,0 +1,85 @@
+global.o: global.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
+ /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/bits/stdlib.h ../include/global.h ../include/constants.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/bits/stdio2.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/bits/stdlib.h:
+
+../include/global.h:
+
+../include/constants.h:
diff --git a/gtfold-mfe/src/.deps/loader.Po b/gtfold-mfe/src/.deps/loader.Po
new file mode 100644
index 0000000..290868e
--- /dev/null
+++ b/gtfold-mfe/src/.deps/loader.Po
@@ -0,0 +1,367 @@
+loader.o: loader.cc /usr/include/c++/4.4/iostream \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+ /usr/include/features.h /usr/include/bits/predefs.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \
+ /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \
+ /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \
+ /usr/include/c++/4.4/cstddef \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \
+ /usr/include/c++/4.4/bits/char_traits.h \
+ /usr/include/c++/4.4/bits/stl_algobase.h \
+ /usr/include/c++/4.4/bits/functexcept.h \
+ /usr/include/c++/4.4/exception_defines.h \
+ /usr/include/c++/4.4/bits/cpp_type_traits.h \
+ /usr/include/c++/4.4/ext/type_traits.h \
+ /usr/include/c++/4.4/ext/numeric_traits.h \
+ /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
+ /usr/include/c++/4.4/bits/concept_check.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.4/bits/stl_iterator.h \
+ /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.4/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/c++/4.4/bits/ios_base.h \
+ /usr/include/c++/4.4/ext/atomicity.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
+ /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/bits/setjmp.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h \
+ /usr/include/bits/unistd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \
+ /usr/include/c++/4.4/bits/allocator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
+ /usr/include/c++/4.4/bits/ostream_insert.h \
+ /usr/include/c++/4.4/cxxabi-forced.h \
+ /usr/include/c++/4.4/bits/stl_function.h \
+ /usr/include/c++/4.4/backward/binders.h \
+ /usr/include/c++/4.4/bits/basic_string.h \
+ /usr/include/c++/4.4/initializer_list \
+ /usr/include/c++/4.4/bits/basic_string.tcc \
+ /usr/include/c++/4.4/bits/locale_classes.tcc \
+ /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \
+ /usr/include/c++/4.4/bits/basic_ios.h \
+ /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \
+ /usr/include/c++/4.4/bits/streambuf_iterator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \
+ /usr/include/c++/4.4/bits/locale_facets.tcc \
+ /usr/include/c++/4.4/bits/basic_ios.tcc \
+ /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \
+ /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \
+ /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \
+ /usr/include/c++/4.4/bits/fstream.tcc /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/c++/4.4/cstring /usr/include/string.h \
+ /usr/include/bits/string3.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/bits/stdlib.h ../include/data.h \
+ ../include/constants.h ../include/utils.h ../include/constants.h \
+ ../include/global.h ../include/loader.h ../include/data.h
+
+/usr/include/c++/4.4/iostream:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+
+/usr/include/c++/4.4/ostream:
+
+/usr/include/c++/4.4/ios:
+
+/usr/include/c++/4.4/iosfwd:
+
+/usr/include/c++/4.4/bits/stringfwd.h:
+
+/usr/include/c++/4.4/bits/postypes.h:
+
+/usr/include/c++/4.4/cwchar:
+
+/usr/include/c++/4.4/cstddef:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/wchar.h:
+
+/usr/include/stdio.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/wchar.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/wchar2.h:
+
+/usr/include/c++/4.4/exception:
+
+/usr/include/c++/4.4/bits/char_traits.h:
+
+/usr/include/c++/4.4/bits/stl_algobase.h:
+
+/usr/include/c++/4.4/bits/functexcept.h:
+
+/usr/include/c++/4.4/exception_defines.h:
+
+/usr/include/c++/4.4/bits/cpp_type_traits.h:
+
+/usr/include/c++/4.4/ext/type_traits.h:
+
+/usr/include/c++/4.4/ext/numeric_traits.h:
+
+/usr/include/c++/4.4/bits/stl_pair.h:
+
+/usr/include/c++/4.4/bits/move.h:
+
+/usr/include/c++/4.4/bits/concept_check.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+
+/usr/include/c++/4.4/bits/stl_iterator.h:
+
+/usr/include/c++/4.4/debug/debug.h:
+
+/usr/include/c++/4.4/bits/localefwd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+
+/usr/include/c++/4.4/clocale:
+
+/usr/include/locale.h:
+
+/usr/include/bits/locale.h:
+
+/usr/include/c++/4.4/cctype:
+
+/usr/include/ctype.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/c++/4.4/bits/ios_base.h:
+
+/usr/include/c++/4.4/ext/atomicity.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+
+/usr/include/pthread.h:
+
+/usr/include/sched.h:
+
+/usr/include/time.h:
+
+/usr/include/bits/sched.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/signal.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/bits/setjmp.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+/usr/include/bits/unistd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+
+/usr/include/c++/4.4/bits/locale_classes.h:
+
+/usr/include/c++/4.4/string:
+
+/usr/include/c++/4.4/bits/allocator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+
+/usr/include/c++/4.4/ext/new_allocator.h:
+
+/usr/include/c++/4.4/new:
+
+/usr/include/c++/4.4/bits/ostream_insert.h:
+
+/usr/include/c++/4.4/cxxabi-forced.h:
+
+/usr/include/c++/4.4/bits/stl_function.h:
+
+/usr/include/c++/4.4/backward/binders.h:
+
+/usr/include/c++/4.4/bits/basic_string.h:
+
+/usr/include/c++/4.4/initializer_list:
+
+/usr/include/c++/4.4/bits/basic_string.tcc:
+
+/usr/include/c++/4.4/bits/locale_classes.tcc:
+
+/usr/include/c++/4.4/streambuf:
+
+/usr/include/c++/4.4/bits/streambuf.tcc:
+
+/usr/include/c++/4.4/bits/basic_ios.h:
+
+/usr/include/c++/4.4/bits/locale_facets.h:
+
+/usr/include/c++/4.4/cwctype:
+
+/usr/include/wctype.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h:
+
+/usr/include/c++/4.4/bits/streambuf_iterator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h:
+
+/usr/include/c++/4.4/bits/locale_facets.tcc:
+
+/usr/include/c++/4.4/bits/basic_ios.tcc:
+
+/usr/include/c++/4.4/bits/ostream.tcc:
+
+/usr/include/c++/4.4/istream:
+
+/usr/include/c++/4.4/bits/istream.tcc:
+
+/usr/include/c++/4.4/fstream:
+
+/usr/include/c++/4.4/bits/codecvt.h:
+
+/usr/include/c++/4.4/cstdio:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/bits/stdio2.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h:
+
+/usr/include/c++/4.4/bits/fstream.tcc:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/c++/4.4/cstring:
+
+/usr/include/string.h:
+
+/usr/include/bits/string3.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/alloca.h:
+
+/usr/include/bits/stdlib.h:
+
+../include/data.h:
+
+../include/constants.h:
+
+../include/utils.h:
+
+../include/constants.h:
+
+../include/global.h:
+
+../include/loader.h:
+
+../include/data.h:
diff --git a/gtfold-mfe/src/.deps/main.Po b/gtfold-mfe/src/.deps/main.Po
new file mode 100644
index 0000000..df8b6af
--- /dev/null
+++ b/gtfold-mfe/src/.deps/main.Po
@@ -0,0 +1,437 @@
+main.o: main.cc /usr/include/c++/4.4/iostream \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+ /usr/include/features.h /usr/include/bits/predefs.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \
+ /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \
+ /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \
+ /usr/include/c++/4.4/cstddef \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \
+ /usr/include/c++/4.4/bits/char_traits.h \
+ /usr/include/c++/4.4/bits/stl_algobase.h \
+ /usr/include/c++/4.4/bits/functexcept.h \
+ /usr/include/c++/4.4/exception_defines.h \
+ /usr/include/c++/4.4/bits/cpp_type_traits.h \
+ /usr/include/c++/4.4/ext/type_traits.h \
+ /usr/include/c++/4.4/ext/numeric_traits.h \
+ /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
+ /usr/include/c++/4.4/bits/concept_check.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.4/bits/stl_iterator.h \
+ /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.4/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/c++/4.4/bits/ios_base.h \
+ /usr/include/c++/4.4/ext/atomicity.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
+ /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/bits/setjmp.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h \
+ /usr/include/bits/unistd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \
+ /usr/include/c++/4.4/bits/allocator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
+ /usr/include/c++/4.4/bits/ostream_insert.h \
+ /usr/include/c++/4.4/cxxabi-forced.h \
+ /usr/include/c++/4.4/bits/stl_function.h \
+ /usr/include/c++/4.4/backward/binders.h \
+ /usr/include/c++/4.4/bits/basic_string.h \
+ /usr/include/c++/4.4/initializer_list \
+ /usr/include/c++/4.4/bits/basic_string.tcc \
+ /usr/include/c++/4.4/bits/locale_classes.tcc \
+ /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \
+ /usr/include/c++/4.4/bits/basic_ios.h \
+ /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \
+ /usr/include/c++/4.4/bits/streambuf_iterator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \
+ /usr/include/c++/4.4/bits/locale_facets.tcc \
+ /usr/include/c++/4.4/bits/basic_ios.tcc \
+ /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \
+ /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/iomanip \
+ /usr/include/c++/4.4/fstream /usr/include/c++/4.4/bits/codecvt.h \
+ /usr/include/c++/4.4/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \
+ /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
+ /usr/include/bits/stdio2.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \
+ /usr/include/c++/4.4/bits/fstream.tcc /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/sys/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/c++/4.4/sstream \
+ /usr/include/c++/4.4/bits/sstream.tcc /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/string.h \
+ /usr/include/bits/string3.h ../include/main.h \
+ /usr/include/c++/4.4/vector /usr/include/c++/4.4/bits/stl_construct.h \
+ /usr/include/c++/4.4/bits/stl_uninitialized.h \
+ /usr/include/c++/4.4/bits/stl_vector.h \
+ /usr/include/c++/4.4/bits/stl_bvector.h \
+ /usr/include/c++/4.4/bits/vector.tcc ../include/constants.h \
+ ../include/utils.h ../include/loader.h ../include/data.h \
+ ../include/options.h /usr/include/c++/4.4/cstring ../include/global.h \
+ ../include/energy.h ../include/algorithms.h ../include/constraints.h \
+ ../include/traceback.h ../include/subopt_traceback.h \
+ /usr/include/c++/4.4/cassert /usr/include/assert.h \
+ /usr/include/c++/4.4/stack /usr/include/c++/4.4/deque \
+ /usr/include/c++/4.4/bits/stl_deque.h \
+ /usr/include/c++/4.4/bits/deque.tcc \
+ /usr/include/c++/4.4/bits/stl_stack.h /usr/include/c++/4.4/map \
+ /usr/include/c++/4.4/bits/stl_tree.h /usr/include/c++/4.4/bits/stl_map.h \
+ /usr/include/c++/4.4/bits/stl_multimap.h ../include/shapereader.h
+
+/usr/include/c++/4.4/iostream:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+
+/usr/include/c++/4.4/ostream:
+
+/usr/include/c++/4.4/ios:
+
+/usr/include/c++/4.4/iosfwd:
+
+/usr/include/c++/4.4/bits/stringfwd.h:
+
+/usr/include/c++/4.4/bits/postypes.h:
+
+/usr/include/c++/4.4/cwchar:
+
+/usr/include/c++/4.4/cstddef:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/wchar.h:
+
+/usr/include/stdio.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/wchar.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/wchar2.h:
+
+/usr/include/c++/4.4/exception:
+
+/usr/include/c++/4.4/bits/char_traits.h:
+
+/usr/include/c++/4.4/bits/stl_algobase.h:
+
+/usr/include/c++/4.4/bits/functexcept.h:
+
+/usr/include/c++/4.4/exception_defines.h:
+
+/usr/include/c++/4.4/bits/cpp_type_traits.h:
+
+/usr/include/c++/4.4/ext/type_traits.h:
+
+/usr/include/c++/4.4/ext/numeric_traits.h:
+
+/usr/include/c++/4.4/bits/stl_pair.h:
+
+/usr/include/c++/4.4/bits/move.h:
+
+/usr/include/c++/4.4/bits/concept_check.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+
+/usr/include/c++/4.4/bits/stl_iterator.h:
+
+/usr/include/c++/4.4/debug/debug.h:
+
+/usr/include/c++/4.4/bits/localefwd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+
+/usr/include/c++/4.4/clocale:
+
+/usr/include/locale.h:
+
+/usr/include/bits/locale.h:
+
+/usr/include/c++/4.4/cctype:
+
+/usr/include/ctype.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/c++/4.4/bits/ios_base.h:
+
+/usr/include/c++/4.4/ext/atomicity.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+
+/usr/include/pthread.h:
+
+/usr/include/sched.h:
+
+/usr/include/time.h:
+
+/usr/include/bits/sched.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/signal.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/bits/setjmp.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+/usr/include/bits/unistd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+
+/usr/include/c++/4.4/bits/locale_classes.h:
+
+/usr/include/c++/4.4/string:
+
+/usr/include/c++/4.4/bits/allocator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+
+/usr/include/c++/4.4/ext/new_allocator.h:
+
+/usr/include/c++/4.4/new:
+
+/usr/include/c++/4.4/bits/ostream_insert.h:
+
+/usr/include/c++/4.4/cxxabi-forced.h:
+
+/usr/include/c++/4.4/bits/stl_function.h:
+
+/usr/include/c++/4.4/backward/binders.h:
+
+/usr/include/c++/4.4/bits/basic_string.h:
+
+/usr/include/c++/4.4/initializer_list:
+
+/usr/include/c++/4.4/bits/basic_string.tcc:
+
+/usr/include/c++/4.4/bits/locale_classes.tcc:
+
+/usr/include/c++/4.4/streambuf:
+
+/usr/include/c++/4.4/bits/streambuf.tcc:
+
+/usr/include/c++/4.4/bits/basic_ios.h:
+
+/usr/include/c++/4.4/bits/locale_facets.h:
+
+/usr/include/c++/4.4/cwctype:
+
+/usr/include/wctype.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h:
+
+/usr/include/c++/4.4/bits/streambuf_iterator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h:
+
+/usr/include/c++/4.4/bits/locale_facets.tcc:
+
+/usr/include/c++/4.4/bits/basic_ios.tcc:
+
+/usr/include/c++/4.4/bits/ostream.tcc:
+
+/usr/include/c++/4.4/istream:
+
+/usr/include/c++/4.4/bits/istream.tcc:
+
+/usr/include/c++/4.4/iomanip:
+
+/usr/include/c++/4.4/fstream:
+
+/usr/include/c++/4.4/bits/codecvt.h:
+
+/usr/include/c++/4.4/cstdio:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/bits/stdio2.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h:
+
+/usr/include/c++/4.4/bits/fstream.tcc:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/sys/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/c++/4.4/sstream:
+
+/usr/include/c++/4.4/bits/sstream.tcc:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/alloca.h:
+
+/usr/include/bits/stdlib.h:
+
+/usr/include/string.h:
+
+/usr/include/bits/string3.h:
+
+../include/main.h:
+
+/usr/include/c++/4.4/vector:
+
+/usr/include/c++/4.4/bits/stl_construct.h:
+
+/usr/include/c++/4.4/bits/stl_uninitialized.h:
+
+/usr/include/c++/4.4/bits/stl_vector.h:
+
+/usr/include/c++/4.4/bits/stl_bvector.h:
+
+/usr/include/c++/4.4/bits/vector.tcc:
+
+../include/constants.h:
+
+../include/utils.h:
+
+../include/loader.h:
+
+../include/data.h:
+
+../include/options.h:
+
+/usr/include/c++/4.4/cstring:
+
+../include/global.h:
+
+../include/energy.h:
+
+../include/algorithms.h:
+
+../include/constraints.h:
+
+../include/traceback.h:
+
+../include/subopt_traceback.h:
+
+/usr/include/c++/4.4/cassert:
+
+/usr/include/assert.h:
+
+/usr/include/c++/4.4/stack:
+
+/usr/include/c++/4.4/deque:
+
+/usr/include/c++/4.4/bits/stl_deque.h:
+
+/usr/include/c++/4.4/bits/deque.tcc:
+
+/usr/include/c++/4.4/bits/stl_stack.h:
+
+/usr/include/c++/4.4/map:
+
+/usr/include/c++/4.4/bits/stl_tree.h:
+
+/usr/include/c++/4.4/bits/stl_map.h:
+
+/usr/include/c++/4.4/bits/stl_multimap.h:
+
+../include/shapereader.h:
diff --git a/gtfold-mfe/src/.deps/options.Po b/gtfold-mfe/src/.deps/options.Po
new file mode 100644
index 0000000..52acdb4
--- /dev/null
+++ b/gtfold-mfe/src/.deps/options.Po
@@ -0,0 +1,265 @@
+options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+ /usr/include/features.h /usr/include/bits/predefs.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.4/bits/stringfwd.h \
+ /usr/include/c++/4.4/bits/char_traits.h \
+ /usr/include/c++/4.4/bits/stl_algobase.h /usr/include/c++/4.4/cstddef \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/c++/4.4/bits/functexcept.h \
+ /usr/include/c++/4.4/exception_defines.h \
+ /usr/include/c++/4.4/bits/cpp_type_traits.h \
+ /usr/include/c++/4.4/ext/type_traits.h \
+ /usr/include/c++/4.4/ext/numeric_traits.h \
+ /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
+ /usr/include/c++/4.4/bits/concept_check.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.4/bits/stl_iterator.h \
+ /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/postypes.h \
+ /usr/include/c++/4.4/cwchar /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.4/bits/allocator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
+ /usr/include/c++/4.4/exception /usr/include/c++/4.4/bits/localefwd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.4/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.4/iosfwd \
+ /usr/include/c++/4.4/cctype /usr/include/ctype.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ostream_insert.h \
+ /usr/include/c++/4.4/cxxabi-forced.h \
+ /usr/include/c++/4.4/bits/stl_function.h \
+ /usr/include/c++/4.4/backward/binders.h \
+ /usr/include/c++/4.4/bits/basic_string.h \
+ /usr/include/c++/4.4/ext/atomicity.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
+ /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/bits/setjmp.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h \
+ /usr/include/bits/unistd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.4/initializer_list \
+ /usr/include/c++/4.4/bits/basic_string.tcc ../include/constants.h \
+ ../include/data.h ../include/options.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/bits/stdlib.h \
+ /usr/include/c++/4.4/cstring /usr/include/string.h \
+ /usr/include/bits/string3.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \
+ /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
+ /usr/include/bits/stdio2.h
+
+../include/loader.h:
+
+/usr/include/c++/4.4/string:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+
+/usr/include/c++/4.4/bits/stringfwd.h:
+
+/usr/include/c++/4.4/bits/char_traits.h:
+
+/usr/include/c++/4.4/bits/stl_algobase.h:
+
+/usr/include/c++/4.4/cstddef:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/c++/4.4/bits/functexcept.h:
+
+/usr/include/c++/4.4/exception_defines.h:
+
+/usr/include/c++/4.4/bits/cpp_type_traits.h:
+
+/usr/include/c++/4.4/ext/type_traits.h:
+
+/usr/include/c++/4.4/ext/numeric_traits.h:
+
+/usr/include/c++/4.4/bits/stl_pair.h:
+
+/usr/include/c++/4.4/bits/move.h:
+
+/usr/include/c++/4.4/bits/concept_check.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+
+/usr/include/c++/4.4/bits/stl_iterator.h:
+
+/usr/include/c++/4.4/debug/debug.h:
+
+/usr/include/c++/4.4/bits/postypes.h:
+
+/usr/include/c++/4.4/cwchar:
+
+/usr/include/wchar.h:
+
+/usr/include/stdio.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/wchar.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/wchar2.h:
+
+/usr/include/c++/4.4/bits/allocator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+
+/usr/include/c++/4.4/ext/new_allocator.h:
+
+/usr/include/c++/4.4/new:
+
+/usr/include/c++/4.4/exception:
+
+/usr/include/c++/4.4/bits/localefwd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+
+/usr/include/c++/4.4/clocale:
+
+/usr/include/locale.h:
+
+/usr/include/bits/locale.h:
+
+/usr/include/c++/4.4/iosfwd:
+
+/usr/include/c++/4.4/cctype:
+
+/usr/include/ctype.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/c++/4.4/bits/ostream_insert.h:
+
+/usr/include/c++/4.4/cxxabi-forced.h:
+
+/usr/include/c++/4.4/bits/stl_function.h:
+
+/usr/include/c++/4.4/backward/binders.h:
+
+/usr/include/c++/4.4/bits/basic_string.h:
+
+/usr/include/c++/4.4/ext/atomicity.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+
+/usr/include/pthread.h:
+
+/usr/include/sched.h:
+
+/usr/include/time.h:
+
+/usr/include/bits/sched.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/signal.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/bits/setjmp.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+/usr/include/bits/unistd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+
+/usr/include/c++/4.4/initializer_list:
+
+/usr/include/c++/4.4/bits/basic_string.tcc:
+
+../include/constants.h:
+
+../include/data.h:
+
+../include/options.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/alloca.h:
+
+/usr/include/bits/stdlib.h:
+
+/usr/include/c++/4.4/cstring:
+
+/usr/include/string.h:
+
+/usr/include/bits/string3.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/bits/stdio2.h:
diff --git a/gtfold-mfe/src/.deps/shapereader.Po b/gtfold-mfe/src/.deps/shapereader.Po
new file mode 100644
index 0000000..4c5d9af
--- /dev/null
+++ b/gtfold-mfe/src/.deps/shapereader.Po
@@ -0,0 +1,360 @@
+shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+ /usr/include/features.h /usr/include/bits/predefs.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \
+ /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \
+ /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \
+ /usr/include/c++/4.4/cstddef \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \
+ /usr/include/c++/4.4/bits/char_traits.h \
+ /usr/include/c++/4.4/bits/stl_algobase.h \
+ /usr/include/c++/4.4/bits/functexcept.h \
+ /usr/include/c++/4.4/exception_defines.h \
+ /usr/include/c++/4.4/bits/cpp_type_traits.h \
+ /usr/include/c++/4.4/ext/type_traits.h \
+ /usr/include/c++/4.4/ext/numeric_traits.h \
+ /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
+ /usr/include/c++/4.4/bits/concept_check.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.4/bits/stl_iterator.h \
+ /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.4/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/c++/4.4/bits/ios_base.h \
+ /usr/include/c++/4.4/ext/atomicity.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
+ /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/bits/setjmp.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h \
+ /usr/include/bits/unistd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \
+ /usr/include/c++/4.4/bits/allocator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
+ /usr/include/c++/4.4/bits/ostream_insert.h \
+ /usr/include/c++/4.4/cxxabi-forced.h \
+ /usr/include/c++/4.4/bits/stl_function.h \
+ /usr/include/c++/4.4/backward/binders.h \
+ /usr/include/c++/4.4/bits/basic_string.h \
+ /usr/include/c++/4.4/initializer_list \
+ /usr/include/c++/4.4/bits/basic_string.tcc \
+ /usr/include/c++/4.4/bits/locale_classes.tcc \
+ /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \
+ /usr/include/c++/4.4/bits/basic_ios.h \
+ /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \
+ /usr/include/c++/4.4/bits/streambuf_iterator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \
+ /usr/include/c++/4.4/bits/locale_facets.tcc \
+ /usr/include/c++/4.4/bits/basic_ios.tcc \
+ /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \
+ /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \
+ /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \
+ /usr/include/c++/4.4/bits/fstream.tcc /usr/include/string.h \
+ /usr/include/bits/string3.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ ../include/shapereader.h ../include/global.h ../include/constants.h \
+ ../include/options.h /usr/include/c++/4.4/cstring
+
+/usr/include/c++/4.4/iostream:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+
+/usr/include/c++/4.4/ostream:
+
+/usr/include/c++/4.4/ios:
+
+/usr/include/c++/4.4/iosfwd:
+
+/usr/include/c++/4.4/bits/stringfwd.h:
+
+/usr/include/c++/4.4/bits/postypes.h:
+
+/usr/include/c++/4.4/cwchar:
+
+/usr/include/c++/4.4/cstddef:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/wchar.h:
+
+/usr/include/stdio.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/wchar.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/wchar2.h:
+
+/usr/include/c++/4.4/exception:
+
+/usr/include/c++/4.4/bits/char_traits.h:
+
+/usr/include/c++/4.4/bits/stl_algobase.h:
+
+/usr/include/c++/4.4/bits/functexcept.h:
+
+/usr/include/c++/4.4/exception_defines.h:
+
+/usr/include/c++/4.4/bits/cpp_type_traits.h:
+
+/usr/include/c++/4.4/ext/type_traits.h:
+
+/usr/include/c++/4.4/ext/numeric_traits.h:
+
+/usr/include/c++/4.4/bits/stl_pair.h:
+
+/usr/include/c++/4.4/bits/move.h:
+
+/usr/include/c++/4.4/bits/concept_check.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+
+/usr/include/c++/4.4/bits/stl_iterator.h:
+
+/usr/include/c++/4.4/debug/debug.h:
+
+/usr/include/c++/4.4/bits/localefwd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+
+/usr/include/c++/4.4/clocale:
+
+/usr/include/locale.h:
+
+/usr/include/bits/locale.h:
+
+/usr/include/c++/4.4/cctype:
+
+/usr/include/ctype.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/c++/4.4/bits/ios_base.h:
+
+/usr/include/c++/4.4/ext/atomicity.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+
+/usr/include/pthread.h:
+
+/usr/include/sched.h:
+
+/usr/include/time.h:
+
+/usr/include/bits/sched.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/signal.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/bits/setjmp.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+/usr/include/bits/unistd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+
+/usr/include/c++/4.4/bits/locale_classes.h:
+
+/usr/include/c++/4.4/string:
+
+/usr/include/c++/4.4/bits/allocator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+
+/usr/include/c++/4.4/ext/new_allocator.h:
+
+/usr/include/c++/4.4/new:
+
+/usr/include/c++/4.4/bits/ostream_insert.h:
+
+/usr/include/c++/4.4/cxxabi-forced.h:
+
+/usr/include/c++/4.4/bits/stl_function.h:
+
+/usr/include/c++/4.4/backward/binders.h:
+
+/usr/include/c++/4.4/bits/basic_string.h:
+
+/usr/include/c++/4.4/initializer_list:
+
+/usr/include/c++/4.4/bits/basic_string.tcc:
+
+/usr/include/c++/4.4/bits/locale_classes.tcc:
+
+/usr/include/c++/4.4/streambuf:
+
+/usr/include/c++/4.4/bits/streambuf.tcc:
+
+/usr/include/c++/4.4/bits/basic_ios.h:
+
+/usr/include/c++/4.4/bits/locale_facets.h:
+
+/usr/include/c++/4.4/cwctype:
+
+/usr/include/wctype.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h:
+
+/usr/include/c++/4.4/bits/streambuf_iterator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h:
+
+/usr/include/c++/4.4/bits/locale_facets.tcc:
+
+/usr/include/c++/4.4/bits/basic_ios.tcc:
+
+/usr/include/c++/4.4/bits/ostream.tcc:
+
+/usr/include/c++/4.4/istream:
+
+/usr/include/c++/4.4/bits/istream.tcc:
+
+/usr/include/c++/4.4/fstream:
+
+/usr/include/c++/4.4/bits/codecvt.h:
+
+/usr/include/c++/4.4/cstdio:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/bits/stdio2.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h:
+
+/usr/include/c++/4.4/bits/fstream.tcc:
+
+/usr/include/string.h:
+
+/usr/include/bits/string3.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/alloca.h:
+
+/usr/include/bits/stdlib.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+../include/shapereader.h:
+
+../include/global.h:
+
+../include/constants.h:
+
+../include/options.h:
+
+/usr/include/c++/4.4/cstring:
diff --git a/gtfold-mfe/src/.deps/subopt_traceback.Po b/gtfold-mfe/src/.deps/subopt_traceback.Po
new file mode 100644
index 0000000..375a33e
--- /dev/null
+++ b/gtfold-mfe/src/.deps/subopt_traceback.Po
@@ -0,0 +1,351 @@
+subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+ /usr/include/features.h /usr/include/bits/predefs.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.4/cstddef \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/stdio.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
+ ../include/constants.h ../include/energy.h ../include/data.h \
+ ../include/constants.h ../include/utils.h ../include/global.h \
+ ../include/subopt_traceback.h /usr/include/c++/4.4/cassert \
+ /usr/include/assert.h /usr/include/c++/4.4/iostream \
+ /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \
+ /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \
+ /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \
+ /usr/include/c++/4.4/bits/char_traits.h \
+ /usr/include/c++/4.4/bits/stl_algobase.h \
+ /usr/include/c++/4.4/bits/functexcept.h \
+ /usr/include/c++/4.4/exception_defines.h \
+ /usr/include/c++/4.4/bits/cpp_type_traits.h \
+ /usr/include/c++/4.4/ext/type_traits.h \
+ /usr/include/c++/4.4/ext/numeric_traits.h \
+ /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
+ /usr/include/c++/4.4/bits/concept_check.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.4/bits/stl_iterator.h \
+ /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.4/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \
+ /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ios_base.h \
+ /usr/include/c++/4.4/ext/atomicity.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
+ /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/bits/setjmp.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h \
+ /usr/include/bits/unistd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \
+ /usr/include/c++/4.4/bits/allocator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
+ /usr/include/c++/4.4/bits/ostream_insert.h \
+ /usr/include/c++/4.4/cxxabi-forced.h \
+ /usr/include/c++/4.4/bits/stl_function.h \
+ /usr/include/c++/4.4/backward/binders.h \
+ /usr/include/c++/4.4/bits/basic_string.h \
+ /usr/include/c++/4.4/initializer_list \
+ /usr/include/c++/4.4/bits/basic_string.tcc \
+ /usr/include/c++/4.4/bits/locale_classes.tcc \
+ /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \
+ /usr/include/c++/4.4/bits/basic_ios.h \
+ /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \
+ /usr/include/wctype.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \
+ /usr/include/c++/4.4/bits/streambuf_iterator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \
+ /usr/include/c++/4.4/bits/locale_facets.tcc \
+ /usr/include/c++/4.4/bits/basic_ios.tcc \
+ /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \
+ /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/sstream \
+ /usr/include/c++/4.4/bits/sstream.tcc /usr/include/c++/4.4/stack \
+ /usr/include/c++/4.4/deque /usr/include/c++/4.4/bits/stl_construct.h \
+ /usr/include/c++/4.4/bits/stl_uninitialized.h \
+ /usr/include/c++/4.4/bits/stl_deque.h \
+ /usr/include/c++/4.4/bits/deque.tcc \
+ /usr/include/c++/4.4/bits/stl_stack.h /usr/include/c++/4.4/map \
+ /usr/include/c++/4.4/bits/stl_tree.h /usr/include/c++/4.4/bits/stl_map.h \
+ /usr/include/c++/4.4/bits/stl_multimap.h /usr/include/c++/4.4/vector \
+ /usr/include/c++/4.4/bits/stl_vector.h \
+ /usr/include/c++/4.4/bits/stl_bvector.h \
+ /usr/include/c++/4.4/bits/vector.tcc
+
+/usr/include/c++/4.4/cstdio:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+
+/usr/include/c++/4.4/cstddef:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/stdio.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/bits/stdio2.h:
+
+../include/constants.h:
+
+../include/energy.h:
+
+../include/data.h:
+
+../include/constants.h:
+
+../include/utils.h:
+
+../include/global.h:
+
+../include/subopt_traceback.h:
+
+/usr/include/c++/4.4/cassert:
+
+/usr/include/assert.h:
+
+/usr/include/c++/4.4/iostream:
+
+/usr/include/c++/4.4/ostream:
+
+/usr/include/c++/4.4/ios:
+
+/usr/include/c++/4.4/iosfwd:
+
+/usr/include/c++/4.4/bits/stringfwd.h:
+
+/usr/include/c++/4.4/bits/postypes.h:
+
+/usr/include/c++/4.4/cwchar:
+
+/usr/include/bits/wchar.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/wchar2.h:
+
+/usr/include/c++/4.4/exception:
+
+/usr/include/c++/4.4/bits/char_traits.h:
+
+/usr/include/c++/4.4/bits/stl_algobase.h:
+
+/usr/include/c++/4.4/bits/functexcept.h:
+
+/usr/include/c++/4.4/exception_defines.h:
+
+/usr/include/c++/4.4/bits/cpp_type_traits.h:
+
+/usr/include/c++/4.4/ext/type_traits.h:
+
+/usr/include/c++/4.4/ext/numeric_traits.h:
+
+/usr/include/c++/4.4/bits/stl_pair.h:
+
+/usr/include/c++/4.4/bits/move.h:
+
+/usr/include/c++/4.4/bits/concept_check.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+
+/usr/include/c++/4.4/bits/stl_iterator.h:
+
+/usr/include/c++/4.4/debug/debug.h:
+
+/usr/include/c++/4.4/bits/localefwd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+
+/usr/include/c++/4.4/clocale:
+
+/usr/include/locale.h:
+
+/usr/include/bits/locale.h:
+
+/usr/include/c++/4.4/cctype:
+
+/usr/include/ctype.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/c++/4.4/bits/ios_base.h:
+
+/usr/include/c++/4.4/ext/atomicity.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+
+/usr/include/pthread.h:
+
+/usr/include/sched.h:
+
+/usr/include/time.h:
+
+/usr/include/bits/sched.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/signal.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/bits/setjmp.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+/usr/include/bits/unistd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+
+/usr/include/c++/4.4/bits/locale_classes.h:
+
+/usr/include/c++/4.4/string:
+
+/usr/include/c++/4.4/bits/allocator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+
+/usr/include/c++/4.4/ext/new_allocator.h:
+
+/usr/include/c++/4.4/new:
+
+/usr/include/c++/4.4/bits/ostream_insert.h:
+
+/usr/include/c++/4.4/cxxabi-forced.h:
+
+/usr/include/c++/4.4/bits/stl_function.h:
+
+/usr/include/c++/4.4/backward/binders.h:
+
+/usr/include/c++/4.4/bits/basic_string.h:
+
+/usr/include/c++/4.4/initializer_list:
+
+/usr/include/c++/4.4/bits/basic_string.tcc:
+
+/usr/include/c++/4.4/bits/locale_classes.tcc:
+
+/usr/include/c++/4.4/streambuf:
+
+/usr/include/c++/4.4/bits/streambuf.tcc:
+
+/usr/include/c++/4.4/bits/basic_ios.h:
+
+/usr/include/c++/4.4/bits/locale_facets.h:
+
+/usr/include/c++/4.4/cwctype:
+
+/usr/include/wctype.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h:
+
+/usr/include/c++/4.4/bits/streambuf_iterator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h:
+
+/usr/include/c++/4.4/bits/locale_facets.tcc:
+
+/usr/include/c++/4.4/bits/basic_ios.tcc:
+
+/usr/include/c++/4.4/bits/ostream.tcc:
+
+/usr/include/c++/4.4/istream:
+
+/usr/include/c++/4.4/bits/istream.tcc:
+
+/usr/include/c++/4.4/sstream:
+
+/usr/include/c++/4.4/bits/sstream.tcc:
+
+/usr/include/c++/4.4/stack:
+
+/usr/include/c++/4.4/deque:
+
+/usr/include/c++/4.4/bits/stl_construct.h:
+
+/usr/include/c++/4.4/bits/stl_uninitialized.h:
+
+/usr/include/c++/4.4/bits/stl_deque.h:
+
+/usr/include/c++/4.4/bits/deque.tcc:
+
+/usr/include/c++/4.4/bits/stl_stack.h:
+
+/usr/include/c++/4.4/map:
+
+/usr/include/c++/4.4/bits/stl_tree.h:
+
+/usr/include/c++/4.4/bits/stl_map.h:
+
+/usr/include/c++/4.4/bits/stl_multimap.h:
+
+/usr/include/c++/4.4/vector:
+
+/usr/include/c++/4.4/bits/stl_vector.h:
+
+/usr/include/c++/4.4/bits/stl_bvector.h:
+
+/usr/include/c++/4.4/bits/vector.tcc:
diff --git a/gtfold-mfe/src/.deps/traceback.Po b/gtfold-mfe/src/.deps/traceback.Po
new file mode 100644
index 0000000..c8b0c87
--- /dev/null
+++ b/gtfold-mfe/src/.deps/traceback.Po
@@ -0,0 +1,127 @@
+traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
+ /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/bits/stdlib.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/assert.h ../include/data.h ../include/constants.h \
+ ../include/constants.h ../include/constraints.h ../include/energy.h \
+ ../include/data.h ../include/global.h ../include/traceback.h \
+ ../include/utils.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/bits/stdio2.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/bits/stdlib.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/assert.h:
+
+../include/data.h:
+
+../include/constants.h:
+
+../include/constants.h:
+
+../include/constraints.h:
+
+../include/energy.h:
+
+../include/data.h:
+
+../include/global.h:
+
+../include/traceback.h:
+
+../include/utils.h:
diff --git a/gtfold-mfe/src/.deps/utils.Po b/gtfold-mfe/src/.deps/utils.Po
new file mode 100644
index 0000000..61ad5ac
--- /dev/null
+++ b/gtfold-mfe/src/.deps/utils.Po
@@ -0,0 +1,222 @@
+utils.o: utils.cc ../include/utils.h ../include/constants.h \
+ /usr/include/string.h /usr/include/features.h \
+ /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/bits/string3.h \
+ /usr/include/c++/4.4/string \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.4/bits/stringfwd.h \
+ /usr/include/c++/4.4/bits/char_traits.h \
+ /usr/include/c++/4.4/bits/stl_algobase.h /usr/include/c++/4.4/cstddef \
+ /usr/include/c++/4.4/bits/functexcept.h \
+ /usr/include/c++/4.4/exception_defines.h \
+ /usr/include/c++/4.4/bits/cpp_type_traits.h \
+ /usr/include/c++/4.4/ext/type_traits.h \
+ /usr/include/c++/4.4/ext/numeric_traits.h \
+ /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
+ /usr/include/c++/4.4/bits/concept_check.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.4/bits/stl_iterator.h \
+ /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/postypes.h \
+ /usr/include/c++/4.4/cwchar /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/bits/wchar2.h \
+ /usr/include/c++/4.4/bits/allocator.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
+ /usr/include/c++/4.4/exception /usr/include/c++/4.4/bits/localefwd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.4/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.4/iosfwd \
+ /usr/include/c++/4.4/cctype /usr/include/ctype.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ostream_insert.h \
+ /usr/include/c++/4.4/cxxabi-forced.h \
+ /usr/include/c++/4.4/bits/stl_function.h \
+ /usr/include/c++/4.4/backward/binders.h \
+ /usr/include/c++/4.4/bits/basic_string.h \
+ /usr/include/c++/4.4/ext/atomicity.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
+ /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/bits/setjmp.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h \
+ /usr/include/bits/unistd.h \
+ /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.4/initializer_list \
+ /usr/include/c++/4.4/bits/basic_string.tcc
+
+../include/utils.h:
+
+../include/constants.h:
+
+/usr/include/string.h:
+
+/usr/include/features.h:
+
+/usr/include/bits/predefs.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string3.h:
+
+/usr/include/c++/4.4/string:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+
+/usr/include/c++/4.4/bits/stringfwd.h:
+
+/usr/include/c++/4.4/bits/char_traits.h:
+
+/usr/include/c++/4.4/bits/stl_algobase.h:
+
+/usr/include/c++/4.4/cstddef:
+
+/usr/include/c++/4.4/bits/functexcept.h:
+
+/usr/include/c++/4.4/exception_defines.h:
+
+/usr/include/c++/4.4/bits/cpp_type_traits.h:
+
+/usr/include/c++/4.4/ext/type_traits.h:
+
+/usr/include/c++/4.4/ext/numeric_traits.h:
+
+/usr/include/c++/4.4/bits/stl_pair.h:
+
+/usr/include/c++/4.4/bits/move.h:
+
+/usr/include/c++/4.4/bits/concept_check.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+
+/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+
+/usr/include/c++/4.4/bits/stl_iterator.h:
+
+/usr/include/c++/4.4/debug/debug.h:
+
+/usr/include/c++/4.4/bits/postypes.h:
+
+/usr/include/c++/4.4/cwchar:
+
+/usr/include/wchar.h:
+
+/usr/include/stdio.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+
+/usr/include/bits/wchar.h:
+
+/usr/include/bits/wchar2.h:
+
+/usr/include/c++/4.4/bits/allocator.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+
+/usr/include/c++/4.4/ext/new_allocator.h:
+
+/usr/include/c++/4.4/new:
+
+/usr/include/c++/4.4/exception:
+
+/usr/include/c++/4.4/bits/localefwd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+
+/usr/include/c++/4.4/clocale:
+
+/usr/include/locale.h:
+
+/usr/include/bits/locale.h:
+
+/usr/include/c++/4.4/iosfwd:
+
+/usr/include/c++/4.4/cctype:
+
+/usr/include/ctype.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/c++/4.4/bits/ostream_insert.h:
+
+/usr/include/c++/4.4/cxxabi-forced.h:
+
+/usr/include/c++/4.4/bits/stl_function.h:
+
+/usr/include/c++/4.4/backward/binders.h:
+
+/usr/include/c++/4.4/bits/basic_string.h:
+
+/usr/include/c++/4.4/ext/atomicity.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+
+/usr/include/pthread.h:
+
+/usr/include/sched.h:
+
+/usr/include/time.h:
+
+/usr/include/bits/sched.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/signal.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/bits/setjmp.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+/usr/include/bits/unistd.h:
+
+/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+
+/usr/include/c++/4.4/initializer_list:
+
+/usr/include/c++/4.4/bits/basic_string.tcc:
diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile
new file mode 100644
index 0000000..0f50f74
--- /dev/null
+++ b/gtfold-mfe/src/Makefile
@@ -0,0 +1,522 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# src/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+
+pkgdatadir = $(datadir)/gtfold
+pkgincludedir = $(includedir)/gtfold
+pkglibdir = $(libdir)/gtfold
+pkglibexecdir = $(libexecdir)/gtfold
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
+target_triplet = x86_64-unknown-linux-gnu
+bin_PROGRAMS = gtfold$(EXEEXT)
+subdir = src
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/gtfold_config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+am__installdirs = "$(DESTDIR)$(bindir)"
+PROGRAMS = $(bin_PROGRAMS)
+am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
+	options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \
+	energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \
+	subopt_traceback.$(OBJEXT) shapereader.$(OBJEXT)
+gtfold_OBJECTS = $(am_gtfold_OBJECTS)
+gtfold_DEPENDENCIES =
+gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
+	$(LDFLAGS) -o $@
+DEFAULT_INCLUDES = -I. -I$(top_builddir)
+depcomp = $(SHELL) $(top_srcdir)/depcomp
+am__depfiles_maybe = depfiles
+am__mv = mv -f
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+CXXLD = $(CXX)
+CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
+	-o $@
+SOURCES = $(gtfold_SOURCES)
+DIST_SOURCES = $(gtfold_SOURCES)
+ETAGS = etags
+CTAGS = ctags
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -g -O2 -Wall
+CPP = gcc -E
+CPPFLAGS = 
+CXX = g++
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2 -Wall
+CYGPATH_W = echo
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /bin/grep -E
+EXEEXT = 
+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = 
+LIBOBJS = 
+LIBS = -lgomp 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+PACKAGE = gtfold
+PACKAGE_BUGREPORT = 
+PACKAGE_NAME = gtfold
+PACKAGE_STRING = gtfold 1.18
+PACKAGE_TARNAME = gtfold
+PACKAGE_URL = 
+PACKAGE_VERSION = 1.18
+PATH_SEPARATOR = :
+SET_MAKE = 
+SHELL = /bin/bash
+STRIP = 
+VERSION = 1.18
+abs_builddir = /home/zs/git/gtfold/gtfold-mfe/src
+abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/src
+abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
+abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = ${AMTAR} chof - "$$tardir"
+am__untar = ${AMTAR} xf -
+bindir = ${exec_prefix}/bin
+build = x86_64-unknown-linux-gnu
+build_alias = 
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = unknown
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host = x86_64-unknown-linux-gnu
+host_alias = 
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = unknown
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /usr/local
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target = x86_64-unknown-linux-gnu
+target_alias = 
+target_cpu = x86_64
+target_os = linux-gnu
+target_vendor = unknown
+top_build_prefix = ../
+top_builddir = ..
+top_srcdir = ..
+INCLUDES = -I$(top_srcdir) -I$(top_srcdir)/include
+AM_CFLAGS = $(OPENMP_CFLAGS) -DDATADIR='$(datadir)/gtfold'
+AM_CXXFLAGS = -DDATADIR='$(datadir)/gtfold'
+gtfold_SOURCES = \
+	main.cc\
+	loader.cc\
+	utils.cc\
+	options.cc\
+	constraints.cc\
+	global.c\
+	energy.c\
+	algorithms.c \
+	traceback.c \
+	subopt_traceback.cc\
+	shapereader.cc
+
+gtfold_LDFLAGS = 
+gtfold_LDADD = -lm
+CLEANFILES = *~ *.o
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .c .cc .o .obj
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu src/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-binPROGRAMS: $(bin_PROGRAMS)
+	@$(NORMAL_INSTALL)
+	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+	for p in $$list; do echo "$$p $$p"; done | \
+	sed 's/$(EXEEXT)$$//' | \
+	while read p p1; do if test -f $$p; \
+	  then echo "$$p"; echo "$$p"; else :; fi; \
+	done | \
+	sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
+	sed 'N;N;N;s,\n, ,g' | \
+	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
+	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
+	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
+	    else { print "f", $$3 "/" $$4, $$1; } } \
+	  END { for (d in files) print "f", d, files[d] }' | \
+	while read type dir files; do \
+	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+	    test -z "$$files" || { \
+	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+	    } \
+	; done
+
+uninstall-binPROGRAMS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+	files=`for p in $$list; do echo "$$p"; done | \
+	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
+	      -e 's/$$/$(EXEEXT)/' `; \
+	test -n "$$list" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(bindir)" && rm -f $$files
+
+clean-binPROGRAMS:
+	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+gtfold$(EXEEXT): $(gtfold_OBJECTS) $(gtfold_DEPENDENCIES) 
+	@rm -f gtfold$(EXEEXT)
+	$(gtfold_LINK) $(gtfold_OBJECTS) $(gtfold_LDADD) $(LIBS)
+
+mostlyclean-compile:
+	-rm -f *.$(OBJEXT)
+
+distclean-compile:
+	-rm -f *.tab.c
+
+include ./$(DEPDIR)/algorithms.Po
+include ./$(DEPDIR)/constraints.Po
+include ./$(DEPDIR)/energy.Po
+include ./$(DEPDIR)/global.Po
+include ./$(DEPDIR)/loader.Po
+include ./$(DEPDIR)/main.Po
+include ./$(DEPDIR)/options.Po
+include ./$(DEPDIR)/shapereader.Po
+include ./$(DEPDIR)/subopt_traceback.Po
+include ./$(DEPDIR)/traceback.Po
+include ./$(DEPDIR)/utils.Po
+
+.c.o:
+	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+#	source='$<' object='$@' libtool=no \
+#	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
+#	$(COMPILE) -c $<
+
+.c.obj:
+	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+#	source='$<' object='$@' libtool=no \
+#	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
+#	$(COMPILE) -c `$(CYGPATH_W) '$<'`
+
+.cc.o:
+	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+#	source='$<' object='$@' libtool=no \
+#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
+#	$(CXXCOMPILE) -c -o $@ $<
+
+.cc.obj:
+	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+#	source='$<' object='$@' libtool=no \
+#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
+#	$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	mkid -fID $$unique
+tags: TAGS
+
+TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	set x; \
+	here=`pwd`; \
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
+	fi
+ctags: CTAGS
+CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(PROGRAMS)
+installdirs:
+	for dir in "$(DESTDIR)$(bindir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -rf ./$(DEPDIR)
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -rf ./$(DEPDIR)
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
+	clean-generic ctags distclean distclean-compile \
+	distclean-generic distclean-tags distdir dvi dvi-am html \
+	html-am info info-am install install-am install-binPROGRAMS \
+	install-data install-data-am install-dvi install-dvi-am \
+	install-exec install-exec-am install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-compile \
+	mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
+	uninstall-am uninstall-binPROGRAMS
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/gtfold-mfe/src/shapereader.cc b/gtfold-mfe/src/shapereader.cc
new file mode 100644
index 0000000..43083ab
--- /dev/null
+++ b/gtfold-mfe/src/shapereader.cc
@@ -0,0 +1,89 @@
+#include<iostream>
+#include<fstream>
+#include<string.h>
+#include<stdio.h>
+#include <stdlib.h>
+#include <math.h>
+
+#include "shapereader.h"
+#include "global.h"
+#include "options.h"
+
+using namespace std;
+
+double* SHAPEarray;
+int* SHAPEenergies;
+
+void free_shapeArray(int len){
+	free(SHAPEarray);
+}
+
+void print_shapeArray(int len){
+	for(int i=0; i<len; i++){
+		printf("SHAPE value for position %d: %f, energy contribution: %f kcal/mol \n", i, SHAPEarray[i], (double)SHAPEenergies[i]/100);
+	}
+
+}
+
+void readSHAPEarray(const char* filename, int seqlength){
+
+	ifstream infile(filename);
+	SHAPEarray = (double*)malloc(sizeof(double)*(seqlength+1));	
+	SHAPEenergies = (int*)malloc(sizeof(int)*(seqlength+1));
+
+	for(int i = 0; i<seqlength; i++){
+		SHAPEarray[i] = -999;	
+		SHAPEenergies[i] = 0;
+	}
+
+	string line;
+	int position;
+	double  SHAPEnumber;
+	
+	while(getline(infile,line)>0){
+		if(sscanf(line.c_str(), "%d %lf", &position, &SHAPEnumber)==2){
+			if(position < seqlength){
+				SHAPEarray[position] = SHAPEnumber;
+				SHAPEenergies[position] = calcShapeEnergy(SHAPEnumber);
+			}
+			else{
+				printf("Invalid SHAPE position indicator (ignoring line): %s\n", line.c_str()); 
+			}	
+		}else{
+			printf("Invalid line (ignoring): %s\n", line.c_str());
+		}
+	}
+
+}
+
+int getShapeEnergy(int position){
+	if(SHAPE_ENABLED){
+		return SHAPEenergies[position];
+	}	
+	else{
+		return 0;
+	}
+}
+
+int calcShapeEnergy(double shapeNumber){
+//ZS: This function returns the free energy contribution as an integer. 
+	if(shapeNumber<(double)0){
+		return 0;
+	}
+	else{
+		double energy = shapeModel(shapeNumber);
+		return (int)floor(100.0*energy+ .5);
+	}
+}
+
+
+double shapeModel(double SHAPE_value){
+//ZS: This function calculates the free energy contribution due to SHAPE. 
+	double m = 2.6;
+	double b = -0.8;
+	return m*log(SHAPE_value+1)+b;
+}
+
+
+
+

From de4982d3154a87ebbbfdd6c4146915c37fcba2ac Mon Sep 17 00:00:00 2001
From: dsokus <dsokus@gmail.com>
Date: Sat, 7 May 2011 20:07:52 -0400
Subject: [PATCH 111/282] Errors in thermodynamic paramters... commit long
 overdue!! (It is not clear what to do with the misc loop parameters.)

Signed-off-by: dsokus <dsokus@gmail.com>
---
 .../Turner04-errors/Turner04-errors/Makefile  | 405 ++++++++
 .../Turner04-errors/Makefile.am               |  27 +
 .../Turner04-errors/coaxial.dat               |  63 ++
 .../Turner04-errors/coaxstack.dat             |  63 ++
 .../Turner04-errors/dangle.dat                |  72 ++
 .../Turner04-errors/hexaloop.dat              |   6 +
 .../Turner04-errors/Turner04-errors/int11.dat | 101 ++
 .../Turner04-errors/Turner04-errors/int21.dat | 353 +++++++
 .../Turner04-errors/Turner04-errors/int22.dat | 928 ++++++++++++++++++
 .../Turner04-errors/Turner04-errors/loop.dat  |  34 +
 .../Turner04-errors/miscloop.dat              |  48 +
 .../Turner04-errors/Turner04-errors/stack.dat |  63 ++
 .../Turner04-errors/Turner04-errors/tloop.dat |  17 +
 .../Turner04-errors/triloop.dat               |   4 +
 .../Turner04-errors/tstack.dat                |  63 ++
 .../Turner04-errors/tstackcoax.dat            |  63 ++
 .../Turner04-errors/tstackh.dat               |  63 ++
 .../Turner04-errors/tstacki.dat               |  63 ++
 .../Turner04-errors/tstackm.dat               |  63 ++
 19 files changed, 2499 insertions(+)
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/int22.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/loop.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackcoax.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat
 create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat

diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile b/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile
new file mode 100644
index 0000000..ba5abb0
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile
@@ -0,0 +1,405 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# data/Turner04/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+
+pkgdatadir = $(datadir)/gtfold
+pkgincludedir = $(includedir)/gtfold
+pkglibdir = $(libdir)/gtfold
+pkglibexecdir = $(libexecdir)/gtfold
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = i686-pc-cygwin
+host_triplet = i686-pc-cygwin
+target_triplet = i686-pc-cygwin
+subdir = data/Turner04
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/gtfold_config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
+DATA = $(gtfold_data_DATA)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} "/cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe/missing" --run aclocal-1.11
+AMTAR = ${SHELL} "/cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe/missing" --run tar
+AUTOCONF = ${SHELL} "/cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe/missing" --run autoconf
+AUTOHEADER = ${SHELL} "/cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe/missing" --run autoheader
+AUTOMAKE = ${SHELL} "/cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe/missing" --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -g -O2 -Wall
+CPP = gcc -E
+CPPFLAGS = 
+CXX = g++
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2 -Wall
+CYGPATH_W = cygpath -w
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /usr/bin/grep -E
+EXEEXT = .exe
+GREP = /usr/bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = 
+LIBOBJS = 
+LIBS = -lgomp 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} "/cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe/missing" --run makeinfo
+MKDIR_P = /usr/bin/mkdir -p
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+PACKAGE = gtfold
+PACKAGE_BUGREPORT = 
+PACKAGE_NAME = gtfold
+PACKAGE_STRING = gtfold 1.18
+PACKAGE_TARNAME = gtfold
+PACKAGE_URL = 
+PACKAGE_VERSION = 1.18
+PATH_SEPARATOR = :
+SET_MAKE = 
+SHELL = /bin/sh
+STRIP = 
+VERSION = 1.18
+abs_builddir = /cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe/data/Turner04
+abs_srcdir = /cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe/data/Turner04
+abs_top_builddir = /cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe
+abs_top_srcdir = /cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = ${AMTAR} chof - "$$tardir"
+am__untar = ${AMTAR} xf -
+bindir = ${exec_prefix}/bin
+build = i686-pc-cygwin
+build_alias = 
+build_cpu = i686
+build_os = cygwin
+build_vendor = pc
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host = i686-pc-cygwin
+host_alias = 
+host_cpu = i686
+host_os = cygwin
+host_vendor = pc
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} '/cygdrive/c/Documents and Settings/Zsuzsi/Desktop/ash211-gtfold-236e97b/gtfold-mfe/install-sh'
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /usr/bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /usr/local
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target = i686-pc-cygwin
+target_alias = 
+target_cpu = i686
+target_os = cygwin
+target_vendor = pc
+top_build_prefix = ../../
+top_builddir = ../..
+top_srcdir = ../..
+gtfold_datadir = $(datadir)/gtfold/Turner04
+gtfold_data_DATA = \
+	stack.dat\
+	miscloop.dat\
+	dangle.dat\
+	loop.dat\
+	coaxial.dat\
+	coaxstack.dat\
+	hexaloop.dat\
+	int11.dat\
+	int21.dat\
+	int22.dat\
+	tloop.dat\
+	triloop.dat\
+	tstack.dat\
+	tstackcoax.dat\
+	tstackh.dat\
+	tstacki.dat\
+	tstackm.dat
+
+EXTRA_DIST = $(gtfold_data_DATA)
+CLEANFILES = *~
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Turner04/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu data/Turner04/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-gtfold_dataDATA: $(gtfold_data_DATA)
+	@$(NORMAL_INSTALL)
+	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
+	done
+
+uninstall-gtfold_dataDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(DATA)
+installdirs:
+	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am: install-gtfold_dataDATA
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-gtfold_dataDATA
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+	distclean-generic distdir dvi dvi-am html html-am info info-am \
+	install install-am install-data install-data-am install-dvi \
+	install-dvi-am install-exec install-exec-am \
+	install-gtfold_dataDATA install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+	pdf-am ps ps-am uninstall uninstall-am \
+	uninstall-gtfold_dataDATA
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am b/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am
new file mode 100644
index 0000000..302a135
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am
@@ -0,0 +1,27 @@
+## Process this file with automake to produce Makefile.in
+
+gtfold_datadir = $(datadir)/@PACKAGE@/Turner04
+
+gtfold_data_DATA = \
+	stack.dat\
+	miscloop.dat\
+	dangle.dat\
+	loop.dat\
+	coaxial.dat\
+	coaxstack.dat\
+	hexaloop.dat\
+	int11.dat\
+	int21.dat\
+	int22.dat\
+	tloop.dat\
+	triloop.dat\
+	tstack.dat\
+	tstackcoax.dat\
+	tstackh.dat\
+	tstacki.dat\
+	tstackm.dat
+
+EXTRA_DIST = $(gtfold_data_DATA)
+
+CLEANFILES = *~
+
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat
new file mode 100644
index 0000000..1fb3051
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat
@@ -0,0 +1,63 @@
+Data Arangement:
+                 Y          
+         ------------------ 
+     (X)  A    C    G    U  
+         ------------------ 
+             5' ==> 3'      
+                AX          
+                AY
+             3' <== 5'      
+     (A)  .    .    .    .  
+     (C)  .    .    .    .  
+     (G)  .    .    .    .  
+     (U) -0.7 -0.1 -0.7 -0.1
+--------------------------------
+ERRORS IN STACKING ENERGIES :
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------  
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U 
+------------------  ------------------  ------------------  ------------------  
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'    
+       AX                  AX                  AX                  AX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5' 
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------  
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U 
+------------------  ------------------  ------------------  ------------------  
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'    
+       CX                  CX                  CX                  CX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'  
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------  
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U 
+------------------  ------------------  ------------------  ------------------  
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'    
+       GX                  GX                  GX                  GX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'  
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------  
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U 
+------------------  ------------------  ------------------  ------------------  
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'    
+       UX                  UX                  UX                  UX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'  
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
\ No newline at end of file
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat
new file mode 100644
index 0000000..cef509d
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat
@@ -0,0 +1,63 @@
+Data Arangement:
+                 Y
+         ------------------
+     (X)  A    C    G    U
+         ------------------
+             5' ==> 3'
+                AX
+                AY
+             3' <== 5'
+     (A)  .    .    .    .
+     (C)  .    .    .    .
+     (G)  .    .    .    .
+     (U) -0.7 -0.1 -0.7 -0.1
+--------------------------------
+ERRORS IN STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS.
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       AX                  AX                  AX                  AX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       CX                  CX                  CX                  CX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       GX                  GX                  GX                  GX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       UX                  UX                  UX                  UX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
\ No newline at end of file
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat
new file mode 100644
index 0000000..7c9161b
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat
@@ -0,0 +1,72 @@
+        X                   X                   X                   X
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       AX                  AX                  AX                  AX
+       A                   C                   G                   U
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        X                   X                   X                   X
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       CX                  CX                  CX                  CX
+       A                   C                   G                   U
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+ 0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        X                   X                   X                   X
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       GX                  GX                  GX                  GX
+       A                   C                   G                   U
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        X                   X                   X                   X
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       UX                  UX                  UX                  UX
+       A                   C                   G                   U
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        X                   X                   X                   X
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       A                   A                   A                   A
+       AX                  CX                  GX                  UX
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+ 0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        X                   X                   X                   X
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       C                   C                   C                   C
+       AX                  CX                  GX                  UX
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        X                   X                   X                   X
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       G                   G                   G                   G
+       AX                  CX                  GX                  UX
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        X                   X                   X                   X
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       U                   U                   U                   U
+       AX                  CX                  GX                  UX
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat
new file mode 100644
index 0000000..66eb771
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat
@@ -0,0 +1,6 @@
+ Seq    Energy
+ -------------
+ ACAGUGCU	0
+ ACAGUGAU	0
+ ACAGUUCU	0
+ ACAGUACU	0
\ No newline at end of file
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat
new file mode 100644
index 0000000..67aa76a
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat
@@ -0,0 +1,101 @@
+Data table for symetric interior loops of size 2 
+Free energies at 37 degrees for RNA 
+Data Arrangement: 
+            Y 
+    ------------------ 
+(X)  A    C    G    U   
+    ------------------ 
+        5' --> 3' 
+            X 
+           A A 
+           U U 
+            Y 
+        3' <-- 5' 
+(A)  .    .    .    .    
+(C)  .    .    .    .    
+(G)  .    .    .    .    
+(U)  .    .    .    .    
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A A                     A C                     A G                     A U                     A G                     A U         
+           U U                     U G                     U C                     U A                     U U                     U G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C A                     C C                     C G                     C U                     C G                     C U         
+           G U                     G G                     G C                     G A                     G U                     G G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00 -0.00  0.00 -0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G A                     G C                     G G                     G U                     G G                     G U         
+           C U                     C G                     C C                     C A                     C U                     C G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U A                     U C                     U G                     U U                     U G                     U U         
+           A U                     A G                     A C                     A A                     A U                     A G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G A                     G C                     G G                     G U                     G G                     G U         
+           U U                     U G                     U C                     U A                     U U                     U G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U A                     U C                     U G                     U U                     U G                     U U         
+           G U                     G G                     G C                     G A                     G U                     G G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00  0.00  0.00 -0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat
new file mode 100644
index 0000000..9966877
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat
@@ -0,0 +1,353 @@
+Data tables for asymmetric interior loops of size 3 
+Free energies at 37 degrees for RNA 
+Data arrangement: 
+            Y 
+    ------------------ 
+(X)  A    C    G    U   
+    ------------------ 
+        5' --> 3' 
+            X 
+           A  A 
+           U  U 
+            YA 
+        3' <-- 5' 
+(A)  .    .    .    .    
+(C)  .    .    .    .    
+(G)  .    .    .    .    
+(U)  .    .    .    .    
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
+  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/int22.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int22.dat
new file mode 100644
index 0000000..5189f6b
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int22.dat
@@ -0,0 +1,928 @@
+Data tables for symetric interior loops of size 4
+Free energies at 37 degrees for RNA
+Data arrangement:
+                                Y
+     ----------------------------------------------------------------
+(X)   A   A   A   A   C   C   C   C   G   G   G   G   U   U   U   U
+      A   C   G   U   A   C   G   U   A   C   G   U   A   C   G   U
+     ----------------------------------------------------------------
+                           5' ------> 3'
+                            A \/ \_/ A
+                            U /\  |  U
+                           3' <------ 5'
+(AA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(AC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(AG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(AU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(CA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(CC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(CG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(CU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(GA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(GC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(GG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(GU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(UA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(UC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(UG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+(UU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .  
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   A \/ \_/ A
+                                   U /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   A \/ \_/ C
+                                   U /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   A \/ \_/ G
+                                   U /\  |  C
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   A \/ \_/ G
+                                   U /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   A \/ \_/ U
+                                   U /\  |  A
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   A \/ \_/ U
+                                   U /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   C \/ \_/ A
+                                   G /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   C \/ \_/ C
+                                   G /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   C \/ \_/ G
+                                   G /\  |  C
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   C \/ \_/ G
+                                   G /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   C \/ \_/ U
+                                   G /\  |  A
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   C \/ \_/ U
+                                   G /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ A
+                                   C /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ C
+                                   C /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ G
+                                   C /\  |  C
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ G
+                                   C /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ U
+                                   C /\  |  A
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ U
+                                   C /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ A
+                                   U /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ C
+                                   U /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ G
+                                   U /\  |  C
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ G
+                                   U /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ U
+                                   U /\  |  A
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   G \/ \_/ U
+                                   U /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ A
+                                   A /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ C
+                                   A /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ G
+                                   A /\  |  C
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ G
+                                   A /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ U
+                                   A /\  |  A
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ U
+                                   A /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ A
+                                   G /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ C
+                                   G /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ G
+                                   G /\  |  C
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ G
+                                   G /\  |  U
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ U
+                                   G /\  |  A
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+                                       Y
+ ------------------------------------------------------------------------------
+   A    A    A    A    C    C    C    C    G    G    G    G    U    U    U    U  
+   A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U  
+ ------------------------------------------------------------------------------
+                                  5' ------> 3'
+                                   U \/ \_/ U
+                                   G /\  |  G
+                                  3' <------ 5'
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+  0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/loop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/loop.dat
new file mode 100644
index 0000000..bfdbaaf
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/loop.dat
@@ -0,0 +1,34 @@
+DESTABILIZING ENERGIES BY SIZE OF LOOP (INTERPOLATE WHERE NEEDED)
+hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges
+SIZE         INTERNAL          BULGE            HAIRPIN
+-------------------------------------------------------
+1              0                 0.08             0
+2              0                 1.3              0
+3              0                 1.9              0.2 
+4              0.1               0			  0.1	
+5              0.1               0                0.2
+6              0.1               0                0.1
+7              0.1               0                0.2
+8              0                 0                0.2
+9              0                 0                0.2
+10             0                 0                0
+11             0                 0                0
+12             0                 0                0
+13             0                 0                0
+14             0                 0                0
+15             0                 0                0
+16             0                 0                0
+17             0                 0                0
+18             0                 0                0
+19             0                 0                0
+20             0                 0                0
+21             0                 0                0
+22             0                 0                0
+23             0                 0                0
+24             0                 0                0
+25             0                 0                0
+26             0                 0                0
+27             0                 0                0
+28             0                 0                0
+29             0                 0                0
+30             0                 0                0
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat
new file mode 100644
index 0000000..c9b76e9
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat
@@ -0,0 +1,48 @@
+Miscellaneous free energy rules
+-------------------------------
+Extrapolation for large loops based on polymer theory
+internal, bulge or hairpin loops > 30: dS(T)=dS(30)+param*ln(n/30)
+--> 
+1.079
+asymmetric internal loops: the ninio equation
+the maximum correction
+--> 
+3.0
+the f(m) array (see Ninio for details)
+-->
+ .6  .6  .6  .6
+multibranched loops
+  offset,  per nuc penalty,  helix penalty
+--> 
+    9.3          -.0                 -.9
+efn2 multibranched loops
+   offset,  per nuc penalty,  helix penalty
+-->
+     9.3         0.0              -0.9
+miscloop asym
+-->
+0.9
+multiloop strain
+--> 
+0.44
+terminal AU penalty
+--> 
+ 0.5
+bonus for GGG hairpin
+--> 
+-2.2
+c hairpin slope
+--> 
+0.3
+c hairpin intercept
+--> 
+0.24
+c hairpin of 3
+--> 
+1.5
+Intermolecular initiation free energy
+--> 
+4.1
+Bonus for Single C bulges adjacent to C
+-->
+0.3
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat
new file mode 100644
index 0000000..81fa1e6
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat
@@ -0,0 +1,63 @@
+Data Arangement:
+                 Y          
+         ------------------ 
+     (X)  A    C    G    U  
+         ------------------ 
+             5' ==> 3'      
+                AX          
+                AY
+             3' <== 5'      
+     (A)  0    0    0    0  
+     (C)  0    0    0    0  
+     (G)  0    0    0    0  
+     (U) -0.7 -0.1 -0.7 -0.1
+--------------------------------
+STACKING ENERGIES :
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------  
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U 
+------------------  ------------------  ------------------  ------------------  
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'    
+       AX                  AX                  AX                  AX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'  
+ 0    0    0     0   0    0    0     0   0    0    0     0    0    0    0  0.03
+ 0    0    0     0   0    0    0    0    0    0    0    0     0    0  0.06   0  
+ 0    0    0     0   0    0    0     0   0     0   0     0    0  0.07   0  0.32
+  0   0     0   0     0   0     0   0     0   0     0   0   0.08   0  0.24   0   
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------  
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U 
+------------------  ------------------  ------------------  ------------------  
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'    
+       CX                  CX                  CX                  CX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'  
+ 0    0    0     0   0    0    0     0    0    0    0  0.07  0    0    0     0  
+ 0    0     0   0    0    0     0   0     0    0  0.07   0   0    0     0   0   
+ 0     0   0     0   0     0   0     0    0  0.09   0  0.27  0     0   0     0  
+  0   0     0   0     0   0     0   0   0.06   0  0.24   0    0   0     0   0   
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------  
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U 
+------------------  ------------------  ------------------  ------------------  
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'    
+       GX                  GX                  GX                  GX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'  
+ 0    0    0     0    0    0    0  0.06  0    0    0     0    0    0    0  0.28
+ 0    0     0   0     0    0  0.08   0   0    0     0   0     0    0  0.25   0  
+ 0     0   0     0    0  0.07   0  0.27  0     0   0     0    0  0.25   0  0.96 
+  0   0     0   0   0.06   0  0.25   0    0   0     0   0   0.24   0  0.56   0    
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------  
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U 
+------------------  ------------------  ------------------  ------------------  
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'    
+       UX                  UX                  UX                  UX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'  
+  0    0    0  0.09  0    0    0     0    0    0    0  0.30   0    0    0     0  
+  0    0  0.06   0   0    0     0   0     0    0 0.27   0    0    0     0   0   
+  0  0.07   0  0.30  0     0   0     0    0  0.24   0 0.48    0     0   0     0  
+0.03   0  0.28   0    0   0     0   0    0.32   0  0.96   0   0   0     0   0   
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat
new file mode 100644
index 0000000..3a63c62
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat
@@ -0,0 +1,17 @@
+ Seq    Energy
+ -------------
+CUACGG	0
+CUCCGG	0
+CUUCGG	0
+CCAAGG	0
+CCCAGG	0
+CCGAGG	0
+CCUAGG	0
+CCACGG	0
+CCGCGG	0
+CCUCGG	0
+CUAAGG	0
+CUCAGG	0
+CUUAGG	0
+CUGCGG	0
+CAACGG	0
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat
new file mode 100644
index 0000000..e66a4b6
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat
@@ -0,0 +1,4 @@
+ Seq    Energy
+ -------------
+CAACG	0
+GUUAC	0
\ No newline at end of file
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat
new file mode 100644
index 0000000..6ab5d45
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat
@@ -0,0 +1,63 @@
+Data Arangement:
+                 Y
+         ------------------
+     (X)  A    C    G    U
+         ------------------
+             5' ==> 3'
+                AX
+                AY
+             3' <== 5'
+     (A)  .    .    .    .
+     (C)  .    .    .    .
+     (G)  .    .    .    .
+     (U) -0.7 -0.1 -0.7 -0.1
+--------------------------------
+STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS.
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       AX                  AX                  AX                  AX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       CX                  CX                  CX                  CX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       GX                  GX                  GX                  GX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       UX                  UX                  UX                  UX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackcoax.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackcoax.dat
new file mode 100644
index 0000000..6ab5d45
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackcoax.dat
@@ -0,0 +1,63 @@
+Data Arangement:
+                 Y
+         ------------------
+     (X)  A    C    G    U
+         ------------------
+             5' ==> 3'
+                AX
+                AY
+             3' <== 5'
+     (A)  .    .    .    .
+     (C)  .    .    .    .
+     (G)  .    .    .    .
+     (U) -0.7 -0.1 -0.7 -0.1
+--------------------------------
+STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS.
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       AX                  AX                  AX                  AX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       CX                  CX                  CX                  CX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       GX                  GX                  GX                  GX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       UX                  UX                  UX                  UX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat
new file mode 100644
index 0000000..6ab5d45
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat
@@ -0,0 +1,63 @@
+Data Arangement:
+                 Y
+         ------------------
+     (X)  A    C    G    U
+         ------------------
+             5' ==> 3'
+                AX
+                AY
+             3' <== 5'
+     (A)  .    .    .    .
+     (C)  .    .    .    .
+     (G)  .    .    .    .
+     (U) -0.7 -0.1 -0.7 -0.1
+--------------------------------
+STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS.
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       AX                  AX                  AX                  AX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       CX                  CX                  CX                  CX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       GX                  GX                  GX                  GX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       UX                  UX                  UX                  UX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat
new file mode 100644
index 0000000..6ab5d45
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat
@@ -0,0 +1,63 @@
+Data Arangement:
+                 Y
+         ------------------
+     (X)  A    C    G    U
+         ------------------
+             5' ==> 3'
+                AX
+                AY
+             3' <== 5'
+     (A)  .    .    .    .
+     (C)  .    .    .    .
+     (G)  .    .    .    .
+     (U) -0.7 -0.1 -0.7 -0.1
+--------------------------------
+STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS.
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       AX                  AX                  AX                  AX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       CX                  CX                  CX                  CX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       GX                  GX                  GX                  GX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       UX                  UX                  UX                  UX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat
new file mode 100644
index 0000000..6ab5d45
--- /dev/null
+++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat
@@ -0,0 +1,63 @@
+Data Arangement:
+                 Y
+         ------------------
+     (X)  A    C    G    U
+         ------------------
+             5' ==> 3'
+                AX
+                AY
+             3' <== 5'
+     (A)  .    .    .    .
+     (C)  .    .    .    .
+     (G)  .    .    .    .
+     (U) -0.7 -0.1 -0.7 -0.1
+--------------------------------
+STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS.
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       AX                  AX                  AX                  AX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       CX                  CX                  CX                  CX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       GX                  GX                  GX                  GX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+        Y                   Y                   Y                   Y
+------------------  ------------------  ------------------  ------------------
+ A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
+------------------  ------------------  ------------------  ------------------
+    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
+       UX                  UX                  UX                  UX
+       AY                  CY                  GY                  UY
+    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
+0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0

From 0e3f085ba7c44f6b953b44298969d9104be4ff72 Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Sun, 8 May 2011 03:17:13 +0200
Subject: [PATCH 112/282] Contact distance implemented + missing SHAPE header
 included again in algorithms.c

---
 gtfold-mfe/include/constraints.h   | 1 +
 gtfold-mfe/src/.deps/algorithms.Po | 3 +++
 gtfold-mfe/src/algorithms.c        | 3 ++-
 gtfold-mfe/src/constraints.cc      | 6 ++++++
 4 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h
index a6b3370..8743d88 100644
--- a/gtfold-mfe/include/constraints.h
+++ b/gtfold-mfe/include/constraints.h
@@ -34,6 +34,7 @@ int check_pair(int i, int j) ;
 int check_stack(int i, int j) ;
 int check_hairpin(int i, int j) ;
 int can_dangle(int i);
+int withinCD(int i, int j);
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/src/.deps/algorithms.Po b/gtfold-mfe/src/.deps/algorithms.Po
index b84c3b7..c737d2e 100644
--- a/gtfold-mfe/src/.deps/algorithms.Po
+++ b/gtfold-mfe/src/.deps/algorithms.Po
@@ -22,6 +22,7 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
  ../include/constants.h ../include/utils.h ../include/constants.h \
  ../include/energy.h ../include/data.h ../include/global.h \
  ../include/algorithms.h ../include/constraints.h \
+ ../include/shapereader.h \
  /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/omp.h
 
 /usr/include/stdio.h:
@@ -128,4 +129,6 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
 
 ../include/constraints.h:
 
+../include/shapereader.h:
+
 /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/omp.h:
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index eef7105..8986603 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -30,6 +30,7 @@
 #include "global.h"
 #include "algorithms.h"
 #include "constraints.h"
+#include "shapereader.h"
 
 #ifdef _OPENMP   
 #include "omp.h"
@@ -56,7 +57,7 @@ int calculate(int len, int nThreads) {
 			j = i + b;
 			int flag = 0, newWM = INFINITY_; 
 
-			if (canPair(RNA[i], RNA[j])) {
+			if (canPair(RNA[i], RNA[j]) && withinCD(i,j)) {
 				flag = 1;
 				int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin
 				int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index f97d214..0dd931d 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -451,5 +451,11 @@ int check_hairpin(int i, int j) {
 		//return is_ss(i,j) || force_pair(i,j) || force_pair(j,i);
 	}	
 	else return 0;
+}
 
+int withinCD(int i, int j){
+	if (LIMIT_DISTANCE){	
+		return j-i+1>contactDistance;
+	}
+	else return 1;
 }

From ff9ec67037510adabad78fba9e137d0d12ecfcb1 Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Sun, 8 May 2011 03:26:55 +0200
Subject: [PATCH 113/282] Removed unnecessary output

---
 gtfold-mfe/src/main.cc | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 8ab8888..b8edbf3 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -65,10 +65,6 @@ void init_fold(string seq) {
 		init_constraints(constraintsFile.c_str(), len);
 	}
 
-	if (LIMIT_DISTANCE){
-		printf("Limit distance is currently not implemented.");
-	}
-
 	if (SHAPE_ENABLED) {
 		readSHAPEarray(shapeFile.c_str(),len);
 	}

From 48ee2aafe9f74c8164b90e892dfda25083490aac Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Mon, 9 May 2011 01:03:22 +0200
Subject: [PATCH 114/282] Fixed pseudoknotted constraint issue (issue nr. 3)

---
 gtfold-mfe/src/constraints.cc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 0dd931d..e0913f5 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -116,7 +116,8 @@ static int load_constraints(const char* constr_file, int verbose=0) {
 	if(v_fbp.size()>1){
 		std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
 		for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) {
-			if (v_fbp[ii].second!=0&&v_fbp[ii].second <= v_fbp[ii+1].second) {
+			if (v_fbp[ii].second!=0&&v_fbp[ii].second <= v_fbp[ii+1].second
+				&& v_fbp[ii].second >= v_fbp[ii+1].first) {
 				fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n");
 				exit(-1);
 			}

From 0d865669b29582ae27cdc1c2387b34c166676ce5 Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Sat, 14 May 2011 05:22:49 +0200
Subject: [PATCH 115/282] Fix to forcing constraints, traceback error, and some
 small problems in the multiloop optimization.

---
 gtfold-mfe/src/.deps/traceback.Po |  4 +++-
 gtfold-mfe/src/algorithms.c       | 37 ++++++++++++++++++++--------
 gtfold-mfe/src/constraints.cc     | 11 +++++----
 gtfold-mfe/src/traceback.c        | 40 +++++++++++++++++++++++--------
 4 files changed, 67 insertions(+), 25 deletions(-)

diff --git a/gtfold-mfe/src/.deps/traceback.Po b/gtfold-mfe/src/.deps/traceback.Po
index c8b0c87..c475c0e 100644
--- a/gtfold-mfe/src/.deps/traceback.Po
+++ b/gtfold-mfe/src/.deps/traceback.Po
@@ -22,7 +22,7 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/assert.h ../include/data.h ../include/constants.h \
  ../include/constants.h ../include/constraints.h ../include/energy.h \
  ../include/data.h ../include/global.h ../include/traceback.h \
- ../include/utils.h
+ ../include/utils.h ../include/shapereader.h
 
 /usr/include/stdio.h:
 
@@ -125,3 +125,5 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \
 ../include/traceback.h:
 
 ../include/utils.h:
+
+../include/shapereader.h:
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 8986603..b1d9b6c 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -56,7 +56,6 @@ int calculate(int len, int nThreads) {
 		for (i = 1; i <= len - b; i++) {
 			j = i + b;
 			int flag = 0, newWM = INFINITY_; 
-
 			if (canPair(RNA[i], RNA[j]) && withinCD(i,j)) {
 				flag = 1;
 				int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin
@@ -65,14 +64,23 @@ int calculate(int len, int nThreads) {
 					int p=0, q=0;
 					int VBIij = INFINITY_;
 
+					int found_forced_pair = 0;
 					for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
 						int minq = j-i+p-MAXLOOP-2;
 						if (minq < p+1+TURN) minq = p+1+TURN;
 						for (q = minq; q < j; q++) {
 							if (!canPair(RNA[p], RNA[q])) continue;
 							if (check_iloop(i,j,p,q)) continue;
+							if(force_pair1(p,q)){
+							//ZS: if we know a pair should be forced, we should 
+							//just enforce it and not care about other options.
+								VBIij = eL(i,j,p,q) + V(p,q); 
+								found_forced_pair = 1;
+								break; 
+							}	
 							VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
 						}
+						if(found_forced_pair){break;}
 					}
 					VBI(i,j) = check_pair(i,j)?INFINITY_:VBIij;
 				} 	// Internal Loop END
@@ -87,7 +95,12 @@ int calculate(int len, int nThreads) {
 						VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1));	
 						VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2));	
 						VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2));	
-						newWM = MIN(newWM, VMij);
+						//ZS: I don't think the following line is being checked in traceback, so 
+						//if you enable it, sometimes huge parts of the structure will not be possible
+						//to trace. 
+						//I don't know if it should be here or not. If it is here, it should be in traceback
+						//too. For now, I am removing it! 
+						//newWM = MIN(newWM, VMij);
 					}
 
 					int d3 = can_dangle(j-1)?Ed3(i,j,j-1):INFINITY_;
@@ -108,20 +121,24 @@ int calculate(int len, int nThreads) {
 
 			if (j-i > 4) {	// WM BEGIN
 				int h; 
-				if (!flag) {
+				//ZS: if we know that i,j are pairing, we just have to set WM(i,j) = V(i,j) in the best possible way.
+				//Conversely, we only need to find the best partitioning if we know that i,j are not forced to pair.
+
+				//Prashant's original code had if(!flag) here... I don't know what that was supposed to do?
+				if (!force_pair1(i,j)) {
 					for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
 						newWM = MIN(newWM, WMU(i,h-1) + WML(h,j));
 					}
 				}
 				
 				newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
-				newWM = can_dangle(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): INFINITY_; 
-				newWM = can_dangle(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM) : INFINITY_; 
-				newWM = (can_dangle(i)&&can_dangle(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM): INFINITY_;
-				
-				newWM = can_dangle(i)?MIN(WMU(i+1,j) + Ec, newWM):INFINITY_;
-				newWM = can_dangle(j)?MIN(WML(i,j-1) + Ec, newWM):INFINITY_;
 
+				//ZS: if i,j are forced to pair then can_dangle(i) and can_dangle(j) will be false 
+				newWM = can_dangle(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): newWM; 
+				newWM = can_dangle(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM) : newWM; 
+				newWM = (can_dangle(i)&&can_dangle(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM): newWM;
+				newWM = can_dangle(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM;
+				newWM = can_dangle(j)?MIN(WML(i,j-1) + Ec, newWM):newWM;
 				WMU(i,j) = WML(i,j) = newWM;
 			} // WM END
 		}
@@ -147,7 +164,7 @@ int calculate(int len, int nThreads) {
 				else if	(Wj==Wijd && force_pair1(i,j-1))
 				  branch = 1;	
 				else if	(force_pair1(i+1,j))
-					branch = 1;
+				  branch = 1;
 			}
 		}
 		W[j] = branch?Wj:MIN(Wj, W[j-1]);
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index e0913f5..aca5419 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -377,10 +377,13 @@ int force_ss1(int i){
 
 int force_ssregion1(int i, int j){
 	if(CONS_ENABLED){
+		int value = 1;
 		for(int p = i; p<j; p++){
-			if(BP(p,p)==3){return 1;}
+			if(BP(p,p)!=3){
+				value= 0;
+			}
 		}
-		return 0;
+		return value;
 	}
 	else return 0;
 }
@@ -390,7 +393,7 @@ int check_iloop(int i, int j, int p, int q) {
 	if (CONS_ENABLED){
 		//Need to check that i,j and p,q pairs are allowed, 
 		//and single-stranded regions between i,p and q,j are allowed
-		return check_pair(i,j)&&check_pair(p,q)&&check_ssregion(i,p)&&check_ssregion(q,j);
+		return check_pair(i,j)||check_pair(p,q)||check_ssregion(i,p)||check_ssregion(q,j);
 	}
 		//Original code (Prashant's):
 		//return is_ss(i,p) || is_ss(q,j);
@@ -447,7 +450,7 @@ int check_hairpin(int i, int j) {
 	//1 when a hairpin with i,j as closing pair isn't allowed.
 	if (CONS_ENABLED){
 		//Need to check if pair is allowed and if anything pairs between them
-		return check_pair(i,j)&&check_ssregion(i,j);
+		return check_pair(i,j)||check_ssregion(i,j);
 		//Original code (Prashant's)
 		//return is_ss(i,j) || force_pair(i,j) || force_pair(j,i);
 	}	
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 6fdc806..9d7290e 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -28,6 +28,7 @@
 #include "global.h"
 #include "traceback.h"
 #include "utils.h"
+#include "shapereader.h"
 
 int verbose = -1;
 int total_en = 0;
@@ -60,12 +61,14 @@ void traceW(int j) {
 	
 	if (j == 0 || j == 1) return;
 
+	
+
 	for (i = 1; i < j && !done; i++) {
 		if (j-i < TURN) continue;
 
 		wim1 = MIN(0, W[i-1]);
 		flag = 1;
-		if (wim1 != W[i-1]) flag = 0;
+		if (wim1 != W[i-1]) flag = 0; //ZS: flag is false if the free energy of the best structure to W[i] is 0 --> all should be ss 
 
 		Widjd = Wijd =  Widj = INFINITY_;
 		Wij = V(i,j) + auPenalty(i, j) + wim1;
@@ -76,7 +79,8 @@ void traceW(int j) {
 		Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
 
 		if (W[j] == Wj) {
-			if (W[j] == Wij) { 
+			//if we know W[j] is pairing with something
+			if (W[j] == Wij || force_pair1(i,j)){ 
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i, j, auPenalty(i, j)/100.00);
@@ -86,7 +90,7 @@ void traceW(int j) {
 				traceV(i, j);
 				if (flag || force_ssregion1(1,i)) traceW(i - 1);
 				break;
-			} else if (W[j] == Widjd && can_dangle(i) && can_dangle(j)) { 
+			} else if ((W[j] == Widjd && can_dangle(i) && can_dangle(j)) || force_pair1(i+1,j-1)) { 
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
@@ -96,7 +100,7 @@ void traceW(int j) {
 				traceV(i + 1, j - 1);
 				if (flag || force_ssregion1(1,i)) traceW(i - 1);
 				break;
-			} else if (W[j] == Wijd && can_dangle(j)) { 
+			} else if ((W[j] == Wijd && can_dangle(j))||force_pair1(i,j-1)) { 
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
@@ -106,7 +110,7 @@ void traceW(int j) {
 				traceV(i, j - 1);
 				if (flag || force_ssregion1(1,i)) traceW(i - 1);
 				break;
-			} else if (W[j] == Widj && can_dangle(i)) { 
+			} else if ((W[j] == Widj && can_dangle(i))||force_pair1(i+1,j)) { 
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
@@ -126,14 +130,15 @@ void traceW(int j) {
 }
 
 int traceV(int i, int j) {
+
 	int a, b, c, d, Vij;
 	if (j-i < TURN)  return INFINITY_;
 
-	a = eH(i, j);
-	b = eS(i, j) + V(i + 1, j - 1);
+	a = eH(i, j)+getShapeEnergy(i) + getShapeEnergy(j);
+	b = eS(i, j) + V(i + 1, j - 1) + getShapeEnergy(i) + getShapeEnergy(j);
 	if (eS(i, j) == 0) b = INFINITY_;
-	c = VBI(i,j);
-	d = VM(i,j);
+	c = VBI(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
+	d = VM(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
 	
 	Vij = MIN(MIN(a, b), MIN(c, d));
 	
@@ -251,6 +256,7 @@ int traceVM(int i, int j) {
 				done = 1;
 				eVM += traceWM(i + 2, h - 1);
 				eVM += traceWM(h, j - 2);
+
 				break;
 			}
 		}
@@ -260,7 +266,6 @@ int traceVM(int i, int j) {
 }
 
 int traceWM(int i, int j) {
-
 	int done;
 	int h1, h;
 	int eWM = 0; 
@@ -312,5 +317,20 @@ int traceWM(int i, int j) {
 			}
 		}
 	}
+	//ZS: This is for debugging purposes. 
+	if(!done){
+		printf("ERROR: WM couldn't be traced!\n");
+		printf("%d %d \n", i, j);
+		printf("WM(i,j) = %d\n", WM(i,j));
+		printf("candangle i? %d\n", can_dangle(i));
+		printf("candangle j? %d\n", can_dangle(j));
+		printf("The options were: \n"); 
+		printf("Option 1 %d \n" , V(i,j) + auPenalty(i, j) + Eb);
+		printf("Option 2 %d \n" , V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec);
+		printf("Option 3 %d \n", V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec);
+		printf("Option 4 %d \n", V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec);
+		printf("Option 5 %d \n", WM(i + 1,j) + Ec );
+		printf("Option 6 %d \n", WM(i,j - 1) + Ec);
+	}
 	return eWM;
 }

From e6877be5ebb72d32820036ca534db0f22203c63b Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Sat, 14 May 2011 15:37:42 +0200
Subject: [PATCH 116/282] fix to tracing W[i] even if it has positive energy,
 in the special case that something is forced to pair within it

---
 gtfold-mfe/src/traceback.c | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 9d7290e..9c961e8 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -68,7 +68,9 @@ void traceW(int j) {
 
 		wim1 = MIN(0, W[i-1]);
 		flag = 1;
-		if (wim1 != W[i-1]) flag = 0; //ZS: flag is false if the free energy of the best structure to W[i] is 0 --> all should be ss 
+		if (wim1 != W[i-1] && !check_ssregion(1,i)) flag = 0; 
+		//ZS: flag is false if the free energy of the best structure to W[i] is > 0 --> all should be ss 
+		//UNLESS there is at least one base that is forced to pair in that region, this is revealed by check_ssregion(1,i)
 
 		Widjd = Wijd =  Widj = INFINITY_;
 		Wij = V(i,j) + auPenalty(i, j) + wim1;
@@ -123,7 +125,7 @@ void traceW(int j) {
 			}
 		}
 	}
-		
+
 	if (W[j] == W[j - 1] && !done) traceW(j-1);
 
 	return;

From 4d8be8a072ebee2fdd357dc8c570ed059a7129aa Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Sat, 14 May 2011 16:19:27 +0200
Subject: [PATCH 117/282] fixed an out-of-scope reference in unconstrained
 predictions, and added verification function to check that prediction
 fulfills constraint criteria

---
 gtfold-mfe/include/constraints.h |  1 +
 gtfold-mfe/src/constraints.cc    | 80 ++++++++++++++++++++++++++++++--
 gtfold-mfe/src/main.cc           | 10 ++++
 gtfold-mfe/src/traceback.c       |  2 +-
 4 files changed, 88 insertions(+), 5 deletions(-)

diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h
index 8743d88..045ebad 100644
--- a/gtfold-mfe/include/constraints.h
+++ b/gtfold-mfe/include/constraints.h
@@ -35,6 +35,7 @@ int check_stack(int i, int j) ;
 int check_hairpin(int i, int j) ;
 int can_dangle(int i);
 int withinCD(int i, int j);
+int verify_structure();
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index aca5419..86814b8 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -263,6 +263,76 @@ int init_constraints(const char* constr_file,int length) {
 	return 0;
 }
 
+int verify_structure(){
+	//ZS: This method returns true if the structure (global.h) is consistent with
+	//the constraints, and false if it is not.
+	
+	if(CONS_ENABLED){
+	int errorhappened = 0;
+	int it, k;
+	//Check prohibited constraints
+	if(nPBP != 0){
+		for(it = 0; it < nPBP; it++){
+			if(PBP[it][2] < 1 || PBP[it][1] == 0){
+				//printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
+				continue;
+			}
+			for(k = 1; k <= PBP[it][2]; k++){
+				//correct answer: strcuture(PBP[it][0]+k-1) != structure(PBP[it][1]-(k-1))
+				if(structure[PBP[it][0]+k-1] == PBP[it][1]-(k-1) || structure[PBP[it][1]-(k-1)] == PBP[it][0]+k-1){	
+					errorhappened = 1; 
+					printf("Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]);
+					break;
+				}
+			}
+		}	
+	}
+
+	//Check forced constraints
+	if(nFBP != 0){
+		for(it = 0; it<nFBP; it++){
+			if(FBP[it][2] < 1){
+				//printf("Invalid entry (F: %d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
+				continue;
+			}
+
+			for(k = 1; k<=FBP[it][2]; k++){
+				int i1 = FBP[it][0]+k-1;
+				int j1 = FBP[it][1]-k+1;
+				if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){
+					//printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
+					continue;			
+				}
+				if(FBP[it][1]!=0&&(j1-i1 < TURN)){
+					//printf("Can't force (%d, %d) to pair (turn too tight) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
+					continue;
+				}
+				if(FBP[it][1] == 0){
+					//force single-stranded
+					if(structure[FBP[it][0]] != 0){
+						printf("Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
+						errorhappened = 1;
+					}
+				}
+				else{
+					if(structure[FBP[it][0]+k-1] != FBP[it][1]-(k-1) || structure[FBP[it][1]-(k-1)] != FBP[it][0]+k-1){
+						printf("Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
+						errorhappened = 1;
+					}
+					
+				}
+			}
+		}
+	}
+		return errorhappened?0:1;
+	}
+	else{
+		return 1;
+	}
+		 
+}
+
+
 void free_constraints(int len) {
 	free(BP);
 }
@@ -419,10 +489,12 @@ int check_pair(int i, int j) {
 int check_ssregion(int i, int j){
 //ZS: This function returns 1 if any nucleotide between i and j is forced to pair with something
 //(i and j are NOT included in the check)
-	for(int p = i+1; p<j; p++){
-		if(BP(p,p)==4) return 1;
-	}
-	return 0;
+	if(CONS_ENABLED){
+		for(int p = i+1; p<j; p++){
+			if(BP(p,p)==4) return 1;
+		}
+		return 0;}
+	else{ return 0; }
 }
 
 int can_dangle(int i){
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index b8edbf3..6394068 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -246,6 +246,16 @@ int main(int argc, char** argv) {
 	save_ct_file(outputFile, seq, energy);
 	printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str());
 
+
+	if(CONS_ENABLED && VERBOSE){
+		printf("Verifying that structure fulfills constraint criteria... ");
+		if(verify_structure()){
+			printf("OK\n");
+		}
+		else{
+			printf("ERROR: NOT OK!!\n");
+		}
+	}
 	// release the malloc'd arrays
 	free_fold(seq.length());
 
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 9c961e8..7d25b32 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -62,8 +62,8 @@ void traceW(int j) {
 	if (j == 0 || j == 1) return;
 
 	
-
 	for (i = 1; i < j && !done; i++) {
+
 		if (j-i < TURN) continue;
 
 		wim1 = MIN(0, W[i-1]);

From ee47c2402f37184533ea44a937f2354f59f2aeb2 Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Tue, 17 May 2011 02:57:28 +0200
Subject: [PATCH 118/282] fix to prohibited constraints

---
 gtfold-mfe/src/algorithms.c   |  3 +++
 gtfold-mfe/src/constraints.cc | 20 ++++++++++++++++++++
 gtfold-mfe/src/main.cc        |  3 +++
 3 files changed, 26 insertions(+)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index b1d9b6c..c7b9a3d 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -39,6 +39,9 @@
 int calculate(int len, int nThreads) { 
 	int b, i, j;
 
+
+//	printf("%d\n", BP(1145, 13));
+
 #ifdef _OPENMP
 	if (nThreads>0) omp_set_num_threads(nThreads);
 #endif
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 86814b8..3d50a5f 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -174,6 +174,17 @@ int init_constraints(const char* constr_file,int length) {
 	
 	//ZS: set prohibited basepairs
 	if(nPBP != 0){
+		int temp;
+		//Make sure smallest one is first 
+		for(it = 0; it < nPBP; it++){
+			if(PBP[it][0] > PBP[it][1]){
+				temp = PBP[it][0];	
+				PBP[it][0] = PBP[it][1];
+				PBP[it][1] = temp;
+			}
+			printf("%d\n", it);
+		}
+
 		for(it = 0; it < nPBP; it++){
 			if(PBP[it][2] < 1 || PBP[it][1] == 0){
 				printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
@@ -194,6 +205,15 @@ int init_constraints(const char* constr_file,int length) {
 	//ZS: set forced basepairs and single-stranded nucleotides
 
 	if(nFBP != 0){
+		int temp; 
+		for(it  = 0; it < nFBP; it++){
+			if(FBP[it][0] > FBP[it][1]){
+				temp = FBP[it][0];
+				FBP[it][0] = FBP[it][1];
+				FBP[it][1] = temp; 
+			}
+			printf("%d\n", it);
+		}
 		for(it = 0; it<nFBP; it++){
 			if(FBP[it][2] < 1){
 				printf("Invalid entry (F: %d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 6394068..9294cbf 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -254,6 +254,9 @@ int main(int argc, char** argv) {
 		}
 		else{
 			printf("ERROR: NOT OK!!\n");
+			fprintf(stderr, "ERROR: Structure does not fulfill constraint criteria.\n");
+			fprintf(stderr, "Structure file: %s\n", outputFile.c_str());
+			fprintf(stderr, "Constraint file: %s\n", constraintsFile.c_str());
 		}
 	}
 	// release the malloc'd arrays

From 42c5b93abce4788759d0ac70ab37e3203006dfbe Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Tue, 17 May 2011 09:53:30 -0400
Subject: [PATCH 119/282] I need to move this to another computer to go to a
 ballgame

---
 gtfold-mfe/src/partition-dangle.cc | 57 ++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 gtfold-mfe/src/partition-dangle.cc

diff --git a/gtfold-mfe/src/partition-dangle.cc b/gtfold-mfe/src/partition-dangle.cc
new file mode 100644
index 0000000..53b889e
--- /dev/null
+++ b/gtfold-mfe/src/partition-dangle.cc
@@ -0,0 +1,57 @@
+/**s1 -> partial_external
+*  s2 -> partial_multi
+*  s3 -> partial_multi2
+*  u1 -> u_helper
+*  f -> cond_dangle (conditional)
+**/
+
+/**TODO cond_dangle, ed3, ed5,**/
+
+/**
+*  For each spot in partial_external at index h,j we'll need:
+**/
+
+double RT = 0.00198721 * 310.15;
+
+int l;
+
+for(l = i+2; l < j; l++){
+	upm[i][j] += up[i+1][l] * exp(-(a + 2 * c + /**TODO terminal pair i+1,l**/)/RT) *
+				(exp(-ed3(i+1,l,l+1)/RT) * 
+				u_helper[l+2][j-1] + 
+				u_helper[l+1][j-1] -
+				u_helper[l+2][j-1]);
+	if(l != i+2){ //goes from i + 2 < l < j
+		upm[i][j] += up[i + 2][l] * 
+					exp(-(a + 2c + b + ed3(j,i,i + 1) + /**TODO terminal pair i+2, l**/)/RT) *
+					(exp(-ed3(i+2,l,l+1)/RT)*u_helper[l+2][j-1] + u_helper[l+1][j-1]  - 
+					u_helper[l+2][j-1]);
+
+		if(l != j - 1){
+			upm[i][j] += exp(-ed3(j,i,i+1)/RT)*exp(-(a + 2 * c + (h - i -1) * b)/RT) * 
+						partial_multi[l][j]; 
+			//Changed h in the paper to l it makes no difference
+			//other than unifying loops
+		}
+	}
+}
+
+
+for(l = h+1; l < j; l++){
+	partial_external[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) *
+				(exp(-ed3(h,l,l+1)/RT)*u_helper[l+2,j-1] + u_helper[l+1][j] -
+				u_helper[l+2][j]);
+
+	partial_multi[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) *
+				(exp(-ed3(h,l,l+1)/RT)*u_helper[l+2,j-1] + u_helper[l+1][j-1] -
+				u_helper[l+2][j-1]);
+
+	partial_multi2[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) *
+				(cond_dangle(j + 1, h, l)*exp(-(j-l) * b / RT) + exp(-ed3(h,l,l + 1)/RT)*u_helper(l+2,j)
+				+u_helper(l + 1,j) - u1(l + 2,j));
+				
+}
+/** partial_multi2 goes up to j **/
+partial_multi2[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) *
+				(cond_dangle(j + 1, h, l)*exp(-(j-l) * b / RT) + exp(-ed3(h,l,l + 1)/RT)*u_helper(l+2,j)
+				+u_helper(l + 1,j) - u1(l + 3,j));

From 83f7fe5caa4b99e7ff571c52b1d1c6700ab154e2 Mon Sep 17 00:00:00 2001
From: Joshua Anderson <josh@lilLime.(none)>
Date: Wed, 18 May 2011 09:17:43 -0400
Subject: [PATCH 120/282] First draft of matrix filling

---
 gtfold-mfe/src/partition-dangle.cc | 159 +++++++++++++++++++++--------
 1 file changed, 116 insertions(+), 43 deletions(-)

diff --git a/gtfold-mfe/src/partition-dangle.cc b/gtfold-mfe/src/partition-dangle.cc
index 53b889e..d07064c 100644
--- a/gtfold-mfe/src/partition-dangle.cc
+++ b/gtfold-mfe/src/partition-dangle.cc
@@ -1,57 +1,130 @@
+//The paper (Dirks, Pierce) offhandedly mentions a G-U terminal pair penalty
+//I don't think we do that...
+
 /**s1 -> partial_external
 *  s2 -> partial_multi
 *  s3 -> partial_multi2
-*  u1 -> u_helper
+*  u1 -> u_multi
 *  f -> cond_dangle (conditional)
 **/
 
-/**TODO cond_dangle, ed3, ed5,**/
+#include energy.h
 
-/**
-*  For each spot in partial_external at index h,j we'll need:
-**/
 
-double RT = 0.00198721 * 310.15;
-
-int l;
-
-for(l = i+2; l < j; l++){
-	upm[i][j] += up[i+1][l] * exp(-(a + 2 * c + /**TODO terminal pair i+1,l**/)/RT) *
-				(exp(-ed3(i+1,l,l+1)/RT) * 
-				u_helper[l+2][j-1] + 
-				u_helper[l+1][j-1] -
-				u_helper[l+2][j-1]);
-	if(l != i+2){ //goes from i + 2 < l < j
-		upm[i][j] += up[i + 2][l] * 
-					exp(-(a + 2c + b + ed3(j,i,i + 1) + /**TODO terminal pair i+2, l**/)/RT) *
-					(exp(-ed3(i+2,l,l+1)/RT)*u_helper[l+2][j-1] + u_helper[l+1][j-1]  - 
-					u_helper[l+2][j-1]);
-
-		if(l != j - 1){
-			upm[i][j] += exp(-ed3(j,i,i+1)/RT)*exp(-(a + 2 * c + (h - i -1) * b)/RT) * 
-						partial_multi[l][j]; 
-			//Changed h in the paper to l it makes no difference
-			//other than unifying loops
-		}
-	}
+int cond_dangle(int j, int h, int l){
+	return j - 1 == l ? 1 : exp(-Ed3(h,l,l+1)/RT);
 }
 
+double RT = (0.00198721 * 310.15)/100.00; 
+//So that we don't have the /100 in every exponent
+//Seeing as we missed some last time
+
+int seg_length;
+int i;
+for(seg_length = MIN_TURN; seg_length < len; len ++){
+	for(i = 1; i < seg_length - MIN_TURN; i++){
+		j = i + seg_length;
+		int l;
+		/**
+		*  For each spot in partial_external at index h,j we'll need:
+		**/
+		for(l = i+2; l < j; l++){
+			upm[i][j] += up[i+1][l] * exp(-(Ea + 2 * Ec + auPenalty(i + 1,l)/RT)) *
+						(exp(-Ed3(i + 1,l,l+1)/RT) * u_multi[l + 2][j - 1] + 
+						u_multi[l + 1][j - 1] -
+						u_multi[l + 2][j - 1]);
+			if(l != i+2){ //goes from i + 2 < l < j
+				upm[i][j] += up[i + 2][l] * 
+						exp(-(Ea + 2 * Ec + Eb + Ed3(j,i,i + 1) + auPenalty(i + 2, l))/RT) *
+						(exp(-Ed3(i + 2,l,l + 1)/RT)*u_multi[l + 2][j - 1] + 
+						u_multi[l + 1][j - 1]  - 
+						u_multi[l + 2][j - 1]);
 
-for(l = h+1; l < j; l++){
-	partial_external[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) *
-				(exp(-ed3(h,l,l+1)/RT)*u_helper[l+2,j-1] + u_helper[l+1][j] -
-				u_helper[l+2][j]);
+				if(l != j - 1){
+					upm[i][j] += exp(-Ed3(j,i,i + 1)/RT)*exp(-(Ea + 2 * Ec + (l - i - 1) * Eb)/RT) * 
+								partial_multi[l][j]; 
+					//Changed h in the paper to l it makes no difference
+					//other than unifying loops
+				}
+			}
+		}
 
-	partial_multi[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) *
-				(exp(-ed3(h,l,l+1)/RT)*u_helper[l+2,j-1] + u_helper[l+1][j-1] -
-				u_helper[l+2][j-1]);
 
-	partial_multi2[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) *
-				(cond_dangle(j + 1, h, l)*exp(-(j-l) * b / RT) + exp(-ed3(h,l,l + 1)/RT)*u_helper(l+2,j)
-				+u_helper(l + 1,j) - u1(l + 2,j));
-				
+		up[i][j] += exp(-eh(i,j)/RT) + exp(-es(i,j)/RT) * up[i + 1][j - 1] + upm[i][j];
+		for(l = j - 1; l > i + 1; l--){
+			if((j - l) - 2> MAX_LOOP){
+				break;
+			}
+			for(h = i + 1 ; h < l; h++){
+				if(!(i == h - 1 && j == l - 1)){ //If this is true we have a stack
+					up[i][j] += exp(-ebi(i,j,h,l)/RT);
+				}
+				if((j - l) + (h - i) - 2> MAX_LOOP){
+					break;
+				}
+			}
+		}
+
+		for(l = i + 1; l <= j ; l++){
+			u_multi[i][j] += up[i][l] * exp(-(Ec + auPenalty(i,l))/RT) *
+					(cond_dangle(j + 1, i, l) * exp(-(j - l) * Eb/RT) + 
+					exp(-Ed3(i,l,l + 1)/RT) * u_multi[l + 2][j] + 
+					u_multi[l + 1][j] -
+					u_multi[l + 2][j]);
+			if(l != i+1){	
+				u_multi[i][j] += up[i + 1][j]*exp(-(Ec + Eb + auPenalty(i + 1,l))/RT)*
+						(cond_dangle(j + 1, i + 1, l) * exp(-(j - l)*Eb/RT) + 
+						exp(-Ed3(i + 1,l,l + 1)/RT) * u_multi[l + 2][j] + 
+						u_multi[l + 1][j] - 
+						u_multi[l + 2][j]);
+				if(l != j){
+					u_multi[i][j] += exp(-(Ec + (h - i) * Eb)/RT) * partial_multi2[l][j];
+
+				}
+			}
+		}
+
+
+		int h = i; //To stay consistant with the notation in the paper.
+
+		for(l = h+1; l < j; l++){
+			partial_external[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
+						(exp(-Ed3(h,l,l + 1)/RT)*u[l + 2,j - 1] + 
+						u[l + 1][j] -
+						u[l + 2][j]);
+
+			partial_multi[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
+						(exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j - 1] + 
+						u_multi[l + 1][j - 1] -
+						u_multi[l + 2][j - 1]);
+
+			partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
+						(cond_dangle(j + 1, h, l)*exp(-(j - l) * Eb / RT) + 
+						exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j] + 
+						u_multi[l + 1][j] - 
+						u_multi[l + 2][j]);
+						
+		}
+		/** partial_multi2 goes up to j **/
+		partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
+					(cond_dangle(j + 1, h, l)*exp(-(j-l) * Eb / RT) + 
+					exp(-Ed3(h,l,l + 1)/RT) * u_multi[l + 2][j] + 
+					u_multi[l + 1][j] - 
+					u_multi[l + 2][j]);
+
+		//Finally we do the u matrix
+		u[i][j] = 1 + up[i][j]*exp(-auPenalty(i,j) /RT);
+
+		for(l = i + 1; l < j; l++){
+			//Replaced l with h in the next line to unify loops
+			u[i][j] += up[l][j] * exp(-(Ed5(l, j , l - 1) + auPenalty(h,j))/RT)
+
+			u[i][j] += exp(-(auPenalty(i,l))/RT)*(exp(-Ed3(i,l,l + 1)/RT) * u[l + 2][j] +
+				   u[l + 1][j] - u[l + 2][j]);
+			if(l != j - 1) {
+				u[i][j] += partial_external[l][j];
+			}
+				   
+		}
+	}
 }
-/** partial_multi2 goes up to j **/
-partial_multi2[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) *
-				(cond_dangle(j + 1, h, l)*exp(-(j-l) * b / RT) + exp(-ed3(h,l,l + 1)/RT)*u_helper(l+2,j)
-				+u_helper(l + 1,j) - u1(l + 3,j));

From d814038e5fc3aab31b13ad257a79dcb725a8d10a Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Wed, 18 May 2011 17:32:30 -0400
Subject: [PATCH 121/282] Compiles does not link

---
 gtfold-mfe/Makefile                      |  24 +-
 gtfold-mfe/configure                     | 343 +++++++++++-----------
 gtfold-mfe/include/Makefile.am           |   2 +-
 gtfold-mfe/include/Makefile.in           |   2 +-
 gtfold-mfe/src/.deps/algorithms.Po       |  33 ++-
 gtfold-mfe/src/.deps/constraints.Po      | 311 ++++++++++----------
 gtfold-mfe/src/.deps/energy.Po           |  33 ++-
 gtfold-mfe/src/.deps/global.Po           |  23 +-
 gtfold-mfe/src/.deps/loader.Po           | 286 +++++++++---------
 gtfold-mfe/src/.deps/main.Po             | 352 +++++++++++------------
 gtfold-mfe/src/.deps/options.Po          | 197 +++++++------
 gtfold-mfe/src/.deps/shapereader.Po      | 282 +++++++++---------
 gtfold-mfe/src/.deps/subopt_traceback.Po | 321 ++++++++++-----------
 gtfold-mfe/src/.deps/traceback.Po        |  23 +-
 gtfold-mfe/src/.deps/utils.Po            | 185 ++++++------
 gtfold-mfe/src/Makefile                  |  29 +-
 gtfold-mfe/src/Makefile.am               |   1 +
 gtfold-mfe/src/Makefile.in               |   5 +-
 gtfold-mfe/src/algorithms-partition.c    |   1 -
 gtfold-mfe/src/partition-dangle.cc       | 130 ---------
 20 files changed, 1241 insertions(+), 1342 deletions(-)
 delete mode 100644 gtfold-mfe/src/partition-dangle.cc

diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile
index 75480ce..cdd52e6 100644
--- a/gtfold-mfe/Makefile
+++ b/gtfold-mfe/Makefile
@@ -126,12 +126,12 @@ DIST_ARCHIVES = $(distdir).tar.gz
 GZIP_ENV = --best
 distuninstallcheck_listfiles = find . -type f -print
 distcleancheck_listfiles = find . -type f -print
-ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = gawk
+ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = mawk
 CC = gcc
 CCDEPMODE = depmode=gcc3
 CFLAGS = -g -O2 -Wall
@@ -158,7 +158,7 @@ LDFLAGS =
 LIBOBJS = 
 LIBS = -lgomp 
 LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
 MKDIR_P = /bin/mkdir -p
 OBJEXT = o
 OPENMP_CFLAGS = -fopenmp
@@ -174,10 +174,10 @@ SET_MAKE =
 SHELL = /bin/bash
 STRIP = 
 VERSION = 1.18
-abs_builddir = /home/zs/git/gtfold/gtfold-mfe
-abs_srcdir = /home/zs/git/gtfold/gtfold-mfe
-abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
-abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe
+abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
+abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
+abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
 ac_ct_CC = gcc
 ac_ct_CXX = g++
 am__include = include
@@ -205,7 +205,7 @@ host_vendor = unknown
 htmldir = ${docdir}
 includedir = ${prefix}/include
 infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
 libdir = ${exec_prefix}/lib
 libexecdir = ${exec_prefix}/libexec
 localedir = ${datarootdir}/locale
diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure
index da30cd9..c5acafe 100755
--- a/gtfold-mfe/configure
+++ b/gtfold-mfe/configure
@@ -1,11 +1,11 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.65 for gtfold 1.18.
+# Generated by GNU Autoconf 2.67 for gtfold 1.18.
 #
 #
 # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-# Inc.
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
+# Foundation, Inc.
 #
 #
 # This configure script is free software; the Free Software Foundation
@@ -316,7 +316,7 @@ $as_echo X"$as_dir" |
       test -d "$as_dir" && break
     done
     test -z "$as_dirs" || eval "mkdir $as_dirs"
-  } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir"
+  } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
 
 
 } # as_fn_mkdir_p
@@ -356,19 +356,19 @@ else
 fi # as_fn_arith
 
 
-# as_fn_error ERROR [LINENO LOG_FD]
-# ---------------------------------
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
 # Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
 # provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-# script with status $?, using 1 if that was 0.
+# script with STATUS, using 1 if that was 0.
 as_fn_error ()
 {
-  as_status=$?; test $as_status -eq 0 && as_status=1
-  if test "$3"; then
-    as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-    $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3
+  as_status=$1; test $as_status -eq 0 && as_status=1
+  if test "$4"; then
+    as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+    $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
   fi
-  $as_echo "$as_me: error: $1" >&2
+  $as_echo "$as_me: error: $2" >&2
   as_fn_exit $as_status
 } # as_fn_error
 
@@ -530,7 +530,7 @@ test -n "$DJDIR" || exec 7<&0 </dev/null
 exec 6>&1
 
 # Name of the host.
-# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
 # so uname gets run too.
 ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
 
@@ -778,8 +778,9 @@ do
   fi
 
   case $ac_option in
-  *=*)	ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
-  *)	ac_optarg=yes ;;
+  *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+  *=)   ac_optarg= ;;
+  *)    ac_optarg=yes ;;
   esac
 
   # Accept the important Cygnus configure options, so we can diagnose typos.
@@ -824,7 +825,7 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error "invalid feature name: $ac_useropt"
+      as_fn_error $? "invalid feature name: $ac_useropt"
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -850,7 +851,7 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error "invalid feature name: $ac_useropt"
+      as_fn_error $? "invalid feature name: $ac_useropt"
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -1054,7 +1055,7 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error "invalid package name: $ac_useropt"
+      as_fn_error $? "invalid package name: $ac_useropt"
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -1070,7 +1071,7 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error "invalid package name: $ac_useropt"
+      as_fn_error $? "invalid package name: $ac_useropt"
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -1100,8 +1101,8 @@ do
   | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
     x_libraries=$ac_optarg ;;
 
-  -*) as_fn_error "unrecognized option: \`$ac_option'
-Try \`$0 --help' for more information."
+  -*) as_fn_error $? "unrecognized option: \`$ac_option'
+Try \`$0 --help' for more information"
     ;;
 
   *=*)
@@ -1109,7 +1110,7 @@ Try \`$0 --help' for more information."
     # Reject names that are not valid shell variable names.
     case $ac_envvar in #(
       '' | [0-9]* | *[!_$as_cr_alnum]* )
-      as_fn_error "invalid variable name: \`$ac_envvar'" ;;
+      as_fn_error $? "invalid variable name: \`$ac_envvar'" ;;
     esac
     eval $ac_envvar=\$ac_optarg
     export $ac_envvar ;;
@@ -1127,13 +1128,13 @@ done
 
 if test -n "$ac_prev"; then
   ac_option=--`echo $ac_prev | sed 's/_/-/g'`
-  as_fn_error "missing argument to $ac_option"
+  as_fn_error $? "missing argument to $ac_option"
 fi
 
 if test -n "$ac_unrecognized_opts"; then
   case $enable_option_checking in
     no) ;;
-    fatal) as_fn_error "unrecognized options: $ac_unrecognized_opts" ;;
+    fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;;
     *)     $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;;
   esac
 fi
@@ -1156,7 +1157,7 @@ do
     [\\/$]* | ?:[\\/]* )  continue;;
     NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
   esac
-  as_fn_error "expected an absolute directory name for --$ac_var: $ac_val"
+  as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val"
 done
 
 # There might be people who depend on the old broken behavior: `$host'
@@ -1170,8 +1171,8 @@ target=$target_alias
 if test "x$host_alias" != x; then
   if test "x$build_alias" = x; then
     cross_compiling=maybe
-    $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
-    If a cross compiler is detected then cross compile mode will be used." >&2
+    $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host.
+    If a cross compiler is detected then cross compile mode will be used" >&2
   elif test "x$build_alias" != "x$host_alias"; then
     cross_compiling=yes
   fi
@@ -1186,9 +1187,9 @@ test "$silent" = yes && exec 6>/dev/null
 ac_pwd=`pwd` && test -n "$ac_pwd" &&
 ac_ls_di=`ls -di .` &&
 ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
-  as_fn_error "working directory cannot be determined"
+  as_fn_error $? "working directory cannot be determined"
 test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
-  as_fn_error "pwd does not report name of working directory"
+  as_fn_error $? "pwd does not report name of working directory"
 
 
 # Find the source files, if location was not specified.
@@ -1227,11 +1228,11 @@ else
 fi
 if test ! -r "$srcdir/$ac_unique_file"; then
   test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
-  as_fn_error "cannot find sources ($ac_unique_file) in $srcdir"
+  as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
 fi
 ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
 ac_abs_confdir=`(
-	cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error "$ac_msg"
+	cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
 	pwd)`
 # When building in place, set srcdir=.
 if test "$ac_abs_confdir" = "$ac_pwd"; then
@@ -1271,7 +1272,7 @@ Configuration:
       --help=short        display options specific to this package
       --help=recursive    display the short help of all the included packages
   -V, --version           display version information and exit
-  -q, --quiet, --silent   do not print \`checking...' messages
+  -q, --quiet, --silent   do not print \`checking ...' messages
       --cache-file=FILE   cache test results in FILE [disabled]
   -C, --config-cache      alias for \`--cache-file=config.cache'
   -n, --no-create         do not create output files
@@ -1421,9 +1422,9 @@ test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
 gtfold configure 1.18
-generated by GNU Autoconf 2.65
+generated by GNU Autoconf 2.67
 
-Copyright (C) 2009 Free Software Foundation, Inc.
+Copyright (C) 2010 Free Software Foundation, Inc.
 This configure script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it.
 _ACEOF
@@ -1577,7 +1578,7 @@ $as_echo "$ac_try_echo"; } >&5
     mv -f conftest.er1 conftest.err
   fi
   $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; } >/dev/null && {
+  test $ac_status = 0; } > conftest.i && {
 	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
 	 test ! -s conftest.err
        }; then :
@@ -1643,10 +1644,10 @@ fi
 ac_fn_c_check_header_mongrel ()
 {
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+  if eval "test \"\${$3+set}\"" = set; then :
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 fi
 eval ac_res=\$$3
@@ -1682,7 +1683,7 @@ if ac_fn_c_try_cpp "$LINENO"; then :
 else
   ac_header_preproc=no
 fi
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.err conftest.i conftest.$ac_ext
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
 $as_echo "$ac_header_preproc" >&6; }
 
@@ -1709,7 +1710,7 @@ $as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
 esac
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   eval "$3=\$ac_header_compiler"
@@ -1731,7 +1732,7 @@ ac_fn_c_check_header_compile ()
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -1762,7 +1763,7 @@ ac_fn_c_check_type ()
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   eval "$3=no"
@@ -1815,7 +1816,7 @@ ac_fn_c_check_func ()
   as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
 $as_echo_n "checking for $2... " >&6; }
-if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${$3+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -1878,7 +1879,7 @@ This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
 It was created by gtfold $as_me 1.18, which was
-generated by GNU Autoconf 2.65.  Invocation command line was
+generated by GNU Autoconf 2.67.  Invocation command line was
 
   $ $0 $@
 
@@ -1988,11 +1989,9 @@ trap 'exit_status=$?
   {
     echo
 
-    cat <<\_ASBOX
-## ---------------- ##
+    $as_echo "## ---------------- ##
 ## Cache variables. ##
-## ---------------- ##
-_ASBOX
+## ---------------- ##"
     echo
     # The following way of writing the cache mishandles newlines in values,
 (
@@ -2026,11 +2025,9 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
 )
     echo
 
-    cat <<\_ASBOX
-## ----------------- ##
+    $as_echo "## ----------------- ##
 ## Output variables. ##
-## ----------------- ##
-_ASBOX
+## ----------------- ##"
     echo
     for ac_var in $ac_subst_vars
     do
@@ -2043,11 +2040,9 @@ _ASBOX
     echo
 
     if test -n "$ac_subst_files"; then
-      cat <<\_ASBOX
-## ------------------- ##
+      $as_echo "## ------------------- ##
 ## File substitutions. ##
-## ------------------- ##
-_ASBOX
+## ------------------- ##"
       echo
       for ac_var in $ac_subst_files
       do
@@ -2061,11 +2056,9 @@ _ASBOX
     fi
 
     if test -s confdefs.h; then
-      cat <<\_ASBOX
-## ----------- ##
+      $as_echo "## ----------- ##
 ## confdefs.h. ##
-## ----------- ##
-_ASBOX
+## ----------- ##"
       echo
       cat confdefs.h
       echo
@@ -2120,7 +2113,12 @@ _ACEOF
 ac_site_file1=NONE
 ac_site_file2=NONE
 if test -n "$CONFIG_SITE"; then
-  ac_site_file1=$CONFIG_SITE
+  # We do not want a PATH search for config.site.
+  case $CONFIG_SITE in #((
+    -*)  ac_site_file1=./$CONFIG_SITE;;
+    */*) ac_site_file1=$CONFIG_SITE;;
+    *)   ac_site_file1=./$CONFIG_SITE;;
+  esac
 elif test "x$prefix" != xNONE; then
   ac_site_file1=$prefix/share/config.site
   ac_site_file2=$prefix/etc/config.site
@@ -2135,7 +2133,11 @@ do
     { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
 $as_echo "$as_me: loading site script $ac_site_file" >&6;}
     sed 's/^/| /' "$ac_site_file" >&5
-    . "$ac_site_file"
+    . "$ac_site_file" \
+      || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "failed to load site script $ac_site_file
+See \`config.log' for more details" "$LINENO" 5 ; }
   fi
 done
 
@@ -2211,7 +2213,7 @@ if $ac_cache_corrupted; then
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
   { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
 $as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
-  as_fn_error "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+  as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
 fi
 ## -------------------- ##
 ## Main body of script. ##
@@ -2232,16 +2234,22 @@ ac_config_headers="$ac_config_headers gtfold_config.h"
 
 ac_aux_dir=
 for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
-  for ac_t in install-sh install.sh shtool; do
-    if test -f "$ac_dir/$ac_t"; then
-      ac_aux_dir=$ac_dir
-      ac_install_sh="$ac_aux_dir/$ac_t -c"
-      break 2
-    fi
-  done
+  if test -f "$ac_dir/install-sh"; then
+    ac_aux_dir=$ac_dir
+    ac_install_sh="$ac_aux_dir/install-sh -c"
+    break
+  elif test -f "$ac_dir/install.sh"; then
+    ac_aux_dir=$ac_dir
+    ac_install_sh="$ac_aux_dir/install.sh -c"
+    break
+  elif test -f "$ac_dir/shtool"; then
+    ac_aux_dir=$ac_dir
+    ac_install_sh="$ac_aux_dir/shtool install -c"
+    break
+  fi
 done
 if test -z "$ac_aux_dir"; then
-  as_fn_error "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
+  as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
 fi
 
 # These three variables are undocumented and unsupported,
@@ -2255,7 +2263,7 @@ ac_configure="$SHELL $ac_aux_dir/configure"  # Please don't use this var.
 
 # Make sure we can run config.sub.
 $SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
-  as_fn_error "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
+  as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
 $as_echo_n "checking build system type... " >&6; }
@@ -2266,16 +2274,16 @@ else
 test "x$ac_build_alias" = x &&
   ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
 test "x$ac_build_alias" = x &&
-  as_fn_error "cannot guess build type; you must specify one" "$LINENO" 5
+  as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
 ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
-  as_fn_error "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
+  as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
 
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
 $as_echo "$ac_cv_build" >&6; }
 case $ac_cv_build in
 *-*-*) ;;
-*) as_fn_error "invalid value of canonical build" "$LINENO" 5;;
+*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;;
 esac
 build=$ac_cv_build
 ac_save_IFS=$IFS; IFS='-'
@@ -2300,7 +2308,7 @@ else
   ac_cv_host=$ac_cv_build
 else
   ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
-    as_fn_error "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
+    as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
 fi
 
 fi
@@ -2308,7 +2316,7 @@ fi
 $as_echo "$ac_cv_host" >&6; }
 case $ac_cv_host in
 *-*-*) ;;
-*) as_fn_error "invalid value of canonical host" "$LINENO" 5;;
+*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;;
 esac
 host=$ac_cv_host
 ac_save_IFS=$IFS; IFS='-'
@@ -2333,7 +2341,7 @@ else
   ac_cv_target=$ac_cv_host
 else
   ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` ||
-    as_fn_error "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5
+    as_fn_error $? "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5
 fi
 
 fi
@@ -2341,7 +2349,7 @@ fi
 $as_echo "$ac_cv_target" >&6; }
 case $ac_cv_target in
 *-*-*) ;;
-*) as_fn_error "invalid value of canonical target" "$LINENO" 5;;
+*) as_fn_error $? "invalid value of canonical target" "$LINENO" 5 ;;
 esac
 target=$ac_cv_target
 ac_save_IFS=$IFS; IFS='-'
@@ -2471,11 +2479,11 @@ am_lf='
 '
 case `pwd` in
   *[\\\"\#\$\&\'\`$am_lf]*)
-    as_fn_error "unsafe absolute working directory name" "$LINENO" 5;;
+    as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;;
 esac
 case $srcdir in
   *[\\\"\#\$\&\'\`$am_lf\ \	]*)
-    as_fn_error "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
+    as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;;
 esac
 
 # Do `set' in a subshell so we don't clobber the current shell's
@@ -2497,7 +2505,7 @@ if (
       # if, for instance, CONFIG_SHELL is bash and it inherits a
       # broken ls alias from the environment.  This has actually
       # happened.  Such a system could not be considered "sane".
-      as_fn_error "ls -t appears to fail.  Make sure there is not a broken
+      as_fn_error $? "ls -t appears to fail.  Make sure there is not a broken
 alias in your environment" "$LINENO" 5
    fi
 
@@ -2507,7 +2515,7 @@ then
    # Ok.
    :
 else
-   as_fn_error "newly created file is older than distributed files!
+   as_fn_error $? "newly created file is older than distributed files!
 Check your system clock" "$LINENO" 5
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
@@ -2745,7 +2753,7 @@ done
 $as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
 set x ${MAKE-make}
 ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
-if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then :
+if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then :
   $as_echo_n "(cached) " >&6
 else
   cat >conftest.make <<\_ACEOF
@@ -2753,7 +2761,7 @@ SHELL = /bin/sh
 all:
 	@echo '@@@%%%=$(MAKE)=@@@%%%'
 _ACEOF
-# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
+# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
 case `${MAKE-make} -f conftest.make 2>/dev/null` in
   *@@@%%%=?*=@@@%%%*)
     eval ac_cv_prog_make_${ac_make}_set=yes;;
@@ -2787,7 +2795,7 @@ if test "`cd $srcdir && pwd`" != "`pwd`"; then
   am__isrc=' -I$(srcdir)'
   # test to see if srcdir already configured
   if test -f $srcdir/config.status; then
-    as_fn_error "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+    as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
   fi
 fi
 
@@ -2849,7 +2857,7 @@ if test "${enable_64bit+set}" = set; then :
   enableval=$enable_64bit; case "${enableval}" in
     "" | y | ye | yes) gtfold_cv_enable_64bit=yes ;;
     n | no) gtfold_cv_enable_64bit=no ;;
-    *) as_fn_error "bad value ${enableval} for --enable-64bit" "$LINENO" 5 ;;
+    *) as_fn_error $? "bad value ${enableval} for --enable-64bit" "$LINENO" 5  ;;
   esac
 else
   gtfold_cv_enable_64bit=no
@@ -2978,8 +2986,8 @@ fi
 
 test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "no acceptable C compiler found in \$PATH
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5 ; }
 
 # Provide some information about the compiler.
 $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
@@ -3093,9 +3101,8 @@ sed 's/^/| /' conftest.$ac_ext >&5
 
 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ as_fn_set_status 77
-as_fn_error "C compiler cannot create executables
-See \`config.log' for more details." "$LINENO" 5; }; }
+as_fn_error 77 "C compiler cannot create executables
+See \`config.log' for more details" "$LINENO" 5 ; }
 else
   { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
 $as_echo "yes" >&6; }
@@ -3137,8 +3144,8 @@ done
 else
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "cannot compute suffix of executables: cannot compile and link
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 rm -f conftest conftest$ac_cv_exeext
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
@@ -3195,9 +3202,9 @@ $as_echo "$ac_try_echo"; } >&5
     else
 	{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "cannot run C compiled programs.
+as_fn_error $? "cannot run C compiled programs.
 If you meant to cross compile, use \`--host'.
-See \`config.log' for more details." "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5 ; }
     fi
   fi
 fi
@@ -3248,8 +3255,8 @@ sed 's/^/| /' conftest.$ac_ext >&5
 
 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "cannot compute suffix of object files: cannot compile
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 rm -f conftest.$ac_cv_objext conftest.$ac_ext
 fi
@@ -4199,7 +4206,7 @@ else
   # Broken: fails on valid input.
 continue
 fi
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.err conftest.i conftest.$ac_ext
 
   # OK, works on sane cases.  Now check whether nonexistent headers
   # can be detected and how.
@@ -4215,11 +4222,11 @@ else
 ac_preproc_ok=:
 break
 fi
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.err conftest.i conftest.$ac_ext
 
 done
 # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.i conftest.err conftest.$ac_ext
 if $ac_preproc_ok; then :
   break
 fi
@@ -4258,7 +4265,7 @@ else
   # Broken: fails on valid input.
 continue
 fi
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.err conftest.i conftest.$ac_ext
 
   # OK, works on sane cases.  Now check whether nonexistent headers
   # can be detected and how.
@@ -4274,18 +4281,18 @@ else
 ac_preproc_ok=:
 break
 fi
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.err conftest.i conftest.$ac_ext
 
 done
 # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
-rm -f conftest.err conftest.$ac_ext
+rm -f conftest.i conftest.err conftest.$ac_ext
 if $ac_preproc_ok; then :
 
 else
   { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "C preprocessor \"$CPP\" fails sanity check
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details" "$LINENO" 5 ; }
 fi
 
 ac_ext=c
@@ -4346,7 +4353,7 @@ esac
   done
 IFS=$as_save_IFS
   if test -z "$ac_cv_path_GREP"; then
-    as_fn_error "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+    as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
   fi
 else
   ac_cv_path_GREP=$GREP
@@ -4412,7 +4419,7 @@ esac
   done
 IFS=$as_save_IFS
   if test -z "$ac_cv_path_EGREP"; then
-    as_fn_error "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+    as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
   fi
 else
   ac_cv_path_EGREP=$EGREP
@@ -4546,8 +4553,7 @@ do :
   as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
 ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
 "
-eval as_val=\$$as_ac_Header
-   if test "x$as_val" = x""yes; then :
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
   cat >>confdefs.h <<_ACEOF
 #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
 _ACEOF
@@ -4561,8 +4567,7 @@ for ac_header in stdlib.h string.h sys/time.h
 do :
   as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
 ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
-eval as_val=\$$as_ac_Header
-   if test "x$as_val" = x""yes; then :
+if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
   cat >>confdefs.h <<_ACEOF
 #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
 _ACEOF
@@ -5073,8 +5078,7 @@ for ac_func in floor gettimeofday pow
 do :
   as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
 ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
-eval as_val=\$$as_ac_var
-   if test "x$as_val" = x""yes; then :
+if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
   cat >>confdefs.h <<_ACEOF
 #define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
 _ACEOF
@@ -5089,7 +5093,7 @@ if test "${enable_debug+set}" = set; then :
     "" | y | ye | yes) debug=true;
 		       CFLAGS=$(echo $CFLAGS -g | sed -e 's/-O\|-O2\|-O3//g') ;;
     n | no) debug=false ;;
-    *) as_fn_error "bad value ${enableval} for --enable-debug" "$LINENO" 5 ;;
+    *) as_fn_error $? "bad value ${enableval} for --enable-debug" "$LINENO" 5  ;;
   esac
 else
   debug=false
@@ -5192,6 +5196,7 @@ DEFS=-DHAVE_CONFIG_H
 
 ac_libobjs=
 ac_ltlibobjs=
+U=
 for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
   # 1. Remove the extension, and $U if already installed.
   ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
@@ -5215,19 +5220,19 @@ else
 fi
 
 if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
-  as_fn_error "conditional \"AMDEP\" was never defined.
+  as_fn_error $? "conditional \"AMDEP\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5
 fi
 if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
-  as_fn_error "conditional \"am__fastdepCC\" was never defined.
+  as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5
 fi
 if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
-  as_fn_error "conditional \"am__fastdepCXX\" was never defined.
+  as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5
 fi
 if test -z "${GTFOLD_DEBUG_TRUE}" && test -z "${GTFOLD_DEBUG_FALSE}"; then
-  as_fn_error "conditional \"GTFOLD_DEBUG\" was never defined.
+  as_fn_error $? "conditional \"GTFOLD_DEBUG\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5
 fi
 
@@ -5377,19 +5382,19 @@ export LANGUAGE
 (unset CDPATH) >/dev/null 2>&1 && unset CDPATH
 
 
-# as_fn_error ERROR [LINENO LOG_FD]
-# ---------------------------------
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
 # Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
 # provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-# script with status $?, using 1 if that was 0.
+# script with STATUS, using 1 if that was 0.
 as_fn_error ()
 {
-  as_status=$?; test $as_status -eq 0 && as_status=1
-  if test "$3"; then
-    as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-    $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3
+  as_status=$1; test $as_status -eq 0 && as_status=1
+  if test "$4"; then
+    as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+    $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
   fi
-  $as_echo "$as_me: error: $1" >&2
+  $as_echo "$as_me: error: $2" >&2
   as_fn_exit $as_status
 } # as_fn_error
 
@@ -5585,7 +5590,7 @@ $as_echo X"$as_dir" |
       test -d "$as_dir" && break
     done
     test -z "$as_dirs" || eval "mkdir $as_dirs"
-  } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir"
+  } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
 
 
 } # as_fn_mkdir_p
@@ -5639,7 +5644,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # values after options handling.
 ac_log="
 This file was extended by gtfold $as_me 1.18, which was
-generated by GNU Autoconf 2.65.  Invocation command line was
+generated by GNU Autoconf 2.67.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
   CONFIG_HEADERS  = $CONFIG_HEADERS
@@ -5705,10 +5710,10 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
 gtfold config.status 1.18
-configured by $0, generated by GNU Autoconf 2.65,
+configured by $0, generated by GNU Autoconf 2.67,
   with options \\"\$ac_cs_config\\"
 
-Copyright (C) 2009 Free Software Foundation, Inc.
+Copyright (C) 2010 Free Software Foundation, Inc.
 This config.status script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it."
 
@@ -5726,11 +5731,16 @@ ac_need_defaults=:
 while test $# != 0
 do
   case $1 in
-  --*=*)
+  --*=?*)
     ac_option=`expr "X$1" : 'X\([^=]*\)='`
     ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
     ac_shift=:
     ;;
+  --*=)
+    ac_option=`expr "X$1" : 'X\([^=]*\)='`
+    ac_optarg=
+    ac_shift=:
+    ;;
   *)
     ac_option=$1
     ac_optarg=$2
@@ -5752,6 +5762,7 @@ do
     $ac_shift
     case $ac_optarg in
     *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+    '') as_fn_error $? "missing file argument" ;;
     esac
     as_fn_append CONFIG_FILES " '$ac_optarg'"
     ac_need_defaults=false;;
@@ -5764,7 +5775,7 @@ do
     ac_need_defaults=false;;
   --he | --h)
     # Conflict between --help and --header
-    as_fn_error "ambiguous option: \`$1'
+    as_fn_error $? "ambiguous option: \`$1'
 Try \`$0 --help' for more information.";;
   --help | --hel | -h )
     $as_echo "$ac_cs_usage"; exit ;;
@@ -5773,7 +5784,7 @@ Try \`$0 --help' for more information.";;
     ac_cs_silent=: ;;
 
   # This is an error.
-  -*) as_fn_error "unrecognized option: \`$1'
+  -*) as_fn_error $? "unrecognized option: \`$1'
 Try \`$0 --help' for more information." ;;
 
   *) as_fn_append ac_config_targets " $1"
@@ -5837,7 +5848,7 @@ do
     "data/Turner04/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner04/Makefile" ;;
     "data/Andronescu/Makefile") CONFIG_FILES="$CONFIG_FILES data/Andronescu/Makefile" ;;
 
-  *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
+  *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;;
   esac
 done
 
@@ -5875,7 +5886,7 @@ $debug ||
 {
   tmp=./conf$$-$RANDOM
   (umask 077 && mkdir "$tmp")
-} || as_fn_error "cannot create a temporary directory in ." "$LINENO" 5
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
 
 # Set up the scripts for CONFIG_FILES section.
 # No need to generate them if there are no CONFIG_FILES.
@@ -5892,7 +5903,7 @@ if test "x$ac_cr" = x; then
 fi
 ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
 if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
-  ac_cs_awk_cr='\r'
+  ac_cs_awk_cr='\\r'
 else
   ac_cs_awk_cr=$ac_cr
 fi
@@ -5906,18 +5917,18 @@ _ACEOF
   echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
   echo "_ACEOF"
 } >conf$$subs.sh ||
-  as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5
-ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'`
+  as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
 ac_delim='%!_!# '
 for ac_last_try in false false false false false :; do
   . ./conf$$subs.sh ||
-    as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5
+    as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
 
   ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
   if test $ac_delim_n = $ac_delim_num; then
     break
   elif $ac_last_try; then
-    as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5
+    as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
   else
     ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
   fi
@@ -6006,20 +6017,28 @@ if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
 else
   cat
 fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
-  || as_fn_error "could not setup config files machinery" "$LINENO" 5
+  || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
 _ACEOF
 
-# VPATH may cause trouble with some makes, so we remove $(srcdir),
-# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
 # trailing colons and then remove the whole line if VPATH becomes empty
 # (actually we leave an empty line to preserve line numbers).
 if test "x$srcdir" = x.; then
-  ac_vpsub='/^[	 ]*VPATH[	 ]*=/{
-s/:*\$(srcdir):*/:/
-s/:*\${srcdir}:*/:/
-s/:*@srcdir@:*/:/
-s/^\([^=]*=[	 ]*\):*/\1/
+  ac_vpsub='/^[	 ]*VPATH[	 ]*=[	 ]*/{
+h
+s///
+s/^/:/
+s/[	 ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
 s/:*$//
+x
+s/\(=[	 ]*\).*/\1/
+G
+s/\n//
 s/^[^=]*=[	 ]*$//
 }'
 fi
@@ -6047,7 +6066,7 @@ for ac_last_try in false false :; do
   if test -z "$ac_t"; then
     break
   elif $ac_last_try; then
-    as_fn_error "could not make $CONFIG_HEADERS" "$LINENO" 5
+    as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
   else
     ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
   fi
@@ -6132,7 +6151,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 _ACAWK
 _ACEOF
 cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-  as_fn_error "could not setup config headers machinery" "$LINENO" 5
+  as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
 fi # test -n "$CONFIG_HEADERS"
 
 
@@ -6145,7 +6164,7 @@ do
   esac
   case $ac_mode$ac_tag in
   :[FHL]*:*);;
-  :L* | :C*:*) as_fn_error "invalid tag \`$ac_tag'" "$LINENO" 5;;
+  :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;;
   :[FH]-) ac_tag=-:-;;
   :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
   esac
@@ -6173,7 +6192,7 @@ do
 	   [\\/$]*) false;;
 	   *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
 	   esac ||
-	   as_fn_error "cannot find input file: \`$ac_f'" "$LINENO" 5;;
+	   as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;;
       esac
       case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
       as_fn_append ac_file_inputs " '$ac_f'"
@@ -6200,7 +6219,7 @@ $as_echo "$as_me: creating $ac_file" >&6;}
 
     case $ac_tag in
     *:-:* | *:-) cat >"$tmp/stdin" \
-      || as_fn_error "could not create $ac_file" "$LINENO" 5 ;;
+      || as_fn_error $? "could not create $ac_file" "$LINENO" 5  ;;
     esac
     ;;
   esac
@@ -6337,22 +6356,22 @@ s&@MKDIR_P@&$ac_MKDIR_P&;t t
 $ac_datarootdir_hack
 "
 eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \
-  || as_fn_error "could not create $ac_file" "$LINENO" 5
+  || as_fn_error $? "could not create $ac_file" "$LINENO" 5
 
 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
   { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
   { ac_out=`sed -n '/^[	 ]*datarootdir[	 ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined.  Please make sure it is defined." >&5
+which seems to be undefined.  Please make sure it is defined" >&5
 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined.  Please make sure it is defined." >&2;}
+which seems to be undefined.  Please make sure it is defined" >&2;}
 
   rm -f "$tmp/stdin"
   case $ac_file in
   -) cat "$tmp/out" && rm -f "$tmp/out";;
   *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
   esac \
-  || as_fn_error "could not create $ac_file" "$LINENO" 5
+  || as_fn_error $? "could not create $ac_file" "$LINENO" 5
  ;;
   :H)
   #
@@ -6363,19 +6382,19 @@ which seems to be undefined.  Please make sure it is defined." >&2;}
       $as_echo "/* $configure_input  */" \
       && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs"
     } >"$tmp/config.h" \
-      || as_fn_error "could not create $ac_file" "$LINENO" 5
+      || as_fn_error $? "could not create $ac_file" "$LINENO" 5
     if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then
       { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
 $as_echo "$as_me: $ac_file is unchanged" >&6;}
     else
       rm -f "$ac_file"
       mv "$tmp/config.h" "$ac_file" \
-	|| as_fn_error "could not create $ac_file" "$LINENO" 5
+	|| as_fn_error $? "could not create $ac_file" "$LINENO" 5
     fi
   else
     $as_echo "/* $configure_input  */" \
       && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \
-      || as_fn_error "could not create -" "$LINENO" 5
+      || as_fn_error $? "could not create -" "$LINENO" 5
   fi
 # Compute "$ac_file"'s index in $config_headers.
 _am_arg="$ac_file"
@@ -6525,7 +6544,7 @@ _ACEOF
 ac_clean_files=$ac_clean_files_save
 
 test $ac_write_fail = 0 ||
-  as_fn_error "write failure creating $CONFIG_STATUS" "$LINENO" 5
+  as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
 
 
 # configure is writing to config.log, and then calls config.status.
@@ -6546,7 +6565,7 @@ if test "$no_create" != yes; then
   exec 5>>config.log
   # Use ||, not &&, to avoid exiting from the if with $? = 1, which
   # would make configure fail if this is the last instruction.
-  $ac_cs_success || as_fn_exit $?
+  $ac_cs_success || as_fn_exit 1
 fi
 if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am
index 545325a..b73b2f6 100644
--- a/gtfold-mfe/include/Makefile.am
+++ b/gtfold-mfe/include/Makefile.am
@@ -1,3 +1,3 @@
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h
 
 CLEANFILES = *~
diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in
index 1fc5099..a0bf52b 100644
--- a/gtfold-mfe/include/Makefile.in
+++ b/gtfold-mfe/include/Makefile.in
@@ -155,7 +155,7 @@ target_vendor = @target_vendor@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h
 CLEANFILES = *~
 all: all-am
 
diff --git a/gtfold-mfe/src/.deps/algorithms.Po b/gtfold-mfe/src/.deps/algorithms.Po
index c737d2e..d5d1ad2 100644
--- a/gtfold-mfe/src/.deps/algorithms.Po
+++ b/gtfold-mfe/src/.deps/algorithms.Po
@@ -2,10 +2,10 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \
  /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
@@ -15,15 +15,16 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/time.h /usr/include/bits/time.h /usr/include/xlocale.h \
  /usr/include/sys/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/endian.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
  /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
- /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/assert.h \
- ../include/constants.h ../include/utils.h ../include/constants.h \
- ../include/energy.h ../include/data.h ../include/global.h \
- ../include/algorithms.h ../include/constraints.h \
- ../include/shapereader.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/omp.h
+ /usr/include/sys/types.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/bits/stdlib.h /usr/include/assert.h ../include/constants.h \
+ ../include/utils.h ../include/constants.h ../include/energy.h \
+ ../include/data.h ../include/global.h ../include/algorithms.h \
+ ../include/constraints.h ../include/shapereader.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/omp.h
 
 /usr/include/stdio.h:
 
@@ -39,7 +40,7 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
 /usr/include/bits/types.h:
 
@@ -51,7 +52,7 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/wchar.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/stdio_lim.h:
 
@@ -95,7 +96,9 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/stdlib.h:
 
-/usr/include/sys/types.h:
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
 
 /usr/include/endian.h:
 
@@ -103,6 +106,8 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/bits/byteswap.h:
 
+/usr/include/sys/types.h:
+
 /usr/include/sys/sysmacros.h:
 
 /usr/include/bits/pthreadtypes.h:
@@ -131,4 +136,4 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
 
 ../include/shapereader.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/omp.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/omp.h:
diff --git a/gtfold-mfe/src/.deps/constraints.Po b/gtfold-mfe/src/.deps/constraints.Po
index ec27b91..891773e 100644
--- a/gtfold-mfe/src/.deps/constraints.Po
+++ b/gtfold-mfe/src/.deps/constraints.Po
@@ -2,7 +2,7 @@ constraints.o: constraints.cc /usr/include/stdlib.h \
  /usr/include/features.h /usr/include/bits/predefs.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
  /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
  /usr/include/endian.h /usr/include/bits/endian.h \
  /usr/include/bits/byteswap.h /usr/include/xlocale.h \
@@ -14,81 +14,82 @@ constraints.o: constraints.cc /usr/include/stdlib.h \
  /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/string.h \
  /usr/include/bits/string3.h /usr/include/stdio.h /usr/include/libio.h \
  /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/c++/4.4/iostream \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \
- /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \
- /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \
- /usr/include/c++/4.4/cstddef /usr/include/bits/wchar.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \
- /usr/include/c++/4.4/bits/char_traits.h \
- /usr/include/c++/4.4/bits/stl_algobase.h \
- /usr/include/c++/4.4/bits/functexcept.h \
- /usr/include/c++/4.4/exception_defines.h \
- /usr/include/c++/4.4/bits/cpp_type_traits.h \
- /usr/include/c++/4.4/ext/type_traits.h \
- /usr/include/c++/4.4/ext/numeric_traits.h \
- /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
- /usr/include/c++/4.4/bits/concept_check.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.4/bits/stl_iterator.h \
- /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.4/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \
- /usr/include/ctype.h /usr/include/c++/4.4/bits/ios_base.h \
- /usr/include/c++/4.4/ext/atomicity.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/c++/4.5/iostream \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \
+ /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \
+ /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \
+ /usr/include/c++/4.5/cstddef /usr/include/bits/wchar.h \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \
+ /usr/include/c++/4.5/bits/char_traits.h \
+ /usr/include/c++/4.5/bits/stl_algobase.h \
+ /usr/include/c++/4.5/bits/functexcept.h \
+ /usr/include/c++/4.5/exception_defines.h \
+ /usr/include/c++/4.5/bits/cpp_type_traits.h \
+ /usr/include/c++/4.5/ext/type_traits.h \
+ /usr/include/c++/4.5/ext/numeric_traits.h \
+ /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
+ /usr/include/c++/4.5/bits/concept_check.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.5/bits/stl_iterator.h \
+ /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.5/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \
+ /usr/include/ctype.h /usr/include/c++/4.5/bits/ios_base.h \
+ /usr/include/c++/4.5/ext/atomicity.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
  /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
- /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \
+ /usr/include/bits/setjmp.h /usr/include/unistd.h \
  /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
  /usr/include/bits/confname.h /usr/include/getopt.h \
  /usr/include/bits/unistd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \
- /usr/include/c++/4.4/bits/allocator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
- /usr/include/c++/4.4/bits/ostream_insert.h \
- /usr/include/c++/4.4/cxxabi-forced.h \
- /usr/include/c++/4.4/bits/stl_function.h \
- /usr/include/c++/4.4/backward/binders.h \
- /usr/include/c++/4.4/bits/basic_string.h \
- /usr/include/c++/4.4/initializer_list \
- /usr/include/c++/4.4/bits/basic_string.tcc \
- /usr/include/c++/4.4/bits/locale_classes.tcc \
- /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \
- /usr/include/c++/4.4/bits/basic_ios.h \
- /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \
+ /usr/include/c++/4.5/bits/allocator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
+ /usr/include/c++/4.5/bits/ostream_insert.h \
+ /usr/include/c++/4.5/cxxabi-forced.h \
+ /usr/include/c++/4.5/bits/stl_function.h \
+ /usr/include/c++/4.5/backward/binders.h \
+ /usr/include/c++/4.5/bits/basic_string.h \
+ /usr/include/c++/4.5/initializer_list \
+ /usr/include/c++/4.5/bits/basic_string.tcc \
+ /usr/include/c++/4.5/bits/locale_classes.tcc \
+ /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \
+ /usr/include/c++/4.5/bits/basic_ios.h \
+ /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \
  /usr/include/wctype.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \
- /usr/include/c++/4.4/bits/streambuf_iterator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \
- /usr/include/c++/4.4/bits/locale_facets.tcc \
- /usr/include/c++/4.4/bits/basic_ios.tcc \
- /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \
- /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \
- /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \
- /usr/include/c++/4.4/bits/fstream.tcc /usr/include/c++/4.4/vector \
- /usr/include/c++/4.4/bits/stl_construct.h \
- /usr/include/c++/4.4/bits/stl_uninitialized.h \
- /usr/include/c++/4.4/bits/stl_vector.h \
- /usr/include/c++/4.4/bits/stl_bvector.h \
- /usr/include/c++/4.4/bits/vector.tcc /usr/include/c++/4.4/algorithm \
- /usr/include/c++/4.4/bits/stl_algo.h /usr/include/c++/4.4/cstdlib \
- /usr/include/c++/4.4/bits/algorithmfwd.h \
- /usr/include/c++/4.4/bits/stl_heap.h \
- /usr/include/c++/4.4/bits/stl_tempbuf.h ../include/global.h \
- ../include/constants.h ../include/options.h /usr/include/c++/4.4/cstring \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \
+ /usr/include/c++/4.5/bits/streambuf_iterator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \
+ /usr/include/c++/4.5/bits/locale_facets.tcc \
+ /usr/include/c++/4.5/bits/basic_ios.tcc \
+ /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \
+ /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \
+ /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \
+ /usr/include/c++/4.5/bits/fstream.tcc /usr/include/c++/4.5/vector \
+ /usr/include/c++/4.5/bits/stl_construct.h \
+ /usr/include/c++/4.5/bits/stl_uninitialized.h \
+ /usr/include/c++/4.5/bits/stl_vector.h \
+ /usr/include/c++/4.5/bits/stl_bvector.h \
+ /usr/include/c++/4.5/bits/vector.tcc /usr/include/c++/4.5/algorithm \
+ /usr/include/c++/4.5/utility /usr/include/c++/4.5/bits/stl_relops.h \
+ /usr/include/c++/4.5/bits/stl_algo.h /usr/include/c++/4.5/cstdlib \
+ /usr/include/c++/4.5/bits/algorithmfwd.h \
+ /usr/include/c++/4.5/bits/stl_heap.h \
+ /usr/include/c++/4.5/bits/stl_tempbuf.h ../include/global.h \
+ ../include/constants.h ../include/options.h /usr/include/c++/4.5/cstring \
  ../include/constraints.h
 
 /usr/include/stdlib.h:
@@ -105,7 +106,7 @@ constraints.o: constraints.cc /usr/include/stdlib.h \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
 /usr/include/bits/waitflags.h:
 
@@ -155,7 +156,7 @@ constraints.o: constraints.cc /usr/include/stdlib.h \
 
 /usr/include/wchar.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/stdio_lim.h:
 
@@ -165,83 +166,83 @@ constraints.o: constraints.cc /usr/include/stdlib.h \
 
 /usr/include/bits/stdio2.h:
 
-/usr/include/c++/4.4/iostream:
+/usr/include/c++/4.5/iostream:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
 
-/usr/include/c++/4.4/ostream:
+/usr/include/c++/4.5/ostream:
 
-/usr/include/c++/4.4/ios:
+/usr/include/c++/4.5/ios:
 
-/usr/include/c++/4.4/iosfwd:
+/usr/include/c++/4.5/iosfwd:
 
-/usr/include/c++/4.4/bits/stringfwd.h:
+/usr/include/c++/4.5/bits/stringfwd.h:
 
-/usr/include/c++/4.4/bits/postypes.h:
+/usr/include/c++/4.5/bits/postypes.h:
 
-/usr/include/c++/4.4/cwchar:
+/usr/include/c++/4.5/cwchar:
 
-/usr/include/c++/4.4/cstddef:
+/usr/include/c++/4.5/cstddef:
 
 /usr/include/bits/wchar.h:
 
 /usr/include/bits/wchar2.h:
 
-/usr/include/c++/4.4/exception:
+/usr/include/c++/4.5/exception:
 
-/usr/include/c++/4.4/bits/char_traits.h:
+/usr/include/c++/4.5/bits/char_traits.h:
 
-/usr/include/c++/4.4/bits/stl_algobase.h:
+/usr/include/c++/4.5/bits/stl_algobase.h:
 
-/usr/include/c++/4.4/bits/functexcept.h:
+/usr/include/c++/4.5/bits/functexcept.h:
 
-/usr/include/c++/4.4/exception_defines.h:
+/usr/include/c++/4.5/exception_defines.h:
 
-/usr/include/c++/4.4/bits/cpp_type_traits.h:
+/usr/include/c++/4.5/bits/cpp_type_traits.h:
 
-/usr/include/c++/4.4/ext/type_traits.h:
+/usr/include/c++/4.5/ext/type_traits.h:
 
-/usr/include/c++/4.4/ext/numeric_traits.h:
+/usr/include/c++/4.5/ext/numeric_traits.h:
 
-/usr/include/c++/4.4/bits/stl_pair.h:
+/usr/include/c++/4.5/bits/stl_pair.h:
 
-/usr/include/c++/4.4/bits/move.h:
+/usr/include/c++/4.5/bits/move.h:
 
-/usr/include/c++/4.4/bits/concept_check.h:
+/usr/include/c++/4.5/bits/concept_check.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
 
-/usr/include/c++/4.4/bits/stl_iterator.h:
+/usr/include/c++/4.5/bits/stl_iterator.h:
 
-/usr/include/c++/4.4/debug/debug.h:
+/usr/include/c++/4.5/debug/debug.h:
 
-/usr/include/c++/4.4/bits/localefwd.h:
+/usr/include/c++/4.5/bits/localefwd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
 
-/usr/include/c++/4.4/clocale:
+/usr/include/c++/4.5/clocale:
 
 /usr/include/locale.h:
 
 /usr/include/bits/locale.h:
 
-/usr/include/c++/4.4/cctype:
+/usr/include/c++/4.5/cctype:
 
 /usr/include/ctype.h:
 
-/usr/include/c++/4.4/bits/ios_base.h:
+/usr/include/c++/4.5/bits/ios_base.h:
 
-/usr/include/c++/4.4/ext/atomicity.h:
+/usr/include/c++/4.5/ext/atomicity.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
 
 /usr/include/pthread.h:
 
@@ -249,8 +250,6 @@ constraints.o: constraints.cc /usr/include/stdlib.h \
 
 /usr/include/bits/sched.h:
 
-/usr/include/signal.h:
-
 /usr/include/bits/setjmp.h:
 
 /usr/include/unistd.h:
@@ -265,99 +264,103 @@ constraints.o: constraints.cc /usr/include/stdlib.h \
 
 /usr/include/bits/unistd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
 
-/usr/include/c++/4.4/bits/locale_classes.h:
+/usr/include/c++/4.5/bits/locale_classes.h:
 
-/usr/include/c++/4.4/string:
+/usr/include/c++/4.5/string:
 
-/usr/include/c++/4.4/bits/allocator.h:
+/usr/include/c++/4.5/bits/allocator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
 
-/usr/include/c++/4.4/ext/new_allocator.h:
+/usr/include/c++/4.5/ext/new_allocator.h:
 
-/usr/include/c++/4.4/new:
+/usr/include/c++/4.5/new:
 
-/usr/include/c++/4.4/bits/ostream_insert.h:
+/usr/include/c++/4.5/bits/ostream_insert.h:
 
-/usr/include/c++/4.4/cxxabi-forced.h:
+/usr/include/c++/4.5/cxxabi-forced.h:
 
-/usr/include/c++/4.4/bits/stl_function.h:
+/usr/include/c++/4.5/bits/stl_function.h:
 
-/usr/include/c++/4.4/backward/binders.h:
+/usr/include/c++/4.5/backward/binders.h:
 
-/usr/include/c++/4.4/bits/basic_string.h:
+/usr/include/c++/4.5/bits/basic_string.h:
 
-/usr/include/c++/4.4/initializer_list:
+/usr/include/c++/4.5/initializer_list:
 
-/usr/include/c++/4.4/bits/basic_string.tcc:
+/usr/include/c++/4.5/bits/basic_string.tcc:
 
-/usr/include/c++/4.4/bits/locale_classes.tcc:
+/usr/include/c++/4.5/bits/locale_classes.tcc:
 
-/usr/include/c++/4.4/streambuf:
+/usr/include/c++/4.5/streambuf:
 
-/usr/include/c++/4.4/bits/streambuf.tcc:
+/usr/include/c++/4.5/bits/streambuf.tcc:
 
-/usr/include/c++/4.4/bits/basic_ios.h:
+/usr/include/c++/4.5/bits/basic_ios.h:
 
-/usr/include/c++/4.4/bits/locale_facets.h:
+/usr/include/c++/4.5/bits/locale_facets.h:
 
-/usr/include/c++/4.4/cwctype:
+/usr/include/c++/4.5/cwctype:
 
 /usr/include/wctype.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h:
+
+/usr/include/c++/4.5/bits/streambuf_iterator.h:
+
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h:
 
-/usr/include/c++/4.4/bits/streambuf_iterator.h:
+/usr/include/c++/4.5/bits/locale_facets.tcc:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h:
+/usr/include/c++/4.5/bits/basic_ios.tcc:
 
-/usr/include/c++/4.4/bits/locale_facets.tcc:
+/usr/include/c++/4.5/bits/ostream.tcc:
 
-/usr/include/c++/4.4/bits/basic_ios.tcc:
+/usr/include/c++/4.5/istream:
 
-/usr/include/c++/4.4/bits/ostream.tcc:
+/usr/include/c++/4.5/bits/istream.tcc:
 
-/usr/include/c++/4.4/istream:
+/usr/include/c++/4.5/fstream:
 
-/usr/include/c++/4.4/bits/istream.tcc:
+/usr/include/c++/4.5/bits/codecvt.h:
 
-/usr/include/c++/4.4/fstream:
+/usr/include/c++/4.5/cstdio:
 
-/usr/include/c++/4.4/bits/codecvt.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h:
 
-/usr/include/c++/4.4/cstdio:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h:
+/usr/include/c++/4.5/bits/fstream.tcc:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h:
+/usr/include/c++/4.5/vector:
 
-/usr/include/c++/4.4/bits/fstream.tcc:
+/usr/include/c++/4.5/bits/stl_construct.h:
 
-/usr/include/c++/4.4/vector:
+/usr/include/c++/4.5/bits/stl_uninitialized.h:
 
-/usr/include/c++/4.4/bits/stl_construct.h:
+/usr/include/c++/4.5/bits/stl_vector.h:
 
-/usr/include/c++/4.4/bits/stl_uninitialized.h:
+/usr/include/c++/4.5/bits/stl_bvector.h:
 
-/usr/include/c++/4.4/bits/stl_vector.h:
+/usr/include/c++/4.5/bits/vector.tcc:
 
-/usr/include/c++/4.4/bits/stl_bvector.h:
+/usr/include/c++/4.5/algorithm:
 
-/usr/include/c++/4.4/bits/vector.tcc:
+/usr/include/c++/4.5/utility:
 
-/usr/include/c++/4.4/algorithm:
+/usr/include/c++/4.5/bits/stl_relops.h:
 
-/usr/include/c++/4.4/bits/stl_algo.h:
+/usr/include/c++/4.5/bits/stl_algo.h:
 
-/usr/include/c++/4.4/cstdlib:
+/usr/include/c++/4.5/cstdlib:
 
-/usr/include/c++/4.4/bits/algorithmfwd.h:
+/usr/include/c++/4.5/bits/algorithmfwd.h:
 
-/usr/include/c++/4.4/bits/stl_heap.h:
+/usr/include/c++/4.5/bits/stl_heap.h:
 
-/usr/include/c++/4.4/bits/stl_tempbuf.h:
+/usr/include/c++/4.5/bits/stl_tempbuf.h:
 
 ../include/global.h:
 
@@ -365,6 +368,6 @@ constraints.o: constraints.cc /usr/include/stdlib.h \
 
 ../include/options.h:
 
-/usr/include/c++/4.4/cstring:
+/usr/include/c++/4.5/cstring:
 
 ../include/constraints.h:
diff --git a/gtfold-mfe/src/.deps/energy.Po b/gtfold-mfe/src/.deps/energy.Po
index 7c1467f..daea2c1 100644
--- a/gtfold-mfe/src/.deps/energy.Po
+++ b/gtfold-mfe/src/.deps/energy.Po
@@ -2,16 +2,17 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \
  /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
- /usr/include/sys/types.h /usr/include/bits/types.h \
- /usr/include/bits/typesizes.h /usr/include/time.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
  /usr/include/bits/sigset.h /usr/include/bits/time.h \
  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
  /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/stdio.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \
  /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
@@ -35,15 +36,11 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
-/usr/include/sys/types.h:
-
-/usr/include/bits/types.h:
+/usr/include/bits/waitflags.h:
 
-/usr/include/bits/typesizes.h:
-
-/usr/include/time.h:
+/usr/include/bits/waitstatus.h:
 
 /usr/include/endian.h:
 
@@ -51,6 +48,14 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \
 
 /usr/include/bits/byteswap.h:
 
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
 /usr/include/sys/select.h:
 
 /usr/include/bits/select.h:
@@ -75,7 +80,7 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \
 
 /usr/include/wchar.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/stdio_lim.h:
 
diff --git a/gtfold-mfe/src/.deps/global.Po b/gtfold-mfe/src/.deps/global.Po
index e2d1748..613e0c5 100644
--- a/gtfold-mfe/src/.deps/global.Po
+++ b/gtfold-mfe/src/.deps/global.Po
@@ -2,15 +2,16 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -30,7 +31,7 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
 /usr/include/bits/types.h:
 
@@ -42,7 +43,7 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/wchar.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/stdio_lim.h:
 
@@ -54,9 +55,9 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/stdlib.h:
 
-/usr/include/sys/types.h:
+/usr/include/bits/waitflags.h:
 
-/usr/include/time.h:
+/usr/include/bits/waitstatus.h:
 
 /usr/include/endian.h:
 
@@ -64,6 +65,10 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/bits/byteswap.h:
 
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
 /usr/include/sys/select.h:
 
 /usr/include/bits/select.h:
diff --git a/gtfold-mfe/src/.deps/loader.Po b/gtfold-mfe/src/.deps/loader.Po
index 290868e..41da0fe 100644
--- a/gtfold-mfe/src/.deps/loader.Po
+++ b/gtfold-mfe/src/.deps/loader.Po
@@ -1,98 +1,98 @@
-loader.o: loader.cc /usr/include/c++/4.4/iostream \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+loader.o: loader.cc /usr/include/c++/4.5/iostream \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
  /usr/include/features.h /usr/include/bits/predefs.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \
- /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \
- /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \
- /usr/include/c++/4.4/cstddef \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \
+ /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \
+ /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \
+ /usr/include/c++/4.5/cstddef \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
  /usr/include/wchar.h /usr/include/stdio.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/wchar.h /usr/include/xlocale.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \
- /usr/include/c++/4.4/bits/char_traits.h \
- /usr/include/c++/4.4/bits/stl_algobase.h \
- /usr/include/c++/4.4/bits/functexcept.h \
- /usr/include/c++/4.4/exception_defines.h \
- /usr/include/c++/4.4/bits/cpp_type_traits.h \
- /usr/include/c++/4.4/ext/type_traits.h \
- /usr/include/c++/4.4/ext/numeric_traits.h \
- /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
- /usr/include/c++/4.4/bits/concept_check.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.4/bits/stl_iterator.h \
- /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.4/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \
+ /usr/include/c++/4.5/bits/char_traits.h \
+ /usr/include/c++/4.5/bits/stl_algobase.h \
+ /usr/include/c++/4.5/bits/functexcept.h \
+ /usr/include/c++/4.5/exception_defines.h \
+ /usr/include/c++/4.5/bits/cpp_type_traits.h \
+ /usr/include/c++/4.5/ext/type_traits.h \
+ /usr/include/c++/4.5/ext/numeric_traits.h \
+ /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
+ /usr/include/c++/4.5/bits/concept_check.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.5/bits/stl_iterator.h \
+ /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.5/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \
  /usr/include/ctype.h /usr/include/bits/types.h \
  /usr/include/bits/typesizes.h /usr/include/endian.h \
  /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/c++/4.4/bits/ios_base.h \
- /usr/include/c++/4.4/ext/atomicity.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/c++/4.5/bits/ios_base.h \
+ /usr/include/c++/4.5/ext/atomicity.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
  /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
- /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
- /usr/include/bits/setjmp.h /usr/include/unistd.h \
- /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
- /usr/include/bits/confname.h /usr/include/getopt.h \
- /usr/include/bits/unistd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \
- /usr/include/c++/4.4/bits/allocator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
- /usr/include/c++/4.4/bits/ostream_insert.h \
- /usr/include/c++/4.4/cxxabi-forced.h \
- /usr/include/c++/4.4/bits/stl_function.h \
- /usr/include/c++/4.4/backward/binders.h \
- /usr/include/c++/4.4/bits/basic_string.h \
- /usr/include/c++/4.4/initializer_list \
- /usr/include/c++/4.4/bits/basic_string.tcc \
- /usr/include/c++/4.4/bits/locale_classes.tcc \
- /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \
- /usr/include/c++/4.4/bits/basic_ios.h \
- /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h /usr/include/bits/unistd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \
+ /usr/include/c++/4.5/bits/allocator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
+ /usr/include/c++/4.5/bits/ostream_insert.h \
+ /usr/include/c++/4.5/cxxabi-forced.h \
+ /usr/include/c++/4.5/bits/stl_function.h \
+ /usr/include/c++/4.5/backward/binders.h \
+ /usr/include/c++/4.5/bits/basic_string.h \
+ /usr/include/c++/4.5/initializer_list \
+ /usr/include/c++/4.5/bits/basic_string.tcc \
+ /usr/include/c++/4.5/bits/locale_classes.tcc \
+ /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \
+ /usr/include/c++/4.5/bits/basic_ios.h \
+ /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \
  /usr/include/wctype.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \
- /usr/include/c++/4.4/bits/streambuf_iterator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \
- /usr/include/c++/4.4/bits/locale_facets.tcc \
- /usr/include/c++/4.4/bits/basic_ios.tcc \
- /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \
- /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \
- /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \
+ /usr/include/c++/4.5/bits/streambuf_iterator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \
+ /usr/include/c++/4.5/bits/locale_facets.tcc \
+ /usr/include/c++/4.5/bits/basic_ios.tcc \
+ /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \
+ /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \
+ /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \
  /usr/include/libio.h /usr/include/_G_config.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \
- /usr/include/c++/4.4/bits/fstream.tcc /usr/include/math.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \
+ /usr/include/c++/4.5/bits/fstream.tcc /usr/include/math.h \
  /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
  /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
- /usr/include/c++/4.4/cstring /usr/include/string.h \
+ /usr/include/c++/4.5/cstring /usr/include/string.h \
  /usr/include/bits/string3.h /usr/include/stdlib.h \
  /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
  /usr/include/sys/types.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/sys/sysmacros.h \
- /usr/include/alloca.h /usr/include/bits/stdlib.h ../include/data.h \
- ../include/constants.h ../include/utils.h ../include/constants.h \
- ../include/global.h ../include/loader.h ../include/data.h
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/bits/stdlib.h ../include/data.h ../include/constants.h \
+ ../include/utils.h ../include/constants.h ../include/global.h \
+ ../include/loader.h ../include/data.h
 
-/usr/include/c++/4.4/iostream:
+/usr/include/c++/4.5/iostream:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
 
 /usr/include/features.h:
 
@@ -106,29 +106,29 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
 
-/usr/include/c++/4.4/ostream:
+/usr/include/c++/4.5/ostream:
 
-/usr/include/c++/4.4/ios:
+/usr/include/c++/4.5/ios:
 
-/usr/include/c++/4.4/iosfwd:
+/usr/include/c++/4.5/iosfwd:
 
-/usr/include/c++/4.4/bits/stringfwd.h:
+/usr/include/c++/4.5/bits/stringfwd.h:
 
-/usr/include/c++/4.4/bits/postypes.h:
+/usr/include/c++/4.5/bits/postypes.h:
 
-/usr/include/c++/4.4/cwchar:
+/usr/include/c++/4.5/cwchar:
 
-/usr/include/c++/4.4/cstddef:
+/usr/include/c++/4.5/cstddef:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
 /usr/include/wchar.h:
 
 /usr/include/stdio.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/wchar.h:
 
@@ -136,47 +136,47 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/wchar2.h:
 
-/usr/include/c++/4.4/exception:
+/usr/include/c++/4.5/exception:
 
-/usr/include/c++/4.4/bits/char_traits.h:
+/usr/include/c++/4.5/bits/char_traits.h:
 
-/usr/include/c++/4.4/bits/stl_algobase.h:
+/usr/include/c++/4.5/bits/stl_algobase.h:
 
-/usr/include/c++/4.4/bits/functexcept.h:
+/usr/include/c++/4.5/bits/functexcept.h:
 
-/usr/include/c++/4.4/exception_defines.h:
+/usr/include/c++/4.5/exception_defines.h:
 
-/usr/include/c++/4.4/bits/cpp_type_traits.h:
+/usr/include/c++/4.5/bits/cpp_type_traits.h:
 
-/usr/include/c++/4.4/ext/type_traits.h:
+/usr/include/c++/4.5/ext/type_traits.h:
 
-/usr/include/c++/4.4/ext/numeric_traits.h:
+/usr/include/c++/4.5/ext/numeric_traits.h:
 
-/usr/include/c++/4.4/bits/stl_pair.h:
+/usr/include/c++/4.5/bits/stl_pair.h:
 
-/usr/include/c++/4.4/bits/move.h:
+/usr/include/c++/4.5/bits/move.h:
 
-/usr/include/c++/4.4/bits/concept_check.h:
+/usr/include/c++/4.5/bits/concept_check.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
 
-/usr/include/c++/4.4/bits/stl_iterator.h:
+/usr/include/c++/4.5/bits/stl_iterator.h:
 
-/usr/include/c++/4.4/debug/debug.h:
+/usr/include/c++/4.5/debug/debug.h:
 
-/usr/include/c++/4.4/bits/localefwd.h:
+/usr/include/c++/4.5/bits/localefwd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
 
-/usr/include/c++/4.4/clocale:
+/usr/include/c++/4.5/clocale:
 
 /usr/include/locale.h:
 
 /usr/include/bits/locale.h:
 
-/usr/include/c++/4.4/cctype:
+/usr/include/c++/4.5/cctype:
 
 /usr/include/ctype.h:
 
@@ -190,13 +190,13 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/byteswap.h:
 
-/usr/include/c++/4.4/bits/ios_base.h:
+/usr/include/c++/4.5/bits/ios_base.h:
 
-/usr/include/c++/4.4/ext/atomicity.h:
+/usr/include/c++/4.5/ext/atomicity.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
 
 /usr/include/pthread.h:
 
@@ -208,10 +208,6 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/time.h:
 
-/usr/include/signal.h:
-
-/usr/include/bits/sigset.h:
-
 /usr/include/bits/pthreadtypes.h:
 
 /usr/include/bits/setjmp.h:
@@ -228,69 +224,69 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/unistd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
 
-/usr/include/c++/4.4/bits/locale_classes.h:
+/usr/include/c++/4.5/bits/locale_classes.h:
 
-/usr/include/c++/4.4/string:
+/usr/include/c++/4.5/string:
 
-/usr/include/c++/4.4/bits/allocator.h:
+/usr/include/c++/4.5/bits/allocator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
 
-/usr/include/c++/4.4/ext/new_allocator.h:
+/usr/include/c++/4.5/ext/new_allocator.h:
 
-/usr/include/c++/4.4/new:
+/usr/include/c++/4.5/new:
 
-/usr/include/c++/4.4/bits/ostream_insert.h:
+/usr/include/c++/4.5/bits/ostream_insert.h:
 
-/usr/include/c++/4.4/cxxabi-forced.h:
+/usr/include/c++/4.5/cxxabi-forced.h:
 
-/usr/include/c++/4.4/bits/stl_function.h:
+/usr/include/c++/4.5/bits/stl_function.h:
 
-/usr/include/c++/4.4/backward/binders.h:
+/usr/include/c++/4.5/backward/binders.h:
 
-/usr/include/c++/4.4/bits/basic_string.h:
+/usr/include/c++/4.5/bits/basic_string.h:
 
-/usr/include/c++/4.4/initializer_list:
+/usr/include/c++/4.5/initializer_list:
 
-/usr/include/c++/4.4/bits/basic_string.tcc:
+/usr/include/c++/4.5/bits/basic_string.tcc:
 
-/usr/include/c++/4.4/bits/locale_classes.tcc:
+/usr/include/c++/4.5/bits/locale_classes.tcc:
 
-/usr/include/c++/4.4/streambuf:
+/usr/include/c++/4.5/streambuf:
 
-/usr/include/c++/4.4/bits/streambuf.tcc:
+/usr/include/c++/4.5/bits/streambuf.tcc:
 
-/usr/include/c++/4.4/bits/basic_ios.h:
+/usr/include/c++/4.5/bits/basic_ios.h:
 
-/usr/include/c++/4.4/bits/locale_facets.h:
+/usr/include/c++/4.5/bits/locale_facets.h:
 
-/usr/include/c++/4.4/cwctype:
+/usr/include/c++/4.5/cwctype:
 
 /usr/include/wctype.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h:
 
-/usr/include/c++/4.4/bits/streambuf_iterator.h:
+/usr/include/c++/4.5/bits/streambuf_iterator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h:
 
-/usr/include/c++/4.4/bits/locale_facets.tcc:
+/usr/include/c++/4.5/bits/locale_facets.tcc:
 
-/usr/include/c++/4.4/bits/basic_ios.tcc:
+/usr/include/c++/4.5/bits/basic_ios.tcc:
 
-/usr/include/c++/4.4/bits/ostream.tcc:
+/usr/include/c++/4.5/bits/ostream.tcc:
 
-/usr/include/c++/4.4/istream:
+/usr/include/c++/4.5/istream:
 
-/usr/include/c++/4.4/bits/istream.tcc:
+/usr/include/c++/4.5/bits/istream.tcc:
 
-/usr/include/c++/4.4/fstream:
+/usr/include/c++/4.5/fstream:
 
-/usr/include/c++/4.4/bits/codecvt.h:
+/usr/include/c++/4.5/bits/codecvt.h:
 
-/usr/include/c++/4.4/cstdio:
+/usr/include/c++/4.5/cstdio:
 
 /usr/include/libio.h:
 
@@ -304,11 +300,11 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/stdio2.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h:
 
-/usr/include/c++/4.4/bits/fstream.tcc:
+/usr/include/c++/4.5/bits/fstream.tcc:
 
 /usr/include/math.h:
 
@@ -328,7 +324,7 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/mathinline.h:
 
-/usr/include/c++/4.4/cstring:
+/usr/include/c++/4.5/cstring:
 
 /usr/include/string.h:
 
@@ -346,6 +342,8 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/select.h:
 
+/usr/include/bits/sigset.h:
+
 /usr/include/sys/sysmacros.h:
 
 /usr/include/alloca.h:
diff --git a/gtfold-mfe/src/.deps/main.Po b/gtfold-mfe/src/.deps/main.Po
index df8b6af..73ec5ce 100644
--- a/gtfold-mfe/src/.deps/main.Po
+++ b/gtfold-mfe/src/.deps/main.Po
@@ -1,114 +1,114 @@
-main.o: main.cc /usr/include/c++/4.4/iostream \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+main.o: main.cc /usr/include/c++/4.5/iostream \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
  /usr/include/features.h /usr/include/bits/predefs.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \
- /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \
- /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \
- /usr/include/c++/4.4/cstddef \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \
+ /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \
+ /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \
+ /usr/include/c++/4.5/cstddef \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
  /usr/include/wchar.h /usr/include/stdio.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/wchar.h /usr/include/xlocale.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \
- /usr/include/c++/4.4/bits/char_traits.h \
- /usr/include/c++/4.4/bits/stl_algobase.h \
- /usr/include/c++/4.4/bits/functexcept.h \
- /usr/include/c++/4.4/exception_defines.h \
- /usr/include/c++/4.4/bits/cpp_type_traits.h \
- /usr/include/c++/4.4/ext/type_traits.h \
- /usr/include/c++/4.4/ext/numeric_traits.h \
- /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
- /usr/include/c++/4.4/bits/concept_check.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.4/bits/stl_iterator.h \
- /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.4/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \
+ /usr/include/c++/4.5/bits/char_traits.h \
+ /usr/include/c++/4.5/bits/stl_algobase.h \
+ /usr/include/c++/4.5/bits/functexcept.h \
+ /usr/include/c++/4.5/exception_defines.h \
+ /usr/include/c++/4.5/bits/cpp_type_traits.h \
+ /usr/include/c++/4.5/ext/type_traits.h \
+ /usr/include/c++/4.5/ext/numeric_traits.h \
+ /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
+ /usr/include/c++/4.5/bits/concept_check.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.5/bits/stl_iterator.h \
+ /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.5/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \
  /usr/include/ctype.h /usr/include/bits/types.h \
  /usr/include/bits/typesizes.h /usr/include/endian.h \
  /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/c++/4.4/bits/ios_base.h \
- /usr/include/c++/4.4/ext/atomicity.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/c++/4.5/bits/ios_base.h \
+ /usr/include/c++/4.5/ext/atomicity.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
  /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
- /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
- /usr/include/bits/setjmp.h /usr/include/unistd.h \
- /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
- /usr/include/bits/confname.h /usr/include/getopt.h \
- /usr/include/bits/unistd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \
- /usr/include/c++/4.4/bits/allocator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
- /usr/include/c++/4.4/bits/ostream_insert.h \
- /usr/include/c++/4.4/cxxabi-forced.h \
- /usr/include/c++/4.4/bits/stl_function.h \
- /usr/include/c++/4.4/backward/binders.h \
- /usr/include/c++/4.4/bits/basic_string.h \
- /usr/include/c++/4.4/initializer_list \
- /usr/include/c++/4.4/bits/basic_string.tcc \
- /usr/include/c++/4.4/bits/locale_classes.tcc \
- /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \
- /usr/include/c++/4.4/bits/basic_ios.h \
- /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h /usr/include/bits/unistd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \
+ /usr/include/c++/4.5/bits/allocator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
+ /usr/include/c++/4.5/bits/ostream_insert.h \
+ /usr/include/c++/4.5/cxxabi-forced.h \
+ /usr/include/c++/4.5/bits/stl_function.h \
+ /usr/include/c++/4.5/backward/binders.h \
+ /usr/include/c++/4.5/bits/basic_string.h \
+ /usr/include/c++/4.5/initializer_list \
+ /usr/include/c++/4.5/bits/basic_string.tcc \
+ /usr/include/c++/4.5/bits/locale_classes.tcc \
+ /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \
+ /usr/include/c++/4.5/bits/basic_ios.h \
+ /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \
  /usr/include/wctype.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \
- /usr/include/c++/4.4/bits/streambuf_iterator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \
- /usr/include/c++/4.4/bits/locale_facets.tcc \
- /usr/include/c++/4.4/bits/basic_ios.tcc \
- /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \
- /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/iomanip \
- /usr/include/c++/4.4/fstream /usr/include/c++/4.4/bits/codecvt.h \
- /usr/include/c++/4.4/cstdio /usr/include/libio.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \
+ /usr/include/c++/4.5/bits/streambuf_iterator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \
+ /usr/include/c++/4.5/bits/locale_facets.tcc \
+ /usr/include/c++/4.5/bits/basic_ios.tcc \
+ /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \
+ /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/iomanip \
+ /usr/include/c++/4.5/fstream /usr/include/c++/4.5/bits/codecvt.h \
+ /usr/include/c++/4.5/cstdio /usr/include/libio.h \
  /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \
  /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
  /usr/include/bits/stdio2.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \
- /usr/include/c++/4.4/bits/fstream.tcc /usr/include/math.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \
+ /usr/include/c++/4.5/bits/fstream.tcc /usr/include/math.h \
  /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
  /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
  /usr/include/sys/time.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/c++/4.4/sstream \
- /usr/include/c++/4.4/bits/sstream.tcc /usr/include/stdlib.h \
- /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
- /usr/include/sys/types.h /usr/include/sys/sysmacros.h \
- /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/string.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/c++/4.5/sstream /usr/include/c++/4.5/bits/sstream.tcc \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/bits/stdlib.h /usr/include/string.h \
  /usr/include/bits/string3.h ../include/main.h \
- /usr/include/c++/4.4/vector /usr/include/c++/4.4/bits/stl_construct.h \
- /usr/include/c++/4.4/bits/stl_uninitialized.h \
- /usr/include/c++/4.4/bits/stl_vector.h \
- /usr/include/c++/4.4/bits/stl_bvector.h \
- /usr/include/c++/4.4/bits/vector.tcc ../include/constants.h \
+ /usr/include/c++/4.5/vector /usr/include/c++/4.5/bits/stl_construct.h \
+ /usr/include/c++/4.5/bits/stl_uninitialized.h \
+ /usr/include/c++/4.5/bits/stl_vector.h \
+ /usr/include/c++/4.5/bits/stl_bvector.h \
+ /usr/include/c++/4.5/bits/vector.tcc ../include/constants.h \
  ../include/utils.h ../include/loader.h ../include/data.h \
- ../include/options.h /usr/include/c++/4.4/cstring ../include/global.h \
+ ../include/options.h /usr/include/c++/4.5/cstring ../include/global.h \
  ../include/energy.h ../include/algorithms.h ../include/constraints.h \
  ../include/traceback.h ../include/subopt_traceback.h \
- /usr/include/c++/4.4/cassert /usr/include/assert.h \
- /usr/include/c++/4.4/stack /usr/include/c++/4.4/deque \
- /usr/include/c++/4.4/bits/stl_deque.h \
- /usr/include/c++/4.4/bits/deque.tcc \
- /usr/include/c++/4.4/bits/stl_stack.h /usr/include/c++/4.4/map \
- /usr/include/c++/4.4/bits/stl_tree.h /usr/include/c++/4.4/bits/stl_map.h \
- /usr/include/c++/4.4/bits/stl_multimap.h ../include/shapereader.h
+ /usr/include/c++/4.5/cassert /usr/include/assert.h \
+ /usr/include/c++/4.5/stack /usr/include/c++/4.5/deque \
+ /usr/include/c++/4.5/bits/stl_deque.h \
+ /usr/include/c++/4.5/bits/deque.tcc \
+ /usr/include/c++/4.5/bits/stl_stack.h /usr/include/c++/4.5/map \
+ /usr/include/c++/4.5/bits/stl_tree.h /usr/include/c++/4.5/bits/stl_map.h \
+ /usr/include/c++/4.5/bits/stl_multimap.h ../include/shapereader.h
 
-/usr/include/c++/4.4/iostream:
+/usr/include/c++/4.5/iostream:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
 
 /usr/include/features.h:
 
@@ -122,29 +122,29 @@ main.o: main.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
 
-/usr/include/c++/4.4/ostream:
+/usr/include/c++/4.5/ostream:
 
-/usr/include/c++/4.4/ios:
+/usr/include/c++/4.5/ios:
 
-/usr/include/c++/4.4/iosfwd:
+/usr/include/c++/4.5/iosfwd:
 
-/usr/include/c++/4.4/bits/stringfwd.h:
+/usr/include/c++/4.5/bits/stringfwd.h:
 
-/usr/include/c++/4.4/bits/postypes.h:
+/usr/include/c++/4.5/bits/postypes.h:
 
-/usr/include/c++/4.4/cwchar:
+/usr/include/c++/4.5/cwchar:
 
-/usr/include/c++/4.4/cstddef:
+/usr/include/c++/4.5/cstddef:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
 /usr/include/wchar.h:
 
 /usr/include/stdio.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/wchar.h:
 
@@ -152,47 +152,47 @@ main.o: main.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/wchar2.h:
 
-/usr/include/c++/4.4/exception:
+/usr/include/c++/4.5/exception:
 
-/usr/include/c++/4.4/bits/char_traits.h:
+/usr/include/c++/4.5/bits/char_traits.h:
 
-/usr/include/c++/4.4/bits/stl_algobase.h:
+/usr/include/c++/4.5/bits/stl_algobase.h:
 
-/usr/include/c++/4.4/bits/functexcept.h:
+/usr/include/c++/4.5/bits/functexcept.h:
 
-/usr/include/c++/4.4/exception_defines.h:
+/usr/include/c++/4.5/exception_defines.h:
 
-/usr/include/c++/4.4/bits/cpp_type_traits.h:
+/usr/include/c++/4.5/bits/cpp_type_traits.h:
 
-/usr/include/c++/4.4/ext/type_traits.h:
+/usr/include/c++/4.5/ext/type_traits.h:
 
-/usr/include/c++/4.4/ext/numeric_traits.h:
+/usr/include/c++/4.5/ext/numeric_traits.h:
 
-/usr/include/c++/4.4/bits/stl_pair.h:
+/usr/include/c++/4.5/bits/stl_pair.h:
 
-/usr/include/c++/4.4/bits/move.h:
+/usr/include/c++/4.5/bits/move.h:
 
-/usr/include/c++/4.4/bits/concept_check.h:
+/usr/include/c++/4.5/bits/concept_check.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
 
-/usr/include/c++/4.4/bits/stl_iterator.h:
+/usr/include/c++/4.5/bits/stl_iterator.h:
 
-/usr/include/c++/4.4/debug/debug.h:
+/usr/include/c++/4.5/debug/debug.h:
 
-/usr/include/c++/4.4/bits/localefwd.h:
+/usr/include/c++/4.5/bits/localefwd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
 
-/usr/include/c++/4.4/clocale:
+/usr/include/c++/4.5/clocale:
 
 /usr/include/locale.h:
 
 /usr/include/bits/locale.h:
 
-/usr/include/c++/4.4/cctype:
+/usr/include/c++/4.5/cctype:
 
 /usr/include/ctype.h:
 
@@ -206,13 +206,13 @@ main.o: main.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/byteswap.h:
 
-/usr/include/c++/4.4/bits/ios_base.h:
+/usr/include/c++/4.5/bits/ios_base.h:
 
-/usr/include/c++/4.4/ext/atomicity.h:
+/usr/include/c++/4.5/ext/atomicity.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
 
 /usr/include/pthread.h:
 
@@ -224,10 +224,6 @@ main.o: main.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/time.h:
 
-/usr/include/signal.h:
-
-/usr/include/bits/sigset.h:
-
 /usr/include/bits/pthreadtypes.h:
 
 /usr/include/bits/setjmp.h:
@@ -244,71 +240,71 @@ main.o: main.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/unistd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
 
-/usr/include/c++/4.4/bits/locale_classes.h:
+/usr/include/c++/4.5/bits/locale_classes.h:
 
-/usr/include/c++/4.4/string:
+/usr/include/c++/4.5/string:
 
-/usr/include/c++/4.4/bits/allocator.h:
+/usr/include/c++/4.5/bits/allocator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
 
-/usr/include/c++/4.4/ext/new_allocator.h:
+/usr/include/c++/4.5/ext/new_allocator.h:
 
-/usr/include/c++/4.4/new:
+/usr/include/c++/4.5/new:
 
-/usr/include/c++/4.4/bits/ostream_insert.h:
+/usr/include/c++/4.5/bits/ostream_insert.h:
 
-/usr/include/c++/4.4/cxxabi-forced.h:
+/usr/include/c++/4.5/cxxabi-forced.h:
 
-/usr/include/c++/4.4/bits/stl_function.h:
+/usr/include/c++/4.5/bits/stl_function.h:
 
-/usr/include/c++/4.4/backward/binders.h:
+/usr/include/c++/4.5/backward/binders.h:
 
-/usr/include/c++/4.4/bits/basic_string.h:
+/usr/include/c++/4.5/bits/basic_string.h:
 
-/usr/include/c++/4.4/initializer_list:
+/usr/include/c++/4.5/initializer_list:
 
-/usr/include/c++/4.4/bits/basic_string.tcc:
+/usr/include/c++/4.5/bits/basic_string.tcc:
 
-/usr/include/c++/4.4/bits/locale_classes.tcc:
+/usr/include/c++/4.5/bits/locale_classes.tcc:
 
-/usr/include/c++/4.4/streambuf:
+/usr/include/c++/4.5/streambuf:
 
-/usr/include/c++/4.4/bits/streambuf.tcc:
+/usr/include/c++/4.5/bits/streambuf.tcc:
 
-/usr/include/c++/4.4/bits/basic_ios.h:
+/usr/include/c++/4.5/bits/basic_ios.h:
 
-/usr/include/c++/4.4/bits/locale_facets.h:
+/usr/include/c++/4.5/bits/locale_facets.h:
 
-/usr/include/c++/4.4/cwctype:
+/usr/include/c++/4.5/cwctype:
 
 /usr/include/wctype.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h:
 
-/usr/include/c++/4.4/bits/streambuf_iterator.h:
+/usr/include/c++/4.5/bits/streambuf_iterator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h:
 
-/usr/include/c++/4.4/bits/locale_facets.tcc:
+/usr/include/c++/4.5/bits/locale_facets.tcc:
 
-/usr/include/c++/4.4/bits/basic_ios.tcc:
+/usr/include/c++/4.5/bits/basic_ios.tcc:
 
-/usr/include/c++/4.4/bits/ostream.tcc:
+/usr/include/c++/4.5/bits/ostream.tcc:
 
-/usr/include/c++/4.4/istream:
+/usr/include/c++/4.5/istream:
 
-/usr/include/c++/4.4/bits/istream.tcc:
+/usr/include/c++/4.5/bits/istream.tcc:
 
-/usr/include/c++/4.4/iomanip:
+/usr/include/c++/4.5/iomanip:
 
-/usr/include/c++/4.4/fstream:
+/usr/include/c++/4.5/fstream:
 
-/usr/include/c++/4.4/bits/codecvt.h:
+/usr/include/c++/4.5/bits/codecvt.h:
 
-/usr/include/c++/4.4/cstdio:
+/usr/include/c++/4.5/cstdio:
 
 /usr/include/libio.h:
 
@@ -322,11 +318,11 @@ main.o: main.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/stdio2.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h:
 
-/usr/include/c++/4.4/bits/fstream.tcc:
+/usr/include/c++/4.5/bits/fstream.tcc:
 
 /usr/include/math.h:
 
@@ -352,9 +348,11 @@ main.o: main.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/select.h:
 
-/usr/include/c++/4.4/sstream:
+/usr/include/bits/sigset.h:
+
+/usr/include/c++/4.5/sstream:
 
-/usr/include/c++/4.4/bits/sstream.tcc:
+/usr/include/c++/4.5/bits/sstream.tcc:
 
 /usr/include/stdlib.h:
 
@@ -376,17 +374,17 @@ main.o: main.cc /usr/include/c++/4.4/iostream \
 
 ../include/main.h:
 
-/usr/include/c++/4.4/vector:
+/usr/include/c++/4.5/vector:
 
-/usr/include/c++/4.4/bits/stl_construct.h:
+/usr/include/c++/4.5/bits/stl_construct.h:
 
-/usr/include/c++/4.4/bits/stl_uninitialized.h:
+/usr/include/c++/4.5/bits/stl_uninitialized.h:
 
-/usr/include/c++/4.4/bits/stl_vector.h:
+/usr/include/c++/4.5/bits/stl_vector.h:
 
-/usr/include/c++/4.4/bits/stl_bvector.h:
+/usr/include/c++/4.5/bits/stl_bvector.h:
 
-/usr/include/c++/4.4/bits/vector.tcc:
+/usr/include/c++/4.5/bits/vector.tcc:
 
 ../include/constants.h:
 
@@ -398,7 +396,7 @@ main.o: main.cc /usr/include/c++/4.4/iostream \
 
 ../include/options.h:
 
-/usr/include/c++/4.4/cstring:
+/usr/include/c++/4.5/cstring:
 
 ../include/global.h:
 
@@ -412,26 +410,26 @@ main.o: main.cc /usr/include/c++/4.4/iostream \
 
 ../include/subopt_traceback.h:
 
-/usr/include/c++/4.4/cassert:
+/usr/include/c++/4.5/cassert:
 
 /usr/include/assert.h:
 
-/usr/include/c++/4.4/stack:
+/usr/include/c++/4.5/stack:
 
-/usr/include/c++/4.4/deque:
+/usr/include/c++/4.5/deque:
 
-/usr/include/c++/4.4/bits/stl_deque.h:
+/usr/include/c++/4.5/bits/stl_deque.h:
 
-/usr/include/c++/4.4/bits/deque.tcc:
+/usr/include/c++/4.5/bits/deque.tcc:
 
-/usr/include/c++/4.4/bits/stl_stack.h:
+/usr/include/c++/4.5/bits/stl_stack.h:
 
-/usr/include/c++/4.4/map:
+/usr/include/c++/4.5/map:
 
-/usr/include/c++/4.4/bits/stl_tree.h:
+/usr/include/c++/4.5/bits/stl_tree.h:
 
-/usr/include/c++/4.4/bits/stl_map.h:
+/usr/include/c++/4.5/bits/stl_map.h:
 
-/usr/include/c++/4.4/bits/stl_multimap.h:
+/usr/include/c++/4.5/bits/stl_multimap.h:
 
 ../include/shapereader.h:
diff --git a/gtfold-mfe/src/.deps/options.Po b/gtfold-mfe/src/.deps/options.Po
index 52acdb4..7d4de3a 100644
--- a/gtfold-mfe/src/.deps/options.Po
+++ b/gtfold-mfe/src/.deps/options.Po
@@ -1,74 +1,73 @@
-options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+options.o: options.cc ../include/loader.h /usr/include/c++/4.5/string \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
  /usr/include/features.h /usr/include/bits/predefs.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.4/bits/stringfwd.h \
- /usr/include/c++/4.4/bits/char_traits.h \
- /usr/include/c++/4.4/bits/stl_algobase.h /usr/include/c++/4.4/cstddef \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
- /usr/include/c++/4.4/bits/functexcept.h \
- /usr/include/c++/4.4/exception_defines.h \
- /usr/include/c++/4.4/bits/cpp_type_traits.h \
- /usr/include/c++/4.4/ext/type_traits.h \
- /usr/include/c++/4.4/ext/numeric_traits.h \
- /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
- /usr/include/c++/4.4/bits/concept_check.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.4/bits/stl_iterator.h \
- /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/postypes.h \
- /usr/include/c++/4.4/cwchar /usr/include/wchar.h /usr/include/stdio.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.5/bits/stringfwd.h \
+ /usr/include/c++/4.5/bits/char_traits.h \
+ /usr/include/c++/4.5/bits/stl_algobase.h /usr/include/c++/4.5/cstddef \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
+ /usr/include/c++/4.5/bits/functexcept.h \
+ /usr/include/c++/4.5/exception_defines.h \
+ /usr/include/c++/4.5/bits/cpp_type_traits.h \
+ /usr/include/c++/4.5/ext/type_traits.h \
+ /usr/include/c++/4.5/ext/numeric_traits.h \
+ /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
+ /usr/include/c++/4.5/bits/concept_check.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.5/bits/stl_iterator.h \
+ /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/postypes.h \
+ /usr/include/c++/4.5/cwchar /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/wchar.h /usr/include/xlocale.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.4/bits/allocator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
- /usr/include/c++/4.4/exception /usr/include/c++/4.4/bits/localefwd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.4/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.4/iosfwd \
- /usr/include/c++/4.4/cctype /usr/include/ctype.h \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.5/bits/allocator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
+ /usr/include/c++/4.5/exception /usr/include/c++/4.5/bits/localefwd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.5/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.5/iosfwd \
+ /usr/include/c++/4.5/cctype /usr/include/ctype.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ostream_insert.h \
- /usr/include/c++/4.4/cxxabi-forced.h \
- /usr/include/c++/4.4/bits/stl_function.h \
- /usr/include/c++/4.4/backward/binders.h \
- /usr/include/c++/4.4/bits/basic_string.h \
- /usr/include/c++/4.4/ext/atomicity.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ostream_insert.h \
+ /usr/include/c++/4.5/cxxabi-forced.h \
+ /usr/include/c++/4.5/bits/stl_function.h \
+ /usr/include/c++/4.5/backward/binders.h \
+ /usr/include/c++/4.5/bits/basic_string.h \
+ /usr/include/c++/4.5/ext/atomicity.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
  /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
- /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
- /usr/include/bits/setjmp.h /usr/include/unistd.h \
- /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
- /usr/include/bits/confname.h /usr/include/getopt.h \
- /usr/include/bits/unistd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.4/initializer_list \
- /usr/include/c++/4.4/bits/basic_string.tcc ../include/constants.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h /usr/include/bits/unistd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.5/initializer_list \
+ /usr/include/c++/4.5/bits/basic_string.tcc ../include/constants.h \
  ../include/data.h ../include/options.h /usr/include/stdlib.h \
  /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
  /usr/include/sys/types.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/sys/sysmacros.h \
- /usr/include/alloca.h /usr/include/bits/stdlib.h \
- /usr/include/c++/4.4/cstring /usr/include/string.h \
- /usr/include/bits/string3.h /usr/include/libio.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/bits/stdlib.h /usr/include/c++/4.5/cstring \
+ /usr/include/string.h /usr/include/bits/string3.h /usr/include/libio.h \
  /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \
  /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
  /usr/include/bits/stdio2.h
 
 ../include/loader.h:
 
-/usr/include/c++/4.4/string:
+/usr/include/c++/4.5/string:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
 
 /usr/include/features.h:
 
@@ -82,51 +81,51 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
 
-/usr/include/c++/4.4/bits/stringfwd.h:
+/usr/include/c++/4.5/bits/stringfwd.h:
 
-/usr/include/c++/4.4/bits/char_traits.h:
+/usr/include/c++/4.5/bits/char_traits.h:
 
-/usr/include/c++/4.4/bits/stl_algobase.h:
+/usr/include/c++/4.5/bits/stl_algobase.h:
 
-/usr/include/c++/4.4/cstddef:
+/usr/include/c++/4.5/cstddef:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
-/usr/include/c++/4.4/bits/functexcept.h:
+/usr/include/c++/4.5/bits/functexcept.h:
 
-/usr/include/c++/4.4/exception_defines.h:
+/usr/include/c++/4.5/exception_defines.h:
 
-/usr/include/c++/4.4/bits/cpp_type_traits.h:
+/usr/include/c++/4.5/bits/cpp_type_traits.h:
 
-/usr/include/c++/4.4/ext/type_traits.h:
+/usr/include/c++/4.5/ext/type_traits.h:
 
-/usr/include/c++/4.4/ext/numeric_traits.h:
+/usr/include/c++/4.5/ext/numeric_traits.h:
 
-/usr/include/c++/4.4/bits/stl_pair.h:
+/usr/include/c++/4.5/bits/stl_pair.h:
 
-/usr/include/c++/4.4/bits/move.h:
+/usr/include/c++/4.5/bits/move.h:
 
-/usr/include/c++/4.4/bits/concept_check.h:
+/usr/include/c++/4.5/bits/concept_check.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
 
-/usr/include/c++/4.4/bits/stl_iterator.h:
+/usr/include/c++/4.5/bits/stl_iterator.h:
 
-/usr/include/c++/4.4/debug/debug.h:
+/usr/include/c++/4.5/debug/debug.h:
 
-/usr/include/c++/4.4/bits/postypes.h:
+/usr/include/c++/4.5/bits/postypes.h:
 
-/usr/include/c++/4.4/cwchar:
+/usr/include/c++/4.5/cwchar:
 
 /usr/include/wchar.h:
 
 /usr/include/stdio.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/wchar.h:
 
@@ -134,29 +133,29 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \
 
 /usr/include/bits/wchar2.h:
 
-/usr/include/c++/4.4/bits/allocator.h:
+/usr/include/c++/4.5/bits/allocator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
 
-/usr/include/c++/4.4/ext/new_allocator.h:
+/usr/include/c++/4.5/ext/new_allocator.h:
 
-/usr/include/c++/4.4/new:
+/usr/include/c++/4.5/new:
 
-/usr/include/c++/4.4/exception:
+/usr/include/c++/4.5/exception:
 
-/usr/include/c++/4.4/bits/localefwd.h:
+/usr/include/c++/4.5/bits/localefwd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
 
-/usr/include/c++/4.4/clocale:
+/usr/include/c++/4.5/clocale:
 
 /usr/include/locale.h:
 
 /usr/include/bits/locale.h:
 
-/usr/include/c++/4.4/iosfwd:
+/usr/include/c++/4.5/iosfwd:
 
-/usr/include/c++/4.4/cctype:
+/usr/include/c++/4.5/cctype:
 
 /usr/include/ctype.h:
 
@@ -170,21 +169,21 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \
 
 /usr/include/bits/byteswap.h:
 
-/usr/include/c++/4.4/bits/ostream_insert.h:
+/usr/include/c++/4.5/bits/ostream_insert.h:
 
-/usr/include/c++/4.4/cxxabi-forced.h:
+/usr/include/c++/4.5/cxxabi-forced.h:
 
-/usr/include/c++/4.4/bits/stl_function.h:
+/usr/include/c++/4.5/bits/stl_function.h:
 
-/usr/include/c++/4.4/backward/binders.h:
+/usr/include/c++/4.5/backward/binders.h:
 
-/usr/include/c++/4.4/bits/basic_string.h:
+/usr/include/c++/4.5/bits/basic_string.h:
 
-/usr/include/c++/4.4/ext/atomicity.h:
+/usr/include/c++/4.5/ext/atomicity.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
 
 /usr/include/pthread.h:
 
@@ -196,10 +195,6 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \
 
 /usr/include/bits/time.h:
 
-/usr/include/signal.h:
-
-/usr/include/bits/sigset.h:
-
 /usr/include/bits/pthreadtypes.h:
 
 /usr/include/bits/setjmp.h:
@@ -216,11 +211,11 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \
 
 /usr/include/bits/unistd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
 
-/usr/include/c++/4.4/initializer_list:
+/usr/include/c++/4.5/initializer_list:
 
-/usr/include/c++/4.4/bits/basic_string.tcc:
+/usr/include/c++/4.5/bits/basic_string.tcc:
 
 ../include/constants.h:
 
@@ -240,13 +235,15 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \
 
 /usr/include/bits/select.h:
 
+/usr/include/bits/sigset.h:
+
 /usr/include/sys/sysmacros.h:
 
 /usr/include/alloca.h:
 
 /usr/include/bits/stdlib.h:
 
-/usr/include/c++/4.4/cstring:
+/usr/include/c++/4.5/cstring:
 
 /usr/include/string.h:
 
diff --git a/gtfold-mfe/src/.deps/shapereader.Po b/gtfold-mfe/src/.deps/shapereader.Po
index 4c5d9af..aa9b3a0 100644
--- a/gtfold-mfe/src/.deps/shapereader.Po
+++ b/gtfold-mfe/src/.deps/shapereader.Po
@@ -1,97 +1,97 @@
-shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+shapereader.o: shapereader.cc /usr/include/c++/4.5/iostream \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
  /usr/include/features.h /usr/include/bits/predefs.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \
- /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \
- /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \
- /usr/include/c++/4.4/cstddef \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \
+ /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \
+ /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \
+ /usr/include/c++/4.5/cstddef \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
  /usr/include/wchar.h /usr/include/stdio.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/wchar.h /usr/include/xlocale.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \
- /usr/include/c++/4.4/bits/char_traits.h \
- /usr/include/c++/4.4/bits/stl_algobase.h \
- /usr/include/c++/4.4/bits/functexcept.h \
- /usr/include/c++/4.4/exception_defines.h \
- /usr/include/c++/4.4/bits/cpp_type_traits.h \
- /usr/include/c++/4.4/ext/type_traits.h \
- /usr/include/c++/4.4/ext/numeric_traits.h \
- /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
- /usr/include/c++/4.4/bits/concept_check.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.4/bits/stl_iterator.h \
- /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.4/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \
+ /usr/include/c++/4.5/bits/char_traits.h \
+ /usr/include/c++/4.5/bits/stl_algobase.h \
+ /usr/include/c++/4.5/bits/functexcept.h \
+ /usr/include/c++/4.5/exception_defines.h \
+ /usr/include/c++/4.5/bits/cpp_type_traits.h \
+ /usr/include/c++/4.5/ext/type_traits.h \
+ /usr/include/c++/4.5/ext/numeric_traits.h \
+ /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
+ /usr/include/c++/4.5/bits/concept_check.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.5/bits/stl_iterator.h \
+ /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.5/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \
  /usr/include/ctype.h /usr/include/bits/types.h \
  /usr/include/bits/typesizes.h /usr/include/endian.h \
  /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/c++/4.4/bits/ios_base.h \
- /usr/include/c++/4.4/ext/atomicity.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/c++/4.5/bits/ios_base.h \
+ /usr/include/c++/4.5/ext/atomicity.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
  /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
- /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
- /usr/include/bits/setjmp.h /usr/include/unistd.h \
- /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
- /usr/include/bits/confname.h /usr/include/getopt.h \
- /usr/include/bits/unistd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \
- /usr/include/c++/4.4/bits/allocator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
- /usr/include/c++/4.4/bits/ostream_insert.h \
- /usr/include/c++/4.4/cxxabi-forced.h \
- /usr/include/c++/4.4/bits/stl_function.h \
- /usr/include/c++/4.4/backward/binders.h \
- /usr/include/c++/4.4/bits/basic_string.h \
- /usr/include/c++/4.4/initializer_list \
- /usr/include/c++/4.4/bits/basic_string.tcc \
- /usr/include/c++/4.4/bits/locale_classes.tcc \
- /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \
- /usr/include/c++/4.4/bits/basic_ios.h \
- /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h /usr/include/bits/unistd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \
+ /usr/include/c++/4.5/bits/allocator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
+ /usr/include/c++/4.5/bits/ostream_insert.h \
+ /usr/include/c++/4.5/cxxabi-forced.h \
+ /usr/include/c++/4.5/bits/stl_function.h \
+ /usr/include/c++/4.5/backward/binders.h \
+ /usr/include/c++/4.5/bits/basic_string.h \
+ /usr/include/c++/4.5/initializer_list \
+ /usr/include/c++/4.5/bits/basic_string.tcc \
+ /usr/include/c++/4.5/bits/locale_classes.tcc \
+ /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \
+ /usr/include/c++/4.5/bits/basic_ios.h \
+ /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \
  /usr/include/wctype.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \
- /usr/include/c++/4.4/bits/streambuf_iterator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \
- /usr/include/c++/4.4/bits/locale_facets.tcc \
- /usr/include/c++/4.4/bits/basic_ios.tcc \
- /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \
- /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \
- /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \
+ /usr/include/c++/4.5/bits/streambuf_iterator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \
+ /usr/include/c++/4.5/bits/locale_facets.tcc \
+ /usr/include/c++/4.5/bits/basic_ios.tcc \
+ /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \
+ /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \
+ /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \
  /usr/include/libio.h /usr/include/_G_config.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \
- /usr/include/c++/4.4/bits/fstream.tcc /usr/include/string.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \
+ /usr/include/c++/4.5/bits/fstream.tcc /usr/include/string.h \
  /usr/include/bits/string3.h /usr/include/stdlib.h \
  /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
  /usr/include/sys/types.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/sys/sysmacros.h \
- /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/math.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/sys/sysmacros.h /usr/include/alloca.h \
+ /usr/include/bits/stdlib.h /usr/include/math.h \
  /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
  /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
  ../include/shapereader.h ../include/global.h ../include/constants.h \
- ../include/options.h /usr/include/c++/4.4/cstring
+ ../include/options.h /usr/include/c++/4.5/cstring
 
-/usr/include/c++/4.4/iostream:
+/usr/include/c++/4.5/iostream:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
 
 /usr/include/features.h:
 
@@ -105,29 +105,29 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
 
-/usr/include/c++/4.4/ostream:
+/usr/include/c++/4.5/ostream:
 
-/usr/include/c++/4.4/ios:
+/usr/include/c++/4.5/ios:
 
-/usr/include/c++/4.4/iosfwd:
+/usr/include/c++/4.5/iosfwd:
 
-/usr/include/c++/4.4/bits/stringfwd.h:
+/usr/include/c++/4.5/bits/stringfwd.h:
 
-/usr/include/c++/4.4/bits/postypes.h:
+/usr/include/c++/4.5/bits/postypes.h:
 
-/usr/include/c++/4.4/cwchar:
+/usr/include/c++/4.5/cwchar:
 
-/usr/include/c++/4.4/cstddef:
+/usr/include/c++/4.5/cstddef:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
 /usr/include/wchar.h:
 
 /usr/include/stdio.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/wchar.h:
 
@@ -135,47 +135,47 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/wchar2.h:
 
-/usr/include/c++/4.4/exception:
+/usr/include/c++/4.5/exception:
 
-/usr/include/c++/4.4/bits/char_traits.h:
+/usr/include/c++/4.5/bits/char_traits.h:
 
-/usr/include/c++/4.4/bits/stl_algobase.h:
+/usr/include/c++/4.5/bits/stl_algobase.h:
 
-/usr/include/c++/4.4/bits/functexcept.h:
+/usr/include/c++/4.5/bits/functexcept.h:
 
-/usr/include/c++/4.4/exception_defines.h:
+/usr/include/c++/4.5/exception_defines.h:
 
-/usr/include/c++/4.4/bits/cpp_type_traits.h:
+/usr/include/c++/4.5/bits/cpp_type_traits.h:
 
-/usr/include/c++/4.4/ext/type_traits.h:
+/usr/include/c++/4.5/ext/type_traits.h:
 
-/usr/include/c++/4.4/ext/numeric_traits.h:
+/usr/include/c++/4.5/ext/numeric_traits.h:
 
-/usr/include/c++/4.4/bits/stl_pair.h:
+/usr/include/c++/4.5/bits/stl_pair.h:
 
-/usr/include/c++/4.4/bits/move.h:
+/usr/include/c++/4.5/bits/move.h:
 
-/usr/include/c++/4.4/bits/concept_check.h:
+/usr/include/c++/4.5/bits/concept_check.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
 
-/usr/include/c++/4.4/bits/stl_iterator.h:
+/usr/include/c++/4.5/bits/stl_iterator.h:
 
-/usr/include/c++/4.4/debug/debug.h:
+/usr/include/c++/4.5/debug/debug.h:
 
-/usr/include/c++/4.4/bits/localefwd.h:
+/usr/include/c++/4.5/bits/localefwd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
 
-/usr/include/c++/4.4/clocale:
+/usr/include/c++/4.5/clocale:
 
 /usr/include/locale.h:
 
 /usr/include/bits/locale.h:
 
-/usr/include/c++/4.4/cctype:
+/usr/include/c++/4.5/cctype:
 
 /usr/include/ctype.h:
 
@@ -189,13 +189,13 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/byteswap.h:
 
-/usr/include/c++/4.4/bits/ios_base.h:
+/usr/include/c++/4.5/bits/ios_base.h:
 
-/usr/include/c++/4.4/ext/atomicity.h:
+/usr/include/c++/4.5/ext/atomicity.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
 
 /usr/include/pthread.h:
 
@@ -207,10 +207,6 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/time.h:
 
-/usr/include/signal.h:
-
-/usr/include/bits/sigset.h:
-
 /usr/include/bits/pthreadtypes.h:
 
 /usr/include/bits/setjmp.h:
@@ -227,69 +223,69 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/unistd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
 
-/usr/include/c++/4.4/bits/locale_classes.h:
+/usr/include/c++/4.5/bits/locale_classes.h:
 
-/usr/include/c++/4.4/string:
+/usr/include/c++/4.5/string:
 
-/usr/include/c++/4.4/bits/allocator.h:
+/usr/include/c++/4.5/bits/allocator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
 
-/usr/include/c++/4.4/ext/new_allocator.h:
+/usr/include/c++/4.5/ext/new_allocator.h:
 
-/usr/include/c++/4.4/new:
+/usr/include/c++/4.5/new:
 
-/usr/include/c++/4.4/bits/ostream_insert.h:
+/usr/include/c++/4.5/bits/ostream_insert.h:
 
-/usr/include/c++/4.4/cxxabi-forced.h:
+/usr/include/c++/4.5/cxxabi-forced.h:
 
-/usr/include/c++/4.4/bits/stl_function.h:
+/usr/include/c++/4.5/bits/stl_function.h:
 
-/usr/include/c++/4.4/backward/binders.h:
+/usr/include/c++/4.5/backward/binders.h:
 
-/usr/include/c++/4.4/bits/basic_string.h:
+/usr/include/c++/4.5/bits/basic_string.h:
 
-/usr/include/c++/4.4/initializer_list:
+/usr/include/c++/4.5/initializer_list:
 
-/usr/include/c++/4.4/bits/basic_string.tcc:
+/usr/include/c++/4.5/bits/basic_string.tcc:
 
-/usr/include/c++/4.4/bits/locale_classes.tcc:
+/usr/include/c++/4.5/bits/locale_classes.tcc:
 
-/usr/include/c++/4.4/streambuf:
+/usr/include/c++/4.5/streambuf:
 
-/usr/include/c++/4.4/bits/streambuf.tcc:
+/usr/include/c++/4.5/bits/streambuf.tcc:
 
-/usr/include/c++/4.4/bits/basic_ios.h:
+/usr/include/c++/4.5/bits/basic_ios.h:
 
-/usr/include/c++/4.4/bits/locale_facets.h:
+/usr/include/c++/4.5/bits/locale_facets.h:
 
-/usr/include/c++/4.4/cwctype:
+/usr/include/c++/4.5/cwctype:
 
 /usr/include/wctype.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h:
 
-/usr/include/c++/4.4/bits/streambuf_iterator.h:
+/usr/include/c++/4.5/bits/streambuf_iterator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h:
 
-/usr/include/c++/4.4/bits/locale_facets.tcc:
+/usr/include/c++/4.5/bits/locale_facets.tcc:
 
-/usr/include/c++/4.4/bits/basic_ios.tcc:
+/usr/include/c++/4.5/bits/basic_ios.tcc:
 
-/usr/include/c++/4.4/bits/ostream.tcc:
+/usr/include/c++/4.5/bits/ostream.tcc:
 
-/usr/include/c++/4.4/istream:
+/usr/include/c++/4.5/istream:
 
-/usr/include/c++/4.4/bits/istream.tcc:
+/usr/include/c++/4.5/bits/istream.tcc:
 
-/usr/include/c++/4.4/fstream:
+/usr/include/c++/4.5/fstream:
 
-/usr/include/c++/4.4/bits/codecvt.h:
+/usr/include/c++/4.5/bits/codecvt.h:
 
-/usr/include/c++/4.4/cstdio:
+/usr/include/c++/4.5/cstdio:
 
 /usr/include/libio.h:
 
@@ -303,11 +299,11 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/stdio2.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h:
 
-/usr/include/c++/4.4/bits/fstream.tcc:
+/usr/include/c++/4.5/bits/fstream.tcc:
 
 /usr/include/string.h:
 
@@ -325,6 +321,8 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/bits/select.h:
 
+/usr/include/bits/sigset.h:
+
 /usr/include/sys/sysmacros.h:
 
 /usr/include/alloca.h:
@@ -357,4 +355,4 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \
 
 ../include/options.h:
 
-/usr/include/c++/4.4/cstring:
+/usr/include/c++/4.5/cstring:
diff --git a/gtfold-mfe/src/.deps/subopt_traceback.Po b/gtfold-mfe/src/.deps/subopt_traceback.Po
index 375a33e..6dac6fe 100644
--- a/gtfold-mfe/src/.deps/subopt_traceback.Po
+++ b/gtfold-mfe/src/.deps/subopt_traceback.Po
@@ -1,96 +1,95 @@
-subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
+subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.5/cstdio \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
  /usr/include/features.h /usr/include/bits/predefs.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.4/cstddef \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.5/cstddef \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
  /usr/include/stdio.h /usr/include/bits/types.h \
  /usr/include/bits/typesizes.h /usr/include/libio.h \
  /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
  ../include/constants.h ../include/energy.h ../include/data.h \
  ../include/constants.h ../include/utils.h ../include/global.h \
- ../include/subopt_traceback.h /usr/include/c++/4.4/cassert \
- /usr/include/assert.h /usr/include/c++/4.4/iostream \
- /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \
- /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \
- /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \
+ ../include/subopt_traceback.h /usr/include/c++/4.5/cassert \
+ /usr/include/assert.h /usr/include/c++/4.5/iostream \
+ /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \
+ /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \
+ /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \
  /usr/include/bits/wchar.h /usr/include/xlocale.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \
- /usr/include/c++/4.4/bits/char_traits.h \
- /usr/include/c++/4.4/bits/stl_algobase.h \
- /usr/include/c++/4.4/bits/functexcept.h \
- /usr/include/c++/4.4/exception_defines.h \
- /usr/include/c++/4.4/bits/cpp_type_traits.h \
- /usr/include/c++/4.4/ext/type_traits.h \
- /usr/include/c++/4.4/ext/numeric_traits.h \
- /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
- /usr/include/c++/4.4/bits/concept_check.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.4/bits/stl_iterator.h \
- /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.4/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \
+ /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \
+ /usr/include/c++/4.5/bits/char_traits.h \
+ /usr/include/c++/4.5/bits/stl_algobase.h \
+ /usr/include/c++/4.5/bits/functexcept.h \
+ /usr/include/c++/4.5/exception_defines.h \
+ /usr/include/c++/4.5/bits/cpp_type_traits.h \
+ /usr/include/c++/4.5/ext/type_traits.h \
+ /usr/include/c++/4.5/ext/numeric_traits.h \
+ /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
+ /usr/include/c++/4.5/bits/concept_check.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.5/bits/stl_iterator.h \
+ /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.5/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \
  /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ios_base.h \
- /usr/include/c++/4.4/ext/atomicity.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ios_base.h \
+ /usr/include/c++/4.5/ext/atomicity.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
  /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
- /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
- /usr/include/bits/setjmp.h /usr/include/unistd.h \
- /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
- /usr/include/bits/confname.h /usr/include/getopt.h \
- /usr/include/bits/unistd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \
- /usr/include/c++/4.4/bits/allocator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
- /usr/include/c++/4.4/bits/ostream_insert.h \
- /usr/include/c++/4.4/cxxabi-forced.h \
- /usr/include/c++/4.4/bits/stl_function.h \
- /usr/include/c++/4.4/backward/binders.h \
- /usr/include/c++/4.4/bits/basic_string.h \
- /usr/include/c++/4.4/initializer_list \
- /usr/include/c++/4.4/bits/basic_string.tcc \
- /usr/include/c++/4.4/bits/locale_classes.tcc \
- /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \
- /usr/include/c++/4.4/bits/basic_ios.h \
- /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h /usr/include/bits/unistd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \
+ /usr/include/c++/4.5/bits/allocator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
+ /usr/include/c++/4.5/bits/ostream_insert.h \
+ /usr/include/c++/4.5/cxxabi-forced.h \
+ /usr/include/c++/4.5/bits/stl_function.h \
+ /usr/include/c++/4.5/backward/binders.h \
+ /usr/include/c++/4.5/bits/basic_string.h \
+ /usr/include/c++/4.5/initializer_list \
+ /usr/include/c++/4.5/bits/basic_string.tcc \
+ /usr/include/c++/4.5/bits/locale_classes.tcc \
+ /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \
+ /usr/include/c++/4.5/bits/basic_ios.h \
+ /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \
  /usr/include/wctype.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \
- /usr/include/c++/4.4/bits/streambuf_iterator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \
- /usr/include/c++/4.4/bits/locale_facets.tcc \
- /usr/include/c++/4.4/bits/basic_ios.tcc \
- /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \
- /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/sstream \
- /usr/include/c++/4.4/bits/sstream.tcc /usr/include/c++/4.4/stack \
- /usr/include/c++/4.4/deque /usr/include/c++/4.4/bits/stl_construct.h \
- /usr/include/c++/4.4/bits/stl_uninitialized.h \
- /usr/include/c++/4.4/bits/stl_deque.h \
- /usr/include/c++/4.4/bits/deque.tcc \
- /usr/include/c++/4.4/bits/stl_stack.h /usr/include/c++/4.4/map \
- /usr/include/c++/4.4/bits/stl_tree.h /usr/include/c++/4.4/bits/stl_map.h \
- /usr/include/c++/4.4/bits/stl_multimap.h /usr/include/c++/4.4/vector \
- /usr/include/c++/4.4/bits/stl_vector.h \
- /usr/include/c++/4.4/bits/stl_bvector.h \
- /usr/include/c++/4.4/bits/vector.tcc
-
-/usr/include/c++/4.4/cstdio:
-
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
-
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \
+ /usr/include/c++/4.5/bits/streambuf_iterator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \
+ /usr/include/c++/4.5/bits/locale_facets.tcc \
+ /usr/include/c++/4.5/bits/basic_ios.tcc \
+ /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \
+ /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/sstream \
+ /usr/include/c++/4.5/bits/sstream.tcc /usr/include/c++/4.5/stack \
+ /usr/include/c++/4.5/deque /usr/include/c++/4.5/bits/stl_construct.h \
+ /usr/include/c++/4.5/bits/stl_uninitialized.h \
+ /usr/include/c++/4.5/bits/stl_deque.h \
+ /usr/include/c++/4.5/bits/deque.tcc \
+ /usr/include/c++/4.5/bits/stl_stack.h /usr/include/c++/4.5/map \
+ /usr/include/c++/4.5/bits/stl_tree.h /usr/include/c++/4.5/bits/stl_map.h \
+ /usr/include/c++/4.5/bits/stl_multimap.h /usr/include/c++/4.5/vector \
+ /usr/include/c++/4.5/bits/stl_vector.h \
+ /usr/include/c++/4.5/bits/stl_bvector.h \
+ /usr/include/c++/4.5/bits/vector.tcc
+
+/usr/include/c++/4.5/cstdio:
+
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
+
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
 
 /usr/include/features.h:
 
@@ -104,11 +103,11 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
 
-/usr/include/c++/4.4/cstddef:
+/usr/include/c++/4.5/cstddef:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
 /usr/include/stdio.h:
 
@@ -122,7 +121,7 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \
 
 /usr/include/wchar.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/stdio_lim.h:
 
@@ -146,23 +145,23 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \
 
 ../include/subopt_traceback.h:
 
-/usr/include/c++/4.4/cassert:
+/usr/include/c++/4.5/cassert:
 
 /usr/include/assert.h:
 
-/usr/include/c++/4.4/iostream:
+/usr/include/c++/4.5/iostream:
 
-/usr/include/c++/4.4/ostream:
+/usr/include/c++/4.5/ostream:
 
-/usr/include/c++/4.4/ios:
+/usr/include/c++/4.5/ios:
 
-/usr/include/c++/4.4/iosfwd:
+/usr/include/c++/4.5/iosfwd:
 
-/usr/include/c++/4.4/bits/stringfwd.h:
+/usr/include/c++/4.5/bits/stringfwd.h:
 
-/usr/include/c++/4.4/bits/postypes.h:
+/usr/include/c++/4.5/bits/postypes.h:
 
-/usr/include/c++/4.4/cwchar:
+/usr/include/c++/4.5/cwchar:
 
 /usr/include/bits/wchar.h:
 
@@ -170,47 +169,47 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \
 
 /usr/include/bits/wchar2.h:
 
-/usr/include/c++/4.4/exception:
+/usr/include/c++/4.5/exception:
 
-/usr/include/c++/4.4/bits/char_traits.h:
+/usr/include/c++/4.5/bits/char_traits.h:
 
-/usr/include/c++/4.4/bits/stl_algobase.h:
+/usr/include/c++/4.5/bits/stl_algobase.h:
 
-/usr/include/c++/4.4/bits/functexcept.h:
+/usr/include/c++/4.5/bits/functexcept.h:
 
-/usr/include/c++/4.4/exception_defines.h:
+/usr/include/c++/4.5/exception_defines.h:
 
-/usr/include/c++/4.4/bits/cpp_type_traits.h:
+/usr/include/c++/4.5/bits/cpp_type_traits.h:
 
-/usr/include/c++/4.4/ext/type_traits.h:
+/usr/include/c++/4.5/ext/type_traits.h:
 
-/usr/include/c++/4.4/ext/numeric_traits.h:
+/usr/include/c++/4.5/ext/numeric_traits.h:
 
-/usr/include/c++/4.4/bits/stl_pair.h:
+/usr/include/c++/4.5/bits/stl_pair.h:
 
-/usr/include/c++/4.4/bits/move.h:
+/usr/include/c++/4.5/bits/move.h:
 
-/usr/include/c++/4.4/bits/concept_check.h:
+/usr/include/c++/4.5/bits/concept_check.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
 
-/usr/include/c++/4.4/bits/stl_iterator.h:
+/usr/include/c++/4.5/bits/stl_iterator.h:
 
-/usr/include/c++/4.4/debug/debug.h:
+/usr/include/c++/4.5/debug/debug.h:
 
-/usr/include/c++/4.4/bits/localefwd.h:
+/usr/include/c++/4.5/bits/localefwd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
 
-/usr/include/c++/4.4/clocale:
+/usr/include/c++/4.5/clocale:
 
 /usr/include/locale.h:
 
 /usr/include/bits/locale.h:
 
-/usr/include/c++/4.4/cctype:
+/usr/include/c++/4.5/cctype:
 
 /usr/include/ctype.h:
 
@@ -220,13 +219,13 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \
 
 /usr/include/bits/byteswap.h:
 
-/usr/include/c++/4.4/bits/ios_base.h:
+/usr/include/c++/4.5/bits/ios_base.h:
 
-/usr/include/c++/4.4/ext/atomicity.h:
+/usr/include/c++/4.5/ext/atomicity.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
 
 /usr/include/pthread.h:
 
@@ -238,10 +237,6 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \
 
 /usr/include/bits/time.h:
 
-/usr/include/signal.h:
-
-/usr/include/bits/sigset.h:
-
 /usr/include/bits/pthreadtypes.h:
 
 /usr/include/bits/setjmp.h:
@@ -258,94 +253,94 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \
 
 /usr/include/bits/unistd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
 
-/usr/include/c++/4.4/bits/locale_classes.h:
+/usr/include/c++/4.5/bits/locale_classes.h:
 
-/usr/include/c++/4.4/string:
+/usr/include/c++/4.5/string:
 
-/usr/include/c++/4.4/bits/allocator.h:
+/usr/include/c++/4.5/bits/allocator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
 
-/usr/include/c++/4.4/ext/new_allocator.h:
+/usr/include/c++/4.5/ext/new_allocator.h:
 
-/usr/include/c++/4.4/new:
+/usr/include/c++/4.5/new:
 
-/usr/include/c++/4.4/bits/ostream_insert.h:
+/usr/include/c++/4.5/bits/ostream_insert.h:
 
-/usr/include/c++/4.4/cxxabi-forced.h:
+/usr/include/c++/4.5/cxxabi-forced.h:
 
-/usr/include/c++/4.4/bits/stl_function.h:
+/usr/include/c++/4.5/bits/stl_function.h:
 
-/usr/include/c++/4.4/backward/binders.h:
+/usr/include/c++/4.5/backward/binders.h:
 
-/usr/include/c++/4.4/bits/basic_string.h:
+/usr/include/c++/4.5/bits/basic_string.h:
 
-/usr/include/c++/4.4/initializer_list:
+/usr/include/c++/4.5/initializer_list:
 
-/usr/include/c++/4.4/bits/basic_string.tcc:
+/usr/include/c++/4.5/bits/basic_string.tcc:
 
-/usr/include/c++/4.4/bits/locale_classes.tcc:
+/usr/include/c++/4.5/bits/locale_classes.tcc:
 
-/usr/include/c++/4.4/streambuf:
+/usr/include/c++/4.5/streambuf:
 
-/usr/include/c++/4.4/bits/streambuf.tcc:
+/usr/include/c++/4.5/bits/streambuf.tcc:
 
-/usr/include/c++/4.4/bits/basic_ios.h:
+/usr/include/c++/4.5/bits/basic_ios.h:
 
-/usr/include/c++/4.4/bits/locale_facets.h:
+/usr/include/c++/4.5/bits/locale_facets.h:
 
-/usr/include/c++/4.4/cwctype:
+/usr/include/c++/4.5/cwctype:
 
 /usr/include/wctype.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h:
 
-/usr/include/c++/4.4/bits/streambuf_iterator.h:
+/usr/include/c++/4.5/bits/streambuf_iterator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h:
 
-/usr/include/c++/4.4/bits/locale_facets.tcc:
+/usr/include/c++/4.5/bits/locale_facets.tcc:
 
-/usr/include/c++/4.4/bits/basic_ios.tcc:
+/usr/include/c++/4.5/bits/basic_ios.tcc:
 
-/usr/include/c++/4.4/bits/ostream.tcc:
+/usr/include/c++/4.5/bits/ostream.tcc:
 
-/usr/include/c++/4.4/istream:
+/usr/include/c++/4.5/istream:
 
-/usr/include/c++/4.4/bits/istream.tcc:
+/usr/include/c++/4.5/bits/istream.tcc:
 
-/usr/include/c++/4.4/sstream:
+/usr/include/c++/4.5/sstream:
 
-/usr/include/c++/4.4/bits/sstream.tcc:
+/usr/include/c++/4.5/bits/sstream.tcc:
 
-/usr/include/c++/4.4/stack:
+/usr/include/c++/4.5/stack:
 
-/usr/include/c++/4.4/deque:
+/usr/include/c++/4.5/deque:
 
-/usr/include/c++/4.4/bits/stl_construct.h:
+/usr/include/c++/4.5/bits/stl_construct.h:
 
-/usr/include/c++/4.4/bits/stl_uninitialized.h:
+/usr/include/c++/4.5/bits/stl_uninitialized.h:
 
-/usr/include/c++/4.4/bits/stl_deque.h:
+/usr/include/c++/4.5/bits/stl_deque.h:
 
-/usr/include/c++/4.4/bits/deque.tcc:
+/usr/include/c++/4.5/bits/deque.tcc:
 
-/usr/include/c++/4.4/bits/stl_stack.h:
+/usr/include/c++/4.5/bits/stl_stack.h:
 
-/usr/include/c++/4.4/map:
+/usr/include/c++/4.5/map:
 
-/usr/include/c++/4.4/bits/stl_tree.h:
+/usr/include/c++/4.5/bits/stl_tree.h:
 
-/usr/include/c++/4.4/bits/stl_map.h:
+/usr/include/c++/4.5/bits/stl_map.h:
 
-/usr/include/c++/4.4/bits/stl_multimap.h:
+/usr/include/c++/4.5/bits/stl_multimap.h:
 
-/usr/include/c++/4.4/vector:
+/usr/include/c++/4.5/vector:
 
-/usr/include/c++/4.4/bits/stl_vector.h:
+/usr/include/c++/4.5/bits/stl_vector.h:
 
-/usr/include/c++/4.4/bits/stl_bvector.h:
+/usr/include/c++/4.5/bits/stl_bvector.h:
 
-/usr/include/c++/4.4/bits/vector.tcc:
+/usr/include/c++/4.5/bits/vector.tcc:
diff --git a/gtfold-mfe/src/.deps/traceback.Po b/gtfold-mfe/src/.deps/traceback.Po
index c475c0e..28cf049 100644
--- a/gtfold-mfe/src/.deps/traceback.Po
+++ b/gtfold-mfe/src/.deps/traceback.Po
@@ -2,15 +2,16 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -38,7 +39,7 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
 /usr/include/bits/types.h:
 
@@ -50,7 +51,7 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/wchar.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/stdio_lim.h:
 
@@ -62,9 +63,9 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/stdlib.h:
 
-/usr/include/sys/types.h:
+/usr/include/bits/waitflags.h:
 
-/usr/include/time.h:
+/usr/include/bits/waitstatus.h:
 
 /usr/include/endian.h:
 
@@ -72,6 +73,10 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \
 
 /usr/include/bits/byteswap.h:
 
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
 /usr/include/sys/select.h:
 
 /usr/include/bits/select.h:
diff --git a/gtfold-mfe/src/.deps/utils.Po b/gtfold-mfe/src/.deps/utils.Po
index 61ad5ac..d92a43a 100644
--- a/gtfold-mfe/src/.deps/utils.Po
+++ b/gtfold-mfe/src/.deps/utils.Po
@@ -3,57 +3,56 @@ utils.o: utils.cc ../include/utils.h ../include/constants.h \
  /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
  /usr/include/xlocale.h /usr/include/bits/string3.h \
- /usr/include/c++/4.4/string \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.4/bits/stringfwd.h \
- /usr/include/c++/4.4/bits/char_traits.h \
- /usr/include/c++/4.4/bits/stl_algobase.h /usr/include/c++/4.4/cstddef \
- /usr/include/c++/4.4/bits/functexcept.h \
- /usr/include/c++/4.4/exception_defines.h \
- /usr/include/c++/4.4/bits/cpp_type_traits.h \
- /usr/include/c++/4.4/ext/type_traits.h \
- /usr/include/c++/4.4/ext/numeric_traits.h \
- /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \
- /usr/include/c++/4.4/bits/concept_check.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.4/bits/stl_iterator.h \
- /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/postypes.h \
- /usr/include/c++/4.4/cwchar /usr/include/wchar.h /usr/include/stdio.h \
- /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \
+ /usr/include/c++/4.5/string \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
+ /usr/include/c++/4.5/bits/stringfwd.h \
+ /usr/include/c++/4.5/bits/char_traits.h \
+ /usr/include/c++/4.5/bits/stl_algobase.h /usr/include/c++/4.5/cstddef \
+ /usr/include/c++/4.5/bits/functexcept.h \
+ /usr/include/c++/4.5/exception_defines.h \
+ /usr/include/c++/4.5/bits/cpp_type_traits.h \
+ /usr/include/c++/4.5/ext/type_traits.h \
+ /usr/include/c++/4.5/ext/numeric_traits.h \
+ /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
+ /usr/include/c++/4.5/bits/concept_check.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
+ /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/4.5/bits/stl_iterator.h \
+ /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/postypes.h \
+ /usr/include/c++/4.5/cwchar /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
  /usr/include/bits/wchar.h /usr/include/bits/wchar2.h \
- /usr/include/c++/4.4/bits/allocator.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \
- /usr/include/c++/4.4/exception /usr/include/c++/4.4/bits/localefwd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.4/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.4/iosfwd \
- /usr/include/c++/4.4/cctype /usr/include/ctype.h \
+ /usr/include/c++/4.5/bits/allocator.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
+ /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
+ /usr/include/c++/4.5/exception /usr/include/c++/4.5/bits/localefwd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
+ /usr/include/c++/4.5/clocale /usr/include/locale.h \
+ /usr/include/bits/locale.h /usr/include/c++/4.5/iosfwd \
+ /usr/include/c++/4.5/cctype /usr/include/ctype.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ostream_insert.h \
- /usr/include/c++/4.4/cxxabi-forced.h \
- /usr/include/c++/4.4/bits/stl_function.h \
- /usr/include/c++/4.4/backward/binders.h \
- /usr/include/c++/4.4/bits/basic_string.h \
- /usr/include/c++/4.4/ext/atomicity.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \
+ /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ostream_insert.h \
+ /usr/include/c++/4.5/cxxabi-forced.h \
+ /usr/include/c++/4.5/bits/stl_function.h \
+ /usr/include/c++/4.5/backward/binders.h \
+ /usr/include/c++/4.5/bits/basic_string.h \
+ /usr/include/c++/4.5/ext/atomicity.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
  /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \
- /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \
- /usr/include/bits/setjmp.h /usr/include/unistd.h \
- /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
- /usr/include/bits/confname.h /usr/include/getopt.h \
- /usr/include/bits/unistd.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.4/initializer_list \
- /usr/include/c++/4.4/bits/basic_string.tcc
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h /usr/include/bits/unistd.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
+ /usr/include/c++/4.5/initializer_list \
+ /usr/include/c++/4.5/bits/basic_string.tcc
 
 ../include/utils.h:
 
@@ -73,89 +72,89 @@ utils.o: utils.cc ../include/utils.h ../include/constants.h \
 
 /usr/include/gnu/stubs-64.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
 
 /usr/include/xlocale.h:
 
 /usr/include/bits/string3.h:
 
-/usr/include/c++/4.4/string:
+/usr/include/c++/4.5/string:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
 
-/usr/include/c++/4.4/bits/stringfwd.h:
+/usr/include/c++/4.5/bits/stringfwd.h:
 
-/usr/include/c++/4.4/bits/char_traits.h:
+/usr/include/c++/4.5/bits/char_traits.h:
 
-/usr/include/c++/4.4/bits/stl_algobase.h:
+/usr/include/c++/4.5/bits/stl_algobase.h:
 
-/usr/include/c++/4.4/cstddef:
+/usr/include/c++/4.5/cstddef:
 
-/usr/include/c++/4.4/bits/functexcept.h:
+/usr/include/c++/4.5/bits/functexcept.h:
 
-/usr/include/c++/4.4/exception_defines.h:
+/usr/include/c++/4.5/exception_defines.h:
 
-/usr/include/c++/4.4/bits/cpp_type_traits.h:
+/usr/include/c++/4.5/bits/cpp_type_traits.h:
 
-/usr/include/c++/4.4/ext/type_traits.h:
+/usr/include/c++/4.5/ext/type_traits.h:
 
-/usr/include/c++/4.4/ext/numeric_traits.h:
+/usr/include/c++/4.5/ext/numeric_traits.h:
 
-/usr/include/c++/4.4/bits/stl_pair.h:
+/usr/include/c++/4.5/bits/stl_pair.h:
 
-/usr/include/c++/4.4/bits/move.h:
+/usr/include/c++/4.5/bits/move.h:
 
-/usr/include/c++/4.4/bits/concept_check.h:
+/usr/include/c++/4.5/bits/concept_check.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_types.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
 
-/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h:
+/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
 
-/usr/include/c++/4.4/bits/stl_iterator.h:
+/usr/include/c++/4.5/bits/stl_iterator.h:
 
-/usr/include/c++/4.4/debug/debug.h:
+/usr/include/c++/4.5/debug/debug.h:
 
-/usr/include/c++/4.4/bits/postypes.h:
+/usr/include/c++/4.5/bits/postypes.h:
 
-/usr/include/c++/4.4/cwchar:
+/usr/include/c++/4.5/cwchar:
 
 /usr/include/wchar.h:
 
 /usr/include/stdio.h:
 
-/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h:
+/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
 
 /usr/include/bits/wchar.h:
 
 /usr/include/bits/wchar2.h:
 
-/usr/include/c++/4.4/bits/allocator.h:
+/usr/include/c++/4.5/bits/allocator.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
 
-/usr/include/c++/4.4/ext/new_allocator.h:
+/usr/include/c++/4.5/ext/new_allocator.h:
 
-/usr/include/c++/4.4/new:
+/usr/include/c++/4.5/new:
 
-/usr/include/c++/4.4/exception:
+/usr/include/c++/4.5/exception:
 
-/usr/include/c++/4.4/bits/localefwd.h:
+/usr/include/c++/4.5/bits/localefwd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
 
-/usr/include/c++/4.4/clocale:
+/usr/include/c++/4.5/clocale:
 
 /usr/include/locale.h:
 
 /usr/include/bits/locale.h:
 
-/usr/include/c++/4.4/iosfwd:
+/usr/include/c++/4.5/iosfwd:
 
-/usr/include/c++/4.4/cctype:
+/usr/include/c++/4.5/cctype:
 
 /usr/include/ctype.h:
 
@@ -169,21 +168,21 @@ utils.o: utils.cc ../include/utils.h ../include/constants.h \
 
 /usr/include/bits/byteswap.h:
 
-/usr/include/c++/4.4/bits/ostream_insert.h:
+/usr/include/c++/4.5/bits/ostream_insert.h:
 
-/usr/include/c++/4.4/cxxabi-forced.h:
+/usr/include/c++/4.5/cxxabi-forced.h:
 
-/usr/include/c++/4.4/bits/stl_function.h:
+/usr/include/c++/4.5/bits/stl_function.h:
 
-/usr/include/c++/4.4/backward/binders.h:
+/usr/include/c++/4.5/backward/binders.h:
 
-/usr/include/c++/4.4/bits/basic_string.h:
+/usr/include/c++/4.5/bits/basic_string.h:
 
-/usr/include/c++/4.4/ext/atomicity.h:
+/usr/include/c++/4.5/ext/atomicity.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
 
 /usr/include/pthread.h:
 
@@ -195,10 +194,6 @@ utils.o: utils.cc ../include/utils.h ../include/constants.h \
 
 /usr/include/bits/time.h:
 
-/usr/include/signal.h:
-
-/usr/include/bits/sigset.h:
-
 /usr/include/bits/pthreadtypes.h:
 
 /usr/include/bits/setjmp.h:
@@ -215,8 +210,8 @@ utils.o: utils.cc ../include/utils.h ../include/constants.h \
 
 /usr/include/bits/unistd.h:
 
-/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h:
+/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
 
-/usr/include/c++/4.4/initializer_list:
+/usr/include/c++/4.5/initializer_list:
 
-/usr/include/c++/4.4/bits/basic_string.tcc:
+/usr/include/c++/4.5/bits/basic_string.tcc:
diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile
index 0f50f74..53081de 100644
--- a/gtfold-mfe/src/Makefile
+++ b/gtfold-mfe/src/Makefile
@@ -51,7 +51,8 @@ PROGRAMS = $(bin_PROGRAMS)
 am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
 	options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \
 	energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \
-	subopt_traceback.$(OBJEXT) shapereader.$(OBJEXT)
+	subopt_traceback.$(OBJEXT) partition-dangle.$(OBJEXT) \
+	shapereader.$(OBJEXT)
 gtfold_OBJECTS = $(am_gtfold_OBJECTS)
 gtfold_DEPENDENCIES =
 gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
@@ -74,12 +75,12 @@ DIST_SOURCES = $(gtfold_SOURCES)
 ETAGS = etags
 CTAGS = ctags
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = gawk
+ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = mawk
 CC = gcc
 CCDEPMODE = depmode=gcc3
 CFLAGS = -g -O2 -Wall
@@ -106,7 +107,7 @@ LDFLAGS =
 LIBOBJS = 
 LIBS = -lgomp 
 LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
 MKDIR_P = /bin/mkdir -p
 OBJEXT = o
 OPENMP_CFLAGS = -fopenmp
@@ -122,10 +123,10 @@ SET_MAKE =
 SHELL = /bin/bash
 STRIP = 
 VERSION = 1.18
-abs_builddir = /home/zs/git/gtfold/gtfold-mfe/src
-abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/src
-abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
-abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/src
+abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/src
+abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
+abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
 ac_ct_CC = gcc
 ac_ct_CXX = g++
 am__include = include
@@ -153,7 +154,7 @@ host_vendor = unknown
 htmldir = ${docdir}
 includedir = ${prefix}/include
 infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
 libdir = ${exec_prefix}/lib
 libexecdir = ${exec_prefix}/libexec
 localedir = ${datarootdir}/locale
@@ -191,6 +192,7 @@ gtfold_SOURCES = \
 	algorithms.c \
 	traceback.c \
 	subopt_traceback.cc\
+	partition-dangle.c\
 	shapereader.cc
 
 gtfold_LDFLAGS = 
@@ -284,6 +286,7 @@ include ./$(DEPDIR)/global.Po
 include ./$(DEPDIR)/loader.Po
 include ./$(DEPDIR)/main.Po
 include ./$(DEPDIR)/options.Po
+include ./$(DEPDIR)/partition-dangle.Po
 include ./$(DEPDIR)/shapereader.Po
 include ./$(DEPDIR)/subopt_traceback.Po
 include ./$(DEPDIR)/traceback.Po
diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am
index 1dea460..797391e 100644
--- a/gtfold-mfe/src/Makefile.am
+++ b/gtfold-mfe/src/Makefile.am
@@ -16,6 +16,7 @@ gtfold_SOURCES = \
 	algorithms.c \
 	traceback.c \
 	subopt_traceback.cc\
+	partition-dangle.c\
 	shapereader.cc
 
 gtfold_LDFLAGS = 
diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in
index 8d3f880..0de321f 100644
--- a/gtfold-mfe/src/Makefile.in
+++ b/gtfold-mfe/src/Makefile.in
@@ -51,7 +51,8 @@ PROGRAMS = $(bin_PROGRAMS)
 am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
 	options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \
 	energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \
-	subopt_traceback.$(OBJEXT) shapereader.$(OBJEXT)
+	subopt_traceback.$(OBJEXT) partition-dangle.$(OBJEXT) \
+	shapereader.$(OBJEXT)
 gtfold_OBJECTS = $(am_gtfold_OBJECTS)
 gtfold_DEPENDENCIES =
 gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
@@ -191,6 +192,7 @@ gtfold_SOURCES = \
 	algorithms.c \
 	traceback.c \
 	subopt_traceback.cc\
+	partition-dangle.c\
 	shapereader.cc
 
 gtfold_LDFLAGS = 
@@ -284,6 +286,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/loader.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@
diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c
index f87e190..c39128e 100644
--- a/gtfold-mfe/src/algorithms-partition.c
+++ b/gtfold-mfe/src/algorithms-partition.c
@@ -217,7 +217,6 @@ double **mallocTwoD(int r, int c) {
             return NULL;
         }
     }
-
     return arr;
 }
 
diff --git a/gtfold-mfe/src/partition-dangle.cc b/gtfold-mfe/src/partition-dangle.cc
deleted file mode 100644
index d07064c..0000000
--- a/gtfold-mfe/src/partition-dangle.cc
+++ /dev/null
@@ -1,130 +0,0 @@
-//The paper (Dirks, Pierce) offhandedly mentions a G-U terminal pair penalty
-//I don't think we do that...
-
-/**s1 -> partial_external
-*  s2 -> partial_multi
-*  s3 -> partial_multi2
-*  u1 -> u_multi
-*  f -> cond_dangle (conditional)
-**/
-
-#include energy.h
-
-
-int cond_dangle(int j, int h, int l){
-	return j - 1 == l ? 1 : exp(-Ed3(h,l,l+1)/RT);
-}
-
-double RT = (0.00198721 * 310.15)/100.00; 
-//So that we don't have the /100 in every exponent
-//Seeing as we missed some last time
-
-int seg_length;
-int i;
-for(seg_length = MIN_TURN; seg_length < len; len ++){
-	for(i = 1; i < seg_length - MIN_TURN; i++){
-		j = i + seg_length;
-		int l;
-		/**
-		*  For each spot in partial_external at index h,j we'll need:
-		**/
-		for(l = i+2; l < j; l++){
-			upm[i][j] += up[i+1][l] * exp(-(Ea + 2 * Ec + auPenalty(i + 1,l)/RT)) *
-						(exp(-Ed3(i + 1,l,l+1)/RT) * u_multi[l + 2][j - 1] + 
-						u_multi[l + 1][j - 1] -
-						u_multi[l + 2][j - 1]);
-			if(l != i+2){ //goes from i + 2 < l < j
-				upm[i][j] += up[i + 2][l] * 
-						exp(-(Ea + 2 * Ec + Eb + Ed3(j,i,i + 1) + auPenalty(i + 2, l))/RT) *
-						(exp(-Ed3(i + 2,l,l + 1)/RT)*u_multi[l + 2][j - 1] + 
-						u_multi[l + 1][j - 1]  - 
-						u_multi[l + 2][j - 1]);
-
-				if(l != j - 1){
-					upm[i][j] += exp(-Ed3(j,i,i + 1)/RT)*exp(-(Ea + 2 * Ec + (l - i - 1) * Eb)/RT) * 
-								partial_multi[l][j]; 
-					//Changed h in the paper to l it makes no difference
-					//other than unifying loops
-				}
-			}
-		}
-
-
-		up[i][j] += exp(-eh(i,j)/RT) + exp(-es(i,j)/RT) * up[i + 1][j - 1] + upm[i][j];
-		for(l = j - 1; l > i + 1; l--){
-			if((j - l) - 2> MAX_LOOP){
-				break;
-			}
-			for(h = i + 1 ; h < l; h++){
-				if(!(i == h - 1 && j == l - 1)){ //If this is true we have a stack
-					up[i][j] += exp(-ebi(i,j,h,l)/RT);
-				}
-				if((j - l) + (h - i) - 2> MAX_LOOP){
-					break;
-				}
-			}
-		}
-
-		for(l = i + 1; l <= j ; l++){
-			u_multi[i][j] += up[i][l] * exp(-(Ec + auPenalty(i,l))/RT) *
-					(cond_dangle(j + 1, i, l) * exp(-(j - l) * Eb/RT) + 
-					exp(-Ed3(i,l,l + 1)/RT) * u_multi[l + 2][j] + 
-					u_multi[l + 1][j] -
-					u_multi[l + 2][j]);
-			if(l != i+1){	
-				u_multi[i][j] += up[i + 1][j]*exp(-(Ec + Eb + auPenalty(i + 1,l))/RT)*
-						(cond_dangle(j + 1, i + 1, l) * exp(-(j - l)*Eb/RT) + 
-						exp(-Ed3(i + 1,l,l + 1)/RT) * u_multi[l + 2][j] + 
-						u_multi[l + 1][j] - 
-						u_multi[l + 2][j]);
-				if(l != j){
-					u_multi[i][j] += exp(-(Ec + (h - i) * Eb)/RT) * partial_multi2[l][j];
-
-				}
-			}
-		}
-
-
-		int h = i; //To stay consistant with the notation in the paper.
-
-		for(l = h+1; l < j; l++){
-			partial_external[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
-						(exp(-Ed3(h,l,l + 1)/RT)*u[l + 2,j - 1] + 
-						u[l + 1][j] -
-						u[l + 2][j]);
-
-			partial_multi[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
-						(exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j - 1] + 
-						u_multi[l + 1][j - 1] -
-						u_multi[l + 2][j - 1]);
-
-			partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
-						(cond_dangle(j + 1, h, l)*exp(-(j - l) * Eb / RT) + 
-						exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j] + 
-						u_multi[l + 1][j] - 
-						u_multi[l + 2][j]);
-						
-		}
-		/** partial_multi2 goes up to j **/
-		partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
-					(cond_dangle(j + 1, h, l)*exp(-(j-l) * Eb / RT) + 
-					exp(-Ed3(h,l,l + 1)/RT) * u_multi[l + 2][j] + 
-					u_multi[l + 1][j] - 
-					u_multi[l + 2][j]);
-
-		//Finally we do the u matrix
-		u[i][j] = 1 + up[i][j]*exp(-auPenalty(i,j) /RT);
-
-		for(l = i + 1; l < j; l++){
-			//Replaced l with h in the next line to unify loops
-			u[i][j] += up[l][j] * exp(-(Ed5(l, j , l - 1) + auPenalty(h,j))/RT)
-
-			u[i][j] += exp(-(auPenalty(i,l))/RT)*(exp(-Ed3(i,l,l + 1)/RT) * u[l + 2][j] +
-				   u[l + 1][j] - u[l + 2][j]);
-			if(l != j - 1) {
-				u[i][j] += partial_external[l][j];
-			}
-				   
-		}
-	}
-}

From 294a55615f0b0230046db1af2b390e4f2751c07f Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Fri, 20 May 2011 11:13:29 -0400
Subject: [PATCH 122/282] Finished writing all probability functions

---
 gtfold-mfe/src/random-sample.cc | 187 ++++++++++++++++++++++++++++++++
 1 file changed, 187 insertions(+)
 create mode 100644 gtfold-mfe/src/random-sample.cc

diff --git a/gtfold-mfe/src/random-sample.cc b/gtfold-mfe/src/random-sample.cc
new file mode 100644
index 0000000..3290e38
--- /dev/null
+++ b/gtfold-mfe/src/random-sample.cc
@@ -0,0 +1,187 @@
+#include <math.h>
+#include <stdlib.h>
+
+#include "parition-dangle.h"
+#include "energy.h"
+
+double RT=(0.00198721 * 310.15)/100.00; 
+
+double randdouble(){
+	    return rand()/(double(RAND_MAX)+1);
+} 
+
+//P_0
+double single_stranded_prob(int i, int j, dangle_struct d_struct){
+	return 1 / d_struct.u[i][j];
+}
+
+//P_{ij}
+double ends_pair_prob(int i, int j, dangle_struct d_struct){
+	return d_struct.up[i][j] * exp(-auPenalty(i,j)/RT)/d_struct.u[i][j];
+}
+
+//P_{hj}
+double prob_h_pairs_with_5_end
+		(int i, int h, int j, dangle_struct d_struct){
+
+	return d_struct.up[h][j] * 
+			exp(-(ed5(h,j,h - 1) + 
+			auPenalty(h,j))/RT) /
+			d_struct.u[i][j];
+}
+
+//P_{il}
+double prob_l_pairs_with_3_end
+	(int i, int l, int j dangle_struct d_struct){
+
+	return d_struct.up[i][l] * exp(-auPenalty(i,l)/RT) *
+			(exp(-Ed3(i,l,l+1)/RT) * d_struct.u[l + 2][j] +
+			d_struct.u[l + 1][j] -
+			d_struct.u[l + 2][j]) /
+			d_struct.u[i][j];
+}
+
+//P_{s1h}
+double prob_h_pairs_in_ij(int i, int h, int j, dangle_struct d_struct){
+	return d_struct.s1[h][j] / d_struct.u[i][j];
+}
+
+//P_{hl}
+//This is the probability h pairs with l 
+//**Given that h pairs before j**
+double prob_h_pairs_with_l(int h, int l, int j, dangle_struct d_struct){
+	return d_struct.up[h][l] * exp(-(Ed5(h,l,h - 1) + auPenalty(h,l))/RT) *
+			(exp(-Ed3(h,l,l + 1)/RT) * d_struct.u[l + 2][j] +
+			d_struct.u[l + 1][j] -
+			d_struct.u[l + 2][j]) /
+			d_struct.s1[h][j];
+}
+
+//Q_{ijH}
+double prob_ij_pair_is_hairpin(int i, int j, dangle_struct d_struct){
+	return exp(-eH(i,j)/RT)/d_struct.up[i][j];
+}
+
+//Q_{ijS}
+double prob_ij_pair_is_stack(int i, int j, dangle_struct d_struct){
+	return exp(-eS(i,j)/RT) * d_struct.up[i + 1][j - 1]/d_struct.u[i][j];
+}
+//To find Q_{ijBl} take the rest of the probabilities and subtract
+//them from 1.
+
+//Q_{ijM}
+double prob_ij_pair_is_multiloop(int i, int j, dangle_struct d_struct){
+	return d_struct.upm[i][j]/d_struct.up[i][j];
+}
+
+//This the probability hl closes a multiloop
+//**GIVEN IJ CLOSES A MULTILOOP**
+double prob_ijhl_is_internal_loop
+	(int i, int j, int h, int l, double partition_sum, dangle_struct d_struct){
+	return exp(-eL(i,j,h,l)/RT) * d_struct.up[h][l] / partition_sum;
+}
+
+//P_{ij(1+1)l}
+double first_multi_prob_pair_next_base
+	(int i, int l, int j, dangle_struct d_struct){
+	return d_struct.up[i + 1][l] * 
+			(exp( - (Ea + 2 * Ec + auPenalty(i + 1, l))/RT) *
+			(exp(-Ed3(i + 1,l,l +1))/RT) * d_struct.u1[l + 2][j - 1] +
+			d_struct.u1[l + 1][j - 1] -
+			d_struct.u1[l + 1][j - 1]) /
+			d_struct.upm[i][j];
+}
+
+//P_{ij(1+2)l}
+double first_multi_prob_pair_after_base
+	(int i, int l, int j, dangle_struct d_struct){
+	
+	return d_struct[i + 2][l] * 
+			exp(-(Ea + 2 * Ec + Eb + Ed3(j, i, i + 1) + auPenalty(i + 2,l))/RT) *
+			(exp(-Ed3(i + 2,l,l+1)/RT) * d_struct.u1[l + 2][j - 1] +
+			d_struct.u1[l + 1][j - 1] -
+			d_struct.u1[l + 2][j - 1]) /
+			d_struct.upm[i][j];
+}
+
+//P_{ijs2h)
+double first_multi_prob_pair_rest_base(int i, int h, int j, dangle_struct d_struct){
+	return exp(-(Ea + 2 * Ec + (h - i - 1) * b + Ed3(j,i,i+1))/RT) *
+			d_struct.s2[h][j] / d_struct.upm[i][j];
+}
+//P_{ijhl}
+double first_multi_prob_base_rest
+	(int i, int h, int l, int j, dangle_struct d_struct){
+	
+	return d_struct.up[h][l] * exp(-(Ed5(h,l,h-1) + auPenalty(h,l))/RT) * 
+			(exp( -Ed3(h,l,l+1)/RT) * d_struct.u1[l + 2][j - 1] +
+			d_struct.u1[l + 1][j - 1] -
+			d_struct.u1[l + 2][j - 1])/d_struct.s2[h][j];
+}
+
+//Q_{(l1 + 1)(j -1)(l1 +1)}
+double rest_multi_prob_next_base_pairs
+	(int l1, int l, int j, dangle_struct d_struct){
+	
+	return d_struct.up[l1 +1][l] * exp( - (Ec + auPenalty(l1 + 1, l))/RT)
+			(cond_dangle(j, l1 + 1, l) * exp( -(j - 1 - l) * Eb /RT) +
+			exp(-(j - 1 - l) * Eb) / RT + 
+			exp(-Ed3(l1 + 1, l, l + 1)/RT) * d_struct.u1[l + 2][j - 1] +
+			d_struct.u1[l + 1][j - 1] -
+			d_struct.u1[l + 1][j - 1]) /
+			d_struct.u1[l1 + 1][j - 1];
+}
+
+//Q_{(l1 + 1)(j - 1)(l1 + 2)l}
+double rest_multi_prob_after_base_pairs
+	(int l1, int l, int j, dangle_struct d_struct){
+	
+	return d_struct.up[l1 + 2][l] * exp(-(Ec + Eb + auPenalty(l1 + 2,l))/RT) *
+			(cond_dangle(j, l1 + 2, l) * exp( -(j - 1 - l) * Eb / RT) +
+			exp(-Ed3(l1 + 1,l ,l + 1)/RT) * d_struct.u1[l + 2][j - 1] +
+			d_struct.u1[l + 1][j - 1] - 
+			d_struct.u1[l + 2][j - 1]) /
+			d_struct.u1[l1 + 1][j - 1];
+			
+}
+
+//Q_{(l1 + 1)(j - 1)s3h}
+double rest_multi_prob_rest_base_pairs
+	(int l1, int h, int j, dangle_struct d_struct){
+	
+	return exp( -(Ec + (h - l1 - 1) * Eb)/RT) * d_struct.s3[h][j - 1] /
+			d_struct.u1[l1 + 1][j - 1];
+}
+
+//Q_{(j-1)hl}
+//GIVEN THAT H PAIRS BEFORE J
+double rest_multi_prob_h_pairs_with_l
+	(int l1, int h, int l, int j, dangle_struct d_struct){
+	
+	return d_struct.up[h][l] * exp(-(Ed5(h,l,h - 1) + auPenalty(h,l))/RT) *
+			(cond_dangle(j,h,l) * exp(-(j - 1 -l) * Eb/RT) + 
+			exp(-Ed3(h,l,l + 1)/RT) * d_struct.u1[l + 2][j - 1] +
+			d_struct.u1[l + 1][j - 1] -
+			d_struct.u1[l + 2][j - 1]) /
+			d_struct.s3[h][j - 1];
+}
+
+int there_is_another_helix(int h2, int l2, int j, dangle_struct d_struct){
+	double counter = randdouble();
+	double coin-flip = cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) /
+					  (cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) + 
+					exp(Ed3(h2,l2,l2 + 1)/RT) * d_struct.u1[l2 + 2][j - 1] +
+					d_struct.u1[l2 + 1][j - 1] -
+					d_struct.u1[l2 + 2][j - 1]);
+	
+	//If I was slick and mean I would have put
+		
+	//return counter > coin-flip
+
+	if(counter <= coin-flip){
+		return 0;
+	}
+	else{
+		return 1;
+	}
+}

From 9008ee9021e249c35d620b6042064c49470f76aa Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 20 May 2011 13:24:55 -0400
Subject: [PATCH 123/282] fixed internal loop calculation

---
 gtfold-mfe/src/algorithms.c | 36 ++++++++++++++++++++++++++++++++++--
 1 file changed, 34 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index a10f0f7..0dcf4cb 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -63,17 +63,49 @@ int calculate(int len, int nThreads) {
 				if (j-i > 6) {  // Internal Loop BEGIN
 					int p=0, q=0;
 					int VBIij = INFINITY_;
-
 					for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
 						int minq = j-i+p-MAXLOOP-2;
 						if (minq < p+1+TURN) minq = p+1+TURN;
-						for (q = minq; q < j; q++) {
+						int maxq = (p==i+1)?(j-2):(j-1);
+						for (q = minq; q <= maxq; q++) {
 							if (!canPair(RNA[p], RNA[q])) continue;
 							if (check_iloop(i,j,p,q)) continue;
 							VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
 						}
 					}
 					VBI(i,j) = check_pair(i,j)?INFINITY_:VBIij;
+					
+					/*
+					int ip,jp;
+					int ifinal, jfinal, temp;
+
+					ip = i + 1;
+					int thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); // Minimum size of a hairpin loop is 3. So, start jp from ip+4 
+					for (jp = thres1; jp <= j - 2; jp++) {
+						if (canPair(RNA[ip], RNA[jp])) {
+							temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; // Energy of internal loop closed by (i,j) and (ip,jp) + the energy of structure closed by (ip, jp)
+							if (VBIij > temp) {
+								VBIij = temp;
+								ifinal = ip;
+								jfinal = jp;
+							}
+						}
+					}
+
+					for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) {
+						thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4);
+						for (jp = thres1; jp <= j - 1; jp++) {
+							if (canPair(RNA[ip], RNA[jp])) {
+								temp = eL(i, j, ip, jp) + V[indx[ip] + jp];
+								if (VBIij > temp) {
+									VBIij = temp;
+									ifinal = ip;
+									jfinal = jp;
+								}
+							}
+						}
+					} */
+
 				} 	// Internal Loop END
 				
 				if (j-i > 10) {	 // Multi Loop BEGIN

From 9e0612c75ec5e17b4b1fb96ff307a7c457d20f0f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 23 May 2011 12:40:34 -0400
Subject: [PATCH 124/282] removed flag optimization

---
 gtfold-mfe/src/algorithms.c | 45 +++++--------------------------------
 1 file changed, 5 insertions(+), 40 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 0dcf4cb..7f76aa5 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -54,12 +54,12 @@ int calculate(int len, int nThreads) {
 #endif
 		for (i = 1; i <= len - b; i++) {
 			j = i + b;
-			int flag = 0, newWM = INFINITY_; 
+			int newWM = INFINITY_; 
 
 			if (canPair(RNA[i], RNA[j])) {
-				flag = 1;
 				int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin
 				int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack
+				
 				if (j-i > 6) {  // Internal Loop BEGIN
 					int p=0, q=0;
 					int VBIij = INFINITY_;
@@ -74,38 +74,6 @@ int calculate(int len, int nThreads) {
 						}
 					}
 					VBI(i,j) = check_pair(i,j)?INFINITY_:VBIij;
-					
-					/*
-					int ip,jp;
-					int ifinal, jfinal, temp;
-
-					ip = i + 1;
-					int thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); // Minimum size of a hairpin loop is 3. So, start jp from ip+4 
-					for (jp = thres1; jp <= j - 2; jp++) {
-						if (canPair(RNA[ip], RNA[jp])) {
-							temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; // Energy of internal loop closed by (i,j) and (ip,jp) + the energy of structure closed by (ip, jp)
-							if (VBIij > temp) {
-								VBIij = temp;
-								ifinal = ip;
-								jfinal = jp;
-							}
-						}
-					}
-
-					for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) {
-						thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4);
-						for (jp = thres1; jp <= j - 1; jp++) {
-							if (canPair(RNA[ip], RNA[jp])) {
-								temp = eL(i, j, ip, jp) + V[indx[ip] + jp];
-								if (VBIij > temp) {
-									VBIij = temp;
-									ifinal = ip;
-									jfinal = jp;
-								}
-							}
-						}
-					} */
-
 				} 	// Internal Loop END
 				
 				if (j-i > 10) {	 // Multi Loop BEGIN
@@ -118,7 +86,6 @@ int calculate(int len, int nThreads) {
 						VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1));	
 						VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2));	
 						VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2));	
-						newWM = MIN(newWM, VMij);
 					}
 
 					int d3 = Ed3(i,j,j-1);
@@ -138,12 +105,10 @@ int calculate(int len, int nThreads) {
 
 			if (j-i > 4) {	// WM BEGIN
 				int h; 
-				if (!flag) {
-					for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
-						newWM = MIN(newWM, WMU(i,h-1) + WML(h,j));
-					}
+				for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
+					newWM = MIN(newWM, WMU(i,h-1) + WML(h,j));
 				}
-				
+
 				newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
 				newWM = check_base(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): INFINITY_; 
 				newWM = check_base(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM) : INFINITY_; 

From b85fbafbcaed713ea2358c77aee7d65d4a5492a6 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 23 May 2011 16:44:42 -0400
Subject: [PATCH 125/282] added -p option to allow

---
 gtfold-mfe/src/constraints.cc | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index d3cd01b..1e840cc 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -24,8 +24,8 @@ bool compare_bp(const std::pair<int,int>& o1,
 
 
 static int load_constraints(const char* constr_file, int verbose=0) {
+    fprintf(stdout, "- Running with constraints %s\n", constr_file);
 	std::ifstream cfcons;
-    fprintf(stdout, "- Running with constraints\n");
 
     cfcons.open(constr_file, std::ios::in);
     if (cfcons == 0) {
@@ -83,7 +83,7 @@ static int load_constraints(const char* constr_file, int verbose=0) {
             pit++;
         }
     }
-
+	/*
 	std::vector<std::pair<int,int> > v_fbp;
 	for(it=0; it< nFBP; it++) {
 		for(int k=1;k<= FBP[it][2];k++)
@@ -100,7 +100,7 @@ static int load_constraints(const char* constr_file, int verbose=0) {
 
 		}
 	}
-
+*/
 
     return 0;
 }

From 3e117e6079ee36b712e57c5920cacaec3be41827 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 23 May 2011 16:45:22 -0400
Subject: [PATCH 126/282] added -p option to allow dir name for param files

---
 gtfold-mfe/src/loader.cc  |  6 +-----
 gtfold-mfe/src/main.cc    |  6 ++++--
 gtfold-mfe/src/options.cc | 21 ++++++++++++++++-----
 3 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 18066c6..e8354a1 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -76,8 +76,7 @@ int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loo
 float prelog;
 
 void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
-
-#ifndef GENBIN
+	cout << userdatalogic << ' ' << userdatadir << std::endl;
 	if (!userdatalogic) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
@@ -85,9 +84,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	} else {
 		EN_DATADIR.assign(userdatadir);
 	}
-#else
-	EN_DATADIR = "data";
-#endif
 
 	//Handle the ending forward slash case
 	if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') {
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index e976d49..a67c887 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -39,6 +39,8 @@
 #include "constraints.h"
 #include "traceback.h"
 #include "subopt_traceback.h"
+#include "shapereader.h"
+
 
 using namespace std;
 
@@ -173,7 +175,7 @@ int main(int argc, char** argv) {
 	std::string seq;
 	int energy;
 	double t1;
-
+	
 	print_header();
 
 	parse_options(argc, argv);
@@ -184,7 +186,7 @@ int main(int argc, char** argv) {
 	}
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
-	readThermodynamicParameters("Turner99",false);
+	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR);
 
 	printRunConfiguration(seq);
 	
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 1bc103c..a8be69b 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -5,8 +5,9 @@ using namespace std;
 
 bool ILSA;
 bool NOISOLATE;
-bool USERDATA;
-bool PARAMS;
+//bool USERDATA;
+//bool PARAMS;
+bool PARAM_DIR = false;
 bool LIMIT_DISTANCE;
 bool BPP_ENABLED;
 bool SUBOPT_ENABLED;
@@ -15,7 +16,8 @@ bool VERBOSE = false;
 
 string seqfile = "";
 string constraintsFile = "";
-string outputFile = "";
+string outputFile = ""; 
+string paramDir = "Turner99"; // default value
 
 int suboptDelta = -1;
 int nThreads = -1;
@@ -34,7 +36,8 @@ void help() {
     printf("                        Load constraints from FILE.  See Constraint syntax below\n");
     printf("   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n");
     printf("                        limit is given, base pairs can be over any distance\n");
-    printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
+    printf("   -p  --paramdir DIR   Path to directory from where parameters are to be read\n");
+   	printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
     printf("   -t, --threads num    Limit number of threads used\n");
 
@@ -83,7 +86,15 @@ void parse_options(int argc, char** argv) {
 					outputFile = argv[++i];
 				else
 					help();
-			} else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
+			} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+				if(i < argc) {
+					paramDir = argv[++i];
+					PARAM_DIR = true;
+				}
+				else
+					help();
+			}
+		   	else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
 				if(i < argc)
 					nThreads = atoi(argv[++i]);
 				else

From 7e421b5762cd36e09ad88c4a948c9a8135c2be33 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 23 May 2011 16:46:23 -0400
Subject: [PATCH 127/282] added -p option to allow dir name for param files

---
 gtfold-mfe/include/options.h | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 7772be1..1e46851 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -10,17 +10,19 @@ using namespace std;
 
 extern bool ILSA; 
 extern bool NOISOLATE;
-extern bool USERDATA;
-extern bool PARAMS;
+//extern bool USERDATA;
+//extern bool PARAMS;
 extern bool LIMIT_DISTANCE;
 extern bool BPP_ENABLED;
 extern bool SUBOPT_ENABLED;
 extern bool CONS_ENABLED;
 extern bool VERBOSE;
+extern bool PARAM_DIR;
 
 extern string seqfile;
 extern string constraintsFile;
 extern string outputFile;
+extern string paramDir;
 
 extern int suboptDelta;
 extern int nThreads;

From ec8dcb9830516cb8ffb57e7105ceac2c69a4c9bf Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 23 May 2011 23:04:06 -0400
Subject: [PATCH 128/282] removed unrequired header

---
 gtfold-mfe/src/main.cc | 2 --
 1 file changed, 2 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index a67c887..2327ca0 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -39,8 +39,6 @@
 #include "constraints.h"
 #include "traceback.h"
 #include "subopt_traceback.h"
-#include "shapereader.h"
-
 
 using namespace std;
 

From fd23a9d001a671efcbb43be6e8695ef7b7c1dd7d Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 23 May 2011 23:14:55 -0400
Subject: [PATCH 129/282] removed cout statement

---
 gtfold-mfe/src/loader.cc | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index e8354a1..c68ee22 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -76,7 +76,6 @@ int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loo
 float prelog;
 
 void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
-	cout << userdatalogic << ' ' << userdatadir << std::endl;
 	if (!userdatalogic) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";

From 14e822e63e4fa717a423d343a482ca3eb944a32b Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Tue, 24 May 2011 15:05:02 +0200
Subject: [PATCH 130/282] fixed MFE and constraints. constraint check included
 with -v option

---
 gtfold-mfe/include/constraints.h |  24 ++---
 gtfold-mfe/src/algorithms.c      | 180 +++++++++++++------------------
 gtfold-mfe/src/constraints.cc    | 140 ++++++++----------------
 gtfold-mfe/src/traceback.c       |  86 ++++++---------
 4 files changed, 163 insertions(+), 267 deletions(-)

diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h
index 045ebad..9805dbd 100644
--- a/gtfold-mfe/include/constraints.h
+++ b/gtfold-mfe/include/constraints.h
@@ -21,19 +21,17 @@ void print_constraints(int length) ;
 #ifdef __cplusplus
 extern "C" {
 #endif
-//int is_ss(int i, int j); 
-//int prohibit_base(int i) ;
-int check_ssregion(int i, int j);
-//int check_base(int i) ;
-//int force_pair(int i, int j) ;
-int force_pair1(int i, int j) ;
-int force_ss1(int i);
-int force_ssregion1(int i, int j);
-int check_iloop(int i, int j, int p, int q) ;
-int check_pair(int i, int j) ;
-int check_stack(int i, int j) ;
-int check_hairpin(int i, int j) ;
-int can_dangle(int i);
+int canStack(int i, int j);
+int canSS(int i);
+int canSSregion(int i, int j);
+int canHairpin(int i, int j);
+int canILoop(int i, int j, int p, int q);
+
+int forceSS(int i);
+int forceSSregion(int i, int j);
+int forcePair(int i, int j);
+
+
 int withinCD(int i, int j);
 int verify_structure();
 #ifdef __cplusplus
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index c7b9a3d..c5a71c5 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -1,29 +1,24 @@
 /*
- GTfold: compute minimum free energy of RNA secondary structure
- Copyright (C) 2008  David A. Bader
- http://www.cc.gatech.edu/~bader
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+GTfold: compute minimum free energy of RNA secondary structure
+Copyright (C) 2008 David A. Bader
+http://www.cc.gatech.edu/~bader
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
 */ 
-
 #include <stdio.h>
 #include <math.h>
 #include <time.h>
 #include <sys/time.h>
 #include <stdlib.h>
 #include <assert.h>
-
 #include "constants.h"
 #include "utils.h"
 #include "energy.h"
@@ -31,27 +26,19 @@
 #include "algorithms.h"
 #include "constraints.h"
 #include "shapereader.h"
-
-#ifdef _OPENMP   
+#ifdef _OPENMP 
 #include "omp.h"
 #endif
-
 int calculate(int len, int nThreads) { 
 	int b, i, j;
-
-
-//	printf("%d\n", BP(1145, 13));
-
 #ifdef _OPENMP
 	if (nThreads>0) omp_set_num_threads(nThreads);
 #endif
-
 #ifdef _OPENMP
 #pragma omp parallel
 #pragma omp master
 	fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
 #endif
-
 	for (b = TURN+1; b <= len-1; b++) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
@@ -59,119 +46,104 @@ int calculate(int len, int nThreads) {
 		for (i = 1; i <= len - b; i++) {
 			j = i + b;
 			int flag = 0, newWM = INFINITY_; 
-			if (canPair(RNA[i], RNA[j]) && withinCD(i,j)) {
+			if (canPair(RNA[i], RNA[j])) {
 				flag = 1;
-				int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin
-				int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack
-				if (j-i > 6) {  // Internal Loop BEGIN
+				int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
+				int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack
+				if (j-i > 6) { // Internal Loop BEGIN
 					int p=0, q=0;
 					int VBIij = INFINITY_;
-
-					int found_forced_pair = 0;
 					for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
 						int minq = j-i+p-MAXLOOP-2;
 						if (minq < p+1+TURN) minq = p+1+TURN;
-						for (q = minq; q < j; q++) {
+						int maxq = (p==i+1)?(j-2):(j-1);
+						for (q = minq; q <= maxq; q++) {
 							if (!canPair(RNA[p], RNA[q])) continue;
-							if (check_iloop(i,j,p,q)) continue;
-							if(force_pair1(p,q)){
-							//ZS: if we know a pair should be forced, we should 
-							//just enforce it and not care about other options.
-								VBIij = eL(i,j,p,q) + V(p,q); 
-								found_forced_pair = 1;
-								break; 
-							}	
+							if (!canILoop(i,j,p,q)) continue;
 							VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
 						}
-						if(found_forced_pair){break;}
 					}
-					VBI(i,j) = check_pair(i,j)?INFINITY_:VBIij;
-				} 	// Internal Loop END
-				
-				if (j-i > 10) {	 // Multi Loop BEGIN
+					VBI(i,j) = VBIij;
+					V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
+
+				} // Internal Loop END
+				if (j-i > 10) { // Multi Loop BEGIN
 					int h;
 					int VMij, VMijd, VMidj, VMidjd;
 					VMij = VMijd = VMidj = VMidjd = INFINITY_;
-
 					for (h = i+TURN+1; h <= j-1-TURN; h++) { 
-						VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1));		
-						VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1));	
-						VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2));	
-						VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2));	
-						//ZS: I don't think the following line is being checked in traceback, so 
-						//if you enable it, sometimes huge parts of the structure will not be possible
-						//to trace. 
-						//I don't know if it should be here or not. If it is here, it should be in traceback
-						//too. For now, I am removing it! 
-						//newWM = MIN(newWM, VMij);
+						VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); 
+						VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); 
+						VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); 
+						VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); 
 					}
-
-					int d3 = can_dangle(j-1)?Ed3(i,j,j-1):INFINITY_;
-					int d5 = can_dangle(i+1)?Ed5(i,j,i+1):INFINITY_;
-
+					int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
+					int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
 					VMij = MIN(VMij, (VMidj + d5 +Ec)) ;
 					VMij = MIN(VMij, (VMijd + d3 +Ec));
-					VMij = MIN(VMij, (VMidjd + d5 +  d3+ 2*Ec));
+					VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec));
 					VMij = VMij + Ea + Eb + auPenalty(i,j);
-					VM(i,j) = check_pair(i,j)?INFINITY_:VMij;
+					VM(i,j) = canStack(i,j)?VMij:INFINITY_;
 				} // Multi Loop END
-
-				V(i,j) = check_pair(i,j)?INFINITY_:MIN4(eh,es,VBI(i,j),VM(i,j));
-				V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
+				V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j));
 			}
-			else
-				V(i,j) = INFINITY_;
-
-			if (j-i > 4) {	// WM BEGIN
+			else V(i,j) = INFINITY_;
+			if (j-i > 4) { // WM BEGIN
 				int h; 
-				//ZS: if we know that i,j are pairing, we just have to set WM(i,j) = V(i,j) in the best possible way.
-				//Conversely, we only need to find the best partitioning if we know that i,j are not forced to pair.
-
-				//Prashant's original code had if(!flag) here... I don't know what that was supposed to do?
-				if (!force_pair1(i,j)) {
-					for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
-						newWM = MIN(newWM, WMU(i,h-1) + WML(h,j));
-					}
+				for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
+					//ZS: This sum corresponds to when i,j are NOT paired with each other.
+					//So we need to make sure only terms where i,j aren't pairing are considered. 
+					newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM;
 				}
-				
 				newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
-
-				//ZS: if i,j are forced to pair then can_dangle(i) and can_dangle(j) will be false 
-				newWM = can_dangle(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): newWM; 
-				newWM = can_dangle(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM) : newWM; 
-				newWM = (can_dangle(i)&&can_dangle(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM): newWM;
-				newWM = can_dangle(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM;
-				newWM = can_dangle(j)?MIN(WML(i,j-1) + Ec, newWM):newWM;
+				newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
+				newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
+				newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; //i,j dangle
+				newWM = canSS(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; //i dangle
+				newWM = canSS(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; //j dangle
 				WMU(i,j) = WML(i,j) = newWM;
 			} // WM END
 		}
 	}
-
-	for (j = TURN+2; j <= len; j++)	{
-		int i, branch=0, Wj, Widjd, Wijd, Widj, Wij, Wim1;
+	for (j = TURN+2; j <= len; j++) {
+		int i, must_branch=0, Wj, Widjd, Wijd, Widj, Wij, Wim1;
 		Wj = INFINITY_;
 		for (i = 1; i < j-TURN; i++) {
 			Wij = Widjd = Wijd = Widj = INFINITY_;
 			Wim1 = MIN(0, W[i-1]); 
 			Wij = V(i, j) + auPenalty(i, j) + Wim1;
-			Widjd = (can_dangle(i)&&can_dangle(j))?(V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1):INFINITY_;
-			Wijd = can_dangle(j)?(V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1):INFINITY_;
-			Widj =  (can_dangle(i))?(V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1):INFINITY_;
+			Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:Widjd;
+			Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd;
+			Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj;
 			Wj = MIN(MIN4(Wij, Widjd, Wijd, Widj), Wj); 
-			
+	
+			/*
 			if (Wj<INFINITY_) {
-				if (Wj==Wij && force_pair1(i,j))
-				   branch = 1;
-				else if	(Wj==Widjd && force_pair1(i+1,j-1))
-				   branch = 1;
-				else if	(Wj==Wijd && force_pair1(i,j-1))
-				  branch = 1;	
-				else if	(force_pair1(i+1,j))
-				  branch = 1;
+				if (Wj==Wij && forcePair(i,j))
+				must_branch = 1;
+				else if (Wj==Widjd && forcePair(i+1,j-1))
+				must_branch = 1;
+				else if (Wj==Wijd && forcePair(i,j-1))
+				must_branch = 1; 
+				else if (forcePair(i+1,j))
+				must_branch = 1;
 			}
+			*/
+			if(i==296&&j==301){
+				printf("Option 1: %d\n", W[j-1]);
+				printf("Option 2: %d = V(i,j) + W(i-1) = %d +%d = %d\n", W[j], V(i,j), W[i-1], V(i,j) + W[i-1]);
+			}
+		}
+		//W[j] = branch?Wj:MIN(Wj, W[j-1]);
+		W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj;
+		if(j==301){
+			printf("Final option 1: %d\n", W[j-1]);
+			printf("Final option 2: %d\n", Wj);
+			printf("canSS(j): %d\n", canSS(j));
+			printf("chosen: %d\n", W[j]);
+			printf("canHairpin(i,j): %d\n", canHairpin(295,305));
+			printf("eH(i,j): %d\n", eH(295,305));
 		}
-		W[j] = branch?Wj:MIN(Wj, W[j-1]);
 	}
-
 	return W[len];
 }
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 3d50a5f..4a5810a 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -301,7 +301,7 @@ int verify_structure(){
 				//correct answer: strcuture(PBP[it][0]+k-1) != structure(PBP[it][1]-(k-1))
 				if(structure[PBP[it][0]+k-1] == PBP[it][1]-(k-1) || structure[PBP[it][1]-(k-1)] == PBP[it][0]+k-1){	
 					errorhappened = 1; 
-					printf("Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]);
+					fprintf(stderr, "Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]);
 					break;
 				}
 			}
@@ -330,13 +330,13 @@ int verify_structure(){
 				if(FBP[it][1] == 0){
 					//force single-stranded
 					if(structure[FBP[it][0]] != 0){
-						printf("Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
+						fprintf(stderr, "Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
 						errorhappened = 1;
 					}
 				}
 				else{
 					if(structure[FBP[it][0]+k-1] != FBP[it][1]-(k-1) || structure[FBP[it][1]-(k-1)] != FBP[it][0]+k-1){
-						printf("Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
+						fprintf(stderr, "Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
 						errorhappened = 1;
 					}
 					
@@ -401,123 +401,75 @@ void print_constraints(int len) {
 			printf(".");
 			break;
 		default:
-			printf("ERROR in constraint value, debugging info: i=%d, BP(i,i)=%d",i,BP(i,i));break;
+			fprintf(stderr,"ERROR in constraint value, debugging info: i=%d, BP(i,i)=%d",i,BP(i,i));break;
 	    }  
     }
     printf("\n");
  
 }
-/* Original Prashant's code commented out
-int is_ss(int i, int j) {
-
-	if (CONS_ENABLED) {
-		int it;
-		for (it = i + 1; it < j; it++) {
-			if (BP[it] > 0) return 1;
-		}
-		return 0;
-	}
-	else
-		return 0;
-
-return 0;
-}
-
-
-int prohibit_base(int i) {
-//	return (BP[i] == -1);
-return 0;
-}
-
-*/
-//int check_base(int i) {
-
-//	if (CONS_ENABLED) 
-//		return (BP[i] <= 0);
-//	else
-//		return 1;
-
-//return 1;
-//}
-
-/*int force_pair(int i, int j) {
-
-		return (BP[i] > 0 && j != BP[i]);
-
-return 0;
-}*/
-
-int force_pair1(int i, int j) {
-//ZS: this function returns true if a pair between i and j is forced.
 
+int forcePair(int i, int j) {
+//ZS: this function returns true if the pair i-j is forced.
 	if (CONS_ENABLED) 
 		return BP(i,j)==1;
 	else
 		return 0;
 }
 
-int force_ss1(int i){
-//ZS: this function returns true if a base is forced to be single-stranded 
-
+int forceSS(int i){
+//ZS: this function returns true if base i is forced to be single-stranded 
 	if(CONS_ENABLED)
 		return BP(i,i)==3;
 	else 
 		return 0;
 }
 
-int force_ssregion1(int i, int j){
+int forceSSregion(int i, int j){
+	//ZS: This returns 1 if all nucleotides between i and j are forced to be single-stranded, 0 if there is at least one that is not
 	if(CONS_ENABLED){
-		int value = 1;
 		for(int p = i; p<j; p++){
 			if(BP(p,p)!=3){
-				value= 0;
+				return 0;
 			}
 		}
-		return value;
+		return 1;
 	}
 	else return 0;
 }
 
-int check_iloop(int i, int j, int p, int q) {
-//ZS: This function returns 1 if internal loop with pairs i,j and p,q is not allowed.
+int canILoop(int i, int j, int p, int q) {
+//ZS: This function returns 1 if internal loop with pairs i,j and p,q is allowed, 0 if not allowed
 	if (CONS_ENABLED){
 		//Need to check that i,j and p,q pairs are allowed, 
 		//and single-stranded regions between i,p and q,j are allowed
-		return check_pair(i,j)||check_pair(p,q)||check_ssregion(i,p)||check_ssregion(q,j);
+		return canStack(i,j) && canStack(p,q) && canSSregion(i,p) && canSSregion(q,j);
 	}
-		//Original code (Prashant's):
-		//return is_ss(i,p) || is_ss(q,j);
 	else 
-		return 0;
+		return 1;
 }
 
-int check_pair(int i, int j) {
-//ZS: This function returns 1 if i and j are not allowed
-//to pair according to the constraints. 
-	if (CONS_ENABLED){ 
-		//can't pair if i,j is prohibited or i or j are forced to be single-stranded
-		if(BP(i,j)==2||BP(i,i)==3||BP(j,j)==3) return 1;
-		//can't pair if i or j are forced to pair with something other than each other
-		if((BP(i,i)==4||BP(j,j)==4)&&BP(i,j)!=1) return 1;	
-		else return 0;
-		//Original code (Prashant's):
-		//return prohibit_base(i) || prohibit_base(j) || force_pair(i,j) || force_pair(j,i);
-	}
-	else return 0;
+int canHairpin(int i, int j) {
+	//ZS: Returns 1 if a hairpin between i,j is allowed, 0 if not allowed
+	if (CONS_ENABLED){
+		//Need to check if pair is allowed and if anything pairs between them
+		return canStack(i,j) && canSSregion(i,j);
+	}	
+	else return 1;
 }
 
-int check_ssregion(int i, int j){
-//ZS: This function returns 1 if any nucleotide between i and j is forced to pair with something
+int canSSregion(int i, int j){
+//ZS: This function returns 0 if any nucleotide between i and j is forced to pair with something
 //(i and j are NOT included in the check)
 	if(CONS_ENABLED){
 		for(int p = i+1; p<j; p++){
-			if(BP(p,p)==4) return 1;
+			if(BP(p,p)==4) return 0;
 		}
-		return 0;}
-	else{ return 0; }
+		return 1;}
+	else{ return 1; }
 }
 
-int can_dangle(int i){
+int canSS(int i){
+	//ZS: This function returns 0 if i is forced to pair with something, 1 if it can be single stranded. 
 	if (CONS_ENABLED){
 		return BP(i,i)!=4;
 	}
@@ -526,30 +478,22 @@ int can_dangle(int i){
 	}
 }
 
-int check_stack(int i, int j) {
-	if (CONS_ENABLED){
-		//Just need to check if pair is allowed
-		return check_pair(i,j);
-		//Original code (Prashant's)
-		//return force_pair(i,j) || force_pair(j,i);
+int canStack(int i, int j) {
+// ZS: This function returns 1 if an i,j pair is allowed, 0 if not allowed
+// (Unfortunately the more intuitive "canPair" name is already used to mark complementary nucleotides so 
+// I couldn't use that again) 
+	if (CONS_ENABLED){ 
+		//can't pair if i,j is prohibited, or i or j are forced to be single-stranded
+		if(BP(i,j)==2||BP(i,i)==3||BP(j,j)==3) return 0;
+		//can't pair if i or j are forced to pair with something other than each other
+		if((BP(i,i)==4||BP(j,j)==4)&&BP(i,j)!=1) return 0;	
+		else return 1;
 	}
-	else return 0;
-}
-
-int check_hairpin(int i, int j) {
-
-	//ZS: According to algorithms.c, this should return 
-	//1 when a hairpin with i,j as closing pair isn't allowed.
-	if (CONS_ENABLED){
-		//Need to check if pair is allowed and if anything pairs between them
-		return check_pair(i,j)||check_ssregion(i,j);
-		//Original code (Prashant's)
-		//return is_ss(i,j) || force_pair(i,j) || force_pair(j,i);
-	}	
-	else return 0;
+	else return 1;
 }
 
 int withinCD(int i, int j){
+	//ZS: This function returns 1 if i and j are within the required contact distance from each other. 
 	if (LIMIT_DISTANCE){	
 		return j-i+1>contactDistance;
 	}
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 7d25b32..15a2f0c 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -61,28 +61,24 @@ void traceW(int j) {
 	
 	if (j == 0 || j == 1) return;
 
-	
 	for (i = 1; i < j && !done; i++) {
-
 		if (j-i < TURN) continue;
 
 		wim1 = MIN(0, W[i-1]);
 		flag = 1;
-		if (wim1 != W[i-1] && !check_ssregion(1,i)) flag = 0; 
-		//ZS: flag is false if the free energy of the best structure to W[i] is > 0 --> all should be ss 
-		//UNLESS there is at least one base that is forced to pair in that region, this is revealed by check_ssregion(1,i)
+		if ( wim1 != W[i-1]) flag = 0;
 
 		Widjd = Wijd =  Widj = INFINITY_;
 		Wij = V(i,j) + auPenalty(i, j) + wim1;
-		Widjd =(can_dangle(i)&&can_dangle(j))?(V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1): INFINITY_;
-		Wijd = (can_dangle(j))?(V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1):INFINITY_;
-		Widj = (can_dangle(i))?(V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1):INFINITY_;
+		Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1;
+		Wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
+		Widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
 		Wj_temp=Wj;
+		
 		Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
 
 		if (W[j] == Wj) {
-			//if we know W[j] is pairing with something
-			if (W[j] == Wij || force_pair1(i,j)){ 
+			if (W[j] == Wij) { 
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i, j, auPenalty(i, j)/100.00);
@@ -90,9 +86,9 @@ void traceW(int j) {
 				structure[i] = j;
 				structure[j] = i;
 				traceV(i, j);
-				if (flag || force_ssregion1(1,i)) traceW(i - 1);
+				if (flag ) traceW(i - 1);
 				break;
-			} else if ((W[j] == Widjd && can_dangle(i) && can_dangle(j)) || force_pair1(i+1,j-1)) { 
+			} else if (W[j] == Widjd) { 
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
@@ -100,9 +96,9 @@ void traceW(int j) {
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
 				traceV(i + 1, j - 1);
-				if (flag || force_ssregion1(1,i)) traceW(i - 1);
+				if (flag ) traceW(i - 1);
 				break;
-			} else if ((W[j] == Wijd && can_dangle(j))||force_pair1(i,j-1)) { 
+			} else if (W[j] == Wijd) { 
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
@@ -110,9 +106,9 @@ void traceW(int j) {
 				structure[i] = j - 1;
 				structure[j - 1] = i;
 				traceV(i, j - 1);
-				if (flag || force_ssregion1(1,i)) traceW(i - 1);
+				if (flag ) traceW(i - 1);
 				break;
-			} else if ((W[j] == Widj && can_dangle(i))||force_pair1(i+1,j)) { 
+			} else if (W[j] == Widj){
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
@@ -120,29 +116,31 @@ void traceW(int j) {
 				structure[i + 1] = j;
 				structure[j] = i + 1;
 				traceV(i + 1, j);
-				if (flag || force_ssregion1(1,i)) traceW(i - 1);
+				if (flag ) traceW(i - 1);
 				break;
 			}
 		}
 	}
-
+		
 	if (W[j] == W[j - 1] && !done) traceW(j-1);
 
 	return;
 }
 
 int traceV(int i, int j) {
-
 	int a, b, c, d, Vij;
 	if (j-i < TURN)  return INFINITY_;
 
-	a = eH(i, j)+getShapeEnergy(i) + getShapeEnergy(j);
-	b = eS(i, j) + V(i + 1, j - 1) + getShapeEnergy(i) + getShapeEnergy(j);
+	a = canHairpin(i,j)?eH(i, j)+ getShapeEnergy(i) + getShapeEnergy(j):INFINITY_;
+	b = canStack(i,j)?eS(i, j) + V(i + 1, j - 1) + getShapeEnergy(i) + getShapeEnergy(j):INFINITY_;
 	if (eS(i, j) == 0) b = INFINITY_;
-	c = VBI(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
-	d = VM(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
+	c = canStack(i,j)?VBI(i,j) + getShapeEnergy(i) + getShapeEnergy(j):INFINITY_;
+	d = canStack(i,j)?VM(i,j) + getShapeEnergy(i) + getShapeEnergy(j):INFINITY_;
+	
+	
 	
-	Vij = MIN(MIN(a, b), MIN(c, d));
+	//Vij = MIN(MIN(a, b), MIN(c, d));
+	Vij = V(i,j);
 	
 	if (Vij == a && Vij != b && Vij != c && Vij != d) { 
 		if (verbose == 1) 
@@ -183,7 +181,6 @@ int traceVBI(int i, int j) {
 
 	for (ip = i + 1; ip < j - 1; ip++) {
 		for (jp = ip + 1; jp < j; jp++) {
-			if (check_iloop(i,j,ip,jp)) continue;
 			el = eL(i, j, ip, jp);
 			v = V(ip, jp);
 			VBIij_temp = el + v;
@@ -227,7 +224,7 @@ int traceVM(int i, int j) {
 		}
 	}
 
-	if (can_dangle(i+1)) {
+	//if (check_base(i+1)) {
 		for (h = i + 3; h <= j - 1 && !done; h++) {
 			A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1); 
 			if (A_temp == VMij) {
@@ -237,9 +234,9 @@ int traceVM(int i, int j) {
 				break;
 			}
 		}
-	}
+	//}
 
-	if (can_dangle(j-1)) {
+	//if (check_base(j-1)) {
 		for (h = i + 2; h <= j - 2 && !done; h++) { 
 			A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1);
 			if (A_temp == VMij) {
@@ -249,25 +246,25 @@ int traceVM(int i, int j) {
 				break;
 			}
 		}
-	}
+	//}
 
-	if (can_dangle(i+1)&&can_dangle(j-1)) {
+	//if (check_base(i+1)&&check_base(j-1)) {
 		for (h = i + 3; h <= j - 2 && !done; h++) { 
 			A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
 			if (A_temp == VMij) {
 				done = 1;
 				eVM += traceWM(i + 2, h - 1);
 				eVM += traceWM(h, j - 2);
-
 				break;
 			}
 		}
-	}
+	//}
 
 	return eVM;
 }
 
 int traceWM(int i, int j) {
+
 	int done;
 	int h1, h;
 	int eWM = 0; 
@@ -295,44 +292,29 @@ int traceWM(int i, int j) {
 				structure[i] = j;
 				structure[j] = i;
 				eWM += traceV(i, j);
-			} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && can_dangle(i)) { 
+			} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec) { 
 				done = 1;
 				eWM += traceV(i + 1, j);
 				structure[i + 1] = j;
 				structure[j] = i + 1;
-			} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec && can_dangle(j) ) { 
+			} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec ) { 
 				done = 1;
 				eWM += traceV(i, j - 1);
 				structure[i] = j - 1;
 				structure[j - 1] = i;
-			} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec && can_dangle(i) && can_dangle(j)) { 
+			} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec) { 
 				done = 1;
 				eWM += traceV(i + 1, j - 1);
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
-			} else if (WM(i,j) == WM(i + 1,j) + Ec && can_dangle(i)) { 
+			} else if (WM(i,j) == WM(i + 1,j) + Ec) { 
 				done = 1;
 				eWM += traceWM(i + 1, j);
-			} else if (WM(i,j) == WM(i,j - 1) + Ec && can_dangle(j)) { 
+			} else if (WM(i,j) == WM(i,j - 1) + Ec) { 
 				done = 1;
 				eWM += traceWM(i, j - 1);
 			}
 		}
 	}
-	//ZS: This is for debugging purposes. 
-	if(!done){
-		printf("ERROR: WM couldn't be traced!\n");
-		printf("%d %d \n", i, j);
-		printf("WM(i,j) = %d\n", WM(i,j));
-		printf("candangle i? %d\n", can_dangle(i));
-		printf("candangle j? %d\n", can_dangle(j));
-		printf("The options were: \n"); 
-		printf("Option 1 %d \n" , V(i,j) + auPenalty(i, j) + Eb);
-		printf("Option 2 %d \n" , V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec);
-		printf("Option 3 %d \n", V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec);
-		printf("Option 4 %d \n", V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec);
-		printf("Option 5 %d \n", WM(i + 1,j) + Ec );
-		printf("Option 6 %d \n", WM(i,j - 1) + Ec);
-	}
 	return eWM;
 }

From 3eee5c204703337e9539eecf53a3438dd82870ff Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Tue, 24 May 2011 18:13:27 +0200
Subject: [PATCH 131/282] Fixed constraints, removed unnecessary output

---
 gtfold-mfe/src/.deps/energy.Po |  5 +++-
 gtfold-mfe/src/algorithms.c    | 30 ++-------------------
 gtfold-mfe/src/constraints.cc  |  2 --
 gtfold-mfe/src/energy.c        |  7 +++--
 gtfold-mfe/src/traceback.c     | 49 ++++++++++++++++++----------------
 5 files changed, 37 insertions(+), 56 deletions(-)

diff --git a/gtfold-mfe/src/.deps/energy.Po b/gtfold-mfe/src/.deps/energy.Po
index 7c1467f..de8d5e9 100644
--- a/gtfold-mfe/src/.deps/energy.Po
+++ b/gtfold-mfe/src/.deps/energy.Po
@@ -19,7 +19,8 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
  ../include/energy.h ../include/data.h ../include/constants.h \
- ../include/utils.h ../include/global.h ../include/constants.h
+ ../include/utils.h ../include/global.h ../include/constants.h \
+ ../include/shapereader.h
 
 /usr/include/stdlib.h:
 
@@ -114,3 +115,5 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \
 ../include/global.h:
 
 ../include/constants.h:
+
+../include/shapereader.h:
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index c5a71c5..59a1824 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -49,7 +49,7 @@ int calculate(int len, int nThreads) {
 			if (canPair(RNA[i], RNA[j])) {
 				flag = 1;
 				int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
-				int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack
+				int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack
 				if (j-i > 6) { // Internal Loop BEGIN
 					int p=0, q=0;
 					int VBIij = INFINITY_;
@@ -106,7 +106,7 @@ int calculate(int len, int nThreads) {
 		}
 	}
 	for (j = TURN+2; j <= len; j++) {
-		int i, must_branch=0, Wj, Widjd, Wijd, Widj, Wij, Wim1;
+		int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
 		Wj = INFINITY_;
 		for (i = 1; i < j-TURN; i++) {
 			Wij = Widjd = Wijd = Widj = INFINITY_;
@@ -116,34 +116,8 @@ int calculate(int len, int nThreads) {
 			Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd;
 			Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj;
 			Wj = MIN(MIN4(Wij, Widjd, Wijd, Widj), Wj); 
-	
-			/*
-			if (Wj<INFINITY_) {
-				if (Wj==Wij && forcePair(i,j))
-				must_branch = 1;
-				else if (Wj==Widjd && forcePair(i+1,j-1))
-				must_branch = 1;
-				else if (Wj==Wijd && forcePair(i,j-1))
-				must_branch = 1; 
-				else if (forcePair(i+1,j))
-				must_branch = 1;
-			}
-			*/
-			if(i==296&&j==301){
-				printf("Option 1: %d\n", W[j-1]);
-				printf("Option 2: %d = V(i,j) + W(i-1) = %d +%d = %d\n", W[j], V(i,j), W[i-1], V(i,j) + W[i-1]);
-			}
 		}
-		//W[j] = branch?Wj:MIN(Wj, W[j-1]);
 		W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj;
-		if(j==301){
-			printf("Final option 1: %d\n", W[j-1]);
-			printf("Final option 2: %d\n", Wj);
-			printf("canSS(j): %d\n", canSS(j));
-			printf("chosen: %d\n", W[j]);
-			printf("canHairpin(i,j): %d\n", canHairpin(295,305));
-			printf("eH(i,j): %d\n", eH(295,305));
-		}
 	}
 	return W[len];
 }
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 4a5810a..a2f1042 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -182,7 +182,6 @@ int init_constraints(const char* constr_file,int length) {
 				PBP[it][0] = PBP[it][1];
 				PBP[it][1] = temp;
 			}
-			printf("%d\n", it);
 		}
 
 		for(it = 0; it < nPBP; it++){
@@ -212,7 +211,6 @@ int init_constraints(const char* constr_file,int length) {
 				FBP[it][0] = FBP[it][1];
 				FBP[it][1] = temp; 
 			}
-			printf("%d\n", it);
 		}
 		for(it = 0; it<nFBP; it++){
 			if(FBP[it][2] < 1){
diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 80f37c3..6d0f375 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -6,6 +6,7 @@
 #include "utils.h"
 #include "global.h"
 #include "constants.h"
+#include "shapereader.h"
 
 int *V; 
 int *VV; 
@@ -153,7 +154,8 @@ inline int eL(int i, int j, int ip, int jp) {
 			energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]);
 		} else if (size == 1) {
 			energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])]
-				+ bulge[size] + eparam[2]; /* mans */
+				+ bulge[size] + eparam[2] +
+				+ getShapeEnergy(i) + getShapeEnergy(j) + getShapeEnergy(ip) + getShapeEnergy(jp);
 		}
 	} else {
 		/* Internal loop */
@@ -325,7 +327,8 @@ inline int eS(int i, int j)
 {
 	int energy;
 	/*  not sure about eparam[1], come from MFold.. = 0 */
-	energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i+1], RNA[j-1])] + eparam[1];
+	energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i+1], RNA[j-1])] + eparam[1] 
+		+ getShapeEnergy(i) + getShapeEnergy(j) + getShapeEnergy(i+1) + getShapeEnergy(j-1) ;
 
 	return energy;
 }
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 15a2f0c..60ce3da 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -46,6 +46,7 @@ void trace(int len, int vbose) {
 	}
 
 	printf("\n");
+	
 	traceW(len);
 	printf("- sum of energy of Loops:   	  %12.2f kcal/mol\n", total_en/100.0);
 	printf("- sum of energy of External Loop: %12.2f kcal/mol\n", total_ex/100.0);
@@ -66,19 +67,19 @@ void traceW(int j) {
 
 		wim1 = MIN(0, W[i-1]);
 		flag = 1;
-		if ( wim1 != W[i-1]) flag = 0;
+		if ( wim1 != W[i-1] && canSSregion(0,i)) flag = 0;
 
 		Widjd = Wijd =  Widj = INFINITY_;
 		Wij = V(i,j) + auPenalty(i, j) + wim1;
 		Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1;
 		Wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
 		Widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
-		Wj_temp=Wj;
+		//Wj_temp=Wj;
 		
-		Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
+		//Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
 
-		if (W[j] == Wj) {
-			if (W[j] == Wij) { 
+		//if (W[j] == Wj) {
+			if ((W[j] == Wij && canStack(i,j)) || forcePair(i,j)) { 
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i, j, auPenalty(i, j)/100.00);
@@ -88,7 +89,7 @@ void traceW(int j) {
 				traceV(i, j);
 				if (flag ) traceW(i - 1);
 				break;
-			} else if (W[j] == Widjd) { 
+			} else if ((W[j] == Widjd && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
@@ -98,7 +99,7 @@ void traceW(int j) {
 				traceV(i + 1, j - 1);
 				if (flag ) traceW(i - 1);
 				break;
-			} else if (W[j] == Wijd) { 
+			} else if ((W[j] == Wijd && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) { 	
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
@@ -108,7 +109,7 @@ void traceW(int j) {
 				traceV(i, j - 1);
 				if (flag ) traceW(i - 1);
 				break;
-			} else if (W[j] == Widj){
+			} else if ((W[j] == Widj && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){
 				done = 1;
 				if (verbose == 1) 
 					printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
@@ -119,7 +120,7 @@ void traceW(int j) {
 				if (flag ) traceW(i - 1);
 				break;
 			}
-		}
+		//}
 	}
 		
 	if (W[j] == W[j - 1] && !done) traceW(j-1);
@@ -131,11 +132,11 @@ int traceV(int i, int j) {
 	int a, b, c, d, Vij;
 	if (j-i < TURN)  return INFINITY_;
 
-	a = canHairpin(i,j)?eH(i, j)+ getShapeEnergy(i) + getShapeEnergy(j):INFINITY_;
-	b = canStack(i,j)?eS(i, j) + V(i + 1, j - 1) + getShapeEnergy(i) + getShapeEnergy(j):INFINITY_;
+	a = canHairpin(i,j)?eH(i, j):INFINITY_;
+	b = canStack(i,j)?eS(i, j) + V(i + 1, j - 1):INFINITY_;
 	if (eS(i, j) == 0) b = INFINITY_;
-	c = canStack(i,j)?VBI(i,j) + getShapeEnergy(i) + getShapeEnergy(j):INFINITY_;
-	d = canStack(i,j)?VM(i,j) + getShapeEnergy(i) + getShapeEnergy(j):INFINITY_;
+	c = canStack(i,j)?VBI(i,j):INFINITY_;
+	d = canStack(i,j)?VM(i,j):INFINITY_;
 	
 	
 	
@@ -184,7 +185,7 @@ int traceVBI(int i, int j) {
 			el = eL(i, j, ip, jp);
 			v = V(ip, jp);
 			VBIij_temp = el + v;
-			if (VBIij_temp == VBI(i,j)) {
+			if (VBIij_temp == VBI(i,j) || forcePair(ip,jp)){
 				ifinal = ip;
 				jfinal = jp;
 				break;
@@ -227,7 +228,7 @@ int traceVM(int i, int j) {
 	//if (check_base(i+1)) {
 		for (h = i + 3; h <= j - 1 && !done; h++) {
 			A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1); 
-			if (A_temp == VMij) {
+			if (A_temp == VMij && canSS(i+1) ) {
 				done = 1;
 				eVM += traceWM(i + 2, h - 1);
 				eVM += traceWM(h, j - 1);
@@ -239,7 +240,7 @@ int traceVM(int i, int j) {
 	//if (check_base(j-1)) {
 		for (h = i + 2; h <= j - 2 && !done; h++) { 
 			A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1);
-			if (A_temp == VMij) {
+			if (A_temp == VMij && canSS(j-1)) {
 				done = 1;
 				eVM += traceWM(i + 1, h - 1);
 				eVM += traceWM(h, j - 2);
@@ -251,7 +252,7 @@ int traceVM(int i, int j) {
 	//if (check_base(i+1)&&check_base(j-1)) {
 		for (h = i + 3; h <= j - 2 && !done; h++) { 
 			A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
-			if (A_temp == VMij) {
+			if (A_temp == VMij && canSS(i+1) && canSS(j-1)) {
 				done = 1;
 				eVM += traceWM(i + 2, h - 1);
 				eVM += traceWM(h, j - 2);
@@ -286,35 +287,37 @@ int traceWM(int i, int j) {
 		if (h1 != 0) {
 			eWM += traceWM(i, h);
 			eWM += traceWM(h + 1, j);
+			done = 1;
 		} else {
-			if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb) { 
+			if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) { 
 				done = 1;
 				structure[i] = j;
 				structure[j] = i;
 				eWM += traceV(i, j);
-			} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec) { 
+			} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) &&  canStack(i+1,j)) { 
 				done = 1;
 				eWM += traceV(i + 1, j);
 				structure[i + 1] = j;
 				structure[j] = i + 1;
-			} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec ) { 
+			} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec && canSS(j) && canStack(i,j-1)) { 
 				done = 1;
 				eWM += traceV(i, j - 1);
 				structure[i] = j - 1;
 				structure[j - 1] = i;
-			} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec) { 
+			} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) { 
 				done = 1;
 				eWM += traceV(i + 1, j - 1);
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
-			} else if (WM(i,j) == WM(i + 1,j) + Ec) { 
+			} else if (WM(i,j) == WM(i + 1,j) + Ec && canSS(i)) { 
 				done = 1;
 				eWM += traceWM(i + 1, j);
-			} else if (WM(i,j) == WM(i,j - 1) + Ec) { 
+			} else if (WM(i,j) == WM(i,j - 1) + Ec && canSS(j)) { 
 				done = 1;
 				eWM += traceWM(i, j - 1);
 			}
 		}
 	}
+	if(!done){fprintf(stderr, "ERROR: WM(%d,%d) could not be traced!\n", i,j);}
 	return eWM;
 }

From 15915e54be38565095ee888f274c863d98d60b22 Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Wed, 25 May 2011 03:55:47 +0200
Subject: [PATCH 132/282] merged Prashant's rewrite branch

---
 gtfold-mfe/data/Turner99/Makefile.am  |  15 +
 gtfold-mfe/data/Turner99/Makefile.in  |  13 +
 gtfold-mfe/data/Turner99/dangle.DAT   |   8 +
 gtfold-mfe/data/Turner99/int11.DAT    |  24 +
 gtfold-mfe/data/Turner99/int21.DAT    |  96 +++
 gtfold-mfe/data/Turner99/int22.DAT    | 576 ++++++++++++++++
 gtfold-mfe/data/Turner99/loop.DAT     |  30 +
 gtfold-mfe/data/Turner99/miscloop.DAT |  12 +
 gtfold-mfe/data/Turner99/sint2.DAT    |  24 +
 gtfold-mfe/data/Turner99/sint4.DAT    | 576 ++++++++++++++++
 gtfold-mfe/data/Turner99/stack.DAT    |  16 +
 gtfold-mfe/data/Turner99/tloop.DAT    |  30 +
 gtfold-mfe/data/Turner99/tstackh.DAT  |  16 +
 gtfold-mfe/data/Turner99/tstacki.DAT  |  16 +
 gtfold-mfe/data/Turner99/tstackm.DAT  |  16 +
 gtfold-mfe/include/loader.h           |  20 +-
 gtfold-mfe/include/options.h          |  11 +
 gtfold-mfe/scripts/dats2DATs.py       |  53 ++
 gtfold-mfe/src/algorithms.c           |  23 +
 gtfold-mfe/src/constraints.cc         |  57 +-
 gtfold-mfe/src/energy.c               |  46 +-
 gtfold-mfe/src/loader.cc              | 949 +++++++-------------------
 gtfold-mfe/src/main.cc                |  14 +-
 gtfold-mfe/src/options.cc             |  26 +-
 24 files changed, 1921 insertions(+), 746 deletions(-)
 create mode 100644 gtfold-mfe/data/Turner99/dangle.DAT
 create mode 100644 gtfold-mfe/data/Turner99/int11.DAT
 create mode 100644 gtfold-mfe/data/Turner99/int21.DAT
 create mode 100644 gtfold-mfe/data/Turner99/int22.DAT
 create mode 100644 gtfold-mfe/data/Turner99/loop.DAT
 create mode 100644 gtfold-mfe/data/Turner99/miscloop.DAT
 create mode 100644 gtfold-mfe/data/Turner99/sint2.DAT
 create mode 100644 gtfold-mfe/data/Turner99/sint4.DAT
 create mode 100644 gtfold-mfe/data/Turner99/stack.DAT
 create mode 100644 gtfold-mfe/data/Turner99/tloop.DAT
 create mode 100644 gtfold-mfe/data/Turner99/tstackh.DAT
 create mode 100644 gtfold-mfe/data/Turner99/tstacki.DAT
 create mode 100644 gtfold-mfe/data/Turner99/tstackm.DAT
 create mode 100755 gtfold-mfe/scripts/dats2DATs.py

diff --git a/gtfold-mfe/data/Turner99/Makefile.am b/gtfold-mfe/data/Turner99/Makefile.am
index 4cf8fa7..cb09a05 100644
--- a/gtfold-mfe/data/Turner99/Makefile.am
+++ b/gtfold-mfe/data/Turner99/Makefile.am
@@ -3,6 +3,19 @@
 gtfold_datadir = $(datadir)/@PACKAGE@/Turner99
 
 gtfold_data_DATA = \
+	stack.DAT\
+	miscloop.DAT\
+	dangle.DAT\
+	loop.DAT\
+	int11.DAT\
+	int21.DAT\
+	int22.DAT\
+	sint2.DAT\
+	sint4.DAT\
+	tloop.DAT\
+	tstackh.DAT\
+	tstacki.DAT\
+	tstackm.DAT\
 	stack.dat\
 	miscloop.dat\
 	dangle.dat\
@@ -23,6 +36,8 @@ gtfold_data_DATA = \
 	tstacki.dat\
 	tstackm.dat
 
+
+
 EXTRA_DIST = $(gtfold_data_DATA)
 
 CLEANFILES = *~
diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in
index d9a1eb3..d042a79 100644
--- a/gtfold-mfe/data/Turner99/Makefile.in
+++ b/gtfold-mfe/data/Turner99/Makefile.in
@@ -176,6 +176,19 @@ top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 gtfold_datadir = $(datadir)/@PACKAGE@/Turner99
 gtfold_data_DATA = \
+	stack.DAT\
+	miscloop.DAT\
+	dangle.DAT\
+	loop.DAT\
+	int11.DAT\
+	int21.DAT\
+	int22.DAT\
+	sint2.DAT\
+	sint4.DAT\
+	tloop.DAT\
+	tstackh.DAT\
+	tstacki.DAT\
+	tstackm.DAT\
 	stack.dat\
 	miscloop.dat\
 	dangle.dat\
diff --git a/gtfold-mfe/data/Turner99/dangle.DAT b/gtfold-mfe/data/Turner99/dangle.DAT
new file mode 100644
index 0000000..9fb7c28
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/dangle.DAT
@@ -0,0 +1,8 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.80	-0.50	-0.80	-0.60
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.70	-0.80	-1.70	-1.20	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-1.10	-0.40	-1.30	-0.60	inf 	inf 	inf 	inf	-0.80	-0.50	-0.80	-0.60
+-0.70	-0.10	-0.70	-0.10	inf 	inf 	inf 	inf	-0.70	-0.10	-0.70	-0.10	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.30	-0.10	-0.20	-0.20
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.20	-0.30	-0.0	-0.0	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-0.50	-0.30	-0.20	-0.10	inf 	inf 	inf 	inf	-0.30	-0.10	-0.20	-0.20
+-0.30	-0.30	-0.40	-0.20	inf 	inf 	inf 	inf	-0.30	-0.30	-0.40	-0.20	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/Turner99/int11.DAT b/gtfold-mfe/data/Turner99/int11.DAT
new file mode 100644
index 0000000..96eabfd
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/int11.DAT
@@ -0,0 +1,24 @@
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.50	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.20	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.10	1.10	1.10	1.10	0.40	-0.40	0.40	0.40	1.10	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.30	0.50	0.40	0.50	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	-0.10	0.40	-1.70	0.40	0.40	0.40	-1.40	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.00	0.40	-0.30	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.80	0.40	0.40	0.40	0.40	0.30	-0.10	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	0.40	-0.40	0.50	0.40	0.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	0.40	0.40	-2.10	0.40	0.40	0.40	-1.70	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	-0.70	0.40	0.50	0.40	-0.30	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.80	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.50	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
diff --git a/gtfold-mfe/data/Turner99/int21.DAT b/gtfold-mfe/data/Turner99/int21.DAT
new file mode 100644
index 0000000..0dfe3c4
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/int21.DAT
@@ -0,0 +1,96 @@
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.20	3.00	2.40	4.80	2.30	2.20	1.10	4.00	2.40	2.20	1.60	4.00	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80
+3.10	3.00	4.80	3.00	2.30	2.20	4.00	2.20	2.30	2.20	4.00	2.20	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00
+2.50	4.80	1.60	4.80	1.70	4.00	0.80	4.00	1.70	4.00	0.80	4.00	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+2.90	2.50	2.40	4.80	2.10	1.70	1.60	4.00	2.10	1.70	1.60	4.00	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80
+3.00	3.30	4.80	3.00	2.20	2.50	4.00	2.20	2.20	2.50	4.00	2.20	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	3.00	4.80	2.10	4.00	2.20	4.00	1.50	4.00	2.20	4.00	1.30	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10
+1.80	1.40	1.20	4.80	0.80	0.60	0.40	4.00	1.00	0.60	0.40	4.00	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+1.60	4.80	3.00	4.80	0.80	4.00	2.20	4.00	0.80	4.00	2.20	4.00	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+3.30	2.70	4.80	3.00	2.50	1.90	4.00	2.20	2.50	1.90	4.00	2.20	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	2.50	4.80	2.00	4.00	1.70	4.00	1.20	4.00	1.70	4.00	1.20	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00
+3.20	3.00	2.40	4.80	2.40	2.20	1.60	4.00	2.50	2.20	2.10	4.00	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80
+3.10	3.00	4.80	3.00	2.30	2.20	4.00	2.20	2.30	2.20	4.00	2.20	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00
+2.50	4.80	1.60	4.80	1.70	4.00	0.80	4.00	1.70	4.00	0.80	4.00	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+2.90	2.50	2.40	4.80	2.10	1.70	1.60	4.00	2.10	1.70	1.60	4.00	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80
+3.00	3.30	4.80	3.00	2.20	2.50	4.00	2.20	2.20	2.50	4.00	2.20	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	3.00	4.80	2.10	4.00	2.20	4.00	1.30	4.00	2.20	4.00	1.20	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10
+1.80	1.40	1.20	4.80	1.00	0.60	0.40	4.00	1.20	0.60	0.40	4.00	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+1.60	4.80	3.00	4.80	0.80	4.00	2.20	4.00	0.80	4.00	2.20	4.00	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+3.30	2.70	4.80	3.00	2.50	1.90	4.00	2.20	2.50	1.90	4.00	2.20	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	2.50	4.80	2.00	4.00	1.70	4.00	1.20	4.00	1.70	4.00	1.20	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
diff --git a/gtfold-mfe/data/Turner99/int22.DAT b/gtfold-mfe/data/Turner99/int22.DAT
new file mode 100644
index 0000000..9691143
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/int22.DAT
@@ -0,0 +1,576 @@
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
+  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
+  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
+  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
+  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
+  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
+  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
+  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
+  0.50  1.10 -0.30  2.00  1.10  1.70  2.00  0.70  0.40  2.00  1.00  0.10  2.00  1.80 -0.50  1.50 
+  0.60  1.50  0.10  2.00  1.10  1.50  2.00  0.50  0.50  2.00  1.40 -0.70  2.00  1.50 -0.60  0.00 
+  0.00 -0.70 -1.60  2.00 -1.00 -0.60  2.00  0.20 -0.70  2.00  0.00 -0.80  2.00  1.20 -0.60  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.00 -0.70  2.00  1.00  1.00  2.00  0.00  0.70  2.00  0.90 -1.90  2.00  1.10 -1.50 -0.20 
+  2.20  1.30  0.70  2.00  1.90  1.30  2.00  0.30  0.70  2.00  1.80 -0.30  2.00  1.40 -0.20 -0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.00  1.20  0.40  2.00  1.10  1.20  2.00  1.70  1.00  2.00  1.70 -0.70  2.00  1.20 -0.30  0.20 
+ -0.20 -0.40 -1.70  2.00  0.70  1.10  2.00  0.20 -0.50  2.00  0.00 -0.90  2.00  1.20 -1.30  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
+  0.90  0.00  0.30  2.00 -0.10  1.00  2.00  0.00  0.60  2.00  0.90 -3.00  2.00  1.00 -2.40  0.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.00  1.20  0.40  2.00  1.10  1.20  2.00  0.20  0.50  2.00  1.70 -0.70  2.00  1.20 -0.10  0.40 
+ -0.10 -1.60 -1.60  2.00 -1.60 -0.60  2.00 -1.60 -0.60  2.00 -0.70 -4.40  2.00 -0.50 -4.10 -1.00 
+  1.40  0.30  0.50  2.00  0.30  0.30  2.00  0.10  1.40  2.00  1.20 -1.00  2.00  0.30  0.10  0.60 
+  1.30  1.20  0.30  2.00  1.60  2.10  2.00  1.90  0.30  2.00  1.00 -0.40  2.00  1.90  1.10  1.40 
+  1.60  1.50  0.60  2.00  2.00  1.80  2.00  1.70  0.60  2.00  1.40 -1.10  2.00  1.70  0.40  0.80 
+  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.20  1.10  0.20  2.00  1.50  1.40  2.00  1.20  0.20  2.00  0.90 -1.50  2.00  1.20  0.00  0.30 
+  2.10  1.40  1.50  2.00  1.80  1.70  2.00  1.50  1.50  2.00  1.80 -0.20  2.00  1.50  1.30  0.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
+  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
+  1.10  0.00  0.90  2.00  0.40  1.30  2.00  1.10  0.90  2.00  0.90 -2.60  2.00  1.10 -1.10  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
+ -0.40 -1.50 -0.60  2.00 -1.10 -0.20  2.00 -0.40 -0.60  2.00 -0.70 -4.20  2.00 -0.40 -2.60 -0.50 
+  1.40  0.30  1.30  2.00  0.80  0.60  2.00  0.50  1.30  2.00  1.20 -0.50  2.00  0.50  1.10 -0.40 
+  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
+  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
+  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
+  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
+  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
+  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
+  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
+  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
+  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
+  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
+  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
+  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
+  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
+  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
+  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
+  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
+  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.20  0.90 -0.80  2.00  0.90  0.90  2.00  0.00 -0.20  2.00  0.80 -2.00  2.00  1.00 -1.60  0.20 
+  0.10 -0.10 -1.90  2.00 -0.20  0.90  2.00 -0.10 -1.30  2.00 -0.20 -1.30  2.00  0.90 -0.90  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.20  1.00 -0.80  2.00  0.90  1.00  2.00  0.00 -0.10  2.00  0.90 -1.90  2.00  1.00 -1.50  0.20 
+  1.80  1.00  0.20  2.00  0.90  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.00 -0.50  0.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.00  0.30  2.00  1.00  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.10 -0.50  0.30 
+ -0.50 -0.80 -2.60  2.00 -0.80  0.20  2.00 -0.80 -1.90  2.00 -0.90 -1.90  2.00  0.30 -1.50  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
+ -0.30 -1.50 -1.50  2.00 -1.60 -0.50  2.00 -1.50 -0.90  2.00 -0.60 -4.50  2.00 -0.50 -4.10 -0.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  0.80  0.00 -0.80  2.00  0.00  0.00  2.00 -1.00 -0.10  2.00  0.50 -1.90  2.00  0.00 -1.50 -0.70 
+ -0.70 -1.90 -1.90  2.00 -2.00 -0.90  2.00 -1.90 -1.30  2.00 -1.00 -4.90  2.00 -0.90 -4.50 -0.90 
+  1.50  0.20  0.30  2.00  0.20  0.20  2.00 -0.70  0.90  2.00  1.10 -0.90  2.00  0.30 -0.50 -0.50 
+  0.50  1.30 -0.20  2.00  0.60  2.20  2.00  2.00  0.00  2.00  1.10 -0.10  2.00  2.00  0.90  1.40 
+  1.10  1.00  0.70  2.00  1.10  1.90  2.00  1.10 -1.00  2.00  0.80 -1.60  2.00  1.10 -0.10  0.30 
+  0.40  0.70 -0.50  2.00  0.50  0.70  2.00  0.50 -0.70  2.00 -0.20 -0.60  2.00  1.00  0.60  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  1.00 -0.40  2.00  1.50  1.30  2.00  1.20 -0.70  2.00  0.90 -1.60  2.00  1.20  0.00  0.30 
+  1.70  1.00  1.10  2.00  1.50  1.30  2.00  1.20 -0.60  2.00  1.50 -0.60  2.00  1.20  1.00  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.10  1.20  2.00  1.50  1.40  2.00  1.20  1.20  2.00  1.50 -0.50  2.00  1.20  1.00  0.30 
+ -0.30 -0.70 -1.70  2.00  0.10  0.70  2.00  0.40 -1.60  2.00 -0.90 -1.60  2.00  0.40  0.30  0.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
+ -0.50 -1.50 -1.30  2.00 -0.60 -0.20  2.00 -0.10 -0.60  2.00 -0.60 -4.10  2.00 -0.30 -2.40  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  0.70  0.00  0.20  2.00  0.50  0.30  2.00  0.20  0.20  2.00  0.50 -1.60  2.00  1.70  0.00  0.10 
+  0.10 -1.90 -0.90  2.00 -0.70 -0.30  2.00 -0.70 -0.80  2.00 -1.00 -4.40  2.00 -0.70 -3.00 -1.00 
+  1.50 -0.20  0.90  2.00  0.00 -0.10  2.00  0.40  0.90  2.00  1.10 -1.00  2.00  0.20  0.60  0.60 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
+  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
+  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
+  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
+  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
+  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
+  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
+  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
+  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
+  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
+  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
+  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
+  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
+  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
+  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
+  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
+  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
+  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
+  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
+  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
+  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
+  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
+  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
+  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
+  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
+  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80
diff --git a/gtfold-mfe/data/Turner99/loop.DAT b/gtfold-mfe/data/Turner99/loop.DAT
new file mode 100644
index 0000000..bc9a352
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/loop.DAT
@@ -0,0 +1,30 @@
+1	inf	3.80	inf
+2	inf	2.80	inf
+3	inf	3.20	5.70
+4	1.70	3.60	5.60
+5	1.80	4.00	5.60
+6	2.00	4.40	5.40
+7	2.20	4.60	5.90
+8	2.30	4.70	5.60
+9	2.40	4.80	6.40
+10	2.50	4.90	6.50
+11	2.60	5.00	6.60
+12	2.70	5.10	6.70
+13	2.80	5.20	6.80
+14	2.90	5.30	6.90
+15	3.00	5.40	6.90
+16	3.00	5.40	7.00
+17	3.10	5.50	7.10
+18	3.10	5.50	7.10
+19	3.20	5.60	7.20
+20	3.30	5.70	7.20
+21	3.30	5.70	7.30
+22	3.40	5.80	7.30
+23	3.40	5.80	7.40
+24	3.40	5.80	7.40
+25	3.50	5.90	7.50
+26	3.50	5.90	7.50
+27	3.60	6.00	7.50
+28	3.60	6.00	7.60
+29	3.60	6.00	7.60
+30	3.70	6.10	7.70
diff --git a/gtfold-mfe/data/Turner99/miscloop.DAT b/gtfold-mfe/data/Turner99/miscloop.DAT
new file mode 100644
index 0000000..2ba7508
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/miscloop.DAT
@@ -0,0 +1,12 @@
+1.079
+3.00
+.50	.50	.50	.50
+3.40	.00	.40
+10.10	-0.30	-0.30
+0.50
+-2.20
+0.30
+1.60
+1.40
+4.10
+1
diff --git a/gtfold-mfe/data/Turner99/sint2.DAT b/gtfold-mfe/data/Turner99/sint2.DAT
new file mode 100644
index 0000000..96eabfd
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/sint2.DAT
@@ -0,0 +1,24 @@
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.50	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.20	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.10	1.10	1.10	1.10	0.40	-0.40	0.40	0.40	1.10	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.30	0.50	0.40	0.50	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	-0.10	0.40	-1.70	0.40	0.40	0.40	-1.40	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.00	0.40	-0.30	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.80	0.40	0.40	0.40	0.40	0.30	-0.10	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	0.40	-0.40	0.50	0.40	0.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	0.40	0.40	-2.10	0.40	0.40	0.40	-1.70	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	-0.70	0.40	0.50	0.40	-0.30	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.80	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.50	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
diff --git a/gtfold-mfe/data/Turner99/sint4.DAT b/gtfold-mfe/data/Turner99/sint4.DAT
new file mode 100644
index 0000000..c878345
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/sint4.DAT
@@ -0,0 +1,576 @@
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.00	1.70	0.00	2.00	1.70	1.70	2.00	0.70	0.60	2.00	1.60	-1.20	2.00	1.80	-0.80	1.00
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	-0.10	2.00	1.60	1.60	2.00	0.60	0.50	2.00	1.50	-1.30	2.00	1.70	-0.90	0.90
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.20	-0.60	2.00	1.10	1.80	2.00	0.80	0.00	2.00	1.10	-0.70	2.00	1.80	-0.30	1.40
+1.70	0.40	0.50	2.00	0.40	1.40	2.00	0.50	1.10	2.00	1.30	-2.50	2.00	1.50	-2.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.70	-0.50	-0.50	2.00	-0.60	0.50	2.00	-0.50	0.10	2.00	0.40	-3.50	2.00	0.50	-3.10	0.50
+2.00	0.80	0.80	2.00	0.70	0.80	2.00	-0.20	1.50	2.00	1.70	-0.30	2.00	0.80	0.10	0.00
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+1.90	1.80	0.90	2.00	2.20	2.10	2.00	1.90	0.90	2.00	1.60	-0.80	2.00	1.90	0.70	1.00
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.70	0.80	2.00	2.10	2.00	2.00	1.80	0.80	2.00	1.50	-0.90	2.00	1.80	0.60	0.90
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.30	1.20	0.30	2.00	1.70	2.10	2.00	2.00	0.30	2.00	1.10	-0.40	2.00	2.00	1.10	1.50
+1.60	0.50	1.40	2.00	0.90	1.80	2.00	1.60	1.40	2.00	1.30	-2.10	2.00	1.60	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.60	-0.50	0.40	2.00	0.00	0.80	2.00	0.70	0.40	2.00	0.40	-3.10	2.00	0.70	-1.60	0.60
+1.90	0.80	1.80	2.00	1.30	1.10	2.00	1.00	1.80	2.00	1.70	0.00	2.00	1.00	1.60	0.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.00	1.60	1.00	2.00	2.00	2.60	2.00	2.60	1.00	2.00	1.40	0.20	2.00	2.30	1.50	2.20
+2.40	1.90	1.30	2.00	2.40	2.40	2.00	2.40	1.30	2.00	1.70	-0.40	2.00	2.10	0.80	1.50
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.50	0.90	2.00	1.90	1.90	2.00	1.90	0.90	2.00	1.30	-0.90	2.00	1.60	0.40	1.10
+2.80	1.80	2.20	2.00	2.20	2.20	2.00	2.20	2.20	2.00	2.20	0.40	2.00	1.90	1.70	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+1.80	0.40	1.60	2.00	0.80	1.80	2.00	1.80	1.60	2.00	1.20	-2.00	2.00	1.50	-0.70	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+0.30	-1.10	0.10	2.00	-0.70	0.30	2.00	0.30	0.10	2.00	-0.30	-3.50	2.00	0.00	-2.20	0.30
+2.20	0.70	1.90	2.00	1.20	1.20	2.00	1.20	1.90	2.00	1.50	0.20	2.00	0.90	1.50	0.30
+0.50	1.10	-0.30	2.00	1.10	1.70	2.00	0.70	0.40	2.00	1.00	0.10	2.00	1.80	-0.50	1.50
+0.60	1.50	0.10	2.00	1.10	1.50	2.00	0.50	0.50	2.00	1.40	-0.70	2.00	1.50	-0.60	0.00
+0.00	-0.70	-1.60	2.00	-1.00	-0.60	2.00	0.20	-0.70	2.00	0.00	-0.80	2.00	1.20	-0.60	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.30	1.00	-0.70	2.00	1.00	1.00	2.00	0.00	0.70	2.00	0.90	-1.90	2.00	1.10	-1.50	-0.20
+2.20	1.30	0.70	2.00	1.90	1.30	2.00	0.30	0.70	2.00	1.80	-0.30	2.00	1.40	-0.20	-0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.00	1.20	0.40	2.00	1.10	1.20	2.00	1.70	1.00	2.00	1.70	-0.70	2.00	1.20	-0.30	0.20
+-0.20	-0.40	-1.70	2.00	0.70	1.10	2.00	0.20	-0.50	2.00	0.00	-0.90	2.00	1.20	-1.30	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.10	0.90	-0.90	2.00	0.80	1.50	2.00	0.50	-0.20	2.00	0.80	-1.00	2.00	1.50	-0.60	1.10
+0.90	0.00	0.30	2.00	-0.10	1.00	2.00	0.00	0.60	2.00	0.90	-3.00	2.00	1.00	-2.40	0.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.00	1.20	0.40	2.00	1.10	1.20	2.00	0.20	0.50	2.00	1.70	-0.70	2.00	1.20	-0.10	0.40
+-0.10	-1.60	-1.60	2.00	-1.60	-0.60	2.00	-1.60	-0.60	2.00	-0.70	-4.40	2.00	-0.50	-4.10	-1.00
+1.40	0.30	0.50	2.00	0.30	0.30	2.00	0.10	1.40	2.00	1.20	-1.00	2.00	0.30	0.10	0.60
+1.30	1.20	0.30	2.00	1.60	2.10	2.00	1.90	0.30	2.00	1.00	-0.40	2.00	1.90	1.10	1.40
+1.60	1.50	0.60	2.00	2.00	1.80	2.00	1.70	0.60	2.00	1.40	-1.10	2.00	1.70	0.40	0.80
+0.30	0.20	-0.70	2.00	0.60	1.50	2.00	1.30	-0.70	2.00	0.00	-0.60	2.00	1.30	0.90	1.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.20	1.10	0.20	2.00	1.50	1.40	2.00	1.20	0.20	2.00	0.90	-1.50	2.00	1.20	0.00	0.30
+2.10	1.40	1.50	2.00	1.80	1.70	2.00	1.50	1.50	2.00	1.80	-0.20	2.00	1.50	1.30	0.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.20	1.30	2.00	1.70	1.50	2.00	1.40	1.30	2.00	1.70	-0.40	2.00	1.40	1.10	0.50
+0.30	0.20	-0.70	2.00	0.60	1.50	2.00	1.30	-0.70	2.00	0.00	-0.60	2.00	1.30	0.90	1.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.00	0.90	0.00	2.00	1.40	1.80	2.00	1.70	0.00	2.00	0.80	-0.70	2.00	1.70	0.90	1.20
+1.10	0.00	0.90	2.00	0.40	1.30	2.00	1.10	0.90	2.00	0.90	-2.60	2.00	1.10	-1.10	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.20	1.30	2.00	1.70	1.50	2.00	1.40	1.30	2.00	1.70	-0.40	2.00	1.40	1.10	0.50
+-0.40	-1.50	-0.60	2.00	-1.10	-0.20	2.00	-0.40	-0.60	2.00	-0.70	-4.20	2.00	-0.40	-2.60	-0.50
+1.40	0.30	1.30	2.00	0.80	0.60	2.00	0.50	1.30	2.00	1.20	-0.50	2.00	0.50	1.10	-0.40
+2.00	1.80	0.80	2.00	1.90	2.30	2.00	2.30	0.80	2.00	1.30	0.60	2.00	2.30	1.60	1.90
+2.40	2.10	1.10	2.00	2.20	2.10	2.00	2.10	1.10	2.00	1.70	0.00	2.00	2.10	0.90	1.30
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.70	0.70	2.00	1.80	1.60	2.00	1.60	0.70	2.00	1.20	-0.50	2.00	1.60	0.50	0.80
+2.80	2.00	2.00	2.00	2.10	1.90	2.00	1.90	2.00	2.00	2.10	0.80	2.00	1.90	1.80	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+1.80	0.60	1.40	2.00	0.70	1.50	2.00	1.50	1.40	2.00	1.10	-1.60	2.00	1.50	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+0.30	-0.90	-0.10	2.00	-0.80	0.00	2.00	0.00	-0.10	2.00	-0.40	-3.10	2.00	0.00	-2.10	0.00
+2.20	0.90	1.80	2.00	1.00	0.90	2.00	0.90	1.80	2.00	1.50	0.60	2.00	0.90	1.60	0.10
+2.00	1.60	1.00	2.00	2.00	2.60	2.00	2.60	1.00	2.00	1.40	0.20	2.00	2.30	1.50	2.20
+2.40	1.90	1.30	2.00	2.40	2.40	2.00	2.40	1.30	2.00	1.70	-0.40	2.00	2.10	0.80	1.50
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.50	0.90	2.00	1.90	1.90	2.00	1.90	0.90	2.00	1.30	-0.90	2.00	1.60	0.40	1.10
+2.80	1.80	2.20	2.00	2.20	2.20	2.00	2.20	2.20	2.00	2.20	0.40	2.00	1.90	1.70	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+1.80	0.40	1.60	2.00	0.80	1.80	2.00	1.80	1.60	2.00	1.20	-2.00	2.00	1.50	-0.70	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+0.30	-1.10	0.10	2.00	-0.70	0.30	2.00	0.30	0.10	2.00	-0.30	-3.50	2.00	0.00	-2.20	0.30
+2.20	0.70	1.90	2.00	1.20	1.20	2.00	1.20	1.90	2.00	1.50	0.20	2.00	0.90	1.50	0.30
+2.00	1.80	0.80	2.00	1.90	2.30	2.00	2.30	0.80	2.00	1.30	0.60	2.00	2.30	1.60	1.90
+2.40	2.10	1.10	2.00	2.20	2.10	2.00	2.10	1.10	2.00	1.70	0.00	2.00	2.10	0.90	1.30
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.70	0.70	2.00	1.80	1.60	2.00	1.60	0.70	2.00	1.20	-0.50	2.00	1.60	0.50	0.80
+2.80	2.00	2.00	2.00	2.10	1.90	2.00	1.90	2.00	2.00	2.10	0.80	2.00	1.90	1.80	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+1.80	0.60	1.40	2.00	0.70	1.50	2.00	1.50	1.40	2.00	1.10	-1.60	2.00	1.50	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+0.30	-0.90	-0.10	2.00	-0.80	0.00	2.00	0.00	-0.10	2.00	-0.40	-3.10	2.00	0.00	-2.10	0.00
+2.20	0.90	1.80	2.00	1.00	0.90	2.00	0.90	1.80	2.00	1.50	0.60	2.00	0.90	1.60	0.10
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+1.80	1.40	0.80	2.00	1.80	1.80	2.00	1.80	0.80	2.00	1.20	-1.00	2.00	1.50	0.30	1.00
+0.70	0.30	-0.30	2.00	0.70	1.70	2.00	1.70	-0.30	2.00	0.10	-0.30	2.00	1.40	1.00	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.40	0.80	2.00	1.90	1.90	2.00	1.90	0.80	2.00	1.20	-0.90	2.00	1.60	0.30	1.00
+2.50	1.40	1.80	2.00	1.90	1.90	2.00	1.90	1.80	2.00	1.80	0.10	2.00	1.60	1.30	1.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.50	1.90	2.00	1.90	1.90	2.00	1.90	1.90	2.00	1.90	0.10	2.00	1.60	1.40	1.10
+0.10	-0.30	-0.90	2.00	0.10	1.10	2.00	1.10	-0.90	2.00	-0.50	-0.90	2.00	0.80	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+0.40	-1.10	0.10	2.00	-0.60	0.40	2.00	0.40	0.10	2.00	-0.30	-3.50	2.00	0.10	-2.20	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.40	0.90	2.00	0.90	0.90	2.00	0.90	0.90	2.00	0.80	-0.90	2.00	0.60	0.40	0.00
+0.00	-1.50	-0.30	2.00	-1.00	0.00	2.00	0.00	-0.30	2.00	-0.70	-3.90	2.00	-0.30	-2.60	-0.10
+2.10	0.70	1.90	2.00	1.10	1.10	2.00	1.10	1.90	2.00	1.50	0.10	2.00	0.80	1.40	0.30
+1.50	1.20	-0.50	2.00	1.20	1.80	2.00	0.80	0.10	2.00	1.10	-0.70	2.00	1.90	-0.30	1.50
+1.20	0.90	-0.80	2.00	0.90	0.90	2.00	0.00	-0.20	2.00	0.80	-2.00	2.00	1.00	-1.60	0.20
+0.10	-0.10	-1.90	2.00	-0.20	0.90	2.00	-0.10	-1.30	2.00	-0.20	-1.30	2.00	0.90	-0.90	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.20	1.00	-0.80	2.00	0.90	1.00	2.00	0.00	-0.10	2.00	0.90	-1.90	2.00	1.00	-1.50	0.20
+1.80	1.00	0.20	2.00	0.90	1.00	2.00	0.00	0.90	2.00	1.50	-0.90	2.00	1.00	-0.50	0.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.00	0.30	2.00	1.00	1.00	2.00	0.00	0.90	2.00	1.50	-0.90	2.00	1.10	-0.50	0.30
+-0.50	-0.80	-2.60	2.00	-0.80	0.20	2.00	-0.80	-1.90	2.00	-0.90	-1.90	2.00	0.30	-1.50	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.10	0.90	-0.90	2.00	0.80	1.50	2.00	0.50	-0.20	2.00	0.80	-1.00	2.00	1.50	-0.60	1.10
+-0.30	-1.50	-1.50	2.00	-1.60	-0.50	2.00	-1.50	-0.90	2.00	-0.60	-4.50	2.00	-0.50	-4.10	-0.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+0.80	0.00	-0.80	2.00	0.00	0.00	2.00	-1.00	-0.10	2.00	0.50	-1.90	2.00	0.00	-1.50	-0.70
+-0.70	-1.90	-1.90	2.00	-2.00	-0.90	2.00	-1.90	-1.30	2.00	-1.00	-4.90	2.00	-0.90	-4.50	-0.90
+1.50	0.20	0.30	2.00	0.20	0.20	2.00	-0.70	0.90	2.00	1.10	-0.90	2.00	0.30	-0.50	-0.50
+0.50	1.30	-0.20	2.00	0.60	2.20	2.00	2.00	0.00	2.00	1.10	-0.10	2.00	2.00	0.90	1.40
+1.10	1.00	0.70	2.00	1.10	1.90	2.00	1.10	-1.00	2.00	0.80	-1.60	2.00	1.10	-0.10	0.30
+0.40	0.70	-0.50	2.00	0.50	0.70	2.00	0.50	-0.70	2.00	-0.20	-0.60	2.00	1.00	0.60	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.10	1.00	-0.40	2.00	1.50	1.30	2.00	1.20	-0.70	2.00	0.90	-1.60	2.00	1.20	0.00	0.30
+1.70	1.00	1.10	2.00	1.50	1.30	2.00	1.20	-0.60	2.00	1.50	-0.60	2.00	1.20	1.00	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.10	1.20	2.00	1.50	1.40	2.00	1.20	1.20	2.00	1.50	-0.50	2.00	1.20	1.00	0.30
+-0.30	-0.70	-1.70	2.00	0.10	0.70	2.00	0.40	-1.60	2.00	-0.90	-1.60	2.00	0.40	0.30	0.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.00	0.90	0.00	2.00	1.40	1.80	2.00	1.70	0.00	2.00	0.80	-0.70	2.00	1.70	0.90	1.20
+-0.50	-1.50	-1.30	2.00	-0.60	-0.20	2.00	-0.10	-0.60	2.00	-0.60	-4.10	2.00	-0.30	-2.40	0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+0.70	0.00	0.20	2.00	0.50	0.30	2.00	0.20	0.20	2.00	0.50	-1.60	2.00	1.70	0.00	0.10
+0.10	-1.90	-0.90	2.00	-0.70	-0.30	2.00	-0.70	-0.80	2.00	-1.00	-4.40	2.00	-0.70	-3.00	-1.00
+1.50	-0.20	0.90	2.00	0.00	-0.10	2.00	0.40	0.90	2.00	1.10	-1.00	2.00	0.20	0.60	0.60
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+1.80	1.60	0.60	2.00	1.70	1.50	2.00	1.50	0.60	2.00	1.10	-0.60	2.00	1.50	0.40	0.70
+0.70	0.50	-0.50	2.00	0.60	1.40	2.00	1.40	-0.50	2.00	0.00	0.10	2.00	1.40	1.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	0.60	2.00	1.70	1.60	2.00	1.60	0.60	2.00	1.20	-0.50	2.00	1.60	0.40	0.80
+2.50	1.60	1.60	2.00	1.70	1.60	2.00	1.60	1.60	2.00	1.80	0.50	2.00	1.60	1.40	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.70	1.70	2.00	1.80	1.60	2.00	1.60	1.70	2.00	1.80	0.50	2.00	1.60	1.50	0.80
+0.10	-0.10	-1.10	2.00	0.00	0.80	2.00	0.80	-1.10	2.00	-0.60	-0.50	2.00	0.80	0.50	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+0.40	-0.90	-0.10	2.00	-0.80	0.10	2.00	0.10	-0.10	2.00	-0.30	-3.10	2.00	0.10	-2.10	0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.60	0.70	2.00	0.70	0.60	2.00	0.60	0.70	2.00	0.80	-0.50	2.00	0.60	0.50	-0.20
+0.00	-1.30	-0.50	2.00	-1.20	-0.30	2.00	-0.30	-0.50	2.00	-0.70	-3.50	2.00	-0.30	-2.50	-0.30
+2.10	0.90	1.70	2.00	1.00	0.80	2.00	0.80	1.70	2.00	1.40	0.50	2.00	0.80	1.50	0.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+1.80	1.40	0.80	2.00	1.80	1.80	2.00	1.80	0.80	2.00	1.20	-1.00	2.00	1.50	0.30	1.00
+0.70	0.30	-0.30	2.00	0.70	1.70	2.00	1.70	-0.30	2.00	0.10	-0.30	2.00	1.40	1.00	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.40	0.80	2.00	1.90	1.90	2.00	1.90	0.80	2.00	1.20	-0.90	2.00	1.60	0.30	1.00
+2.50	1.40	1.80	2.00	1.90	1.90	2.00	1.90	1.80	2.00	1.80	0.10	2.00	1.60	1.30	1.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.50	1.90	2.00	1.90	1.90	2.00	1.90	1.90	2.00	1.90	0.10	2.00	1.60	1.40	1.10
+0.10	-0.30	-0.90	2.00	0.10	1.10	2.00	1.10	-0.90	2.00	-0.50	-0.90	2.00	0.80	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+0.40	-1.10	0.10	2.00	-0.60	0.40	2.00	0.40	0.10	2.00	-0.30	-3.50	2.00	0.10	-2.20	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.40	0.90	2.00	0.90	0.90	2.00	0.90	0.90	2.00	0.80	-0.90	2.00	0.60	0.40	0.00
+0.00	-1.50	-0.30	2.00	-1.00	0.00	2.00	0.00	-0.30	2.00	-0.70	-3.90	2.00	-0.30	-2.60	-0.10
+2.10	0.70	1.90	2.00	1.10	1.10	2.00	1.10	1.90	2.00	1.50	0.10	2.00	0.80	1.40	0.30
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+1.80	1.60	0.60	2.00	1.70	1.50	2.00	1.50	0.60	2.00	1.10	-0.60	2.00	1.50	0.40	0.70
+0.70	0.50	-0.50	2.00	0.60	1.40	2.00	1.40	-0.50	2.00	0.00	0.10	2.00	1.40	1.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	0.60	2.00	1.70	1.60	2.00	1.60	0.60	2.00	1.20	-0.50	2.00	1.60	0.40	0.80
+2.50	1.60	1.60	2.00	1.70	1.60	2.00	1.60	1.60	2.00	1.80	0.50	2.00	1.60	1.40	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.70	1.70	2.00	1.80	1.60	2.00	1.60	1.70	2.00	1.80	0.50	2.00	1.60	1.50	0.80
+0.10	-0.10	-1.10	2.00	0.00	0.80	2.00	0.80	-1.10	2.00	-0.60	-0.50	2.00	0.80	0.50	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+0.40	-0.90	-0.10	2.00	-0.80	0.10	2.00	0.10	-0.10	2.00	-0.30	-3.10	2.00	0.10	-2.10	0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.60	0.70	2.00	0.70	0.60	2.00	0.60	0.70	2.00	0.80	-0.50	2.00	0.60	0.50	-0.20
+0.00	-1.30	-0.50	2.00	-1.20	-0.30	2.00	-0.30	-0.50	2.00	-0.70	-3.50	2.00	-0.30	-2.50	-0.30
+2.10	0.90	1.70	2.00	1.00	0.80	2.00	0.80	1.70	2.00	1.40	0.50	2.00	0.80	1.50	0.00
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.10	1.90	0.10	2.00	1.80	1.90	2.00	0.90	0.70	2.00	1.80	-1.00	2.00	1.90	-0.60	1.10
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.70	1.40	-0.30	2.00	1.40	1.40	2.00	0.40	0.30	2.00	1.30	-1.50	2.00	1.50	-1.10	0.70
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	1.20	-0.50	2.00	1.20	1.80	2.00	0.80	0.10	2.00	1.10	-0.70	2.00	1.90	-0.30	1.50
+1.60	0.30	0.40	2.00	0.30	1.30	2.00	0.40	1.00	2.00	1.20	-2.60	2.00	1.40	-2.20	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+0.30	-0.90	-0.90	2.00	-1.00	0.10	2.00	-0.90	-0.30	2.00	0.00	-3.90	2.00	0.10	-3.50	0.10
+2.30	1.00	1.10	2.00	1.00	1.00	2.00	0.00	1.70	2.00	1.90	-0.10	2.00	1.10	0.30	0.30
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+2.00	1.90	1.00	2.00	2.40	2.20	2.00	2.10	1.00	2.00	1.80	-0.70	2.00	2.10	0.80	1.20
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.60	1.50	0.60	2.00	1.90	1.80	2.00	1.60	0.60	2.00	1.30	-1.10	2.00	1.60	0.40	0.70
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.30	0.40	2.00	1.70	2.20	2.00	2.00	0.40	2.00	1.10	-0.30	2.00	2.00	1.20	1.50
+1.50	0.40	1.30	2.00	0.80	1.70	2.00	1.50	1.30	2.00	1.20	-2.20	2.00	1.50	-0.70	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+0.20	-0.90	0.00	2.00	-0.40	0.40	2.00	0.30	0.00	2.00	0.00	-3.50	2.00	0.30	-2.00	0.20
+2.20	1.10	2.00	2.00	1.50	1.40	2.00	1.20	2.00	2.00	1.90	0.30	2.00	1.20	1.80	0.30
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.00	1.70	0.00	2.00	1.70	1.70	2.00	0.70	0.60	2.00	1.60	-1.20	2.00	1.80	-0.80	1.00
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	-0.10	2.00	1.60	1.60	2.00	0.60	0.50	2.00	1.50	-1.30	2.00	1.70	-0.90	0.90
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.20	-0.60	2.00	1.10	1.80	2.00	0.80	0.00	2.00	1.10	-0.70	2.00	1.80	-0.30	1.40
+1.70	0.40	0.50	2.00	0.40	1.40	2.00	0.50	1.10	2.00	1.30	-2.50	2.00	1.50	-2.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.70	-0.50	-0.50	2.00	-0.60	0.50	2.00	-0.50	0.10	2.00	0.40	-3.50	2.00	0.50	-3.10	0.50
+2.00	0.80	0.80	2.00	0.70	0.80	2.00	-0.20	1.50	2.00	1.70	-0.30	2.00	0.80	0.10	0.00
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+1.90	1.80	0.90	2.00	2.20	2.10	2.00	1.90	0.90	2.00	1.60	-0.80	2.00	1.90	0.70	1.00
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.70	0.80	2.00	2.10	2.00	2.00	1.80	0.80	2.00	1.50	-0.90	2.00	1.80	0.60	0.90
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.30	1.20	0.30	2.00	1.70	2.10	2.00	2.00	0.30	2.00	1.10	-0.40	2.00	2.00	1.10	1.50
+1.60	0.50	1.40	2.00	0.90	1.80	2.00	1.60	1.40	2.00	1.30	-2.10	2.00	1.60	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.60	-0.50	0.40	2.00	0.00	0.80	2.00	0.70	0.40	2.00	0.40	-3.10	2.00	0.70	-1.60	0.60
+1.90	0.80	1.80	2.00	1.30	1.10	2.00	1.00	1.80	2.00	1.70	0.00	2.00	1.00	1.60	0.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.10	1.90	0.10	2.00	1.80	1.90	2.00	0.90	0.70	2.00	1.80	-1.00	2.00	1.90	-0.60	1.10
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.70	1.40	-0.30	2.00	1.40	1.40	2.00	0.40	0.30	2.00	1.30	-1.50	2.00	1.50	-1.10	0.70
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	1.20	-0.50	2.00	1.20	1.80	2.00	0.80	0.10	2.00	1.10	-0.70	2.00	1.90	-0.30	1.50
+1.60	0.30	0.40	2.00	0.30	1.30	2.00	0.40	1.00	2.00	1.20	-2.60	2.00	1.40	-2.20	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+0.30	-0.90	-0.90	2.00	-1.00	0.10	2.00	-0.90	-0.30	2.00	0.00	-3.90	2.00	0.10	-3.50	0.10
+2.30	1.00	1.10	2.00	1.00	1.00	2.00	0.00	1.70	2.00	1.90	-0.10	2.00	1.10	0.30	0.30
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+2.00	1.90	1.00	2.00	2.40	2.20	2.00	2.10	1.00	2.00	1.80	-0.70	2.00	2.10	0.80	1.20
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.60	1.50	0.60	2.00	1.90	1.80	2.00	1.60	0.60	2.00	1.30	-1.10	2.00	1.60	0.40	0.70
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.30	0.40	2.00	1.70	2.20	2.00	2.00	0.40	2.00	1.10	-0.30	2.00	2.00	1.20	1.50
+1.50	0.40	1.30	2.00	0.80	1.70	2.00	1.50	1.30	2.00	1.20	-2.20	2.00	1.50	-0.70	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+0.20	-0.90	0.00	2.00	-0.40	0.40	2.00	0.30	0.00	2.00	0.00	-3.50	2.00	0.30	-2.00	0.20
+2.20	1.10	2.00	2.00	1.50	1.40	2.00	1.20	2.00	2.00	1.90	0.30	2.00	1.20	1.80	0.30
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
diff --git a/gtfold-mfe/data/Turner99/stack.DAT b/gtfold-mfe/data/Turner99/stack.DAT
new file mode 100644
index 0000000..04a6889
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/stack.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.90
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.20	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.10	inf	-0.60
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.10	inf	-1.40	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.10	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-3.30	inf 	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.40	inf	-1.40	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.10	inf	-2.10	inf 	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.40	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.30
+inf 	inf 	inf 	inf 	inf 	inf	-3.40	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.50	inf
+inf 	inf 	inf 	inf 	inf	-3.30	inf	-1.50	inf 	inf 	inf 	inf 	inf	-2.10	inf	-0.50
+inf 	inf 	inf 	inf	-2.20	inf	-2.50	inf 	inf 	inf 	inf 	inf	-1.40	inf	1.30	inf
+inf 	inf 	inf	-1.30	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.00	inf 	inf 	inf 	inf
+inf 	inf	-2.40	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.50	inf 	inf 	inf 	inf 	inf
+inf	-2.10	inf	-1.00	inf 	inf 	inf 	inf 	inf	-1.40	inf	0.30	inf 	inf 	inf 	inf
+-0.90	inf	-1.30	inf 	inf 	inf 	inf 	inf	-0.60	inf	-0.50	inf 	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/Turner99/tloop.DAT b/gtfold-mfe/data/Turner99/tloop.DAT
new file mode 100644
index 0000000..dda2750
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/tloop.DAT
@@ -0,0 +1,30 @@
+GGGGAC	-3.00
+GGUGAC	-3.00
+CGAAAG	-3.00
+GGAGAC	-3.00
+CGCAAG	-3.00
+GGAAAC	-3.00
+CGGAAG	-3.00
+CUUCGG	-3.00
+CGUGAG	-3.00
+CGAAGG	-2.50
+CUACGG	-2.50
+GGCAAC	-2.50
+CGCGAG	-2.50
+UGAGAG	-2.50
+CGAGAG	-2.00
+AGAAAU	-2.00
+CGUAAG	-2.00
+CUAACG	-2.00
+UGAAAG	-2.00
+GGAAGC	-1.50
+GGGAAC	-1.50
+UGAAAA	-1.50
+AGCAAU	-1.50
+AGUAAU	-1.50
+CGGGAG	-1.50
+AGUGAU	-1.50
+GGCGAC	-1.50
+GGGAGC	-1.50
+GUGAAC	-1.50
+UGGAAA	-1.50
diff --git a/gtfold-mfe/data/Turner99/tstackh.DAT b/gtfold-mfe/data/Turner99/tstackh.DAT
new file mode 100644
index 0000000..7648650
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/tstackh.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.30	-0.50	-0.30	-0.30
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.10	-0.20	-1.50	-0.20
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.10	-1.20	-0.20	0.20
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.30	-0.30	-0.60	-1.10
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.50	-1.50	-1.40	-1.80	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.00	-0.90	-2.90	-0.80	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.20	-2.00	-1.60	-1.10	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.70	-1.40	-1.80	-2.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-1.10	-1.50	-1.30	-2.10	inf 	inf 	inf 	inf	0.20	-0.50	-0.30	-0.30
+inf 	inf 	inf 	inf	-1.10	-0.70	-2.40	-0.50	inf 	inf 	inf 	inf	-0.10	-0.20	-1.50	-0.20
+inf 	inf 	inf 	inf	-2.40	-2.90	-1.40	-1.20	inf 	inf 	inf 	inf	-0.90	-1.10	-0.30	0.00
+inf 	inf 	inf 	inf	-1.90	-1.00	-2.20	-1.50	inf 	inf 	inf 	inf	-0.30	-0.30	-0.40	-1.10
+-0.50	-0.30	-0.60	-0.50	inf 	inf 	inf 	inf	-0.50	-0.30	-0.60	-0.50	inf 	inf 	inf 	inf
+-0.20	-0.10	-1.20	-0.00	inf 	inf 	inf 	inf	-0.20	-0.10	-1.70	0.00	inf 	inf 	inf 	inf
+-1.40	-1.20	-0.70	-0.20	inf 	inf 	inf 	inf	-0.80	-1.20	-0.30	-0.70	inf 	inf 	inf 	inf
+-0.30	-0.10	-0.50	-0.80	inf 	inf 	inf 	inf	-0.60	-0.10	-0.60	-0.80	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/Turner99/tstacki.DAT b/gtfold-mfe/data/Turner99/tstacki.DAT
new file mode 100644
index 0000000..dd7b5da
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/tstacki.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	0.70	0.70	-0.40	0.70
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.70
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.40	0.70	0.70	0.70
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.00
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.00	-0.00	-1.10	-0.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.10	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.70	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-0.00	-0.00	-1.10	-0.00	inf 	inf 	inf 	inf	0.70	0.70	-0.40	0.70
+inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.70
+inf 	inf 	inf 	inf	-1.10	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf	-0.40	0.70	0.70	0.70
+inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.70	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.00
+0.70	0.70	-0.40	0.70	inf 	inf 	inf 	inf	0.70	0.70	-0.40	0.70	inf 	inf 	inf 	inf
+0.70	0.70	0.70	0.70	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.70	inf 	inf 	inf 	inf
+-0.40	0.70	0.70	0.70	inf 	inf 	inf 	inf	-0.40	0.70	0.70	0.70	inf 	inf 	inf 	inf
+0.70	0.70	0.70	0.00	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.00	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/Turner99/tstackm.DAT b/gtfold-mfe/data/Turner99/tstackm.DAT
new file mode 100644
index 0000000..b850f80
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/tstackm.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf	-1.00	inf 	inf 	inf	-1.00	inf 	inf 	inf	-2.20	-0.80	-1.00	-0.80	-0.90
+inf 	inf	-1.50	inf 	inf 	inf	-1.50	inf 	inf 	inf	-2.70	inf	-0.60	-0.70	-2.20	-0.70
+inf	-1.50	inf	-1.00	inf	-1.50	inf	-1.00	inf	-2.70	inf	-2.20	-0.80	-2.10	-0.80	-0.80
+-1.00	inf	-1.50	inf	-1.00	inf	-1.50	inf	-2.20	inf	-2.70	inf	-1.10	-0.80	-1.10	-0.80
+inf 	inf 	inf	-1.00	inf 	inf 	inf	-1.00	-1.70	-1.70	-1.70	-1.70	inf 	inf 	inf	-1.00
+inf 	inf	-1.50	inf 	inf 	inf	-1.50	inf	-1.00	-1.10	-3.30	-0.80	inf 	inf	-1.50	inf
+inf	-1.50	inf	-1.00	inf	-1.50	inf	-1.00	-1.70	-2.40	-1.70	-1.70	inf	-1.50	inf	-1.00
+-1.00	inf	-1.50	inf	-1.00	inf	-1.50	inf	-1.60	-1.40	-1.60	-1.20	-1.00	inf	-1.50	inf
+inf 	inf 	inf	-2.20	-1.10	-1.50	-1.30	-1.90	inf 	inf 	inf	-1.00	-0.80	-1.00	-0.80	-1.30
+inf 	inf	-2.70	inf	-1.10	-0.70	-3.40	-0.50	inf 	inf	-1.50	inf	-0.60	-0.70	-2.50	-0.70
+inf	-2.70	inf	-2.20	-1.60	-3.30	-1.40	-1.30	inf	-1.50	inf	-1.00	-0.80	-2.10	-0.80	-0.80
+-2.20	inf	-2.70	inf	-1.70	-1.00	-2.00	-0.70	-1.00	inf	-1.50	inf	-1.40	-0.80	1.30	-0.80
+-1.00	-0.80	-1.10	-1.30	inf 	inf 	inf	-1.00	-1.00	-0.80	-1.10	-1.00	inf 	inf 	inf	-2.00
+-0.70	-0.60	-2.40	-0.50	inf 	inf	-1.50	inf	-0.70	-0.60	-1.50	-0.50	inf 	inf	-2.50	inf
+-1.10	-2.10	-1.20	-1.00	inf	-1.50	inf	-1.00	-0.70	-1.40	-0.80	0.30	inf	-2.50	inf	-2.00
+-0.90	-0.60	-1.40	-0.50	-1.00	inf	-1.50	inf	-0.50	-0.60	-0.50	-0.50	-2.00	inf	-2.50	inf
diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h
index 20a0708..f8fdc78 100644
--- a/gtfold-mfe/include/loader.h
+++ b/gtfold-mfe/include/loader.h
@@ -27,16 +27,16 @@
 
 void readThermodynamicParameters(const char *userdatadir,bool userdatalogic);
 
-int initStackValues(std::string fileName);
-int initMiscloopValues(std::string fileName);
-int initDangleValues(std::string fileName);
-int initLoopValues(std::string fileName);
-int initTstkhValues(std::string fileName);
-int initTstkiValues(std::string fileName);
-int initTloopValues(std::string fileName);
-int initInt21Values(std::string fileName);
-int initInt22Values(std::string fileName);
-int initInt11Values(std::string fileName);
+int initStackValues(const std::string& fileName, const std::string& dirPath);
+int initMiscloopValues(const std::string& fileName, const std::string& dirPath);
+int initDangleValues(const std::string& fileName, const std::string& dirPath);
+int initLoopValues(const std::string& fileName, const std::string& dirPath);
+int initTstkhValues(const std::string& fileName, const std::string& dirPath);
+int initTstkiValues(const std::string& fileName, const std::string& dirPath);
+int initTloopValues(const std::string& fileName, const std::string& dirPath);
+int initInt21Values(const std::string& fileName, const std::string& dirPath);
+int initInt22Values(const std::string& fileName, const std::string& dirPath);
+int initInt11Values(const std::string& fileName, const std::string& dirPath);
 
 extern std::string EN_DATADIR;
 
diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 1bfbb5a..79cb62b 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -10,18 +10,29 @@ using namespace std;
 
 extern bool ILSA;
 extern bool NOISOLATE;
+<<<<<<< .merge_file_N36WcI
 extern bool USERDATA;
 extern bool PARAMS;
+=======
+//extern bool USERDATA;
+//extern bool PARAMS;
+extern bool LIMIT_DISTANCE;
+>>>>>>> .merge_file_qTispI
 extern bool BPP_ENABLED;
 extern bool SUBOPT_ENABLED;
 extern bool CONS_ENABLED;
 extern bool VERBOSE;
+<<<<<<< .merge_file_N36WcI
 extern bool SHAPE_ENABLED;
+=======
+extern bool PARAM_DIR;
+>>>>>>> .merge_file_qTispI
 
 extern string seqfile;
 extern string constraintsFile;
 extern string shapeFile;
 extern string outputFile;
+extern string paramDir;
 
 extern int suboptDelta;
 extern int nThreads;
diff --git a/gtfold-mfe/scripts/dats2DATs.py b/gtfold-mfe/scripts/dats2DATs.py
new file mode 100755
index 0000000..e488b84
--- /dev/null
+++ b/gtfold-mfe/scripts/dats2DATs.py
@@ -0,0 +1,53 @@
+import os, sys, re
+
+# read in arguments from command line
+if len(sys.argv) != 3:
+    print "need directory names"
+    print "Usage: dats2DATs.py <source_dir> <target_dir>"
+source_dir_name = sys.argv[1]
+target_dir_name = sys.argv[2]
+
+# this function opens a .dat formatted file and returns a string with .DAT file format
+def dat2DAT(file_name, num_cols, num_rows):
+	num_data_rows_seen = 0
+	DAT_content = ""
+	file = open(file_name,'r')
+
+	for line in file.readlines() :
+		if re.match('[\d\-\.\s]+\n', line) and not re.match('[\s\-]*\n', line):
+			# If the line contains only digits, negative signs, dots, and white space
+			# and does not contain ony dashes and whitespace convert the line to .DAT format
+			DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line)
+			DAT_line = re.sub('\s+\-','\t-', DAT_line)
+			DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line)
+			DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line)
+			DAT_line = DAT_line.lstrip().rstrip()+"\n"
+			DAT_content += DAT_line
+
+	return DAT_content
+
+for file_prefix in ["dangle", "int11", "int21", "int22", "loop", "miscloop", "sint2", "sint4", "stack", "tstackh", "tstacki", "tstackm"]:
+	file_name = source_dir_name+"/"+file_prefix+".dat"
+	output_file_path = target_dir_name+"/"+file_prefix+".DAT"
+	output_file = open(output_file_path, 'w')
+	output_file.write(dat2DAT(file_name, 16, 16))
+	#print dat2DAT(file_name, 16, 16)
+
+file_name = source_dir_name+"/tloop.dat"
+output_file_path = target_dir_name+"/tloop.DAT"
+DAT_content = ""
+file = open(file_name,'r')
+
+for line in file.readlines() :
+	if re.match('[\d\-\.\sACGU]+\n', line) and not re.match('[\s\-]*\n', line):
+		# If the line contains only digits, negative signs, dots, and white space or ACGU
+		# and does not contain ony dashes and whitespace convert the line to .DAT format
+		DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line)
+		DAT_line = re.sub('\s+\-','\t-', DAT_line)
+		DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line)
+		DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line)
+		DAT_line = DAT_line.lstrip().rstrip()+"\n"
+		DAT_content += DAT_line
+output_file = open(output_file_path, 'w')
+output_file.write(DAT_content)
+	
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 59a1824..65ac5f0 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -45,12 +45,22 @@ int calculate(int len, int nThreads) {
 #endif
 		for (i = 1; i <= len - b; i++) {
 			j = i + b;
+<<<<<<< .merge_file_vD135I
 			int flag = 0, newWM = INFINITY_; 
 			if (canPair(RNA[i], RNA[j])) {
 				flag = 1;
 				int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
 				int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack
 				if (j-i > 6) { // Internal Loop BEGIN
+=======
+			int newWM = INFINITY_; 
+
+			if (canPair(RNA[i], RNA[j])) {
+				int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin
+				int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack
+				
+				if (j-i > 6) {  // Internal Loop BEGIN
+>>>>>>> .merge_file_o95D9I
 					int p=0, q=0;
 					int VBIij = INFINITY_;
 					for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
@@ -72,10 +82,17 @@ int calculate(int len, int nThreads) {
 					int VMij, VMijd, VMidj, VMidjd;
 					VMij = VMijd = VMidj = VMidjd = INFINITY_;
 					for (h = i+TURN+1; h <= j-1-TURN; h++) { 
+<<<<<<< .merge_file_vD135I
 						VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); 
 						VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); 
 						VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); 
 						VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); 
+=======
+						VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1));		
+						VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1));	
+						VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2));	
+						VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2));	
+>>>>>>> .merge_file_o95D9I
 					}
 					int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
 					int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
@@ -91,10 +108,16 @@ int calculate(int len, int nThreads) {
 			if (j-i > 4) { // WM BEGIN
 				int h; 
 				for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
+<<<<<<< .merge_file_vD135I
 					//ZS: This sum corresponds to when i,j are NOT paired with each other.
 					//So we need to make sure only terms where i,j aren't pairing are considered. 
 					newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM;
 				}
+=======
+					newWM = MIN(newWM, WMU(i,h-1) + WML(h,j));
+				}
+
+>>>>>>> .merge_file_o95D9I
 				newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
 				newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
 				newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index a2f1042..c8d9055 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -44,7 +44,12 @@ bool compare_bp(const std::pair<int,int>& o1,
 
 
 static int load_constraints(const char* constr_file, int verbose=0) {
+<<<<<<< .merge_file_FGxfkH
 	
+=======
+    fprintf(stdout, "- Running with constraints %s\n", constr_file);
+	std::ifstream cfcons;
+>>>>>>> .merge_file_mYvNsH
 
 	fprintf(stdout, "- Running with constraints\n");
 
@@ -106,12 +111,13 @@ static int load_constraints(const char* constr_file, int verbose=0) {
             pit++;
         }
     }
-
+	/*
 	std::vector<std::pair<int,int> > v_fbp;
 	for(it=0; it< nFBP; it++) {
 		for(int k=1;k<= FBP[it][2];k++)
 			v_fbp.push_back(std::pair<int,int>(FBP[it][0]+k-1, FBP[it][1]-k+1));
 	}
+<<<<<<< .merge_file_FGxfkH
 	
 	if(v_fbp.size()>1){
 		std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
@@ -126,6 +132,21 @@ static int load_constraints(const char* constr_file, int verbose=0) {
 	}
 
   
+=======
+
+	if (v_fbp.size() > 1) {
+		std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
+		for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) {
+			if (v_fbp[ii].second <= v_fbp[ii+1].second) {
+				fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n");
+				exit(-1);
+			}
+
+		}
+	}
+*/
+
+>>>>>>> .merge_file_mYvNsH
     return 0;
 }
 
@@ -170,6 +191,7 @@ int init_constraints(const char* constr_file,int length) {
 			}
 		}
 	}
+<<<<<<< .merge_file_FGxfkH
 
 	
 	//ZS: set prohibited basepairs
@@ -188,6 +210,13 @@ int init_constraints(const char* constr_file,int length) {
 			if(PBP[it][2] < 1 || PBP[it][1] == 0){
 				printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
 				continue;
+=======
+	if (nFBP != 0) {
+		for (it = 0; it < nFBP; it++) {
+			if (FBP[it][2] < 1) {
+				printf("Invalid entry (%d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
+				continue; // TODO: report and exit here
+>>>>>>> .merge_file_mYvNsH
 			}
 		
 			for(k = 1; k <= PBP[it][2]; k++){
@@ -222,6 +251,7 @@ int init_constraints(const char* constr_file,int length) {
 			for(k = 1; k<=FBP[it][2]; k++){
 				int i1 = FBP[it][0]+k-1;
 				int j1 = FBP[it][1]-k+1;
+<<<<<<< .merge_file_FGxfkH
 				if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){
 					printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
 					continue;			
@@ -274,6 +304,18 @@ int init_constraints(const char* constr_file,int length) {
 					BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1;
 					
 				}
+=======
+				if (!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])) {
+					printf("Can't constrain (%d,%d)\n", FBP[it][0]+k-1, FBP[it][1]-k+1);
+					continue; // TODO: report and exit here
+				}
+				if (j1-i1 < TURN) {
+					printf("Can't constrain (%d,%d)\n", i1, j1);
+					continue; // TODO: report and exit here
+				}	
+				BP[FBP[it][0]+k-1] = FBP[it][1]+1-k;
+				BP[FBP[it][1]+1-k] = FBP[it][0]+k-1;
+>>>>>>> .merge_file_mYvNsH
 			}
 		}
 	}
@@ -406,10 +448,23 @@ void print_constraints(int len) {
  
 }
 
+<<<<<<< .merge_file_FGxfkH
 int forcePair(int i, int j) {
 //ZS: this function returns true if the pair i-j is forced.
 	if (CONS_ENABLED) 
 		return BP(i,j)==1;
+=======
+
+
+int is_ss(int i, int j) {
+	if (CONS_ENABLED) {
+		int it;
+		for (it = i + 1; it < j; it++) {
+			if (BP[it] > 0) return 1;
+		}
+		return 0;
+	}
+>>>>>>> .merge_file_mYvNsH
 	else
 		return 0;
 }
diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 6d0f375..1118794 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -17,8 +17,9 @@ int *VM;
 int **WM; 
 int *indx; 
 
-void create_tables(int len)
-{	
+int alloc_flag = 0;
+
+void create_tables(int len) {	
 	V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
 	if (V == NULL) {
 		perror("Cannot allocate variable 'V'");
@@ -75,12 +76,13 @@ void create_tables(int len)
 		exit(-1);
 	}
 
+	alloc_flag = 1;
+	
 	init_tables(len);
 }
 
 
-void init_tables(int len) 
-{
+void init_tables(int len) {
 	int i, j, LLL;
 	
 	for (i = 0; i <= len; i++) {
@@ -106,21 +108,21 @@ void init_tables(int len)
 	return;
 }
 
-void free_tables(int len)
-{
-	free(indx);
-	
-	int i;
-	for (i = 0; i <= len; i++)
-	         free(WM[i]);
-	free(WM);
-
-	free(VM);
-	free(VBI);
-	free(V);
-	free(VV);
-	free(VV1);
-	free(W);
+void free_tables(int len) {
+	if (alloc_flag == 1) {
+		free(indx);
+
+		int i;
+		for (i = 0; i <= len; i++) free(WM[i]);
+		free(WM);
+
+		free(VM);
+		free(VBI);
+		free(V);
+		free(VV);
+		free(VV1);
+		free(W);
+	}
 }
 
 
@@ -217,8 +219,7 @@ inline int eL(int i, int j, int ip, int jp) {
 	return energy;
 }
 
-inline int eH(int i, int j) 
-{
+inline int eH(int i, int j) {
 	/*  Hairpin loop for all the bases between i and j */
 	/*  size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */
 	int size;
@@ -323,8 +324,7 @@ inline int eH(int i, int j)
 	return energy;
 }
 
-inline int eS(int i, int j) 
-{
+inline int eS(int i, int j) {
 	int energy;
 	/*  not sure about eparam[1], come from MFold.. = 0 */
 	energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i+1], RNA[j-1])] + eparam[1] 
diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index f916f3c..c68ee22 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -20,6 +20,7 @@
 #include <iostream>
 #include <fstream>
 #include <istream>
+#include <sstream>
 #include <math.h>
 
 #include <cstring>
@@ -75,198 +76,102 @@ int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loo
 float prelog;
 
 void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
-
-#ifndef GENBIN
-	if (!userdatalogic) 
-	{
+	if (!userdatalogic) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
 		EN_DATADIR += userdatadir;
-	} else 
-	{
+	} else {
 		EN_DATADIR.assign(userdatadir);
 	}
-#else
-	EN_DATADIR = "data";
-#endif
 
 	//Handle the ending forward slash case
 	if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') {
 		EN_DATADIR += "/";
 	}
 
-	initMiscloopValues("miscloop.dat");
-	// miscloop.dat - Miscellaneous loop file
-	initStackValues("stack.dat");
-	// stack.dat - free energies for base pair stacking
-	initDangleValues("dangle.dat");
-	// dangle.dat - single base stacking free energies
-	initLoopValues("loop.dat");
-	// loop.dat - entropic component for internal, bulge and hairpin loops.
-	initTstkhValues("tstackh.dat");
-	// tstackh.dat - free energies for terminal mismatch stacking in hairpin loops
-	initTstkiValues("tstacki.dat");
-	// tstacki.dat - free energies for terminal mismatch stacking in internal loops
-	initTloopValues("tloop.dat");
-	// tloop.dat - free energies for distinguished tetraloops
-	initInt21Values("int21.dat");
-	// int21.dat - free energies for 2 x 1 interior loops
-	initInt22Values("int22.dat");
-	// int22.dat - free energies for 2 x 2 interior loops
-	initInt11Values("int11.dat");
-	// int11.dat - free energies for 1 x 1 interior loops
+	initMiscloopValues("miscloop.DAT", EN_DATADIR);
+	initDangleValues("dangle.DAT", EN_DATADIR);
+	initStackValues("stack.DAT", EN_DATADIR);
+	initLoopValues("loop.DAT", EN_DATADIR);
+	initTstkhValues("tstackh.DAT", EN_DATADIR);
+	initTstkiValues("tstacki.DAT", EN_DATADIR);
+	initTloopValues("tloop.DAT", EN_DATADIR);
+	initInt21Values("int21.DAT", EN_DATADIR);
+	initInt22Values("int22.DAT", EN_DATADIR);
+	initInt11Values("int11.DAT", EN_DATADIR);
 }
 
+int initStackValues(const string& fileName, const string& dirPath)  { 
+	std::string filePath;
+	std::ifstream cf;
 
- int initStackValues(string fileName) {
-
-	ifstream cf; //cf = current file
-	int i, j, k, l;
-	int ii, jj, kk, ll;
-	int index;
-	char currentLine[256];
-	string currentString;
-	string s;
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
 
-	// Initialize the array with INFINITY
-	for (i = 0; i < 4; i++) {
-		for (j = 0; j < 4; j++) {
-			for (k = 0; k < 4; k++) {
-				for (l = 0; l < 4; l++) {
+	for (int i = 0; i < 4; i++) {
+		for (int j = 0; j < 4; j++) {
+			for (int k = 0; k < 4; k++) {
+				for (int l = 0; l < 2; l++) {
 					stack[fourBaseIndex(i,j,k,l)] = INFINITY_;
 				}
 			}
 		}
 	}
-
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-
-	// Read the thermodynamic parameters.
-	// The 24 first lines are junk we don't need
-	for (index = 1; index <= 15; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	i = 0;
-	kk = 0;
-	ii = 0;
-	jj = 0;
-	ll = 0;
-
-	while (i < 16) {
-
-		if (i % 4 == 0)
-			for (index = 1; index < 9; index++)
-				cf.getline(currentLine, 256);
-
-		cf.getline(currentLine, 256);
-		s = currentLine;
-		j = 0;
-
-		ll = 0;
-		jj = 0;
-
-		int z = 0;
-		int r = 0;
-
-		while (s[z] != '\0') {
-
-			if (s[z] == ' ')
-				z++;
-
-			else if (s[z] == '.') {
-				z++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
-				r++;
-				if (r % 4 == 0)
-					jj++;
-			} else {
-				char value[10];
-				int x = 0;
-
-				while (s[z] != ' ' && s[z] != '\0') {
-					value[x++] = s[z++];
-				}
-
-				value[x] = '\0';
-
-				int temp = (int) floor(100.0 * atof(value) + .5);
-				stack[fourBaseIndex(ii,jj,kk,ll)] = temp;
-				r++;
-				z++;
-				if (r % 4 == 0)
-					jj++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
+	
+	int count = 0;
+
+	while (cf.good()) {
+		int i, j, k, l;
+		
+		std::string line;
+		std::stringstream ss;
+
+		getline(cf, line);
+		ss << line;
+		if (line.empty()) continue;
+
+		i = count/4;
+		k = count%4;
+		
+		for (int cols = 0; cols < 16; cols++) {
+			std::string val;
+			ss >> val;
+			j = cols/4;
+			l = cols%4; 		
+			if (!(val == "inf")) {
+				stack[fourBaseIndex(i,j,k,l)]  = (int) floor(100.0 * atof(val.c_str()) + .5);
 			}
-		}
-		i++;
-		if (!(i % 4))
-			ii++;
-
-		/*    jj = 1; */
-		kk = (i % 4);
-
+		}	
+		++count;
 	}
-	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
+	
 	return 0;
 }
 
- int initMiscloopValues(string fileName) {
-	/*
-	 miscloop.dat - Miscellaneous loop file. Contains :
-	 1. Extrapolation for large loops based on polymer theory
-	 2. Asymmetric internal loop correction parameters.
-	 3. the f(m) array (see Ninio for details)
-	 4. Paremeters for multibranch loops
-	 5. Paremeters for multibranch loops (for efn2 only)
-	 6. Terminal AU or GU penalty
-	 7. Bonus for GGG hairpin
-	 8,9,10. C hairpin rules: a) slope  b) intercept c) value for size 3
-	 11. Intermolecular initiation free energy
-	 12. GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on or off)
-	 */
+int initMiscloopValues(const string& fileName, const string& dirpath) {
+	std::string filePath;
+	std::ifstream cf;
 
-	char currentWord[256];
-	string s;
-	ifstream cf; //cf = current file
+	filePath = dirpath + fileName;
+	cf.open(filePath.c_str(), ios::in);
 
-	fileName = EN_DATADIR + fileName;
-#if 0
-	cout << "Getting miscloop values from " << fileName << endl;
-#endif
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
+	if (!cf.good()) {
+		std::cerr << "File open failed - " << filePath << std::endl;
+		cf.close();
+		exit(-1);		
 	}
-	s = "";
 
-	cf >> currentWord;
+	char currentWord[256];
+	std::string s;
+
 	for (int index = 1; index < 13; index++) { // There are total 12 values to read in.
-		while (strcmp(currentWord, "-->")) {
-			cf >> currentWord;
-		}
 		if (index == 1) {
 			cf >> currentWord;
 			prelog = 100 * atof(currentWord);
-			//cout << "prelog = " << prelog << endl;
 		}
 		if (index == 2) {
 			cf >> currentWord;
 			maxpen = int(atof(currentWord) * 100.0 + .5);
-			//cout << "maxpen = " << maxpen << endl;
 		}
 		if (index == 3) {
 			for (int count = 1; count <= 4; count++) {
@@ -292,7 +197,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 				s = currentWord;
 				multConst[count - 1] = (int) (atof(s.c_str()) * 100 + 0.5);
 				eparam[table[count]] = (int) (atof(s.c_str()) * 100 + 0.5);
-				//cout << "\n multi " << multConst[count-1];
 			}
 		}
 		if (index == 5) {
@@ -336,150 +240,86 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 		}
 	}
 
-	cf.close();
+	cf.close();	 
+
 	return 0;
 }
 
- int initDangleValues(string fileName) {
-	ifstream cf; //cf = current file
-	char currentLine[256];
-	string currentString;
-	string s;
-	int index;
-	int i, j, k, l;
-	int ii, jj, kk, ll; // ii = 1st base, jj = 2nd base, kk = 3rd base, ll = 1 up or 2 low
-
-	for (i = 0; i < 4; i++) {
-		for (j = 0; j < 4; j++) {
-			for (k = 0; k < 4; k++) {
-				for (l = 0; l < 2; l++) {
+int initDangleValues(const std::string& fileName, 
+					  const std::string& dirPath) { 
+	std::string filePath;
+	std::ifstream cf;
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+
+	for (int i = 0; i < 4; i++) {
+		for (int j = 0; j < 4; j++) {
+			for (int k = 0; k < 4; k++) {
+				for (int l = 0; l < 2; l++) {
 					dangle[i][j][k][l] = INFINITY_;
 				}
 			}
 		}
 	}
-
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-
-	// The 8 first lines are junk
-	for (index = 1; index <= 8; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	// 8 lines of useful data
-	i = 0;
-	ii = 0;
-	jj = 0;
-	kk = 0;
-	ll = 0;
-
-	while (i < 8) {
-
-		if (i != 0)
-			for (index = 1; index < 9; index++)
-				cf.getline(currentLine, 256);
-
-		cf.getline(currentLine, 256);
-		s = currentLine;
-		j = 0;
-
-		jj = 0;
-
-		int z = 0;
-		int r = 0;
-
-		while (s[z] != '\0') {
-
-			if (s[z] == ' ')
-				z++;
-
-			else if (s[z] == '.') {
-				z++;
-				kk++;
-				if (kk == 4)
-					kk = 0;
-				r++;
-				if (r % 4 == 0)
-					jj++;
-			} else {
-				char value[10];
-				int x = 0;
-
-				while (s[z] != ' ' && s[z] != '\0') {
-					value[x++] = s[z++];
-				}
-
-				value[x] = '\0';
-
-				int temp = (int) floor(100.0 * atof(value) + .5);
-				//if ( temp == 0 )	temp = -1;
-				dangle[ii][jj][kk][ll] = temp;
-				//cout<< "\n " << temp << "  "<< ii <<" "<< jj << " "<< kk << " " << ll ;
-				r++;
-				z++;
-				if (r % 4 == 0)
-					jj++;
-				kk++;
-				if (kk == 4)
-					kk = 0;
-
+	
+	int count = 0;
+
+	while (cf.good()) {
+		int i, j, k, l;
+		
+		std::string line;
+		std::stringstream ss;
+
+		getline(cf, line);
+		ss << line;
+		if (line.empty()) continue;
+
+		i = count%4;
+		l = count/4;
+		
+		for (int cols = 0; cols < 16; cols++) {
+			std::string val;
+
+			j = cols/4;
+			ss >> val;
+			k = cols%4; 		
+			if (!(val == "inf")) {
+				dangle[i][j][k][l] = (int) floor(100.0 * atof(val.c_str()) + .5);
 			}
-
-		}
-
-		i++;
-		ii++;
-		if (ii == 4)
-			ii = 0;
-
-		if (i == 4)
-			ll = 1;
-
+		}	
+		++count;
 	}
-	cf.close();
-
-#if 0
-	cout << " Done!" << endl;
-#endif
+	
 	return 0;
 }
 
- int initLoopValues(string fileName) {
+int initLoopValues( const string& fileName, const string& dirPath) {
 	// algorithm.c, line 2996
 	ifstream cf; // current file
-	char currentLine[256];
+	std::string filePath;
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+	
+	//char currentLine[256];
 	char currentWord[256];
 	string s;
-	int index;
+	int index= 0;
 	int tempValue = 0;
 
-#if 0
-	cout << "Getting loop values...";
-#endif
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
 	if (cf.fail()) {
 		cerr << "File open failed" << endl;
 		exit(-1);
 	}
-	// The 4 first lines are junk we don't need
-	for (index = 1; index <= 4; index++) {
-		cf.getline(currentLine, 256);
-		//s = currentLine;
-		//cout << s << endl;
-	}
+
 	while (index < 30) {
 		for (int j = 1; j <= 4; j++) {
 			cf >> currentWord;
 			if (j == 1)
 				index = atoi(currentWord);
 			if (j > 1) {
-				if (strcmp(currentWord, ".")) {
+				if (strcmp(currentWord, "inf")) {
 					tempValue = (int) (100 * atof(currentWord) + 0.5);
 				} else {
 					tempValue = INFINITY_;
@@ -500,228 +340,111 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	}
 	cf.close();
 
-#if 0
-	cout << " Done!" << endl;
-#endif
 	return 0;
 }
 
- int initTstkhValues(string fileName) {
-	ifstream cf; //cf = current file
-	int i, j, k, l;
-	int ii, jj, kk, ll;
-	int index;
-	char currentLine[256];
-	string currentString;
-	string s;
+int initTstkhValues(const std::string& fileName, const std::string& dirPath) {
+	std::string filePath;
+	std::ifstream cf;
 
-	for (i = 0; i < 4; i++) {
-		for (j = 0; j < 4; j++) {
-			for (k = 0; k < 4; k++) {
-				for (l = 0; l < 4; l++) {
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+
+	for (int i = 0; i < 4; i++) {
+		for (int j = 0; j < 4; j++) {
+			for (int k = 0; k < 4; k++) {
+				for (int l = 0; l < 2; l++) {
 					tstkh[fourBaseIndex(i,j,k,l)] = INFINITY_;
 				}
 			}
 		}
 	}
-
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-
-	// The 27 first lines are junk we don't need
-	for (index = 1; index <= 15; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	i = 0;
-	kk = 0;
-	ii = 0;
-	jj = 0;
-	ll = 0;
-
-	while (i < 16) {
-
-		if (i % 4 == 0)
-			for (index = 1; index < 9; index++)
-				cf.getline(currentLine, 256);
-
-		cf.getline(currentLine, 256);
-		s = currentLine;
-		j = 0;
-
-		ll = 0;
-		jj = 0;
-
-		int z = 0;
-		int r = 0;
-
-		while (s[z] != '\0') {
-
-			if (s[z] == ' ')
-				z++;
-
-			else if (s[z] == '.') {
-				z++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
-				r++;
-				if (r % 4 == 0)
-					jj++;
-			}
-
-			else {
-				char value[10];
-				int x = 0;
-
-				while (s[z] != ' ' && s[z] != '\0') {
-					value[x++] = s[z++];
-				}
-
-				value[x] = '\0';
-
-				int temp = (int) floor(100.0 * atof(value) + .5);
-				tstkh[fourBaseIndex(ii,jj,kk,ll)] = temp;
-
-				r++;
-				z++;
-				if (r % 4 == 0)
-					jj++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
+	
+	int count = 0;
+
+	while (cf.good()) {
+		int i, j, k, l;
+		
+		std::string line;
+		std::stringstream ss;
+
+		getline(cf, line);
+		ss << line;
+		if (line.empty()) continue;
+
+		i = count/4;
+		k = count%4;
+		
+		for (int cols = 0; cols < 16; cols++) {
+			std::string val;
+			ss >> val;
+			j = cols/4;
+			l = cols%4; 		
+			if (!(val == "inf")) {
+				tstkh[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5);
 			}
-		}
-		i++;
-		if (!(i % 4))
-			ii++;
-
-		jj = 0;
-		kk = (i % 4);
-
+		}	
+		++count;
 	}
-
-	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
+	
 	return 0;
 }
 
- int initTstkiValues(string fileName) {
-	ifstream cf; //cf = current file
-	int i, j, k, l;
-	int ii, jj, kk, ll;
-	int index;
-	char currentLine[256];
-	string currentString;
-	string s;
 
-	for (i = 0; i < 4; i++) {
-		for (j = 0; j < 4; j++) {
-			for (k = 0; k < 4; k++) {
-				for (l = 0; l < 4; l++) {
+int initTstkiValues(const std::string& fileName, const std::string& dirPath) {
+	std::string filePath;
+	std::ifstream cf;
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+
+	for (int i = 0; i < 4; i++) {
+		for (int j = 0; j < 4; j++) {
+			for (int k = 0; k < 4; k++) {
+				for (int l = 0; l < 2; l++) {
 					tstki[fourBaseIndex(i,j,k,l)] = INFINITY_;
 				}
 			}
 		}
 	}
 
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-
-	// The 27 first lines are junk we don't need
-	for (index = 1; index <= 15; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	i = 0;
-	kk = 0;
-	ii = 0;
-	jj = 0;
-	ll = 0;
-
-	while (i < 16) {
+	int count = 0;
 
-		if (i % 4 == 0)
-			for (index = 1; index < 9; index++)
-				cf.getline(currentLine, 256);
-
-		cf.getline(currentLine, 256);
-		s = currentLine;
-		j = 0;
-
-		ll = 0;
-		jj = 0;
+	while (cf.good()) {
+		int i, j, k, l;
 
-		int z = 0;
-		int r = 0;
+		std::string line;
+		std::stringstream ss;
 
-		while (s[z] != '\0') {
+		getline(cf, line);
+		ss << line;
+		if (line.empty()) continue;
 
-			if (s[z] == ' ')
-				z++;
+		i = count/4;
+		k = count%4;
 
-			else if (s[z] == '.') {
-				z++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
-				r++;
-				if (r % 4 == 0)
-					jj++;
+		for (int cols = 0; cols < 16; cols++) {
+			std::string val;
+			ss >> val;
+			j = cols/4;
+			l = cols%4; 		
+			if (!(val == "inf")) {
+				tstki[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5);
 			}
-
-			else {
-				char value[10];
-				int x = 0;
-
-				while (s[z] != ' ' && s[z] != '\0') {
-					value[x++] = s[z++];
-				}
-
-				value[x] = '\0';
-
-				int temp = (int) floor(100.0 * atof(value) + .5);
-				tstki[fourBaseIndex(ii,jj,kk,ll)] = temp;
-
-				//cout << "\n temp " << temp << " " <<ii << " "<< jj << " "<< kk << " " << ll;
-				r++;
-				z++;
-				if (r % 4 == 0)
-					jj++;
-				ll++;
-				if (ll == 4)
-					ll = 0;
-			}
-		}
-		i++;
-		if (!(i % 4))
-			ii++;
-
-		jj = 0;
-		kk = (i % 4);
-
+		}	
+		++count;
 	}
 
-	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
 	return 0;
 }
 
-//SH: Rewritten as an error was being generated by this function.
- int initTloopValues(string fileName) {
-	ifstream cf;
+int initTloopValues(const std::string& fileName, const std::string& dirPath) {
+	std::string filePath;
+	std::ifstream cf;
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+
 	int count;
 	char currentLine[256];
 	char currentSeqNumbers[7];
@@ -732,20 +455,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 
 	string s, temp;
 
-#if 0
-	cout << "Getting tloop values...";
-#endif
-
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
-		exit(-1);
-	}
-	// skip 2 lines
-	cf.getline(currentLine, 256);
-	cf.getline(currentLine, 256);
-
 	numoftloops = 0;
 
 	while (!cf.eof() && (++(numoftloops) < maxtloop)) {
@@ -759,33 +468,23 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 		for (count = 0; count < 6; count++) {
 			temp = currentLine[count + clindex];
 			currentSeqNumbers[count] = baseToDigit(temp.c_str());
-			//cout << currentSeqNumbers[count];
-			//cout << currentLine[count+1];
 		}
-		//cout << endl;
 		clindex=clindex+7;
 		while(currentLine[clindex]== ' ') clindex++;
 		count = 0;
 		while(currentLine[clindex+count]!=' '&&currentLine[clindex+count]!='\0') {
 			currentValue[count] = currentLine[count + clindex];
 			count++;
-			//cout << currentValue[count];
 		}
-		//cout << endl;
 
 		tloop[numoftloops][0] = (int) atoi(currentSeqNumbers);
 		tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5);
-		//cout << " --  "<< tloop[numoftloops][0] << " | " << tloop[numoftloops][1] << endl;
 	}
 	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
 	return 0;
 }
 
- int initInt22Values(string fileName) {
-
+int initInt22Values(const std::string& fileName, const std::string& dirPath) {
 	//Read the 2x2 internal loops
 	//key iloop22[a][b][c][d][j][l][k][m] =
 	//a j l b
@@ -803,66 +502,36 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 									iloop22[i][j][k][r][q][t][y][z] = INFINITY_;
 
 	ifstream cf;
-	int index, flag;
 	char currentLine[256], currentValue[6];
-	string s, s1, s2, temp;
-	string sre;
 
 	int base[4];
 	int l, m;
 
-#if 0
-	cout << "Getting Int22 values...";
-#endif
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
-	if (cf.fail()) {
-		cerr << "File open failed" << endl;
+	string filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+	if (!cf.good()) {
+		cerr << "File open failed " << endl;
 		exit(-1);
 	}
 
-	// Get rid of the 38 1st lines
-	for (index = 1; index < 28; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	sre = "Y";
-	flag = 0;
-
-	for (index = 1; index <= 36; index++) { // 36 tables 16x16
-		// Go to the beginning of the tables
-		while (!flag) {
-			cf.getline(currentLine, 256);
+	const char* str[] = {"A-U","C-G","G-C","U-A","G-U","U-G"};
+	
 
-			s = currentLine;
+	int outer, inner;
 
-			int z = 0;
-			while (s[z] != '\0') {
+	for (int index = 1; index <= 36; index++) { // 36 tables 16x16
+		std::stringstream ss1;
+		std::string s ;
 
-				if (s[z] == 'Y')
-					flag = 1;
-
-				z++;
-			}
-		}
-		flag = 0;
-
-		// We skip 5 lines
-		for (i = 0; i < 5; ++i) {
-			cf.getline(currentLine, 256);
-		}
- 
-		// get the closing bases
-		cf.getline(currentLine, 256);
-		s1 = currentLine;
-		cf.getline(currentLine, 256);
-		s2 = currentLine;
-		s = s1 + s2;
-
-		int z = 0;
+		outer = (index-1)/6;
+		inner = (index-1)%6;
+		ss1 << str[outer][0] << '-' << str[inner][0] << '-' << str[outer][2] << '-' <<
+			str[inner][2];
+	    ss1 >> s;	
+		
 		int k = 0;
+		int z = 0;
 		while (s[z] != '\0') {
-
 			if (s[z] == 'A')
 				base[k++] = BASE_A;
 			else if (s[z] == 'C')
@@ -871,22 +540,15 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 				base[k++] = BASE_G;
 			else if (s[z] == 'U')
 				base[k++] = BASE_U;
-
 			z++;
 		}
 
-		cf.getline(currentLine, 256);
-
-		//key iloop22[a][b][c][d][j][l][k][m] =
-		//a j l b
-		//c k m d
-
-
 		for (int rowIndex = 1; rowIndex <= 16; rowIndex++) {
+			cf.getline(currentLine, 256);
+			std::stringstream ss;
+			ss << currentLine;
 			for (int colIndex = 1; colIndex <= 16; colIndex++) {
-				cf >> currentValue;
-				// rowIndex = j*4+k
-				// colIndex = l*4+m
+				ss >> currentValue;	
 
 				j = ((rowIndex - 1) - (rowIndex - 1) % 4) / 4;
 				k = (rowIndex - 1) % 4;
@@ -894,23 +556,17 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 				l = ((colIndex - 1) - (colIndex - 1) % 4) / 4;
 				m = (colIndex - 1) % 4;
 
-				iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m]
-				                                                     = (int) floor(100.0 * atof(currentValue) + 0.5);
-				//int temp = (int) floor(100.0*atof(currentValue)+0.5);
-				//printf("\n temp is : %d    %d %d %d %d   %d  %d   %d %d", temp, base[0], base[2], base[1], base[3], j, k, l, m );
+				iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] 
+					= (int) floor(100.0 * atof(currentValue) + 0.5);
 			}
 		}
 	}
 
 	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
 	return 0;
 }
 
- int initInt21Values(string fileName) {
-
+int initInt21Values(const std::string& fileName, const std::string& dirPath) {
 	// 24x6 arrays of 4x4 values
 	//      c
 	//   a     f
@@ -921,7 +577,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	char currentLine[256];
 	string sre;
 	string s, s1, s2;
-	int a, b, c, d, e, f, g, index;
+	int a, b, c, d, e, f, g;
 	int i, j, k, r, q, t, y;
 	int z;
 
@@ -958,87 +614,44 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	base1[6] = BASE_U + 1;
 	base2[6] = BASE_G + 1;
 
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
+	std::string filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
 	if (cf.fail()) {
 		cerr << "File open failed" << endl;
 		exit(-1);
 	}
 
-	// Get rid of the 18 1st lines
-	for (index = 1; index <= 17; index++) {
-		cf.getline(currentLine, 256);
-	}
-
 	i = 1;
-
 	while (i <= 6) {
-
 		j = 1;
-
 		while (j <= 4) {
-
 			k = 1;
-
-			for (index = 1; index <= 10; index++)
-				cf.getline(currentLine, 256);
-
-			s = currentLine;
-
 			while (k <= 4) {
-
 				cf.getline(currentLine, 256);
-
-				s = currentLine;
-
 				r = 0;
-				z = 0;
 				int jj = 1;
 				d = 1;
-				while (s[z] != '\0') {
-
-					if (s[z] == ' ')
-						z++;
-
-					else if (s[z] == '.') {
-						z++;
-						d++;
-						if (d == 5)
-							d = 1;
-						r++;
-						if (r % 4 == 0)
-							jj++;
-					}
-
-					else {
-						char value[10];
-						int x = 0;
-
-						while (s[z] != ' ' && s[z] != '\0') {
-							value[x++] = s[z++];
-						}
-
-						value[x] = '\0';
-
-						int temp = (int) floor(100.0 * atof(value) + .5);
-						a = base1[i];
-						b = base2[i];
-						f = base1[jj];
-						g = base2[jj];
-						c = k;
-						e = j;
-
-						iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1]
-						                                                  = temp;
-						//printf("\n temp %d, a %d , b %d, c %d, d %d, e %d, f %d, g %d", temp, a, b, c, d, e, f, g);
-						r++;
-						z++;
-						if (r % 4 == 0)
-							jj++;
-						d++;
-						if (d == 5)
-							d = 1;
-					}
+
+				std::stringstream ss;
+				ss << currentLine;
+
+				for (z = 1; z <=24 ; z++) {
+					char value[32];
+					ss >> value;
+					int temp = (int) floor(100.0 * atof(value) + .5);
+					a = base1[i];
+					b = base2[i];
+					f = base1[jj];
+					g = base2[jj];
+					c = k;
+					e = j;
+
+					iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1]
+						= temp;
+					r++;
+					if (r % 4 == 0) jj++;
+					d++;
+					if (d == 5) d = 1;
 				}
 				k++;
 			}
@@ -1050,13 +663,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	return 0;
 }
 
- int initInt11Values(string fileName) {
-
-	//Read the 1x1 internal loops
-	//key iloop11[a][b][c][d][j][l][k][m] =
-	//a b c
-	//d e f
-
+int initInt11Values(const std::string& fileName, const std::string& dirPath) {
 	int i, j, k, r, q, t;
 
 	for (i = 0; i < 4; i++)
@@ -1068,37 +675,20 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 							iloop11[i][j][k][r][q][t] = INFINITY_;
 
 	ifstream cf;
-	int index;
 	char currentLine[256];
 	string s;
 	int base1[7];
 	int base2[7];
 
-	//int j, k, l, m;
 	int a, b, c, d, f;
 
-#if 0
-	cout << "Getting Int11 values...";
-#endif
-	fileName = EN_DATADIR + fileName;
-	cf.open(fileName.c_str(), ios::in);
+	std::string filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
 	if (cf.fail()) {
 		cerr << "File open failed" << endl;
 		exit(-1);
 	}
 
-	// Get rid of the 19 1st lines
-	for (index = 1; index <= 17; index++) {
-		cf.getline(currentLine, 256);
-	}
-
-	/*
-	 Structure of the file:
-	 array of 6x6 arrays
-	 Order:
-	 AU CG GC UA GU UG
-	 */
-
 	base1[1] = BASE_A + 1;
 	base2[1] = BASE_U + 1;
 	base1[2] = BASE_C + 1;
@@ -1117,75 +707,38 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 
 	while (k < 6) {
 		k++;
-		index = 0;
-		for (index = 1; index <= 10; index++) {
-			cf.getline(currentLine, 256);
-		}
-
 		i = 0;
 		b = 1;
 
 		while (i < 4) {
-
 			int jj = 1;
 			++i;
 			cf.getline(currentLine, 256);
-			s = currentLine;
-
 			j = 0;
 
 			int r = 0;
-			int z = 0;
 			int e = 1;
-			while (s[z] != '\0') {
-
-				if (s[z] == ' ')
-					z++;
-
-				else if (s[z] == '.') {
-					z++;
-					e++;
-					if (e == 5)
-						e = 1;
-					r++;
-					if (r % 4 == 0)
-						jj++;
-				}
-
-				else {
-					char value[10];
-					int x = 0;
-
-					while (s[z] != ' ' && s[z] != '\0') {
-						value[x++] = s[z++];
-					}
-
-					value[x] = '\0';
+			std::stringstream ss;
+			ss << currentLine;
 
-					int temp = (int) floor(100.0 * atof(value) + .5);
-					a = base1[k];
-					d = base2[k];
-					c = base1[jj];
-					f = base2[jj];
-					iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp;
-					r++;
-					z++;
-					if (r % 4 == 0)
-						jj++;
-					e++;
-					if (e == 5)
-						e = 1;
-				}
+			for (int z=1; z <= 24; ++z) {
+				char value[32];
+				ss >> value;	
+				int temp = (int) floor(100.0 * atof(value) + .5);
+				a = base1[k];
+				d = base2[k];
+				c = base1[jj];
+				f = base2[jj];
+				iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp;
+				r++;
+				if (r % 4 == 0) jj++;
+				e++;
+				if (e == 5) e = 1;
 			}
 			b++;
 		}
 	}
 
 	cf.close();
-#if 0
-	cout << " Done!" << endl;
-#endif
 	return 0;
 }
-
-
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 9294cbf..2c56804 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -94,16 +94,14 @@ int read_sequence_file(const char* filename, std::string& seq) {
 
 	ifstream fs;
 	fs.open(filename, ios::in);
-	if (fs == NULL)
-		return FAILURE;
+	if (!fs.good()) return FAILURE;
 
 	string line;
-	getline(fs, line);
-	while(line.length() > 0) {
+	while(fs.good()) {
+		getline(fs, line);
 		// exclude lines starting with FASTA comment characters
-		if(line[0] != ';' && line[0] != '>')
+		if(line[0] != ';' && line[0] != '>' && line.length() > 0)
 			seq += line;
-		getline(fs, line);
 	}
 
 	fs.close();
@@ -188,7 +186,7 @@ int main(int argc, char** argv) {
 	std::string seq;
 	int energy;
 	double t1;
-
+	
 	print_header();
 
 	parse_options(argc, argv);
@@ -199,7 +197,7 @@ int main(int argc, char** argv) {
 	}
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
-	readThermodynamicParameters("Turner99",false);
+	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR);
 
 	printRunConfiguration(seq);
 	
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 9ded8dd..565ca5d 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -5,8 +5,9 @@ using namespace std;
 
 bool ILSA;
 bool NOISOLATE;
-bool USERDATA;
-bool PARAMS;
+//bool USERDATA;
+//bool PARAMS;
+bool PARAM_DIR = false;
 bool LIMIT_DISTANCE;
 bool BPP_ENABLED;
 bool SUBOPT_ENABLED;
@@ -16,8 +17,13 @@ bool SHAPE_ENABLED = false;
 
 string seqfile = "";
 string constraintsFile = "";
+<<<<<<< .merge_file_vAQXEJ
 string outputFile = "";
 string shapeFile = "";
+=======
+string outputFile = ""; 
+string paramDir = "Turner99"; // default value
+>>>>>>> .merge_file_058DyL
 
 int suboptDelta = -1;
 int nThreads = -1;
@@ -37,7 +43,8 @@ void help() {
 
     printf("   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n");
     printf("                        limit is given, base pairs can be over any distance\n");
-    printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
+    printf("   -p  --paramdir DIR   Path to directory from where parameters are to be read\n");
+   	printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
     printf("   -t, --threads num    Limit number of threads used\n");
 
@@ -89,7 +96,15 @@ void parse_options(int argc, char** argv) {
 					outputFile = argv[++i];
 				else
 					help();
-			} else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
+			} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+				if(i < argc) {
+					paramDir = argv[++i];
+					PARAM_DIR = true;
+				}
+				else
+					help();
+			}
+		   	else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
 				if(i < argc)
 					nThreads = atoi(argv[++i]);
 				else
@@ -189,7 +204,6 @@ void printRunConfiguration(string seq) {
 
 	printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str());
 	printf("- input file: %s\n", seqfile.c_str());
-	printf("  - sequence length: %d\n", (int)seq.length());
-	printf("  - sequence contents: %s\n", seq.c_str());
+	printf("- sequence length: %d\n", (int)seq.length());
 	printf("- output file: %s\n", outputFile.c_str());
 }

From da4c291ef2289d3ac6aa134b2af16c1e5f985b1a Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Wed, 25 May 2011 15:49:53 +0200
Subject: [PATCH 133/282] Fixed merge errors, should compile now

---
 gtfold-mfe/include/options.h   |  8 -----
 gtfold-mfe/src/.deps/loader.Po |  7 +++-
 gtfold-mfe/src/algorithms.c    | 24 +-------------
 gtfold-mfe/src/constraints.cc  | 58 ++--------------------------------
 gtfold-mfe/src/options.cc      |  5 +--
 gtfold-mfe/src/traceback.c     |  2 +-
 6 files changed, 11 insertions(+), 93 deletions(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 79cb62b..ec0ff7f 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -10,23 +10,15 @@ using namespace std;
 
 extern bool ILSA;
 extern bool NOISOLATE;
-<<<<<<< .merge_file_N36WcI
-extern bool USERDATA;
-extern bool PARAMS;
-=======
 //extern bool USERDATA;
 //extern bool PARAMS;
 extern bool LIMIT_DISTANCE;
->>>>>>> .merge_file_qTispI
 extern bool BPP_ENABLED;
 extern bool SUBOPT_ENABLED;
 extern bool CONS_ENABLED;
 extern bool VERBOSE;
-<<<<<<< .merge_file_N36WcI
 extern bool SHAPE_ENABLED;
-=======
 extern bool PARAM_DIR;
->>>>>>> .merge_file_qTispI
 
 extern string seqfile;
 extern string constraintsFile;
diff --git a/gtfold-mfe/src/.deps/loader.Po b/gtfold-mfe/src/.deps/loader.Po
index 290868e..a00ed8b 100644
--- a/gtfold-mfe/src/.deps/loader.Po
+++ b/gtfold-mfe/src/.deps/loader.Po
@@ -74,7 +74,8 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \
  /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
  /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \
  /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \
- /usr/include/c++/4.4/bits/fstream.tcc /usr/include/math.h \
+ /usr/include/c++/4.4/bits/fstream.tcc /usr/include/c++/4.4/sstream \
+ /usr/include/c++/4.4/bits/sstream.tcc /usr/include/math.h \
  /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
  /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
@@ -310,6 +311,10 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \
 
 /usr/include/c++/4.4/bits/fstream.tcc:
 
+/usr/include/c++/4.4/sstream:
+
+/usr/include/c++/4.4/bits/sstream.tcc:
+
 /usr/include/math.h:
 
 /usr/include/bits/huge_val.h:
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 65ac5f0..1950fc0 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -45,22 +45,12 @@ int calculate(int len, int nThreads) {
 #endif
 		for (i = 1; i <= len - b; i++) {
 			j = i + b;
-<<<<<<< .merge_file_vD135I
 			int flag = 0, newWM = INFINITY_; 
 			if (canPair(RNA[i], RNA[j])) {
 				flag = 1;
 				int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
 				int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack
 				if (j-i > 6) { // Internal Loop BEGIN
-=======
-			int newWM = INFINITY_; 
-
-			if (canPair(RNA[i], RNA[j])) {
-				int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin
-				int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack
-				
-				if (j-i > 6) {  // Internal Loop BEGIN
->>>>>>> .merge_file_o95D9I
 					int p=0, q=0;
 					int VBIij = INFINITY_;
 					for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
@@ -82,17 +72,10 @@ int calculate(int len, int nThreads) {
 					int VMij, VMijd, VMidj, VMidjd;
 					VMij = VMijd = VMidj = VMidjd = INFINITY_;
 					for (h = i+TURN+1; h <= j-1-TURN; h++) { 
-<<<<<<< .merge_file_vD135I
 						VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); 
 						VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); 
 						VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); 
 						VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); 
-=======
-						VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1));		
-						VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1));	
-						VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2));	
-						VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2));	
->>>>>>> .merge_file_o95D9I
 					}
 					int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
 					int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
@@ -108,16 +91,10 @@ int calculate(int len, int nThreads) {
 			if (j-i > 4) { // WM BEGIN
 				int h; 
 				for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
-<<<<<<< .merge_file_vD135I
 					//ZS: This sum corresponds to when i,j are NOT paired with each other.
 					//So we need to make sure only terms where i,j aren't pairing are considered. 
 					newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM;
 				}
-=======
-					newWM = MIN(newWM, WMU(i,h-1) + WML(h,j));
-				}
-
->>>>>>> .merge_file_o95D9I
 				newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
 				newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
 				newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
@@ -144,3 +121,4 @@ int calculate(int len, int nThreads) {
 	}
 	return W[len];
 }
+
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index c8d9055..add3113 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -44,12 +44,7 @@ bool compare_bp(const std::pair<int,int>& o1,
 
 
 static int load_constraints(const char* constr_file, int verbose=0) {
-<<<<<<< .merge_file_FGxfkH
 	
-=======
-    fprintf(stdout, "- Running with constraints %s\n", constr_file);
-	std::ifstream cfcons;
->>>>>>> .merge_file_mYvNsH
 
 	fprintf(stdout, "- Running with constraints\n");
 
@@ -111,13 +106,12 @@ static int load_constraints(const char* constr_file, int verbose=0) {
             pit++;
         }
     }
-	/*
+
 	std::vector<std::pair<int,int> > v_fbp;
 	for(it=0; it< nFBP; it++) {
 		for(int k=1;k<= FBP[it][2];k++)
 			v_fbp.push_back(std::pair<int,int>(FBP[it][0]+k-1, FBP[it][1]-k+1));
 	}
-<<<<<<< .merge_file_FGxfkH
 	
 	if(v_fbp.size()>1){
 		std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
@@ -132,21 +126,6 @@ static int load_constraints(const char* constr_file, int verbose=0) {
 	}
 
   
-=======
-
-	if (v_fbp.size() > 1) {
-		std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
-		for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) {
-			if (v_fbp[ii].second <= v_fbp[ii+1].second) {
-				fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n");
-				exit(-1);
-			}
-
-		}
-	}
-*/
-
->>>>>>> .merge_file_mYvNsH
     return 0;
 }
 
@@ -191,7 +170,6 @@ int init_constraints(const char* constr_file,int length) {
 			}
 		}
 	}
-<<<<<<< .merge_file_FGxfkH
 
 	
 	//ZS: set prohibited basepairs
@@ -210,13 +188,6 @@ int init_constraints(const char* constr_file,int length) {
 			if(PBP[it][2] < 1 || PBP[it][1] == 0){
 				printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
 				continue;
-=======
-	if (nFBP != 0) {
-		for (it = 0; it < nFBP; it++) {
-			if (FBP[it][2] < 1) {
-				printf("Invalid entry (%d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
-				continue; // TODO: report and exit here
->>>>>>> .merge_file_mYvNsH
 			}
 		
 			for(k = 1; k <= PBP[it][2]; k++){
@@ -251,7 +222,6 @@ int init_constraints(const char* constr_file,int length) {
 			for(k = 1; k<=FBP[it][2]; k++){
 				int i1 = FBP[it][0]+k-1;
 				int j1 = FBP[it][1]-k+1;
-<<<<<<< .merge_file_FGxfkH
 				if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){
 					printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
 					continue;			
@@ -304,18 +274,6 @@ int init_constraints(const char* constr_file,int length) {
 					BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1;
 					
 				}
-=======
-				if (!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])) {
-					printf("Can't constrain (%d,%d)\n", FBP[it][0]+k-1, FBP[it][1]-k+1);
-					continue; // TODO: report and exit here
-				}
-				if (j1-i1 < TURN) {
-					printf("Can't constrain (%d,%d)\n", i1, j1);
-					continue; // TODO: report and exit here
-				}	
-				BP[FBP[it][0]+k-1] = FBP[it][1]+1-k;
-				BP[FBP[it][1]+1-k] = FBP[it][0]+k-1;
->>>>>>> .merge_file_mYvNsH
 			}
 		}
 	}
@@ -448,23 +406,10 @@ void print_constraints(int len) {
  
 }
 
-<<<<<<< .merge_file_FGxfkH
 int forcePair(int i, int j) {
 //ZS: this function returns true if the pair i-j is forced.
 	if (CONS_ENABLED) 
 		return BP(i,j)==1;
-=======
-
-
-int is_ss(int i, int j) {
-	if (CONS_ENABLED) {
-		int it;
-		for (it = i + 1; it < j; it++) {
-			if (BP[it] > 0) return 1;
-		}
-		return 0;
-	}
->>>>>>> .merge_file_mYvNsH
 	else
 		return 0;
 }
@@ -552,3 +497,4 @@ int withinCD(int i, int j){
 	}
 	else return 1;
 }
+
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 565ca5d..76cbe44 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -17,13 +17,10 @@ bool SHAPE_ENABLED = false;
 
 string seqfile = "";
 string constraintsFile = "";
-<<<<<<< .merge_file_vAQXEJ
 string outputFile = "";
 string shapeFile = "";
-=======
-string outputFile = ""; 
 string paramDir = "Turner99"; // default value
->>>>>>> .merge_file_058DyL
+
 
 int suboptDelta = -1;
 int nThreads = -1;
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 60ce3da..445c851 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -54,7 +54,7 @@ void trace(int len, int vbose) {
 }
 
 void traceW(int j) {
-	int done, i, Wj,Wj_temp;
+	int done, i, Wj;
 	int wim1, flag, Widjd, Wijd, Widj, Wij;
 	Wj = INFINITY_;
 	flag = 1;

From a5ebd1672b168bcdfb047186c310f1f1b0e38ed9 Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Wed, 25 May 2011 16:48:05 +0200
Subject: [PATCH 134/282] replaced data Makefiles with Prashant's version

---
 gtfold-mfe/Makefile     | 2 +-
 gtfold-mfe/src/Makefile | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile
index 75480ce..8bba63d 100644
--- a/gtfold-mfe/Makefile
+++ b/gtfold-mfe/Makefile
@@ -214,7 +214,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /usr/local
+prefix = /home/zs/gtfold
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile
index 0f50f74..c79eea5 100644
--- a/gtfold-mfe/src/Makefile
+++ b/gtfold-mfe/src/Makefile
@@ -162,7 +162,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /usr/local
+prefix = /home/zs/gtfold
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin

From b4b005510bf27baba412743718d80077793da46c Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Wed, 25 May 2011 16:51:01 +0200
Subject: [PATCH 135/282] trying to commit data Makefiles again

---
 gtfold-mfe/test.txt | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 gtfold-mfe/test.txt

diff --git a/gtfold-mfe/test.txt b/gtfold-mfe/test.txt
deleted file mode 100644
index 229c9b9..0000000
--- a/gtfold-mfe/test.txt
+++ /dev/null
@@ -1 +0,0 @@
-this is to test how my Git setup works  - Zs
\ No newline at end of file

From ecf119af1c35f4f5b7e2718744e30955e26c5625 Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Wed, 25 May 2011 16:53:21 +0200
Subject: [PATCH 136/282] ...and once more..?

---
 gtfold-mfe/data/Andronescu/Makefile | 399 +++++++++++++++++++++
 gtfold-mfe/data/Makefile            | 536 ++++++++++++++++++++++++++++
 gtfold-mfe/data/Turner04/Makefile   | 405 +++++++++++++++++++++
 gtfold-mfe/data/Turner99/Makefile   | 420 ++++++++++++++++++++++
 gtfold-mfe/include/Makefile         | 388 ++++++++++++++++++++
 5 files changed, 2148 insertions(+)
 create mode 100644 gtfold-mfe/data/Andronescu/Makefile
 create mode 100644 gtfold-mfe/data/Makefile
 create mode 100644 gtfold-mfe/data/Turner04/Makefile
 create mode 100644 gtfold-mfe/data/Turner99/Makefile
 create mode 100644 gtfold-mfe/include/Makefile

diff --git a/gtfold-mfe/data/Andronescu/Makefile b/gtfold-mfe/data/Andronescu/Makefile
new file mode 100644
index 0000000..ece5bb2
--- /dev/null
+++ b/gtfold-mfe/data/Andronescu/Makefile
@@ -0,0 +1,399 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# data/Andronescu/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+
+pkgdatadir = $(datadir)/gtfold
+pkgincludedir = $(includedir)/gtfold
+pkglibdir = $(libdir)/gtfold
+pkglibexecdir = $(libexecdir)/gtfold
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
+target_triplet = x86_64-unknown-linux-gnu
+subdir = data/Andronescu
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/gtfold_config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
+DATA = $(gtfold_data_DATA)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -g -O2 -Wall
+CPP = gcc -E
+CPPFLAGS = 
+CXX = g++
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2 -Wall
+CYGPATH_W = echo
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /bin/grep -E
+EXEEXT = 
+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = 
+LIBOBJS = 
+LIBS = -lgomp 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+PACKAGE = gtfold
+PACKAGE_BUGREPORT = 
+PACKAGE_NAME = gtfold
+PACKAGE_STRING = gtfold 1.18
+PACKAGE_TARNAME = gtfold
+PACKAGE_URL = 
+PACKAGE_VERSION = 1.18
+PATH_SEPARATOR = :
+SET_MAKE = 
+SHELL = /bin/bash
+STRIP = 
+VERSION = 1.18
+abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data/Andronescu
+abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data/Andronescu
+abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
+abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = ${AMTAR} chof - "$$tardir"
+am__untar = ${AMTAR} xf -
+bindir = ${exec_prefix}/bin
+build = x86_64-unknown-linux-gnu
+build_alias = 
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = unknown
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host = x86_64-unknown-linux-gnu
+host_alias = 
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = unknown
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /home/zs/gtfold
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target = x86_64-unknown-linux-gnu
+target_alias = 
+target_cpu = x86_64
+target_os = linux-gnu
+target_vendor = unknown
+top_build_prefix = ../../
+top_builddir = ../..
+top_srcdir = ../..
+gtfold_datadir = $(datadir)/gtfold/Andronescu
+gtfold_data_DATA = \
+	stack.dat\
+	miscloop.dat\
+	dangle.dat\
+	loop.dat\
+	int11.dat\
+	int21.dat\
+	int22.dat\
+	tloop.dat\
+	triloop.dat\
+	tstackh.dat\
+	tstacki.dat
+
+EXTRA_DIST = $(gtfold_data_DATA)
+CLEANFILES = *~
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Andronescu/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu data/Andronescu/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-gtfold_dataDATA: $(gtfold_data_DATA)
+	@$(NORMAL_INSTALL)
+	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
+	done
+
+uninstall-gtfold_dataDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(DATA)
+installdirs:
+	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am: install-gtfold_dataDATA
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-gtfold_dataDATA
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+	distclean-generic distdir dvi dvi-am html html-am info info-am \
+	install install-am install-data install-data-am install-dvi \
+	install-dvi-am install-exec install-exec-am \
+	install-gtfold_dataDATA install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+	pdf-am ps ps-am uninstall uninstall-am \
+	uninstall-gtfold_dataDATA
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/gtfold-mfe/data/Makefile b/gtfold-mfe/data/Makefile
new file mode 100644
index 0000000..90fd188
--- /dev/null
+++ b/gtfold-mfe/data/Makefile
@@ -0,0 +1,536 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# data/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+pkgdatadir = $(datadir)/gtfold
+pkgincludedir = $(includedir)/gtfold
+pkglibdir = $(libdir)/gtfold
+pkglibexecdir = $(libexecdir)/gtfold
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
+target_triplet = x86_64-unknown-linux-gnu
+subdir = data
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/gtfold_config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
+	html-recursive info-recursive install-data-recursive \
+	install-dvi-recursive install-exec-recursive \
+	install-html-recursive install-info-recursive \
+	install-pdf-recursive install-ps-recursive install-recursive \
+	installcheck-recursive installdirs-recursive pdf-recursive \
+	ps-recursive uninstall-recursive
+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
+  distclean-recursive maintainer-clean-recursive
+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+	$(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
+	distdir
+ETAGS = etags
+CTAGS = ctags
+DIST_SUBDIRS = $(SUBDIRS)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+am__relativize = \
+  dir0=`pwd`; \
+  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
+  sed_rest='s,^[^/]*/*,,'; \
+  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
+  sed_butlast='s,/*[^/]*$$,,'; \
+  while test -n "$$dir1"; do \
+    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
+    if test "$$first" != "."; then \
+      if test "$$first" = ".."; then \
+        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
+        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
+      else \
+        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
+        if test "$$first2" = "$$first"; then \
+          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
+        else \
+          dir2="../$$dir2"; \
+        fi; \
+        dir0="$$dir0"/"$$first"; \
+      fi; \
+    fi; \
+    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
+  done; \
+  reldir="$$dir2"
+ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -g -O2 -Wall
+CPP = gcc -E
+CPPFLAGS = 
+CXX = g++
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2 -Wall
+CYGPATH_W = echo
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /bin/grep -E
+EXEEXT = 
+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = 
+LIBOBJS = 
+LIBS = -lgomp 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+PACKAGE = gtfold
+PACKAGE_BUGREPORT = 
+PACKAGE_NAME = gtfold
+PACKAGE_STRING = gtfold 1.18
+PACKAGE_TARNAME = gtfold
+PACKAGE_URL = 
+PACKAGE_VERSION = 1.18
+PATH_SEPARATOR = :
+SET_MAKE = 
+SHELL = /bin/bash
+STRIP = 
+VERSION = 1.18
+abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data
+abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data
+abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
+abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = ${AMTAR} chof - "$$tardir"
+am__untar = ${AMTAR} xf -
+bindir = ${exec_prefix}/bin
+build = x86_64-unknown-linux-gnu
+build_alias = 
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = unknown
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host = x86_64-unknown-linux-gnu
+host_alias = 
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = unknown
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /home/zs/gtfold
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target = x86_64-unknown-linux-gnu
+target_alias = 
+target_cpu = x86_64
+target_os = linux-gnu
+target_vendor = unknown
+top_build_prefix = ../
+top_builddir = ..
+top_srcdir = ..
+SUBDIRS = Turner04 Turner99 Andronescu
+all: all-recursive
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu data/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+
+# This directory's subdirectories are mostly independent; you can cd
+# into them and run `make' without going through this Makefile.
+# To change the values of `make' variables: instead of editing Makefiles,
+# (1) if the variable is set in `config.status', edit `config.status'
+#     (which will cause the Makefiles to be regenerated when you run `make');
+# (2) otherwise, pass the desired values on the `make' command line.
+$(RECURSIVE_TARGETS):
+	@fail= failcom='exit 1'; \
+	for f in x $$MAKEFLAGS; do \
+	  case $$f in \
+	    *=* | --[!k]*);; \
+	    *k*) failcom='fail=yes';; \
+	  esac; \
+	done; \
+	dot_seen=no; \
+	target=`echo $@ | sed s/-recursive//`; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    dot_seen=yes; \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  || eval $$failcom; \
+	done; \
+	if test "$$dot_seen" = "no"; then \
+	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
+	fi; test -z "$$fail"
+
+$(RECURSIVE_CLEAN_TARGETS):
+	@fail= failcom='exit 1'; \
+	for f in x $$MAKEFLAGS; do \
+	  case $$f in \
+	    *=* | --[!k]*);; \
+	    *k*) failcom='fail=yes';; \
+	  esac; \
+	done; \
+	dot_seen=no; \
+	case "$@" in \
+	  distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
+	  *) list='$(SUBDIRS)' ;; \
+	esac; \
+	rev=''; for subdir in $$list; do \
+	  if test "$$subdir" = "."; then :; else \
+	    rev="$$subdir $$rev"; \
+	  fi; \
+	done; \
+	rev="$$rev ."; \
+	target=`echo $@ | sed s/-recursive//`; \
+	for subdir in $$rev; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  || eval $$failcom; \
+	done && test -z "$$fail"
+tags-recursive:
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
+	done
+ctags-recursive:
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
+	done
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	mkid -fID $$unique
+tags: TAGS
+
+TAGS: tags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	set x; \
+	here=`pwd`; \
+	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
+	  include_option=--etags-include; \
+	  empty_fix=.; \
+	else \
+	  include_option=--include; \
+	  empty_fix=; \
+	fi; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    test ! -f $$subdir/TAGS || \
+	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
+	  fi; \
+	done; \
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
+	fi
+ctags: CTAGS
+CTAGS: ctags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    test -d "$(distdir)/$$subdir" \
+	    || $(MKDIR_P) "$(distdir)/$$subdir" \
+	    || exit 1; \
+	  fi; \
+	done
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
+	    $(am__relativize); \
+	    new_distdir=$$reldir; \
+	    dir1=$$subdir; dir2="$(top_distdir)"; \
+	    $(am__relativize); \
+	    new_top_distdir=$$reldir; \
+	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
+	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
+	    ($(am__cd) $$subdir && \
+	      $(MAKE) $(AM_MAKEFLAGS) \
+	        top_distdir="$$new_top_distdir" \
+	        distdir="$$new_distdir" \
+		am__remove_distdir=: \
+		am__skip_length_check=: \
+		am__skip_mode_fix=: \
+	        distdir) \
+	      || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-recursive
+all-am: Makefile
+installdirs: installdirs-recursive
+installdirs-am:
+install: install-recursive
+install-exec: install-exec-recursive
+install-data: install-data-recursive
+uninstall: uninstall-recursive
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-recursive
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-recursive
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-recursive
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+html-am:
+
+info: info-recursive
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-recursive
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-recursive
+
+install-html-am:
+
+install-info: install-info-recursive
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-recursive
+
+install-pdf-am:
+
+install-ps: install-ps-recursive
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-recursive
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-recursive
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-recursive
+
+pdf-am:
+
+ps: ps-recursive
+
+ps-am:
+
+uninstall-am:
+
+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
+	install-am install-strip tags-recursive
+
+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
+	all all-am check check-am clean clean-generic ctags \
+	ctags-recursive distclean distclean-generic distclean-tags \
+	distdir dvi dvi-am html html-am info info-am install \
+	install-am install-data install-data-am install-dvi \
+	install-dvi-am install-exec install-exec-am install-html \
+	install-html-am install-info install-info-am install-man \
+	install-pdf install-pdf-am install-ps install-ps-am \
+	install-strip installcheck installcheck-am installdirs \
+	installdirs-am maintainer-clean maintainer-clean-generic \
+	mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \
+	tags-recursive uninstall uninstall-am
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/gtfold-mfe/data/Turner04/Makefile b/gtfold-mfe/data/Turner04/Makefile
new file mode 100644
index 0000000..d64ce66
--- /dev/null
+++ b/gtfold-mfe/data/Turner04/Makefile
@@ -0,0 +1,405 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# data/Turner04/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+
+pkgdatadir = $(datadir)/gtfold
+pkgincludedir = $(includedir)/gtfold
+pkglibdir = $(libdir)/gtfold
+pkglibexecdir = $(libexecdir)/gtfold
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
+target_triplet = x86_64-unknown-linux-gnu
+subdir = data/Turner04
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/gtfold_config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
+DATA = $(gtfold_data_DATA)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -g -O2 -Wall
+CPP = gcc -E
+CPPFLAGS = 
+CXX = g++
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2 -Wall
+CYGPATH_W = echo
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /bin/grep -E
+EXEEXT = 
+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = 
+LIBOBJS = 
+LIBS = -lgomp 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+PACKAGE = gtfold
+PACKAGE_BUGREPORT = 
+PACKAGE_NAME = gtfold
+PACKAGE_STRING = gtfold 1.18
+PACKAGE_TARNAME = gtfold
+PACKAGE_URL = 
+PACKAGE_VERSION = 1.18
+PATH_SEPARATOR = :
+SET_MAKE = 
+SHELL = /bin/bash
+STRIP = 
+VERSION = 1.18
+abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data/Turner04
+abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data/Turner04
+abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
+abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = ${AMTAR} chof - "$$tardir"
+am__untar = ${AMTAR} xf -
+bindir = ${exec_prefix}/bin
+build = x86_64-unknown-linux-gnu
+build_alias = 
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = unknown
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host = x86_64-unknown-linux-gnu
+host_alias = 
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = unknown
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /home/zs/gtfold
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target = x86_64-unknown-linux-gnu
+target_alias = 
+target_cpu = x86_64
+target_os = linux-gnu
+target_vendor = unknown
+top_build_prefix = ../../
+top_builddir = ../..
+top_srcdir = ../..
+gtfold_datadir = $(datadir)/gtfold/Turner04
+gtfold_data_DATA = \
+	stack.dat\
+	miscloop.dat\
+	dangle.dat\
+	loop.dat\
+	coaxial.dat\
+	coaxstack.dat\
+	hexaloop.dat\
+	int11.dat\
+	int21.dat\
+	int22.dat\
+	tloop.dat\
+	triloop.dat\
+	tstack.dat\
+	tstackcoax.dat\
+	tstackh.dat\
+	tstacki.dat\
+	tstackm.dat
+
+EXTRA_DIST = $(gtfold_data_DATA)
+CLEANFILES = *~
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Turner04/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu data/Turner04/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-gtfold_dataDATA: $(gtfold_data_DATA)
+	@$(NORMAL_INSTALL)
+	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
+	done
+
+uninstall-gtfold_dataDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(DATA)
+installdirs:
+	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am: install-gtfold_dataDATA
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-gtfold_dataDATA
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+	distclean-generic distdir dvi dvi-am html html-am info info-am \
+	install install-am install-data install-data-am install-dvi \
+	install-dvi-am install-exec install-exec-am \
+	install-gtfold_dataDATA install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+	pdf-am ps ps-am uninstall uninstall-am \
+	uninstall-gtfold_dataDATA
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/gtfold-mfe/data/Turner99/Makefile b/gtfold-mfe/data/Turner99/Makefile
new file mode 100644
index 0000000..413b605
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/Makefile
@@ -0,0 +1,420 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# data/Turner99/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+
+pkgdatadir = $(datadir)/gtfold
+pkgincludedir = $(includedir)/gtfold
+pkglibdir = $(libdir)/gtfold
+pkglibexecdir = $(libexecdir)/gtfold
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
+target_triplet = x86_64-unknown-linux-gnu
+subdir = data/Turner99
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/gtfold_config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
+DATA = $(gtfold_data_DATA)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -g -O2 -Wall
+CPP = gcc -E
+CPPFLAGS = 
+CXX = g++
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2 -Wall
+CYGPATH_W = echo
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /bin/grep -E
+EXEEXT = 
+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = 
+LIBOBJS = 
+LIBS = -lgomp 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+PACKAGE = gtfold
+PACKAGE_BUGREPORT = 
+PACKAGE_NAME = gtfold
+PACKAGE_STRING = gtfold 1.18
+PACKAGE_TARNAME = gtfold
+PACKAGE_URL = 
+PACKAGE_VERSION = 1.18
+PATH_SEPARATOR = :
+SET_MAKE = 
+SHELL = /bin/bash
+STRIP = 
+VERSION = 1.18
+abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data/Turner99
+abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data/Turner99
+abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
+abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = ${AMTAR} chof - "$$tardir"
+am__untar = ${AMTAR} xf -
+bindir = ${exec_prefix}/bin
+build = x86_64-unknown-linux-gnu
+build_alias = 
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = unknown
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host = x86_64-unknown-linux-gnu
+host_alias = 
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = unknown
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /home/zs/gtfold
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target = x86_64-unknown-linux-gnu
+target_alias = 
+target_cpu = x86_64
+target_os = linux-gnu
+target_vendor = unknown
+top_build_prefix = ../../
+top_builddir = ../..
+top_srcdir = ../..
+gtfold_datadir = $(datadir)/gtfold/Turner99
+gtfold_data_DATA = \
+	stack.DAT\
+	miscloop.DAT\
+	dangle.DAT\
+	loop.DAT\
+	int11.DAT\
+	int21.DAT\
+	int22.DAT\
+	sint2.DAT\
+	sint4.DAT\
+	tloop.DAT\
+	tstackh.DAT\
+	tstacki.DAT\
+	tstackm.DAT\
+	stack.dat\
+	miscloop.dat\
+	dangle.dat\
+	loop.dat\
+	asint1x2.dat\
+	coaxial.dat\
+	coaxstack.dat\
+	int11.dat\
+	int21.dat\
+	int22.dat\
+	sint2.dat\
+	sint4.dat\
+	tloop.dat\
+	triloop.dat\
+	tstack.dat\
+	tstackcoax.dat\
+	tstackh.dat\
+	tstacki.dat\
+	tstackm.dat
+
+EXTRA_DIST = $(gtfold_data_DATA)
+CLEANFILES = *~
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Turner99/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu data/Turner99/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-gtfold_dataDATA: $(gtfold_data_DATA)
+	@$(NORMAL_INSTALL)
+	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
+	done
+
+uninstall-gtfold_dataDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(DATA)
+installdirs:
+	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am: install-gtfold_dataDATA
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-gtfold_dataDATA
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+	distclean-generic distdir dvi dvi-am html html-am info info-am \
+	install install-am install-data install-data-am install-dvi \
+	install-dvi-am install-exec install-exec-am \
+	install-gtfold_dataDATA install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+	pdf-am ps ps-am uninstall uninstall-am \
+	uninstall-gtfold_dataDATA
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/gtfold-mfe/include/Makefile b/gtfold-mfe/include/Makefile
new file mode 100644
index 0000000..6318aff
--- /dev/null
+++ b/gtfold-mfe/include/Makefile
@@ -0,0 +1,388 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# include/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+
+pkgdatadir = $(datadir)/gtfold
+pkgincludedir = $(includedir)/gtfold
+pkglibdir = $(libdir)/gtfold
+pkglibexecdir = $(libexecdir)/gtfold
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
+target_triplet = x86_64-unknown-linux-gnu
+subdir = include
+DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
+	$(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/gtfold_config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
+HEADERS = $(noinst_HEADERS)
+ETAGS = etags
+CTAGS = ctags
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -g -O2 -Wall
+CPP = gcc -E
+CPPFLAGS = 
+CXX = g++
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2 -Wall
+CYGPATH_W = echo
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /bin/grep -E
+EXEEXT = 
+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = 
+LIBOBJS = 
+LIBS = -lgomp 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+PACKAGE = gtfold
+PACKAGE_BUGREPORT = 
+PACKAGE_NAME = gtfold
+PACKAGE_STRING = gtfold 1.18
+PACKAGE_TARNAME = gtfold
+PACKAGE_URL = 
+PACKAGE_VERSION = 1.18
+PATH_SEPARATOR = :
+SET_MAKE = 
+SHELL = /bin/bash
+STRIP = 
+VERSION = 1.18
+abs_builddir = /home/zs/git/gtfold/gtfold-mfe/include
+abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/include
+abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
+abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = ${AMTAR} chof - "$$tardir"
+am__untar = ${AMTAR} xf -
+bindir = ${exec_prefix}/bin
+build = x86_64-unknown-linux-gnu
+build_alias = 
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = unknown
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host = x86_64-unknown-linux-gnu
+host_alias = 
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = unknown
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /home/zs/gtfold
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target = x86_64-unknown-linux-gnu
+target_alias = 
+target_cpu = x86_64
+target_os = linux-gnu
+target_vendor = unknown
+top_build_prefix = ../
+top_builddir = ..
+top_srcdir = ..
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h
+CLEANFILES = *~
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu include/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu include/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	mkid -fID $$unique
+tags: TAGS
+
+TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	set x; \
+	here=`pwd`; \
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
+	fi
+ctags: CTAGS
+CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(HEADERS)
+installdirs:
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am:
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
+	ctags distclean distclean-generic distclean-tags distdir dvi \
+	dvi-am html html-am info info-am install install-am \
+	install-data install-data-am install-dvi install-dvi-am \
+	install-exec install-exec-am install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+	pdf-am ps ps-am tags uninstall uninstall-am
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:

From 7227e162d9e6f8d2c42b110749e252b61227f8a6 Mon Sep 17 00:00:00 2001
From: Zsuzsanna Sukosd <dsokus@gmail.com>
Date: Wed, 25 May 2011 18:17:37 +0200
Subject: [PATCH 137/282] fixed lost support for contact distance

---
 gtfold-mfe/Makefile                 |  2 +-
 gtfold-mfe/data/Andronescu/Makefile |  2 +-
 gtfold-mfe/data/Makefile            |  2 +-
 gtfold-mfe/data/Turner04/Makefile   |  2 +-
 gtfold-mfe/data/Turner99/Makefile   |  2 +-
 gtfold-mfe/include/Makefile         |  2 +-
 gtfold-mfe/src/.deps/global.Po      |  5 ++++-
 gtfold-mfe/src/Makefile             |  2 +-
 gtfold-mfe/src/algorithms.c         |  2 ++
 gtfold-mfe/src/constraints.cc       | 12 ++++++------
 gtfold-mfe/src/global.c             |  1 +
 11 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile
index 8bba63d..608a49b 100644
--- a/gtfold-mfe/Makefile
+++ b/gtfold-mfe/Makefile
@@ -214,7 +214,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/gtfold
+prefix = /home/zs/dsgtfold
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/data/Andronescu/Makefile b/gtfold-mfe/data/Andronescu/Makefile
index ece5bb2..b2fd9ef 100644
--- a/gtfold-mfe/data/Andronescu/Makefile
+++ b/gtfold-mfe/data/Andronescu/Makefile
@@ -159,7 +159,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/gtfold
+prefix = /home/zs/dsgtfold
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/data/Makefile b/gtfold-mfe/data/Makefile
index 90fd188..0331574 100644
--- a/gtfold-mfe/data/Makefile
+++ b/gtfold-mfe/data/Makefile
@@ -175,7 +175,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/gtfold
+prefix = /home/zs/dsgtfold
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/data/Turner04/Makefile b/gtfold-mfe/data/Turner04/Makefile
index d64ce66..382eac6 100644
--- a/gtfold-mfe/data/Turner04/Makefile
+++ b/gtfold-mfe/data/Turner04/Makefile
@@ -159,7 +159,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/gtfold
+prefix = /home/zs/dsgtfold
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/data/Turner99/Makefile b/gtfold-mfe/data/Turner99/Makefile
index 413b605..0fee0e5 100644
--- a/gtfold-mfe/data/Turner99/Makefile
+++ b/gtfold-mfe/data/Turner99/Makefile
@@ -159,7 +159,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/gtfold
+prefix = /home/zs/dsgtfold
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/include/Makefile b/gtfold-mfe/include/Makefile
index 6318aff..ced6c10 100644
--- a/gtfold-mfe/include/Makefile
+++ b/gtfold-mfe/include/Makefile
@@ -140,7 +140,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/gtfold
+prefix = /home/zs/dsgtfold
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/src/.deps/global.Po b/gtfold-mfe/src/.deps/global.Po
index e2d1748..a407344 100644
--- a/gtfold-mfe/src/.deps/global.Po
+++ b/gtfold-mfe/src/.deps/global.Po
@@ -14,7 +14,8 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
- /usr/include/bits/stdlib.h ../include/global.h ../include/constants.h
+ /usr/include/bits/stdlib.h ../include/global.h ../include/constants.h \
+ ../include/constraints.h
 
 /usr/include/stdio.h:
 
@@ -83,3 +84,5 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \
 ../include/global.h:
 
 ../include/constants.h:
+
+../include/constraints.h:
diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile
index c79eea5..6385554 100644
--- a/gtfold-mfe/src/Makefile
+++ b/gtfold-mfe/src/Makefile
@@ -162,7 +162,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/gtfold
+prefix = /home/zs/dsgtfold
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 1950fc0..3262322 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -39,6 +39,8 @@ int calculate(int len, int nThreads) {
 #pragma omp master
 	fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
 #endif
+
+
 	for (b = TURN+1; b <= len-1; b++) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index add3113..45d6280 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -443,7 +443,7 @@ int canILoop(int i, int j, int p, int q) {
 		return canStack(i,j) && canStack(p,q) && canSSregion(i,p) && canSSregion(q,j);
 	}
 	else 
-		return 1;
+		return withinCD(i,j) && withinCD(p,q);
 }
 
 int canHairpin(int i, int j) {
@@ -452,7 +452,7 @@ int canHairpin(int i, int j) {
 		//Need to check if pair is allowed and if anything pairs between them
 		return canStack(i,j) && canSSregion(i,j);
 	}	
-	else return 1;
+	else return withinCD(i,j);
 }
 
 int canSSregion(int i, int j){
@@ -485,15 +485,15 @@ int canStack(int i, int j) {
 		if(BP(i,j)==2||BP(i,i)==3||BP(j,j)==3) return 0;
 		//can't pair if i or j are forced to pair with something other than each other
 		if((BP(i,i)==4||BP(j,j)==4)&&BP(i,j)!=1) return 0;	
-		else return 1;
+		else return withinCD(i,j);
 	}
-	else return 1;
+	else return withinCD(i,j);
 }
 
 int withinCD(int i, int j){
 	//ZS: This function returns 1 if i and j are within the required contact distance from each other. 
-	if (LIMIT_DISTANCE){	
-		return j-i+1>contactDistance;
+	if (LIMIT_DISTANCE){
+		return (j-i>=contactDistance);
 	}
 	else return 1;
 }
diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c
index 5197c1e..a83c475 100644
--- a/gtfold-mfe/src/global.c
+++ b/gtfold-mfe/src/global.c
@@ -2,6 +2,7 @@
 #include <stdlib.h>
 
 #include "global.h"
+#include "constraints.h"
 
 unsigned char *RNA; 
 int *structure; 

From 71de763ded642d0c33a60c7bb66590e888c3ed32 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 7 Jun 2011 17:53:53 -0400
Subject: [PATCH 138/282] testing

---
 gtfold-mfe/src/algorithms.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 3262322..91191dc 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -12,7 +12,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 GNU General Public License for more details.
 You should have received a copy of the GNU General Public License
 along with this program. If not, see <http://www.gnu.org/licenses/>.
-*/ 
+*/
+
 #include <stdio.h>
 #include <math.h>
 #include <time.h>

From f3fdde6ada0a7aff0e7cbfcd3191c7bdd9567294 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 7 Jun 2011 17:58:26 -0400
Subject: [PATCH 139/282] change to speedup multiloop calculations

---
 gtfold-mfe/include/energy.h |  8 ++-----
 gtfold-mfe/src/algorithms.c | 44 ++++++++++++++++++-------------------
 gtfold-mfe/src/energy.c     | 41 +++++++++++++++++-----------------
 3 files changed, 44 insertions(+), 49 deletions(-)

diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h
index c5fdb1f..5b7b5cc 100644
--- a/gtfold-mfe/include/energy.h
+++ b/gtfold-mfe/include/energy.h
@@ -4,24 +4,20 @@
 #include "data.h"
 
 extern int *V; 
-extern int *VV; 
-extern int *VV1; 
 extern int *W; 
 extern int *VBI; 
 extern int *VM; 
 extern int **WM; 
-extern int *WMu; 
-extern int *WMl; 
+extern int **WMPrime; 
 extern int *indx; 
 
 
 #define V(i,j) V[indx[j]+i]
 #define VM(i,j) VM[indx[j]+i]
 #define WM(i,j) WM[i][j]
+#define WMPrime(i,j) WMPrime[i][j]
 #define WMU(i,j) WM[i][j]
 #define WML(i,j) WM[j][i]
-//#define WMU(i,j) WMu[indx[j]+i]
-//#define WML(i,j) WMl[indx[j]+i]
 #define VBI(i,j) VBI[indx[j]+i]
 
 #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0)
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 91191dc..0fd0c72 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -12,8 +12,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 GNU General Public License for more details.
 You should have received a copy of the GNU General Public License
 along with this program. If not, see <http://www.gnu.org/licenses/>.
-*/
-
+*/ 
 #include <stdio.h>
 #include <math.h>
 #include <time.h>
@@ -41,19 +40,19 @@ int calculate(int len, int nThreads) {
 	fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
 #endif
 
-
 	for (b = TURN+1; b <= len-1; b++) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
 #endif
 		for (i = 1; i <= len - b; i++) {
 			j = i + b;
-			int flag = 0, newWM = INFINITY_; 
+			int newWM = INFINITY_; 
 			if (canPair(RNA[i], RNA[j])) {
-				flag = 1;
 				int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
-				int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack
-				if (j-i > 6) { // Internal Loop BEGIN
+				
+        int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack
+				
+        if (j-i > 6) { // Internal Loop BEGIN
 					int p=0, q=0;
 					int VBIij = INFINITY_;
 					for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
@@ -68,18 +67,14 @@ int calculate(int len, int nThreads) {
 					}
 					VBI(i,j) = VBIij;
 					V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
-
 				} // Internal Loop END
-				if (j-i > 10) { // Multi Loop BEGIN
-					int h;
-					int VMij, VMijd, VMidj, VMidjd;
-					VMij = VMijd = VMidj = VMidjd = INFINITY_;
-					for (h = i+TURN+1; h <= j-1-TURN; h++) { 
-						VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); 
-						VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); 
-						VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); 
-						VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); 
-					}
+				
+        if (j-i > 10) { // Multi Loop BEGIN
+					int VMij =  WMPrime[i+1][j-1]; 
+					int VMidj = WMPrime[i+2][j-1]; 
+					int VMijd = WMPrime[i+1][j-2]; 
+					int VMidjd = WMPrime[i+2][j-2]; 
+          
 					int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
 					int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
 					VMij = MIN(VMij, (VMidj + d5 +Ec)) ;
@@ -88,16 +83,21 @@ int calculate(int len, int nThreads) {
 					VMij = VMij + Ea + Eb + auPenalty(i,j);
 					VM(i,j) = canStack(i,j)?VMij:INFINITY_;
 				} // Multi Loop END
-				V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j));
+				
+        V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j));
 			}
 			else V(i,j) = INFINITY_;
-			if (j-i > 4) { // WM BEGIN
+			
+      if (j-i > 4) { // WM BEGIN
 				int h; 
 				for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
 					//ZS: This sum corresponds to when i,j are NOT paired with each other.
 					//So we need to make sure only terms where i,j aren't pairing are considered. 
-					newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM;
+					// Added auxillary storage WMPrime to speedup multiloop calculations
+          WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); 
+					//newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM;
 				}
+				newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM;
 				newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
 				newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
 				newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
@@ -108,6 +108,7 @@ int calculate(int len, int nThreads) {
 			} // WM END
 		}
 	}
+
 	for (j = TURN+2; j <= len; j++) {
 		int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
 		Wj = INFINITY_;
@@ -124,4 +125,3 @@ int calculate(int len, int nThreads) {
 	}
 	return W[len];
 }
-
diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 1118794..9450f92 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -9,12 +9,11 @@
 #include "shapereader.h"
 
 int *V; 
-int *VV; 
-int *VV1; 
 int *W; 
 int *VBI; 
 int *VM; 
 int **WM; 
+int **WMPrime; 
 int *indx; 
 
 int alloc_flag = 0;
@@ -26,18 +25,6 @@ void create_tables(int len) {
 		exit(-1);
 	}
 
-	VV1 = (int *) malloc((len+ 1)*sizeof(int));
-	if (VV1 == NULL) {
-		perror("Cannot allocate variable 'V'");
-		exit(-1);
-	}
-
-	VV = (int *) malloc((len+ 1)*sizeof(int));
-	if (VV == NULL) {
-		perror("Cannot allocate variable 'V'");
-		exit(-1);
-	}
-	
 	int i;
 	WM = (int **) malloc((len+1)* sizeof(int *));
 	if (WM == NULL) {
@@ -50,7 +37,20 @@ void create_tables(int len) {
 			perror("Cannot allocate variable 'WM[i]'");
 			exit(-1);
 		}   
+	}
+
+  WMPrime = (int **) malloc((len+1)* sizeof(int *));
+	if (WMPrime == NULL) {
+		perror("Cannot allocate variable 'WM'");
+		exit(-1);
 	}   
+	for (i = 0; i <= len; i++) {
+		WMPrime[i] = (int *)malloc((len+1)* sizeof(int));
+		if (WMPrime[i] == NULL) {
+			perror("Cannot allocate variable 'WM[i]'");
+			exit(-1);
+		}   
+	}
 
 	VM = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
 	if (VM == NULL) {
@@ -87,15 +87,13 @@ void init_tables(int len) {
 	
 	for (i = 0; i <= len; i++) {
 		W[i] = INFINITY_; 
-		VV[i] = INFINITY_;
-		VV1[i] = INFINITY_;
-		for (j = 0; j <= len; j++) 
+		for (j = 0; j <= len; j++) {
 			WM[i][j] = INFINITY_;
+			WMPrime[i][j] = INFINITY_;
+    }
 	}
 	
-	
 	LLL = (len)*(len+1)/2 + 1;
-
 	for (i = 0; i < LLL; i++) {
 		V[i] = INFINITY_;
 		VM[i] = INFINITY_;
@@ -116,11 +114,12 @@ void free_tables(int len) {
 		for (i = 0; i <= len; i++) free(WM[i]);
 		free(WM);
 
+		for (i = 0; i <= len; i++) free(WMPrime[i]);
+		free(WMPrime);
+
 		free(VM);
 		free(VBI);
 		free(V);
-		free(VV);
-		free(VV1);
 		free(W);
 	}
 }

From 7b9fe56de9247ae20d5d9c6a8a078dcb170b6bcc Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Sat, 11 Jun 2011 18:52:01 -0400
Subject: [PATCH 140/282] Bugfix in partition. Random sample now compiles,
 links

---
 gtfold-mfe/include/Makefile.am        |   2 +-
 gtfold-mfe/include/Makefile.in        |   2 +-
 gtfold-mfe/include/energy.h           |   1 +
 gtfold-mfe/include/partition-dangle.h |  19 ++
 gtfold-mfe/include/random-sample.h    |  15 +
 gtfold-mfe/src/Makefile               |   7 +-
 gtfold-mfe/src/Makefile.am            |   2 +
 gtfold-mfe/src/Makefile.in            |   7 +-
 gtfold-mfe/src/algorithms-partition.c |  23 +-
 gtfold-mfe/src/partition-dangle.c     | 197 +++++++++++++
 gtfold-mfe/src/random-sample.cc       | 394 +++++++++++++++++++++++++-
 11 files changed, 642 insertions(+), 27 deletions(-)
 create mode 100644 gtfold-mfe/include/partition-dangle.h
 create mode 100644 gtfold-mfe/include/random-sample.h
 create mode 100644 gtfold-mfe/src/partition-dangle.c

diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am
index b73b2f6..ee1eb98 100644
--- a/gtfold-mfe/include/Makefile.am
+++ b/gtfold-mfe/include/Makefile.am
@@ -1,3 +1,3 @@
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-paritition.h
 
 CLEANFILES = *~
diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in
index a0bf52b..3565a69 100644
--- a/gtfold-mfe/include/Makefile.in
+++ b/gtfold-mfe/include/Makefile.in
@@ -155,7 +155,7 @@ target_vendor = @target_vendor@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-paritition.h
 CLEANFILES = *~
 all: all-am
 
diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h
index c5fdb1f..f8d7c77 100644
--- a/gtfold-mfe/include/energy.h
+++ b/gtfold-mfe/include/energy.h
@@ -23,6 +23,7 @@ extern int *indx;
 //#define WMU(i,j) WMu[indx[j]+i]
 //#define WML(i,j) WMl[indx[j]+i]
 #define VBI(i,j) VBI[indx[j]+i]
+#define RT ((0.00198721 * 310.15)/100.00)
 
 #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0)
 
diff --git a/gtfold-mfe/include/partition-dangle.h b/gtfold-mfe/include/partition-dangle.h
new file mode 100644
index 0000000..e483aa1
--- /dev/null
+++ b/gtfold-mfe/include/partition-dangle.h
@@ -0,0 +1,19 @@
+#ifndef _PARTITION_DANGLE_H
+#define _PARTITION_DANGLE_H
+
+
+typedef struct partition_d{
+	double ** u;
+	double ** up;
+	double ** upm;
+	double ** s1;
+	double ** s2;
+	double ** s3;
+	double ** u1;
+	int length;
+}dangle_struct;
+
+double cond_dangle(int j, int h, int l);
+void fill_partition_arrays_d(dangle_struct part_struct);
+
+#endif
diff --git a/gtfold-mfe/include/random-sample.h b/gtfold-mfe/include/random-sample.h
new file mode 100644
index 0000000..4a68889
--- /dev/null
+++ b/gtfold-mfe/include/random-sample.h
@@ -0,0 +1,15 @@
+#ifndef _RANDOM_SAMPLE_H
+#define _RANDOM_SAMPLE_H
+
+#include <list>
+
+using namespace std;
+
+typedef struct sub_seq_t{
+	int start;
+	int end;
+	int paired;
+}sub_seq;
+
+void multi_loop_strand(int i, int j, dangle_struct d_struct, int * structure, list<sub_seq> * stack);
+#endif
diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile
index 53081de..8d533f1 100644
--- a/gtfold-mfe/src/Makefile
+++ b/gtfold-mfe/src/Makefile
@@ -51,7 +51,8 @@ PROGRAMS = $(bin_PROGRAMS)
 am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
 	options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \
 	energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \
-	subopt_traceback.$(OBJEXT) partition-dangle.$(OBJEXT) \
+	subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \
+	partition-dangle.$(OBJEXT) random-sample.$(OBJEXT) \
 	shapereader.$(OBJEXT)
 gtfold_OBJECTS = $(am_gtfold_OBJECTS)
 gtfold_DEPENDENCIES =
@@ -192,7 +193,9 @@ gtfold_SOURCES = \
 	algorithms.c \
 	traceback.c \
 	subopt_traceback.cc\
+	algorithms-partition.c\
 	partition-dangle.c\
+	random-sample.cc\
 	shapereader.cc
 
 gtfold_LDFLAGS = 
@@ -279,6 +282,7 @@ mostlyclean-compile:
 distclean-compile:
 	-rm -f *.tab.c
 
+include ./$(DEPDIR)/algorithms-partition.Po
 include ./$(DEPDIR)/algorithms.Po
 include ./$(DEPDIR)/constraints.Po
 include ./$(DEPDIR)/energy.Po
@@ -287,6 +291,7 @@ include ./$(DEPDIR)/loader.Po
 include ./$(DEPDIR)/main.Po
 include ./$(DEPDIR)/options.Po
 include ./$(DEPDIR)/partition-dangle.Po
+include ./$(DEPDIR)/random-sample.Po
 include ./$(DEPDIR)/shapereader.Po
 include ./$(DEPDIR)/subopt_traceback.Po
 include ./$(DEPDIR)/traceback.Po
diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am
index 797391e..aaa9481 100644
--- a/gtfold-mfe/src/Makefile.am
+++ b/gtfold-mfe/src/Makefile.am
@@ -16,7 +16,9 @@ gtfold_SOURCES = \
 	algorithms.c \
 	traceback.c \
 	subopt_traceback.cc\
+	algorithms-partition.c\
 	partition-dangle.c\
+	random-sample.cc\
 	shapereader.cc
 
 gtfold_LDFLAGS = 
diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in
index 0de321f..8b6d90d 100644
--- a/gtfold-mfe/src/Makefile.in
+++ b/gtfold-mfe/src/Makefile.in
@@ -51,7 +51,8 @@ PROGRAMS = $(bin_PROGRAMS)
 am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
 	options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \
 	energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \
-	subopt_traceback.$(OBJEXT) partition-dangle.$(OBJEXT) \
+	subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \
+	partition-dangle.$(OBJEXT) random-sample.$(OBJEXT) \
 	shapereader.$(OBJEXT)
 gtfold_OBJECTS = $(am_gtfold_OBJECTS)
 gtfold_DEPENDENCIES =
@@ -192,7 +193,9 @@ gtfold_SOURCES = \
 	algorithms.c \
 	traceback.c \
 	subopt_traceback.cc\
+	algorithms-partition.c\
 	partition-dangle.c\
+	random-sample.cc\
 	shapereader.cc
 
 gtfold_LDFLAGS = 
@@ -279,6 +282,7 @@ mostlyclean-compile:
 distclean-compile:
 	-rm -f *.tab.c
 
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/constraints.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/energy.Po@am__quote@
@@ -287,6 +291,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/random-sample.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@
diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c
index c39128e..1ed7895 100644
--- a/gtfold-mfe/src/algorithms-partition.c
+++ b/gtfold-mfe/src/algorithms-partition.c
@@ -16,7 +16,6 @@
 
 
 // Boltzmann constant (R) * Standard 37C temperature (T in Kelvin)
-double RT = 0.00198721 * 310.15;
 
 // Based on pseudocode in figure 6 in 
 //
@@ -67,18 +66,18 @@ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) {
 
                 // NOTE: eH returns an integer encoded as fixed point.  So a
                 // return value of 115 represents raw value 115/100 = 1.15
-                QB[i][j] = exp(-eH(i,j)/100.0/RT);
+                QB[i][j] = exp(-eH(i,j)/RT);
 
                 for(d=i+1; d<=j-4; ++d) {
                     for(e=d+4; e<=j-1; ++e) {
                         
                 if(d == i + 1 && e == j -1)
-                    QB[i][j] += exp(-eS(i,j)/100.0/RT)*QB[d][e];
+                    QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e];
                 else 
-                    QB[i][j] += exp(-eL(i,j,d,e)/100.0/RT)*QB[d][e];
+                    QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e];
 
                         QB[i][j] += QM[i+1][d-1]*QB[d][e] *
-                            exp(-(a + b + c*(j-e-1))/100.0/RT);
+                            exp(-(a + b + c*(j-e-1))/RT);
                     }
                 }
             }
@@ -88,8 +87,8 @@ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) {
             for(d=i; d<=j-4; ++d) {
                 for(e=d+4; e<=j; ++e) {
                     Q[i][j] += Q[i][d-1]*QB[d][e];
-                    QM[i][j] += exp(-(b+c*(d-i)+c*(j-e))/100.0) * QB[d][e];
-                    QM[i][j] += QM[i][d-1] * QB[d][e] * exp(-(b+c*(j-e))/100.0/RT);
+                    QM[i][j] += exp(-(b+c*(d-i)+c*(j-e))/RT) * QB[d][e];
+                    QM[i][j] += QM[i][d-1] * QB[d][e] * exp(-(b+c*(j-e))/RT);
                 }
             }
         }
@@ -137,22 +136,22 @@ void fillBasePairProbabilities(int length, int *structure, double **Q, double **
                     tempBuffer = P[i][j]*QB[h][l]/QB[i][j];
 
                     if(i == h-1 && j == l+1) //of which stacked pairs are a special case
-                        tempBuffer *= exp(-eS(i,j)/100.0/RT);
+                        tempBuffer *= exp(-eS(i,j)/RT);
                     else
-                        tempBuffer *= exp(-eL(i,j,h,l)/100.0/RT);
+                        tempBuffer *= exp(-eL(i,j,h,l)/RT);
 
                     P[h][l] += tempBuffer;
 
                     // third term
                     tempBuffer = 0; // Start over for multiloops
                     if(j - l > 3)
-                        tempBuffer += exp(-((h-i-1)*c/100.0/RT)) * QM[l+1][j-1];
+                        tempBuffer += exp(-((h-i-1)*c/RT)) * QM[l+1][j-1];
                     if(h - i > 3)
-                        tempBuffer += exp(-((j-l-1)*c/100.0/RT)) * QM[i+1][h-1];
+                        tempBuffer += exp(-((j-l-1)*c/RT)) * QM[i+1][h-1];
                     if(j - l > 3 && h - i > 3)
                         tempBuffer += QM[i+1][h-1] * QM[l+1][j-1];
 
-                    tempBuffer *= P[i][j] * QB[h][l] / QB[i][j] * exp(-(a+b)/100.0/RT);
+                    tempBuffer *= P[i][j] * QB[h][l] / QB[i][j] * exp(-(a+b)/RT);
 
                     P[h][l] += tempBuffer;
                 }
diff --git a/gtfold-mfe/src/partition-dangle.c b/gtfold-mfe/src/partition-dangle.c
new file mode 100644
index 0000000..df677fc
--- /dev/null
+++ b/gtfold-mfe/src/partition-dangle.c
@@ -0,0 +1,197 @@
+//Attempting to follow Ding and Lawrence as closely as possible
+
+/**s1 -> partial_external
+*  s2 -> partial_multi
+*  s3 -> partial_multi2
+*  u1 -> u_multi
+*  f -> cond_dangle (conditional)
+*  ebi -> eL
+**/
+
+#include <math.h>
+#include <stdlib.h>
+
+#include "energy.h"
+#include "utils.h"
+#include "global.h"
+#include "data.h"
+#include "algorithms-partition.h"
+#include "partition-dangle.h"
+
+#define MIN_TURN 4
+#define MAX_LOOP 30
+
+//double RT = (0.00198721 * 310.15)/100.00; 
+
+double cond_dangle(int j, int h, int l){
+	if(j - 1 == l)
+		return 1;
+	else 
+		return exp(-Ed3(h,l,l+1)/RT);
+}
+
+dangle_struct malloc_partition_arrays_d(int length){
+	dangle_struct ret_struct;
+	ret_struct.length = length;
+	
+	//Add 1 since we're not zero indexed
+	ret_struct.u = mallocTwoD(length + 1, length + 1); 
+	ret_struct.up = mallocTwoD(length + 1, length + 1); 
+	ret_struct.upm = mallocTwoD(length + 1, length + 1); 
+	ret_struct.u1 = mallocTwoD(length + 1, length + 1); 
+	ret_struct.s1 = mallocTwoD(length + 1, length + 1); 
+	ret_struct.s2 = mallocTwoD(length + 1, length + 1); 
+	ret_struct.s3 = mallocTwoD(length + 1, length + 1); 
+
+	int i,j;
+
+	for(i = 0; i < length + 1; i++){
+		for(j = 0; j < length + 1; j++){
+			ret_struct.u[i][j] = 1;
+			ret_struct.up[i][j] = 0;
+			ret_struct.upm[i][j] = 0;
+			ret_struct.u1[i][j] = 0;
+			ret_struct.s1[i][j] = 0;
+			ret_struct.s2[i][j] = 0;
+			ret_struct.s3[i][j] = 0;
+		}
+	}
+	return ret_struct;
+}
+
+void free_partition_arrays_d(struct partition_d part)
+{
+	freeTwoD(part.u, part.length, part.length);
+	freeTwoD(part.up, part.length, part.length);
+	freeTwoD(part.upm, part.length, part.length);
+	freeTwoD(part.u1, part.length, part.length);
+	freeTwoD(part.s1, part.length, part.length);
+	freeTwoD(part.s2, part.length, part.length);
+	freeTwoD(part.s3, part.length, part.length);
+}
+
+void fill_partition_arrays_d(dangle_struct part_struct){
+	//So that we don't have the /100 in every exponent
+	//Seeing as we missed some last time
+
+	double ** partial_external = part_struct.s1;
+	double ** partial_multi = part_struct.s2;
+	double ** partial_multi2 = part_struct.s3;
+	double ** u_multi = part_struct.u1;
+	double ** u = part_struct.u;
+	double ** up = part_struct.up;
+	double ** upm = part_struct.upm;
+	int len = part_struct.length;
+
+	int seg_length;
+	int i,j;
+
+	for(seg_length = MIN_TURN; seg_length <= len; len++){
+		//Insert parallelism here.
+		for(i = 1; i < len - seg_length; i++){
+			j = i + seg_length - 1;
+
+			int l;
+			if(canPair(i,j)){
+				for(l = i+2; l < j; l++){
+					upm[i][j] += up[i+1][l] * exp(-(Ea + 2 * Ec + auPenalty(i + 1,l)/RT)) *
+								(exp(-Ed3(i + 1,l,l+1)/RT) * u_multi[l + 2][j - 1] + 
+								u_multi[l + 1][j - 1] -
+								u_multi[l + 2][j - 1]);
+					if(l != i+2){ //goes from i + 2 < l < j
+						upm[i][j] += up[i + 2][l] * 
+								exp(-(Ea + 2 * Ec + Eb + Ed3(j,i,i + 1) + auPenalty(i + 2, l))/RT) *
+								(exp(-Ed3(i + 2,l,l + 1)/RT)*u_multi[l + 2][j - 1] + 
+								u_multi[l + 1][j - 1]  - 
+								u_multi[l + 2][j - 1]);
+
+						if(l != j - 1){
+							upm[i][j] += exp(-Ed3(j,i,i + 1)/RT)*exp(-(Ea + 2 * Ec + (l - i - 1) * Eb)/RT) * 
+										partial_multi[l][j]; 
+							//Changed h in the paper to l it makes no difference
+							//other than unifying loops
+						}
+					}
+				}
+
+
+				up[i][j] += exp(-eH(i,j)/RT) + exp(-eS(i,j)/RT) * up[i + 1][j - 1] + upm[i][j];
+				for(l = j - 1; l > i + 1; l--){
+					if((j - l) - 2> MAX_LOOP){
+						break;
+					}
+					int h;
+					for(h = i + 1 ; h < l; h++){
+						if(!(i == h - 1 && j == l - 1)){ //If this is true we have a stack
+							up[i][j] += exp(-eL(i,j,h,l)/RT);
+						}
+						if((j - l) + (h - i) - 2 > MAX_LOOP){
+							break;
+						}
+					}
+				}
+			}//End checkpair conditional
+
+			for(l = i + 1; l <= j ; l++){
+				u_multi[i][j] += up[i][l] * exp(-(Ec + auPenalty(i,l))/RT) *
+						(cond_dangle(j + 1,i,l) * exp(-(j - l) * Eb/RT) + 
+						exp(-Ed3(i,l,l + 1)/RT) * u_multi[l + 2][j] + 
+						u_multi[l + 1][j] -
+						u_multi[l + 2][j]);
+				if(l != i+1){	
+					u_multi[i][j] += up[i + 1][j]*exp(-(Ec + Eb + auPenalty(i + 1,l))/RT)*
+							(cond_dangle(j + 1, i + 1, l) * exp(-(j - l)*Eb/RT) + 
+							exp(-Ed3(i + 1,l,l + 1)/RT) * u_multi[l + 2][j] + 
+							u_multi[l + 1][j] - 
+							u_multi[l + 2][j]);
+					if(l != j){
+						u_multi[i][j] += exp(-(Ec + (l - i) * Eb)/RT) * partial_multi2[l][j];
+
+					}
+				}
+			}
+
+
+			int h = i; //To stay consistant with the notation in the paper.
+
+			for(l = h+1; l < j; l++){
+				partial_external[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
+							(exp(-Ed3(h,l,l + 1)/RT)*u[l + 2][j - 1] + 
+							u[l + 1][j] -
+							u[l + 2][j]);
+
+				partial_multi[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
+							(exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j - 1] + 
+							u_multi[l + 1][j - 1] -
+							u_multi[l + 2][j - 1]);
+
+				partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
+							(cond_dangle(j + 1, h, l)*exp(-(j - l) * Eb / RT) + 
+							exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j] + 
+							u_multi[l + 1][j] - 
+							u_multi[l + 2][j]);
+							
+			}
+			/** partial_multi2 goes up to j **/
+			partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) *
+						(cond_dangle(j + 1, h, l)*exp(-(j-l) * Eb / RT) + 
+						exp(-Ed3(h,l,l + 1)/RT) * u_multi[l + 2][j] + 
+						u_multi[l + 1][j] - 
+						u_multi[l + 2][j]);
+
+			//Finally we do the u matrix
+			u[i][j] = 1 + up[i][j]*exp(-auPenalty(i,j) /RT);
+
+			for(l = i + 1; l < j; l++){
+				//Replaced l with h in the next line to unify loops
+				u[i][j] += up[l][j] * exp(-(Ed5(l, j , l - 1) + auPenalty(h,j))/RT);
+
+				u[i][j] += exp(-(auPenalty(i,l))/RT)*(exp(-Ed3(i,l,l + 1)/RT) * u[l + 2][j] +
+					   u[l + 1][j] - u[l + 2][j]);
+				if(l != j - 1) {
+					u[i][j] += partial_external[l][j];
+				}
+			}
+		}//end of minor (paralellizeable) for loop
+	}//End of major for loop
+}
diff --git a/gtfold-mfe/src/random-sample.cc b/gtfold-mfe/src/random-sample.cc
index 3290e38..ff53afa 100644
--- a/gtfold-mfe/src/random-sample.cc
+++ b/gtfold-mfe/src/random-sample.cc
@@ -1,10 +1,29 @@
 #include <math.h>
 #include <stdlib.h>
+#include <list>
 
-#include "parition-dangle.h"
+#include "partition-dangle.h"
+#include "algorithms-partition.h"
 #include "energy.h"
+#include "random-sample.h"
 
-double RT=(0.00198721 * 310.15)/100.00; 
+using namespace std;
+
+#define MIN_TURN 4
+
+//double RT=(0.00198721 * 310.15)/100.00; 
+
+
+//I don't know why not having this function
+//gives me a link error it should get this function
+//from partition-dangle
+
+double cond_dangle(int j, int h, int l){
+	if(j - 1 == l)
+		return 1;
+	else 
+		return exp(-Ed3(h,l,l+1)/RT);
+}
 
 double randdouble(){
 	    return rand()/(double(RAND_MAX)+1);
@@ -25,14 +44,14 @@ double prob_h_pairs_with_5_end
 		(int i, int h, int j, dangle_struct d_struct){
 
 	return d_struct.up[h][j] * 
-			exp(-(ed5(h,j,h - 1) + 
+			exp(-(Ed5(h,j,h - 1) + 
 			auPenalty(h,j))/RT) /
 			d_struct.u[i][j];
 }
 
 //P_{il}
 double prob_l_pairs_with_3_end
-	(int i, int l, int j dangle_struct d_struct){
+	(int i, int l, int j, dangle_struct d_struct){
 
 	return d_struct.up[i][l] * exp(-auPenalty(i,l)/RT) *
 			(exp(-Ed3(i,l,l+1)/RT) * d_struct.u[l + 2][j] +
@@ -96,7 +115,7 @@ double first_multi_prob_pair_next_base
 double first_multi_prob_pair_after_base
 	(int i, int l, int j, dangle_struct d_struct){
 	
-	return d_struct[i + 2][l] * 
+	return d_struct.up[i + 2][l] * 
 			exp(-(Ea + 2 * Ec + Eb + Ed3(j, i, i + 1) + auPenalty(i + 2,l))/RT) *
 			(exp(-Ed3(i + 2,l,l+1)/RT) * d_struct.u1[l + 2][j - 1] +
 			d_struct.u1[l + 1][j - 1] -
@@ -106,7 +125,7 @@ double first_multi_prob_pair_after_base
 
 //P_{ijs2h)
 double first_multi_prob_pair_rest_base(int i, int h, int j, dangle_struct d_struct){
-	return exp(-(Ea + 2 * Ec + (h - i - 1) * b + Ed3(j,i,i+1))/RT) *
+	return exp(-(Ea + 2 * Ec + (h - i - 1) * Eb + Ed3(j,i,i+1))/RT) *
 			d_struct.s2[h][j] / d_struct.upm[i][j];
 }
 //P_{ijhl}
@@ -120,10 +139,9 @@ double first_multi_prob_base_rest
 }
 
 //Q_{(l1 + 1)(j -1)(l1 +1)}
-double rest_multi_prob_next_base_pairs
-	(int l1, int l, int j, dangle_struct d_struct){
+double rest_multi_prob_next_base_pairs (int l1, int l, int j, dangle_struct d_struct){
 	
-	return d_struct.up[l1 +1][l] * exp( - (Ec + auPenalty(l1 + 1, l))/RT)
+	return d_struct.up[l1 +1][l] * exp(-(Ec + auPenalty(l1 + 1, l))/RT) *
 			(cond_dangle(j, l1 + 1, l) * exp( -(j - 1 - l) * Eb /RT) +
 			exp(-(j - 1 - l) * Eb) / RT + 
 			exp(-Ed3(l1 + 1, l, l + 1)/RT) * d_struct.u1[l + 2][j - 1] +
@@ -166,9 +184,10 @@ double rest_multi_prob_h_pairs_with_l
 			d_struct.s3[h][j - 1];
 }
 
+//P_{Bh2l2}
 int there_is_another_helix(int h2, int l2, int j, dangle_struct d_struct){
 	double counter = randdouble();
-	double coin-flip = cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) /
+	double coin_flip = cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) /
 					  (cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) + 
 					exp(Ed3(h2,l2,l2 + 1)/RT) * d_struct.u1[l2 + 2][j - 1] +
 					d_struct.u1[l2 + 1][j - 1] -
@@ -178,10 +197,363 @@ int there_is_another_helix(int h2, int l2, int j, dangle_struct d_struct){
 		
 	//return counter > coin-flip
 
-	if(counter <= coin-flip){
+	if(counter <= coin_flip){
 		return 0;
 	}
 	else{
 		return 1;
 	}
 }
+
+void single_stranded(int i, int j, int * structure){
+	for(;i <= j; i++)
+	{
+		structure[i] = 0;
+	}
+}
+
+void unknown_strand(int i, int j, dangle_struct d_struct, int * structure, list<sub_seq> * stack){
+//Unknown strand from i,j
+	double counter = randdouble();
+	counter -= single_stranded_prob(i, j, d_struct);
+	if (counter <= 0){
+		single_stranded(i,j, structure);
+		return;
+	}
+	counter -= ends_pair_prob(i, j, d_struct);
+	if(counter <= 0){
+		sub_seq seq;
+		seq.start = i;
+		seq.end = j;
+		seq.paired = 1;
+		//put i j on paired and push i j on stack as paired
+		
+		structure[i] = j;
+		structure[j] = i;
+		stack->push_front(seq);
+		return;
+	}
+	for (int h = i + MIN_TURN; h < j; h++){
+		counter -= prob_h_pairs_with_5_end(i,h,j,d_struct);
+		if(counter < 0){
+			sub_seq seq1;
+			sub_seq seq2;
+
+			seq1.start = i;
+			seq1.end = h;
+			seq1.paired = 1;
+
+			seq2.start = h + 1;
+			seq2.end = j;
+			seq2.paired = 0;
+			
+			//Push i h as paired and h + 1 to j as unknown
+			structure[i] = h;
+			structure[h] = i;
+			stack->push_front(seq1);
+			stack->push_front(seq2);
+			return;
+		}
+	}
+
+	for(int l = i + 1; l <= j - MIN_TURN; l++){
+		counter -= prob_l_pairs_with_3_end(i,l,j,d_struct);
+		if (counter < 0){
+			
+			sub_seq seq;
+			seq.start = l;
+			seq.end = j;
+			seq.paired = 1;
+
+			//put from i to l - 1 as unpaired and push l and j as paired
+			single_stranded(i, l - 1, structure);
+			structure[l] = j;
+			structure[j] = l;
+			stack->push_front(seq);
+			return;
+		}
+	}
+	int h; //The loop is just to find h we need it later
+	for(h = i + 1; i <= j - MIN_TURN - 1; h++){
+		counter -= prob_h_pairs_in_ij(i,h,j,d_struct);
+		if(counter < 0)
+		{
+			break;
+		}
+	}
+
+	//Now to find l
+	counter = randdouble(); //reset counter, this is a seperate case
+	for(int l = h + MIN_TURN; l <= j - MIN_TURN; l++){
+		counter -= prob_h_pairs_with_l(h,l,j,d_struct);	
+		if (counter < 0){
+			sub_seq seq1;
+			sub_seq seq2;
+			
+			seq1.start = h;
+			seq1.end = l;
+			seq1.paired = 1;
+
+			seq2.start = l + 1;
+			seq2.end = j;
+			seq2.paired = 0;
+
+			//set from i to h - 1 as single stranded
+			//Push h l as paired and l + 1 to j
+			//as unknown.
+
+			single_stranded(i, h - 1, structure);
+			structure[h] = l;
+			structure[l] = h;
+			stack->push_front(seq1);
+			stack->push_front(seq2);
+			return;
+		}	
+	}
+	//If we hit here, that's bad
+}
+
+void paired_strand(int i, int j, dangle_struct d_struct, int * structure, list<sub_seq> * stack){
+	double counter = randdouble();
+	double cumulative_prob = 0;
+
+ 
+	cumulative_prob = prob_ij_pair_is_hairpin(i,j,d_struct);
+	if(counter - cumulative_prob < 0){
+		//i + 1, j - 1 is single stranded
+		single_stranded(i + 1, j - 1, structure);
+		return;
+	}
+
+	cumulative_prob += prob_ij_pair_is_stack(i,j,d_struct);
+	if(counter - cumulative_prob < 0){
+		sub_seq seq;
+		seq.start = i + 1;
+		seq.end = j - 1;
+		seq.paired = 1;
+
+		//i + 1, j - 1 is pushed as stack
+		stack->push_front(seq);
+		structure[i + 1] = j - 1;
+		structure[j - 1] = i + 1;
+		return;
+	}
+
+	cumulative_prob += prob_ij_pair_is_multiloop(i,j,d_struct);
+	if(counter - cumulative_prob < 0){
+		multi_loop_strand(i,j,d_struct,structure,stack);
+		return;
+	}
+
+	//else we know we have an internal loop.
+	//The probabilities should work out so that
+	//we never get more than 30 base internal loops.
+	//Might need to put guards in here.
+	counter = randdouble();
+	for(int h = i + 1; h < j; h++){
+		for(int l = h + MIN_TURN; l < j; l++){
+			if(!(h == i + 1 && l == j - 1)) //Don't want a stack
+				counter -= exp(-eL(i,j,h,l)/RT) * d_struct.up[h][l] / (1 - cumulative_prob); 
+				if(counter < 0){
+					sub_seq	seq;
+					seq.start = h;
+					seq.end = l;
+					seq.paired = 1;
+
+					//hl goes on the stack as a pair and the rest of the internal loop
+					//gets put on a single stranded
+
+					stack->push_front(seq);
+					structure[h] = l;
+					structure[l] = h;
+					single_stranded(i + 1, h - 1,structure);
+					single_stranded(l + 1, j - 1,structure);
+				}
+		}
+	}
+}
+
+//It returns where it stops.
+int multi_first_loop(int i, int j, dangle_struct d_struct, int * structure, list<sub_seq> * stack){
+	double counter = randdouble();
+	for(int l= i + MIN_TURN + 1; l < j - 1; l++){
+		counter -= first_multi_prob_pair_next_base(i,l,j,d_struct);
+		if(counter < 0){
+			sub_seq seq;
+			seq.start = i + 1;
+			seq.end = l;
+			seq.paired = 1;
+
+			//Under this condition i + 1 pairs with l;
+			
+			stack->push_front(seq);
+			structure[i + 1] = l;
+			structure[l] = i + 1;
+			return l + 1;
+		}
+	}
+	for(int l = i + MIN_TURN + 2; l < j - 1; l++){
+		counter -= first_multi_prob_pair_after_base(i,l,j,d_struct);
+		if(counter < 0){
+			sub_seq seq;
+			seq.start = i + 2;
+			seq.end = l;
+			seq.paired = 1;
+
+			//Under this condition i + 2 pairs with l;
+			//and i + 1 is unpaired
+			
+			stack->push_front(seq);
+			structure[i + 1] = 0;
+			structure[i + 2] = l;
+			structure[l] = i + 2;
+			return l + 1;
+		}
+	}
+	
+	//We need h after this loop so we declare it here.
+	int h;
+	for(h = i + 3; h < j - 1; h ++){
+		counter -= first_multi_prob_pair_rest_base(i,h,j,d_struct);
+		if(counter < 0){
+			break;
+		}
+	}
+	
+	//Now h is the opening base in a base pair now we need to find the closing one
+	//So first we start a new counter
+	counter = randdouble();
+	for (int l = h + MIN_TURN; l < j - 1; l++){
+		counter -= first_multi_prob_base_rest(i,h,l,j,d_struct);
+		if(counter < 0){
+			sub_seq seq;
+			seq.start = h;
+			seq.end = l;
+			seq.paired = 1;
+			
+			//H pairs with l and i + 1 to h - 1 is single stranded
+			single_stranded(i + 1, h - 1, structure);
+			stack->push_front(seq);
+			structure[h] = l;
+			structure[l] = h;
+			return l + 1;
+		}
+	}
+	
+	return -1; //We have an underflow or calculation error.
+}
+
+void multi_loop_strand(int i, int j, dangle_struct d_struct, int * structure, list<sub_seq> * stack){
+	int l1 = multi_first_loop(i,j,d_struct, structure,stack);//l1 is the name of the closing base of the first loop
+	int h1 = i;
+	int notdone = 1;
+	int breakflag = 0;
+	
+	while(notdone){
+		double counter = randdouble();
+		for(int l = l1 + MIN_TURN + 1; l < j - 1; l++){
+			counter -= rest_multi_prob_next_base_pairs(l1,l,j,d_struct);
+			if(counter < 0){
+				sub_seq seq;
+				seq.start = l1 + 1;
+				seq.end = l;
+				seq.paired = 1;
+
+				//Under this condition i + 1 pairs with l;
+				
+				stack->push_front(seq);
+				structure[l1 + 1] = l;
+				structure[l] = i + 1;
+				h1 = l1 + 1;
+				l1 = l;
+				breakflag = 1;
+				break;
+			}
+		}
+		if(breakflag){
+			notdone = there_is_another_helix(h1, l1, j, d_struct);
+			breakflag = 0;
+			continue; //Starts while loop over
+		}
+		for(int l = l1 + MIN_TURN + 2; l < j - 1; l++){
+			counter -= rest_multi_prob_after_base_pairs(l1,l,j,d_struct);
+			if(counter < 0){
+				sub_seq seq;
+				seq.start = l1 + 2;
+				seq.end = l;
+				seq.paired = 1;
+
+				//Under this condition i + 2 pairs with l;
+				//and i + 1 is unpaired
+				
+				stack->push_front(seq);
+				structure[l1 + 1] = 0;
+				structure[l1 + 2] = l;
+				structure[l] = l1 + 2;
+				h1 = l1 + 2;
+				l1 = l;
+				breakflag = 1;
+				break;
+			}
+		}
+		if(breakflag){
+			notdone = there_is_another_helix(h1, l1, j, d_struct);
+			breakflag = 0;
+			continue; //Starts while loop over
+		}
+		//We need h after this loop so we declare it here.
+		int h;
+		for(h = l1 + 3; h < j - 1; h ++){
+			counter -= rest_multi_prob_rest_base_pairs(i,h,j,d_struct);
+			if(counter < 0){
+				break;
+			}
+		}
+		
+		//Now h is the opening base in a base pair now we need to find the closing one
+		//So first we start a new counter
+		counter = randdouble();
+		for (int l = h + MIN_TURN; l < j - 1; l++){
+			counter -= rest_multi_prob_h_pairs_with_l(l1,h,l,j,d_struct);
+			if(counter < 0){
+				sub_seq seq;
+				seq.start = h;
+				seq.end = l;
+				seq.paired = 1;
+				
+				//H pairs with l and i + 1 to h - 1 is single stranded
+				single_stranded(l1 + 1, h - 1, structure);
+				stack->push_front(seq);
+				structure[h] = l;
+				structure[l] = h;
+				l1 = l + 1;
+				h1 = h;
+			}
+		}
+		notdone = there_is_another_helix(h1, l1, j, d_struct);
+	}//End while
+}//End function
+
+
+void sample_structure(int * structure, dangle_struct d_struct){
+	sub_seq seq;
+	seq.start = 1;
+	seq.end = d_struct.length;
+	seq.paired = 0;
+
+	list<sub_seq> da_stack;
+	da_stack.push_front(seq);
+	while(!da_stack.empty()){
+		sub_seq cur_seq = da_stack.front();
+		if(cur_seq.paired)
+		{
+			paired_strand(cur_seq.start, cur_seq.end, d_struct, structure, &da_stack);
+		}
+		else
+		{
+			unknown_strand(cur_seq.start, cur_seq.end, d_struct, structure, &da_stack);
+		}
+		da_stack.pop_front();
+	}
+	
+}

From 142e6c6580b6e0d733eefd4d10c1b697ff1f6e5b Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Thu, 16 Jun 2011 11:55:09 -0400
Subject: [PATCH 141/282] I believe my automake is broken, but bpp
 theoretically re-integrated

---
 gtfold-mfe/INSTALL                        | 228 ++++++++++++++++----
 gtfold-mfe/aclocal.m4                     |  12 --
 gtfold-mfe/config.guess                   | 248 ++++++++++------------
 gtfold-mfe/config.sub                     | 102 +++++++--
 gtfold-mfe/configure                      |   1 -
 gtfold-mfe/configure.in                   |  34 ++-
 gtfold-mfe/depcomp                        |  87 ++++++--
 gtfold-mfe/include/Makefile.am            |   2 +-
 gtfold-mfe/include/Makefile.in            |   2 +-
 gtfold-mfe/include/algorithms-partition.h |  18 +-
 gtfold-mfe/include/partition-dangle.h     |   1 +
 gtfold-mfe/install-sh                     |   5 +-
 gtfold-mfe/missing                        |  49 +++--
 gtfold-mfe/src/.deps/main.Po              |  15 +-
 gtfold-mfe/src/Makefile                   |   4 +-
 gtfold-mfe/src/Makefile.am                |   4 +-
 gtfold-mfe/src/Makefile.in                |   4 +-
 gtfold-mfe/src/algorithms-partition.c     |   4 +-
 gtfold-mfe/src/main.cc                    |  25 +++
 gtfold-mfe/src/random-sample.cc           |   4 +-
 20 files changed, 540 insertions(+), 309 deletions(-)
 mode change 100644 => 100755 gtfold-mfe/config.guess
 mode change 100644 => 100755 gtfold-mfe/config.sub
 mode change 100644 => 100755 gtfold-mfe/depcomp
 mode change 100644 => 100755 gtfold-mfe/missing

diff --git a/gtfold-mfe/INSTALL b/gtfold-mfe/INSTALL
index 54caf7c..7d1c323 100644
--- a/gtfold-mfe/INSTALL
+++ b/gtfold-mfe/INSTALL
@@ -1,13 +1,25 @@
-Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software
-Foundation, Inc.
+Installation Instructions
+*************************
 
-   This file is free documentation; the Free Software Foundation gives
-unlimited permission to copy, distribute and modify it.
+Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
+2006, 2007, 2008, 2009 Free Software Foundation, Inc.
+
+   Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved.  This file is offered as-is,
+without warranty of any kind.
 
 Basic Installation
 ==================
 
-   These are generic installation instructions.
+   Briefly, the shell commands `./configure; make; make install' should
+configure, build, and install this package.  The following
+more-detailed instructions are generic; see the `README' file for
+instructions specific to this package.  Some packages provide this
+`INSTALL' file but do not implement all of the features documented
+below.  The lack of an optional feature in a given package is not
+necessarily a bug.  More recommendations for GNU packages can be found
+in *note Makefile Conventions: (standards)Makefile Conventions.
 
    The `configure' shell script attempts to guess correct values for
 various system-dependent variables used during compilation.  It uses
@@ -20,9 +32,9 @@ debugging `configure').
 
    It can also use an optional file (typically called `config.cache'
 and enabled with `--cache-file=config.cache' or simply `-C') that saves
-the results of its tests to speed up reconfiguring.  (Caching is
+the results of its tests to speed up reconfiguring.  Caching is
 disabled by default to prevent problems with accidental use of stale
-cache files.)
+cache files.
 
    If you need to do unusual things to compile the package, please try
 to figure out how `configure' could check whether to do them, and mail
@@ -32,30 +44,37 @@ some point `config.cache' contains results you don't want to keep, you
 may remove or edit it.
 
    The file `configure.ac' (or `configure.in') is used to create
-`configure' by a program called `autoconf'.  You only need
-`configure.ac' if you want to change it or regenerate `configure' using
-a newer version of `autoconf'.
+`configure' by a program called `autoconf'.  You need `configure.ac' if
+you want to change it or regenerate `configure' using a newer version
+of `autoconf'.
 
-The simplest way to compile this package is:
+   The simplest way to compile this package is:
 
   1. `cd' to the directory containing the package's source code and type
-     `./configure' to configure the package for your system.  If you're
-     using `csh' on an old version of System V, you might need to type
-     `sh ./configure' instead to prevent `csh' from trying to execute
-     `configure' itself.
+     `./configure' to configure the package for your system.
 
-     Running `configure' takes awhile.  While running, it prints some
-     messages telling which features it is checking for.
+     Running `configure' might take a while.  While running, it prints
+     some messages telling which features it is checking for.
 
   2. Type `make' to compile the package.
 
   3. Optionally, type `make check' to run any self-tests that come with
-     the package.
+     the package, generally using the just-built uninstalled binaries.
 
   4. Type `make install' to install the programs and any data files and
-     documentation.
-
-  5. You can remove the program binaries and object files from the
+     documentation.  When installing into a prefix owned by root, it is
+     recommended that the package be configured and built as a regular
+     user, and only the `make install' phase executed with root
+     privileges.
+
+  5. Optionally, type `make installcheck' to repeat any self-tests, but
+     this time using the binaries in their final installed location.
+     This target does not install anything.  Running this target as a
+     regular user, particularly if the prior `make install' required
+     root privileges, verifies that the installation completed
+     correctly.
+
+  6. You can remove the program binaries and object files from the
      source code directory by typing `make clean'.  To also remove the
      files that `configure' created (so you can compile the package for
      a different kind of computer), type `make distclean'.  There is
@@ -64,6 +83,16 @@ The simplest way to compile this package is:
      all sorts of other programs in order to regenerate files that came
      with the distribution.
 
+  7. Often, you can also type `make uninstall' to remove the installed
+     files again.  In practice, not all packages have tested that
+     uninstallation works correctly, even though it is required by the
+     GNU Coding Standards.
+
+  8. Some packages, particularly those that use Automake, provide `make
+     distcheck', which can by used by developers to test that all other
+     targets like `make install' and `make uninstall' work correctly.
+     This target is generally not run by end users.
+
 Compilers and Options
 =====================
 
@@ -75,7 +104,7 @@ for details on some of the pertinent environment variables.
 by setting variables in the command line or in the environment.  Here
 is an example:
 
-     ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix
+     ./configure CC=c99 CFLAGS=-g LIBS=-lposix
 
    *Note Defining Variables::, for more details.
 
@@ -84,44 +113,89 @@ Compiling For Multiple Architectures
 
    You can compile the package for more than one kind of computer at the
 same time, by placing the object files for each architecture in their
-own directory.  To do this, you must use a version of `make' that
-supports the `VPATH' variable, such as GNU `make'.  `cd' to the
+own directory.  To do this, you can use GNU `make'.  `cd' to the
 directory where you want the object files and executables to go and run
 the `configure' script.  `configure' automatically checks for the
-source code in the directory that `configure' is in and in `..'.
+source code in the directory that `configure' is in and in `..'.  This
+is known as a "VPATH" build.
 
-   If you have to use a `make' that does not support the `VPATH'
-variable, you have to compile the package for one architecture at a
-time in the source code directory.  After you have installed the
-package for one architecture, use `make distclean' before reconfiguring
-for another architecture.
+   With a non-GNU `make', it is safer to compile the package for one
+architecture at a time in the source code directory.  After you have
+installed the package for one architecture, use `make distclean' before
+reconfiguring for another architecture.
+
+   On MacOS X 10.5 and later systems, you can create libraries and
+executables that work on multiple system types--known as "fat" or
+"universal" binaries--by specifying multiple `-arch' options to the
+compiler but only a single `-arch' option to the preprocessor.  Like
+this:
+
+     ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+                 CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+                 CPP="gcc -E" CXXCPP="g++ -E"
+
+   This is not guaranteed to produce working output in all cases, you
+may have to build one architecture at a time and combine the results
+using the `lipo' tool if you have problems.
 
 Installation Names
 ==================
 
-   By default, `make install' will install the package's files in
-`/usr/local/bin', `/usr/local/man', etc.  You can specify an
-installation prefix other than `/usr/local' by giving `configure' the
-option `--prefix=PATH'.
+   By default, `make install' installs the package's commands under
+`/usr/local/bin', include files under `/usr/local/include', etc.  You
+can specify an installation prefix other than `/usr/local' by giving
+`configure' the option `--prefix=PREFIX', where PREFIX must be an
+absolute file name.
 
    You can specify separate installation prefixes for
 architecture-specific files and architecture-independent files.  If you
-give `configure' the option `--exec-prefix=PATH', the package will use
-PATH as the prefix for installing programs and libraries.
-Documentation and other data files will still use the regular prefix.
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files still use the regular prefix.
 
    In addition, if you use an unusual directory layout you can give
-options like `--bindir=PATH' to specify different values for particular
+options like `--bindir=DIR' to specify different values for particular
 kinds of files.  Run `configure --help' for a list of the directories
-you can set and what kinds of files go in them.
+you can set and what kinds of files go in them.  In general, the
+default for these options is expressed in terms of `${prefix}', so that
+specifying just `--prefix' will affect all of the other directory
+specifications that were not explicitly provided.
+
+   The most portable way to affect installation locations is to pass the
+correct locations to `configure'; however, many packages provide one or
+both of the following shortcuts of passing variable assignments to the
+`make install' command line to change installation locations without
+having to reconfigure or recompile.
+
+   The first method involves providing an override variable for each
+affected directory.  For example, `make install
+prefix=/alternate/directory' will choose an alternate location for all
+directory configuration variables that were expressed in terms of
+`${prefix}'.  Any directories that were specified during `configure',
+but not in terms of `${prefix}', must each be overridden at install
+time for the entire installation to be relocated.  The approach of
+makefile variable overrides for each directory variable is required by
+the GNU Coding Standards, and ideally causes no recompilation.
+However, some platforms have known limitations with the semantics of
+shared libraries that end up requiring recompilation when using this
+method, particularly noticeable in packages that use GNU Libtool.
+
+   The second method involves providing the `DESTDIR' variable.  For
+example, `make install DESTDIR=/alternate/directory' will prepend
+`/alternate/directory' before all installation names.  The approach of
+`DESTDIR' overrides is not required by the GNU Coding Standards, and
+does not work on platforms that have drive letters.  On the other hand,
+it does better at avoiding recompilation issues, and works well even
+when some directory options were not specified in terms of `${prefix}'
+at `configure' time.
+
+Optional Features
+=================
 
    If the package supports it, you can cause programs to be installed
 with an extra prefix or suffix on their names by giving `configure' the
 option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
 
-Optional Features
-=================
-
    Some packages pay attention to `--enable-FEATURE' options to
 `configure', where FEATURE indicates an optional part of the package.
 They may also pay attention to `--with-PACKAGE' options, where PACKAGE
@@ -134,6 +208,45 @@ find the X include and library files automatically, but if it doesn't,
 you can use the `configure' options `--x-includes=DIR' and
 `--x-libraries=DIR' to specify their locations.
 
+   Some packages offer the ability to configure how verbose the
+execution of `make' will be.  For these packages, running `./configure
+--enable-silent-rules' sets the default to minimal output, which can be
+overridden with `make V=1'; while running `./configure
+--disable-silent-rules' sets the default to verbose, which can be
+overridden with `make V=0'.
+
+Particular systems
+==================
+
+   On HP-UX, the default C compiler is not ANSI C compatible.  If GNU
+CC is not installed, it is recommended to use the following options in
+order to use an ANSI C compiler:
+
+     ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
+
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+
+   On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
+parse its `<wchar.h>' header file.  The option `-nodtk' can be used as
+a workaround.  If GNU CC is not installed, it is therefore recommended
+to try
+
+     ./configure CC="cc"
+
+and if that doesn't work, try
+
+     ./configure CC="cc -nodtk"
+
+   On Solaris, don't put `/usr/ucb' early in your `PATH'.  This
+directory contains several dysfunctional programs; working variants of
+these programs are available in `/usr/bin'.  So, if you need `/usr/ucb'
+in your `PATH', put it _after_ `/usr/bin'.
+
+   On Haiku, software installed for all users goes in `/boot/common',
+not `/usr/local'.  It is recommended to use the following options:
+
+     ./configure --prefix=/boot/common
+
 Specifying the System Type
 ==========================
 
@@ -149,14 +262,15 @@ type, such as `sun4', or a canonical name which has the form:
 
 where SYSTEM can have one of these forms:
 
-     OS KERNEL-OS
+     OS
+     KERNEL-OS
 
    See the file `config.sub' for the possible values of each field.  If
 `config.sub' isn't included in this package, then this package doesn't
 need to know the machine type.
 
    If you are _building_ compiler tools for cross-compiling, you should
-use the `--target=TYPE' option to select the type of system they will
+use the option `--target=TYPE' to select the type of system they will
 produce code for.
 
    If you want to _use_ a cross compiler, that generates code for a
@@ -186,9 +300,14 @@ them in the `configure' command line, using `VAR=value'.  For example:
 
      ./configure CC=/usr/local2/bin/gcc
 
-will cause the specified gcc to be used as the C compiler (unless it is
+causes the specified `gcc' to be used as the C compiler (unless it is
 overridden in the site shell script).
 
+Unfortunately, this technique does not work for `CONFIG_SHELL' due to
+an Autoconf bug.  Until the bug is fixed you can use this workaround:
+
+     CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
+
 `configure' Invocation
 ======================
 
@@ -197,7 +316,14 @@ operates.
 
 `--help'
 `-h'
-     Print a summary of the options to `configure', and exit.
+     Print a summary of all of the options to `configure', and exit.
+
+`--help=short'
+`--help=recursive'
+     Print a summary of the options unique to this package's
+     `configure', and exit.  The `short' variant lists options used
+     only in the top level, while the `recursive' variant lists options
+     also present in any nested packages.
 
 `--version'
 `-V'
@@ -224,6 +350,16 @@ operates.
      Look for the package's source code in directory DIR.  Usually
      `configure' can determine that directory automatically.
 
+`--prefix=DIR'
+     Use DIR as the installation prefix.  *note Installation Names::
+     for more details, including other options available for fine-tuning
+     the installation locations.
+
+`--no-create'
+`-n'
+     Run the configure checks, but stop before creating any output
+     files.
+
 `configure' also accepts some other, not widely useful, options.  Run
 `configure --help' for more details.
 
diff --git a/gtfold-mfe/aclocal.m4 b/gtfold-mfe/aclocal.m4
index f5a02ce..eba341b 100644
--- a/gtfold-mfe/aclocal.m4
+++ b/gtfold-mfe/aclocal.m4
@@ -406,18 +406,6 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
      [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
 ])
 
-# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005
-# Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# serial 8
-
-# AM_CONFIG_HEADER is obsolete.  It has been replaced by AC_CONFIG_HEADERS.
-AU_DEFUN([AM_CONFIG_HEADER], [AC_CONFIG_HEADERS($@)])
-
 # Do all the work for Automake.                             -*- Autoconf -*-
 
 # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
diff --git a/gtfold-mfe/config.guess b/gtfold-mfe/config.guess
old mode 100644
new mode 100755
index ca2a03c..c2246a4
--- a/gtfold-mfe/config.guess
+++ b/gtfold-mfe/config.guess
@@ -1,10 +1,10 @@
 #! /bin/sh
 # Attempt to guess a canonical system name.
 #   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-#   2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008
+#   2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010
 #   Free Software Foundation, Inc.
 
-timestamp='2008-01-08'
+timestamp='2009-12-30'
 
 # This file is free software; you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by
@@ -27,16 +27,16 @@ timestamp='2008-01-08'
 # the same distribution terms that you use for the rest of that program.
 
 
-# Originally written by Per Bothner <per@bothner.com>.
-# Please send patches to <config-patches@gnu.org>.  Submit a context
-# diff and a properly formatted ChangeLog entry.
+# Originally written by Per Bothner.  Please send patches (context
+# diff format) to <config-patches@gnu.org> and include a ChangeLog
+# entry.
 #
 # This script attempts to guess a canonical system name similar to
 # config.sub.  If it succeeds, it prints the system name on stdout, and
 # exits with 0.  Otherwise, it exits with 1.
 #
-# The plan is that this can be called by configure scripts if you
-# don't specify an explicit build system type.
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
 
 me=`echo "$0" | sed -e 's,.*/,,'`
 
@@ -56,8 +56,9 @@ version="\
 GNU config.guess ($timestamp)
 
 Originally written by Per Bothner.
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
-2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,
+2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free
+Software Foundation, Inc.
 
 This is free software; see the source for copying conditions.  There is NO
 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -170,7 +171,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
 	    arm*|i386|m68k|ns32k|sh3*|sparc|vax)
 		eval $set_cc_for_build
 		if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
-			| grep __ELF__ >/dev/null
+			| grep -q __ELF__
 		then
 		    # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
 		    # Return netbsd for either.  FIX?
@@ -324,14 +325,33 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
 	case `/usr/bin/uname -p` in
 	    sparc) echo sparc-icl-nx7; exit ;;
 	esac ;;
+    s390x:SunOS:*:*)
+	echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+	exit ;;
     sun4H:SunOS:5.*:*)
 	echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
 	exit ;;
     sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
 	echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
 	exit ;;
+    i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*)
+	echo i386-pc-auroraux${UNAME_RELEASE}
+	exit ;;
     i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
-	echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+	eval $set_cc_for_build
+	SUN_ARCH="i386"
+	# If there is a compiler, see if it is configured for 64-bit objects.
+	# Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
+	# This test works for both compilers.
+	if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+	    if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
+		(CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+		grep IS_64BIT_ARCH >/dev/null
+	    then
+		SUN_ARCH="x86_64"
+	    fi
+	fi
+	echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
 	exit ;;
     sun4*:SunOS:6*:*)
 	# According to config.sub, this is the proper way to canonicalize
@@ -640,7 +660,7 @@ EOF
 	    # => hppa64-hp-hpux11.23
 
 	    if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
-		grep __LP64__ >/dev/null
+		grep -q __LP64__
 	    then
 		HP_ARCH="hppa2.0w"
 	    else
@@ -791,12 +811,12 @@ EOF
     i*:PW*:*)
 	echo ${UNAME_MACHINE}-pc-pw32
 	exit ;;
-    *:Interix*:[3456]*)
+    *:Interix*:*)
     	case ${UNAME_MACHINE} in
 	    x86)
 		echo i586-pc-interix${UNAME_RELEASE}
 		exit ;;
-	    EM64T | authenticamd)
+	    authenticamd | genuineintel | EM64T)
 		echo x86_64-unknown-interix${UNAME_RELEASE}
 		exit ;;
 	    IA64)
@@ -806,6 +826,9 @@ EOF
     [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
 	echo i${UNAME_MACHINE}-pc-mks
 	exit ;;
+    8664:Windows_NT:*)
+	echo x86_64-pc-mks
+	exit ;;
     i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
 	# How do we know it's Interix rather than the generic POSIX subsystem?
 	# It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
@@ -835,6 +858,20 @@ EOF
     i*86:Minix:*:*)
 	echo ${UNAME_MACHINE}-pc-minix
 	exit ;;
+    alpha:Linux:*:*)
+	case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
+	  EV5)   UNAME_MACHINE=alphaev5 ;;
+	  EV56)  UNAME_MACHINE=alphaev56 ;;
+	  PCA56) UNAME_MACHINE=alphapca56 ;;
+	  PCA57) UNAME_MACHINE=alphapca56 ;;
+	  EV6)   UNAME_MACHINE=alphaev6 ;;
+	  EV67)  UNAME_MACHINE=alphaev67 ;;
+	  EV68*) UNAME_MACHINE=alphaev68 ;;
+        esac
+	objdump --private-headers /bin/sh | grep -q ld.so.1
+	if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
+	echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+	exit ;;
     arm*:Linux:*:*)
 	eval $set_cc_for_build
 	if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
@@ -857,6 +894,17 @@ EOF
     frv:Linux:*:*)
     	echo frv-unknown-linux-gnu
 	exit ;;
+    i*86:Linux:*:*)
+	LIBC=gnu
+	eval $set_cc_for_build
+	sed 's/^	//' << EOF >$dummy.c
+	#ifdef __dietlibc__
+	LIBC=dietlibc
+	#endif
+EOF
+	eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
+	echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
+	exit ;;
     ia64:Linux:*:*)
 	echo ${UNAME_MACHINE}-unknown-linux-gnu
 	exit ;;
@@ -866,74 +914,33 @@ EOF
     m68*:Linux:*:*)
 	echo ${UNAME_MACHINE}-unknown-linux-gnu
 	exit ;;
-    mips:Linux:*:*)
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-	#undef CPU
-	#undef mips
-	#undef mipsel
-	#if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
-	CPU=mipsel
-	#else
-	#if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
-	CPU=mips
-	#else
-	CPU=
-	#endif
-	#endif
-EOF
-	eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
-	    /^CPU/{
-		s: ::g
-		p
-	    }'`"
-	test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
-	;;
-    mips64:Linux:*:*)
+    mips:Linux:*:* | mips64:Linux:*:*)
 	eval $set_cc_for_build
 	sed 's/^	//' << EOF >$dummy.c
 	#undef CPU
-	#undef mips64
-	#undef mips64el
+	#undef ${UNAME_MACHINE}
+	#undef ${UNAME_MACHINE}el
 	#if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
-	CPU=mips64el
+	CPU=${UNAME_MACHINE}el
 	#else
 	#if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
-	CPU=mips64
+	CPU=${UNAME_MACHINE}
 	#else
 	CPU=
 	#endif
 	#endif
 EOF
-	eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
-	    /^CPU/{
-		s: ::g
-		p
-	    }'`"
+	eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
 	test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
 	;;
     or32:Linux:*:*)
 	echo or32-unknown-linux-gnu
 	exit ;;
-    ppc:Linux:*:*)
-	echo powerpc-unknown-linux-gnu
-	exit ;;
-    ppc64:Linux:*:*)
-	echo powerpc64-unknown-linux-gnu
+    padre:Linux:*:*)
+	echo sparc-unknown-linux-gnu
 	exit ;;
-    alpha:Linux:*:*)
-	case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
-	  EV5)   UNAME_MACHINE=alphaev5 ;;
-	  EV56)  UNAME_MACHINE=alphaev56 ;;
-	  PCA56) UNAME_MACHINE=alphapca56 ;;
-	  PCA57) UNAME_MACHINE=alphapca56 ;;
-	  EV6)   UNAME_MACHINE=alphaev6 ;;
-	  EV67)  UNAME_MACHINE=alphaev67 ;;
-	  EV68*) UNAME_MACHINE=alphaev68 ;;
-        esac
-	objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null
-	if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
-	echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+    parisc64:Linux:*:* | hppa64:Linux:*:*)
+	echo hppa64-unknown-linux-gnu
 	exit ;;
     parisc:Linux:*:* | hppa:Linux:*:*)
 	# Look for CPU level
@@ -943,8 +950,11 @@ EOF
 	  *)    echo hppa-unknown-linux-gnu ;;
 	esac
 	exit ;;
-    parisc64:Linux:*:* | hppa64:Linux:*:*)
-	echo hppa64-unknown-linux-gnu
+    ppc64:Linux:*:*)
+	echo powerpc64-unknown-linux-gnu
+	exit ;;
+    ppc:Linux:*:*)
+	echo powerpc-unknown-linux-gnu
 	exit ;;
     s390:Linux:*:* | s390x:Linux:*:*)
 	echo ${UNAME_MACHINE}-ibm-linux
@@ -967,69 +977,6 @@ EOF
     xtensa*:Linux:*:*)
     	echo ${UNAME_MACHINE}-unknown-linux-gnu
 	exit ;;
-    i*86:Linux:*:*)
-	# The BFD linker knows what the default object file format is, so
-	# first see if it will tell us. cd to the root directory to prevent
-	# problems with other programs or directories called `ld' in the path.
-	# Set LC_ALL=C to ensure ld outputs messages in English.
-	ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \
-			 | sed -ne '/supported targets:/!d
-				    s/[ 	][ 	]*/ /g
-				    s/.*supported targets: *//
-				    s/ .*//
-				    p'`
-        case "$ld_supported_targets" in
-	  elf32-i386)
-		TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu"
-		;;
-	  a.out-i386-linux)
-		echo "${UNAME_MACHINE}-pc-linux-gnuaout"
-		exit ;;
-	  coff-i386)
-		echo "${UNAME_MACHINE}-pc-linux-gnucoff"
-		exit ;;
-	  "")
-		# Either a pre-BFD a.out linker (linux-gnuoldld) or
-		# one that does not give us useful --help.
-		echo "${UNAME_MACHINE}-pc-linux-gnuoldld"
-		exit ;;
-	esac
-	# Determine whether the default compiler is a.out or elf
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-	#include <features.h>
-	#ifdef __ELF__
-	# ifdef __GLIBC__
-	#  if __GLIBC__ >= 2
-	LIBC=gnu
-	#  else
-	LIBC=gnulibc1
-	#  endif
-	# else
-	LIBC=gnulibc1
-	# endif
-	#else
-	#if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC)
-	LIBC=gnu
-	#else
-	LIBC=gnuaout
-	#endif
-	#endif
-	#ifdef __dietlibc__
-	LIBC=dietlibc
-	#endif
-EOF
-	eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
-	    /^LIBC/{
-		s: ::g
-		p
-	    }'`"
-	test x"${LIBC}" != x && {
-		echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
-		exit
-	}
-	test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; }
-	;;
     i*86:DYNIX/ptx:4*:*)
 	# ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
 	# earlier versions are messed up and put the nodename in both
@@ -1058,7 +1005,7 @@ EOF
     i*86:syllable:*:*)
 	echo ${UNAME_MACHINE}-pc-syllable
 	exit ;;
-    i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*)
+    i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
 	echo i386-unknown-lynxos${UNAME_RELEASE}
 	exit ;;
     i*86:*DOS:*:*)
@@ -1102,8 +1049,11 @@ EOF
     pc:*:*:*)
 	# Left here for compatibility:
         # uname -m prints for DJGPP always 'pc', but it prints nothing about
-        # the processor, so we play safe by assuming i386.
-	echo i386-pc-msdosdjgpp
+        # the processor, so we play safe by assuming i586.
+	# Note: whatever this is, it MUST be the same as what config.sub
+	# prints for the "djgpp" host, or else GDB configury will decide that
+	# this is a cross-build.
+	echo i586-pc-msdosdjgpp
         exit ;;
     Intel:Mach:3*:*)
 	echo i386-pc-mach3
@@ -1141,6 +1091,16 @@ EOF
     3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
         /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
           && { echo i486-ncr-sysv4; exit; } ;;
+    NCR*:*:4.2:* | MPRAS*:*:4.2:*)
+	OS_REL='.3'
+	test -r /etc/.relid \
+	    && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+	/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+	    && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+	/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+	    && { echo i586-ncr-sysv4.3${OS_REL}; exit; }
+	/bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
+	    && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
     m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
 	echo m68k-unknown-lynxos${UNAME_RELEASE}
 	exit ;;
@@ -1153,7 +1113,7 @@ EOF
     rs6000:LynxOS:2.*:*)
 	echo rs6000-unknown-lynxos${UNAME_RELEASE}
 	exit ;;
-    PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*)
+    PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
 	echo powerpc-unknown-lynxos${UNAME_RELEASE}
 	exit ;;
     SM[BE]S:UNIX_SV:*:*)
@@ -1216,6 +1176,9 @@ EOF
     BePC:BeOS:*:*)	# BeOS running on Intel PC compatible.
 	echo i586-pc-beos
 	exit ;;
+    BePC:Haiku:*:*)	# Haiku running on Intel PC compatible.
+	echo i586-pc-haiku
+	exit ;;
     SX-4:SUPER-UX:*:*)
 	echo sx4-nec-superux${UNAME_RELEASE}
 	exit ;;
@@ -1243,6 +1206,16 @@ EOF
     *:Darwin:*:*)
 	UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
 	case $UNAME_PROCESSOR in
+	    i386)
+		eval $set_cc_for_build
+		if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+		  if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
+		      (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+		      grep IS_64BIT_ARCH >/dev/null
+		  then
+		      UNAME_PROCESSOR="x86_64"
+		  fi
+		fi ;;
 	    unknown) UNAME_PROCESSOR=powerpc ;;
 	esac
 	echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
@@ -1324,6 +1297,9 @@ EOF
     i*86:rdos:*:*)
 	echo ${UNAME_MACHINE}-pc-rdos
 	exit ;;
+    i*86:AROS:*:*)
+	echo ${UNAME_MACHINE}-pc-aros
+	exit ;;
 esac
 
 #echo '(No uname command or uname output not recognized.)' 1>&2
@@ -1484,9 +1460,9 @@ This script, last modified $timestamp, has failed to recognize
 the operating system you are using. It is advised that you
 download the most up to date version of the config scripts from
 
-  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
+  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
 and
-  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub
+  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
 
 If the version you run ($0) is already up to date, please
 send the following data and any information you think might be
diff --git a/gtfold-mfe/config.sub b/gtfold-mfe/config.sub
old mode 100644
new mode 100755
index 6759825..c2d1257
--- a/gtfold-mfe/config.sub
+++ b/gtfold-mfe/config.sub
@@ -1,10 +1,10 @@
 #! /bin/sh
 # Configuration validation subroutine script.
 #   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-#   2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008
+#   2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010
 #   Free Software Foundation, Inc.
 
-timestamp='2008-01-16'
+timestamp='2010-01-22'
 
 # This file is (in principle) common to ALL GNU software.
 # The presence of a machine in this file suggests that SOME GNU software
@@ -32,13 +32,16 @@ timestamp='2008-01-16'
 
 
 # Please send patches to <config-patches@gnu.org>.  Submit a context
-# diff and a properly formatted ChangeLog entry.
+# diff and a properly formatted GNU ChangeLog entry.
 #
 # Configuration subroutine to validate and canonicalize a configuration type.
 # Supply the specified configuration type as an argument.
 # If it is invalid, we print an error message on stderr and exit with code 1.
 # Otherwise, we print the canonical config type on stdout and succeed.
 
+# You can get the latest version of this script from:
+# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+
 # This file is supposed to be the same for all GNU packages
 # and recognize all the CPU types, system types and aliases
 # that are meaningful with *any* GNU software.
@@ -72,8 +75,9 @@ Report bugs and patches to <config-patches@gnu.org>."
 version="\
 GNU config.sub ($timestamp)
 
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
-2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000,
+2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free
+Software Foundation, Inc.
 
 This is free software; see the source for copying conditions.  There is NO
 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -122,6 +126,7 @@ maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
 case $maybe_os in
   nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \
   uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \
+  kopensolaris*-gnu* | \
   storm-chaos* | os2-emx* | rtmk-nova*)
     os=-$maybe_os
     basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
@@ -148,10 +153,13 @@ case $os in
 	-convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
 	-c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
 	-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
-	-apple | -axis | -knuth | -cray)
+	-apple | -axis | -knuth | -cray | -microblaze)
 		os=
 		basic_machine=$1
 		;;
+        -bluegene*)
+	        os=-cnk
+		;;
 	-sim | -cisco | -oki | -wec | -winbond)
 		os=
 		basic_machine=$1
@@ -249,13 +257,16 @@ case $basic_machine in
 	| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
 	| i370 | i860 | i960 | ia64 \
 	| ip2k | iq2000 \
+	| lm32 \
 	| m32c | m32r | m32rle | m68000 | m68k | m88k \
-	| maxq | mb | microblaze | mcore | mep \
+	| maxq | mb | microblaze | mcore | mep | metag \
 	| mips | mipsbe | mipseb | mipsel | mipsle \
 	| mips16 \
 	| mips64 | mips64el \
-	| mips64vr | mips64vrel \
+	| mips64octeon | mips64octeonel \
 	| mips64orion | mips64orionel \
+	| mips64r5900 | mips64r5900el \
+	| mips64vr | mips64vrel \
 	| mips64vr4100 | mips64vr4100el \
 	| mips64vr4300 | mips64vr4300el \
 	| mips64vr5000 | mips64vr5000el \
@@ -268,6 +279,7 @@ case $basic_machine in
 	| mipsisa64sr71k | mipsisa64sr71kel \
 	| mipstx39 | mipstx39el \
 	| mn10200 | mn10300 \
+	| moxie \
 	| mt \
 	| msp430 \
 	| nios | nios2 \
@@ -276,20 +288,22 @@ case $basic_machine in
 	| pdp10 | pdp11 | pj | pjl \
 	| powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
 	| pyramid \
+	| rx \
 	| score \
-	| sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
+	| sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
 	| sh64 | sh64le \
 	| sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
 	| sparcv8 | sparcv9 | sparcv9b | sparcv9v \
 	| spu | strongarm \
 	| tahoe | thumb | tic4x | tic80 | tron \
+	| ubicom32 \
 	| v850 | v850e \
 	| we32k \
 	| x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \
-	| z8k)
+	| z8k | z80)
 		basic_machine=$basic_machine-unknown
 		;;
-	m6811 | m68hc11 | m6812 | m68hc12)
+	m6811 | m68hc11 | m6812 | m68hc12 | picochip)
 		# Motorola 68HC11/12.
 		basic_machine=$basic_machine-unknown
 		os=-none
@@ -329,14 +343,17 @@ case $basic_machine in
 	| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
 	| i*86-* | i860-* | i960-* | ia64-* \
 	| ip2k-* | iq2000-* \
+	| lm32-* \
 	| m32c-* | m32r-* | m32rle-* \
 	| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
-	| m88110-* | m88k-* | maxq-* | mcore-* \
+	| m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \
 	| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
 	| mips16-* \
 	| mips64-* | mips64el-* \
-	| mips64vr-* | mips64vrel-* \
+	| mips64octeon-* | mips64octeonel-* \
 	| mips64orion-* | mips64orionel-* \
+	| mips64r5900-* | mips64r5900el-* \
+	| mips64vr-* | mips64vrel-* \
 	| mips64vr4100-* | mips64vr4100el-* \
 	| mips64vr4300-* | mips64vr4300el-* \
 	| mips64vr5000-* | mips64vr5000el-* \
@@ -357,21 +374,23 @@ case $basic_machine in
 	| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
 	| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
 	| pyramid-* \
-	| romp-* | rs6000-* \
-	| sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
+	| romp-* | rs6000-* | rx-* \
+	| sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
 	| shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
 	| sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
 	| sparclite-* \
 	| sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \
 	| tahoe-* | thumb-* \
 	| tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+	| tile-* | tilegx-* \
 	| tron-* \
+	| ubicom32-* \
 	| v850-* | v850e-* | vax-* \
 	| we32k-* \
 	| x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \
 	| xstormy16-* | xtensa*-* \
 	| ymp-* \
-	| z8k-*)
+	| z8k-* | z80-*)
 		;;
 	# Recognize the basic CPU types without company name, with glob match.
 	xtensa*)
@@ -439,6 +458,10 @@ case $basic_machine in
 		basic_machine=m68k-apollo
 		os=-bsd
 		;;
+	aros)
+		basic_machine=i386-pc
+		os=-aros
+		;;
 	aux)
 		basic_machine=m68k-apple
 		os=-aux
@@ -455,10 +478,18 @@ case $basic_machine in
 		basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
 		os=-linux
 		;;
+	bluegene*)
+		basic_machine=powerpc-ibm
+		os=-cnk
+		;;
 	c90)
 		basic_machine=c90-cray
 		os=-unicos
 		;;
+        cegcc)
+		basic_machine=arm-unknown
+		os=-cegcc
+		;;
 	convex-c1)
 		basic_machine=c1-convex
 		os=-bsd
@@ -526,6 +557,10 @@ case $basic_machine in
 		basic_machine=m88k-motorola
 		os=-sysv3
 		;;
+	dicos)
+		basic_machine=i686-pc
+		os=-dicos
+		;;
 	djgpp)
 		basic_machine=i586-pc
 		os=-msdosdjgpp
@@ -699,6 +734,9 @@ case $basic_machine in
 		basic_machine=ns32k-utek
 		os=-sysv
 		;;
+        microblaze)
+		basic_machine=microblaze-xilinx
+		;;
 	mingw32)
 		basic_machine=i386-pc
 		os=-mingw32
@@ -1049,6 +1087,11 @@ case $basic_machine in
 		basic_machine=tic6x-unknown
 		os=-coff
 		;;
+        # This must be matched before tile*.
+        tilegx*)
+		basic_machine=tilegx-unknown
+		os=-linux-gnu
+		;;
 	tile*)
 		basic_machine=tile-unknown
 		os=-linux-gnu
@@ -1128,6 +1171,10 @@ case $basic_machine in
 		basic_machine=z8k-unknown
 		os=-sim
 		;;
+	z80-*-coff)
+		basic_machine=z80-unknown
+		os=-sim
+		;;
 	none)
 		basic_machine=none-none
 		os=-none
@@ -1166,7 +1213,7 @@ case $basic_machine in
 	we32k)
 		basic_machine=we32k-att
 		;;
-	sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele)
+	sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele)
 		basic_machine=sh-unknown
 		;;
 	sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
@@ -1216,6 +1263,9 @@ case $os in
         # First match some system type aliases
         # that might get confused with valid system types.
 	# -solaris* is a basic system type, with this one exception.
+        -auroraux)
+	        os=-auroraux
+		;;
 	-solaris1 | -solaris1.*)
 		os=`echo $os | sed -e 's|solaris1|sunos4|'`
 		;;
@@ -1236,10 +1286,11 @@ case $os in
 	# Each alternative MUST END IN A *, to match a version number.
 	# -sysv* is not here because it comes later, after sysvr4.
 	-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
-	      | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\
-	      | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
+	      | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
+	      | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \
+	      | -sym* | -kopensolaris* \
 	      | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
-	      | -aos* \
+	      | -aos* | -aros* \
 	      | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
 	      | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
 	      | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
@@ -1248,7 +1299,7 @@ case $os in
 	      | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
 	      | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
 	      | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
-	      | -chorusos* | -chorusrdb* \
+	      | -chorusos* | -chorusrdb* | -cegcc* \
 	      | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
 	      | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
 	      | -uxpv* | -beos* | -mpeix* | -udk* \
@@ -1258,7 +1309,7 @@ case $os in
 	      | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
 	      | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
 	      | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
-	      | -skyos* | -haiku* | -rdos* | -toppers* | -drops*)
+	      | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*)
 	# Remember, each alternative MUST END IN *, to match a version number.
 		;;
 	-qnx*)
@@ -1388,6 +1439,11 @@ case $os in
 	-zvmoe)
 		os=-zvmoe
 		;;
+	-dicos*)
+		os=-dicos
+		;;
+        -nacl*)
+	        ;;
 	-none)
 		;;
 	*)
@@ -1585,7 +1641,7 @@ case $basic_machine in
 			-sunos*)
 				vendor=sun
 				;;
-			-aix*)
+			-cnk*|-aix*)
 				vendor=ibm
 				;;
 			-beos*)
diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure
index c5acafe..679f8a1 100755
--- a/gtfold-mfe/configure
+++ b/gtfold-mfe/configure
@@ -2372,7 +2372,6 @@ test -n "$target_alias" &&
     NONENONEs,x,x, &&
   program_prefix=${target_alias}-
 
-
 am__api_version='1.11'
 
 # Find a good install program.  We prefer a C program (faster),
diff --git a/gtfold-mfe/configure.in b/gtfold-mfe/configure.in
index b5b456b..ef1ddde 100644
--- a/gtfold-mfe/configure.in
+++ b/gtfold-mfe/configure.in
@@ -1,8 +1,8 @@
 dnl Process this file with autoconf to produce a configure script.
 
-dnl AC_PREREQ(1.8)
+dnl AC_PREREQ([2.67])
 dnl AC 2.62 needed for OpenMP
-AC_PREREQ(2.62)
+AC_PREREQ([2.67])
 
 dnl AC_INIT (package, version, [bug-report-email], [tarname])
 AC_INIT([gtfold],[1.18])
@@ -12,11 +12,11 @@ dnl specified by --srcdir is the right one
 AC_CONFIG_SRCDIR([README])
 
 dnl Specify a header configuration file
-AM_CONFIG_HEADER(gtfold_config.h)
+AC_CONFIG_HEADERS([gtfold_config.h])
 
 dnl Compute the canonical host-system type variable, host, and its
 dnl three individual parts host_cpu, host_vendor, and host_os.
-AC_CANONICAL_SYSTEM
+AC_CANONICAL_TARGET
 
 dnl Initialize Automake
 AM_INIT_AUTOMAKE
@@ -62,7 +62,7 @@ dnl Check for libraries
 AC_CHECK_LIB(m, log2, AC_DEFINE([HAVE_LOG2],[],[log2 function is present]))
 
 dnl Check for header files
-AC_STDC_HEADERS
+AC_HEADER_STDC
 #AC_CHECK_HEADERS(sys/resource.h)
 #AC_CHECK_HEADERS(getopt.h)
 AC_CHECK_HEADERS([stdlib.h string.h sys/time.h])
@@ -101,25 +101,21 @@ dnl are not a part of the standard Autoconf tests:
 
 If Sun cc is present, define appropriate compiler flags  
 AC_MSG_CHECKING(for Sun C compiler)
-AC_TRY_COMPILE([], [#ifndef __SUNPRO_C
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __SUNPRO_C
                     #include "error: this is not a Sun C compiler."
                     #endif 
-                   ],
-		   [AC_MSG_RESULT(yes)
-                    gtfold_cv_check_sunpro_cc=yes],
-		   [AC_MSG_RESULT(no)
+                   ]])],[AC_MSG_RESULT(yes)
+                    gtfold_cv_check_sunpro_cc=yes],[AC_MSG_RESULT(no)
                     gtfold_cv_check_sunpro_cc=no])
 
 if test "$gtfold_cv_check_sunpro_cc" == "yes";
 then
 	AC_MSG_CHECKING(for Sun C compiler architecture target)
-	AC_TRY_COMPILE([], [#ifndef __sparc
+	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparc
                     #include "error: this is not a Sun Sparc processor."
                     #endif 
-                   ],
-		   [AC_MSG_RESULT(yes)
-                    gtfold_cv_check_sun_sparc=yes],
-		   [AC_MSG_RESULT(no)
+                   ]])],[AC_MSG_RESULT(yes)
+                    gtfold_cv_check_sun_sparc=yes],[AC_MSG_RESULT(no)
                     gtfold_cv_check_sun_sparc=no])
 fi
 
@@ -128,13 +124,11 @@ then
 	if test "$gtfold_cv_check_sun_sparc" == "yes";
 	then	
 		AC_MSG_CHECKING(for Sun sparc v9 architecture)
-		AC_TRY_COMPILE([], [#ifndef __sparcv9
+		AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparcv9
 				    #include "error: this is not a Sun Sparc V9 processor."
 				    #endif 
-				    ],		    
-				    [AC_MSG_RESULT(yes)
-				    gtfold_cv_check_sun_sparcv9=yes],
-				    [AC_MSG_RESULT(no)
+				    ]])],[AC_MSG_RESULT(yes)
+				    gtfold_cv_check_sun_sparcv9=yes],[AC_MSG_RESULT(no)
 				    gtfold_cv_check_sun_sparcv9=no])
         fi				    
 fi
diff --git a/gtfold-mfe/depcomp b/gtfold-mfe/depcomp
old mode 100644
new mode 100755
index e5f9736..df8eea7
--- a/gtfold-mfe/depcomp
+++ b/gtfold-mfe/depcomp
@@ -1,10 +1,10 @@
 #! /bin/sh
 # depcomp - compile a program generating dependencies as side-effects
 
-scriptversion=2007-03-29.01
+scriptversion=2009-04-28.21; # UTC
 
-# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software
-# Foundation, Inc.
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
+# Software Foundation, Inc.
 
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -17,9 +17,7 @@ scriptversion=2007-03-29.01
 # GNU General Public License for more details.
 
 # You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 # As a special exception to the GNU General Public License, if you
 # distribute this file as part of a program that contains a
@@ -87,6 +85,15 @@ if test "$depmode" = dashXmstdout; then
    depmode=dashmstdout
 fi
 
+cygpath_u="cygpath -u -f -"
+if test "$depmode" = msvcmsys; then
+   # This is just like msvisualcpp but w/o cygpath translation.
+   # Just convert the backslash-escaped backslashes to single forward
+   # slashes to satisfy depend.m4
+   cygpath_u="sed s,\\\\\\\\,/,g"
+   depmode=msvisualcpp
+fi
+
 case "$depmode" in
 gcc3)
 ## gcc 3 implements dependency tracking that does exactly what
@@ -192,14 +199,14 @@ sgi)
 ' < "$tmpdepfile" \
     | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
     tr '
-' ' ' >> $depfile
-    echo >> $depfile
+' ' ' >> "$depfile"
+    echo >> "$depfile"
 
     # The second pass generates a dummy entry for each header file.
     tr ' ' '
 ' < "$tmpdepfile" \
    | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
-   >> $depfile
+   >> "$depfile"
   else
     # The sourcefile does not contain any dependencies, so just
     # store a dummy comment line, to avoid errors with the Makefile
@@ -328,7 +335,12 @@ hp2)
   if test -f "$tmpdepfile"; then
     sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
     # Add `dependent.h:' lines.
-    sed -ne '2,${; s/^ *//; s/ \\*$//; s/$/:/; p;}' "$tmpdepfile" >> "$depfile"
+    sed -ne '2,${
+	       s/^ *//
+	       s/ \\*$//
+	       s/$/:/
+	       p
+	     }' "$tmpdepfile" >> "$depfile"
   else
     echo "#dummy" > "$depfile"
   fi
@@ -404,7 +416,7 @@ dashmstdout)
 
   # Remove the call to Libtool.
   if test "$libtool" = yes; then
-    while test $1 != '--mode=compile'; do
+    while test "X$1" != 'X--mode=compile'; do
       shift
     done
     shift
@@ -455,32 +467,39 @@ makedepend)
   "$@" || exit $?
   # Remove any Libtool call
   if test "$libtool" = yes; then
-    while test $1 != '--mode=compile'; do
+    while test "X$1" != 'X--mode=compile'; do
       shift
     done
     shift
   fi
   # X makedepend
   shift
-  cleared=no
-  for arg in "$@"; do
+  cleared=no eat=no
+  for arg
+  do
     case $cleared in
     no)
       set ""; shift
       cleared=yes ;;
     esac
+    if test $eat = yes; then
+      eat=no
+      continue
+    fi
     case "$arg" in
     -D*|-I*)
       set fnord "$@" "$arg"; shift ;;
     # Strip any option that makedepend may not understand.  Remove
     # the object too, otherwise makedepend will parse it as a source file.
+    -arch)
+      eat=yes ;;
     -*|$object)
       ;;
     *)
       set fnord "$@" "$arg"; shift ;;
     esac
   done
-  obj_suffix="`echo $object | sed 's/^.*\././'`"
+  obj_suffix=`echo "$object" | sed 's/^.*\././'`
   touch "$tmpdepfile"
   ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
   rm -f "$depfile"
@@ -500,7 +519,7 @@ cpp)
 
   # Remove the call to Libtool.
   if test "$libtool" = yes; then
-    while test $1 != '--mode=compile'; do
+    while test "X$1" != 'X--mode=compile'; do
       shift
     done
     shift
@@ -538,13 +557,27 @@ cpp)
 
 msvisualcpp)
   # Important note: in order to support this mode, a compiler *must*
-  # always write the preprocessed file to stdout, regardless of -o,
-  # because we must use -o when running libtool.
+  # always write the preprocessed file to stdout.
   "$@" || exit $?
+
+  # Remove the call to Libtool.
+  if test "$libtool" = yes; then
+    while test "X$1" != 'X--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+
   IFS=" "
   for arg
   do
     case "$arg" in
+    -o)
+      shift
+      ;;
+    $object)
+      shift
+      ;;
     "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
 	set fnord "$@"
 	shift
@@ -557,16 +590,23 @@ msvisualcpp)
 	;;
     esac
   done
-  "$@" -E |
-  sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
+  "$@" -E 2>/dev/null |
+  sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
   rm -f "$depfile"
   echo "$object : \\" > "$depfile"
-  . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::	\1 \\:p' >> "$depfile"
+  sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::	\1 \\:p' >> "$depfile"
   echo "	" >> "$depfile"
-  . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+  sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
   rm -f "$tmpdepfile"
   ;;
 
+msvcmsys)
+  # This case exists only to let depend.m4 do its work.  It works by
+  # looking at the text of this script.  This case will never be run,
+  # since it is checked for above.
+  exit 1
+  ;;
+
 none)
   exec "$@"
   ;;
@@ -585,5 +625,6 @@ exit 0
 # eval: (add-hook 'write-file-hooks 'time-stamp)
 # time-stamp-start: "scriptversion="
 # time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
 # End:
diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am
index ee1eb98..a03865e 100644
--- a/gtfold-mfe/include/Makefile.am
+++ b/gtfold-mfe/include/Makefile.am
@@ -1,3 +1,3 @@
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-paritition.h
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h
 
 CLEANFILES = *~
diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in
index 3565a69..44a1859 100644
--- a/gtfold-mfe/include/Makefile.in
+++ b/gtfold-mfe/include/Makefile.in
@@ -155,7 +155,7 @@ target_vendor = @target_vendor@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-paritition.h
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h
 CLEANFILES = *~
 all: all-am
 
diff --git a/gtfold-mfe/include/algorithms-partition.h b/gtfold-mfe/include/algorithms-partition.h
index b45d656..77c2377 100644
--- a/gtfold-mfe/include/algorithms-partition.h
+++ b/gtfold-mfe/include/algorithms-partition.h
@@ -5,8 +5,14 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
-
-
+/*
+typedef struct _pFuncData {
+    int len;
+    double** QB;
+    double** Q;
+    double** QM;
+} p_func_data;
+*/
 void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM);
 void fillBasePairProbabilities(int length, int *structure, double **Q, double **QB, double **QM, double**P);
 void printBasePairProbabilities(int n, int *structure, double **P);
@@ -16,14 +22,6 @@ double probabilityUnpaired(int length, int i, double **P);
 double **mallocTwoD(int r, int c);
 void freeTwoD(double** arr, int r, int c);
 
-typedef struct _pFuncData {
-    int len;
-    double** QB;
-    double** Q;
-    double** QM;
-
-    // TODO: probability function stuff here
-} pFuncData;
 
 
 #ifdef __cplusplus
diff --git a/gtfold-mfe/include/partition-dangle.h b/gtfold-mfe/include/partition-dangle.h
index e483aa1..1fb8a3b 100644
--- a/gtfold-mfe/include/partition-dangle.h
+++ b/gtfold-mfe/include/partition-dangle.h
@@ -14,6 +14,7 @@ typedef struct partition_d{
 }dangle_struct;
 
 double cond_dangle(int j, int h, int l);
+dangle_struct malloc_partition_arrays_d(int len);
 void fill_partition_arrays_d(dangle_struct part_struct);
 
 #endif
diff --git a/gtfold-mfe/install-sh b/gtfold-mfe/install-sh
index a5897de..6781b98 100755
--- a/gtfold-mfe/install-sh
+++ b/gtfold-mfe/install-sh
@@ -1,7 +1,7 @@
 #!/bin/sh
 # install - install a program, script, or datafile
 
-scriptversion=2006-12-25.00
+scriptversion=2009-04-28.21; # UTC
 
 # This originates from X11R5 (mit/util/scripts/install.sh), which was
 # later released in X11R6 (xc/config/util/install.sh) with the
@@ -515,5 +515,6 @@ done
 # eval: (add-hook 'write-file-hooks 'time-stamp)
 # time-stamp-start: "scriptversion="
 # time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
 # End:
diff --git a/gtfold-mfe/missing b/gtfold-mfe/missing
old mode 100644
new mode 100755
index 1c8ff70..28055d2
--- a/gtfold-mfe/missing
+++ b/gtfold-mfe/missing
@@ -1,10 +1,10 @@
 #! /bin/sh
 # Common stub for a few missing GNU programs while installing.
 
-scriptversion=2006-05-10.23
+scriptversion=2009-04-28.21; # UTC
 
-# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006
-#   Free Software Foundation, Inc.
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009 Free Software Foundation, Inc.
 # Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
 
 # This program is free software; you can redistribute it and/or modify
@@ -18,9 +18,7 @@ scriptversion=2006-05-10.23
 # GNU General Public License for more details.
 
 # You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 # As a special exception to the GNU General Public License, if you
 # distribute this file as part of a program that contains a
@@ -89,6 +87,9 @@ Supported PROGRAM values:
   tar          try tar, gnutar, gtar, then tar without non-portable flags
   yacc         create \`y.tab.[ch]', if possible, from existing .[ch]
 
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+
 Send bug reports to <bug-automake@gnu.org>."
     exit $?
     ;;
@@ -106,15 +107,22 @@ Send bug reports to <bug-automake@gnu.org>."
 
 esac
 
+# normalize program name to check for.
+program=`echo "$1" | sed '
+  s/^gnu-//; t
+  s/^gnu//; t
+  s/^g//; t'`
+
 # Now exit if we have it, but it failed.  Also exit now if we
 # don't have it and --version was passed (most likely to detect
-# the program).
+# the program).  This is about non-GNU programs, so use $1 not
+# $program.
 case $1 in
-  lex|yacc)
+  lex*|yacc*)
     # Not GNU programs, they don't have --version.
     ;;
 
-  tar)
+  tar*)
     if test -n "$run"; then
        echo 1>&2 "ERROR: \`tar' requires --run"
        exit 1
@@ -138,7 +146,7 @@ esac
 
 # If it does not exist, or fails to run (possibly an outdated version),
 # try to emulate it.
-case $1 in
+case $program in
   aclocal*)
     echo 1>&2 "\
 WARNING: \`$1' is $msg.  You should only need it if
@@ -148,7 +156,7 @@ WARNING: \`$1' is $msg.  You should only need it if
     touch aclocal.m4
     ;;
 
-  autoconf)
+  autoconf*)
     echo 1>&2 "\
 WARNING: \`$1' is $msg.  You should only need it if
          you modified \`${configure_ac}'.  You might want to install the
@@ -157,7 +165,7 @@ WARNING: \`$1' is $msg.  You should only need it if
     touch configure
     ;;
 
-  autoheader)
+  autoheader*)
     echo 1>&2 "\
 WARNING: \`$1' is $msg.  You should only need it if
          you modified \`acconfig.h' or \`${configure_ac}'.  You might want
@@ -187,7 +195,7 @@ WARNING: \`$1' is $msg.  You should only need it if
 	   while read f; do touch "$f"; done
     ;;
 
-  autom4te)
+  autom4te*)
     echo 1>&2 "\
 WARNING: \`$1' is needed, but is $msg.
          You might have modified some files without having the
@@ -210,7 +218,7 @@ WARNING: \`$1' is needed, but is $msg.
     fi
     ;;
 
-  bison|yacc)
+  bison*|yacc*)
     echo 1>&2 "\
 WARNING: \`$1' $msg.  You should only need it if
          you modified a \`.y' file.  You may need the \`Bison' package
@@ -240,7 +248,7 @@ WARNING: \`$1' $msg.  You should only need it if
     fi
     ;;
 
-  lex|flex)
+  lex*|flex*)
     echo 1>&2 "\
 WARNING: \`$1' is $msg.  You should only need it if
          you modified a \`.l' file.  You may need the \`Flex' package
@@ -263,7 +271,7 @@ WARNING: \`$1' is $msg.  You should only need it if
     fi
     ;;
 
-  help2man)
+  help2man*)
     echo 1>&2 "\
 WARNING: \`$1' is $msg.  You should only need it if
 	 you modified a dependency of a manual page.  You may need the
@@ -277,11 +285,11 @@ WARNING: \`$1' is $msg.  You should only need it if
     else
 	test -z "$file" || exec >$file
 	echo ".ab help2man is required to generate this page"
-	exit 1
+	exit $?
     fi
     ;;
 
-  makeinfo)
+  makeinfo*)
     echo 1>&2 "\
 WARNING: \`$1' is $msg.  You should only need it if
          you modified a \`.texi' or \`.texinfo' file, or any other file
@@ -310,7 +318,7 @@ WARNING: \`$1' is $msg.  You should only need it if
     touch $file
     ;;
 
-  tar)
+  tar*)
     shift
 
     # We have already tried tar in the generic part.
@@ -363,5 +371,6 @@ exit 0
 # eval: (add-hook 'write-file-hooks 'time-stamp)
 # time-stamp-start: "scriptversion="
 # time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
 # End:
diff --git a/gtfold-mfe/src/.deps/main.Po b/gtfold-mfe/src/.deps/main.Po
index 73ec5ce..64c9b68 100644
--- a/gtfold-mfe/src/.deps/main.Po
+++ b/gtfold-mfe/src/.deps/main.Po
@@ -94,11 +94,12 @@ main.o: main.cc /usr/include/c++/4.5/iostream \
  /usr/include/c++/4.5/bits/vector.tcc ../include/constants.h \
  ../include/utils.h ../include/loader.h ../include/data.h \
  ../include/options.h /usr/include/c++/4.5/cstring ../include/global.h \
- ../include/energy.h ../include/algorithms.h ../include/constraints.h \
- ../include/traceback.h ../include/subopt_traceback.h \
- /usr/include/c++/4.5/cassert /usr/include/assert.h \
- /usr/include/c++/4.5/stack /usr/include/c++/4.5/deque \
- /usr/include/c++/4.5/bits/stl_deque.h \
+ ../include/energy.h ../include/algorithms.h \
+ ../include/algorithms-partition.h ../include/partition-dangle.h \
+ ../include/constraints.h ../include/traceback.h \
+ ../include/subopt_traceback.h /usr/include/c++/4.5/cassert \
+ /usr/include/assert.h /usr/include/c++/4.5/stack \
+ /usr/include/c++/4.5/deque /usr/include/c++/4.5/bits/stl_deque.h \
  /usr/include/c++/4.5/bits/deque.tcc \
  /usr/include/c++/4.5/bits/stl_stack.h /usr/include/c++/4.5/map \
  /usr/include/c++/4.5/bits/stl_tree.h /usr/include/c++/4.5/bits/stl_map.h \
@@ -404,6 +405,10 @@ main.o: main.cc /usr/include/c++/4.5/iostream \
 
 ../include/algorithms.h:
 
+../include/algorithms-partition.h:
+
+../include/partition-dangle.h:
+
 ../include/constraints.h:
 
 ../include/traceback.h:
diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile
index 8d533f1..e7c9193 100644
--- a/gtfold-mfe/src/Makefile
+++ b/gtfold-mfe/src/Makefile
@@ -190,8 +190,8 @@ gtfold_SOURCES = \
 	constraints.cc\
 	global.c\
 	energy.c\
-	algorithms.c \
-	traceback.c \
+	algorithms.c\
+	traceback.c\
 	subopt_traceback.cc\
 	algorithms-partition.c\
 	partition-dangle.c\
diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am
index aaa9481..428951a 100644
--- a/gtfold-mfe/src/Makefile.am
+++ b/gtfold-mfe/src/Makefile.am
@@ -13,8 +13,8 @@ gtfold_SOURCES = \
 	constraints.cc\
 	global.c\
 	energy.c\
-	algorithms.c \
-	traceback.c \
+	algorithms.c\
+	traceback.c\
 	subopt_traceback.cc\
 	algorithms-partition.c\
 	partition-dangle.c\
diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in
index 8b6d90d..e8e0471 100644
--- a/gtfold-mfe/src/Makefile.in
+++ b/gtfold-mfe/src/Makefile.in
@@ -190,8 +190,8 @@ gtfold_SOURCES = \
 	constraints.cc\
 	global.c\
 	energy.c\
-	algorithms.c \
-	traceback.c \
+	algorithms.c\
+	traceback.c\
 	subopt_traceback.cc\
 	algorithms-partition.c\
 	partition-dangle.c\
diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c
index 1ed7895..77e4fdf 100644
--- a/gtfold-mfe/src/algorithms-partition.c
+++ b/gtfold-mfe/src/algorithms-partition.c
@@ -30,7 +30,9 @@
  * @param QM Matrix
  *
  */
-void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) {
+
+
+void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) {
 
     // multiConst[3] is a global variable with 3 values: a, b, c for the
     // experimental constants
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 6394068..c970d59 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -36,6 +36,8 @@
 #include "global.h"
 #include "energy.h"
 #include "algorithms.h"
+#include "algorithms-partition.h"
+#include "partition-dangle.h"
 #include "constraints.h"
 #include "traceback.h"
 #include "subopt_traceback.h"
@@ -259,5 +261,28 @@ int main(int argc, char** argv) {
 	// release the malloc'd arrays
 	free_fold(seq.length());
 
+	if(BPP_ENABLED){
+		printf("Calculating partition function\n");
+		double ** Q,  **QM, **QB, **P;
+		Q = mallocTwoD(seq.length() + 1, seq.length() + 1);
+		QM = mallocTwoD(seq.length() + 1, seq.length() + 1);
+		QB = mallocTwoD(seq.length() + 1, seq.length() + 1);
+		P = mallocTwoD(seq.length() + 1, seq.length() + 1);
+
+		fill_partition_fn_arrays(seq.length(), Q, QB, QM);
+		fillBasePairProbabilities(seq.length(), structure, Q, QB, QM, P);
+		printBasePairProbabilities(seq.length(), structure, P);
+
+		freeTwoD(Q, seq.length() + 1, seq.length() + 1);
+		freeTwoD(QM, seq.length() + 1, seq.length() + 1);
+		freeTwoD(QB, seq.length() + 1, seq.length() + 1);
+		freeTwoD(P, seq.length() + 1, seq.length() + 1);
+	}
+/*
+	dangle_struct partition;
+	partition = malloc_partition_arrays_d(seq.length());
+	fill_partition_arrays_d(partition);
+	printf("Done with the partition functioni.\n");
+*/
 	return EXIT_SUCCESS;
 }
diff --git a/gtfold-mfe/src/random-sample.cc b/gtfold-mfe/src/random-sample.cc
index ff53afa..c336b68 100644
--- a/gtfold-mfe/src/random-sample.cc
+++ b/gtfold-mfe/src/random-sample.cc
@@ -18,12 +18,12 @@ using namespace std;
 //gives me a link error it should get this function
 //from partition-dangle
 
-double cond_dangle(int j, int h, int l){
+/*double cond_dangle(int j, int h, int l){
 	if(j - 1 == l)
 		return 1;
 	else 
 		return exp(-Ed3(h,l,l+1)/RT);
-}
+}*/
 
 double randdouble(){
 	    return rand()/(double(RAND_MAX)+1);

From b491b38e5c5095c46bd2acf0b10dcbd0e15b3211 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 16 Jun 2011 16:09:56 -0400
Subject: [PATCH 142/282] added new macro

---
 gtfold-mfe/include/utils.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gtfold-mfe/include/utils.h b/gtfold-mfe/include/utils.h
index dbe0fa7..8b33655 100644
--- a/gtfold-mfe/include/utils.h
+++ b/gtfold-mfe/include/utils.h
@@ -7,6 +7,7 @@
 #define MIN(X,Y) ((X) < (Y) ? (X) : (Y))
 #define MAX(X,Y) ((X) > (Y) ? (X) : (Y))
 #define MIN4(W,X,Y,Z) MIN(MIN(W,X),MIN(Y,Z))
+#define MIN3(W,X,Y) MIN(MIN(W,X),Y)
 
 char baseToDigit(const char* base) ;
 unsigned char encode(char base);

From 265ac33c2db2f6255ccb6db848faadf3ebed3e8f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 16 Jun 2011 16:14:28 -0400
Subject: [PATCH 143/282] added new macro

---
 gtfold-mfe/include/data.h | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/gtfold-mfe/include/data.h b/gtfold-mfe/include/data.h
index d88382f..c0875eb 100644
--- a/gtfold-mfe/include/data.h
+++ b/gtfold-mfe/include/data.h
@@ -59,6 +59,11 @@ extern int init;
 extern int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
 extern float prelog;
 
+extern int tstackm[5][5][6][6];
+extern int tstacke[5][5][6][6];
+extern int tstacki23[5][5][5][5];
+
+
 #define fourBaseIndex(a, b, c, d) (((a) << 6) + ((b) << 4) + ((c) << 2) + (d))
 
 #endif

From f192620c4fa87055a4576b4d0498ee7f95d2d42d Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 16 Jun 2011 16:17:05 -0400
Subject: [PATCH 144/282] added -m option

---
 gtfold-mfe/include/options.h | 1 +
 gtfold-mfe/src/options.cc    | 4 ++++
 2 files changed, 5 insertions(+)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index ec0ff7f..0862b03 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -19,6 +19,7 @@ extern bool CONS_ENABLED;
 extern bool VERBOSE;
 extern bool SHAPE_ENABLED;
 extern bool PARAM_DIR;
+extern bool T_MISMATCH;
 
 extern string seqfile;
 extern string constraintsFile;
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 76cbe44..1545f60 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -14,6 +14,7 @@ bool SUBOPT_ENABLED;
 bool CONS_ENABLED = false;
 bool VERBOSE = false;
 bool SHAPE_ENABLED = false;
+bool T_MISMATCH = false;
 
 string seqfile = "";
 string constraintsFile = "";
@@ -41,6 +42,7 @@ void help() {
     printf("   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n");
     printf("                        limit is given, base pairs can be over any distance\n");
     printf("   -p  --paramdir DIR   Path to directory from where parameters are to be read\n");
+    printf("   -m   			    enable terminal mismatch calculations\n");
    	printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
     printf("   -t, --threads num    Limit number of threads used\n");
@@ -100,6 +102,8 @@ void parse_options(int argc, char** argv) {
 				}
 				else
 					help();
+			} else if (strcmp(argv[i], "-m") == 0) {
+                T_MISMATCH = true;
 			}
 		   	else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
 				if(i < argc)

From 4c9b019122d63aa205119c5ffa42fabfc0bbac70 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 16 Jun 2011 16:18:40 -0400
Subject: [PATCH 145/282] added energy functions to support unafold mode

---
 gtfold-mfe/include/energy.h |   5 +-
 gtfold-mfe/src/energy.c     | 151 ++++++++++++++++++++++++++----------
 2 files changed, 113 insertions(+), 43 deletions(-)

diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h
index 5b7b5cc..7ccf999 100644
--- a/gtfold-mfe/include/energy.h
+++ b/gtfold-mfe/include/energy.h
@@ -10,7 +10,7 @@ extern int *VM;
 extern int **WM; 
 extern int **WMPrime; 
 extern int *indx; 
-
+extern int **PP; 
 
 #define V(i,j) V[indx[j]+i]
 #define VM(i,j) VM[indx[j]+i]
@@ -36,6 +36,9 @@ int auPenalty(int i, int j);
 int eS(int i, int j);
 int eH(int i, int j);
 int eL(int i, int j, int ip, int jp);
+int eL1(int i, int j, int ip, int jp);
+int Estackm(int i, int j);
+int Estacke(int i, int j);
 
 void create_tables(int len);
 void init_tables(int len);
diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 9450f92..985d47a 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -15,6 +15,7 @@ int *VM;
 int **WM; 
 int **WMPrime; 
 int *indx; 
+int **PP; 
 
 int alloc_flag = 0;
 
@@ -39,7 +40,20 @@ void create_tables(int len) {
 		}   
 	}
 
-  WMPrime = (int **) malloc((len+1)* sizeof(int *));
+	PP = (int **) malloc((len+1)* sizeof(int *));
+	if (PP == NULL) {
+		perror("Cannot allocate variable 'WM'");
+		exit(-1);
+	}   
+	for (i = 0; i <= len; i++) {
+		PP[i] = (int *)malloc((len+1)* sizeof(int));
+		if (PP[i] == NULL) {
+			perror("Cannot allocate variable 'WM[i]'");
+			exit(-1);
+		}   
+	}
+
+  	WMPrime = (int **) malloc((len+1)* sizeof(int *));
 	if (WMPrime == NULL) {
 		perror("Cannot allocate variable 'WM'");
 		exit(-1);
@@ -90,7 +104,8 @@ void init_tables(int len) {
 		for (j = 0; j <= len; j++) {
 			WM[i][j] = INFINITY_;
 			WMPrime[i][j] = INFINITY_;
-    }
+    		PP[i][j] = 0;
+		}
 	}
 	
 	LLL = (len)*(len+1)/2 + 1;
@@ -129,6 +144,67 @@ inline int Ed3(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][1];}
 inline int Ed5(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][0]; }
 inline int auPenalty(int i, int j) { return auPen(RNA[i], RNA[j]);}
 
+inline int eL1(int i, int j, int ii, int jj) {
+	int loopSize1, loopSize2;
+	int loopEnergy, asPenalty;
+
+	loopSize1 = ii - i - 1;
+	loopSize2 = j - jj - 1;
+	if (loopSize1 + loopSize2 > MAXLOOP)
+		return INFINITY_;
+
+	if (loopSize1 == 0) {
+		if (loopSize2 == 1)
+			return bulge[1] + stack[fourBaseIndex(RNA[i], RNA[j], RNA[ii], RNA[jj])];
+		else if (loopSize2 <= 30)
+			return bulge[loopSize2] + auPenalty(i, j) + auPenalty(ii, jj);
+		else
+			return bulge[30] + (int)floor(prelog*log((double) loopSize2 / 30)) + auPenalty(i, j) + auPenalty(ii, jj);
+	}
+	else if (loopSize2 == 0) {
+		if (loopSize1 == 1)
+			return bulge[1] + stack[fourBaseIndex(RNA[i], RNA[j], RNA[ii], RNA[jj])];
+		else if (loopSize1 <= 30)
+			return bulge[loopSize1] + auPenalty(i, j) + auPenalty(ii, jj);
+		else
+			return bulge[30] + (int)floor(prelog* log((double) loopSize1 / 30)) + auPenalty(i, j) + auPenalty(ii, jj);
+	}
+	else if (loopSize1 == 1 && loopSize2 == 1)
+		return iloop11[RNA[i]][RNA[i + 1]][RNA[ii]][RNA[j]][RNA[j - 1]][RNA[jj]];
+	else if (loopSize1 == 1 && loopSize2 == 2)
+		return iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ii]][RNA[jj]];
+	else if (loopSize1 == 2 && loopSize2 == 1)
+		return iloop21[RNA[jj]][RNA[ii]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]];
+	else if (loopSize1 == 2 && loopSize2 == 2)
+		return iloop22[RNA[i]][RNA[ii]][RNA[j]][RNA[jj]][RNA[i+1]][RNA[i+2]][RNA[j-1]][RNA[j-2]];
+	else if ((loopSize1 == 2 && loopSize2 == 3) ||
+			 (loopSize1 == 3 && loopSize2 == 2)) {
+		return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] +
+			tstacki23[RNA[jj]][RNA[ii]][RNA[jj + 1]][RNA[ii - 1]];
+	}
+	else {
+		if (loopSize1 + loopSize2 <= 30)
+			loopEnergy = inter[loopSize1 + loopSize2];
+		else
+			loopEnergy = inter[30] + (int)floor(prelog* log((double) (loopSize1 + loopSize2) / 30));
+		
+		if (gail && (loopSize1 == 1 || loopSize2 == 1)) {
+			loopEnergy += tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)];
+			loopEnergy += tstki[fourBaseIndex(RNA[jj], RNA[ii], BASE_A, BASE_A)];
+		}
+		else {
+			loopEnergy += tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])];
+			loopEnergy += tstki[fourBaseIndex(RNA[jj], RNA[ii], RNA[jj + 1], RNA[ii - 1])];
+		}
+		asPenalty = abs(loopSize1 - loopSize2)*poppen[MIN3(2, loopSize1, loopSize2) - 1];
+		asPenalty = MIN(asPenalty, maxpen);
+
+		loopEnergy += asPenalty;
+
+		return loopEnergy;
+	}
+}
+
 inline int eL(int i, int j, int ip, int jp) {
 	int energy;
 	int size1, size2, size;
@@ -165,53 +241,36 @@ inline int eL(int i, int j, int ip, int jp) {
 		if (size > 30) {
 			loginc = (int) floor(prelog * log((double) size / 30.0));
 
-			/* Please check what should be the difference in the following two options. Is it correct?*/
 			if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/
 
-				energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j
-											 - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp
-																		  + 1], RNA[ip - 1])] + inter[30] + loginc + eparam[3]
-											 + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1,
-																						 size2))]));
+				energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + 
+					tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[30] + loginc +
+				   	eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))]));
 			} else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/
-				energy
-					= tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]
-					+ tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A,
-										  BASE_A)] + inter[30] + loginc
-					+ eparam[3] + MIN(maxpen, (lopsided
-											   * poppen[MIN(2, MIN(size1, size2))]));
+				energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A,
+										  BASE_A)] + inter[30] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))]));
 			}
 		}
-		/* if size is not > 30, we have a looooot of cases... */
-		else if (size1 == 2 && size2 == 2) {
-			/* 2x2 internal loop */
-			energy
-				= iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i
-				+ 2]][RNA[j - 1]][RNA[j - 2]];
+		else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */
+			energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]];
+			if (i==1 && j==22) printf("2x2 loop at %d %d %d\n", i,j, energy);
 		} else if (size1 == 1 && size2 == 2) {
-			energy
-				= iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]];
-		} else if (size1 == 2 && size2 == 1) {
-			/* 1x2 internal loop */
-			energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i
-				+ 1]][RNA[j]][RNA[i]];
-		} else if (size == 2) {
-			/* 1*1 internal loops */
-			energy
-				= iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]];
-		} else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0)  */
-			energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]
-				+ tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)]
-				+ inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided
-																  * poppen[MIN(2, MIN(size1, size2))]));
+			energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]];
+		} else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */
+			energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]];
+		} else if (size == 2) { /* 1*1 internal loops */
+			energy = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]];
+		} else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) {
+			return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] +
+				tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]];
+		}
+		else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0)  */
+			energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)]
+				+ inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))]));
 		} else { /* General Internal loops */
-			energy
-				= tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1],
-									  RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp],
-																		 RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size]
-										  + loginc + eparam[3] /* AM: I don't understand this eparam value, I think they do not play any role currently. Please look in loader.cc file, for what value have been assinged to various elements of eparam array */
-										  + MIN(maxpen,
-												(lopsided * poppen[MIN(2, MIN(size1, size2))])); /*  */
+			energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size]
+										  + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); 
+		
 		}
 	}
 
@@ -331,3 +390,11 @@ inline int eS(int i, int j) {
 
 	return energy;
 }
+
+inline int Estackm(int i, int j) {
+	return tstackm[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]];
+}
+
+inline int Estacke(int i, int j) {
+	return tstacke[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]];
+}

From 7ff348f3cc6fe9eee24f7b7d00a77b6467b7aa95 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 16 Jun 2011 16:22:08 -0400
Subject: [PATCH 146/282] added function to load tstacke tstackm tstacki23
 enegery values

---
 gtfold-mfe/include/loader.h |   5 +-
 gtfold-mfe/src/loader.cc    | 182 +++++++++++++++++++++++++++++++-----
 2 files changed, 163 insertions(+), 24 deletions(-)

diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h
index f8fdc78..c7eff12 100644
--- a/gtfold-mfe/include/loader.h
+++ b/gtfold-mfe/include/loader.h
@@ -25,7 +25,7 @@
 #include "constants.h"
 #include "data.h"
 
-void readThermodynamicParameters(const char *userdatadir,bool userdatalogic);
+void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int t_mismatch);
 
 int initStackValues(const std::string& fileName, const std::string& dirPath);
 int initMiscloopValues(const std::string& fileName, const std::string& dirPath);
@@ -37,6 +37,9 @@ int initTloopValues(const std::string& fileName, const std::string& dirPath);
 int initInt21Values(const std::string& fileName, const std::string& dirPath);
 int initInt22Values(const std::string& fileName, const std::string& dirPath);
 int initInt11Values(const std::string& fileName, const std::string& dirPath);
+int	initTstkmValues(const std::string& fileName, const std::string& dirPath);
+int	initTstkeValues(const std::string& fileName, const std::string& dirPath);
+int	initTstk23Values(const std::string& fileName, const std::string& dirPath);
 
 extern std::string EN_DATADIR;
 
diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index c68ee22..66e0ff0 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -34,7 +34,6 @@
 
 #define xstr(s) str(s)
 #define str(s) #s
-//#define GENBIN 1
 
 using namespace std;
 
@@ -53,14 +52,20 @@ int tstkh[256]; /* Terminal mismatch energy used in the calculations of hairpin
 int tstki[256]; /* Terminal mismatch energy used in the calculations of internal loops */
 int tloop[maxtloop + 1][2];
 int numoftloops;
-int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */
 int iloop21[5][5][5][5][5][5][5]; /* 2*1 internal loops */
+int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */
 int iloop11[5][5][5][5][5][5]; /* 1*1 internal loops */
-int coax[6][6][6][6];
-int tstackcoax[6][6][6][6];
-int coaxstack[6][6][6][6];
-int tstack[6][6][6][6];
-int tstkm[6][6][6][6];
+
+//int coax[6][6][6][6];
+//int tstackcoax[6][6][6][6];
+//int coaxstack[6][6][6][6];
+//int tstack[6][6][6][6];
+//int tstkm[6][6][6][6];
+
+int tstackm[5][5][6][6];
+int tstacke[5][5][6][6];
+int tstacki23[5][5][5][5];
+
 int auend;
 int gubonus;
 int cint; /* cint, cslope, c3 are used for poly C hairpin loops */
@@ -75,7 +80,7 @@ int init;
 int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
 float prelog;
 
-void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
+void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int t_mismatch=0) {
 	if (!userdatalogic) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
@@ -96,9 +101,19 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) {
 	initTstkhValues("tstackh.DAT", EN_DATADIR);
 	initTstkiValues("tstacki.DAT", EN_DATADIR);
 	initTloopValues("tloop.DAT", EN_DATADIR);
-	initInt21Values("int21.DAT", EN_DATADIR);
-	initInt22Values("int22.DAT", EN_DATADIR);
-	initInt11Values("int11.DAT", EN_DATADIR);
+
+	if (t_mismatch) {
+		initInt21Values("asint1x2.DAT", EN_DATADIR);
+		initInt22Values("sint4.DAT", EN_DATADIR);
+		initInt11Values("sint2.DAT", EN_DATADIR);
+		initTstkmValues("tstackm.DAT", EN_DATADIR);
+		initTstkeValues("tstacke.DAT", EN_DATADIR);
+		initTstk23Values("tstacki23.DAT", EN_DATADIR);
+	} else {
+		initInt21Values("int21.DAT", EN_DATADIR);
+		initInt22Values("int22.DAT", EN_DATADIR);
+		initInt11Values("int11.DAT", EN_DATADIR);
+	}
 }
 
 int initStackValues(const string& fileName, const string& dirPath)  { 
@@ -111,7 +126,7 @@ int initStackValues(const string& fileName, const string& dirPath)  {
 	for (int i = 0; i < 4; i++) {
 		for (int j = 0; j < 4; j++) {
 			for (int k = 0; k < 4; k++) {
-				for (int l = 0; l < 2; l++) {
+				for (int l = 0; l < 4; l++) {
 					stack[fourBaseIndex(i,j,k,l)] = INFINITY_;
 				}
 			}
@@ -309,7 +324,7 @@ int initLoopValues( const string& fileName, const string& dirPath) {
 	int tempValue = 0;
 
 	if (cf.fail()) {
-		cerr << "File open failed" << endl;
+		cerr << "File open failed " << filePath << endl;
 		exit(-1);
 	}
 
@@ -343,6 +358,119 @@ int initLoopValues( const string& fileName, const string& dirPath) {
 	return 0;
 }
 
+int initTstk23Values(const std::string& fileName, const std::string& dirPath) {
+	int i1, j1, i2, j2;                                                              
+	std::string filePath;
+	std::ifstream cf;
+	std::string val;						
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+
+	if (cf.fail()) {
+		cerr << "File open failed " << filePath << endl;
+		exit(-1);
+	}
+
+	for (i1 = 0; i1 < 5; ++i1)
+		for (i2 = 0; i2 < 5; ++i2)
+			for (j1 = 0; j1 < 5; ++j1)
+				for (j2 = 0; j2 < 5; ++j2)
+					if (i1 == 4 || j1 == 4)
+						tstacki23[i1][j1][i2][j2] = INFINITY_;
+					else if (i2 == 4 || j2 == 4)
+						tstacki23[i1][j1][i2][j2] = 0;
+					else {
+						cf >> val;
+						tstacki23[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): 
+							((int) floor(100.0 * atof(val.c_str()) + .5));
+					}
+	cf.close();
+
+	return 0;
+}
+
+
+
+
+int initTstkeValues(const std::string& fileName, const std::string& dirPath) {
+	int i1, j1, i2, j2;                                                              
+	std::string filePath;
+	std::ifstream cf;
+	std::string val;						
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+
+	if (cf.fail()) {
+		cerr << "File open failed " << filePath << endl;
+		exit(-1);
+	}
+
+	for (i1 = 0; i1 < 5; ++i1) {                                    
+		for (i2 = 0; i2 < 6; ++i2) {                                                     
+			for (j1 = 0; j1 < 5; ++j1) {                                                   
+				for (j2 = 0; j2 < 6; ++j2) {                                                      
+					if (i1 == 4 || j1 == 4)                                                       
+						tstacke[i1][j1][i2][j2] = INFINITY_;                                         
+					else if (i2 == 5 || j2 == 5)                                                  
+						tstacke[i1][j1][i2][j2] = INFINITY_;                                         
+					else if (i2 == 4 || j2 == 4)                                                  
+						tstacke[i1][j1][i2][j2] = 0;                                                
+					else { 
+						cf >> val;
+						tstacke[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): 
+							((int) floor(100.0 * atof(val.c_str()) + .5));
+					}
+				}
+			}
+		}			
+	}
+
+	cf.close();
+
+	return 0;
+}
+
+int initTstkmValues(const std::string& fileName, const std::string& dirPath) {
+	int i1, j1, i2, j2;                                                              
+	std::string filePath;
+	std::ifstream cf;
+	std::string val;						
+
+	filePath = dirPath + fileName;
+	cf.open(filePath.c_str(), ios::in);
+	
+	if (cf.fail()) {
+		cerr << "File open failed " << filePath << endl;
+		exit(-1);
+	}
+
+	for (i1 = 0; i1 < 5; ++i1) {                                    
+		for (i2 = 0; i2 < 6; ++i2) {                                                     
+			for (j1 = 0; j1 < 5; ++j1) {                                                   
+				for (j2 = 0; j2 < 6; ++j2) {                                                      
+					if (i1 == 4 || j1 == 4)                                                       
+						tstackm[i1][j1][i2][j2] = INFINITY_;                                         
+					else if (i2 == 5 || j2 == 5)                                                  
+						tstackm[i1][j1][i2][j2] = INFINITY_;                                         
+					else if (i2 == 4 || j2 == 4)                                                  
+						tstackm[i1][j1][i2][j2] = 0;                                                
+					else { 
+						cf >> val;
+						tstackm[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): 
+							((int) floor(100.0 * atof(val.c_str()) + .5));
+					}
+				}
+			}
+		}			
+	}
+
+	cf.close();
+
+	return 0;
+}
+
 int initTstkhValues(const std::string& fileName, const std::string& dirPath) {
 	std::string filePath;
 	std::ifstream cf;
@@ -476,9 +604,11 @@ int initTloopValues(const std::string& fileName, const std::string& dirPath) {
 			currentValue[count] = currentLine[count + clindex];
 			count++;
 		}
-
+		
 		tloop[numoftloops][0] = (int) atoi(currentSeqNumbers);
-		tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5);
+		
+		if (!(strcmp(currentValue,"inf")==0)) 
+			tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5);
 	}
 	cf.close();
 	return 0;
@@ -510,7 +640,7 @@ int initInt22Values(const std::string& fileName, const std::string& dirPath) {
 	string filePath = dirPath + fileName;
 	cf.open(filePath.c_str(), ios::in);
 	if (!cf.good()) {
-		cerr << "File open failed " << endl;
+		cerr << "File open failed " << filePath << endl;
 		exit(-1);
 	}
 
@@ -556,8 +686,9 @@ int initInt22Values(const std::string& fileName, const std::string& dirPath) {
 				l = ((colIndex - 1) - (colIndex - 1) % 4) / 4;
 				m = (colIndex - 1) % 4;
 
-				iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] 
-					= (int) floor(100.0 * atof(currentValue) + 0.5);
+				if (!(strcmp(currentValue,"inf")==0)) 
+					iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] 
+						= (int) floor(100.0 * atof(currentValue) + 0.5);
 			}
 		}
 	}
@@ -617,7 +748,7 @@ int initInt21Values(const std::string& fileName, const std::string& dirPath) {
 	std::string filePath = dirPath + fileName;
 	cf.open(filePath.c_str(), ios::in);
 	if (cf.fail()) {
-		cerr << "File open failed" << endl;
+		cerr << "File open failed" << filePath << endl;
 		exit(-1);
 	}
 
@@ -646,8 +777,8 @@ int initInt21Values(const std::string& fileName, const std::string& dirPath) {
 					c = k;
 					e = j;
 
-					iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1]
-						= temp;
+					if (!(strcmp(value,"inf")==0)) 
+						iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] = temp;
 					r++;
 					if (r % 4 == 0) jj++;
 					d++;
@@ -663,6 +794,7 @@ int initInt21Values(const std::string& fileName, const std::string& dirPath) {
 	return 0;
 }
 
+
 int initInt11Values(const std::string& fileName, const std::string& dirPath) {
 	int i, j, k, r, q, t;
 
@@ -685,7 +817,7 @@ int initInt11Values(const std::string& fileName, const std::string& dirPath) {
 	std::string filePath = dirPath + fileName;
 	cf.open(filePath.c_str(), ios::in);
 	if (cf.fail()) {
-		cerr << "File open failed" << endl;
+		cerr << "File open failed " << filePath << endl;
 		exit(-1);
 	}
 
@@ -729,7 +861,10 @@ int initInt11Values(const std::string& fileName, const std::string& dirPath) {
 				d = base2[k];
 				c = base1[jj];
 				f = base2[jj];
-				iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp;
+				
+				if (!(strcmp(value,"inf")==0)) 
+					iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp;
+				
 				r++;
 				if (r % 4 == 0) jj++;
 				e++;
@@ -740,5 +875,6 @@ int initInt11Values(const std::string& fileName, const std::string& dirPath) {
 	}
 
 	cf.close();
+	
 	return 0;
 }

From e0ab3434577a985c29871cca3fe9248374a74e9b Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 16 Jun 2011 16:26:55 -0400
Subject: [PATCH 147/282] added change to handle unafold mode

---
 gtfold-mfe/src/main.cc | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 2c56804..18489d1 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -169,11 +169,18 @@ void print_header() {
  * @param outputFile The file to save to
  * @param energy The MFE energy (multiplied by 100)
  */
-void save_ct_file(string outputFile, string seq, int energy) {
+void save_ct_file(string outputFile, string seq, int energy, string seqfile) {
+	if(seqfile.find("/") != string::npos) {
+		size_t pos = seqfile.find_last_of("/");
+		seqfile.erase(0,pos+1);
+	}
+	if(seqfile.find(".") != string::npos)
+		seqfile.erase(seqfile.rfind("."));
 	ofstream outfile;
 	outfile.open(outputFile.c_str());
 
 	outfile << seq.length() << "\t  dG = " << energy/100.0 << endl;
+	//outfile << seq.length() << "\tdG = " << energy/100.0 << "\t" << seqfile << endl;
 
 	unsigned int i = 1;
 	for(i=1; i <= seq.length(); i++)
@@ -197,7 +204,7 @@ int main(int argc, char** argv) {
 	}
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
-	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR);
+	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, T_MISMATCH);
 
 	printRunConfiguration(seq);
 	
@@ -207,7 +214,7 @@ int main(int argc, char** argv) {
 	fflush(stdout);
 
 	t1 = get_seconds();
-	energy = calculate(seq.length(), nThreads);
+	energy = calculate(seq.length(), nThreads, T_MISMATCH);
 	t1 = get_seconds() - t1;
 	
 	printf("Done.\n\n");
@@ -227,7 +234,7 @@ int main(int argc, char** argv) {
 	}
 	
 	t1 = get_seconds();
-	trace(seq.length(), VERBOSE);
+	trace(seq.length(), VERBOSE, T_MISMATCH);
 	t1 = get_seconds() - t1;
 
 	printf("\n");
@@ -241,7 +248,7 @@ int main(int argc, char** argv) {
 		print_shapeArray(seq.length());
 	
 
-	save_ct_file(outputFile, seq, energy);
+	save_ct_file(outputFile, seq, energy,seqfile);
 	printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str());
 
 

From 2ed0a6459b6d4b903687a5f0164ab01957d74ae9 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 16 Jun 2011 16:29:29 -0400
Subject: [PATCH 148/282] added changes to handle unafold mode

---
 gtfold-mfe/include/algorithms.h |   2 +-
 gtfold-mfe/include/traceback.h  |   2 +-
 gtfold-mfe/src/algorithms.c     | 215 ++++++++++++++++++++++++--------
 gtfold-mfe/src/traceback.c      | 213 +++++++++++++++++--------------
 4 files changed, 283 insertions(+), 149 deletions(-)

diff --git a/gtfold-mfe/include/algorithms.h b/gtfold-mfe/include/algorithms.h
index 336e443..9b3dee0 100644
--- a/gtfold-mfe/include/algorithms.h
+++ b/gtfold-mfe/include/algorithms.h
@@ -23,7 +23,7 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
-	int calculate(int len, int nThreads);
+	int calculate(int len, int nThreads, int t_mismatch);
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/include/traceback.h b/gtfold-mfe/include/traceback.h
index a8bd6c4..47a4f19 100644
--- a/gtfold-mfe/include/traceback.h
+++ b/gtfold-mfe/include/traceback.h
@@ -26,7 +26,7 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
-	void trace(int len, int vbose);
+	void trace(int len, int vbose, int t_mismatch);
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 0fd0c72..4bf8cc0 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -29,7 +29,79 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
 #ifdef _OPENMP 
 #include "omp.h"
 #endif
-int calculate(int len, int nThreads) { 
+
+//#define DEBUG 1
+
+void initializeMatrix(int len) {
+	int i, j;
+
+	for (i = 1; i <= len; ++i) 
+		for (j = len; j >= i; --j) 
+			if (canPair(RNA[i],RNA[j]) && j-i >= TURN) 
+				PP[i][j]  = 1;
+}
+
+void prefilter(int len, int prefilter1, int prefilter2) {
+	char** in;
+	int i, j, k, count;
+
+	in = (char**)malloc(len*sizeof(char*));
+	for (i = 1; i <= len; ++i) in[i - 1] = (char*)malloc(len*sizeof(char));
+
+	for (i = 1; i <= len - prefilter2 + 1; ++i)
+		for (j = len; j >= prefilter2 && j >= i; --j) {
+			count = 0;
+			for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k)
+				if (PP[i + k][j - k] == 1) ++count;
+			if (count >= prefilter1)
+				for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k)
+					++in[i + k - 1][j - k - 1];
+		}
+
+	for (i = 1; i <= len; ++i) {
+		for (j = len; j >= i; --j)
+			if (!in[i - 1][j - 1]) PP[i][j] = 0;
+		free(in[i - 1]);
+	}
+
+	free(in);
+}
+
+int calcVBI(int i, int j) {
+	int p=0, q=0;
+	int VBIij = INFINITY_;
+
+	for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
+		int minq = j-i+p-MAXLOOP-2;
+		if (minq < p+1+TURN) minq = p+1+TURN;
+		int maxq = (p==(i+1))?(j-2):(j-1);
+
+		for (q = minq; q <= maxq; q++) {
+			if (PP[p][q]==0) continue;
+			if (!canILoop(i,j,p,q)) continue;
+			VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
+		}
+	}
+
+	return VBIij;
+}
+
+int calcVBI2(int i, int j, int  len) {
+	int d, ii, jj; 
+	int energy = INFINITY_;
+
+	for (d = j-i-3; d >= TURN+1 && d >= j-i-2-MAXLOOP; --d) 
+		for (ii = i + 1; ii < j - d && ii <= len; ++ii)
+		{    
+			jj = d + ii;
+			if (PP[ii][jj]==1)
+				energy = MIN(energy, eL(i, j, ii, jj) + V(ii, jj));
+		}    
+
+	return energy;
+}
+
+int calculate(int len, int nThreads, int t_mismatch) { 
 	int b, i, j;
 #ifdef _OPENMP
 	if (nThreads>0) omp_set_num_threads(nThreads);
@@ -40,6 +112,11 @@ int calculate(int len, int nThreads) {
 	fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
 #endif
 
+	initializeMatrix(len);
+	if (t_mismatch) {
+		prefilter(len,2,2);
+	}
+
 	for (b = TURN+1; b <= len-1; b++) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
@@ -47,65 +124,67 @@ int calculate(int len, int nThreads) {
 		for (i = 1; i <= len - b; i++) {
 			j = i + b;
 			int newWM = INFINITY_; 
-			if (canPair(RNA[i], RNA[j])) {
+			
+			if (PP[i][j]==1) {
 				int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
-				
-        int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack
-				
-        if (j-i > 6) { // Internal Loop BEGIN
-					int p=0, q=0;
-					int VBIij = INFINITY_;
-					for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
-						int minq = j-i+p-MAXLOOP-2;
-						if (minq < p+1+TURN) minq = p+1+TURN;
-						int maxq = (p==i+1)?(j-2):(j-1);
-						for (q = minq; q <= maxq; q++) {
-							if (!canPair(RNA[p], RNA[q])) continue;
-							if (!canILoop(i,j,p,q)) continue;
-							VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
-						}
-					}
-					VBI(i,j) = VBIij;
-					V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
-				} // Internal Loop END
-				
-        if (j-i > 10) { // Multi Loop BEGIN
-					int VMij =  WMPrime[i+1][j-1]; 
-					int VMidj = WMPrime[i+2][j-1]; 
-					int VMijd = WMPrime[i+1][j-2]; 
-					int VMidjd = WMPrime[i+2][j-2]; 
-          
-					int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
-					int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
-					VMij = MIN(VMij, (VMidj + d5 +Ec)) ;
-					VMij = MIN(VMij, (VMijd + d3 +Ec));
+				int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack
+
+				// Internal Loop BEGIN
+				VBI(i,j) = calcVBI(i,j);
+				V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
+				// Internal Loop END
+
+				// Multi Loop BEGIN
+				int VMij =  WMPrime[i+1][j-1]; 
+				int VMidj = WMPrime[i+2][j-1]; 
+				int VMijd = WMPrime[i+1][j-2]; 
+				int VMidjd = WMPrime[i+2][j-2]; 
+
+				int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
+				int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
+				VMij = MIN(VMij, (VMidj + d5 +Ec)) ;
+				VMij = MIN(VMij, (VMijd + d3 +Ec));
+
+				if (t_mismatch) {
+					VMij = MIN(VMij, (VMidjd + Estackm(i,j) + 2*Ec));
+				} else {
 					VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec));
-					VMij = VMij + Ea + Eb + auPenalty(i,j);
-					VM(i,j) = canStack(i,j)?VMij:INFINITY_;
-				} // Multi Loop END
-				
-        V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j));
+				}
+
+				VMij = VMij + Ea + Eb + auPenalty(i,j);
+				VM(i,j) = canStack(i,j)?VMij:INFINITY_;
+				// Multi Loop END
+
+				V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j));
 			}
 			else V(i,j) = INFINITY_;
+
+			int h; 
+			for (h = i+TURN+1 ; h <= j-TURN-2; h++) {
+				// Added auxillary storage WMPrime to speedup multiloop calculations
+				WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); 
+				//newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM;
+			}
 			
-      if (j-i > 4) { // WM BEGIN
-				int h; 
-				for (h = i+TURN+1 ; h <= j-TURN-1; h++) {
-					//ZS: This sum corresponds to when i,j are NOT paired with each other.
-					//So we need to make sure only terms where i,j aren't pairing are considered. 
-					// Added auxillary storage WMPrime to speedup multiloop calculations
-          WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); 
-					//newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM;
-				}
-				newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM;
-				newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
-				newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
-				newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
+			//ZS: This sum corresponds to when i,j are NOT paired with each other.
+			//So we need to make sure only terms where i,j aren't pairing are considered. 
+			newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM;
+			
+			newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
+			newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
+			newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
+
+			if (t_mismatch) {
+				if (i<j-TURN-2)
+					newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; 
+			}
+			else {
 				newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; //i,j dangle
-				newWM = canSS(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; //i dangle
-				newWM = canSS(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; //j dangle
-				WMU(i,j) = WML(i,j) = newWM;
-			} // WM END
+			}
+
+			newWM = canSS(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; //i dangle
+			newWM = canSS(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; //j dangle
+			WMU(i,j) = WML(i,j) = newWM;
 		}
 	}
 
@@ -116,12 +195,38 @@ int calculate(int len, int nThreads) {
 			Wij = Widjd = Wijd = Widj = INFINITY_;
 			Wim1 = MIN(0, W[i-1]); 
 			Wij = V(i, j) + auPenalty(i, j) + Wim1;
-			Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:Widjd;
+		
+			if (t_mismatch) {
+				Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Estacke(j-1,i+1) + Wim1:Widjd;
+			} else {
+				Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:Widjd;
+			}
+			
 			Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd;
 			Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj;
 			Wj = MIN(MIN4(Wij, Widjd, Wijd, Widj), Wj); 
 		}
 		W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj;
 	}
+
+#ifdef DEBUG
+	FILE* file = fopen("VM.txt", "w");
+	int ii, jj;
+	for (ii = 1; ii <= len; ++ii) {    
+		for (jj = 1; jj <= len; ++jj) {
+			fprintf(file, "%d %d %d\n",ii,jj,VM(ii,jj));
+		}
+	}    
+	fclose(file);
+	
+ 	file = fopen("WM.txt", "w");
+	for (ii = 1; ii <= len; ++ii) {    
+		for (jj = 1; jj <= len; ++jj) {
+			fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj));
+		}
+	}    
+	fclose(file);
+#endif
+	
 	return W[len];
 }
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 445c851..e4357d7 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -33,10 +33,12 @@
 int verbose = -1;
 int total_en = 0;
 int total_ex = 0;
+int t_mismatch = 0;
 
-void trace(int len, int vbose) {
+void trace(int len, int vbose, int t_mismatch_) {
 	int i;
 	verbose = vbose;
+	t_mismatch = t_mismatch_;
 	for (i = 0; i < len+1; i++)
 		structure[i] = 0;
 
@@ -71,56 +73,69 @@ void traceW(int j) {
 
 		Widjd = Wijd =  Widj = INFINITY_;
 		Wij = V(i,j) + auPenalty(i, j) + wim1;
-		Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1;
+		
+		if (t_mismatch) {
+			Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Estacke(j-1,i+1) + wim1;
+		}
+		else {
+			Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1;
+		}
+
 		Wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
 		Widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
-		//Wj_temp=Wj;
-		
-		//Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
 
-		//if (W[j] == Wj) {
-			if ((W[j] == Wij && canStack(i,j)) || forcePair(i,j)) { 
-				done = 1;
-				if (verbose == 1) 
-					printf("i %5d j %5d ExtLoop   %12.2f\n", i, j, auPenalty(i, j)/100.00);
-				total_ex += auPenalty(i, j);
-				structure[i] = j;
-				structure[j] = i;
-				traceV(i, j);
-				if (flag ) traceW(i - 1);
-				break;
-			} else if ((W[j] == Widjd && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
-				done = 1;
-				if (verbose == 1) 
-					printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
-				total_ex += (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
-				structure[i + 1] = j - 1;
-				structure[j - 1] = i + 1;
-				traceV(i + 1, j - 1);
-				if (flag ) traceW(i - 1);
-				break;
-			} else if ((W[j] == Wijd && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) { 	
-				done = 1;
-				if (verbose == 1) 
-					printf("i %5d j %5d ExtLoop   %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
-				total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
-				structure[i] = j - 1;
-				structure[j - 1] = i;
-				traceV(i, j - 1);
-				if (flag ) traceW(i - 1);
-				break;
-			} else if ((W[j] == Widj && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){
-				done = 1;
-				if (verbose == 1) 
-					printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
-				total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
-				structure[i + 1] = j;
-				structure[j] = i + 1;
-				traceV(i + 1, j);
-				if (flag ) traceW(i - 1);
-				break;
-			}
-		//}
+		if ((W[j] == Wij && canStack(i,j)) || forcePair(i,j)) { 
+			done = 1;
+			if (verbose == 1) 
+				printf("i %5d j %5d ExtLoop   %12.2f\n", i, j, auPenalty(i, j)/100.00);
+			total_ex += auPenalty(i, j);
+			structure[i] = j;
+			structure[j] = i;
+			traceV(i, j);
+			if (flag ) traceW(i - 1);
+			break;
+		} else if ((W[j] == Widjd && t_mismatch && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
+			done = 1;
+			if (verbose == 1) 
+				printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Estacke(j-1,i+1))/100.00);
+			total_ex += (auPenalty(i+1, j-1) + Estacke(j-1,i+1));
+			structure[i + 1] = j - 1;
+			structure[j - 1] = i + 1;
+			traceV(i + 1, j - 1);
+			if (flag ) traceW(i - 1);
+			break;
+		}
+	   	else if ((W[j] == Widjd && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
+			done = 1;
+			if (verbose == 1) 
+				printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
+			total_ex += (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
+			structure[i + 1] = j - 1;
+			structure[j - 1] = i + 1;
+			traceV(i + 1, j - 1);
+			if (flag ) traceW(i - 1);
+			break;
+		} else if ((W[j] == Wijd && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) { 	
+			done = 1;
+			if (verbose == 1) 
+				printf("i %5d j %5d ExtLoop   %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
+			total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
+			structure[i] = j - 1;
+			structure[j - 1] = i;
+			traceV(i, j - 1);
+			if (flag ) traceW(i - 1);
+			break;
+		} else if ((W[j] == Widj && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){
+			done = 1;
+			if (verbose == 1) 
+				printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
+			total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
+			structure[i + 1] = j;
+			structure[j] = i + 1;
+			traceV(i + 1, j);
+			if (flag ) traceW(i - 1);
+			break;
+		}
 	}
 		
 	if (W[j] == W[j - 1] && !done) traceW(j-1);
@@ -133,17 +148,15 @@ int traceV(int i, int j) {
 	if (j-i < TURN)  return INFINITY_;
 
 	a = canHairpin(i,j)?eH(i, j):INFINITY_;
+	// TODO 
+	// if (eS(i, j) == 0) b = INFINITY_;
 	b = canStack(i,j)?eS(i, j) + V(i + 1, j - 1):INFINITY_;
-	if (eS(i, j) == 0) b = INFINITY_;
 	c = canStack(i,j)?VBI(i,j):INFINITY_;
 	d = canStack(i,j)?VM(i,j):INFINITY_;
 	
-	
-	
-	//Vij = MIN(MIN(a, b), MIN(c, d));
 	Vij = V(i,j);
-	
-	if (Vij == a && Vij != b && Vij != c && Vij != d) { 
+
+	if (Vij == a ) { 
 		if (verbose == 1) 
 			printf("i %5d j %5d Hairpin   %12.2f\n", i, j, eH(i, j)/100.00);
 		total_en += eH(i,j);
@@ -161,13 +174,14 @@ int traceV(int i, int j) {
 			printf("i %5d j %5d IntLoop  ", i, j);
 		traceVBI(i, j);
 		return Vij;
-	} else if (Vij == d && Vij != a && Vij != b && Vij != c) { 
+	} else if (Vij == d) { 
 		int eVM = traceVM(i, j);
 		if (verbose ==1) 
 			printf("i %5d j %5d MultiLoop %12.2f\n", i, j, (Vij-eVM)/100.0);
 		total_en += (Vij-eVM);
 		return Vij;
-	} 
+	}
+
 	return 0;
 }
 
@@ -206,7 +220,6 @@ int traceVBI(int i, int j) {
 }
 
 int traceVM(int i, int j) {
-
 	int done;
 	int h;
 	int A_temp;
@@ -215,41 +228,18 @@ int traceVM(int i, int j) {
 	done = 0;
 	int VMij = VM(i,j);
 
-	for (h = i + 2; h <= j - 1 && !done; h++) {
-		A_temp = WM(i+1,h-1) + WM(h,j - 1) + Ea + Eb + auPenalty(i, j);
-		if (A_temp == VMij) { 
-			done = 1;
-			eVM += traceWM(i + 1, h - 1);
-			eVM += traceWM(h, j - 1);
-			break;
-		}
-	}
-
-	//if (check_base(i+1)) {
-		for (h = i + 3; h <= j - 1 && !done; h++) {
-			A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1); 
-			if (A_temp == VMij && canSS(i+1) ) {
+	if (t_mismatch && i<j-TURN-2) {
+		for (h = i + 3; h <= j - 2 && !done; h++) { 
+			A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i,j) + Estackm(i,j);
+			if (A_temp == VMij && canSS(i+1) && canSS(j-1)) {
 				done = 1;
 				eVM += traceWM(i + 2, h - 1);
-				eVM += traceWM(h, j - 1);
-				break;
-			}
-		}
-	//}
-
-	//if (check_base(j-1)) {
-		for (h = i + 2; h <= j - 2 && !done; h++) { 
-			A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1);
-			if (A_temp == VMij && canSS(j-1)) {
-				done = 1;
-				eVM += traceWM(i + 1, h - 1);
 				eVM += traceWM(h, j - 2);
 				break;
 			}
 		}
-	//}
-
-	//if (check_base(i+1)&&check_base(j-1)) {
+	}
+	else {
 		for (h = i + 3; h <= j - 2 && !done; h++) { 
 			A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
 			if (A_temp == VMij && canSS(i+1) && canSS(j-1)) {
@@ -259,9 +249,39 @@ int traceVM(int i, int j) {
 				break;
 			}
 		}
-	//}
+	}
+
+	for (h = i + 2; h <= j - 1 && !done; h++) {
+		A_temp = WM(i+1,h-1) + WM(h,j - 1) + Ea + Eb + auPenalty(i, j);
+		if (A_temp == VMij) { 
+			done = 1;
+			eVM += traceWM(i + 1, h - 1);
+			eVM += traceWM(h, j - 1);
+			break;
+		}
+	}
 
-	return eVM;
+	for (h = i + 3; h <= j - 1 && !done; h++) {
+		A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1); 
+		if (A_temp == VMij && canSS(i+1) ) {
+			done = 1;
+			eVM += traceWM(i + 2, h - 1);
+			eVM += traceWM(h, j - 1);
+			break;
+		}
+	}
+
+	for (h = i + 2; h <= j - 2 && !done; h++) { 
+		A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1);
+		if (A_temp == VMij && canSS(j-1)) {
+			done = 1;
+			eVM += traceWM(i + 1, h - 1);
+			eVM += traceWM(h, j - 2);
+			break;
+		}
+	}
+
+		return eVM;
 }
 
 int traceWM(int i, int j) {
@@ -290,15 +310,15 @@ int traceWM(int i, int j) {
 			done = 1;
 		} else {
 			if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) { 
-				done = 1;
 				structure[i] = j;
 				structure[j] = i;
 				eWM += traceV(i, j);
-			} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) &&  canStack(i+1,j)) { 
 				done = 1;
+			} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) &&  canStack(i+1,j)) { 
 				eWM += traceV(i + 1, j);
 				structure[i + 1] = j;
 				structure[j] = i + 1;
+				done = 1;
 			} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec && canSS(j) && canStack(i,j-1)) { 
 				done = 1;
 				eWM += traceV(i, j - 1);
@@ -309,7 +329,14 @@ int traceWM(int i, int j) {
 				eWM += traceV(i + 1, j - 1);
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
-			} else if (WM(i,j) == WM(i + 1,j) + Ec && canSS(i)) { 
+			}
+		   	else if (WM(i,j) == V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1) && t_mismatch) {
+				done = 1;
+				eWM += traceV(i + 1, j - 1);
+				structure[i + 1] = j - 1;
+				structure[j - 1] = i + 1;
+			}
+			else if (WM(i,j) == WM(i + 1,j) + Ec && canSS(i)) { 
 				done = 1;
 				eWM += traceWM(i + 1, j);
 			} else if (WM(i,j) == WM(i,j - 1) + Ec && canSS(j)) { 
@@ -318,6 +345,8 @@ int traceWM(int i, int j) {
 			}
 		}
 	}
-	if(!done){fprintf(stderr, "ERROR: WM(%d,%d) could not be traced!\n", i,j);}
+	if(!done) { 
+		fprintf(stderr, "ERROR: WM(%d,%d) could not be traced!\n", i,j);
+	}
 	return eWM;
 }

From f9e0200e78d13295742397191727e27179665a45 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 16 Jun 2011 16:31:22 -0400
Subject: [PATCH 149/282] merged ZS bug fix on constraints

---
 gtfold-mfe/src/constraints.cc | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 45d6280..c491068 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -205,8 +205,9 @@ int init_constraints(const char* constr_file,int length) {
 
 	if(nFBP != 0){
 		int temp; 
+		//Make sure smallest one is first, UNLESS forcing single-stranded 
 		for(it  = 0; it < nFBP; it++){
-			if(FBP[it][0] > FBP[it][1]){
+			if(FBP[it][0] > FBP[it][1] && FBP[it][1]!=0){
 				temp = FBP[it][0];
 				FBP[it][0] = FBP[it][1];
 				FBP[it][1] = temp; 
@@ -223,11 +224,11 @@ int init_constraints(const char* constr_file,int length) {
 				int i1 = FBP[it][0]+k-1;
 				int j1 = FBP[it][1]-k+1;
 				if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){
-					printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
+					fprintf(stderr,"Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
 					continue;			
 				}
 				if(FBP[it][1]!=0&&(j1-i1 < TURN)){
-					printf("Can't force (%d, %d) to pair (turn too tight) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
+					fprintf(stderr,"Can't force (%d, %d) to pair (turn too tight) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
 					continue;
 				}
 				if(FBP[it][1] == 0){

From 9cb4ef7ef64aa956a9505d6c3bde5467af58fc8f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 16 Jun 2011 16:39:56 -0400
Subject: [PATCH 150/282] merged ZS changes with SHAPE

---
 gtfold-mfe/src/algorithms.c | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 4bf8cc0..c22da33 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -127,11 +127,10 @@ int calculate(int len, int nThreads, int t_mismatch) {
 			
 			if (PP[i][j]==1) {
 				int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
-				int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack
+				int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack
 
 				// Internal Loop BEGIN
 				VBI(i,j) = calcVBI(i,j);
-				V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j);
 				// Internal Loop END
 
 				// Multi Loop BEGIN

From 25b03068c2d50d282a01062de89685221c30fa5c Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 16 Jun 2011 16:40:47 -0400
Subject: [PATCH 151/282] merged ZS changes with SHAPE

---
 gtfold-mfe/src/shapereader.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/shapereader.cc b/gtfold-mfe/src/shapereader.cc
index 43083ab..fcbcbc5 100644
--- a/gtfold-mfe/src/shapereader.cc
+++ b/gtfold-mfe/src/shapereader.cc
@@ -42,7 +42,7 @@ void readSHAPEarray(const char* filename, int seqlength){
 	
 	while(getline(infile,line)>0){
 		if(sscanf(line.c_str(), "%d %lf", &position, &SHAPEnumber)==2){
-			if(position < seqlength){
+			if(position <= seqlength){
 				SHAPEarray[position] = SHAPEnumber;
 				SHAPEenergies[position] = calcShapeEnergy(SHAPEnumber);
 			}

From 69de0414f0d551bd4e2b22616057e4239eb25068 Mon Sep 17 00:00:00 2001
From: Andrew Ash <ash211@gmail.com>
Date: Thu, 16 Jun 2011 23:29:19 -0700
Subject: [PATCH 152/282] Accessing C declarations from C++ requires the "C"
 extern

---
 gtfold-mfe/include/partition-dangle.h | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/gtfold-mfe/include/partition-dangle.h b/gtfold-mfe/include/partition-dangle.h
index 1fb8a3b..2843a60 100644
--- a/gtfold-mfe/include/partition-dangle.h
+++ b/gtfold-mfe/include/partition-dangle.h
@@ -1,6 +1,9 @@
 #ifndef _PARTITION_DANGLE_H
 #define _PARTITION_DANGLE_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
 
 typedef struct partition_d{
 	double ** u;
@@ -17,4 +20,8 @@ double cond_dangle(int j, int h, int l);
 dangle_struct malloc_partition_arrays_d(int len);
 void fill_partition_arrays_d(dangle_struct part_struct);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif

From 2223754819754809dbab5be0a9add615d34a625d Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Fri, 17 Jun 2011 13:00:06 -0400
Subject: [PATCH 153/282] removed Makefile

---
 gtfold-mfe/src/Makefile | 522 ----------------------------------------
 1 file changed, 522 deletions(-)
 delete mode 100644 gtfold-mfe/src/Makefile

diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile
deleted file mode 100644
index 6385554..0000000
--- a/gtfold-mfe/src/Makefile
+++ /dev/null
@@ -1,522 +0,0 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
-# src/Makefile.  Generated from Makefile.in by configure.
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-
-
-
-pkgdatadir = $(datadir)/gtfold
-pkgincludedir = $(includedir)/gtfold
-pkglibdir = $(libdir)/gtfold
-pkglibexecdir = $(libexecdir)/gtfold
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = x86_64-unknown-linux-gnu
-host_triplet = x86_64-unknown-linux-gnu
-target_triplet = x86_64-unknown-linux-gnu
-bin_PROGRAMS = gtfold$(EXEEXT)
-subdir = src
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-am__installdirs = "$(DESTDIR)$(bindir)"
-PROGRAMS = $(bin_PROGRAMS)
-am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
-	options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \
-	energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \
-	subopt_traceback.$(OBJEXT) shapereader.$(OBJEXT)
-gtfold_OBJECTS = $(am_gtfold_OBJECTS)
-gtfold_DEPENDENCIES =
-gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
-	$(LDFLAGS) -o $@
-DEFAULT_INCLUDES = -I. -I$(top_builddir)
-depcomp = $(SHELL) $(top_srcdir)/depcomp
-am__depfiles_maybe = depfiles
-am__mv = mv -f
-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-CCLD = $(CC)
-LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
-	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
-CXXLD = $(CXX)
-CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-	-o $@
-SOURCES = $(gtfold_SOURCES)
-DIST_SOURCES = $(gtfold_SOURCES)
-ETAGS = etags
-CTAGS = ctags
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = gawk
-CC = gcc
-CCDEPMODE = depmode=gcc3
-CFLAGS = -g -O2 -Wall
-CPP = gcc -E
-CPPFLAGS = 
-CXX = g++
-CXXDEPMODE = depmode=gcc3
-CXXFLAGS = -g -O2 -Wall
-CYGPATH_W = echo
-DEFS = -DHAVE_CONFIG_H
-DEPDIR = .deps
-ECHO_C = 
-ECHO_N = -n
-ECHO_T = 
-EGREP = /bin/grep -E
-EXEEXT = 
-GREP = /bin/grep
-INSTALL = /usr/bin/install -c
-INSTALL_DATA = ${INSTALL} -m 644
-INSTALL_PROGRAM = ${INSTALL}
-INSTALL_SCRIPT = ${INSTALL}
-INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
-LDFLAGS = 
-LIBOBJS = 
-LIBS = -lgomp 
-LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
-MKDIR_P = /bin/mkdir -p
-OBJEXT = o
-OPENMP_CFLAGS = -fopenmp
-PACKAGE = gtfold
-PACKAGE_BUGREPORT = 
-PACKAGE_NAME = gtfold
-PACKAGE_STRING = gtfold 1.18
-PACKAGE_TARNAME = gtfold
-PACKAGE_URL = 
-PACKAGE_VERSION = 1.18
-PATH_SEPARATOR = :
-SET_MAKE = 
-SHELL = /bin/bash
-STRIP = 
-VERSION = 1.18
-abs_builddir = /home/zs/git/gtfold/gtfold-mfe/src
-abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/src
-abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
-abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
-ac_ct_CC = gcc
-ac_ct_CXX = g++
-am__include = include
-am__leading_dot = .
-am__quote = 
-am__tar = ${AMTAR} chof - "$$tardir"
-am__untar = ${AMTAR} xf -
-bindir = ${exec_prefix}/bin
-build = x86_64-unknown-linux-gnu
-build_alias = 
-build_cpu = x86_64
-build_os = linux-gnu
-build_vendor = unknown
-builddir = .
-datadir = ${datarootdir}
-datarootdir = ${prefix}/share
-docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
-dvidir = ${docdir}
-exec_prefix = ${prefix}
-host = x86_64-unknown-linux-gnu
-host_alias = 
-host_cpu = x86_64
-host_os = linux-gnu
-host_vendor = unknown
-htmldir = ${docdir}
-includedir = ${prefix}/include
-infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
-libdir = ${exec_prefix}/lib
-libexecdir = ${exec_prefix}/libexec
-localedir = ${datarootdir}/locale
-localstatedir = ${prefix}/var
-mandir = ${datarootdir}/man
-mkdir_p = /bin/mkdir -p
-oldincludedir = /usr/include
-pdfdir = ${docdir}
-prefix = /home/zs/dsgtfold
-program_transform_name = s,x,x,
-psdir = ${docdir}
-sbindir = ${exec_prefix}/sbin
-sharedstatedir = ${prefix}/com
-srcdir = .
-sysconfdir = ${prefix}/etc
-target = x86_64-unknown-linux-gnu
-target_alias = 
-target_cpu = x86_64
-target_os = linux-gnu
-target_vendor = unknown
-top_build_prefix = ../
-top_builddir = ..
-top_srcdir = ..
-INCLUDES = -I$(top_srcdir) -I$(top_srcdir)/include
-AM_CFLAGS = $(OPENMP_CFLAGS) -DDATADIR='$(datadir)/gtfold'
-AM_CXXFLAGS = -DDATADIR='$(datadir)/gtfold'
-gtfold_SOURCES = \
-	main.cc\
-	loader.cc\
-	utils.cc\
-	options.cc\
-	constraints.cc\
-	global.c\
-	energy.c\
-	algorithms.c \
-	traceback.c \
-	subopt_traceback.cc\
-	shapereader.cc
-
-gtfold_LDFLAGS = 
-gtfold_LDADD = -lm
-CLEANFILES = *~ *.o
-all: all-am
-
-.SUFFIXES:
-.SUFFIXES: .c .cc .o .obj
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu src/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-install-binPROGRAMS: $(bin_PROGRAMS)
-	@$(NORMAL_INSTALL)
-	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
-	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-	for p in $$list; do echo "$$p $$p"; done | \
-	sed 's/$(EXEEXT)$$//' | \
-	while read p p1; do if test -f $$p; \
-	  then echo "$$p"; echo "$$p"; else :; fi; \
-	done | \
-	sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
-	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
-	sed 'N;N;N;s,\n, ,g' | \
-	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
-	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
-	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
-	    else { print "f", $$3 "/" $$4, $$1; } } \
-	  END { for (d in files) print "f", d, files[d] }' | \
-	while read type dir files; do \
-	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
-	    test -z "$$files" || { \
-	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
-	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
-	    } \
-	; done
-
-uninstall-binPROGRAMS:
-	@$(NORMAL_UNINSTALL)
-	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-	files=`for p in $$list; do echo "$$p"; done | \
-	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
-	      -e 's/$$/$(EXEEXT)/' `; \
-	test -n "$$list" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(bindir)" && rm -f $$files
-
-clean-binPROGRAMS:
-	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
-gtfold$(EXEEXT): $(gtfold_OBJECTS) $(gtfold_DEPENDENCIES) 
-	@rm -f gtfold$(EXEEXT)
-	$(gtfold_LINK) $(gtfold_OBJECTS) $(gtfold_LDADD) $(LIBS)
-
-mostlyclean-compile:
-	-rm -f *.$(OBJEXT)
-
-distclean-compile:
-	-rm -f *.tab.c
-
-include ./$(DEPDIR)/algorithms.Po
-include ./$(DEPDIR)/constraints.Po
-include ./$(DEPDIR)/energy.Po
-include ./$(DEPDIR)/global.Po
-include ./$(DEPDIR)/loader.Po
-include ./$(DEPDIR)/main.Po
-include ./$(DEPDIR)/options.Po
-include ./$(DEPDIR)/shapereader.Po
-include ./$(DEPDIR)/subopt_traceback.Po
-include ./$(DEPDIR)/traceback.Po
-include ./$(DEPDIR)/utils.Po
-
-.c.o:
-	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-#	source='$<' object='$@' libtool=no \
-#	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
-#	$(COMPILE) -c $<
-
-.c.obj:
-	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-#	source='$<' object='$@' libtool=no \
-#	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
-#	$(COMPILE) -c `$(CYGPATH_W) '$<'`
-
-.cc.o:
-	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-#	source='$<' object='$@' libtool=no \
-#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
-#	$(CXXCOMPILE) -c -o $@ $<
-
-.cc.obj:
-	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-#	source='$<' object='$@' libtool=no \
-#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
-#	$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	mkid -fID $$unique
-tags: TAGS
-
-TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	set x; \
-	here=`pwd`; \
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	shift; \
-	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-	  test -n "$$unique" || unique=$$empty_fix; \
-	  if test $$# -gt 0; then \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      "$$@" $$unique; \
-	  else \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      $$unique; \
-	  fi; \
-	fi
-ctags: CTAGS
-CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	test -z "$(CTAGS_ARGS)$$unique" \
-	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$unique
-
-GTAGS:
-	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && $(am__cd) $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) "$$here"
-
-distclean-tags:
-	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-am
-all-am: Makefile $(PROGRAMS)
-installdirs:
-	for dir in "$(DESTDIR)$(bindir)"; do \
-	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-	done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
-
-distclean: distclean-am
-	-rm -rf ./$(DEPDIR)
-	-rm -f Makefile
-distclean-am: clean-am distclean-compile distclean-generic \
-	distclean-tags
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am:
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am: install-binPROGRAMS
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
-	-rm -rf ./$(DEPDIR)
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-compile mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-binPROGRAMS
-
-.MAKE: install-am install-strip
-
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
-	clean-generic ctags distclean distclean-compile \
-	distclean-generic distclean-tags distdir dvi dvi-am html \
-	html-am info info-am install install-am install-binPROGRAMS \
-	install-data install-data-am install-dvi install-dvi-am \
-	install-exec install-exec-am install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-compile \
-	mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
-	uninstall-am uninstall-binPROGRAMS
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:

From 92625685f8f946e3b15095bca9ba597a3b18e14f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Fri, 17 Jun 2011 15:10:42 -0400
Subject: [PATCH 154/282] seperate functions eL1(), eL() to handle 2x3 internal
 loop

---
 gtfold-mfe/src/algorithms.c |  26 +++++++-
 gtfold-mfe/src/energy.c     | 126 ++++++++++++++++++++----------------
 2 files changed, 93 insertions(+), 59 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index c22da33..6f4a314 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -86,6 +86,25 @@ int calcVBI(int i, int j) {
 	return VBIij;
 }
 
+int calcVBI1(int i, int j) {
+	int p=0, q=0;
+	int VBIij = INFINITY_;
+
+	for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
+		int minq = j-i+p-MAXLOOP-2;
+		if (minq < p+1+TURN) minq = p+1+TURN;
+		int maxq = (p==(i+1))?(j-2):(j-1);
+
+		for (q = minq; q <= maxq; q++) {
+			if (PP[p][q]==0) continue;
+			if (!canILoop(i,j,p,q)) continue;
+			VBIij = MIN(eL1(i, j, p, q) + V(p,q), VBIij);
+		}
+	}
+
+	return VBIij;
+}
+
 int calcVBI2(int i, int j, int  len) {
 	int d, ii, jj; 
 	int energy = INFINITY_;
@@ -95,7 +114,7 @@ int calcVBI2(int i, int j, int  len) {
 		{    
 			jj = d + ii;
 			if (PP[ii][jj]==1)
-				energy = MIN(energy, eL(i, j, ii, jj) + V(ii, jj));
+				energy = MIN(energy, eL1(i, j, ii, jj) + V(ii, jj));
 		}    
 
 	return energy;
@@ -130,7 +149,10 @@ int calculate(int len, int nThreads, int t_mismatch) {
 				int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack
 
 				// Internal Loop BEGIN
-				VBI(i,j) = calcVBI(i,j);
+				if (t_mismatch) 
+					VBI(i,j) = calcVBI1(i,j);
+				else
+					VBI(i,j) = calcVBI(i,j);
 				// Internal Loop END
 
 				// Multi Loop BEGIN
diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 985d47a..616ad48 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -144,65 +144,76 @@ inline int Ed3(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][1];}
 inline int Ed5(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][0]; }
 inline int auPenalty(int i, int j) { return auPen(RNA[i], RNA[j]);}
 
-inline int eL1(int i, int j, int ii, int jj) {
-	int loopSize1, loopSize2;
-	int loopEnergy, asPenalty;
+inline int eL1(int i, int j, int ip, int jp) {
+	int energy;
+	int size1, size2, size;
+	int loginc; /* SH: Originally unassiged, but needs to be set to 0 so it doesn't throw off later calculations. */
+	int lopsided; /* define the asymmetry of an interior loop */
 
-	loopSize1 = ii - i - 1;
-	loopSize2 = j - jj - 1;
-	if (loopSize1 + loopSize2 > MAXLOOP)
-		return INFINITY_;
+	energy = INFINITY_;
+	loginc = 0;
 
-	if (loopSize1 == 0) {
-		if (loopSize2 == 1)
-			return bulge[1] + stack[fourBaseIndex(RNA[i], RNA[j], RNA[ii], RNA[jj])];
-		else if (loopSize2 <= 30)
-			return bulge[loopSize2] + auPenalty(i, j) + auPenalty(ii, jj);
-		else
-			return bulge[30] + (int)floor(prelog*log((double) loopSize2 / 30)) + auPenalty(i, j) + auPenalty(ii, jj);
-	}
-	else if (loopSize2 == 0) {
-		if (loopSize1 == 1)
-			return bulge[1] + stack[fourBaseIndex(RNA[i], RNA[j], RNA[ii], RNA[jj])];
-		else if (loopSize1 <= 30)
-			return bulge[loopSize1] + auPenalty(i, j) + auPenalty(ii, jj);
-		else
-			return bulge[30] + (int)floor(prelog* log((double) loopSize1 / 30)) + auPenalty(i, j) + auPenalty(ii, jj);
-	}
-	else if (loopSize1 == 1 && loopSize2 == 1)
-		return iloop11[RNA[i]][RNA[i + 1]][RNA[ii]][RNA[j]][RNA[j - 1]][RNA[jj]];
-	else if (loopSize1 == 1 && loopSize2 == 2)
-		return iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ii]][RNA[jj]];
-	else if (loopSize1 == 2 && loopSize2 == 1)
-		return iloop21[RNA[jj]][RNA[ii]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]];
-	else if (loopSize1 == 2 && loopSize2 == 2)
-		return iloop22[RNA[i]][RNA[ii]][RNA[j]][RNA[jj]][RNA[i+1]][RNA[i+2]][RNA[j-1]][RNA[j-2]];
-	else if ((loopSize1 == 2 && loopSize2 == 3) ||
-			 (loopSize1 == 3 && loopSize2 == 2)) {
-		return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] +
-			tstacki23[RNA[jj]][RNA[ii]][RNA[jj + 1]][RNA[ii - 1]];
-	}
-	else {
-		if (loopSize1 + loopSize2 <= 30)
-			loopEnergy = inter[loopSize1 + loopSize2];
-		else
-			loopEnergy = inter[30] + (int)floor(prelog* log((double) (loopSize1 + loopSize2) / 30));
-		
-		if (gail && (loopSize1 == 1 || loopSize2 == 1)) {
-			loopEnergy += tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)];
-			loopEnergy += tstki[fourBaseIndex(RNA[jj], RNA[ii], BASE_A, BASE_A)];
-		}
-		else {
-			loopEnergy += tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])];
-			loopEnergy += tstki[fourBaseIndex(RNA[jj], RNA[ii], RNA[jj + 1], RNA[ii - 1])];
+	/*SH: These calculations used to incorrectly be within the bulge loop code, moved out here. */
+	size1 = ip - i - 1;
+	size2 = j - jp - 1;
+	size = size1 + size2;
+
+	if (size1 == 0 || size2 == 0) {
+		if (size > 30) {
+			/* AM: Does not depend upon i and j and ip and jp - Stacking Energies */
+			loginc = (int) floor(prelog * log((double) size / 30.0));
+			energy = bulge[30] + eparam[2] + loginc + auPen(RNA[i], RNA[j])
+				+ auPen(RNA[ip], RNA[jp]);
+		} else if (size <= 30 && size != 1) {
+			/* Does not depend upon i and j and ip and jp - Stacking Energies  */
+			energy = bulge[size] + eparam[2];
+			energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]);
+		} else if (size == 1) {
+			energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])]
+				+ bulge[size] + eparam[2] +
+				+ getShapeEnergy(i) + getShapeEnergy(j) + getShapeEnergy(ip) + getShapeEnergy(jp);
 		}
-		asPenalty = abs(loopSize1 - loopSize2)*poppen[MIN3(2, loopSize1, loopSize2) - 1];
-		asPenalty = MIN(asPenalty, maxpen);
+	} else {
+		/* Internal loop */
+		lopsided = abs(size1 - size2);
 
-		loopEnergy += asPenalty;
+		if (size > 30) {
+			loginc = (int) floor(prelog * log((double) size / 30.0));
 
-		return loopEnergy;
+			if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/
+
+				energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + 
+					tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[30] + loginc +
+				   	eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))]));
+			} else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/
+				energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A,
+										  BASE_A)] + inter[30] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))]));
+			}
+		}
+		else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */
+			energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]];
+			if (i==1 && j==22) printf("2x2 loop at %d %d %d\n", i,j, energy);
+		} else if (size1 == 1 && size2 == 2) {
+			energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]];
+		} else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */
+			energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]];
+		} else if (size == 2) { /* 1*1 internal loops */
+			energy = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]];
+		} else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) {
+			return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] +
+				tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]];
+		}
+		else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0)  */
+			energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)]
+				+ inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))]));
+		} else { /* General Internal loops */
+			energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size]
+										  + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); 
+		
+		}
 	}
+
+	return energy;
 }
 
 inline int eL(int i, int j, int ip, int jp) {
@@ -260,10 +271,11 @@ inline int eL(int i, int j, int ip, int jp) {
 			energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]];
 		} else if (size == 2) { /* 1*1 internal loops */
 			energy = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]];
-		} else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) {
-			return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] +
-				tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]];
-		}
+		} 
+		//else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) {
+		//	return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] +
+		//		tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]];
+		//}
 		else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0)  */
 			energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)]
 				+ inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))]));

From 92191276d372d3927a1485cb7980a0c58d73b2c0 Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Sun, 19 Jun 2011 15:27:44 -0400
Subject: [PATCH 155/282] Pull from gtfold master

---
 gtfold-mfe/src/algorithms-partition.c | 30 ++++++++++++++++++++-------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c
index 77e4fdf..83d1a4d 100644
--- a/gtfold-mfe/src/algorithms-partition.c
+++ b/gtfold-mfe/src/algorithms-partition.c
@@ -10,6 +10,13 @@
 #include "algorithms-partition.h"
 #include "data.h"
 
+#ifdef _OPENMP   
+#include "omp.h"
+#endif
+
+
+#define DANGLE_DEBUG
+
 // double[][] QB;
 // double[][] Q;
 // double[][] QM;
@@ -58,6 +65,12 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) {
 
     // fill in values in the array
     for(l=1; l<=len; ++l) {
+		//Parrallelize
+		#ifndef DANGLE_DEBUG
+		#ifdef _OPENMP
+		#pragma omp parallel for private (i,j) schedule(guided)
+		#endif
+		#endif
         for(i=1; i<= len-l+1; ++i) {
 
             int j = i+l-1;
@@ -73,13 +86,16 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) {
                 for(d=i+1; d<=j-4; ++d) {
                     for(e=d+4; e<=j-1; ++e) {
                         
-                if(d == i + 1 && e == j -1)
-                    QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e];
-                else 
-                    QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e];
-
-                        QB[i][j] += QM[i+1][d-1]*QB[d][e] *
-                            exp(-(a + b + c*(j-e-1))/RT);
+						if(d == i + 1 && e == j -1){
+							QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e];
+						}
+						else{
+							printf("i: %d j: %d d: %d e: %d\n", i,j,d,e);
+							QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e];
+						}
+
+						QB[i][j] += QM[i+1][d-1]*QB[d][e] *
+									exp(-(a + b + c*(j-e-1))/RT);
                     }
                 }
             }

From 12b006bc6387cc2b60a0937d71fe6df0609466f0 Mon Sep 17 00:00:00 2001
From: Janderson <janderson3@gatech.edu>
Date: Sun, 19 Jun 2011 23:22:45 -0400
Subject: [PATCH 156/282] --bpp option re-integrated.

---
 gtfold-mfe/Makefile                       |   2 +-
 gtfold-mfe/data/Andronescu/Makefile       |  26 ++--
 gtfold-mfe/data/Makefile                  |  26 ++--
 gtfold-mfe/data/Turner04/Makefile         |  26 ++--
 gtfold-mfe/data/Turner99/Makefile         |  26 ++--
 gtfold-mfe/include/Makefile               | 162 +---------------------
 gtfold-mfe/include/algorithms-partition.h |   2 +-
 gtfold-mfe/include/energy.h               |   2 +-
 gtfold-mfe/src/.deps/loader.Po            |  12 +-
 gtfold-mfe/src/algorithms-partition.c     |  51 ++++---
 gtfold-mfe/src/main.cc                    |   8 +-
 11 files changed, 100 insertions(+), 243 deletions(-)

diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile
index f791022..cdd52e6 100644
--- a/gtfold-mfe/Makefile
+++ b/gtfold-mfe/Makefile
@@ -214,7 +214,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/dsgtfold
+prefix = /usr/local
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/data/Andronescu/Makefile b/gtfold-mfe/data/Andronescu/Makefile
index b2fd9ef..8dc0b5c 100644
--- a/gtfold-mfe/data/Andronescu/Makefile
+++ b/gtfold-mfe/data/Andronescu/Makefile
@@ -71,12 +71,12 @@ am__base_list = \
 am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
 DATA = $(gtfold_data_DATA)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = gawk
+ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = mawk
 CC = gcc
 CCDEPMODE = depmode=gcc3
 CFLAGS = -g -O2 -Wall
@@ -103,7 +103,7 @@ LDFLAGS =
 LIBOBJS = 
 LIBS = -lgomp 
 LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
 MKDIR_P = /bin/mkdir -p
 OBJEXT = o
 OPENMP_CFLAGS = -fopenmp
@@ -119,10 +119,10 @@ SET_MAKE =
 SHELL = /bin/bash
 STRIP = 
 VERSION = 1.18
-abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data/Andronescu
-abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data/Andronescu
-abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
-abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data/Andronescu
+abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data/Andronescu
+abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
+abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
 ac_ct_CC = gcc
 ac_ct_CXX = g++
 am__include = include
@@ -150,7 +150,7 @@ host_vendor = unknown
 htmldir = ${docdir}
 includedir = ${prefix}/include
 infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
 libdir = ${exec_prefix}/lib
 libexecdir = ${exec_prefix}/libexec
 localedir = ${datarootdir}/locale
@@ -159,7 +159,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/dsgtfold
+prefix = /usr/local
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/data/Makefile b/gtfold-mfe/data/Makefile
index 0331574..654058c 100644
--- a/gtfold-mfe/data/Makefile
+++ b/gtfold-mfe/data/Makefile
@@ -87,12 +87,12 @@ am__relativize = \
     dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
   done; \
   reldir="$$dir2"
-ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = gawk
+ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = mawk
 CC = gcc
 CCDEPMODE = depmode=gcc3
 CFLAGS = -g -O2 -Wall
@@ -119,7 +119,7 @@ LDFLAGS =
 LIBOBJS = 
 LIBS = -lgomp 
 LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
 MKDIR_P = /bin/mkdir -p
 OBJEXT = o
 OPENMP_CFLAGS = -fopenmp
@@ -135,10 +135,10 @@ SET_MAKE =
 SHELL = /bin/bash
 STRIP = 
 VERSION = 1.18
-abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data
-abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data
-abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
-abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data
+abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data
+abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
+abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
 ac_ct_CC = gcc
 ac_ct_CXX = g++
 am__include = include
@@ -166,7 +166,7 @@ host_vendor = unknown
 htmldir = ${docdir}
 includedir = ${prefix}/include
 infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
 libdir = ${exec_prefix}/lib
 libexecdir = ${exec_prefix}/libexec
 localedir = ${datarootdir}/locale
@@ -175,7 +175,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/dsgtfold
+prefix = /usr/local
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/data/Turner04/Makefile b/gtfold-mfe/data/Turner04/Makefile
index 382eac6..65f56b2 100644
--- a/gtfold-mfe/data/Turner04/Makefile
+++ b/gtfold-mfe/data/Turner04/Makefile
@@ -71,12 +71,12 @@ am__base_list = \
 am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
 DATA = $(gtfold_data_DATA)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = gawk
+ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = mawk
 CC = gcc
 CCDEPMODE = depmode=gcc3
 CFLAGS = -g -O2 -Wall
@@ -103,7 +103,7 @@ LDFLAGS =
 LIBOBJS = 
 LIBS = -lgomp 
 LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
 MKDIR_P = /bin/mkdir -p
 OBJEXT = o
 OPENMP_CFLAGS = -fopenmp
@@ -119,10 +119,10 @@ SET_MAKE =
 SHELL = /bin/bash
 STRIP = 
 VERSION = 1.18
-abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data/Turner04
-abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data/Turner04
-abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
-abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner04
+abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner04
+abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
+abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
 ac_ct_CC = gcc
 ac_ct_CXX = g++
 am__include = include
@@ -150,7 +150,7 @@ host_vendor = unknown
 htmldir = ${docdir}
 includedir = ${prefix}/include
 infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
 libdir = ${exec_prefix}/lib
 libexecdir = ${exec_prefix}/libexec
 localedir = ${datarootdir}/locale
@@ -159,7 +159,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/dsgtfold
+prefix = /usr/local
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/data/Turner99/Makefile b/gtfold-mfe/data/Turner99/Makefile
index 0fee0e5..abc7da4 100644
--- a/gtfold-mfe/data/Turner99/Makefile
+++ b/gtfold-mfe/data/Turner99/Makefile
@@ -71,12 +71,12 @@ am__base_list = \
 am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
 DATA = $(gtfold_data_DATA)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = gawk
+ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
+AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
+AWK = mawk
 CC = gcc
 CCDEPMODE = depmode=gcc3
 CFLAGS = -g -O2 -Wall
@@ -103,7 +103,7 @@ LDFLAGS =
 LIBOBJS = 
 LIBS = -lgomp 
 LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo
+MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
 MKDIR_P = /bin/mkdir -p
 OBJEXT = o
 OPENMP_CFLAGS = -fopenmp
@@ -119,10 +119,10 @@ SET_MAKE =
 SHELL = /bin/bash
 STRIP = 
 VERSION = 1.18
-abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data/Turner99
-abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data/Turner99
-abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
-abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
+abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner99
+abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner99
+abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
+abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
 ac_ct_CC = gcc
 ac_ct_CXX = g++
 am__include = include
@@ -150,7 +150,7 @@ host_vendor = unknown
 htmldir = ${docdir}
 includedir = ${prefix}/include
 infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh
+install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
 libdir = ${exec_prefix}/lib
 libexecdir = ${exec_prefix}/libexec
 localedir = ${datarootdir}/locale
@@ -159,7 +159,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/dsgtfold
+prefix = /usr/local
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
diff --git a/gtfold-mfe/include/Makefile b/gtfold-mfe/include/Makefile
index 8b19e61..596ed80 100644
--- a/gtfold-mfe/include/Makefile
+++ b/gtfold-mfe/include/Makefile
@@ -46,39 +46,9 @@ mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/gtfold_config.h
 CONFIG_CLEAN_FILES =
 CONFIG_CLEAN_VPATH_FILES =
-<<<<<<< HEAD
-am__installdirs = "$(DESTDIR)$(bindir)"
-PROGRAMS = $(bin_PROGRAMS)
-am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
-	options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \
-	energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \
-	subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \
-	partition-dangle.$(OBJEXT) random-sample.$(OBJEXT) \
-	shapereader.$(OBJEXT)
-gtfold_OBJECTS = $(am_gtfold_OBJECTS)
-gtfold_DEPENDENCIES =
-gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
-	$(LDFLAGS) -o $@
-DEFAULT_INCLUDES = -I. -I$(top_builddir)
-depcomp = $(SHELL) $(top_srcdir)/depcomp
-am__depfiles_maybe = depfiles
-am__mv = mv -f
-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-CCLD = $(CC)
-LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
-	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
-CXXLD = $(CXX)
-CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-	-o $@
-SOURCES = $(gtfold_SOURCES)
-DIST_SOURCES = $(gtfold_SOURCES)
-=======
 SOURCES =
 DIST_SOURCES =
 HEADERS = $(noinst_HEADERS)
->>>>>>> gtfold/master
 ETAGS = etags
 CTAGS = ctags
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
@@ -130,17 +100,10 @@ SET_MAKE =
 SHELL = /bin/bash
 STRIP = 
 VERSION = 1.18
-<<<<<<< HEAD
-abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/src
-abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/src
+abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/include
+abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/include
 abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
 abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
-=======
-abs_builddir = /home/zs/git/gtfold/gtfold-mfe/include
-abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/include
-abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe
-abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe
->>>>>>> gtfold/master
 ac_ct_CC = gcc
 ac_ct_CXX = g++
 am__include = include
@@ -177,7 +140,7 @@ mandir = ${datarootdir}/man
 mkdir_p = /bin/mkdir -p
 oldincludedir = /usr/include
 pdfdir = ${docdir}
-prefix = /home/zs/dsgtfold
+prefix = /usr/local
 program_transform_name = s,x,x,
 psdir = ${docdir}
 sbindir = ${exec_prefix}/sbin
@@ -192,33 +155,8 @@ target_vendor = unknown
 top_build_prefix = ../
 top_builddir = ..
 top_srcdir = ..
-<<<<<<< HEAD
-INCLUDES = -I$(top_srcdir) -I$(top_srcdir)/include
-AM_CFLAGS = $(OPENMP_CFLAGS) -DDATADIR='$(datadir)/gtfold'
-AM_CXXFLAGS = -DDATADIR='$(datadir)/gtfold'
-gtfold_SOURCES = \
-	main.cc\
-	loader.cc\
-	utils.cc\
-	options.cc\
-	constraints.cc\
-	global.c\
-	energy.c\
-	algorithms.c\
-	traceback.c\
-	subopt_traceback.cc\
-	algorithms-partition.c\
-	partition-dangle.c\
-	random-sample.cc\
-	shapereader.cc
-
-gtfold_LDFLAGS = 
-gtfold_LDADD = -lm
-CLEANFILES = *~ *.o
-=======
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h
 CLEANFILES = *~
->>>>>>> gtfold/master
 all: all-am
 
 .SUFFIXES:
@@ -252,98 +190,6 @@ $(top_srcdir)/configure:  $(am__configure_deps)
 $(ACLOCAL_M4):  $(am__aclocal_m4_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
 $(am__aclocal_m4_deps):
-<<<<<<< HEAD
-install-binPROGRAMS: $(bin_PROGRAMS)
-	@$(NORMAL_INSTALL)
-	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
-	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-	for p in $$list; do echo "$$p $$p"; done | \
-	sed 's/$(EXEEXT)$$//' | \
-	while read p p1; do if test -f $$p; \
-	  then echo "$$p"; echo "$$p"; else :; fi; \
-	done | \
-	sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
-	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
-	sed 'N;N;N;s,\n, ,g' | \
-	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
-	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
-	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
-	    else { print "f", $$3 "/" $$4, $$1; } } \
-	  END { for (d in files) print "f", d, files[d] }' | \
-	while read type dir files; do \
-	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
-	    test -z "$$files" || { \
-	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
-	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
-	    } \
-	; done
-
-uninstall-binPROGRAMS:
-	@$(NORMAL_UNINSTALL)
-	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-	files=`for p in $$list; do echo "$$p"; done | \
-	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
-	      -e 's/$$/$(EXEEXT)/' `; \
-	test -n "$$list" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(bindir)" && rm -f $$files
-
-clean-binPROGRAMS:
-	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
-gtfold$(EXEEXT): $(gtfold_OBJECTS) $(gtfold_DEPENDENCIES) 
-	@rm -f gtfold$(EXEEXT)
-	$(gtfold_LINK) $(gtfold_OBJECTS) $(gtfold_LDADD) $(LIBS)
-
-mostlyclean-compile:
-	-rm -f *.$(OBJEXT)
-
-distclean-compile:
-	-rm -f *.tab.c
-
-include ./$(DEPDIR)/algorithms-partition.Po
-include ./$(DEPDIR)/algorithms.Po
-include ./$(DEPDIR)/constraints.Po
-include ./$(DEPDIR)/energy.Po
-include ./$(DEPDIR)/global.Po
-include ./$(DEPDIR)/loader.Po
-include ./$(DEPDIR)/main.Po
-include ./$(DEPDIR)/options.Po
-include ./$(DEPDIR)/partition-dangle.Po
-include ./$(DEPDIR)/random-sample.Po
-include ./$(DEPDIR)/shapereader.Po
-include ./$(DEPDIR)/subopt_traceback.Po
-include ./$(DEPDIR)/traceback.Po
-include ./$(DEPDIR)/utils.Po
-
-.c.o:
-	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-#	source='$<' object='$@' libtool=no \
-#	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
-#	$(COMPILE) -c $<
-
-.c.obj:
-	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-#	source='$<' object='$@' libtool=no \
-#	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
-#	$(COMPILE) -c `$(CYGPATH_W) '$<'`
-
-.cc.o:
-	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-#	source='$<' object='$@' libtool=no \
-#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
-#	$(CXXCOMPILE) -c -o $@ $<
-
-.cc.obj:
-	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-#	source='$<' object='$@' libtool=no \
-#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
-#	$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
-=======
->>>>>>> gtfold/master
 
 ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
 	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
diff --git a/gtfold-mfe/include/algorithms-partition.h b/gtfold-mfe/include/algorithms-partition.h
index 77c2377..ef55266 100644
--- a/gtfold-mfe/include/algorithms-partition.h
+++ b/gtfold-mfe/include/algorithms-partition.h
@@ -14,7 +14,7 @@ typedef struct _pFuncData {
 } p_func_data;
 */
 void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM);
-void fillBasePairProbabilities(int length, int *structure, double **Q, double **QB, double **QM, double**P);
+void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, double**P);
 void printBasePairProbabilities(int n, int *structure, double **P);
 
 double probabilityUnpaired(int length, int i, double **P);
diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h
index 026a26a..f742042 100644
--- a/gtfold-mfe/include/energy.h
+++ b/gtfold-mfe/include/energy.h
@@ -19,7 +19,7 @@ extern int **PP;
 #define WMU(i,j) WM[i][j]
 #define WML(i,j) WM[j][i]
 #define VBI(i,j) VBI[indx[j]+i]
-#define RT ((0.00198721 * 310.15)/100.00)
+#define RT ((0.00198721 * 310.15) * 100.00)
 
 #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0)
 
diff --git a/gtfold-mfe/src/.deps/loader.Po b/gtfold-mfe/src/.deps/loader.Po
index 80d3963..926b316 100644
--- a/gtfold-mfe/src/.deps/loader.Po
+++ b/gtfold-mfe/src/.deps/loader.Po
@@ -71,10 +71,10 @@ loader.o: loader.cc /usr/include/c++/4.5/iostream \
  /usr/include/libio.h /usr/include/_G_config.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \
- /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \
- /usr/include/c++/4.4/bits/fstream.tcc /usr/include/c++/4.4/sstream \
- /usr/include/c++/4.4/bits/sstream.tcc /usr/include/math.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \
+ /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \
+ /usr/include/c++/4.5/bits/fstream.tcc /usr/include/c++/4.5/sstream \
+ /usr/include/c++/4.5/bits/sstream.tcc /usr/include/math.h \
  /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
  /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
@@ -307,9 +307,9 @@ loader.o: loader.cc /usr/include/c++/4.5/iostream \
 
 /usr/include/c++/4.5/bits/fstream.tcc:
 
-/usr/include/c++/4.4/sstream:
+/usr/include/c++/4.5/sstream:
 
-/usr/include/c++/4.4/bits/sstream.tcc:
+/usr/include/c++/4.5/bits/sstream.tcc:
 
 /usr/include/math.h:
 
diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c
index 83d1a4d..1492a8e 100644
--- a/gtfold-mfe/src/algorithms-partition.c
+++ b/gtfold-mfe/src/algorithms-partition.c
@@ -15,7 +15,7 @@
 #endif
 
 
-#define DANGLE_DEBUG
+#define MAX_LOOP 30
 
 // double[][] QB;
 // double[][] Q;
@@ -66,36 +66,44 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) {
     // fill in values in the array
     for(l=1; l<=len; ++l) {
 		//Parrallelize
-		#ifndef DANGLE_DEBUG
-		#ifdef _OPENMP
-		#pragma omp parallel for private (i,j) schedule(guided)
-		#endif
-		#endif
-        for(i=1; i<= len-l+1; ++i) {
+		//#ifdef _OPENMP
+		//#pragma omp parallel for private (i,j) schedule(guided)
+		//#endif
+        for(i=1; i<= len - l + 1; i++) {
 
-            int j = i+l-1;
+            int j = i + l - 1;
 
             // QB recursion
             // Only calculate if i and j actually pair
-            if(checkPair(i,j)) {
+            if(canPair(RNA[i],RNA[j])) {
 
                 // NOTE: eH returns an integer encoded as fixed point.  So a
                 // return value of 115 represents raw value 115/100 = 1.15
                 QB[i][j] = exp(-eH(i,j)/RT);
-
+				
                 for(d=i+1; d<=j-4; ++d) {
+					//if(d - i - 1 > MAX_LOOP)
+					//	break;
                     for(e=d+4; e<=j-1; ++e) {
-                        
-						if(d == i + 1 && e == j -1){
-							QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e];
-						}
-						else{
-							printf("i: %d j: %d d: %d e: %d\n", i,j,d,e);
-							QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e];
-						}
 
-						QB[i][j] += QM[i+1][d-1]*QB[d][e] *
-									exp(-(a + b + c*(j-e-1))/RT);
+                      // if(d - i - 1 + j - e - 1 > MAX_LOOP)
+						//	break;
+
+						if(QB[d][e] != 0){ 
+							//more general than chkpair 
+							//if we cant pair, move on
+
+							if(d == i + 1 && e == j -1){
+								QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e];
+							}
+							else{
+								//printf("i: %d j: %d d: %d e: %d\n", i,j,d,e);
+								QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e];
+							}
+
+							QB[i][j] += QM[i+1][d-1]*QB[d][e] *
+										exp(-(a + b + c*(j-e-1))/RT);
+						}
                     }
                 }
             }
@@ -111,6 +119,7 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) {
             }
         }
     }
+	printf("Total partition number: %f", Q[1][len]);
 }
 
 /**
@@ -120,7 +129,7 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) {
  *                  index j. structure[i] = 0 means the nucleotide is
  *                  unpaired.
  */
-void fillBasePairProbabilities(int length, int *structure, double **Q, double **QB, double **QM, double**P) {
+void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, double**P) {
 
 	int d, l, h, i, j;
 	double tempBuffer;
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index ddcd987..a4cfe32 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -266,8 +266,6 @@ int main(int argc, char** argv) {
 			fprintf(stderr, "Constraint file: %s\n", constraintsFile.c_str());
 		}
 	}
-	// release the malloc'd arrays
-	free_fold(seq.length());
 
 	if(BPP_ENABLED){
 		printf("Calculating partition function\n");
@@ -277,8 +275,9 @@ int main(int argc, char** argv) {
 		QB = mallocTwoD(seq.length() + 1, seq.length() + 1);
 		P = mallocTwoD(seq.length() + 1, seq.length() + 1);
 
+	
 		fill_partition_fn_arrays(seq.length(), Q, QB, QM);
-		fillBasePairProbabilities(seq.length(), structure, Q, QB, QM, P);
+		fillBasePairProbabilities(seq.length(), Q, QB, QM, P);
 		printBasePairProbabilities(seq.length(), structure, P);
 
 		freeTwoD(Q, seq.length() + 1, seq.length() + 1);
@@ -286,6 +285,9 @@ int main(int argc, char** argv) {
 		freeTwoD(QB, seq.length() + 1, seq.length() + 1);
 		freeTwoD(P, seq.length() + 1, seq.length() + 1);
 	}
+
+	// release the malloc'd arrays
+	free_fold(seq.length());
 /*
 	dangle_struct partition;
 	partition = malloc_partition_arrays_d(seq.length());

From 7d7dadb6c06bfca7cee48b61aa4bd877b588497e Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Mon, 20 Jun 2011 11:11:50 -0400
Subject: [PATCH 157/282] subopt related changes

---
 gtfold-mfe/src/main.cc             | 37 +++++++++++++++++++------
 gtfold-mfe/src/subopt_traceback.cc | 44 +++++++++++++++---------------
 2 files changed, 50 insertions(+), 31 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 18489d1..7f2ceba 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -163,19 +163,27 @@ void print_header() {
 	printf("Georgia Institute of Technology\n\n");
 }
 
+void save_subopt_file(string outputFile, ss_map_t& ss_data)
+{
+	ofstream outfile;
+	outfile.open(outputFile.c_str());
+	
+	for (ss_map_t::iterator it = ss_data.begin();
+						it != ss_data.end(); ++it) {
+		outfile << it->first << '\t' << it->second/100.0 << std::endl;
+	}
+
+	outfile.close();
+}
+
 /**
  * Save the output to a ct file
  *
  * @param outputFile The file to save to
  * @param energy The MFE energy (multiplied by 100)
  */
-void save_ct_file(string outputFile, string seq, int energy, string seqfile) {
-	if(seqfile.find("/") != string::npos) {
-		size_t pos = seqfile.find_last_of("/");
-		seqfile.erase(0,pos+1);
-	}
-	if(seqfile.find(".") != string::npos)
-		seqfile.erase(seqfile.rfind("."));
+void save_ct_file(string outputFile, string seq, int energy) {
+
 	ofstream outfile;
 	outfile.open(outputFile.c_str());
 
@@ -225,10 +233,21 @@ int main(int argc, char** argv) {
 	
 	if (SUBOPT_ENABLED) {	
 		t1 = get_seconds();
-		subopt_traceback(seq.length(), suboptDelta);
+		ss_map_t subopt_data = subopt_traceback(seq.length(), suboptDelta);
 		t1 = get_seconds() - t1;
 		printf("Subopt traceback running time: %9.6f seconds\n\n", t1);
+		
+		string suboptfile;
+		suboptfile	+= seqfile;
+		if(suboptfile.find("/") != string::npos) {
+			size_t pos = suboptfile.find_last_of("/");
+			suboptfile.erase(0,pos+1);
+		}
+		if(suboptfile.find(".") != string::npos)
+			suboptfile.erase(suboptfile.rfind("."));
+		suboptfile += ".ss";	
 
+		save_subopt_file(suboptfile, subopt_data);	
 		free_fold(seq.length());
 		exit(0);
 	}
@@ -248,7 +267,7 @@ int main(int argc, char** argv) {
 		print_shapeArray(seq.length());
 	
 
-	save_ct_file(outputFile, seq, energy,seqfile);
+	save_ct_file(outputFile, seq, energy);
 	printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str());
 
 
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index 45c72d9..6375f2e 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -84,7 +84,7 @@ void process(ss_map_t& subopt_data, int energy, int len)
 				(*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack, energy);
 			}
 
-			if (gstack.size() == s1 && ps.total() <= energy)
+			if (gstack.size() == s1 && ps.total() == energy)
 			{
 				ps_t ps1(ps);
 				gstack.push(ps1);
@@ -115,7 +115,7 @@ ss_map_t subopt_traceback(int len, int delta)
 void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 {
 	// Hairpin Loop
-	if (eH(i,j) + ps.total()  <= energy )
+	if (eH(i,j) + ps.total()  == energy )
 	{
 		//	std::cout << "Hairpin " << i  << ' ' << j << std::endl;
 		ps_t ps1(ps); 
@@ -125,7 +125,7 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 	}
 
 	// Stack
-	if (eS(i, j) + V(i+1, j-1) + ps.total() <= energy)
+	if (eS(i, j) + V(i+1, j-1) + ps.total() == energy)
 	{
 		//	std::cout << "Stack " << i  << ' ' << j << std::endl;
 		ps_t ps1(ps);
@@ -136,7 +136,7 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 	}
 
 	// Internal Loop
-	if (VBI(i,j) + ps.total() <= energy )
+	if (VBI(i,j) + ps.total() == energy )
 	{
 		//std::cout << "Internal " << i  << ' ' << j << std::endl;
 		ps_t ps1(ps);
@@ -146,7 +146,7 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 	}
 
 	// Multiloop
-	if ( VM(i,j) + ps.total() <= energy )
+	if ( VM(i,j) + ps.total() == energy )
 	{
 		//	std::cout << "Multi " << i  << ' ' << j << std::endl;
 		ps_t ps1(ps);
@@ -167,7 +167,7 @@ void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 
 		for (q = minq; q < j; q++) 
 		{
-			if (V(p, q) + eL(i, j, p, q) + ps.total() <= energy )
+			if (V(p, q) + eL(i, j, p, q) + ps.total() == energy )
 			{
 				ps_t ps1(ps);
 				ps1.push(segment(p, q, lV, V(p, q)));
@@ -187,7 +187,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		int wim1 =  MIN(0, W[i-1]);
 
 		int wij = V(i,j) + auPenalty(i, j) + wim1;
-		if (wij + ps.total() <= energy )
+		if (wij + ps.total() == energy )
 		{
 			ps_t ps1(ps);
 			ps1.push(segment(i, j, lV, V(i,j)));
@@ -197,7 +197,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}		
 
 		int wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
-		if (wijd + ps.total() <= energy )
+		if (wijd + ps.total() == energy )
 		{
 			ps_t ps3(ps);
 			ps3.push(segment(i, j-1, lV, V(i, j-1)));
@@ -207,7 +207,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}	
 
 		int widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
-		if (widj + ps.total() <= energy )
+		if (widj + ps.total() == energy )
 		{
 			ps_t ps4(ps);
 			ps4.push(segment(i+1, j, lV, V(i+1,j)));
@@ -217,7 +217,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}
 
 		int widjd = V(i+1, j-1) + auPenalty(i+1,j-1) + Ed3(j-1, i+1, i) + Ed5(j-1, i+1, j) + wim1;
-		if (widjd + ps.total() <= energy )
+		if (widjd + ps.total() == energy )
 		{
 			ps_t ps2(ps);
 			ps2.push(segment(i+1, j-1, lV, V(i+1,j-1)));
@@ -227,7 +227,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}
 	}
 
-	if (W[j-1] + ps.total() <= energy )
+	if (W[j-1] + ps.total() == energy )
 	{
 		ps_t ps1(ps);
 		ps1.push(segment(1, j-1, lW, W[j-1]));
@@ -276,7 +276,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 		int h = i1; int k = j1;
 
 		int wmij = V(h,k) + auPenalty(h,k) + Eb;
-		if (pss.total() + wmij <= energy )
+		if (pss.total() + wmij == energy )
 		{
 			ps_t ps1(pss);
 			ps1.push_v(segment(h,k,lV, V(h,k)));
@@ -285,7 +285,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 		}
 
 		int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+ Ec ;
-		if (pss.total() + wmijd <= energy )
+		if (pss.total() + wmijd == energy )
 		{
 			ps_t ps1(pss);
 			ps1.push_v(segment(h,k-1,lV, V(h,k-1)));
@@ -294,7 +294,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 		}
 
 		int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + Eb+Ec ;
-		if (pss.total() + wmidj <= energy )
+		if (pss.total() + wmidj == energy )
 		{
 			ps_t ps1(pss);
 			ps1.push_v(segment(h+1, k, lV, V(h+1,k)));
@@ -303,7 +303,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 		}
 
 		int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) +  auPenalty(h+1,k-1) +Eb+ 2*Ec ;
-		if (pss.total() + wmidjd <= energy )
+		if (pss.total() + wmidjd == energy )
 		{
 			ps_t ps1(pss);
 			ps1.push_v(segment(h+1, k-1, lV, V(h+1,k-1)));
@@ -312,7 +312,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 		}
 
 
-		if (pss.total() + WM(i1,j1-1)  + Ec  <= energy )
+		if (pss.total() + WM(i1,j1-1)  + Ec  == energy )
 		{
 			ps_t ps1(pss);
 			ps1.push(segment(i1,j1-1, lWM, WM(i1,j1-1)));		
@@ -320,7 +320,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 			wm_stack.push(ps1);
 		}
 
-		if (pss.total() + WM[i1+1][j1] + Ec <= energy )
+		if (pss.total() + WM[i1+1][j1] + Ec == energy )
 		{
 			ps_t ps1(pss);
 			ps1.push(segment(i1+1,j1, lWM, WM(i1+1,j1)));		
@@ -330,7 +330,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 
 		for (int h = i1+1; h <= j1-1; ++h)
 		{	
-			if (WM(i1,h) + WM(h+1,j1) + pss.total() <= energy )
+			if (WM(i1,h) + WM(h+1,j1) + pss.total() == energy )
 			{
 				ps_t ps1(pss);
 				ps1.push(segment(i1, h, lWM, WM(i1,h)));
@@ -354,7 +354,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		int common = auPenalty(i,j) + Ea + Eb;
 
 		dG = common + WM[i+1][h-1] + WM[h][j-1];
-		if (dG + ps.total()  <= energy )
+		if (dG + ps.total()  == energy )
 		{
 			ps_t ps1(ps);
 			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));
@@ -364,7 +364,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}
 
 		dG =  common + WM[i+2][h-1] + WM[h][j-1] + d5 + Ec;
-		if (dG + ps.total()  <= energy )
+		if (dG + ps.total()  == energy )
 		{
 			ps_t ps1(ps);
 			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
@@ -374,7 +374,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}
 
 		dG = common + WM[i+1][h-1] + WM[h][j-2] + d3 + Ec;
-		if (dG + ps.total()  <= energy )
+		if (dG + ps.total()  == energy )
 		{
 			ps_t ps1(ps);	
 			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));	
@@ -384,7 +384,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}
 
 		dG = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*Ec;
-		if (dG + ps.total()  <= energy )
+		if (dG + ps.total()  == energy )
 		{ 	
 			ps_t ps1(ps);	
 			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	

From 0c9f170140be04511ff9e63b7672b470da2f9df3 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Mon, 20 Jun 2011 11:17:13 -0400
Subject: [PATCH 158/282] added print message

---
 gtfold-mfe/src/main.cc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 7f2ceba..a5c5083 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -246,7 +246,8 @@ int main(int argc, char** argv) {
 		if(suboptfile.find(".") != string::npos)
 			suboptfile.erase(suboptfile.rfind("."));
 		suboptfile += ".ss";	
-
+		
+		printf("Suboptimal structures saved in %s\n", suboptfile.c_str());
 		save_subopt_file(suboptfile, subopt_data);	
 		free_fold(seq.length());
 		exit(0);

From f33cfc986cdcad53b2630e937e5dd0c8efa4e3e7 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Mon, 20 Jun 2011 11:19:50 -0400
Subject: [PATCH 159/282] added .dat files to base_data dir

---
 .../data/Turner99/base_data/asint1x2.dat      | 353 +++++++
 .../data/Turner99/base_data/coaxial.dat       |  63 ++
 .../data/Turner99/base_data/coaxstack.dat     |  63 ++
 gtfold-mfe/data/Turner99/base_data/dangle.dat |  72 ++
 gtfold-mfe/data/Turner99/base_data/int11.dat  | 101 ++
 gtfold-mfe/data/Turner99/base_data/int21.dat  | 353 +++++++
 gtfold-mfe/data/Turner99/base_data/int22.dat  | 928 ++++++++++++++++++
 gtfold-mfe/data/Turner99/base_data/loop.dat   |  34 +
 .../data/Turner99/base_data/miscloop.dat      |  42 +
 gtfold-mfe/data/Turner99/base_data/sint2.dat  | 101 ++
 gtfold-mfe/data/Turner99/base_data/sint4.dat  | 928 ++++++++++++++++++
 gtfold-mfe/data/Turner99/base_data/stack.dat  |  63 ++
 gtfold-mfe/data/Turner99/base_data/tloop.dat  |  32 +
 .../data/Turner99/base_data/triloop.dat       |   2 +
 gtfold-mfe/data/Turner99/base_data/tstack.dat |  63 ++
 .../data/Turner99/base_data/tstackcoax.dat    |  63 ++
 .../data/Turner99/base_data/tstackh.dat       |  63 ++
 .../data/Turner99/base_data/tstacki.dat       |  63 ++
 .../data/Turner99/base_data/tstackm.dat       |  63 ++
 19 files changed, 3450 insertions(+)
 create mode 100644 gtfold-mfe/data/Turner99/base_data/asint1x2.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/coaxial.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/coaxstack.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/dangle.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/int11.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/int21.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/int22.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/loop.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/miscloop.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/sint2.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/sint4.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/stack.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/tloop.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/triloop.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/tstack.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/tstackcoax.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/tstackh.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/tstacki.dat
 create mode 100644 gtfold-mfe/data/Turner99/base_data/tstackm.dat

diff --git a/gtfold-mfe/data/Turner99/base_data/asint1x2.dat b/gtfold-mfe/data/Turner99/base_data/asint1x2.dat
new file mode 100644
index 0000000..d17afd2
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/asint1x2.dat
@@ -0,0 +1,353 @@
+Data tables for asymmetric interior loops of size 3 
+Free energies at 37 degrees for RNA 
+Data arrangement: 
+            Y 
+    ------------------ 
+(X)  A    C    G    U   
+    ------------------ 
+        5' --> 3' 
+            X 
+           A  A 
+           U  U 
+            YA 
+        3' <-- 5' 
+(A)  .    .    .    .    
+(C)  .    .    .    .    
+(G)  .    .    .    .    
+(U)  .    .    .    .    
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
+  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
+  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
+  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.20  3.00  2.40  4.80  2.30  2.20  1.10  4.00  2.40  2.20  1.60  4.00  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80 
+  3.10  3.00  4.80  3.00  2.30  2.20  4.00  2.20  2.30  2.20  4.00  2.20  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00 
+  2.50  4.80  1.60  4.80  1.70  4.00  0.80  4.00  1.70  4.00  0.80  4.00  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.90  2.50  2.40  4.80  2.10  1.70  1.60  4.00  2.10  1.70  1.60  4.00  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80 
+  3.00  3.30  4.80  3.00  2.20  2.50  4.00  2.20  2.20  2.50  4.00  2.20  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  4.80  3.00  4.80  2.10  4.00  2.20  4.00  1.50  4.00  2.20  4.00  1.30  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.80  1.40  1.20  4.80  0.80  0.60  0.40  4.00  1.00  0.60  0.40  4.00  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  1.60  4.80  3.00  4.80  0.80  4.00  2.20  4.00  0.80  4.00  2.20  4.00  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  3.30  2.70  4.80  3.00  2.50  1.90  4.00  2.20  2.50  1.90  4.00  2.20  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  4.80  2.50  4.80  2.00  4.00  1.70  4.00  1.20  4.00  1.70  4.00  1.20  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.20  3.00  2.40  4.80  2.40  2.20  1.60  4.00  2.50  2.20  2.10  4.00  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80 
+  3.10  3.00  4.80  3.00  2.30  2.20  4.00  2.20  2.30  2.20  4.00  2.20  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00 
+  2.50  4.80  1.60  4.80  1.70  4.00  0.80  4.00  1.70  4.00  0.80  4.00  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.90  2.50  2.40  4.80  2.10  1.70  1.60  4.00  2.10  1.70  1.60  4.00  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80 
+  3.00  3.30  4.80  3.00  2.20  2.50  4.00  2.20  2.20  2.50  4.00  2.20  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  4.80  3.00  4.80  2.10  4.00  2.20  4.00  1.30  4.00  2.20  4.00  1.20  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.80  1.40  1.20  4.80  1.00  0.60  0.40  4.00  1.20  0.60  0.40  4.00  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  1.60  4.80  3.00  4.80  0.80  4.00  2.20  4.00  0.80  4.00  2.20  4.00  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  3.30  2.70  4.80  3.00  2.50  1.90  4.00  2.20  2.50  1.90  4.00  2.20  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  4.80  2.50  4.80  2.00  4.00  1.70  4.00  1.20  4.00  1.70  4.00  1.20  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
+  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
+  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
+  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
+  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
+  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
+  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
+  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
+  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
+  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
diff --git a/gtfold-mfe/data/Turner99/base_data/coaxial.dat b/gtfold-mfe/data/Turner99/base_data/coaxial.dat
new file mode 100644
index 0000000..9987fef
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/coaxial.dat
@@ -0,0 +1,63 @@
+Data Arangement: 
+                 Y           
+         ------------------  
+     (X)  A    C    G    U   
+         ------------------  
+             5' ==> 3'       
+                AX           
+                AY 
+             3' <== 5'       
+     (A)   .     .     .     .   
+     (C)   .     .     .     .   
+     (G)   .     .     .     .   
+     (U) -0.70 -0.10 -0.70 -0.10 
+-------------------------------- 
+STACKING ENERGIES : 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         AX                      AX                      AX                      AX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .     .     .     .     .     .     .     .     .   -0.90
+   .     .     .     .     .     .     .     .     .     .     .     .     .     .   -2.20   .   
+   .     .     .     .     .     .     .     .     .     .     .     .     .   -2.10   .   -0.60 
+   .     .     .     .     .     .     .     .     .     .     .     .   -1.10   .   -1.40   .    
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         CX                      CX                      CX                      CX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .     .     .     .     .   -2.10   .     .     .     .   
+   .     .     .     .     .     .     .     .     .     .   -3.30   .     .     .     .     .    
+   .     .     .     .     .     .     .     .     .   -2.40   .   -1.40   .     .     .     .   
+   .     .     .     .     .     .     .     .   -2.10   .   -2.10   .     .     .     .     .    
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         GX                      GX                      GX                      GX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .   -2.40   .     .     .     .     .     .     .   -1.30 
+   .     .     .     .     .     .   -3.40   .     .     .     .     .     .     .   -2.50   .   
+   .     .     .     .     .   -3.30   .   -1.50   .     .     .     .     .   -2.10   .   -0.50  
+   .     .     .     .   -2.20   .   -2.50   .     .     .     .     .   -1.40   .    1.30   .     
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         UX                      UX                      UX                      UX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -1.30   .     .     .     .     .     .     .   -1.00   .     .     .     .   
+   .     .   -2.40   .     .     .     .     .     .     .   -1.50   .     .     .     .     .    
+   .   -2.10   .   -1.00   .     .     .     .     .   -1.40   .    0.30   .     .     .     .   
+ -0.90   .   -1.30   .     .     .     .     .   -0.60   .   -0.50   .     .     .     .     .    
diff --git a/gtfold-mfe/data/Turner99/base_data/coaxstack.dat b/gtfold-mfe/data/Turner99/base_data/coaxstack.dat
new file mode 100644
index 0000000..7125756
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/coaxstack.dat
@@ -0,0 +1,63 @@
+Data Arangement: 
+                 Y           
+         ------------------  
+     (X)  A    C    G    U   
+         ------------------  
+             5' ==> 3'       
+                AX           
+                AY 
+             3' <== 5'       
+     (A)   .     .     .     .   
+     (C)   .     .     .     .   
+     (G)   .     .     .     .   
+     (U) -0.70 -0.10 -0.70 -0.10 
+-------------------------------- 
+STACKING ENERGIES : COAXIAL STACKING ENERGIES
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         AX                      AX                      AX                      AX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .     .     .     .     .     .   -2.10 -2.10 -2.10 -2.50 
+   .     .     .     .     .     .     .     .     .     .     .     .   -2.10 -2.10 -2.50 -2.10 
+   .     .     .     .     .     .     .     .     .     .     .     .   -2.10 -2.50 -2.10 -2.30 
+   .     .     .     .     .     .     .     .     .     .     .     .   -2.50 -2.10 -2.30 -2.10 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         CX                      CX                      CX                      CX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .     .   -2.10 -2.10 -2.10 -2.50   .     .     .     .  
+   .     .     .     .     .     .     .     .   -2.10 -2.10 -2.50 -2.10   .     .     .     . 
+   .     .     .     .     .     .     .     .   -2.10 -2.50 -2.10 -2.30   .     .     .     .  
+   .     .     .     .     .     .     .     .   -2.50 -2.10 -2.30 -2.10   .     .     .     . 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         GX                      GX                      GX                      GX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .   -2.10 -2.10 -2.10 -2.50   .     .     .     .   -2.10 -2.10 -2.10 -2.50 
+   .     .     .     .   -2.10 -2.10 -2.50 -2.10   .     .     .     .   -2.10 -2.10 -2.50 -2.10 
+   .     .     .     .   -2.10 -2.50 -2.10 -2.30   .     .     .     .   -2.10 -2.50 -2.10 -2.30 
+   .     .     .     .   -2.50 -2.10 -2.30 -2.10   .     .     .     .   -2.50 -2.10 -2.30 -2.10 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         UX                      UX                      UX                      UX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+ -2.10 -2.10 -2.10 -2.50   .     .     .     .   -2.10 -2.10 -2.10 -2.50   .     .     .     .  
+ -2.10 -2.10 -2.50 -2.10   .     .     .     .   -2.10 -2.10 -2.50 -2.10   .     .     .     . 
+ -2.10 -2.50 -2.10 -2.30   .     .     .     .   -2.10 -2.50 -2.10 -2.30   .     .     .     .  
+ -2.50 -2.10 -2.30 -2.10   .     .     .     .   -2.50 -2.10 -2.30 -2.10   .     .     .     . 
diff --git a/gtfold-mfe/data/Turner99/base_data/dangle.dat b/gtfold-mfe/data/Turner99/base_data/dangle.dat
new file mode 100644
index 0000000..2f2d2da
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/dangle.dat
@@ -0,0 +1,72 @@
+          X                       X                       X                       X 
+  ------------------      ------------------      ------------------      ------------------ 
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
+  ------------------      ------------------      ------------------      ------------------ 
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+         AX                      AX                      AX                      AX 
+         A                       C                       G                       U 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  .     .     .     .     .     .     .     .     .     .     .     .   -0.80 -0.50 -0.80 -0.60 
+          X                       X                       X                       X 
+  ------------------      ------------------      ------------------      ------------------ 
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
+  ------------------      ------------------      ------------------      ------------------ 
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+         CX                      CX                      CX                      CX 
+         A                       C                       G                       U 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  .     .     .     .     .     .     .     .   -1.70 -0.80 -1.70 -1.20   .     .     .     . 
+          X                       X                       X                       X 
+  ------------------      ------------------      ------------------      ------------------ 
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
+  ------------------      ------------------      ------------------      ------------------ 
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+         GX                      GX                      GX                      GX 
+         A                       C                       G                       U 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  .     .     .     .   -1.10 -0.40 -1.30 -0.60   .     .     .     .   -0.80 -0.50 -0.80 -0.60 
+          X                       X                       X                       X 
+  ------------------      ------------------      ------------------      ------------------ 
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
+  ------------------      ------------------      ------------------      ------------------ 
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+         UX                      UX                      UX                      UX 
+         A                       C                       G                       U 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+-0.70 -0.10 -0.70 -0.10   .     .     .     .   -0.70 -0.10 -0.70 -0.10   .     .     .     . 
+          X                       X                       X                       X 
+  ------------------      ------------------      ------------------      ------------------ 
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
+  ------------------      ------------------      ------------------      ------------------ 
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+         A                       A                       A                       A 
+         AX                      CX                      GX                      UX 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  .     .     .     .     .     .     .     .     .     .     .     .   -0.30 -0.10 -0.20 -0.20 
+          X                       X                       X                       X 
+  ------------------      ------------------      ------------------      ------------------ 
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
+  ------------------      ------------------      ------------------      ------------------ 
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+         C                       C                       C                       C 
+         AX                      CX                      GX                      UX 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  .     .     .     .     .     .     .     .   -0.20 -0.30 -0.0 -0.0   .     .     .     . 
+          X                       X                       X                       X 
+  ------------------      ------------------      ------------------      ------------------ 
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
+  ------------------      ------------------      ------------------      ------------------ 
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+         G                       G                       G                       G 
+         AX                      CX                      GX                      UX 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  .     .     .     .   -0.50 -0.30 -0.20 -0.10   .     .     .     .   -0.30 -0.10 -0.20 -0.20 
+          X                       X                       X                       X 
+  ------------------      ------------------      ------------------      ------------------ 
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
+  ------------------      ------------------      ------------------      ------------------ 
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+         U                       U                       U                       U 
+         AX                      CX                      GX                      UX 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+-0.30 -0.30 -0.40 -0.20   .     .     .     .   -0.30 -0.30 -0.40 -0.20   .     .     .     . 
diff --git a/gtfold-mfe/data/Turner99/base_data/int11.dat b/gtfold-mfe/data/Turner99/base_data/int11.dat
new file mode 100644
index 0000000..3e0f630
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/int11.dat
@@ -0,0 +1,101 @@
+Data table for symetric interior loops of size 2 
+Free energies at 37 degrees for RNA 
+Data Arrangement: 
+            Y 
+    ------------------ 
+(X)  A    C    G    U   
+    ------------------ 
+        5' --> 3' 
+            X 
+           A A 
+           U U 
+            Y 
+        3' <-- 5' 
+(A)  .    .    .    .    
+(C)  .    .    .    .    
+(G)  .    .    .    .    
+(U)  .    .    .    .    
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A A                     A C                     A G                     A U                     A G                     A U         
+           U U                     U G                     U C                     U A                     U U                     U G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
+  1.70  1.70  1.70  1.50  1.10  1.10  1.10  1.00  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.20  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C A                     C C                     C G                     C U                     C G                     C U         
+           G U                     G G                     G C                     G A                     G U                     G G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.10  1.10  1.10  1.10  0.40 -0.40  0.40  0.40  1.10  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+  1.10  1.10  1.10  1.10  0.30  0.50  0.40  0.50  0.40  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+  1.10  1.10 -1.00  1.10 -0.10  0.40 -1.70  0.40  0.40  0.40 -1.40  0.40  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10 
+  1.10  1.10  1.10  1.10  0.40  0.00  0.40 -0.30  0.40  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G A                     G C                     G G                     G U                     G G                     G U         
+           C U                     C G                     C C                     C A                     C U                     C G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.10  1.10  1.10  1.10  0.80  0.40  0.40  0.40  0.40  0.30 -0.10  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+  1.10  1.10  1.10  1.10  0.40  0.40  0.40  0.40 -0.40  0.50  0.40  0.00  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+  1.10  1.10 -1.00  1.10  0.40  0.40 -2.10  0.40  0.40  0.40 -1.70  0.40  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10 
+  1.10  1.10  1.10  1.10  0.40  0.40  0.40 -0.70  0.40  0.50  0.40 -0.30  1.10  1.10  1.10  1.00  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U A                     U C                     U G                     U U                     U G                     U U         
+           A U                     A G                     A C                     A A                     A U                     A G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
+  1.70  1.70  1.70  1.80  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.50  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G A                     G C                     G G                     G U                     G G                     G U         
+           U U                     U G                     U C                     U A                     U U                     U G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U A                     U C                     U G                     U U                     U G                     U U         
+           G U                     G G                     G C                     G A                     G U                     G G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
diff --git a/gtfold-mfe/data/Turner99/base_data/int21.dat b/gtfold-mfe/data/Turner99/base_data/int21.dat
new file mode 100644
index 0000000..d17afd2
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/int21.dat
@@ -0,0 +1,353 @@
+Data tables for asymmetric interior loops of size 3 
+Free energies at 37 degrees for RNA 
+Data arrangement: 
+            Y 
+    ------------------ 
+(X)  A    C    G    U   
+    ------------------ 
+        5' --> 3' 
+            X 
+           A  A 
+           U  U 
+            YA 
+        3' <-- 5' 
+(A)  .    .    .    .    
+(C)  .    .    .    .    
+(G)  .    .    .    .    
+(U)  .    .    .    .    
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
+  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
+  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
+  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.20  3.00  2.40  4.80  2.30  2.20  1.10  4.00  2.40  2.20  1.60  4.00  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80 
+  3.10  3.00  4.80  3.00  2.30  2.20  4.00  2.20  2.30  2.20  4.00  2.20  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00 
+  2.50  4.80  1.60  4.80  1.70  4.00  0.80  4.00  1.70  4.00  0.80  4.00  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.90  2.50  2.40  4.80  2.10  1.70  1.60  4.00  2.10  1.70  1.60  4.00  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80 
+  3.00  3.30  4.80  3.00  2.20  2.50  4.00  2.20  2.20  2.50  4.00  2.20  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  4.80  3.00  4.80  2.10  4.00  2.20  4.00  1.50  4.00  2.20  4.00  1.30  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.80  1.40  1.20  4.80  0.80  0.60  0.40  4.00  1.00  0.60  0.40  4.00  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  1.60  4.80  3.00  4.80  0.80  4.00  2.20  4.00  0.80  4.00  2.20  4.00  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  3.30  2.70  4.80  3.00  2.50  1.90  4.00  2.20  2.50  1.90  4.00  2.20  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  4.80  2.50  4.80  2.00  4.00  1.70  4.00  1.20  4.00  1.70  4.00  1.20  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.20  3.00  2.40  4.80  2.40  2.20  1.60  4.00  2.50  2.20  2.10  4.00  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80 
+  3.10  3.00  4.80  3.00  2.30  2.20  4.00  2.20  2.30  2.20  4.00  2.20  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00 
+  2.50  4.80  1.60  4.80  1.70  4.00  0.80  4.00  1.70  4.00  0.80  4.00  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.90  2.50  2.40  4.80  2.10  1.70  1.60  4.00  2.10  1.70  1.60  4.00  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80 
+  3.00  3.30  4.80  3.00  2.20  2.50  4.00  2.20  2.20  2.50  4.00  2.20  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  4.80  3.00  4.80  2.10  4.00  2.20  4.00  1.30  4.00  2.20  4.00  1.20  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.80  1.40  1.20  4.80  1.00  0.60  0.40  4.00  1.20  0.60  0.40  4.00  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  1.60  4.80  3.00  4.80  0.80  4.00  2.20  4.00  0.80  4.00  2.20  4.00  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  3.30  2.70  4.80  3.00  2.50  1.90  4.00  2.20  2.50  1.90  4.00  2.20  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00 
+  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
+  4.80  2.50  4.80  2.00  4.00  1.70  4.00  1.20  4.00  1.70  4.00  1.20  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
+  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
+  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
+  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
+  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
+  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
+  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
+           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YA                      YA                      YA                      YA                      YA                      YA 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
+  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
+  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YC                      YC                      YC                      YC                      YC                      YC 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
+  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YG                      YG                      YG                      YG                      YG                      YG 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
+           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
+            YU                      YU                      YU                      YU                      YU                      YU 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
+  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
+  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
diff --git a/gtfold-mfe/data/Turner99/base_data/int22.dat b/gtfold-mfe/data/Turner99/base_data/int22.dat
new file mode 100644
index 0000000..2357f6f
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/int22.dat
@@ -0,0 +1,928 @@
+Data tables for symetric interior loops of size 4 
+Free energies at 37 degrees for RNA 
+Data arrangement: 
+                                Y 
+     ---------------------------------------------------------------- 
+(X)   A   A   A   A   C   C   C   C   G   G   G   G   U   U   U   U 
+      A   C   G   U   A   C   G   U   A   C   G   U   A   C   G   U 
+     ---------------------------------------------------------------- 
+                           5' ------> 3' 
+                            A \/ \_/ A 
+                            U /\  |  U 
+                           3' <------ 5' 
+(AA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(AC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(AG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(AU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(CA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(CC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(CG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(CU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(GA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(GC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(GG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(GU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(UA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(UC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(UG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(UU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ A 
+                                           U /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ C 
+                                           U /\  |  G 
+                                          3' <------ 5' 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
+  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
+  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ G 
+                                           U /\  |  C 
+                                          3' <------ 5' 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
+  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
+  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ U 
+                                           U /\  |  A 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ G 
+                                           U /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ U 
+                                           U /\  |  G 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ A 
+                                           G /\  |  U 
+                                          3' <------ 5' 
+  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
+  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
+  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
+  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ C 
+                                           G /\  |  G 
+                                          3' <------ 5' 
+  0.50  1.10 -0.30  2.00  1.10  1.70  2.00  0.70  0.40  2.00  1.00  0.10  2.00  1.80 -0.50  1.50 
+  0.60  1.50  0.10  2.00  1.10  1.50  2.00  0.50  0.50  2.00  1.40 -0.70  2.00  1.50 -0.60  0.00 
+  0.00 -0.70 -1.60  2.00 -1.00 -0.60  2.00  0.20 -0.70  2.00  0.00 -0.80  2.00  1.20 -0.60  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.00 -0.70  2.00  1.00  1.00  2.00  0.00  0.70  2.00  0.90 -1.90  2.00  1.10 -1.50 -0.20 
+  2.20  1.30  0.70  2.00  1.90  1.30  2.00  0.30  0.70  2.00  1.80 -0.30  2.00  1.40 -0.20 -0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.00  1.20  0.40  2.00  1.10  1.20  2.00  1.70  1.00  2.00  1.70 -0.70  2.00  1.20 -0.30  0.20 
+ -0.20 -0.40 -1.70  2.00  0.70  1.10  2.00  0.20 -0.50  2.00  0.00 -0.90  2.00  1.20 -1.30  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
+  0.90  0.00  0.30  2.00 -0.10  1.00  2.00  0.00  0.60  2.00  0.90 -3.00  2.00  1.00 -2.40  0.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.00  1.20  0.40  2.00  1.10  1.20  2.00  0.20  0.50  2.00  1.70 -0.70  2.00  1.20 -0.10  0.40 
+ -0.10 -1.60 -1.60  2.00 -1.60 -0.60  2.00 -1.60 -0.60  2.00 -0.70 -4.40  2.00 -0.50 -4.10 -1.00 
+  1.40  0.30  0.50  2.00  0.30  0.30  2.00  0.10  1.40  2.00  1.20 -1.00  2.00  0.30  0.10  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ G 
+                                           G /\  |  C 
+                                          3' <------ 5' 
+  1.30  1.20  0.30  2.00  1.60  2.10  2.00  1.90  0.30  2.00  1.00 -0.40  2.00  1.90  1.10  1.40 
+  1.60  1.50  0.60  2.00  2.00  1.80  2.00  1.70  0.60  2.00  1.40 -1.10  2.00  1.70  0.40  0.80 
+  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.20  1.10  0.20  2.00  1.50  1.40  2.00  1.20  0.20  2.00  0.90 -1.50  2.00  1.20  0.00  0.30 
+  2.10  1.40  1.50  2.00  1.80  1.70  2.00  1.50  1.50  2.00  1.80 -0.20  2.00  1.50  1.30  0.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
+  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
+  1.10  0.00  0.90  2.00  0.40  1.30  2.00  1.10  0.90  2.00  0.90 -2.60  2.00  1.10 -1.10  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
+ -0.40 -1.50 -0.60  2.00 -1.10 -0.20  2.00 -0.40 -0.60  2.00 -0.70 -4.20  2.00 -0.40 -2.60 -0.50 
+  1.40  0.30  1.30  2.00  0.80  0.60  2.00  0.50  1.30  2.00  1.20 -0.50  2.00  0.50  1.10 -0.40 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ U 
+                                           G /\  |  A 
+                                          3' <------ 5' 
+  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
+  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
+  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
+  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ G 
+                                           G /\  |  U 
+                                          3' <------ 5' 
+  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
+  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
+  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
+  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ U 
+                                           G /\  |  G 
+                                          3' <------ 5' 
+  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
+  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
+  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
+  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ A 
+                                           C /\  |  U 
+                                          3' <------ 5' 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
+  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
+  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
+  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
+  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
+  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ C 
+                                           C /\  |  G 
+                                          3' <------ 5' 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.20  0.90 -0.80  2.00  0.90  0.90  2.00  0.00 -0.20  2.00  0.80 -2.00  2.00  1.00 -1.60  0.20 
+  0.10 -0.10 -1.90  2.00 -0.20  0.90  2.00 -0.10 -1.30  2.00 -0.20 -1.30  2.00  0.90 -0.90  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.20  1.00 -0.80  2.00  0.90  1.00  2.00  0.00 -0.10  2.00  0.90 -1.90  2.00  1.00 -1.50  0.20 
+  1.80  1.00  0.20  2.00  0.90  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.00 -0.50  0.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.00  0.30  2.00  1.00  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.10 -0.50  0.30 
+ -0.50 -0.80 -2.60  2.00 -0.80  0.20  2.00 -0.80 -1.90  2.00 -0.90 -1.90  2.00  0.30 -1.50  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
+ -0.30 -1.50 -1.50  2.00 -1.60 -0.50  2.00 -1.50 -0.90  2.00 -0.60 -4.50  2.00 -0.50 -4.10 -0.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  0.80  0.00 -0.80  2.00  0.00  0.00  2.00 -1.00 -0.10  2.00  0.50 -1.90  2.00  0.00 -1.50 -0.70 
+ -0.70 -1.90 -1.90  2.00 -2.00 -0.90  2.00 -1.90 -1.30  2.00 -1.00 -4.90  2.00 -0.90 -4.50 -0.90 
+  1.50  0.20  0.30  2.00  0.20  0.20  2.00 -0.70  0.90  2.00  1.10 -0.90  2.00  0.30 -0.50 -0.50 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ G 
+                                           C /\  |  C 
+                                          3' <------ 5' 
+  0.50  1.30 -0.20  2.00  0.60  2.20  2.00  2.00  0.00  2.00  1.10 -0.10  2.00  2.00  0.90  1.40 
+  1.10  1.00  0.70  2.00  1.10  1.90  2.00  1.10 -1.00  2.00  0.80 -1.60  2.00  1.10 -0.10  0.30 
+  0.40  0.70 -0.50  2.00  0.50  0.70  2.00  0.50 -0.70  2.00 -0.20 -0.60  2.00  1.00  0.60  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  1.00 -0.40  2.00  1.50  1.30  2.00  1.20 -0.70  2.00  0.90 -1.60  2.00  1.20  0.00  0.30 
+  1.70  1.00  1.10  2.00  1.50  1.30  2.00  1.20 -0.60  2.00  1.50 -0.60  2.00  1.20  1.00  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.10  1.20  2.00  1.50  1.40  2.00  1.20  1.20  2.00  1.50 -0.50  2.00  1.20  1.00  0.30 
+ -0.30 -0.70 -1.70  2.00  0.10  0.70  2.00  0.40 -1.60  2.00 -0.90 -1.60  2.00  0.40  0.30  0.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
+ -0.50 -1.50 -1.30  2.00 -0.60 -0.20  2.00 -0.10 -0.60  2.00 -0.60 -4.10  2.00 -0.30 -2.40  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  0.70  0.00  0.20  2.00  0.50  0.30  2.00  0.20  0.20  2.00  0.50 -1.60  2.00  1.70  0.00  0.10 
+  0.10 -1.90 -0.90  2.00 -0.70 -0.30  2.00 -0.70 -0.80  2.00 -1.00 -4.40  2.00 -0.70 -3.00 -1.00 
+  1.50 -0.20  0.90  2.00  0.00 -0.10  2.00  0.40  0.90  2.00  1.10 -1.00  2.00  0.20  0.60  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ U 
+                                           C /\  |  A 
+                                          3' <------ 5' 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
+  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
+  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
+  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
+  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
+  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ G 
+                                           C /\  |  U 
+                                          3' <------ 5' 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
+  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
+  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
+  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
+  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
+  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ U 
+                                           C /\  |  G 
+                                          3' <------ 5' 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
+  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
+  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
+  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
+  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
+  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ A 
+                                           A /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ C 
+                                           A /\  |  G 
+                                          3' <------ 5' 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
+  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ G 
+                                           A /\  |  C 
+                                          3' <------ 5' 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
+  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
+  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ U 
+                                           A /\  |  A 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ G 
+                                           A /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ U 
+                                           A /\  |  G 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ A 
+                                           U /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ C 
+                                           U /\  |  G 
+                                          3' <------ 5' 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
+  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
+  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ G 
+                                           U /\  |  C 
+                                          3' <------ 5' 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
+  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
+  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ U 
+                                           U /\  |  A 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ G 
+                                           U /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ U 
+                                           U /\  |  G 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ A 
+                                           G /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ C 
+                                           G /\  |  G 
+                                          3' <------ 5' 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
+  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ G 
+                                           G /\  |  C 
+                                          3' <------ 5' 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
+  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
+  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ U 
+                                           G /\  |  A 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ G 
+                                           G /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ U 
+                                           G /\  |  G 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80
diff --git a/gtfold-mfe/data/Turner99/base_data/loop.dat b/gtfold-mfe/data/Turner99/base_data/loop.dat
new file mode 100644
index 0000000..927fbbd
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/loop.dat
@@ -0,0 +1,34 @@
+DESTABILIZING ENERGIES BY SIZE OF LOOP (INTERPOLATE WHERE NEEDED) 
+hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges 
+SIZE         INTERNAL            BULGE            HAIRPIN 
+------------------------------------------------------- 
+1                .                3.80                . 
+2                .                2.80                . 
+3                .                3.20              5.70  
+4              1.70               3.60              5.60 
+5              1.80               4.00              5.60 
+6              2.00               4.40              5.40 
+7              2.20               4.60              5.90 
+8              2.30               4.70              5.60 
+9              2.40               4.80              6.40 
+10             2.50               4.90              6.50 
+11             2.60               5.00              6.60 
+12             2.70               5.10              6.70 
+13             2.80               5.20              6.80 
+14             2.90               5.30              6.90 
+15             3.00               5.40              6.90 
+16             3.00               5.40              7.00 
+17             3.10               5.50              7.10 
+18             3.10               5.50              7.10 
+19             3.20               5.60              7.20 
+20             3.30               5.70              7.20 
+21             3.30               5.70              7.30 
+22             3.40               5.80              7.30 
+23             3.40               5.80              7.40 
+24             3.40               5.80              7.40 
+25             3.50               5.90              7.50 
+26             3.50               5.90              7.50 
+27             3.60               6.00              7.50 
+28             3.60               6.00              7.60 
+29             3.60               6.00              7.60 
+30             3.70               6.10              7.70 
diff --git a/gtfold-mfe/data/Turner99/base_data/miscloop.dat b/gtfold-mfe/data/Turner99/base_data/miscloop.dat
new file mode 100644
index 0000000..cd585c1
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/miscloop.dat
@@ -0,0 +1,42 @@
+Miscellaneous free energy rules 
+------------------------------- 
+Extrapolation for large loops based on polymer theory 
+internal, bulge or hairpin loops > 30: dS(T)=dS(30)+param*ln(n/30) 
+-->  
+1.079 
+asymmetric internal loops: the ninio equation 
+the maximum correction 
+-->  
+3.00 
+the f(m) array (see Ninio for details) 
+--> 
+ .50  .50  .50  .50 
+multibranched loops 
+  offset,  free base penalty,  helix penalty 
+-->  
+    3.40          .00                 .40 
+efn2 multibranched loops 
+   offset,  free base penalty,  helix penalty 
+--> 
+     10.10         -0.30              -0.30  
+terminal AU penalty 
+-->  
+ 0.50 
+bonus for GGG hairpin 
+-->  
+-2.20 
+c hairpin slope 
+-->  
+0.30 
+c hairpin intercept 
+-->  
+1.60 
+c hairpin of 3 
+-->  
+1.40 
+Intermolecular initiation free energy 
+-->  
+4.10 
+GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) 
+-->  
+1 
diff --git a/gtfold-mfe/data/Turner99/base_data/sint2.dat b/gtfold-mfe/data/Turner99/base_data/sint2.dat
new file mode 100644
index 0000000..3e0f630
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/sint2.dat
@@ -0,0 +1,101 @@
+Data table for symetric interior loops of size 2 
+Free energies at 37 degrees for RNA 
+Data Arrangement: 
+            Y 
+    ------------------ 
+(X)  A    C    G    U   
+    ------------------ 
+        5' --> 3' 
+            X 
+           A A 
+           U U 
+            Y 
+        3' <-- 5' 
+(A)  .    .    .    .    
+(C)  .    .    .    .    
+(G)  .    .    .    .    
+(U)  .    .    .    .    
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           A A                     A C                     A G                     A U                     A G                     A U         
+           U U                     U G                     U C                     U A                     U U                     U G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
+  1.70  1.70  1.70  1.50  1.10  1.10  1.10  1.00  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.20  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           C A                     C C                     C G                     C U                     C G                     C U         
+           G U                     G G                     G C                     G A                     G U                     G G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.10  1.10  1.10  1.10  0.40 -0.40  0.40  0.40  1.10  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+  1.10  1.10  1.10  1.10  0.30  0.50  0.40  0.50  0.40  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+  1.10  1.10 -1.00  1.10 -0.10  0.40 -1.70  0.40  0.40  0.40 -1.40  0.40  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10 
+  1.10  1.10  1.10  1.10  0.40  0.00  0.40 -0.30  0.40  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G A                     G C                     G G                     G U                     G G                     G U         
+           C U                     C G                     C C                     C A                     C U                     C G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.10  1.10  1.10  1.10  0.80  0.40  0.40  0.40  0.40  0.30 -0.10  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+  1.10  1.10  1.10  1.10  0.40  0.40  0.40  0.40 -0.40  0.50  0.40  0.00  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+  1.10  1.10 -1.00  1.10  0.40  0.40 -2.10  0.40  0.40  0.40 -1.70  0.40  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10 
+  1.10  1.10  1.10  1.10  0.40  0.40  0.40 -0.70  0.40  0.50  0.40 -0.30  1.10  1.10  1.10  1.00  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U A                     U C                     U G                     U U                     U G                     U U         
+           A U                     A G                     A C                     A A                     A U                     A G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
+  1.70  1.70  1.70  1.80  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.50  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           G A                     G C                     G G                     G U                     G G                     G U         
+           U U                     U G                     U C                     U A                     U U                     U G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+            Y                       Y                       Y                       Y                       Y                       Y 
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
+    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
+        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
+            X                       X                       X                       X                       X                       X 
+           U A                     U C                     U G                     U U                     U G                     U U         
+           G U                     G G                     G C                     G A                     G U                     G G         
+            Y                       Y                       Y                       Y                       Y                       Y 
+        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
+  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
+  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
diff --git a/gtfold-mfe/data/Turner99/base_data/sint4.dat b/gtfold-mfe/data/Turner99/base_data/sint4.dat
new file mode 100644
index 0000000..1939411
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/sint4.dat
@@ -0,0 +1,928 @@
+Data tables for symetric interior loops of size 4 
+Free energies at 37 degrees for RNA 
+Data arrangement: 
+                                Y 
+     ---------------------------------------------------------------- 
+(X)   A   A   A   A   C   C   C   C   G   G   G   G   U   U   U   U 
+      A   C   G   U   A   C   G   U   A   C   G   U   A   C   G   U 
+     ---------------------------------------------------------------- 
+                           5' ------> 3' 
+                            A \/ \_/ A 
+                            U /\  |  U 
+                           3' <------ 5' 
+(AA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(AC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(AG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(AU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(CA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(CC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(CG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(CU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(GA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(GC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(GG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(GU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(UA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(UC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(UG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+(UU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ A 
+                                           U /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ C 
+                                           U /\  |  G 
+                                          3' <------ 5' 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
+  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
+  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ G 
+                                           U /\  |  C 
+                                          3' <------ 5' 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
+  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
+  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ U 
+                                           U /\  |  A 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ G 
+                                           U /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           A \/ \_/ U 
+                                           U /\  |  G 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ A 
+                                           G /\  |  U 
+                                          3' <------ 5' 
+  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
+  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
+  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
+  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ C 
+                                           G /\  |  G 
+                                          3' <------ 5' 
+  0.50  1.10 -0.30  2.00  1.10  1.70  2.00  0.70  0.40  2.00  1.00  0.10  2.00  1.80 -0.50  1.50 
+  0.60  1.50  0.10  2.00  1.10  1.50  2.00  0.50  0.50  2.00  1.40 -0.70  2.00  1.50 -0.60  0.00 
+  0.00 -0.70 -1.60  2.00 -1.00 -0.60  2.00  0.20 -0.70  2.00  0.00 -0.80  2.00  1.20 -0.60  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.00 -0.70  2.00  1.00  1.00  2.00  0.00  0.70  2.00  0.90 -1.90  2.00  1.10 -1.50 -0.20 
+  2.20  1.30  0.70  2.00  1.90  1.30  2.00  0.30  0.70  2.00  1.80 -0.30  2.00  1.40 -0.20 -0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.00  1.20  0.40  2.00  1.10  1.20  2.00  1.70  1.00  2.00  1.70 -0.70  2.00  1.20 -0.30  0.20 
+ -0.20 -0.40 -1.70  2.00  0.70  1.10  2.00  0.20 -0.50  2.00  0.00 -0.90  2.00  1.20 -1.30  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
+  0.90  0.00  0.30  2.00 -0.10  1.00  2.00  0.00  0.60  2.00  0.90 -3.00  2.00  1.00 -2.40  0.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.00  1.20  0.40  2.00  1.10  1.20  2.00  0.20  0.50  2.00  1.70 -0.70  2.00  1.20 -0.10  0.40 
+ -0.10 -1.60 -1.60  2.00 -1.60 -0.60  2.00 -1.60 -0.60  2.00 -0.70 -4.40  2.00 -0.50 -4.10 -1.00 
+  1.40  0.30  0.50  2.00  0.30  0.30  2.00  0.10  1.40  2.00  1.20 -1.00  2.00  0.30  0.10  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ G 
+                                           G /\  |  C 
+                                          3' <------ 5' 
+  1.30  1.20  0.30  2.00  1.60  2.10  2.00  1.90  0.30  2.00  1.00 -0.40  2.00  1.90  1.10  1.40 
+  1.60  1.50  0.60  2.00  2.00  1.80  2.00  1.70  0.60  2.00  1.40 -1.10  2.00  1.70  0.40  0.80 
+  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.20  1.10  0.20  2.00  1.50  1.40  2.00  1.20  0.20  2.00  0.90 -1.50  2.00  1.20  0.00  0.30 
+  2.10  1.40  1.50  2.00  1.80  1.70  2.00  1.50  1.50  2.00  1.80 -0.20  2.00  1.50  1.30  0.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
+  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
+  1.10  0.00  0.90  2.00  0.40  1.30  2.00  1.10  0.90  2.00  0.90 -2.60  2.00  1.10 -1.10  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
+ -0.40 -1.50 -0.60  2.00 -1.10 -0.20  2.00 -0.40 -0.60  2.00 -0.70 -4.20  2.00 -0.40 -2.60 -0.50 
+  1.40  0.30  1.30  2.00  0.80  0.60  2.00  0.50  1.30  2.00  1.20 -0.50  2.00  0.50  1.10 -0.40 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ U 
+                                           G /\  |  A 
+                                          3' <------ 5' 
+  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
+  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
+  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
+  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ G 
+                                           G /\  |  U 
+                                          3' <------ 5' 
+  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
+  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
+  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
+  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           C \/ \_/ U 
+                                           G /\  |  G 
+                                          3' <------ 5' 
+  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
+  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
+  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
+  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ A 
+                                           C /\  |  U 
+                                          3' <------ 5' 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
+  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
+  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
+  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
+  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
+  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ C 
+                                           C /\  |  G 
+                                          3' <------ 5' 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.20  0.90 -0.80  2.00  0.90  0.90  2.00  0.00 -0.20  2.00  0.80 -2.00  2.00  1.00 -1.60  0.20 
+  0.10 -0.10 -1.90  2.00 -0.20  0.90  2.00 -0.10 -1.30  2.00 -0.20 -1.30  2.00  0.90 -0.90  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.20  1.00 -0.80  2.00  0.90  1.00  2.00  0.00 -0.10  2.00  0.90 -1.90  2.00  1.00 -1.50  0.20 
+  1.80  1.00  0.20  2.00  0.90  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.00 -0.50  0.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.00  0.30  2.00  1.00  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.10 -0.50  0.30 
+ -0.50 -0.80 -2.60  2.00 -0.80  0.20  2.00 -0.80 -1.90  2.00 -0.90 -1.90  2.00  0.30 -1.50  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
+ -0.30 -1.50 -1.50  2.00 -1.60 -0.50  2.00 -1.50 -0.90  2.00 -0.60 -4.50  2.00 -0.50 -4.10 -0.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  0.80  0.00 -0.80  2.00  0.00  0.00  2.00 -1.00 -0.10  2.00  0.50 -1.90  2.00  0.00 -1.50 -0.70 
+ -0.70 -1.90 -1.90  2.00 -2.00 -0.90  2.00 -1.90 -1.30  2.00 -1.00 -4.90  2.00 -0.90 -4.50 -0.90 
+  1.50  0.20  0.30  2.00  0.20  0.20  2.00 -0.70  0.90  2.00  1.10 -0.90  2.00  0.30 -0.50 -0.50 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ G 
+                                           C /\  |  C 
+                                          3' <------ 5' 
+  0.50  1.30 -0.20  2.00  0.60  2.20  2.00  2.00  0.00  2.00  1.10 -0.10  2.00  2.00  0.90  1.40 
+  1.10  1.00  0.70  2.00  1.10  1.90  2.00  1.10 -1.00  2.00  0.80 -1.60  2.00  1.10 -0.10  0.30 
+  0.40  0.70 -0.50  2.00  0.50  0.70  2.00  0.50 -0.70  2.00 -0.20 -0.60  2.00  1.00  0.60  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  1.00 -0.40  2.00  1.50  1.30  2.00  1.20 -0.70  2.00  0.90 -1.60  2.00  1.20  0.00  0.30 
+  1.70  1.00  1.10  2.00  1.50  1.30  2.00  1.20 -0.60  2.00  1.50 -0.60  2.00  1.20  1.00  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.10  1.20  2.00  1.50  1.40  2.00  1.20  1.20  2.00  1.50 -0.50  2.00  1.20  1.00  0.30 
+ -0.30 -0.70 -1.70  2.00  0.10  0.70  2.00  0.40 -1.60  2.00 -0.90 -1.60  2.00  0.40  0.30  0.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
+ -0.50 -1.50 -1.30  2.00 -0.60 -0.20  2.00 -0.10 -0.60  2.00 -0.60 -4.10  2.00 -0.30 -2.40  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  0.70  0.00  0.20  2.00  0.50  0.30  2.00  0.20  0.20  2.00  0.50 -1.60  2.00  1.70  0.00  0.10 
+  0.10 -1.90 -0.90  2.00 -0.70 -0.30  2.00 -0.70 -0.80  2.00 -1.00 -4.40  2.00 -0.70 -3.00 -1.00 
+  1.50 -0.20  0.90  2.00  0.00 -0.10  2.00  0.40  0.90  2.00  1.10 -1.00  2.00  0.20  0.60  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ U 
+                                           C /\  |  A 
+                                          3' <------ 5' 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
+  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
+  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
+  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
+  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
+  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ G 
+                                           C /\  |  U 
+                                          3' <------ 5' 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
+  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
+  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
+  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
+  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
+  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ U 
+                                           C /\  |  G 
+                                          3' <------ 5' 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
+  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
+  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
+  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
+  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
+  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ A 
+                                           A /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ C 
+                                           A /\  |  G 
+                                          3' <------ 5' 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
+  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ G 
+                                           A /\  |  C 
+                                          3' <------ 5' 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
+  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
+  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ U 
+                                           A /\  |  A 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ G 
+                                           A /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ U 
+                                           A /\  |  G 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ A 
+                                           U /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ C 
+                                           U /\  |  G 
+                                          3' <------ 5' 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
+  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
+  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ G 
+                                           U /\  |  C 
+                                          3' <------ 5' 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
+  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
+  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ U 
+                                           U /\  |  A 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ G 
+                                           U /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           G \/ \_/ U 
+                                           U /\  |  G 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ A 
+                                           G /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ C 
+                                           G /\  |  G 
+                                          3' <------ 5' 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
+  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ G 
+                                           G /\  |  C 
+                                          3' <------ 5' 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
+  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
+  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ U 
+                                           G /\  |  A 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ G 
+                                           G /\  |  U 
+                                          3' <------ 5' 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+                                               Y 
+   --------------------------------------------------------------------------------------------- 
+    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
+    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
+   --------------------------------------------------------------------------------------------- 
+                                          5' ------> 3' 
+                                           U \/ \_/ U 
+                                           G /\  |  G 
+                                          3' <------ 5' 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
diff --git a/gtfold-mfe/data/Turner99/base_data/stack.dat b/gtfold-mfe/data/Turner99/base_data/stack.dat
new file mode 100644
index 0000000..ba2d3f5
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/stack.dat
@@ -0,0 +1,63 @@
+Data Arangement: 
+                 Y           
+         ------------------  
+     (X)  A    C    G    U   
+         ------------------  
+             5' ==> 3'       
+                AX           
+                AY 
+             3' <== 5'       
+     (A)   .     .     .     .   
+     (C)   .     .     .     .   
+     (G)   .     .     .     .   
+     (U) -0.70 -0.10 -0.70 -0.10 
+-------------------------------- 
+STACKING ENERGIES : 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         AX                      AX                      AX                      AX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .     .     .     .     .     .     .     .     .   -0.90 
+   .     .     .     .     .     .     .     .     .     .     .     .     .     .   -2.20   .   
+   .     .     .     .     .     .     .     .     .     .     .     .     .   -2.10   .   -0.60 
+   .     .     .     .     .     .     .     .     .     .     .     .   -1.10   .   -1.40   .    
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         CX                      CX                      CX                      CX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .     .     .     .     .   -2.10   .     .     .     .   
+   .     .     .     .     .     .     .     .     .     .   -3.30   .     .     .     .     .    
+   .     .     .     .     .     .     .     .     .   -2.40   .   -1.40   .     .     .     .   
+   .     .     .     .     .     .     .     .   -2.10   .   -2.10   .     .     .     .     .    
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         GX                      GX                      GX                      GX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .   -2.40   .     .     .     .     .     .     .   -1.30 
+   .     .     .     .     .     .   -3.40   .     .     .     .     .     .     .   -2.50   .   
+   .     .     .     .     .   -3.30   .   -1.50   .     .     .     .     .   -2.10   .   -0.50  
+   .     .     .     .   -2.20   .   -2.50   .     .     .     .     .   -1.40   .    1.30   .     
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         UX                      UX                      UX                      UX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -1.30   .     .     .     .     .     .     .   -1.00   .     .     .     .   
+   .     .   -2.40   .     .     .     .     .     .     .   -1.50   .     .     .     .     .    
+   .   -2.10   .   -1.00   .     .     .     .     .   -1.40   .    0.30   .     .     .     .   
+ -0.90   .   -1.30   .     .     .     .     .   -0.60   .   -0.50   .     .     .     .     .
diff --git a/gtfold-mfe/data/Turner99/base_data/tloop.dat b/gtfold-mfe/data/Turner99/base_data/tloop.dat
new file mode 100644
index 0000000..ad64bf4
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/tloop.dat
@@ -0,0 +1,32 @@
+ Seq    Energy 
+ ------------- 
+ GGGGAC -3.00 
+ GGUGAC -3.00 
+ CGAAAG -3.00 
+ GGAGAC -3.00 
+ CGCAAG -3.00 
+ GGAAAC -3.00 
+ CGGAAG -3.00 
+ CUUCGG -3.00 
+ CGUGAG -3.00 
+ CGAAGG -2.50 
+ CUACGG -2.50 
+ GGCAAC -2.50 
+ CGCGAG -2.50 
+ UGAGAG -2.50 
+ CGAGAG -2.00 
+ AGAAAU -2.00 
+ CGUAAG -2.00 
+ CUAACG -2.00 
+ UGAAAG -2.00 
+ GGAAGC -1.50 
+ GGGAAC -1.50 
+ UGAAAA -1.50 
+ AGCAAU -1.50 
+ AGUAAU -1.50 
+ CGGGAG -1.50 
+ AGUGAU -1.50 
+ GGCGAC -1.50 
+ GGGAGC -1.50 
+ GUGAAC -1.50 
+ UGGAAA -1.50 
diff --git a/gtfold-mfe/data/Turner99/base_data/triloop.dat b/gtfold-mfe/data/Turner99/base_data/triloop.dat
new file mode 100644
index 0000000..75c3bfc
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/triloop.dat
@@ -0,0 +1,2 @@
+ Seq    Energy 
+ ------------- 
diff --git a/gtfold-mfe/data/Turner99/base_data/tstack.dat b/gtfold-mfe/data/Turner99/base_data/tstack.dat
new file mode 100644
index 0000000..97a4115
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/tstack.dat
@@ -0,0 +1,63 @@
+Data Arangement: 
+                 Y           
+         ------------------  
+     (X)  A    C    G    U   
+         ------------------  
+             5' ==> 3'       
+                AX           
+                AY 
+             3' <== 5'       
+     (A)   .     .     .     .   
+     (C)   .     .     .     .   
+     (G)   .     .     .     .   
+     (U) -0.70 -0.10 -0.70 -0.10 
+-------------------------------- 
+STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         AX                      AX                      AX                      AX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -1.00   .     .     .   -1.00   .     .     .   -2.20 -0.80 -1.00 -0.80   .  
+   .     .   -1.50   .     .     .   -1.50   .     .     .   -2.70   .   -0.60 -0.70   .   -0.70 
+   .   -1.50   .   -1.00   .   -1.50   .   -1.00   .   -2.70   .   -2.20 -0.80   .   -0.80   .  
+ -1.00   .   -1.50   .   -1.00   .   -1.50   .   -2.20   .   -2.70   .     .   -0.80   .   -0.80 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         CX                      CX                      CX                      CX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -1.00   .     .     .   -1.00 -1.50 -1.50 -1.40   .     .     .     .   -1.00 
+   .     .   -1.50   .     .     .   -1.50   .   -1.00 -1.10   .   -0.80   .     .   -1.50   . 
+   .   -1.50   .   -1.00   .   -1.50   .   -1.00 -1.40   .   -1.60   .     .   -1.50   .   -1.00 
+ -1.00   .   -1.50   .   -1.00   .   -1.50   .     .   -1.40   .   -1.20 -1.00   .   -1.50   . 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         GX                      GX                      GX                      GX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -2.20 -1.10 -1.50 -1.30   .     .     .     .   -1.00 -0.30 -1.00 -0.80   .  
+   .     .   -2.70   .   -1.10 -0.70   .   -0.50   .     .   -1.50   .   -0.60 -0.70   .   -0.70 
+   .   -2.70   .   -2.20 -1.60   .   -1.40   .     .   -1.50   .   -1.00 -0.60   .   -0.80   .  
+ -2.20   .   -2.70   .     .   -1.00   .   -0.70 -1.00   .   -1.50   .     .   -0.80   .   -0.80 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         UX                      UX                      UX                      UX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+ -1.00 -0.80 -1.10   .     .     .     .   -1.00 -1.00 -0.80 -1.10   .     .     .     .   -2.00 
+ -0.70 -0.60   .   -0.50   .     .   -1.50   .   -0.70 -0.60   .   -0.50   .     .   -2.50   . 
+ -1.10   .   -1.20   .     .   -1.50   .   -1.00 -0.50   .   -0.80 -0.80   .   -2.50   .   -2.00 
+   .   -0.60   .   -0.50 -1.00   .   -1.50   .     .   -0.60 -1.10 -0.50 -2.00   .   -2.50   .   
diff --git a/gtfold-mfe/data/Turner99/base_data/tstackcoax.dat b/gtfold-mfe/data/Turner99/base_data/tstackcoax.dat
new file mode 100644
index 0000000..b90d0bc
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/tstackcoax.dat
@@ -0,0 +1,63 @@
+Data Arangement: 
+                 Y           
+         ------------------  
+     (X)  A    C    G    U   
+         ------------------  
+             5' ==> 3'       
+                AX           
+                AY 
+             3' <== 5'       
+     (A)   .     .     .     .   
+     (C)   .     .     .     .   
+     (G)   .     .     .     .   
+     (U) -0.70 -0.10 -0.70 -0.10 
+-------------------------------- 
+STACKING ENERGIES : COAXIAL STACKING
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         AX                      AX                      AX                      AX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -1.00   .     .     .   -0.70   .     .     .   -1.10 -0.80 -1.00 -0.80 -0.40 
+   .     .   -1.10   .     .     .   -1.10   .     .     .   -1.60   .   -0.60 -0.70 -1.70 -0.70 
+   .   -1.50   .   -1.00   .   -1.00   .   -0.70   .   -1.40   .   -0.50 -0.80 -1.60 -0.80 -0.10 
+ -0.80   .   -0.30   .   -0.60   .   -0.60   .   -0.80   .   -0.60   .   -0.60 -0.80 -0.90 -0.80 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         CX                      CX                      CX                      CX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -0.80   .     .     .   -0.60 -1.50 -1.50 -1.40 -1.60   .     .     .   -0.60 
+   .     .   -1.50   .     .     .   -0.70   .   -1.00 -1.10 -2.80 -0.80   .     .   -1.00   . 
+   .   -1.50   .   -0.80   .   -1.10   .   -0.60 -1.40 -1.90 -1.60 -0.90   .   -1.40   .   -0.60 
+ -1.00   .   -1.00   .   -0.70   .   -0.70   .   -1.60 -1.40 -1.60 -1.20 -0.80   .   -0.80   . 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         GX                      GX                      GX                      GX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -1.10 -1.10 -1.50 -1.30 -1.90   .     .     .   -1.20 -0.30 -1.00 -0.80 -0.80 
+   .     .   -1.30   .   -1.10 -0.70 -2.90 -0.50   .     .   -1.40   .   -0.60 -0.70 -2.00 -0.70 
+   .   -1.40   .   -1.10 -1.60 -2.80 -1.40 -1.00   .   -1.60   .   -0.80 -0.60 -1.60 -0.80  0.00 
+ -0.80   .   -0.80   .   -1.70 -1.00 -2.00 -0.70 -0.80   .   -0.80   .   -0.90 -0.80  1.80 -0.80 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         UX                      UX                      UX                      UX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+ -1.00 -0.80 -1.10 -0.80   .     .     .   -0.50 -1.00 -0.80 -1.10 -0.50   .     .     .   -0.50 
+ -0.70 -0.60 -1.90 -0.50   .     .   -0.50   .   -0.70 -0.60 -1.00 -0.50   .     .   -0.70   . 
+ -1.10 -1.60 -1.20 -0.50   .   -0.80   .   -0.50 -0.50 -0.90 -0.80  0.80   .   -1.20   .   -0.50 
+ -0.40 -0.60 -0.80 -0.50 -0.70   .   -0.70   .   -0.10 -0.60 -0.00 -0.50 -0.80   .   -0.80   .  
diff --git a/gtfold-mfe/data/Turner99/base_data/tstackh.dat b/gtfold-mfe/data/Turner99/base_data/tstackh.dat
new file mode 100644
index 0000000..6959647
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/tstackh.dat
@@ -0,0 +1,63 @@
+Data Arangement: 
+                 Y           
+         ------------------  
+     (X)  A    C    G    U   
+         ------------------  
+             5' ==> 3'       
+                AX           
+                AY 
+             3' <== 5'       
+     (A)   .     .     .     .   
+     (C)   .     .     .     .   
+     (G)   .     .     .     .   
+     (U) -0.70 -0.10 -0.70 -0.10 
+-------------------------------- 
+STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         AX                      AX                      AX                      AX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .     .     .     .     .     .   -0.30 -0.50 -0.30 -0.30 
+   .     .     .     .     .     .     .     .     .     .     .     .   -0.10 -0.20 -1.50 -0.20 
+   .     .     .     .     .     .     .     .     .     .     .     .   -1.10 -1.20 -0.20  0.20 
+   .     .     .     .     .     .     .     .     .     .     .     .   -0.30 -0.30 -0.60 -1.10 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         CX                      CX                      CX                      CX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .     .   -1.50 -1.50 -1.40 -1.80   .     .     .     .  
+   .     .     .     .     .     .     .     .   -1.00 -0.90 -2.90 -0.80   .     .     .     . 
+   .     .     .     .     .     .     .     .   -2.20 -2.00 -1.60 -1.10   .     .     .     .  
+   .     .     .     .     .     .     .     .   -1.70 -1.40 -1.80 -2.00   .     .     .     . 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         GX                      GX                      GX                      GX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .   -1.10 -1.50 -1.30 -2.10   .     .     .     .    0.20 -0.50 -0.30 -0.30 
+   .     .     .     .   -1.10 -0.70 -2.40 -0.50   .     .     .     .   -0.10 -0.20 -1.50 -0.20 
+   .     .     .     .   -2.40 -2.90 -1.40 -1.20   .     .     .     .   -0.90 -1.10 -0.30  0.00 
+   .     .     .     .   -1.90 -1.00 -2.20 -1.50   .     .     .     .   -0.30 -0.30 -0.40 -1.10 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         UX                      UX                      UX                      UX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+ -0.50 -0.30 -0.60 -0.50   .     .     .     .   -0.50 -0.30 -0.60 -0.50   .     .     .     .  
+ -0.20 -0.10 -1.20 -0.00   .     .     .     .   -0.20 -0.10 -1.70  0.00   .     .     .     . 
+ -1.40 -1.20 -0.70 -0.20   .     .     .     .   -0.80 -1.20 -0.30 -0.70   .     .     .     .  
+ -0.30 -0.10 -0.50 -0.80   .     .     .     .   -0.60 -0.10 -0.60 -0.80   .     .     .     . 
diff --git a/gtfold-mfe/data/Turner99/base_data/tstacki.dat b/gtfold-mfe/data/Turner99/base_data/tstacki.dat
new file mode 100644
index 0000000..bf5d98c
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/tstacki.dat
@@ -0,0 +1,63 @@
+Data Arangement: 
+                 Y           
+         ------------------  
+     (X)  A    C    G    U   
+         ------------------  
+             5' ==> 3'       
+                AX           
+                AY 
+             3' <== 5'       
+     (A)   .     .     .     .   
+     (C)   .     .     .     .   
+     (G)   .     .     .     .   
+     (U) -0.70 -0.10 -0.70 -0.10 
+-------------------------------- 
+STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         AX                      AX                      AX                      AX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .     .     .     .     .     .    0.70  0.70 -0.40  0.70 
+   .     .     .     .     .     .     .     .     .     .     .     .    0.70  0.70  0.70  0.70 
+   .     .     .     .     .     .     .     .     .     .     .     .   -0.40  0.70  0.70  0.70 
+   .     .     .     .     .     .     .     .     .     .     .     .    0.70  0.70  0.70  0.00 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         CX                      CX                      CX                      CX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .     .     .     .     .   -0.00 -0.00 -1.10 -0.00   .     .     .     .  
+   .     .     .     .     .     .     .     .   -0.00 -0.00 -0.00 -0.00   .     .     .     . 
+   .     .     .     .     .     .     .     .   -1.10 -0.00 -0.00 -0.00   .     .     .     .  
+   .     .     .     .     .     .     .     .   -0.00 -0.00 -0.00 -0.70   .     .     .     . 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         GX                      GX                      GX                      GX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .     .   -0.00 -0.00 -1.10 -0.00   .     .     .     .    0.70  0.70 -0.40  0.70 
+   .     .     .     .   -0.00 -0.00 -0.00 -0.00   .     .     .     .    0.70  0.70  0.70  0.70 
+   .     .     .     .   -1.10 -0.00 -0.00 -0.00   .     .     .     .   -0.40  0.70  0.70  0.70 
+   .     .     .     .   -0.00 -0.00 -0.00 -0.70   .     .     .     .    0.70  0.70  0.70  0.00 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         UX                      UX                      UX                      UX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+  0.70  0.70 -0.40  0.70   .     .     .     .    0.70  0.70 -0.40  0.70   .     .     .     .  
+  0.70  0.70  0.70  0.70   .     .     .     .    0.70  0.70  0.70  0.70   .     .     .     . 
+ -0.40  0.70  0.70  0.70   .     .     .     .   -0.40  0.70  0.70  0.70   .     .     .     .  
+  0.70  0.70  0.70  0.00   .     .     .     .    0.70  0.70  0.70  0.00   .     .     .     . 
diff --git a/gtfold-mfe/data/Turner99/base_data/tstackm.dat b/gtfold-mfe/data/Turner99/base_data/tstackm.dat
new file mode 100644
index 0000000..f38c845
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/base_data/tstackm.dat
@@ -0,0 +1,63 @@
+Data Arangement: 
+                 Y           
+         ------------------  
+     (X)  A    C    G    U   
+         ------------------  
+             5' ==> 3'       
+                AX           
+                AY 
+             3' <== 5'       
+     (A)   .     .     .     .   
+     (C)   .     .     .     .   
+     (G)   .     .     .     .   
+     (U) -0.70 -0.10 -0.70 -0.10 
+-------------------------------- 
+STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         AX                      AX                      AX                      AX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -1.00   .     .     .   -1.00   .     .     .   -2.20 -0.80 -1.00 -0.80 -0.90 
+   .     .   -1.50   .     .     .   -1.50   .     .     .   -2.70   .   -0.60 -0.70 -2.20 -0.70 
+   .   -1.50   .   -1.00   .   -1.50   .   -1.00   .   -2.70   .   -2.20 -0.80 -2.10 -0.80 -0.80 
+ -1.00   .   -1.50   .   -1.00   .   -1.50   .   -2.20   .   -2.70   .   -1.10 -0.80 -1.10 -0.80 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         CX                      CX                      CX                      CX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -1.00   .     .     .   -1.00 -1.70 -1.70 -1.70 -1.70   .     .     .   -1.00 
+   .     .   -1.50   .     .     .   -1.50   .   -1.00 -1.10 -3.30 -0.80   .     .   -1.50   . 
+   .   -1.50   .   -1.00   .   -1.50   .   -1.00 -1.70 -2.40 -1.70 -1.70   .   -1.50   .   -1.00 
+ -1.00   .   -1.50   .   -1.00   .   -1.50   .   -1.60 -1.40 -1.60 -1.20 -1.00   .   -1.50   . 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         GX                      GX                      GX                      GX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+   .     .     .   -2.20 -1.10 -1.50 -1.30 -1.90   .     .     .   -1.00 -0.80 -1.00 -0.80 -1.30 
+   .     .   -2.70   .   -1.10 -0.70 -3.40 -0.50   .     .   -1.50   .   -0.60 -0.70 -2.50 -0.70 
+   .   -2.70   .   -2.20 -1.60 -3.30 -1.40 -1.30   .   -1.50   .   -1.00 -0.80 -2.10 -0.80 -0.80 
+ -2.20   .   -2.70   .   -1.70 -1.00 -2.00 -0.70 -1.00   .   -1.50   .   -1.40 -0.80  1.30 -0.80 
+          Y                       Y                       Y                       Y 
+  ------------------      ------------------      ------------------      ------------------   
+   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
+  ------------------      ------------------      ------------------      ------------------   
+      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
+         UX                      UX                      UX                      UX 
+         AY                      CY                      GY                      UY 
+      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
+ -1.00 -0.80 -1.10 -1.30   .     .     .   -1.00 -1.00 -0.80 -1.10 -1.00   .     .     .   -2.00 
+ -0.70 -0.60 -2.40 -0.50   .     .   -1.50   .   -0.70 -0.60 -1.50 -0.50   .     .   -2.50   . 
+ -1.10 -2.10 -1.20 -1.00   .   -1.50   .   -1.00 -0.70 -1.40 -0.80  0.30   .   -2.50   .   -2.00 
+ -0.90 -0.60 -1.40 -0.50 -1.00   .   -1.50   .   -0.50 -0.60 -0.50 -0.50 -2.00   .   -2.50   . 

From 6fcd379ad7f3142572caf34b270c0a1c7e66e28f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Mon, 20 Jun 2011 11:20:55 -0400
Subject: [PATCH 160/282] moved .dat files to base_data dir

---
 gtfold-mfe/data/Turner99/asint1x2.dat   | 353 ---------
 gtfold-mfe/data/Turner99/coaxial.dat    |  63 --
 gtfold-mfe/data/Turner99/coaxstack.dat  |  63 --
 gtfold-mfe/data/Turner99/dangle.dat     |  72 --
 gtfold-mfe/data/Turner99/int11.dat      | 101 ---
 gtfold-mfe/data/Turner99/int21.dat      | 353 ---------
 gtfold-mfe/data/Turner99/int22.dat      | 928 ------------------------
 gtfold-mfe/data/Turner99/loop.dat       |  34 -
 gtfold-mfe/data/Turner99/miscloop.dat   |  42 --
 gtfold-mfe/data/Turner99/sint2.dat      | 101 ---
 gtfold-mfe/data/Turner99/sint4.dat      | 928 ------------------------
 gtfold-mfe/data/Turner99/stack.dat      |  63 --
 gtfold-mfe/data/Turner99/tloop.dat      |  32 -
 gtfold-mfe/data/Turner99/triloop.dat    |   2 -
 gtfold-mfe/data/Turner99/tstack.dat     |  63 --
 gtfold-mfe/data/Turner99/tstackcoax.dat |  63 --
 gtfold-mfe/data/Turner99/tstackh.dat    |  63 --
 gtfold-mfe/data/Turner99/tstacki.dat    |  63 --
 gtfold-mfe/data/Turner99/tstackm.dat    |  63 --
 19 files changed, 3450 deletions(-)
 delete mode 100644 gtfold-mfe/data/Turner99/asint1x2.dat
 delete mode 100644 gtfold-mfe/data/Turner99/coaxial.dat
 delete mode 100644 gtfold-mfe/data/Turner99/coaxstack.dat
 delete mode 100644 gtfold-mfe/data/Turner99/dangle.dat
 delete mode 100644 gtfold-mfe/data/Turner99/int11.dat
 delete mode 100644 gtfold-mfe/data/Turner99/int21.dat
 delete mode 100644 gtfold-mfe/data/Turner99/int22.dat
 delete mode 100644 gtfold-mfe/data/Turner99/loop.dat
 delete mode 100644 gtfold-mfe/data/Turner99/miscloop.dat
 delete mode 100644 gtfold-mfe/data/Turner99/sint2.dat
 delete mode 100644 gtfold-mfe/data/Turner99/sint4.dat
 delete mode 100644 gtfold-mfe/data/Turner99/stack.dat
 delete mode 100644 gtfold-mfe/data/Turner99/tloop.dat
 delete mode 100644 gtfold-mfe/data/Turner99/triloop.dat
 delete mode 100644 gtfold-mfe/data/Turner99/tstack.dat
 delete mode 100644 gtfold-mfe/data/Turner99/tstackcoax.dat
 delete mode 100644 gtfold-mfe/data/Turner99/tstackh.dat
 delete mode 100644 gtfold-mfe/data/Turner99/tstacki.dat
 delete mode 100644 gtfold-mfe/data/Turner99/tstackm.dat

diff --git a/gtfold-mfe/data/Turner99/asint1x2.dat b/gtfold-mfe/data/Turner99/asint1x2.dat
deleted file mode 100644
index d17afd2..0000000
--- a/gtfold-mfe/data/Turner99/asint1x2.dat
+++ /dev/null
@@ -1,353 +0,0 @@
-Data tables for asymmetric interior loops of size 3 
-Free energies at 37 degrees for RNA 
-Data arrangement: 
-            Y 
-    ------------------ 
-(X)  A    C    G    U   
-    ------------------ 
-        5' --> 3' 
-            X 
-           A  A 
-           U  U 
-            YA 
-        3' <-- 5' 
-(A)  .    .    .    .    
-(C)  .    .    .    .    
-(G)  .    .    .    .    
-(U)  .    .    .    .    
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
-  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
-  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
-  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.20  3.00  2.40  4.80  2.30  2.20  1.10  4.00  2.40  2.20  1.60  4.00  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80 
-  3.10  3.00  4.80  3.00  2.30  2.20  4.00  2.20  2.30  2.20  4.00  2.20  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00 
-  2.50  4.80  1.60  4.80  1.70  4.00  0.80  4.00  1.70  4.00  0.80  4.00  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.90  2.50  2.40  4.80  2.10  1.70  1.60  4.00  2.10  1.70  1.60  4.00  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80 
-  3.00  3.30  4.80  3.00  2.20  2.50  4.00  2.20  2.20  2.50  4.00  2.20  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  4.80  3.00  4.80  2.10  4.00  2.20  4.00  1.50  4.00  2.20  4.00  1.30  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.80  1.40  1.20  4.80  0.80  0.60  0.40  4.00  1.00  0.60  0.40  4.00  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  1.60  4.80  3.00  4.80  0.80  4.00  2.20  4.00  0.80  4.00  2.20  4.00  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  3.30  2.70  4.80  3.00  2.50  1.90  4.00  2.20  2.50  1.90  4.00  2.20  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  4.80  2.50  4.80  2.00  4.00  1.70  4.00  1.20  4.00  1.70  4.00  1.20  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.20  3.00  2.40  4.80  2.40  2.20  1.60  4.00  2.50  2.20  2.10  4.00  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80 
-  3.10  3.00  4.80  3.00  2.30  2.20  4.00  2.20  2.30  2.20  4.00  2.20  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00 
-  2.50  4.80  1.60  4.80  1.70  4.00  0.80  4.00  1.70  4.00  0.80  4.00  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.90  2.50  2.40  4.80  2.10  1.70  1.60  4.00  2.10  1.70  1.60  4.00  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80 
-  3.00  3.30  4.80  3.00  2.20  2.50  4.00  2.20  2.20  2.50  4.00  2.20  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  4.80  3.00  4.80  2.10  4.00  2.20  4.00  1.30  4.00  2.20  4.00  1.20  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.80  1.40  1.20  4.80  1.00  0.60  0.40  4.00  1.20  0.60  0.40  4.00  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  1.60  4.80  3.00  4.80  0.80  4.00  2.20  4.00  0.80  4.00  2.20  4.00  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  3.30  2.70  4.80  3.00  2.50  1.90  4.00  2.20  2.50  1.90  4.00  2.20  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  4.80  2.50  4.80  2.00  4.00  1.70  4.00  1.20  4.00  1.70  4.00  1.20  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
-  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
-  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
-  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
-  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
-  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
-  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
-  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
-  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
-  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
diff --git a/gtfold-mfe/data/Turner99/coaxial.dat b/gtfold-mfe/data/Turner99/coaxial.dat
deleted file mode 100644
index 9987fef..0000000
--- a/gtfold-mfe/data/Turner99/coaxial.dat
+++ /dev/null
@@ -1,63 +0,0 @@
-Data Arangement: 
-                 Y           
-         ------------------  
-     (X)  A    C    G    U   
-         ------------------  
-             5' ==> 3'       
-                AX           
-                AY 
-             3' <== 5'       
-     (A)   .     .     .     .   
-     (C)   .     .     .     .   
-     (G)   .     .     .     .   
-     (U) -0.70 -0.10 -0.70 -0.10 
--------------------------------- 
-STACKING ENERGIES : 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         AX                      AX                      AX                      AX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .     .     .     .     .     .     .     .     .   -0.90
-   .     .     .     .     .     .     .     .     .     .     .     .     .     .   -2.20   .   
-   .     .     .     .     .     .     .     .     .     .     .     .     .   -2.10   .   -0.60 
-   .     .     .     .     .     .     .     .     .     .     .     .   -1.10   .   -1.40   .    
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         CX                      CX                      CX                      CX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .     .     .     .     .   -2.10   .     .     .     .   
-   .     .     .     .     .     .     .     .     .     .   -3.30   .     .     .     .     .    
-   .     .     .     .     .     .     .     .     .   -2.40   .   -1.40   .     .     .     .   
-   .     .     .     .     .     .     .     .   -2.10   .   -2.10   .     .     .     .     .    
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         GX                      GX                      GX                      GX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .   -2.40   .     .     .     .     .     .     .   -1.30 
-   .     .     .     .     .     .   -3.40   .     .     .     .     .     .     .   -2.50   .   
-   .     .     .     .     .   -3.30   .   -1.50   .     .     .     .     .   -2.10   .   -0.50  
-   .     .     .     .   -2.20   .   -2.50   .     .     .     .     .   -1.40   .    1.30   .     
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         UX                      UX                      UX                      UX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -1.30   .     .     .     .     .     .     .   -1.00   .     .     .     .   
-   .     .   -2.40   .     .     .     .     .     .     .   -1.50   .     .     .     .     .    
-   .   -2.10   .   -1.00   .     .     .     .     .   -1.40   .    0.30   .     .     .     .   
- -0.90   .   -1.30   .     .     .     .     .   -0.60   .   -0.50   .     .     .     .     .    
diff --git a/gtfold-mfe/data/Turner99/coaxstack.dat b/gtfold-mfe/data/Turner99/coaxstack.dat
deleted file mode 100644
index 7125756..0000000
--- a/gtfold-mfe/data/Turner99/coaxstack.dat
+++ /dev/null
@@ -1,63 +0,0 @@
-Data Arangement: 
-                 Y           
-         ------------------  
-     (X)  A    C    G    U   
-         ------------------  
-             5' ==> 3'       
-                AX           
-                AY 
-             3' <== 5'       
-     (A)   .     .     .     .   
-     (C)   .     .     .     .   
-     (G)   .     .     .     .   
-     (U) -0.70 -0.10 -0.70 -0.10 
--------------------------------- 
-STACKING ENERGIES : COAXIAL STACKING ENERGIES
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         AX                      AX                      AX                      AX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .     .     .     .     .     .   -2.10 -2.10 -2.10 -2.50 
-   .     .     .     .     .     .     .     .     .     .     .     .   -2.10 -2.10 -2.50 -2.10 
-   .     .     .     .     .     .     .     .     .     .     .     .   -2.10 -2.50 -2.10 -2.30 
-   .     .     .     .     .     .     .     .     .     .     .     .   -2.50 -2.10 -2.30 -2.10 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         CX                      CX                      CX                      CX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .     .   -2.10 -2.10 -2.10 -2.50   .     .     .     .  
-   .     .     .     .     .     .     .     .   -2.10 -2.10 -2.50 -2.10   .     .     .     . 
-   .     .     .     .     .     .     .     .   -2.10 -2.50 -2.10 -2.30   .     .     .     .  
-   .     .     .     .     .     .     .     .   -2.50 -2.10 -2.30 -2.10   .     .     .     . 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         GX                      GX                      GX                      GX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .   -2.10 -2.10 -2.10 -2.50   .     .     .     .   -2.10 -2.10 -2.10 -2.50 
-   .     .     .     .   -2.10 -2.10 -2.50 -2.10   .     .     .     .   -2.10 -2.10 -2.50 -2.10 
-   .     .     .     .   -2.10 -2.50 -2.10 -2.30   .     .     .     .   -2.10 -2.50 -2.10 -2.30 
-   .     .     .     .   -2.50 -2.10 -2.30 -2.10   .     .     .     .   -2.50 -2.10 -2.30 -2.10 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         UX                      UX                      UX                      UX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
- -2.10 -2.10 -2.10 -2.50   .     .     .     .   -2.10 -2.10 -2.10 -2.50   .     .     .     .  
- -2.10 -2.10 -2.50 -2.10   .     .     .     .   -2.10 -2.10 -2.50 -2.10   .     .     .     . 
- -2.10 -2.50 -2.10 -2.30   .     .     .     .   -2.10 -2.50 -2.10 -2.30   .     .     .     .  
- -2.50 -2.10 -2.30 -2.10   .     .     .     .   -2.50 -2.10 -2.30 -2.10   .     .     .     . 
diff --git a/gtfold-mfe/data/Turner99/dangle.dat b/gtfold-mfe/data/Turner99/dangle.dat
deleted file mode 100644
index 2f2d2da..0000000
--- a/gtfold-mfe/data/Turner99/dangle.dat
+++ /dev/null
@@ -1,72 +0,0 @@
-          X                       X                       X                       X 
-  ------------------      ------------------      ------------------      ------------------ 
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
-  ------------------      ------------------      ------------------      ------------------ 
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-         AX                      AX                      AX                      AX 
-         A                       C                       G                       U 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  .     .     .     .     .     .     .     .     .     .     .     .   -0.80 -0.50 -0.80 -0.60 
-          X                       X                       X                       X 
-  ------------------      ------------------      ------------------      ------------------ 
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
-  ------------------      ------------------      ------------------      ------------------ 
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-         CX                      CX                      CX                      CX 
-         A                       C                       G                       U 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  .     .     .     .     .     .     .     .   -1.70 -0.80 -1.70 -1.20   .     .     .     . 
-          X                       X                       X                       X 
-  ------------------      ------------------      ------------------      ------------------ 
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
-  ------------------      ------------------      ------------------      ------------------ 
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-         GX                      GX                      GX                      GX 
-         A                       C                       G                       U 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  .     .     .     .   -1.10 -0.40 -1.30 -0.60   .     .     .     .   -0.80 -0.50 -0.80 -0.60 
-          X                       X                       X                       X 
-  ------------------      ------------------      ------------------      ------------------ 
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
-  ------------------      ------------------      ------------------      ------------------ 
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-         UX                      UX                      UX                      UX 
-         A                       C                       G                       U 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
--0.70 -0.10 -0.70 -0.10   .     .     .     .   -0.70 -0.10 -0.70 -0.10   .     .     .     . 
-          X                       X                       X                       X 
-  ------------------      ------------------      ------------------      ------------------ 
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
-  ------------------      ------------------      ------------------      ------------------ 
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-         A                       A                       A                       A 
-         AX                      CX                      GX                      UX 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  .     .     .     .     .     .     .     .     .     .     .     .   -0.30 -0.10 -0.20 -0.20 
-          X                       X                       X                       X 
-  ------------------      ------------------      ------------------      ------------------ 
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
-  ------------------      ------------------      ------------------      ------------------ 
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-         C                       C                       C                       C 
-         AX                      CX                      GX                      UX 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  .     .     .     .     .     .     .     .   -0.20 -0.30 -0.0 -0.0   .     .     .     . 
-          X                       X                       X                       X 
-  ------------------      ------------------      ------------------      ------------------ 
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
-  ------------------      ------------------      ------------------      ------------------ 
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-         G                       G                       G                       G 
-         AX                      CX                      GX                      UX 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  .     .     .     .   -0.50 -0.30 -0.20 -0.10   .     .     .     .   -0.30 -0.10 -0.20 -0.20 
-          X                       X                       X                       X 
-  ------------------      ------------------      ------------------      ------------------ 
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U 
-  ------------------      ------------------      ------------------      ------------------ 
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-         U                       U                       U                       U 
-         AX                      CX                      GX                      UX 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
--0.30 -0.30 -0.40 -0.20   .     .     .     .   -0.30 -0.30 -0.40 -0.20   .     .     .     . 
diff --git a/gtfold-mfe/data/Turner99/int11.dat b/gtfold-mfe/data/Turner99/int11.dat
deleted file mode 100644
index 3e0f630..0000000
--- a/gtfold-mfe/data/Turner99/int11.dat
+++ /dev/null
@@ -1,101 +0,0 @@
-Data table for symetric interior loops of size 2 
-Free energies at 37 degrees for RNA 
-Data Arrangement: 
-            Y 
-    ------------------ 
-(X)  A    C    G    U   
-    ------------------ 
-        5' --> 3' 
-            X 
-           A A 
-           U U 
-            Y 
-        3' <-- 5' 
-(A)  .    .    .    .    
-(C)  .    .    .    .    
-(G)  .    .    .    .    
-(U)  .    .    .    .    
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           A A                     A C                     A G                     A U                     A G                     A U         
-           U U                     U G                     U C                     U A                     U U                     U G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
-  1.70  1.70  1.70  1.50  1.10  1.10  1.10  1.00  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.20  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           C A                     C C                     C G                     C U                     C G                     C U         
-           G U                     G G                     G C                     G A                     G U                     G G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.10  1.10  1.10  1.10  0.40 -0.40  0.40  0.40  1.10  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-  1.10  1.10  1.10  1.10  0.30  0.50  0.40  0.50  0.40  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-  1.10  1.10 -1.00  1.10 -0.10  0.40 -1.70  0.40  0.40  0.40 -1.40  0.40  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10 
-  1.10  1.10  1.10  1.10  0.40  0.00  0.40 -0.30  0.40  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G A                     G C                     G G                     G U                     G G                     G U         
-           C U                     C G                     C C                     C A                     C U                     C G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.10  1.10  1.10  1.10  0.80  0.40  0.40  0.40  0.40  0.30 -0.10  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-  1.10  1.10  1.10  1.10  0.40  0.40  0.40  0.40 -0.40  0.50  0.40  0.00  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-  1.10  1.10 -1.00  1.10  0.40  0.40 -2.10  0.40  0.40  0.40 -1.70  0.40  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10 
-  1.10  1.10  1.10  1.10  0.40  0.40  0.40 -0.70  0.40  0.50  0.40 -0.30  1.10  1.10  1.10  1.00  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U A                     U C                     U G                     U U                     U G                     U U         
-           A U                     A G                     A C                     A A                     A U                     A G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
-  1.70  1.70  1.70  1.80  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.50  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G A                     G C                     G G                     G U                     G G                     G U         
-           U U                     U G                     U C                     U A                     U U                     U G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U A                     U C                     U G                     U U                     U G                     U U         
-           G U                     G G                     G C                     G A                     G U                     G G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
diff --git a/gtfold-mfe/data/Turner99/int21.dat b/gtfold-mfe/data/Turner99/int21.dat
deleted file mode 100644
index d17afd2..0000000
--- a/gtfold-mfe/data/Turner99/int21.dat
+++ /dev/null
@@ -1,353 +0,0 @@
-Data tables for asymmetric interior loops of size 3 
-Free energies at 37 degrees for RNA 
-Data arrangement: 
-            Y 
-    ------------------ 
-(X)  A    C    G    U   
-    ------------------ 
-        5' --> 3' 
-            X 
-           A  A 
-           U  U 
-            YA 
-        3' <-- 5' 
-(A)  .    .    .    .    
-(C)  .    .    .    .    
-(G)  .    .    .    .    
-(U)  .    .    .    .    
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
-  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
-  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
-  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           A  A                    A  C                    A  G                    A  U                    A  G                    A  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.20  3.00  2.40  4.80  2.30  2.20  1.10  4.00  2.40  2.20  1.60  4.00  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80 
-  3.10  3.00  4.80  3.00  2.30  2.20  4.00  2.20  2.30  2.20  4.00  2.20  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00 
-  2.50  4.80  1.60  4.80  1.70  4.00  0.80  4.00  1.70  4.00  0.80  4.00  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.90  2.50  2.40  4.80  2.10  1.70  1.60  4.00  2.10  1.70  1.60  4.00  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80 
-  3.00  3.30  4.80  3.00  2.20  2.50  4.00  2.20  2.20  2.50  4.00  2.20  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  4.80  3.00  4.80  2.10  4.00  2.20  4.00  1.50  4.00  2.20  4.00  1.30  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.80  1.40  1.20  4.80  0.80  0.60  0.40  4.00  1.00  0.60  0.40  4.00  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  1.60  4.80  3.00  4.80  0.80  4.00  2.20  4.00  0.80  4.00  2.20  4.00  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           C  A                    C  C                    C  G                    C  U                    C  G                    C  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  3.30  2.70  4.80  3.00  2.50  1.90  4.00  2.20  2.50  1.90  4.00  2.20  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  4.80  2.50  4.80  2.00  4.00  1.70  4.00  1.20  4.00  1.70  4.00  1.20  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.20  3.00  2.40  4.80  2.40  2.20  1.60  4.00  2.50  2.20  2.10  4.00  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80 
-  3.10  3.00  4.80  3.00  2.30  2.20  4.00  2.20  2.30  2.20  4.00  2.20  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00 
-  2.50  4.80  1.60  4.80  1.70  4.00  0.80  4.00  1.70  4.00  0.80  4.00  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.90  2.50  2.40  4.80  2.10  1.70  1.60  4.00  2.10  1.70  1.60  4.00  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80 
-  3.00  3.30  4.80  3.00  2.20  2.50  4.00  2.20  2.20  2.50  4.00  2.20  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  4.80  3.00  4.80  2.10  4.00  2.20  4.00  1.30  4.00  2.20  4.00  1.20  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.80  1.40  1.20  4.80  1.00  0.60  0.40  4.00  1.20  0.60  0.40  4.00  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  1.60  4.80  3.00  4.80  0.80  4.00  2.20  4.00  0.80  4.00  2.20  4.00  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           C  U                    C  G                    C  C                    C  A                    C  U                    C  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  3.30  2.70  4.80  3.00  2.50  1.90  4.00  2.20  2.50  1.90  4.00  2.20  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00 
-  4.80  4.80  4.80  4.80  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.00  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80 
-  4.80  2.50  4.80  2.00  4.00  1.70  4.00  1.20  4.00  1.70  4.00  1.20  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
-  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
-  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
-  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           A  U                    A  G                    A  C                    A  A                    A  U                    A  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
-  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
-  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
-  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G  A                    G  C                    G  G                    G  U                    G  G                    G  U 
-           U  U                    U  G                    U  C                    U  A                    U  U                    U  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YA                      YA                      YA                      YA                      YA                      YA 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.90  3.70  3.10  5.50  3.20  3.00  2.40  4.80  3.20  3.00  2.40  4.80  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50  3.90  3.70  3.10  5.50 
-  3.80  3.70  5.50  3.70  3.10  3.00  4.80  3.00  3.10  3.00  4.80  3.00  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70  3.80  3.70  5.50  3.70 
-  3.20  5.50  2.30  5.50  2.50  4.80  1.60  4.80  2.50  4.80  1.60  4.80  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50  3.20  5.50  2.30  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YC                      YC                      YC                      YC                      YC                      YC 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  3.60  3.20  3.10  5.50  2.90  2.50  2.40  4.80  2.90  2.50  2.40  4.80  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50  3.60  3.20  3.10  5.50 
-  3.70  4.00  5.50  3.70  3.00  3.30  4.80  3.00  3.00  3.30  4.80  3.00  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70  3.70  4.00  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.70  5.50  2.80  4.80  3.00  4.80  2.10  4.80  3.00  4.80  2.10  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80  5.50  3.70  5.50  2.80 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YG                      YG                      YG                      YG                      YG                      YG 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  2.50  2.10  1.90  5.50  1.80  1.40  1.20  4.80  1.80  1.40  1.20  4.80  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50  2.50  2.10  1.90  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  2.30  5.50  3.70  5.50  1.60  4.80  3.00  4.80  1.60  4.80  3.00  4.80  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50  2.30  5.50  3.70  5.50 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U  A                    U  C                    U  G                    U  U                    U  G                    U  U 
-           G  U                    G  G                    G  C                    G  A                    G  U                    G  G 
-            YU                      YU                      YU                      YU                      YU                      YU 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  4.00  3.40  5.50  3.70  3.30  2.70  4.80  3.00  3.30  2.70  4.80  3.00  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70  4.00  3.40  5.50  3.70 
-  5.50  5.50  5.50  5.50  4.80  4.80  4.80  4.80  4.80  4.80  4.80  4.80  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50  5.50 
-  5.50  3.20  5.50  2.70  4.80  2.50  4.80  2.00  4.80  2.50  4.80  2.00  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70  5.50  3.20  5.50  2.70 
diff --git a/gtfold-mfe/data/Turner99/int22.dat b/gtfold-mfe/data/Turner99/int22.dat
deleted file mode 100644
index 2357f6f..0000000
--- a/gtfold-mfe/data/Turner99/int22.dat
+++ /dev/null
@@ -1,928 +0,0 @@
-Data tables for symetric interior loops of size 4 
-Free energies at 37 degrees for RNA 
-Data arrangement: 
-                                Y 
-     ---------------------------------------------------------------- 
-(X)   A   A   A   A   C   C   C   C   G   G   G   G   U   U   U   U 
-      A   C   G   U   A   C   G   U   A   C   G   U   A   C   G   U 
-     ---------------------------------------------------------------- 
-                           5' ------> 3' 
-                            A \/ \_/ A 
-                            U /\  |  U 
-                           3' <------ 5' 
-(AA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(AC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(AG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(AU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(CA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(CC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(CG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(CU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(GA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(GC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(GG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(GU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(UA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(UC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(UG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(UU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ A 
-                                           U /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
-  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
-  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ C 
-                                           U /\  |  G 
-                                          3' <------ 5' 
-  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
-  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
-  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
-  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
-  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ G 
-                                           U /\  |  C 
-                                          3' <------ 5' 
-  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
-  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
-  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
-  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
-  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ U 
-                                           U /\  |  A 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
-  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
-  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ G 
-                                           U /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
-  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
-  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ U 
-                                           U /\  |  G 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
-  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
-  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ A 
-                                           G /\  |  U 
-                                          3' <------ 5' 
-  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
-  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
-  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
-  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
-  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
-  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
-  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
-  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ C 
-                                           G /\  |  G 
-                                          3' <------ 5' 
-  0.50  1.10 -0.30  2.00  1.10  1.70  2.00  0.70  0.40  2.00  1.00  0.10  2.00  1.80 -0.50  1.50 
-  0.60  1.50  0.10  2.00  1.10  1.50  2.00  0.50  0.50  2.00  1.40 -0.70  2.00  1.50 -0.60  0.00 
-  0.00 -0.70 -1.60  2.00 -1.00 -0.60  2.00  0.20 -0.70  2.00  0.00 -0.80  2.00  1.20 -0.60  0.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.30  1.00 -0.70  2.00  1.00  1.00  2.00  0.00  0.70  2.00  0.90 -1.90  2.00  1.10 -1.50 -0.20 
-  2.20  1.30  0.70  2.00  1.90  1.30  2.00  0.30  0.70  2.00  1.80 -0.30  2.00  1.40 -0.20 -0.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.00  1.20  0.40  2.00  1.10  1.20  2.00  1.70  1.00  2.00  1.70 -0.70  2.00  1.20 -0.30  0.20 
- -0.20 -0.40 -1.70  2.00  0.70  1.10  2.00  0.20 -0.50  2.00  0.00 -0.90  2.00  1.20 -1.30  0.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
-  0.90  0.00  0.30  2.00 -0.10  1.00  2.00  0.00  0.60  2.00  0.90 -3.00  2.00  1.00 -2.40  0.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.00  1.20  0.40  2.00  1.10  1.20  2.00  0.20  0.50  2.00  1.70 -0.70  2.00  1.20 -0.10  0.40 
- -0.10 -1.60 -1.60  2.00 -1.60 -0.60  2.00 -1.60 -0.60  2.00 -0.70 -4.40  2.00 -0.50 -4.10 -1.00 
-  1.40  0.30  0.50  2.00  0.30  0.30  2.00  0.10  1.40  2.00  1.20 -1.00  2.00  0.30  0.10  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ G 
-                                           G /\  |  C 
-                                          3' <------ 5' 
-  1.30  1.20  0.30  2.00  1.60  2.10  2.00  1.90  0.30  2.00  1.00 -0.40  2.00  1.90  1.10  1.40 
-  1.60  1.50  0.60  2.00  2.00  1.80  2.00  1.70  0.60  2.00  1.40 -1.10  2.00  1.70  0.40  0.80 
-  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.20  1.10  0.20  2.00  1.50  1.40  2.00  1.20  0.20  2.00  0.90 -1.50  2.00  1.20  0.00  0.30 
-  2.10  1.40  1.50  2.00  1.80  1.70  2.00  1.50  1.50  2.00  1.80 -0.20  2.00  1.50  1.30  0.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
-  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
-  1.10  0.00  0.90  2.00  0.40  1.30  2.00  1.10  0.90  2.00  0.90 -2.60  2.00  1.10 -1.10  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
- -0.40 -1.50 -0.60  2.00 -1.10 -0.20  2.00 -0.40 -0.60  2.00 -0.70 -4.20  2.00 -0.40 -2.60 -0.50 
-  1.40  0.30  1.30  2.00  0.80  0.60  2.00  0.50  1.30  2.00  1.20 -0.50  2.00  0.50  1.10 -0.40 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ U 
-                                           G /\  |  A 
-                                          3' <------ 5' 
-  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
-  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
-  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
-  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
-  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
-  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
-  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
-  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ G 
-                                           G /\  |  U 
-                                          3' <------ 5' 
-  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
-  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
-  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
-  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
-  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
-  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
-  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
-  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ U 
-                                           G /\  |  G 
-                                          3' <------ 5' 
-  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
-  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
-  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
-  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
-  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
-  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
-  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
-  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ A 
-                                           C /\  |  U 
-                                          3' <------ 5' 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
-  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
-  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
-  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
-  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
-  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
-  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ C 
-                                           C /\  |  G 
-                                          3' <------ 5' 
-  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
-  1.20  0.90 -0.80  2.00  0.90  0.90  2.00  0.00 -0.20  2.00  0.80 -2.00  2.00  1.00 -1.60  0.20 
-  0.10 -0.10 -1.90  2.00 -0.20  0.90  2.00 -0.10 -1.30  2.00 -0.20 -1.30  2.00  0.90 -0.90  0.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.20  1.00 -0.80  2.00  0.90  1.00  2.00  0.00 -0.10  2.00  0.90 -1.90  2.00  1.00 -1.50  0.20 
-  1.80  1.00  0.20  2.00  0.90  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.00 -0.50  0.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.00  0.30  2.00  1.00  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.10 -0.50  0.30 
- -0.50 -0.80 -2.60  2.00 -0.80  0.20  2.00 -0.80 -1.90  2.00 -0.90 -1.90  2.00  0.30 -1.50  0.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
- -0.30 -1.50 -1.50  2.00 -1.60 -0.50  2.00 -1.50 -0.90  2.00 -0.60 -4.50  2.00 -0.50 -4.10 -0.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  0.80  0.00 -0.80  2.00  0.00  0.00  2.00 -1.00 -0.10  2.00  0.50 -1.90  2.00  0.00 -1.50 -0.70 
- -0.70 -1.90 -1.90  2.00 -2.00 -0.90  2.00 -1.90 -1.30  2.00 -1.00 -4.90  2.00 -0.90 -4.50 -0.90 
-  1.50  0.20  0.30  2.00  0.20  0.20  2.00 -0.70  0.90  2.00  1.10 -0.90  2.00  0.30 -0.50 -0.50 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ G 
-                                           C /\  |  C 
-                                          3' <------ 5' 
-  0.50  1.30 -0.20  2.00  0.60  2.20  2.00  2.00  0.00  2.00  1.10 -0.10  2.00  2.00  0.90  1.40 
-  1.10  1.00  0.70  2.00  1.10  1.90  2.00  1.10 -1.00  2.00  0.80 -1.60  2.00  1.10 -0.10  0.30 
-  0.40  0.70 -0.50  2.00  0.50  0.70  2.00  0.50 -0.70  2.00 -0.20 -0.60  2.00  1.00  0.60  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.10  1.00 -0.40  2.00  1.50  1.30  2.00  1.20 -0.70  2.00  0.90 -1.60  2.00  1.20  0.00  0.30 
-  1.70  1.00  1.10  2.00  1.50  1.30  2.00  1.20 -0.60  2.00  1.50 -0.60  2.00  1.20  1.00  0.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.10  1.20  2.00  1.50  1.40  2.00  1.20  1.20  2.00  1.50 -0.50  2.00  1.20  1.00  0.30 
- -0.30 -0.70 -1.70  2.00  0.10  0.70  2.00  0.40 -1.60  2.00 -0.90 -1.60  2.00  0.40  0.30  0.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
- -0.50 -1.50 -1.30  2.00 -0.60 -0.20  2.00 -0.10 -0.60  2.00 -0.60 -4.10  2.00 -0.30 -2.40  0.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  0.70  0.00  0.20  2.00  0.50  0.30  2.00  0.20  0.20  2.00  0.50 -1.60  2.00  1.70  0.00  0.10 
-  0.10 -1.90 -0.90  2.00 -0.70 -0.30  2.00 -0.70 -0.80  2.00 -1.00 -4.40  2.00 -0.70 -3.00 -1.00 
-  1.50 -0.20  0.90  2.00  0.00 -0.10  2.00  0.40  0.90  2.00  1.10 -1.00  2.00  0.20  0.60  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ U 
-                                           C /\  |  A 
-                                          3' <------ 5' 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
-  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
-  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
-  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
-  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
-  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
-  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ G 
-                                           C /\  |  U 
-                                          3' <------ 5' 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
-  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
-  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
-  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
-  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
-  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
-  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ U 
-                                           C /\  |  G 
-                                          3' <------ 5' 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
-  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
-  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
-  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
-  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
-  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
-  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ A 
-                                           A /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
-  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ C 
-                                           A /\  |  G 
-                                          3' <------ 5' 
-  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
-  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
-  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
-  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
-  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
-  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
-  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ G 
-                                           A /\  |  C 
-                                          3' <------ 5' 
-  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
-  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
-  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
-  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
-  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
-  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
-  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ U 
-                                           A /\  |  A 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
-  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ G 
-                                           A /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
-  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ U 
-                                           A /\  |  G 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
-  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ A 
-                                           U /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
-  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
-  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ C 
-                                           U /\  |  G 
-                                          3' <------ 5' 
-  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
-  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
-  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
-  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
-  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ G 
-                                           U /\  |  C 
-                                          3' <------ 5' 
-  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
-  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
-  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
-  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
-  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ U 
-                                           U /\  |  A 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
-  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
-  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ G 
-                                           U /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
-  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
-  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ U 
-                                           U /\  |  G 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
-  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
-  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ A 
-                                           G /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
-  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ C 
-                                           G /\  |  G 
-                                          3' <------ 5' 
-  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
-  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
-  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
-  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
-  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
-  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
-  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ G 
-                                           G /\  |  C 
-                                          3' <------ 5' 
-  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
-  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
-  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
-  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
-  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
-  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
-  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ U 
-                                           G /\  |  A 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
-  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ G 
-                                           G /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
-  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ U 
-                                           G /\  |  G 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
-  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80
diff --git a/gtfold-mfe/data/Turner99/loop.dat b/gtfold-mfe/data/Turner99/loop.dat
deleted file mode 100644
index 927fbbd..0000000
--- a/gtfold-mfe/data/Turner99/loop.dat
+++ /dev/null
@@ -1,34 +0,0 @@
-DESTABILIZING ENERGIES BY SIZE OF LOOP (INTERPOLATE WHERE NEEDED) 
-hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges 
-SIZE         INTERNAL            BULGE            HAIRPIN 
-------------------------------------------------------- 
-1                .                3.80                . 
-2                .                2.80                . 
-3                .                3.20              5.70  
-4              1.70               3.60              5.60 
-5              1.80               4.00              5.60 
-6              2.00               4.40              5.40 
-7              2.20               4.60              5.90 
-8              2.30               4.70              5.60 
-9              2.40               4.80              6.40 
-10             2.50               4.90              6.50 
-11             2.60               5.00              6.60 
-12             2.70               5.10              6.70 
-13             2.80               5.20              6.80 
-14             2.90               5.30              6.90 
-15             3.00               5.40              6.90 
-16             3.00               5.40              7.00 
-17             3.10               5.50              7.10 
-18             3.10               5.50              7.10 
-19             3.20               5.60              7.20 
-20             3.30               5.70              7.20 
-21             3.30               5.70              7.30 
-22             3.40               5.80              7.30 
-23             3.40               5.80              7.40 
-24             3.40               5.80              7.40 
-25             3.50               5.90              7.50 
-26             3.50               5.90              7.50 
-27             3.60               6.00              7.50 
-28             3.60               6.00              7.60 
-29             3.60               6.00              7.60 
-30             3.70               6.10              7.70 
diff --git a/gtfold-mfe/data/Turner99/miscloop.dat b/gtfold-mfe/data/Turner99/miscloop.dat
deleted file mode 100644
index cd585c1..0000000
--- a/gtfold-mfe/data/Turner99/miscloop.dat
+++ /dev/null
@@ -1,42 +0,0 @@
-Miscellaneous free energy rules 
-------------------------------- 
-Extrapolation for large loops based on polymer theory 
-internal, bulge or hairpin loops > 30: dS(T)=dS(30)+param*ln(n/30) 
--->  
-1.079 
-asymmetric internal loops: the ninio equation 
-the maximum correction 
--->  
-3.00 
-the f(m) array (see Ninio for details) 
---> 
- .50  .50  .50  .50 
-multibranched loops 
-  offset,  free base penalty,  helix penalty 
--->  
-    3.40          .00                 .40 
-efn2 multibranched loops 
-   offset,  free base penalty,  helix penalty 
---> 
-     10.10         -0.30              -0.30  
-terminal AU penalty 
--->  
- 0.50 
-bonus for GGG hairpin 
--->  
--2.20 
-c hairpin slope 
--->  
-0.30 
-c hairpin intercept 
--->  
-1.60 
-c hairpin of 3 
--->  
-1.40 
-Intermolecular initiation free energy 
--->  
-4.10 
-GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) 
--->  
-1 
diff --git a/gtfold-mfe/data/Turner99/sint2.dat b/gtfold-mfe/data/Turner99/sint2.dat
deleted file mode 100644
index 3e0f630..0000000
--- a/gtfold-mfe/data/Turner99/sint2.dat
+++ /dev/null
@@ -1,101 +0,0 @@
-Data table for symetric interior loops of size 2 
-Free energies at 37 degrees for RNA 
-Data Arrangement: 
-            Y 
-    ------------------ 
-(X)  A    C    G    U   
-    ------------------ 
-        5' --> 3' 
-            X 
-           A A 
-           U U 
-            Y 
-        3' <-- 5' 
-(A)  .    .    .    .    
-(C)  .    .    .    .    
-(G)  .    .    .    .    
-(U)  .    .    .    .    
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           A A                     A C                     A G                     A U                     A G                     A U         
-           U U                     U G                     U C                     U A                     U U                     U G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
-  1.70  1.70  1.70  1.50  1.10  1.10  1.10  1.00  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.20  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           C A                     C C                     C G                     C U                     C G                     C U         
-           G U                     G G                     G C                     G A                     G U                     G G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.10  1.10  1.10  1.10  0.40 -0.40  0.40  0.40  1.10  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-  1.10  1.10  1.10  1.10  0.30  0.50  0.40  0.50  0.40  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-  1.10  1.10 -1.00  1.10 -0.10  0.40 -1.70  0.40  0.40  0.40 -1.40  0.40  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10 
-  1.10  1.10  1.10  1.10  0.40  0.00  0.40 -0.30  0.40  0.40  0.40  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G A                     G C                     G G                     G U                     G G                     G U         
-           C U                     C G                     C C                     C A                     C U                     C G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.10  1.10  1.10  1.10  0.80  0.40  0.40  0.40  0.40  0.30 -0.10  0.40  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-  1.10  1.10  1.10  1.10  0.40  0.40  0.40  0.40 -0.40  0.50  0.40  0.00  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-  1.10  1.10 -1.00  1.10  0.40  0.40 -2.10  0.40  0.40  0.40 -1.70  0.40  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10 
-  1.10  1.10  1.10  1.10  0.40  0.40  0.40 -0.70  0.40  0.50  0.40 -0.30  1.10  1.10  1.10  1.00  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U A                     U C                     U G                     U U                     U G                     U U         
-           A U                     A G                     A C                     A A                     A U                     A G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
-  1.70  1.70  1.70  1.80  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.50  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           G A                     G C                     G G                     G U                     G G                     G U         
-           U U                     U G                     U C                     U A                     U U                     U G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-            Y                       Y                       Y                       Y                       Y                       Y 
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-     A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U   
-    ------------------      ------------------      ------------------      ------------------      ------------------      ------------------ 
-        5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3' 
-            X                       X                       X                       X                       X                       X 
-           U A                     U C                     U G                     U U                     U G                     U U         
-           G U                     G G                     G C                     G A                     G U                     G G         
-            Y                       Y                       Y                       Y                       Y                       Y 
-        3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5' 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
-  1.70  1.70 -0.40  1.70  1.10  1.10 -1.00  1.10  1.10  1.10 -1.00  1.10  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70  1.70  1.70 -0.40  1.70 
-  1.70  1.70  1.70  1.70  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.10  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70  1.70 
diff --git a/gtfold-mfe/data/Turner99/sint4.dat b/gtfold-mfe/data/Turner99/sint4.dat
deleted file mode 100644
index 1939411..0000000
--- a/gtfold-mfe/data/Turner99/sint4.dat
+++ /dev/null
@@ -1,928 +0,0 @@
-Data tables for symetric interior loops of size 4 
-Free energies at 37 degrees for RNA 
-Data arrangement: 
-                                Y 
-     ---------------------------------------------------------------- 
-(X)   A   A   A   A   C   C   C   C   G   G   G   G   U   U   U   U 
-      A   C   G   U   A   C   G   U   A   C   G   U   A   C   G   U 
-     ---------------------------------------------------------------- 
-                           5' ------> 3' 
-                            A \/ \_/ A 
-                            U /\  |  U 
-                           3' <------ 5' 
-(AA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(AC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(AG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(AU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(CA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(CC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(CG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(CU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(GA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(GC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(GG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(GU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(UA)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(UC)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(UG)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-(UU)  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ A 
-                                           U /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
-  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
-  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ C 
-                                           U /\  |  G 
-                                          3' <------ 5' 
-  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
-  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
-  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
-  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
-  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ G 
-                                           U /\  |  C 
-                                          3' <------ 5' 
-  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
-  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
-  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
-  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
-  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ U 
-                                           U /\  |  A 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
-  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
-  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ G 
-                                           U /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
-  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
-  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           A \/ \_/ U 
-                                           U /\  |  G 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
-  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
-  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ A 
-                                           G /\  |  U 
-                                          3' <------ 5' 
-  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
-  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
-  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
-  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
-  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
-  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
-  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
-  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ C 
-                                           G /\  |  G 
-                                          3' <------ 5' 
-  0.50  1.10 -0.30  2.00  1.10  1.70  2.00  0.70  0.40  2.00  1.00  0.10  2.00  1.80 -0.50  1.50 
-  0.60  1.50  0.10  2.00  1.10  1.50  2.00  0.50  0.50  2.00  1.40 -0.70  2.00  1.50 -0.60  0.00 
-  0.00 -0.70 -1.60  2.00 -1.00 -0.60  2.00  0.20 -0.70  2.00  0.00 -0.80  2.00  1.20 -0.60  0.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.30  1.00 -0.70  2.00  1.00  1.00  2.00  0.00  0.70  2.00  0.90 -1.90  2.00  1.10 -1.50 -0.20 
-  2.20  1.30  0.70  2.00  1.90  1.30  2.00  0.30  0.70  2.00  1.80 -0.30  2.00  1.40 -0.20 -0.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.00  1.20  0.40  2.00  1.10  1.20  2.00  1.70  1.00  2.00  1.70 -0.70  2.00  1.20 -0.30  0.20 
- -0.20 -0.40 -1.70  2.00  0.70  1.10  2.00  0.20 -0.50  2.00  0.00 -0.90  2.00  1.20 -1.30  0.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
-  0.90  0.00  0.30  2.00 -0.10  1.00  2.00  0.00  0.60  2.00  0.90 -3.00  2.00  1.00 -2.40  0.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.00  1.20  0.40  2.00  1.10  1.20  2.00  0.20  0.50  2.00  1.70 -0.70  2.00  1.20 -0.10  0.40 
- -0.10 -1.60 -1.60  2.00 -1.60 -0.60  2.00 -1.60 -0.60  2.00 -0.70 -4.40  2.00 -0.50 -4.10 -1.00 
-  1.40  0.30  0.50  2.00  0.30  0.30  2.00  0.10  1.40  2.00  1.20 -1.00  2.00  0.30  0.10  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ G 
-                                           G /\  |  C 
-                                          3' <------ 5' 
-  1.30  1.20  0.30  2.00  1.60  2.10  2.00  1.90  0.30  2.00  1.00 -0.40  2.00  1.90  1.10  1.40 
-  1.60  1.50  0.60  2.00  2.00  1.80  2.00  1.70  0.60  2.00  1.40 -1.10  2.00  1.70  0.40  0.80 
-  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.20  1.10  0.20  2.00  1.50  1.40  2.00  1.20  0.20  2.00  0.90 -1.50  2.00  1.20  0.00  0.30 
-  2.10  1.40  1.50  2.00  1.80  1.70  2.00  1.50  1.50  2.00  1.80 -0.20  2.00  1.50  1.30  0.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
-  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
-  1.10  0.00  0.90  2.00  0.40  1.30  2.00  1.10  0.90  2.00  0.90 -2.60  2.00  1.10 -1.10  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
- -0.40 -1.50 -0.60  2.00 -1.10 -0.20  2.00 -0.40 -0.60  2.00 -0.70 -4.20  2.00 -0.40 -2.60 -0.50 
-  1.40  0.30  1.30  2.00  0.80  0.60  2.00  0.50  1.30  2.00  1.20 -0.50  2.00  0.50  1.10 -0.40 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ U 
-                                           G /\  |  A 
-                                          3' <------ 5' 
-  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
-  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
-  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
-  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
-  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
-  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
-  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
-  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ G 
-                                           G /\  |  U 
-                                          3' <------ 5' 
-  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
-  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
-  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
-  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
-  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
-  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
-  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
-  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           C \/ \_/ U 
-                                           G /\  |  G 
-                                          3' <------ 5' 
-  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
-  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
-  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
-  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
-  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
-  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
-  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
-  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ A 
-                                           C /\  |  U 
-                                          3' <------ 5' 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
-  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
-  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
-  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
-  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
-  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
-  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ C 
-                                           C /\  |  G 
-                                          3' <------ 5' 
-  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
-  1.20  0.90 -0.80  2.00  0.90  0.90  2.00  0.00 -0.20  2.00  0.80 -2.00  2.00  1.00 -1.60  0.20 
-  0.10 -0.10 -1.90  2.00 -0.20  0.90  2.00 -0.10 -1.30  2.00 -0.20 -1.30  2.00  0.90 -0.90  0.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.20  1.00 -0.80  2.00  0.90  1.00  2.00  0.00 -0.10  2.00  0.90 -1.90  2.00  1.00 -1.50  0.20 
-  1.80  1.00  0.20  2.00  0.90  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.00 -0.50  0.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.00  0.30  2.00  1.00  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.10 -0.50  0.30 
- -0.50 -0.80 -2.60  2.00 -0.80  0.20  2.00 -0.80 -1.90  2.00 -0.90 -1.90  2.00  0.30 -1.50  0.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
- -0.30 -1.50 -1.50  2.00 -1.60 -0.50  2.00 -1.50 -0.90  2.00 -0.60 -4.50  2.00 -0.50 -4.10 -0.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  0.80  0.00 -0.80  2.00  0.00  0.00  2.00 -1.00 -0.10  2.00  0.50 -1.90  2.00  0.00 -1.50 -0.70 
- -0.70 -1.90 -1.90  2.00 -2.00 -0.90  2.00 -1.90 -1.30  2.00 -1.00 -4.90  2.00 -0.90 -4.50 -0.90 
-  1.50  0.20  0.30  2.00  0.20  0.20  2.00 -0.70  0.90  2.00  1.10 -0.90  2.00  0.30 -0.50 -0.50 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ G 
-                                           C /\  |  C 
-                                          3' <------ 5' 
-  0.50  1.30 -0.20  2.00  0.60  2.20  2.00  2.00  0.00  2.00  1.10 -0.10  2.00  2.00  0.90  1.40 
-  1.10  1.00  0.70  2.00  1.10  1.90  2.00  1.10 -1.00  2.00  0.80 -1.60  2.00  1.10 -0.10  0.30 
-  0.40  0.70 -0.50  2.00  0.50  0.70  2.00  0.50 -0.70  2.00 -0.20 -0.60  2.00  1.00  0.60  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.10  1.00 -0.40  2.00  1.50  1.30  2.00  1.20 -0.70  2.00  0.90 -1.60  2.00  1.20  0.00  0.30 
-  1.70  1.00  1.10  2.00  1.50  1.30  2.00  1.20 -0.60  2.00  1.50 -0.60  2.00  1.20  1.00  0.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.10  1.20  2.00  1.50  1.40  2.00  1.20  1.20  2.00  1.50 -0.50  2.00  1.20  1.00  0.30 
- -0.30 -0.70 -1.70  2.00  0.10  0.70  2.00  0.40 -1.60  2.00 -0.90 -1.60  2.00  0.40  0.30  0.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
- -0.50 -1.50 -1.30  2.00 -0.60 -0.20  2.00 -0.10 -0.60  2.00 -0.60 -4.10  2.00 -0.30 -2.40  0.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  0.70  0.00  0.20  2.00  0.50  0.30  2.00  0.20  0.20  2.00  0.50 -1.60  2.00  1.70  0.00  0.10 
-  0.10 -1.90 -0.90  2.00 -0.70 -0.30  2.00 -0.70 -0.80  2.00 -1.00 -4.40  2.00 -0.70 -3.00 -1.00 
-  1.50 -0.20  0.90  2.00  0.00 -0.10  2.00  0.40  0.90  2.00  1.10 -1.00  2.00  0.20  0.60  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ U 
-                                           C /\  |  A 
-                                          3' <------ 5' 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
-  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
-  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
-  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
-  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
-  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
-  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ G 
-                                           C /\  |  U 
-                                          3' <------ 5' 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
-  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
-  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
-  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
-  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
-  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
-  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ U 
-                                           C /\  |  G 
-                                          3' <------ 5' 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
-  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
-  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
-  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
-  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
-  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
-  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ A 
-                                           A /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
-  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ C 
-                                           A /\  |  G 
-                                          3' <------ 5' 
-  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
-  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
-  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
-  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
-  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
-  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
-  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ G 
-                                           A /\  |  C 
-                                          3' <------ 5' 
-  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
-  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
-  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
-  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
-  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
-  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
-  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ U 
-                                           A /\  |  A 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
-  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ G 
-                                           A /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
-  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ U 
-                                           A /\  |  G 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
-  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ A 
-                                           U /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
-  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
-  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ C 
-                                           U /\  |  G 
-                                          3' <------ 5' 
-  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
-  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
-  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
-  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
-  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ G 
-                                           U /\  |  C 
-                                          3' <------ 5' 
-  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
-  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
-  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
-  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
-  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ U 
-                                           U /\  |  A 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
-  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
-  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ G 
-                                           U /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
-  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
-  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           G \/ \_/ U 
-                                           U /\  |  G 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
-  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
-  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ A 
-                                           G /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
-  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ C 
-                                           G /\  |  G 
-                                          3' <------ 5' 
-  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
-  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
-  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
-  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
-  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
-  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
-  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
-  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ G 
-                                           G /\  |  C 
-                                          3' <------ 5' 
-  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
-  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
-  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
-  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
-  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
-  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
-  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
-  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ U 
-                                           G /\  |  A 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
-  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ G 
-                                           G /\  |  U 
-                                          3' <------ 5' 
-  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
-  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
-  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
-  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
-  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
-  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
-                                               Y 
-   --------------------------------------------------------------------------------------------- 
-    A     A     A     A     C     C     C     C     G     G     G     G     U     U     U     U   
-    A     C     G     U     A     C     G     U     A     C     G     U     A     C     G     U   
-   --------------------------------------------------------------------------------------------- 
-                                          5' ------> 3' 
-                                           U \/ \_/ U 
-                                           G /\  |  G 
-                                          3' <------ 5' 
-  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
-  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
-  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
-  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
-  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
-  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
-  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
-  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
diff --git a/gtfold-mfe/data/Turner99/stack.dat b/gtfold-mfe/data/Turner99/stack.dat
deleted file mode 100644
index ba2d3f5..0000000
--- a/gtfold-mfe/data/Turner99/stack.dat
+++ /dev/null
@@ -1,63 +0,0 @@
-Data Arangement: 
-                 Y           
-         ------------------  
-     (X)  A    C    G    U   
-         ------------------  
-             5' ==> 3'       
-                AX           
-                AY 
-             3' <== 5'       
-     (A)   .     .     .     .   
-     (C)   .     .     .     .   
-     (G)   .     .     .     .   
-     (U) -0.70 -0.10 -0.70 -0.10 
--------------------------------- 
-STACKING ENERGIES : 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         AX                      AX                      AX                      AX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .     .     .     .     .     .     .     .     .   -0.90 
-   .     .     .     .     .     .     .     .     .     .     .     .     .     .   -2.20   .   
-   .     .     .     .     .     .     .     .     .     .     .     .     .   -2.10   .   -0.60 
-   .     .     .     .     .     .     .     .     .     .     .     .   -1.10   .   -1.40   .    
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         CX                      CX                      CX                      CX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .     .     .     .     .   -2.10   .     .     .     .   
-   .     .     .     .     .     .     .     .     .     .   -3.30   .     .     .     .     .    
-   .     .     .     .     .     .     .     .     .   -2.40   .   -1.40   .     .     .     .   
-   .     .     .     .     .     .     .     .   -2.10   .   -2.10   .     .     .     .     .    
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         GX                      GX                      GX                      GX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .   -2.40   .     .     .     .     .     .     .   -1.30 
-   .     .     .     .     .     .   -3.40   .     .     .     .     .     .     .   -2.50   .   
-   .     .     .     .     .   -3.30   .   -1.50   .     .     .     .     .   -2.10   .   -0.50  
-   .     .     .     .   -2.20   .   -2.50   .     .     .     .     .   -1.40   .    1.30   .     
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         UX                      UX                      UX                      UX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -1.30   .     .     .     .     .     .     .   -1.00   .     .     .     .   
-   .     .   -2.40   .     .     .     .     .     .     .   -1.50   .     .     .     .     .    
-   .   -2.10   .   -1.00   .     .     .     .     .   -1.40   .    0.30   .     .     .     .   
- -0.90   .   -1.30   .     .     .     .     .   -0.60   .   -0.50   .     .     .     .     .
diff --git a/gtfold-mfe/data/Turner99/tloop.dat b/gtfold-mfe/data/Turner99/tloop.dat
deleted file mode 100644
index ad64bf4..0000000
--- a/gtfold-mfe/data/Turner99/tloop.dat
+++ /dev/null
@@ -1,32 +0,0 @@
- Seq    Energy 
- ------------- 
- GGGGAC -3.00 
- GGUGAC -3.00 
- CGAAAG -3.00 
- GGAGAC -3.00 
- CGCAAG -3.00 
- GGAAAC -3.00 
- CGGAAG -3.00 
- CUUCGG -3.00 
- CGUGAG -3.00 
- CGAAGG -2.50 
- CUACGG -2.50 
- GGCAAC -2.50 
- CGCGAG -2.50 
- UGAGAG -2.50 
- CGAGAG -2.00 
- AGAAAU -2.00 
- CGUAAG -2.00 
- CUAACG -2.00 
- UGAAAG -2.00 
- GGAAGC -1.50 
- GGGAAC -1.50 
- UGAAAA -1.50 
- AGCAAU -1.50 
- AGUAAU -1.50 
- CGGGAG -1.50 
- AGUGAU -1.50 
- GGCGAC -1.50 
- GGGAGC -1.50 
- GUGAAC -1.50 
- UGGAAA -1.50 
diff --git a/gtfold-mfe/data/Turner99/triloop.dat b/gtfold-mfe/data/Turner99/triloop.dat
deleted file mode 100644
index 75c3bfc..0000000
--- a/gtfold-mfe/data/Turner99/triloop.dat
+++ /dev/null
@@ -1,2 +0,0 @@
- Seq    Energy 
- ------------- 
diff --git a/gtfold-mfe/data/Turner99/tstack.dat b/gtfold-mfe/data/Turner99/tstack.dat
deleted file mode 100644
index 97a4115..0000000
--- a/gtfold-mfe/data/Turner99/tstack.dat
+++ /dev/null
@@ -1,63 +0,0 @@
-Data Arangement: 
-                 Y           
-         ------------------  
-     (X)  A    C    G    U   
-         ------------------  
-             5' ==> 3'       
-                AX           
-                AY 
-             3' <== 5'       
-     (A)   .     .     .     .   
-     (C)   .     .     .     .   
-     (G)   .     .     .     .   
-     (U) -0.70 -0.10 -0.70 -0.10 
--------------------------------- 
-STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         AX                      AX                      AX                      AX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -1.00   .     .     .   -1.00   .     .     .   -2.20 -0.80 -1.00 -0.80   .  
-   .     .   -1.50   .     .     .   -1.50   .     .     .   -2.70   .   -0.60 -0.70   .   -0.70 
-   .   -1.50   .   -1.00   .   -1.50   .   -1.00   .   -2.70   .   -2.20 -0.80   .   -0.80   .  
- -1.00   .   -1.50   .   -1.00   .   -1.50   .   -2.20   .   -2.70   .     .   -0.80   .   -0.80 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         CX                      CX                      CX                      CX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -1.00   .     .     .   -1.00 -1.50 -1.50 -1.40   .     .     .     .   -1.00 
-   .     .   -1.50   .     .     .   -1.50   .   -1.00 -1.10   .   -0.80   .     .   -1.50   . 
-   .   -1.50   .   -1.00   .   -1.50   .   -1.00 -1.40   .   -1.60   .     .   -1.50   .   -1.00 
- -1.00   .   -1.50   .   -1.00   .   -1.50   .     .   -1.40   .   -1.20 -1.00   .   -1.50   . 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         GX                      GX                      GX                      GX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -2.20 -1.10 -1.50 -1.30   .     .     .     .   -1.00 -0.30 -1.00 -0.80   .  
-   .     .   -2.70   .   -1.10 -0.70   .   -0.50   .     .   -1.50   .   -0.60 -0.70   .   -0.70 
-   .   -2.70   .   -2.20 -1.60   .   -1.40   .     .   -1.50   .   -1.00 -0.60   .   -0.80   .  
- -2.20   .   -2.70   .     .   -1.00   .   -0.70 -1.00   .   -1.50   .     .   -0.80   .   -0.80 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         UX                      UX                      UX                      UX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
- -1.00 -0.80 -1.10   .     .     .     .   -1.00 -1.00 -0.80 -1.10   .     .     .     .   -2.00 
- -0.70 -0.60   .   -0.50   .     .   -1.50   .   -0.70 -0.60   .   -0.50   .     .   -2.50   . 
- -1.10   .   -1.20   .     .   -1.50   .   -1.00 -0.50   .   -0.80 -0.80   .   -2.50   .   -2.00 
-   .   -0.60   .   -0.50 -1.00   .   -1.50   .     .   -0.60 -1.10 -0.50 -2.00   .   -2.50   .   
diff --git a/gtfold-mfe/data/Turner99/tstackcoax.dat b/gtfold-mfe/data/Turner99/tstackcoax.dat
deleted file mode 100644
index b90d0bc..0000000
--- a/gtfold-mfe/data/Turner99/tstackcoax.dat
+++ /dev/null
@@ -1,63 +0,0 @@
-Data Arangement: 
-                 Y           
-         ------------------  
-     (X)  A    C    G    U   
-         ------------------  
-             5' ==> 3'       
-                AX           
-                AY 
-             3' <== 5'       
-     (A)   .     .     .     .   
-     (C)   .     .     .     .   
-     (G)   .     .     .     .   
-     (U) -0.70 -0.10 -0.70 -0.10 
--------------------------------- 
-STACKING ENERGIES : COAXIAL STACKING
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         AX                      AX                      AX                      AX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -1.00   .     .     .   -0.70   .     .     .   -1.10 -0.80 -1.00 -0.80 -0.40 
-   .     .   -1.10   .     .     .   -1.10   .     .     .   -1.60   .   -0.60 -0.70 -1.70 -0.70 
-   .   -1.50   .   -1.00   .   -1.00   .   -0.70   .   -1.40   .   -0.50 -0.80 -1.60 -0.80 -0.10 
- -0.80   .   -0.30   .   -0.60   .   -0.60   .   -0.80   .   -0.60   .   -0.60 -0.80 -0.90 -0.80 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         CX                      CX                      CX                      CX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -0.80   .     .     .   -0.60 -1.50 -1.50 -1.40 -1.60   .     .     .   -0.60 
-   .     .   -1.50   .     .     .   -0.70   .   -1.00 -1.10 -2.80 -0.80   .     .   -1.00   . 
-   .   -1.50   .   -0.80   .   -1.10   .   -0.60 -1.40 -1.90 -1.60 -0.90   .   -1.40   .   -0.60 
- -1.00   .   -1.00   .   -0.70   .   -0.70   .   -1.60 -1.40 -1.60 -1.20 -0.80   .   -0.80   . 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         GX                      GX                      GX                      GX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -1.10 -1.10 -1.50 -1.30 -1.90   .     .     .   -1.20 -0.30 -1.00 -0.80 -0.80 
-   .     .   -1.30   .   -1.10 -0.70 -2.90 -0.50   .     .   -1.40   .   -0.60 -0.70 -2.00 -0.70 
-   .   -1.40   .   -1.10 -1.60 -2.80 -1.40 -1.00   .   -1.60   .   -0.80 -0.60 -1.60 -0.80  0.00 
- -0.80   .   -0.80   .   -1.70 -1.00 -2.00 -0.70 -0.80   .   -0.80   .   -0.90 -0.80  1.80 -0.80 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         UX                      UX                      UX                      UX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
- -1.00 -0.80 -1.10 -0.80   .     .     .   -0.50 -1.00 -0.80 -1.10 -0.50   .     .     .   -0.50 
- -0.70 -0.60 -1.90 -0.50   .     .   -0.50   .   -0.70 -0.60 -1.00 -0.50   .     .   -0.70   . 
- -1.10 -1.60 -1.20 -0.50   .   -0.80   .   -0.50 -0.50 -0.90 -0.80  0.80   .   -1.20   .   -0.50 
- -0.40 -0.60 -0.80 -0.50 -0.70   .   -0.70   .   -0.10 -0.60 -0.00 -0.50 -0.80   .   -0.80   .  
diff --git a/gtfold-mfe/data/Turner99/tstackh.dat b/gtfold-mfe/data/Turner99/tstackh.dat
deleted file mode 100644
index 6959647..0000000
--- a/gtfold-mfe/data/Turner99/tstackh.dat
+++ /dev/null
@@ -1,63 +0,0 @@
-Data Arangement: 
-                 Y           
-         ------------------  
-     (X)  A    C    G    U   
-         ------------------  
-             5' ==> 3'       
-                AX           
-                AY 
-             3' <== 5'       
-     (A)   .     .     .     .   
-     (C)   .     .     .     .   
-     (G)   .     .     .     .   
-     (U) -0.70 -0.10 -0.70 -0.10 
--------------------------------- 
-STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         AX                      AX                      AX                      AX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .     .     .     .     .     .   -0.30 -0.50 -0.30 -0.30 
-   .     .     .     .     .     .     .     .     .     .     .     .   -0.10 -0.20 -1.50 -0.20 
-   .     .     .     .     .     .     .     .     .     .     .     .   -1.10 -1.20 -0.20  0.20 
-   .     .     .     .     .     .     .     .     .     .     .     .   -0.30 -0.30 -0.60 -1.10 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         CX                      CX                      CX                      CX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .     .   -1.50 -1.50 -1.40 -1.80   .     .     .     .  
-   .     .     .     .     .     .     .     .   -1.00 -0.90 -2.90 -0.80   .     .     .     . 
-   .     .     .     .     .     .     .     .   -2.20 -2.00 -1.60 -1.10   .     .     .     .  
-   .     .     .     .     .     .     .     .   -1.70 -1.40 -1.80 -2.00   .     .     .     . 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         GX                      GX                      GX                      GX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .   -1.10 -1.50 -1.30 -2.10   .     .     .     .    0.20 -0.50 -0.30 -0.30 
-   .     .     .     .   -1.10 -0.70 -2.40 -0.50   .     .     .     .   -0.10 -0.20 -1.50 -0.20 
-   .     .     .     .   -2.40 -2.90 -1.40 -1.20   .     .     .     .   -0.90 -1.10 -0.30  0.00 
-   .     .     .     .   -1.90 -1.00 -2.20 -1.50   .     .     .     .   -0.30 -0.30 -0.40 -1.10 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         UX                      UX                      UX                      UX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
- -0.50 -0.30 -0.60 -0.50   .     .     .     .   -0.50 -0.30 -0.60 -0.50   .     .     .     .  
- -0.20 -0.10 -1.20 -0.00   .     .     .     .   -0.20 -0.10 -1.70  0.00   .     .     .     . 
- -1.40 -1.20 -0.70 -0.20   .     .     .     .   -0.80 -1.20 -0.30 -0.70   .     .     .     .  
- -0.30 -0.10 -0.50 -0.80   .     .     .     .   -0.60 -0.10 -0.60 -0.80   .     .     .     . 
diff --git a/gtfold-mfe/data/Turner99/tstacki.dat b/gtfold-mfe/data/Turner99/tstacki.dat
deleted file mode 100644
index bf5d98c..0000000
--- a/gtfold-mfe/data/Turner99/tstacki.dat
+++ /dev/null
@@ -1,63 +0,0 @@
-Data Arangement: 
-                 Y           
-         ------------------  
-     (X)  A    C    G    U   
-         ------------------  
-             5' ==> 3'       
-                AX           
-                AY 
-             3' <== 5'       
-     (A)   .     .     .     .   
-     (C)   .     .     .     .   
-     (G)   .     .     .     .   
-     (U) -0.70 -0.10 -0.70 -0.10 
--------------------------------- 
-STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         AX                      AX                      AX                      AX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .     .     .     .     .     .    0.70  0.70 -0.40  0.70 
-   .     .     .     .     .     .     .     .     .     .     .     .    0.70  0.70  0.70  0.70 
-   .     .     .     .     .     .     .     .     .     .     .     .   -0.40  0.70  0.70  0.70 
-   .     .     .     .     .     .     .     .     .     .     .     .    0.70  0.70  0.70  0.00 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         CX                      CX                      CX                      CX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .     .     .     .     .   -0.00 -0.00 -1.10 -0.00   .     .     .     .  
-   .     .     .     .     .     .     .     .   -0.00 -0.00 -0.00 -0.00   .     .     .     . 
-   .     .     .     .     .     .     .     .   -1.10 -0.00 -0.00 -0.00   .     .     .     .  
-   .     .     .     .     .     .     .     .   -0.00 -0.00 -0.00 -0.70   .     .     .     . 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         GX                      GX                      GX                      GX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .     .   -0.00 -0.00 -1.10 -0.00   .     .     .     .    0.70  0.70 -0.40  0.70 
-   .     .     .     .   -0.00 -0.00 -0.00 -0.00   .     .     .     .    0.70  0.70  0.70  0.70 
-   .     .     .     .   -1.10 -0.00 -0.00 -0.00   .     .     .     .   -0.40  0.70  0.70  0.70 
-   .     .     .     .   -0.00 -0.00 -0.00 -0.70   .     .     .     .    0.70  0.70  0.70  0.00 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         UX                      UX                      UX                      UX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-  0.70  0.70 -0.40  0.70   .     .     .     .    0.70  0.70 -0.40  0.70   .     .     .     .  
-  0.70  0.70  0.70  0.70   .     .     .     .    0.70  0.70  0.70  0.70   .     .     .     . 
- -0.40  0.70  0.70  0.70   .     .     .     .   -0.40  0.70  0.70  0.70   .     .     .     .  
-  0.70  0.70  0.70  0.00   .     .     .     .    0.70  0.70  0.70  0.00   .     .     .     . 
diff --git a/gtfold-mfe/data/Turner99/tstackm.dat b/gtfold-mfe/data/Turner99/tstackm.dat
deleted file mode 100644
index f38c845..0000000
--- a/gtfold-mfe/data/Turner99/tstackm.dat
+++ /dev/null
@@ -1,63 +0,0 @@
-Data Arangement: 
-                 Y           
-         ------------------  
-     (X)  A    C    G    U   
-         ------------------  
-             5' ==> 3'       
-                AX           
-                AY 
-             3' <== 5'       
-     (A)   .     .     .     .   
-     (C)   .     .     .     .   
-     (G)   .     .     .     .   
-     (U) -0.70 -0.10 -0.70 -0.10 
--------------------------------- 
-STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         AX                      AX                      AX                      AX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -1.00   .     .     .   -1.00   .     .     .   -2.20 -0.80 -1.00 -0.80 -0.90 
-   .     .   -1.50   .     .     .   -1.50   .     .     .   -2.70   .   -0.60 -0.70 -2.20 -0.70 
-   .   -1.50   .   -1.00   .   -1.50   .   -1.00   .   -2.70   .   -2.20 -0.80 -2.10 -0.80 -0.80 
- -1.00   .   -1.50   .   -1.00   .   -1.50   .   -2.20   .   -2.70   .   -1.10 -0.80 -1.10 -0.80 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         CX                      CX                      CX                      CX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -1.00   .     .     .   -1.00 -1.70 -1.70 -1.70 -1.70   .     .     .   -1.00 
-   .     .   -1.50   .     .     .   -1.50   .   -1.00 -1.10 -3.30 -0.80   .     .   -1.50   . 
-   .   -1.50   .   -1.00   .   -1.50   .   -1.00 -1.70 -2.40 -1.70 -1.70   .   -1.50   .   -1.00 
- -1.00   .   -1.50   .   -1.00   .   -1.50   .   -1.60 -1.40 -1.60 -1.20 -1.00   .   -1.50   . 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         GX                      GX                      GX                      GX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
-   .     .     .   -2.20 -1.10 -1.50 -1.30 -1.90   .     .     .   -1.00 -0.80 -1.00 -0.80 -1.30 
-   .     .   -2.70   .   -1.10 -0.70 -3.40 -0.50   .     .   -1.50   .   -0.60 -0.70 -2.50 -0.70 
-   .   -2.70   .   -2.20 -1.60 -3.30 -1.40 -1.30   .   -1.50   .   -1.00 -0.80 -2.10 -0.80 -0.80 
- -2.20   .   -2.70   .   -1.70 -1.00 -2.00 -0.70 -1.00   .   -1.50   .   -1.40 -0.80  1.30 -0.80 
-          Y                       Y                       Y                       Y 
-  ------------------      ------------------      ------------------      ------------------   
-   A    C    G    U        A    C    G    U        A    C    G    U        A    C    G    U  
-  ------------------      ------------------      ------------------      ------------------   
-      5' --> 3'               5' --> 3'               5' --> 3'               5' --> 3'     
-         UX                      UX                      UX                      UX 
-         AY                      CY                      GY                      UY 
-      3' <-- 5'               3' <-- 5'               3' <-- 5'               3' <-- 5'   
- -1.00 -0.80 -1.10 -1.30   .     .     .   -1.00 -1.00 -0.80 -1.10 -1.00   .     .     .   -2.00 
- -0.70 -0.60 -2.40 -0.50   .     .   -1.50   .   -0.70 -0.60 -1.50 -0.50   .     .   -2.50   . 
- -1.10 -2.10 -1.20 -1.00   .   -1.50   .   -1.00 -0.70 -1.40 -0.80  0.30   .   -2.50   .   -2.00 
- -0.90 -0.60 -1.40 -0.50 -1.00   .   -1.50   .   -0.50 -0.60 -0.50 -0.50 -2.00   .   -2.50   . 

From cbaa6e8a13f09b8ff14fbbdd5fad235d8fe474e4 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Mon, 20 Jun 2011 11:23:00 -0400
Subject: [PATCH 161/282] rmeoved .dat entries

---
 gtfold-mfe/data/Turner99/Makefile.am | 22 +---------------------
 gtfold-mfe/data/Turner99/Makefile.in | 24 ++----------------------
 2 files changed, 3 insertions(+), 43 deletions(-)

diff --git a/gtfold-mfe/data/Turner99/Makefile.am b/gtfold-mfe/data/Turner99/Makefile.am
index cb09a05..c8cf6c6 100644
--- a/gtfold-mfe/data/Turner99/Makefile.am
+++ b/gtfold-mfe/data/Turner99/Makefile.am
@@ -15,27 +15,7 @@ gtfold_data_DATA = \
 	tloop.DAT\
 	tstackh.DAT\
 	tstacki.DAT\
-	tstackm.DAT\
-	stack.dat\
-	miscloop.dat\
-	dangle.dat\
-	loop.dat\
-	asint1x2.dat\
-	coaxial.dat\
-	coaxstack.dat\
-	int11.dat\
-	int21.dat\
-	int22.dat\
-	sint2.dat\
-	sint4.dat\
-	tloop.dat\
-	triloop.dat\
-	tstack.dat\
-	tstackcoax.dat\
-	tstackh.dat\
-	tstacki.dat\
-	tstackm.dat
-
+	tstackm.DAT
 
 
 EXTRA_DIST = $(gtfold_data_DATA)
diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in
index d042a79..084882b 100644
--- a/gtfold-mfe/data/Turner99/Makefile.in
+++ b/gtfold-mfe/data/Turner99/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# Makefile.in generated by automake 1.11 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
@@ -112,7 +112,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 SET_MAKE = @SET_MAKE@
@@ -188,26 +187,7 @@ gtfold_data_DATA = \
 	tloop.DAT\
 	tstackh.DAT\
 	tstacki.DAT\
-	tstackm.DAT\
-	stack.dat\
-	miscloop.dat\
-	dangle.dat\
-	loop.dat\
-	asint1x2.dat\
-	coaxial.dat\
-	coaxstack.dat\
-	int11.dat\
-	int21.dat\
-	int22.dat\
-	sint2.dat\
-	sint4.dat\
-	tloop.dat\
-	triloop.dat\
-	tstack.dat\
-	tstackcoax.dat\
-	tstackh.dat\
-	tstacki.dat\
-	tstackm.dat
+	tstackm.DAT
 
 EXTRA_DIST = $(gtfold_data_DATA)
 CLEANFILES = *~

From d2f0de250f17a19dd2fae5887c20ea9b8d92af4f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Tue, 21 Jun 2011 13:51:17 -0400
Subject: [PATCH 162/282] fix for contact dist

---
 gtfold-mfe/src/constraints.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index c491068..08f67bc 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -494,7 +494,7 @@ int canStack(int i, int j) {
 int withinCD(int i, int j){
 	//ZS: This function returns 1 if i and j are within the required contact distance from each other. 
 	if (LIMIT_DISTANCE){
-		return (j-i>=contactDistance);
+		return (j-i<=contactDistance);
 	}
 	else return 1;
 }

From 4da0d65ff0c7adea819294bf54dc4e5b1b283064 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Tue, 21 Jun 2011 13:52:22 -0400
Subject: [PATCH 163/282] fixed subopt, change to take value kCal

---
 gtfold-mfe/include/options.h          |   2 +-
 gtfold-mfe/include/subopt_traceback.h |   8 +-
 gtfold-mfe/src/main.cc                |   2 +-
 gtfold-mfe/src/options.cc             |   6 +-
 gtfold-mfe/src/subopt_traceback.cc    | 128 ++++++++++++++------------
 5 files changed, 76 insertions(+), 70 deletions(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 0862b03..46b3a3a 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -27,7 +27,7 @@ extern string shapeFile;
 extern string outputFile;
 extern string paramDir;
 
-extern int suboptDelta;
+extern float suboptDelta;
 extern int nThreads;
 
 extern bool LIMIT_DISTANCE;
diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h
index a02839e..cccf44e 100644
--- a/gtfold-mfe/include/subopt_traceback.h
+++ b/gtfold-mfe/include/subopt_traceback.h
@@ -217,10 +217,10 @@ void push_to_gstack(ps_stack_t & gs, const ps_t& v);
 
 ss_map_t subopt_traceback(int len, int gap);
 
-void traceV(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); 
-void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs, int energy);
-void traceW(int i, int j, ps_t & ps, ps_stack_t & gs, int energy);
-void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs, int energy);
+void traceV(int i, int j, ps_t & ps, ps_stack_t & gs); 
+void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs);
+void traceW(int i, int j, ps_t & ps, ps_stack_t & gs);
+void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs);
 void traceWM(ps_t& ps, ps_map_t& filter);
 
 #endif
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 87a4c1c..49b3676 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -235,7 +235,7 @@ int main(int argc, char** argv) {
 	
 	if (SUBOPT_ENABLED) {	
 		t1 = get_seconds();
-		ss_map_t subopt_data = subopt_traceback(seq.length(), suboptDelta);
+		ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta);
 		t1 = get_seconds() - t1;
 		printf("Subopt traceback running time: %9.6f seconds\n\n", t1);
 		
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 1545f60..a37ee9a 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -23,7 +23,7 @@ string shapeFile = "";
 string paramDir = "Turner99"; // default value
 
 
-int suboptDelta = -1;
+float suboptDelta = 0.0;
 int nThreads = -1;
 int contactDistance = -1;
 
@@ -118,7 +118,7 @@ void parse_options(int argc, char** argv) {
 			} else if(strcmp(argv[i], "--subopt") == 0) {
 				SUBOPT_ENABLED = true;
 				if(i < argc)
-					suboptDelta = atoi(argv[++i]);
+					suboptDelta = atof(argv[++i]);
 				else
 					help();
 			}
@@ -196,7 +196,7 @@ void printRunConfiguration(string seq) {
 	}
 
 	if (SUBOPT_ENABLED) {
-		printf("+ calculating suboptimal structures within %d kcal/mol of MFE\n", suboptDelta);
+		printf("+ calculating suboptimal structures within %f kcal/mol of MFE\n", suboptDelta);
 		standardRun = false;
 	}
 
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index 6375f2e..1cfe6d5 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -30,7 +30,9 @@
 
 const char* lstr[] = {"W", "V", "VBI", "VM", "WM"};
 
-void (*trace_func[5]) (int i, int j, ps_t& ps, ps_stack_t& gs, int energy);
+void (*trace_func[5]) (int i, int j, ps_t& ps, ps_stack_t& gs);
+int delta = 0;
+int mfe = INFINITY_;
 
 void print_stack(ps_stack_t temp)
 {	
@@ -45,15 +47,14 @@ void print_stack(ps_stack_t temp)
 	std::cout << "}\n";
 }
 
-void process(ss_map_t& subopt_data, int energy, int len)
+void process(ss_map_t& subopt_data, int len)
 {
 	int count = 0 ;
 	ps_stack_t gstack;
 
-	// initialize the partial structure
-	// segment stack = {[1,n]}, label = W, list_bp = {} 
+	// initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} 
 	ps_t first(0, len);
-	first.push(segment(5, len, lW, W[len]));	
+	first.push(segment(1, len, lW, W[len]));	
 	gstack.push(first); // initialize the partial structure stacka
 
 	while (1)
@@ -65,11 +66,17 @@ void process(ss_map_t& subopt_data, int energy, int len)
 
 		if (ps.empty()) 
 		{
-			//std::cout << ps.str << " dG =" << ps.ae_ << std::endl;
-			if (subopt_data.find(ps.str) == subopt_data.end())
+			ss_map_t::iterator it = subopt_data.find(ps.str); 
+			if ( it == subopt_data.end())
 			{
 				subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
 				count++;
+			} else 
+			{
+				int energy = it->second;
+				if (ps.ae_ < energy && (ps.ae_ >= mfe && ps.ae_ >= mfe + delta)) {
+					subopt_data[it->first] = ps.ae_;					
+				}		
 			}
 			continue;
 		}	
@@ -79,12 +86,13 @@ void process(ss_map_t& subopt_data, int energy, int len)
 			ps.pop();
 			size_t s1 = gstack.size();
 
-			if (smt.j_ - smt.i_ >=4)
+			if (smt.j_ - smt.i_ >= TURN)
 			{
-				(*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack, energy);
+				(*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack);
 			}
-
-			if (gstack.size() == s1 && ps.total() == energy)
+			
+			// discard this segment, use remaining ones
+			if (gstack.size() == s1 && ps.total() <= mfe + delta)
 			{
 				ps_t ps1(ps);
 				gstack.push(ps1);
@@ -93,31 +101,27 @@ void process(ss_map_t& subopt_data, int energy, int len)
 	}
 }
 
-ss_map_t subopt_traceback(int len, int delta)
+ss_map_t subopt_traceback(int len, int _delta)
 {
 	trace_func[0] = traceW;
 	trace_func[1] = traceV;
-	trace_func[2] = traceVBI;
 	trace_func[3] = traceVM;
-	//trace_func[4] = traceWM;
 
-	int mfe = W[len];
-	int level = 0; 
+	mfe = W[len];
+	delta = _delta;
 
 	ss_map_t subopt_data;
-
-	for (level = mfe; level <= mfe + delta; level += 10)
-		process(subopt_data, level, len);			
+	process(subopt_data, len);
 
 	return subopt_data;
 }
 
-void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
+void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack)
 {
 	// Hairpin Loop
-	if (eH(i,j) + ps.total()  == energy )
+	if (eH(i,j) + ps.total()  <= mfe + delta )
 	{
-		//	std::cout << "Hairpin " << i  << ' ' << j << std::endl;
+		//std::cout << "Hairpin " << i  << ' ' << j << std::endl;
 		ps_t ps1(ps); 
 		ps1.accumulate(eH(i,j));
 		ps1.update(i, j, '(', ')');
@@ -125,7 +129,7 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 	}
 
 	// Stack
-	if (eS(i, j) + V(i+1, j-1) + ps.total() == energy)
+	if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta)
 	{
 		//	std::cout << "Stack " << i  << ' ' << j << std::endl;
 		ps_t ps1(ps);
@@ -136,19 +140,20 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 	}
 
 	// Internal Loop
-	if (VBI(i,j) + ps.total() == energy )
+	if (VBI(i,j) + ps.total() <= mfe + delta )
 	{
 		//std::cout << "Internal " << i  << ' ' << j << std::endl;
-		ps_t ps1(ps);
-		ps1.push(segment(i, j, lVBI, VBI(i,j)));
-		ps1.update(i, j, '(', ')');
-		push_to_gstack(gstack, ps1);
+		//ps_t ps1(ps);
+		//ps1.push(segment(i, j, lVBI, VBI(i,j)));
+		//ps1.update(i, j, 'i', 'i');
+		//push_to_gstack(gstack, ps1);
+		traceVBI(i,j,ps,gstack);
 	}
 
 	// Multiloop
-	if ( VM(i,j) + ps.total() == energy )
+	if ( VM(i,j) + ps.total() <= mfe + delta )
 	{
-		//	std::cout << "Multi " << i  << ' ' << j << std::endl;
+		//std::cout << "Multi " << i  << ' ' << j << std::endl;
 		ps_t ps1(ps);
 		ps1.push(segment(i, j, lVM, VM(i,j)));
 		ps1.update(i, j, '(', ')');
@@ -157,19 +162,21 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 
 }
 
-void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
+void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack)
 {
 	int p,q;
 	for (p = i+1; p < MIN(j-2-TURN, i+MAXLOOP+1); ++p)
 	{
 		int minq = j-i+p-MAXLOOP-2;
 		if (minq < p+1+TURN) minq = p+1+TURN;
+		int maxq = (p==(i+1))?(j-2):(j-1);
 
-		for (q = minq; q < j; q++) 
+		for (q = minq; q <= maxq; q++) 
 		{
-			if (V(p, q) + eL(i, j, p, q) + ps.total() == energy )
+			if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta && PP[p][q] == 1)
 			{
 				ps_t ps1(ps);
+				ps1.update(i, j, '(', ')');
 				ps1.push(segment(p, q, lV, V(p, q)));
 				ps1.accumulate(eL(i, j, p, q));
 				push_to_gstack(gstack, ps1);
@@ -178,16 +185,14 @@ void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 	}
 }
 
-void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
+void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack)
 {
-	if ( (h>=j) || j == 0 || j == 1) return;
-
-	for (int i = h; i < j; ++i)
+	for (int i = 1; i < j-TURN; ++i)
 	{
 		int wim1 =  MIN(0, W[i-1]);
 
 		int wij = V(i,j) + auPenalty(i, j) + wim1;
-		if (wij + ps.total() == energy )
+		if (wij + ps.total() <= mfe + delta )
 		{
 			ps_t ps1(ps);
 			ps1.push(segment(i, j, lV, V(i,j)));
@@ -195,9 +200,10 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 			ps1.accumulate(auPenalty(i, j));
 			push_to_gstack(gstack, ps1);
 		}		
-
+		
+		
 		int wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
-		if (wijd + ps.total() == energy )
+		if (wijd + ps.total() <= mfe + delta )
 		{
 			ps_t ps3(ps);
 			ps3.push(segment(i, j-1, lV, V(i, j-1)));
@@ -207,7 +213,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}	
 
 		int widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
-		if (widj + ps.total() == energy )
+		if (widj + ps.total() <= mfe + delta )
 		{
 			ps_t ps4(ps);
 			ps4.push(segment(i+1, j, lV, V(i+1,j)));
@@ -217,7 +223,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		}
 
 		int widjd = V(i+1, j-1) + auPenalty(i+1,j-1) + Ed3(j-1, i+1, i) + Ed5(j-1, i+1, j) + wim1;
-		if (widjd + ps.total() == energy )
+		if (widjd + ps.total() <= mfe + delta )
 		{
 			ps_t ps2(ps);
 			ps2.push(segment(i+1, j-1, lV, V(i+1,j-1)));
@@ -225,9 +231,9 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 			ps2.accumulate(auPenalty(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
 			push_to_gstack(gstack, ps2);
 		}
-	}
+	} 
 
-	if (W[j-1] + ps.total() == energy )
+	if (W[j-1] + ps.total() <= mfe + delta )
 	{
 		ps_t ps1(ps);
 		ps1.push(segment(1, j-1, lW, W[j-1]));
@@ -235,7 +241,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 	}	
 }
 
-void traceWM(ps_t& ps, ps_map_t& filter, int energy)
+void traceWM(ps_t& ps, ps_map_t& filter)
 {
 	ps_stack_t wm_stack;
 	wm_stack.push(ps);
@@ -276,7 +282,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 		int h = i1; int k = j1;
 
 		int wmij = V(h,k) + auPenalty(h,k) + Eb;
-		if (pss.total() + wmij == energy )
+		if (pss.total() + wmij <= mfe + delta )
 		{
 			ps_t ps1(pss);
 			ps1.push_v(segment(h,k,lV, V(h,k)));
@@ -285,7 +291,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 		}
 
 		int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+ Ec ;
-		if (pss.total() + wmijd == energy )
+		if (pss.total() + wmijd <= mfe + delta )
 		{
 			ps_t ps1(pss);
 			ps1.push_v(segment(h,k-1,lV, V(h,k-1)));
@@ -294,7 +300,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 		}
 
 		int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + Eb+Ec ;
-		if (pss.total() + wmidj == energy )
+		if (pss.total() + wmidj <= mfe + delta )
 		{
 			ps_t ps1(pss);
 			ps1.push_v(segment(h+1, k, lV, V(h+1,k)));
@@ -303,7 +309,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 		}
 
 		int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) +  auPenalty(h+1,k-1) +Eb+ 2*Ec ;
-		if (pss.total() + wmidjd == energy )
+		if (pss.total() + wmidjd <= mfe + delta )
 		{
 			ps_t ps1(pss);
 			ps1.push_v(segment(h+1, k-1, lV, V(h+1,k-1)));
@@ -312,7 +318,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 		}
 
 
-		if (pss.total() + WM(i1,j1-1)  + Ec  == energy )
+		if (pss.total() + WM(i1,j1-1)  + Ec  <= mfe + delta )
 		{
 			ps_t ps1(pss);
 			ps1.push(segment(i1,j1-1, lWM, WM(i1,j1-1)));		
@@ -320,7 +326,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 			wm_stack.push(ps1);
 		}
 
-		if (pss.total() + WM[i1+1][j1] + Ec == energy )
+		if (pss.total() + WM[i1+1][j1] + Ec <= mfe + delta )
 		{
 			ps_t ps1(pss);
 			ps1.push(segment(i1+1,j1, lWM, WM(i1+1,j1)));		
@@ -330,7 +336,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 
 		for (int h = i1+1; h <= j1-1; ++h)
 		{	
-			if (WM(i1,h) + WM(h+1,j1) + pss.total() == energy )
+			if (WM(i1,h) + WM(h+1,j1) + pss.total() <= mfe + delta )
 			{
 				ps_t ps1(pss);
 				ps1.push(segment(i1, h, lWM, WM(i1,h)));
@@ -341,7 +347,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy)
 	}
 }
 
-void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
+void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack)
 {
 	std::map<std::string, ps_t> filter;
 	int h;	
@@ -354,43 +360,43 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy)
 		int common = auPenalty(i,j) + Ea + Eb;
 
 		dG = common + WM[i+1][h-1] + WM[h][j-1];
-		if (dG + ps.total()  == energy )
+		if (dG + ps.total()  <= mfe + delta )
 		{
 			ps_t ps1(ps);
 			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));
 			ps1.push(segment(h, j-1, lWM, WM[h][j-1]));
 			ps1.accumulate(common) ; 
-			traceWM(ps1, filter, energy);
+			traceWM(ps1, filter);
 		}
 
 		dG =  common + WM[i+2][h-1] + WM[h][j-1] + d5 + Ec;
-		if (dG + ps.total()  == energy )
+		if (dG + ps.total()  <= mfe + delta )
 		{
 			ps_t ps1(ps);
 			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
 			ps1.push(segment(h, j-1, lWM, WM[h][j-1]));	
 			ps1.accumulate(common + d5 + Ec);
-			traceWM(ps1, filter, energy);
+			traceWM(ps1, filter);
 		}
 
 		dG = common + WM[i+1][h-1] + WM[h][j-2] + d3 + Ec;
-		if (dG + ps.total()  == energy )
+		if (dG + ps.total()  <= mfe + delta )
 		{
 			ps_t ps1(ps);	
 			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));	
 			ps1.push(segment(h, j-2, lWM, WM[h][j-2]));	
 			ps1.accumulate(common + d3 + Ec);
-			traceWM(ps1, filter, energy);
+			traceWM(ps1, filter);
 		}
 
 		dG = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*Ec;
-		if (dG + ps.total()  == energy )
+		if (dG + ps.total()  <= mfe + delta )
 		{ 	
 			ps_t ps1(ps);	
 			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
 			ps1.push(segment(h, j-2, lWM, WM[h][j-2]));	
 			ps1.accumulate(common + d3 + d5 + 2*Ec) ;
-			traceWM(ps1, filter, energy);
+			traceWM(ps1, filter);
 		}
 	}
 

From 0ed558f5b3b83838850113236e36be0269d01874 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Wed, 22 Jun 2011 13:41:55 -0400
Subject: [PATCH 164/282] fix for allowable basepair

---
 gtfold-mfe/src/algorithms.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 6f4a314..c428607 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -37,7 +37,7 @@ void initializeMatrix(int len) {
 
 	for (i = 1; i <= len; ++i) 
 		for (j = len; j >= i; --j) 
-			if (canPair(RNA[i],RNA[j]) && j-i >= TURN) 
+			if (canPair(RNA[i],RNA[j]) && j-i > TURN) 
 				PP[i][j]  = 1;
 }
 

From a21bebc689ce891497a423bb885b8e5ac873ff12 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Wed, 22 Jun 2011 13:48:21 -0400
Subject: [PATCH 165/282] subopt changes

---
 gtfold-mfe/src/main.cc             | 18 ++++++++++++------
 gtfold-mfe/src/subopt_traceback.cc |  6 ++++--
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 49b3676..7f11741 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -165,14 +165,20 @@ void print_header() {
 	printf("Georgia Institute of Technology\n\n");
 }
 
-void save_subopt_file(string outputFile, ss_map_t& ss_data)
+void save_subopt_file(string outputFile, ss_map_t& ss_data, 
+		const string& seq, int energy)
 {
 	ofstream outfile;
 	outfile.open(outputFile.c_str());
-	
-	for (ss_map_t::iterator it = ss_data.begin();
-						it != ss_data.end(); ++it) {
-		outfile << it->first << '\t' << it->second/100.0 << std::endl;
+	char buff[1024];
+
+	sprintf(buff,"%s\t%0.2f", seq.c_str(), energy/100.0);
+	outfile << buff << std::endl;
+	for (ss_map_t::iterator it = ss_data.begin(); it!= ss_data.end(); ++it) 
+	{
+		sprintf(buff,"%s %0.2f", (it->first).c_str(), it->second/100.0);
+		//outfile << it->first << '\t' << it->second/100.0 << std::endl;
+		outfile << buff << std::endl;
 	}
 
 	outfile.close();
@@ -250,7 +256,7 @@ int main(int argc, char** argv) {
 		suboptfile += ".ss";	
 		
 		printf("Suboptimal structures saved in %s\n", suboptfile.c_str());
-		save_subopt_file(suboptfile, subopt_data);	
+		save_subopt_file(suboptfile, subopt_data, seq, energy);	
 		free_fold(seq.length());
 		exit(0);
 	}
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index 1cfe6d5..d5e4729 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -66,15 +66,17 @@ void process(ss_map_t& subopt_data, int len)
 
 		if (ps.empty()) 
 		{
+			//std::cout << ps.str << ' ' << ps.ae_/100.0 << std::endl;
 			ss_map_t::iterator it = subopt_data.find(ps.str); 
 			if ( it == subopt_data.end())
 			{
 				subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
 				count++;
-			} else 
+			} 
+			else 
 			{
 				int energy = it->second;
-				if (ps.ae_ < energy && (ps.ae_ >= mfe && ps.ae_ >= mfe + delta)) {
+				if (ps.ae_ < energy && (ps.ae_ >= mfe && ps.ae_ <= mfe + delta)) {
 					subopt_data[it->first] = ps.ae_;					
 				}		
 			}

From e98313ff9119072e16d58fc65134732923d9e325 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 23 Jun 2011 14:05:03 -0400
Subject: [PATCH 166/282] adding UNAfold parameters

---
 gtfold-mfe/data/UNAParams/asint1x2.DAT   |  96 ++++
 gtfold-mfe/data/UNAParams/dangle.DAT     |   8 +
 gtfold-mfe/data/UNAParams/extinction.DAT |  22 +
 gtfold-mfe/data/UNAParams/hexaloop.DAT   |   0
 gtfold-mfe/data/UNAParams/loop.DAT       |  30 ++
 gtfold-mfe/data/UNAParams/miscloop.DAT   |  13 +
 gtfold-mfe/data/UNAParams/sint2.DAT      |  24 +
 gtfold-mfe/data/UNAParams/sint4.DAT      | 576 +++++++++++++++++++++++
 gtfold-mfe/data/UNAParams/stack.DAT      |  16 +
 gtfold-mfe/data/UNAParams/tloop.DAT      |  30 ++
 gtfold-mfe/data/UNAParams/triloop.DAT    |   0
 gtfold-mfe/data/UNAParams/tstacke.DAT    |  16 +
 gtfold-mfe/data/UNAParams/tstackh.DAT    |  16 +
 gtfold-mfe/data/UNAParams/tstacki.DAT    |  16 +
 gtfold-mfe/data/UNAParams/tstacki23.DAT  |  16 +
 gtfold-mfe/data/UNAParams/tstackm.DAT    |  16 +
 16 files changed, 895 insertions(+)
 create mode 100644 gtfold-mfe/data/UNAParams/asint1x2.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/dangle.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/extinction.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/hexaloop.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/loop.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/miscloop.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/sint2.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/sint4.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/stack.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/tloop.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/triloop.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/tstacke.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/tstackh.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/tstacki.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/tstacki23.DAT
 create mode 100644 gtfold-mfe/data/UNAParams/tstackm.DAT

diff --git a/gtfold-mfe/data/UNAParams/asint1x2.DAT b/gtfold-mfe/data/UNAParams/asint1x2.DAT
new file mode 100644
index 0000000..0dfe3c4
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/asint1x2.DAT
@@ -0,0 +1,96 @@
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.20	3.00	2.40	4.80	2.30	2.20	1.10	4.00	2.40	2.20	1.60	4.00	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80
+3.10	3.00	4.80	3.00	2.30	2.20	4.00	2.20	2.30	2.20	4.00	2.20	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00
+2.50	4.80	1.60	4.80	1.70	4.00	0.80	4.00	1.70	4.00	0.80	4.00	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+2.90	2.50	2.40	4.80	2.10	1.70	1.60	4.00	2.10	1.70	1.60	4.00	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80
+3.00	3.30	4.80	3.00	2.20	2.50	4.00	2.20	2.20	2.50	4.00	2.20	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	3.00	4.80	2.10	4.00	2.20	4.00	1.50	4.00	2.20	4.00	1.30	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10
+1.80	1.40	1.20	4.80	0.80	0.60	0.40	4.00	1.00	0.60	0.40	4.00	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+1.60	4.80	3.00	4.80	0.80	4.00	2.20	4.00	0.80	4.00	2.20	4.00	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+3.30	2.70	4.80	3.00	2.50	1.90	4.00	2.20	2.50	1.90	4.00	2.20	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	2.50	4.80	2.00	4.00	1.70	4.00	1.20	4.00	1.70	4.00	1.20	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00
+3.20	3.00	2.40	4.80	2.40	2.20	1.60	4.00	2.50	2.20	2.10	4.00	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80
+3.10	3.00	4.80	3.00	2.30	2.20	4.00	2.20	2.30	2.20	4.00	2.20	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00
+2.50	4.80	1.60	4.80	1.70	4.00	0.80	4.00	1.70	4.00	0.80	4.00	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+2.90	2.50	2.40	4.80	2.10	1.70	1.60	4.00	2.10	1.70	1.60	4.00	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80
+3.00	3.30	4.80	3.00	2.20	2.50	4.00	2.20	2.20	2.50	4.00	2.20	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	3.00	4.80	2.10	4.00	2.20	4.00	1.30	4.00	2.20	4.00	1.20	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10
+1.80	1.40	1.20	4.80	1.00	0.60	0.40	4.00	1.20	0.60	0.40	4.00	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+1.60	4.80	3.00	4.80	0.80	4.00	2.20	4.00	0.80	4.00	2.20	4.00	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+3.30	2.70	4.80	3.00	2.50	1.90	4.00	2.20	2.50	1.90	4.00	2.20	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	2.50	4.80	2.00	4.00	1.70	4.00	1.20	4.00	1.70	4.00	1.20	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
diff --git a/gtfold-mfe/data/UNAParams/dangle.DAT b/gtfold-mfe/data/UNAParams/dangle.DAT
new file mode 100644
index 0000000..704c886
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/dangle.DAT
@@ -0,0 +1,8 @@
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	-0.50	-0.80	-0.60
+inf	inf	inf	inf	inf	inf	inf	inf	-1.70	-0.80	-1.70	-1.20	inf	inf	inf	inf
+inf	inf	inf	inf	-1.10	-0.40	-1.30	-0.60	inf	inf	inf	inf	-0.80	-0.50	-0.80	-0.60
+-0.70	-0.10	-0.70	-0.10	inf	inf	inf	inf	-0.70	-0.10	-0.70	-0.10	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.30	-0.10	-0.20	-0.20
+inf	inf	inf	inf	inf	inf	inf	inf	-0.20	-0.30	-0.00	-0.00	inf	inf	inf	inf
+inf	inf	inf	inf	-0.50	-0.30	-0.20	-0.10	inf	inf	inf	inf	-0.30	-0.10	-0.20	-0.20
+-0.30	-0.30	-0.40	-0.20	inf	inf	inf	inf	-0.30	-0.30	-0.40	-0.20	inf	inf	inf	inf
diff --git a/gtfold-mfe/data/UNAParams/extinction.DAT b/gtfold-mfe/data/UNAParams/extinction.DAT
new file mode 100644
index 0000000..c358304
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/extinction.DAT
@@ -0,0 +1,22 @@
+        
+
+   13650  13650
+   10670  10670
+   12790  12790
+   12140  11420
+   10670  10670
+   7520   7520
+   9390   9390
+   8370   7660
+   12920  12920
+   9190   9190
+   11430  11430
+   10960  10220
+   12520  11780
+   8900   8150
+   10400  9700
+   10110  8610
+    15340  15340
+    7600   7600
+    12160  12160
+    10210  8700
diff --git a/gtfold-mfe/data/UNAParams/hexaloop.DAT b/gtfold-mfe/data/UNAParams/hexaloop.DAT
new file mode 100644
index 0000000..e69de29
diff --git a/gtfold-mfe/data/UNAParams/loop.DAT b/gtfold-mfe/data/UNAParams/loop.DAT
new file mode 100644
index 0000000..bc9a352
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/loop.DAT
@@ -0,0 +1,30 @@
+1	inf	3.80	inf
+2	inf	2.80	inf
+3	inf	3.20	5.70
+4	1.70	3.60	5.60
+5	1.80	4.00	5.60
+6	2.00	4.40	5.40
+7	2.20	4.60	5.90
+8	2.30	4.70	5.60
+9	2.40	4.80	6.40
+10	2.50	4.90	6.50
+11	2.60	5.00	6.60
+12	2.70	5.10	6.70
+13	2.80	5.20	6.80
+14	2.90	5.30	6.90
+15	3.00	5.40	6.90
+16	3.00	5.40	7.00
+17	3.10	5.50	7.10
+18	3.10	5.50	7.10
+19	3.20	5.60	7.20
+20	3.30	5.70	7.20
+21	3.30	5.70	7.30
+22	3.40	5.80	7.30
+23	3.40	5.80	7.40
+24	3.40	5.80	7.40
+25	3.50	5.90	7.50
+26	3.50	5.90	7.50
+27	3.60	6.00	7.50
+28	3.60	6.00	7.60
+29	3.60	6.00	7.60
+30	3.70	6.10	7.70
diff --git a/gtfold-mfe/data/UNAParams/miscloop.DAT b/gtfold-mfe/data/UNAParams/miscloop.DAT
new file mode 100644
index 0000000..da4ef9f
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/miscloop.DAT
@@ -0,0 +1,13 @@
+1.07857764
+3.00
+.50	.50	.50	.50
+3.40	.00	.40
+10.10	-0.30	-0.30
+0.50
+-2.20
+0.30
+1.60
+1.40
+4.10
+1
+37
diff --git a/gtfold-mfe/data/UNAParams/sint2.DAT b/gtfold-mfe/data/UNAParams/sint2.DAT
new file mode 100644
index 0000000..658b46a
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/sint2.DAT
@@ -0,0 +1,24 @@
+1.70	1.70	1.70	inf	1.10	1.10	1.10	inf	1.10	1.10	1.10	inf	1.70	1.70	1.70	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.70	1.70	inf	1.70	1.10	1.10	inf	1.10	1.10	1.10	inf	1.10	1.70	1.70	inf	1.70	inf	inf	inf	inf	inf	inf	inf	inf
+1.70	inf	-0.40	1.70	1.10	inf	-1.00	1.10	1.10	inf	-1.00	1.10	1.70	inf	-0.40	1.70	inf	inf	inf	inf	inf	inf	inf	inf
+inf	1.70	1.70	1.50	inf	1.10	1.10	1.00	inf	1.10	1.10	1.10	inf	1.70	1.70	1.20	inf	inf	inf	inf	inf	inf	inf	inf
+1.10	1.10	1.10	inf	0.40	-0.40	0.40	inf	1.10	0.40	0.40	inf	1.10	1.10	1.10	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.10	1.10	inf	1.10	0.30	0.50	inf	0.50	0.40	0.40	inf	0.40	1.10	1.10	inf	1.10	inf	inf	inf	inf	inf	inf	inf	inf
+1.10	inf	-1.00	1.10	-0.10	inf	-1.70	0.40	0.40	inf	-1.40	0.40	1.10	inf	-1.00	1.10	inf	inf	inf	inf	inf	inf	inf	inf
+inf	1.10	1.10	1.10	inf	0.00	0.40	-0.30	inf	0.40	0.40	0.40	inf	1.10	1.10	1.10	inf	inf	inf	inf	inf	inf	inf	inf
+1.10	1.10	1.10	inf	0.80	0.40	0.40	inf	0.40	0.30	-0.10	inf	1.10	1.10	1.10	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.10	1.10	inf	1.10	0.40	0.40	inf	0.40	-0.40	0.50	inf	0.00	1.10	1.10	inf	1.10	inf	inf	inf	inf	inf	inf	inf	inf
+1.10	inf	-1.00	1.10	0.40	inf	-2.10	0.40	0.40	inf	-1.70	0.40	1.10	inf	-1.00	1.10	inf	inf	inf	inf	inf	inf	inf	inf
+inf	1.10	1.10	1.10	inf	0.40	0.40	-0.70	inf	0.50	0.40	-0.30	inf	1.10	1.10	1.00	inf	inf	inf	inf	inf	inf	inf	inf
+1.70	1.70	1.70	inf	1.10	1.10	1.10	inf	1.10	1.10	1.10	inf	1.70	1.70	1.70	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.70	1.70	inf	1.70	1.10	1.10	inf	1.10	1.10	1.10	inf	1.10	1.70	1.70	inf	1.70	inf	inf	inf	inf	inf	inf	inf	inf
+1.70	inf	-0.40	1.70	1.10	inf	-1.00	1.10	1.10	inf	-1.00	1.10	1.70	inf	-0.40	1.70	inf	inf	inf	inf	inf	inf	inf	inf
+inf	1.70	1.70	1.80	inf	1.10	1.10	1.10	inf	1.10	1.10	1.10	inf	1.70	1.70	1.50	inf	inf	inf	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
diff --git a/gtfold-mfe/data/UNAParams/sint4.DAT b/gtfold-mfe/data/UNAParams/sint4.DAT
new file mode 100644
index 0000000..0b446cd
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/sint4.DAT
@@ -0,0 +1,576 @@
+2.80	2.30	1.70	inf	2.80	3.40	inf	3.40	1.70	inf	2.10	1.00	inf	3.10	2.20	2.90
+2.60	2.20	1.60	inf	2.60	2.60	inf	2.60	1.60	inf	2.00	-0.20	inf	2.30	1.10	1.80
+1.50	1.10	0.50	inf	1.50	2.50	inf	2.50	0.50	inf	0.90	0.50	inf	2.20	1.80	2.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	2.10	1.50	inf	2.50	2.50	inf	2.50	1.50	inf	1.90	-0.30	inf	2.20	1.00	1.70
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.50	1.10	0.50	inf	1.50	2.50	inf	2.50	0.50	inf	0.90	0.50	inf	2.20	1.80	2.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.60	1.00	inf	2.10	2.70	inf	2.70	1.00	inf	1.40	0.30	inf	2.40	1.50	2.20
+2.30	0.90	2.10	inf	1.30	2.30	inf	2.30	2.10	inf	1.70	-1.50	inf	2.00	-0.20	2.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.30	-0.10	1.10	inf	0.30	1.30	inf	1.30	1.10	inf	0.70	-2.50	inf	1.00	-1.20	1.30
+2.70	1.20	2.40	inf	1.70	1.70	inf	1.70	2.40	inf	2.00	0.70	inf	1.40	1.90	0.80
+2.10	1.90	0.10	inf	1.80	2.50	inf	1.50	0.70	inf	1.80	0.00	inf	2.50	0.40	2.10
+2.00	1.70	0.00	inf	1.70	1.70	inf	0.70	0.60	inf	1.60	-1.20	inf	1.80	-0.80	1.00
+0.90	0.60	-1.10	inf	0.60	1.60	inf	0.70	-0.50	inf	0.50	-0.50	inf	1.70	-0.10	1.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.60	-0.10	inf	1.60	1.60	inf	0.60	0.50	inf	1.50	-1.30	inf	1.70	-0.90	0.90
+2.40	1.60	0.80	inf	1.50	1.60	inf	0.60	1.40	inf	2.10	-0.30	inf	1.60	0.10	0.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.40	1.60	0.80	inf	1.50	1.60	inf	0.60	1.40	inf	2.10	-0.30	inf	1.60	0.10	0.80
+0.90	0.60	-1.10	inf	0.60	1.60	inf	0.70	-0.50	inf	0.50	-0.50	inf	1.70	-0.10	1.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.40	1.20	-0.60	inf	1.10	1.80	inf	0.80	0.00	inf	1.10	-0.70	inf	1.80	-0.30	1.40
+1.70	0.40	0.50	inf	0.40	1.40	inf	0.50	1.10	inf	1.30	-2.50	inf	1.50	-2.10	1.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.40	1.60	0.80	inf	1.50	1.60	inf	0.60	1.40	inf	2.10	-0.30	inf	1.60	0.10	0.80
+0.70	-0.50	-0.50	inf	-0.60	0.50	inf	-0.50	0.10	inf	0.40	-3.50	inf	0.50	-3.10	0.50
+2.00	0.80	0.80	inf	0.70	0.80	inf	-0.20	1.50	inf	1.70	-0.30	inf	0.80	0.10	0.00
+2.00	1.90	1.00	inf	2.40	2.80	inf	2.70	1.00	inf	1.80	0.30	inf	2.70	1.80	2.20
+1.90	1.80	0.90	inf	2.20	2.10	inf	1.90	0.90	inf	1.60	-0.80	inf	1.90	0.70	1.00
+0.80	0.70	-0.20	inf	1.10	2.00	inf	1.80	-0.20	inf	0.50	-0.10	inf	1.80	1.40	1.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.70	0.80	inf	2.10	2.00	inf	1.80	0.80	inf	1.50	-0.90	inf	1.80	0.60	0.90
+2.30	1.60	1.70	inf	2.10	1.90	inf	1.80	1.70	inf	2.10	0.00	inf	1.80	1.50	0.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	1.60	1.70	inf	2.10	1.90	inf	1.80	1.70	inf	2.10	0.00	inf	1.80	1.50	0.90
+0.80	0.70	-0.20	inf	1.10	2.00	inf	1.80	-0.20	inf	0.50	-0.10	inf	1.80	1.40	1.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.30	1.20	0.30	inf	1.70	2.10	inf	2.00	0.30	inf	1.10	-0.40	inf	2.00	1.10	1.50
+1.60	0.50	1.40	inf	0.90	1.80	inf	1.60	1.40	inf	1.30	-2.10	inf	1.60	-0.60	1.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	1.60	1.70	inf	2.10	1.90	inf	1.80	1.70	inf	2.10	0.00	inf	1.80	1.50	0.90
+0.60	-0.50	0.40	inf	0.00	0.80	inf	0.70	0.40	inf	0.40	-3.10	inf	0.70	-1.60	0.60
+1.90	0.80	1.80	inf	1.30	1.10	inf	1.00	1.80	inf	1.70	0.00	inf	1.00	1.60	0.10
+2.80	2.50	1.50	inf	2.60	3.10	inf	3.10	1.50	inf	2.10	1.30	inf	3.10	2.30	2.70
+2.60	2.40	1.40	inf	2.50	2.30	inf	2.30	1.40	inf	1.90	0.20	inf	2.30	1.20	1.50
+1.50	1.30	0.30	inf	1.40	2.20	inf	2.20	0.30	inf	0.80	0.90	inf	2.20	1.90	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	2.30	1.30	inf	2.40	2.20	inf	2.20	1.30	inf	1.80	0.10	inf	2.20	1.10	1.40
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.50	1.30	0.30	inf	1.40	2.20	inf	2.20	0.30	inf	0.80	0.90	inf	2.20	1.90	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.80	0.80	inf	1.90	2.40	inf	2.40	0.80	inf	1.40	0.70	inf	2.40	1.60	2.00
+2.30	1.10	1.90	inf	1.20	2.00	inf	2.00	1.90	inf	1.60	-1.10	inf	2.00	-0.10	2.00
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.30	0.10	0.90	inf	0.20	1.00	inf	1.00	0.90	inf	0.70	-2.10	inf	1.00	-1.10	1.10
+2.70	1.40	2.20	inf	1.50	1.40	inf	1.40	2.20	inf	2.00	1.10	inf	1.40	2.00	0.60
+2.80	2.30	1.70	inf	2.80	3.40	inf	3.40	1.70	inf	2.10	1.00	inf	3.10	2.20	2.90
+2.60	2.20	1.60	inf	2.60	2.60	inf	2.60	1.60	inf	2.00	-0.20	inf	2.30	1.10	1.80
+1.50	1.10	0.50	inf	1.50	2.50	inf	2.50	0.50	inf	0.90	0.50	inf	2.20	1.80	2.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	2.10	1.50	inf	2.50	2.50	inf	2.50	1.50	inf	1.90	-0.30	inf	2.20	1.00	1.70
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.50	1.10	0.50	inf	1.50	2.50	inf	2.50	0.50	inf	0.90	0.50	inf	2.20	1.80	2.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.60	1.00	inf	2.10	2.70	inf	2.70	1.00	inf	1.40	0.30	inf	2.40	1.50	2.20
+2.30	0.90	2.10	inf	1.30	2.30	inf	2.30	2.10	inf	1.70	-1.50	inf	2.00	-0.20	2.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.30	-0.10	1.10	inf	0.30	1.30	inf	1.30	1.10	inf	0.70	-2.50	inf	1.00	-1.20	1.30
+2.70	1.20	2.40	inf	1.70	1.70	inf	1.70	2.40	inf	2.00	0.70	inf	1.40	1.90	0.80
+2.80	2.50	1.50	inf	2.60	3.10	inf	3.10	1.50	inf	2.10	1.30	inf	3.10	2.30	2.70
+2.60	2.40	1.40	inf	2.50	2.30	inf	2.30	1.40	inf	1.90	0.20	inf	2.30	1.20	1.50
+1.50	1.30	0.30	inf	1.40	2.20	inf	2.20	0.30	inf	0.80	0.90	inf	2.20	1.90	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	2.30	1.30	inf	2.40	2.20	inf	2.20	1.30	inf	1.80	0.10	inf	2.20	1.10	1.40
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.50	1.30	0.30	inf	1.40	2.20	inf	2.20	0.30	inf	0.80	0.90	inf	2.20	1.90	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.80	0.80	inf	1.90	2.40	inf	2.40	0.80	inf	1.40	0.70	inf	2.40	1.60	2.00
+2.30	1.10	1.90	inf	1.20	2.00	inf	2.00	1.90	inf	1.60	-1.10	inf	2.00	-0.10	2.00
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.30	0.10	0.90	inf	0.20	1.00	inf	1.00	0.90	inf	0.70	-2.10	inf	1.00	-1.10	1.10
+2.70	1.40	2.20	inf	1.50	1.40	inf	1.40	2.20	inf	2.00	1.10	inf	1.40	2.00	0.60
+2.00	1.60	1.00	inf	2.00	2.60	inf	2.60	1.00	inf	1.40	0.20	inf	2.30	1.50	2.20
+2.40	1.90	1.30	inf	2.40	2.40	inf	2.40	1.30	inf	1.70	-0.40	inf	2.10	0.80	1.50
+1.00	0.60	0.00	inf	1.00	2.00	inf	2.00	0.00	inf	0.40	0.00	inf	1.70	1.30	2.00
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.50	0.90	inf	1.90	1.90	inf	1.90	0.90	inf	1.30	-0.90	inf	1.60	0.40	1.10
+2.80	1.80	2.20	inf	2.20	2.20	inf	2.20	2.20	inf	2.20	0.40	inf	1.90	1.70	1.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.70	1.60	2.00	inf	2.10	2.10	inf	2.10	2.00	inf	2.00	0.30	inf	1.80	1.50	1.20
+1.00	0.60	0.00	inf	1.00	2.00	inf	2.00	0.00	inf	0.40	0.00	inf	1.70	1.30	2.00
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.30	0.70	inf	1.80	2.40	inf	2.40	0.70	inf	1.10	0.00	inf	2.10	1.20	1.90
+1.80	0.40	1.60	inf	0.80	1.80	inf	1.80	1.60	inf	1.20	-2.00	inf	1.50	-0.70	1.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.70	1.60	2.00	inf	2.10	2.10	inf	2.10	2.00	inf	2.00	0.30	inf	1.80	1.50	1.20
+0.30	-1.10	0.10	inf	-0.70	0.30	inf	0.30	0.10	inf	-0.30	-3.50	inf	0.00	-2.20	0.30
+2.20	0.70	1.90	inf	1.20	1.20	inf	1.20	1.90	inf	1.50	0.20	inf	0.90	1.50	0.30
+0.50	1.10	-0.30	inf	1.10	1.70	inf	0.70	0.40	inf	1.00	0.10	inf	1.80	-0.50	1.50
+0.60	1.50	0.10	inf	1.10	1.50	inf	0.50	0.50	inf	1.40	-0.70	inf	1.50	-0.60	0.00
+0.00	-0.70	-1.60	inf	-1.00	-0.60	inf	0.20	-0.70	inf	0.00	-0.80	inf	1.20	-0.60	0.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.30	1.00	-0.70	inf	1.00	1.00	inf	0.00	0.70	inf	0.90	-1.90	inf	1.10	-1.50	-0.20
+2.20	1.30	0.70	inf	1.90	1.30	inf	0.30	0.70	inf	1.80	-0.30	inf	1.40	-0.20	-0.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.00	1.20	0.40	inf	1.10	1.20	inf	1.70	1.00	inf	1.70	-0.70	inf	1.20	-0.30	0.20
+-0.20	-0.40	-1.70	inf	0.70	1.10	inf	0.20	-0.50	inf	0.00	-0.90	inf	1.20	-1.30	0.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.10	0.90	-0.90	inf	0.80	1.50	inf	0.50	-0.20	inf	0.80	-1.00	inf	1.50	-0.60	1.10
+0.90	0.00	0.30	inf	-0.10	1.00	inf	0.00	0.60	inf	0.90	-3.00	inf	1.00	-2.40	0.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.00	1.20	0.40	inf	1.10	1.20	inf	0.20	0.50	inf	1.70	-0.70	inf	1.20	-0.10	0.40
+-0.10	-1.60	-1.60	inf	-1.60	-0.60	inf	-1.60	-0.60	inf	-0.70	-4.40	inf	-0.50	-4.10	-1.00
+1.40	0.30	0.50	inf	0.30	0.30	inf	0.10	1.40	inf	1.20	-1.00	inf	0.30	0.10	0.60
+1.30	1.20	0.30	inf	1.60	2.10	inf	1.90	0.30	inf	1.00	-0.40	inf	1.90	1.10	1.40
+1.60	1.50	0.60	inf	2.00	1.80	inf	1.70	0.60	inf	1.40	-1.10	inf	1.70	0.40	0.80
+0.30	0.20	-0.70	inf	0.60	1.50	inf	1.30	-0.70	inf	0.00	-0.60	inf	1.30	0.90	1.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.20	1.10	0.20	inf	1.50	1.40	inf	1.20	0.20	inf	0.90	-1.50	inf	1.20	0.00	0.30
+2.10	1.40	1.50	inf	1.80	1.70	inf	1.50	1.50	inf	1.80	-0.20	inf	1.50	1.30	0.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.20	1.30	inf	1.70	1.50	inf	1.40	1.30	inf	1.70	-0.40	inf	1.40	1.10	0.50
+0.30	0.20	-0.70	inf	0.60	1.50	inf	1.30	-0.70	inf	0.00	-0.60	inf	1.30	0.90	1.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.00	0.90	0.00	inf	1.40	1.80	inf	1.70	0.00	inf	0.80	-0.70	inf	1.70	0.90	1.20
+1.10	0.00	0.90	inf	0.40	1.30	inf	1.10	0.90	inf	0.90	-2.60	inf	1.10	-1.10	1.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.20	1.30	inf	1.70	1.50	inf	1.40	1.30	inf	1.70	-0.40	inf	1.40	1.10	0.50
+-0.40	-1.50	-0.60	inf	-1.10	-0.20	inf	-0.40	-0.60	inf	-0.70	-4.20	inf	-0.40	-2.60	-0.50
+1.40	0.30	1.30	inf	0.80	0.60	inf	0.50	1.30	inf	1.20	-0.50	inf	0.50	1.10	-0.40
+2.00	1.80	0.80	inf	1.90	2.30	inf	2.30	0.80	inf	1.30	0.60	inf	2.30	1.60	1.90
+2.40	2.10	1.10	inf	2.20	2.10	inf	2.10	1.10	inf	1.70	0.00	inf	2.10	0.90	1.30
+1.00	0.80	-0.20	inf	0.90	1.70	inf	1.70	-0.20	inf	0.30	0.40	inf	1.70	1.40	1.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.70	0.70	inf	1.80	1.60	inf	1.60	0.70	inf	1.20	-0.50	inf	1.60	0.50	0.80
+2.80	2.00	2.00	inf	2.10	1.90	inf	1.90	2.00	inf	2.10	0.80	inf	1.90	1.80	1.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.70	1.80	1.80	inf	1.90	1.80	inf	1.80	1.80	inf	2.00	0.70	inf	1.80	1.60	1.00
+1.00	0.80	-0.20	inf	0.90	1.70	inf	1.70	-0.20	inf	0.30	0.40	inf	1.70	1.40	1.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.50	0.50	inf	1.60	2.10	inf	2.10	0.50	inf	1.10	0.40	inf	2.10	1.30	1.70
+1.80	0.60	1.40	inf	0.70	1.50	inf	1.50	1.40	inf	1.10	-1.60	inf	1.50	-0.60	1.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.70	1.80	1.80	inf	1.90	1.80	inf	1.80	1.80	inf	2.00	0.70	inf	1.80	1.60	1.00
+0.30	-0.90	-0.10	inf	-0.80	0.00	inf	0.00	-0.10	inf	-0.40	-3.10	inf	0.00	-2.10	0.00
+2.20	0.90	1.80	inf	1.00	0.90	inf	0.90	1.80	inf	1.50	0.60	inf	0.90	1.60	0.10
+2.00	1.60	1.00	inf	2.00	2.60	inf	2.60	1.00	inf	1.40	0.20	inf	2.30	1.50	2.20
+2.40	1.90	1.30	inf	2.40	2.40	inf	2.40	1.30	inf	1.70	-0.40	inf	2.10	0.80	1.50
+1.00	0.60	0.00	inf	1.00	2.00	inf	2.00	0.00	inf	0.40	0.00	inf	1.70	1.30	2.00
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.50	0.90	inf	1.90	1.90	inf	1.90	0.90	inf	1.30	-0.90	inf	1.60	0.40	1.10
+2.80	1.80	2.20	inf	2.20	2.20	inf	2.20	2.20	inf	2.20	0.40	inf	1.90	1.70	1.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.70	1.60	2.00	inf	2.10	2.10	inf	2.10	2.00	inf	2.00	0.30	inf	1.80	1.50	1.20
+1.00	0.60	0.00	inf	1.00	2.00	inf	2.00	0.00	inf	0.40	0.00	inf	1.70	1.30	2.00
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.30	0.70	inf	1.80	2.40	inf	2.40	0.70	inf	1.10	0.00	inf	2.10	1.20	1.90
+1.80	0.40	1.60	inf	0.80	1.80	inf	1.80	1.60	inf	1.20	-2.00	inf	1.50	-0.70	1.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.70	1.60	2.00	inf	2.10	2.10	inf	2.10	2.00	inf	2.00	0.30	inf	1.80	1.50	1.20
+0.30	-1.10	0.10	inf	-0.70	0.30	inf	0.30	0.10	inf	-0.30	-3.50	inf	0.00	-2.20	0.30
+2.20	0.70	1.90	inf	1.20	1.20	inf	1.20	1.90	inf	1.50	0.20	inf	0.90	1.50	0.30
+2.00	1.80	0.80	inf	1.90	2.30	inf	2.30	0.80	inf	1.30	0.60	inf	2.30	1.60	1.90
+2.40	2.10	1.10	inf	2.20	2.10	inf	2.10	1.10	inf	1.70	0.00	inf	2.10	0.90	1.30
+1.00	0.80	-0.20	inf	0.90	1.70	inf	1.70	-0.20	inf	0.30	0.40	inf	1.70	1.40	1.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.70	0.70	inf	1.80	1.60	inf	1.60	0.70	inf	1.20	-0.50	inf	1.60	0.50	0.80
+2.80	2.00	2.00	inf	2.10	1.90	inf	1.90	2.00	inf	2.10	0.80	inf	1.90	1.80	1.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.70	1.80	1.80	inf	1.90	1.80	inf	1.80	1.80	inf	2.00	0.70	inf	1.80	1.60	1.00
+1.00	0.80	-0.20	inf	0.90	1.70	inf	1.70	-0.20	inf	0.30	0.40	inf	1.70	1.40	1.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.50	0.50	inf	1.60	2.10	inf	2.10	0.50	inf	1.10	0.40	inf	2.10	1.30	1.70
+1.80	0.60	1.40	inf	0.70	1.50	inf	1.50	1.40	inf	1.10	-1.60	inf	1.50	-0.60	1.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.70	1.80	1.80	inf	1.90	1.80	inf	1.80	1.80	inf	2.00	0.70	inf	1.80	1.60	1.00
+0.30	-0.90	-0.10	inf	-0.80	0.00	inf	0.00	-0.10	inf	-0.40	-3.10	inf	0.00	-2.10	0.00
+2.20	0.90	1.80	inf	1.00	0.90	inf	0.90	1.80	inf	1.50	0.60	inf	0.90	1.60	0.10
+2.10	1.70	1.10	inf	2.10	2.70	inf	2.70	1.10	inf	1.50	0.30	inf	2.40	1.60	2.30
+1.80	1.40	0.80	inf	1.80	1.80	inf	1.80	0.80	inf	1.20	-1.00	inf	1.50	0.30	1.00
+0.70	0.30	-0.30	inf	0.70	1.70	inf	1.70	-0.30	inf	0.10	-0.30	inf	1.40	1.00	1.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.40	0.80	inf	1.90	1.90	inf	1.90	0.80	inf	1.20	-0.90	inf	1.60	0.30	1.00
+2.50	1.40	1.80	inf	1.90	1.90	inf	1.90	1.80	inf	1.80	0.10	inf	1.60	1.30	1.00
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	1.50	1.90	inf	1.90	1.90	inf	1.90	1.90	inf	1.90	0.10	inf	1.60	1.40	1.10
+0.10	-0.30	-0.90	inf	0.10	1.10	inf	1.10	-0.90	inf	-0.50	-0.90	inf	0.80	0.40	1.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.30	0.70	inf	1.80	2.40	inf	2.40	0.70	inf	1.10	0.00	inf	2.10	1.20	1.90
+0.40	-1.10	0.10	inf	-0.60	0.40	inf	0.40	0.10	inf	-0.30	-3.50	inf	0.10	-2.20	0.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.50	0.40	0.90	inf	0.90	0.90	inf	0.90	0.90	inf	0.80	-0.90	inf	0.60	0.40	0.00
+0.00	-1.50	-0.30	inf	-1.00	0.00	inf	0.00	-0.30	inf	-0.70	-3.90	inf	-0.30	-2.60	-0.10
+2.10	0.70	1.90	inf	1.10	1.10	inf	1.10	1.90	inf	1.50	0.10	inf	0.80	1.40	0.30
+1.50	1.20	-0.50	inf	1.20	1.80	inf	0.80	0.10	inf	1.10	-0.70	inf	1.90	-0.30	1.50
+1.20	0.90	-0.80	inf	0.90	0.90	inf	0.00	-0.20	inf	0.80	-2.00	inf	1.00	-1.60	0.20
+0.10	-0.10	-1.90	inf	-0.20	0.90	inf	-0.10	-1.30	inf	-0.20	-1.30	inf	0.90	-0.90	0.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.20	1.00	-0.80	inf	0.90	1.00	inf	0.00	-0.10	inf	0.90	-1.90	inf	1.00	-1.50	0.20
+1.80	1.00	0.20	inf	0.90	1.00	inf	0.00	0.90	inf	1.50	-0.90	inf	1.00	-0.50	0.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.00	0.30	inf	1.00	1.00	inf	0.00	0.90	inf	1.50	-0.90	inf	1.10	-0.50	0.30
+-0.50	-0.80	-2.60	inf	-0.80	0.20	inf	-0.80	-1.90	inf	-0.90	-1.90	inf	0.30	-1.50	0.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.10	0.90	-0.90	inf	0.80	1.50	inf	0.50	-0.20	inf	0.80	-1.00	inf	1.50	-0.60	1.10
+-0.30	-1.50	-1.50	inf	-1.60	-0.50	inf	-1.50	-0.90	inf	-0.60	-4.50	inf	-0.50	-4.10	-0.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+0.80	0.00	-0.80	inf	0.00	0.00	inf	-1.00	-0.10	inf	0.50	-1.90	inf	0.00	-1.50	-0.70
+-0.70	-1.90	-1.90	inf	-2.00	-0.90	inf	-1.90	-1.30	inf	-1.00	-4.90	inf	-0.90	-4.50	-0.90
+1.50	0.20	0.30	inf	0.20	0.20	inf	-0.70	0.90	inf	1.10	-0.90	inf	0.30	-0.50	-0.50
+0.50	1.30	-0.20	inf	0.60	2.20	inf	2.00	0.00	inf	1.10	-0.10	inf	2.00	0.90	1.40
+1.10	1.00	0.70	inf	1.10	1.90	inf	1.10	-1.00	inf	0.80	-1.60	inf	1.10	-0.10	0.30
+0.40	0.70	-0.50	inf	0.50	0.70	inf	0.50	-0.70	inf	-0.20	-0.60	inf	1.00	0.60	1.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.10	1.00	-0.40	inf	1.50	1.30	inf	1.20	-0.70	inf	0.90	-1.60	inf	1.20	0.00	0.30
+1.70	1.00	1.10	inf	1.50	1.30	inf	1.20	-0.60	inf	1.50	-0.60	inf	1.20	1.00	0.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.10	1.20	inf	1.50	1.40	inf	1.20	1.20	inf	1.50	-0.50	inf	1.20	1.00	0.30
+-0.30	-0.70	-1.70	inf	0.10	0.70	inf	0.40	-1.60	inf	-0.90	-1.60	inf	0.40	0.30	0.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.00	0.90	0.00	inf	1.40	1.80	inf	1.70	0.00	inf	0.80	-0.70	inf	1.70	0.90	1.20
+-0.50	-1.50	-1.30	inf	-0.60	-0.20	inf	-0.10	-0.60	inf	-0.60	-4.10	inf	-0.30	-2.40	0.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+0.70	0.00	0.20	inf	0.50	0.30	inf	0.20	0.20	inf	0.50	-1.60	inf	1.70	0.00	0.10
+0.10	-1.90	-0.90	inf	-0.70	-0.30	inf	-0.70	-0.80	inf	-1.00	-4.40	inf	-0.70	-3.00	-1.00
+1.50	-0.20	0.90	inf	0.00	-0.10	inf	0.40	0.90	inf	1.10	-1.00	inf	0.20	0.60	0.60
+2.10	1.90	0.90	inf	2.00	2.40	inf	2.40	0.90	inf	1.40	0.70	inf	2.40	1.70	2.00
+1.80	1.60	0.60	inf	1.70	1.50	inf	1.50	0.60	inf	1.10	-0.60	inf	1.50	0.40	0.70
+0.70	0.50	-0.50	inf	0.60	1.40	inf	1.40	-0.50	inf	0.00	0.10	inf	1.40	1.10	1.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.60	0.60	inf	1.70	1.60	inf	1.60	0.60	inf	1.20	-0.50	inf	1.60	0.40	0.80
+2.50	1.60	1.60	inf	1.70	1.60	inf	1.60	1.60	inf	1.80	0.50	inf	1.60	1.40	0.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	1.70	1.70	inf	1.80	1.60	inf	1.60	1.70	inf	1.80	0.50	inf	1.60	1.50	0.80
+0.10	-0.10	-1.10	inf	0.00	0.80	inf	0.80	-1.10	inf	-0.60	-0.50	inf	0.80	0.50	0.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.50	0.50	inf	1.60	2.10	inf	2.10	0.50	inf	1.10	0.40	inf	2.10	1.30	1.70
+0.40	-0.90	-0.10	inf	-0.80	0.10	inf	0.10	-0.10	inf	-0.30	-3.10	inf	0.10	-2.10	0.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.50	0.60	0.70	inf	0.70	0.60	inf	0.60	0.70	inf	0.80	-0.50	inf	0.60	0.50	-0.20
+0.00	-1.30	-0.50	inf	-1.20	-0.30	inf	-0.30	-0.50	inf	-0.70	-3.50	inf	-0.30	-2.50	-0.30
+2.10	0.90	1.70	inf	1.00	0.80	inf	0.80	1.70	inf	1.40	0.50	inf	0.80	1.50	0.00
+2.10	1.70	1.10	inf	2.10	2.70	inf	2.70	1.10	inf	1.50	0.30	inf	2.40	1.60	2.30
+1.80	1.40	0.80	inf	1.80	1.80	inf	1.80	0.80	inf	1.20	-1.00	inf	1.50	0.30	1.00
+0.70	0.30	-0.30	inf	0.70	1.70	inf	1.70	-0.30	inf	0.10	-0.30	inf	1.40	1.00	1.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.40	0.80	inf	1.90	1.90	inf	1.90	0.80	inf	1.20	-0.90	inf	1.60	0.30	1.00
+2.50	1.40	1.80	inf	1.90	1.90	inf	1.90	1.80	inf	1.80	0.10	inf	1.60	1.30	1.00
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	1.50	1.90	inf	1.90	1.90	inf	1.90	1.90	inf	1.90	0.10	inf	1.60	1.40	1.10
+0.10	-0.30	-0.90	inf	0.10	1.10	inf	1.10	-0.90	inf	-0.50	-0.90	inf	0.80	0.40	1.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.30	0.70	inf	1.80	2.40	inf	2.40	0.70	inf	1.10	0.00	inf	2.10	1.20	1.90
+0.40	-1.10	0.10	inf	-0.60	0.40	inf	0.40	0.10	inf	-0.30	-3.50	inf	0.10	-2.20	0.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.50	0.40	0.90	inf	0.90	0.90	inf	0.90	0.90	inf	0.80	-0.90	inf	0.60	0.40	0.00
+0.00	-1.50	-0.30	inf	-1.00	0.00	inf	0.00	-0.30	inf	-0.70	-3.90	inf	-0.30	-2.60	-0.10
+2.10	0.70	1.90	inf	1.10	1.10	inf	1.10	1.90	inf	1.50	0.10	inf	0.80	1.40	0.30
+2.10	1.90	0.90	inf	2.00	2.40	inf	2.40	0.90	inf	1.40	0.70	inf	2.40	1.70	2.00
+1.80	1.60	0.60	inf	1.70	1.50	inf	1.50	0.60	inf	1.10	-0.60	inf	1.50	0.40	0.70
+0.70	0.50	-0.50	inf	0.60	1.40	inf	1.40	-0.50	inf	0.00	0.10	inf	1.40	1.10	1.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.60	0.60	inf	1.70	1.60	inf	1.60	0.60	inf	1.20	-0.50	inf	1.60	0.40	0.80
+2.50	1.60	1.60	inf	1.70	1.60	inf	1.60	1.60	inf	1.80	0.50	inf	1.60	1.40	0.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	1.70	1.70	inf	1.80	1.60	inf	1.60	1.70	inf	1.80	0.50	inf	1.60	1.50	0.80
+0.10	-0.10	-1.10	inf	0.00	0.80	inf	0.80	-1.10	inf	-0.60	-0.50	inf	0.80	0.50	0.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.50	0.50	inf	1.60	2.10	inf	2.10	0.50	inf	1.10	0.40	inf	2.10	1.30	1.70
+0.40	-0.90	-0.10	inf	-0.80	0.10	inf	0.10	-0.10	inf	-0.30	-3.10	inf	0.10	-2.10	0.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.50	0.60	0.70	inf	0.70	0.60	inf	0.60	0.70	inf	0.80	-0.50	inf	0.60	0.50	-0.20
+0.00	-1.30	-0.50	inf	-1.20	-0.30	inf	-0.30	-0.50	inf	-0.70	-3.50	inf	-0.30	-2.50	-0.30
+2.10	0.90	1.70	inf	1.00	0.80	inf	0.80	1.70	inf	1.40	0.50	inf	0.80	1.50	0.00
+2.80	2.30	1.70	inf	2.80	3.40	inf	3.40	1.70	inf	2.10	1.00	inf	3.10	2.20	2.90
+2.80	2.30	1.70	inf	2.80	2.80	inf	2.80	1.70	inf	2.10	0.00	inf	2.50	1.20	1.90
+1.70	1.30	0.70	inf	1.70	2.70	inf	2.70	0.70	inf	1.10	0.70	inf	2.40	2.00	2.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	1.90	1.30	inf	2.30	2.30	inf	2.30	1.30	inf	1.70	-0.50	inf	2.00	0.80	1.50
+3.40	2.30	2.70	inf	2.80	2.80	inf	2.80	2.70	inf	2.70	1.00	inf	2.50	2.20	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.70	1.30	0.70	inf	1.70	2.70	inf	2.70	0.70	inf	1.10	0.70	inf	2.40	2.00	2.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.70	1.10	inf	2.10	2.70	inf	2.70	1.10	inf	1.50	0.30	inf	2.40	1.60	2.30
+2.20	0.80	2.00	inf	1.20	2.20	inf	2.20	2.00	inf	1.60	-1.60	inf	1.90	-0.30	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.40	2.30	2.70	inf	2.80	2.80	inf	2.80	2.70	inf	2.70	1.00	inf	2.50	2.20	1.90
+1.00	-0.50	0.70	inf	0.00	1.00	inf	1.00	0.70	inf	0.30	-2.90	inf	0.70	-1.60	0.90
+2.90	1.50	2.70	inf	1.90	1.90	inf	1.90	2.70	inf	2.30	0.90	inf	1.60	2.20	1.10
+2.10	1.90	0.10	inf	1.80	2.50	inf	1.50	0.70	inf	1.80	0.00	inf	2.50	0.40	2.10
+2.10	1.90	0.10	inf	1.80	1.90	inf	0.90	0.70	inf	1.80	-1.00	inf	1.90	-0.60	1.10
+1.10	0.80	-0.90	inf	0.80	1.80	inf	0.90	-0.30	inf	0.70	-0.30	inf	1.90	0.10	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.70	1.40	-0.30	inf	1.40	1.40	inf	0.40	0.30	inf	1.30	-1.50	inf	1.50	-1.10	0.70
+2.70	1.90	1.10	inf	1.80	1.90	inf	0.90	1.70	inf	2.40	0.00	inf	1.90	0.40	1.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.40	1.60	0.80	inf	1.50	1.60	inf	0.60	1.40	inf	2.10	-0.30	inf	1.60	0.10	0.80
+1.10	0.80	-0.90	inf	0.80	1.80	inf	0.90	-0.30	inf	0.70	-0.30	inf	1.90	0.10	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.50	1.20	-0.50	inf	1.20	1.80	inf	0.80	0.10	inf	1.10	-0.70	inf	1.90	-0.30	1.50
+1.60	0.30	0.40	inf	0.30	1.30	inf	0.40	1.00	inf	1.20	-2.60	inf	1.40	-2.20	1.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.70	1.90	1.10	inf	1.80	1.90	inf	0.90	1.70	inf	2.40	0.00	inf	1.90	0.40	1.10
+0.30	-0.90	-0.90	inf	-1.00	0.10	inf	-0.90	-0.30	inf	0.00	-3.90	inf	0.10	-3.50	0.10
+2.30	1.00	1.10	inf	1.00	1.00	inf	0.00	1.70	inf	1.90	-0.10	inf	1.10	0.30	0.30
+2.00	1.90	1.00	inf	2.40	2.80	inf	2.70	1.00	inf	1.80	0.30	inf	2.70	1.80	2.20
+2.00	1.90	1.00	inf	2.40	2.20	inf	2.10	1.00	inf	1.80	-0.70	inf	2.10	0.80	1.20
+1.00	0.90	0.00	inf	1.30	2.20	inf	2.00	0.00	inf	0.70	0.10	inf	2.00	1.60	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.60	1.50	0.60	inf	1.90	1.80	inf	1.60	0.60	inf	1.30	-1.10	inf	1.60	0.40	0.70
+2.60	1.90	2.00	inf	2.40	2.20	inf	2.10	2.00	inf	2.40	0.30	inf	2.10	1.80	1.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	1.60	1.70	inf	2.10	1.90	inf	1.80	1.70	inf	2.10	0.00	inf	1.80	1.50	0.90
+1.00	0.90	0.00	inf	1.30	2.20	inf	2.00	0.00	inf	0.70	0.10	inf	2.00	1.60	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.40	1.30	0.40	inf	1.70	2.20	inf	2.00	0.40	inf	1.10	-0.30	inf	2.00	1.20	1.50
+1.50	0.40	1.30	inf	0.80	1.70	inf	1.50	1.30	inf	1.20	-2.20	inf	1.50	-0.70	1.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.60	1.90	2.00	inf	2.40	2.20	inf	2.10	2.00	inf	2.40	0.30	inf	2.10	1.80	1.20
+0.20	-0.90	0.00	inf	-0.40	0.40	inf	0.30	0.00	inf	0.00	-3.50	inf	0.30	-2.00	0.20
+2.20	1.10	2.00	inf	1.50	1.40	inf	1.20	2.00	inf	1.90	0.30	inf	1.20	1.80	0.30
+2.80	2.50	1.50	inf	2.60	3.10	inf	3.10	1.50	inf	2.10	1.30	inf	3.10	2.30	2.70
+2.80	2.50	1.50	inf	2.60	2.50	inf	2.50	1.50	inf	2.10	0.30	inf	2.50	1.30	1.70
+1.70	1.50	0.50	inf	1.60	2.40	inf	2.40	0.50	inf	1.00	1.10	inf	2.40	2.10	2.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	2.10	1.10	inf	2.20	2.00	inf	2.00	1.10	inf	1.60	-0.10	inf	2.00	0.90	1.20
+3.40	2.50	2.50	inf	2.60	2.50	inf	2.50	2.50	inf	2.70	1.30	inf	2.50	2.30	1.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.70	1.50	0.50	inf	1.60	2.40	inf	2.40	0.50	inf	1.00	1.10	inf	2.40	2.10	2.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.90	0.90	inf	2.00	2.40	inf	2.40	0.90	inf	1.40	0.70	inf	2.40	1.70	2.00
+2.20	1.00	1.80	inf	1.10	1.90	inf	1.90	1.80	inf	1.50	-1.20	inf	1.90	-0.20	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.40	2.50	2.50	inf	2.60	2.50	inf	2.50	2.50	inf	2.70	1.30	inf	2.50	2.30	1.70
+1.00	-0.30	0.50	inf	-0.20	0.70	inf	0.70	0.50	inf	0.30	-2.50	inf	0.70	-1.50	0.70
+2.90	1.70	2.50	inf	1.80	1.60	inf	1.60	2.50	inf	2.20	1.30	inf	1.60	2.30	0.80
+2.80	2.30	1.70	inf	2.80	3.40	inf	3.40	1.70	inf	2.10	1.00	inf	3.10	2.20	2.90
+2.80	2.30	1.70	inf	2.80	2.80	inf	2.80	1.70	inf	2.10	0.00	inf	2.50	1.20	1.90
+1.70	1.30	0.70	inf	1.70	2.70	inf	2.70	0.70	inf	1.10	0.70	inf	2.40	2.00	2.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	1.90	1.30	inf	2.30	2.30	inf	2.30	1.30	inf	1.70	-0.50	inf	2.00	0.80	1.50
+3.40	2.30	2.70	inf	2.80	2.80	inf	2.80	2.70	inf	2.70	1.00	inf	2.50	2.20	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.70	1.30	0.70	inf	1.70	2.70	inf	2.70	0.70	inf	1.10	0.70	inf	2.40	2.00	2.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.70	1.10	inf	2.10	2.70	inf	2.70	1.10	inf	1.50	0.30	inf	2.40	1.60	2.30
+2.20	0.80	2.00	inf	1.20	2.20	inf	2.20	2.00	inf	1.60	-1.60	inf	1.90	-0.30	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.40	2.30	2.70	inf	2.80	2.80	inf	2.80	2.70	inf	2.70	1.00	inf	2.50	2.20	1.90
+1.00	-0.50	0.70	inf	0.00	1.00	inf	1.00	0.70	inf	0.30	-2.90	inf	0.70	-1.60	0.90
+2.90	1.50	2.70	inf	1.90	1.90	inf	1.90	2.70	inf	2.30	0.90	inf	1.60	2.20	1.10
+2.80	2.50	1.50	inf	2.60	3.10	inf	3.10	1.50	inf	2.10	1.30	inf	3.10	2.30	2.70
+2.80	2.50	1.50	inf	2.60	2.50	inf	2.50	1.50	inf	2.10	0.30	inf	2.50	1.30	1.70
+1.70	1.50	0.50	inf	1.60	2.40	inf	2.40	0.50	inf	1.00	1.10	inf	2.40	2.10	2.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	2.10	1.10	inf	2.20	2.00	inf	2.00	1.10	inf	1.60	-0.10	inf	2.00	0.90	1.20
+3.40	2.50	2.50	inf	2.60	2.50	inf	2.50	2.50	inf	2.70	1.30	inf	2.50	2.30	1.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.70	1.50	0.50	inf	1.60	2.40	inf	2.40	0.50	inf	1.00	1.10	inf	2.40	2.10	2.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.90	0.90	inf	2.00	2.40	inf	2.40	0.90	inf	1.40	0.70	inf	2.40	1.70	2.00
+2.20	1.00	1.80	inf	1.10	1.90	inf	1.90	1.80	inf	1.50	-1.20	inf	1.90	-0.20	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.40	2.50	2.50	inf	2.60	2.50	inf	2.50	2.50	inf	2.70	1.30	inf	2.50	2.30	1.70
+1.00	-0.30	0.50	inf	-0.20	0.70	inf	0.70	0.50	inf	0.30	-2.50	inf	0.70	-1.50	0.70
+2.90	1.70	2.50	inf	1.80	1.60	inf	1.60	2.50	inf	2.20	1.30	inf	1.60	2.30	0.80
+2.80	2.30	1.70	inf	2.80	3.40	inf	3.40	1.70	inf	2.10	1.00	inf	3.10	2.20	2.90
+2.60	2.20	1.60	inf	2.60	2.60	inf	2.60	1.60	inf	2.00	-0.20	inf	2.30	1.10	1.80
+1.50	1.10	0.50	inf	1.50	2.50	inf	2.50	0.50	inf	0.90	0.50	inf	2.20	1.80	2.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	2.10	1.50	inf	2.50	2.50	inf	2.50	1.50	inf	1.90	-0.30	inf	2.20	1.00	1.70
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.50	1.10	0.50	inf	1.50	2.50	inf	2.50	0.50	inf	0.90	0.50	inf	2.20	1.80	2.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.60	1.00	inf	2.10	2.70	inf	2.70	1.00	inf	1.40	0.30	inf	2.40	1.50	2.20
+2.30	0.90	2.10	inf	1.30	2.30	inf	2.30	2.10	inf	1.70	-1.50	inf	2.00	-0.20	2.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.30	-0.10	1.10	inf	0.30	1.30	inf	1.30	1.10	inf	0.70	-2.50	inf	1.00	-1.20	1.30
+2.70	1.20	2.40	inf	1.70	1.70	inf	1.70	2.40	inf	2.00	0.70	inf	1.40	1.90	0.80
+2.10	1.90	0.10	inf	1.80	2.50	inf	1.50	0.70	inf	1.80	0.00	inf	2.50	0.40	2.10
+2.00	1.70	0.00	inf	1.70	1.70	inf	0.70	0.60	inf	1.60	-1.20	inf	1.80	-0.80	1.00
+0.90	0.60	-1.10	inf	0.60	1.60	inf	0.70	-0.50	inf	0.50	-0.50	inf	1.70	-0.10	1.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.90	1.60	-0.10	inf	1.60	1.60	inf	0.60	0.50	inf	1.50	-1.30	inf	1.70	-0.90	0.90
+2.40	1.60	0.80	inf	1.50	1.60	inf	0.60	1.40	inf	2.10	-0.30	inf	1.60	0.10	0.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.40	1.60	0.80	inf	1.50	1.60	inf	0.60	1.40	inf	2.10	-0.30	inf	1.60	0.10	0.80
+0.90	0.60	-1.10	inf	0.60	1.60	inf	0.70	-0.50	inf	0.50	-0.50	inf	1.70	-0.10	1.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.40	1.20	-0.60	inf	1.10	1.80	inf	0.80	0.00	inf	1.10	-0.70	inf	1.80	-0.30	1.40
+1.70	0.40	0.50	inf	0.40	1.40	inf	0.50	1.10	inf	1.30	-2.50	inf	1.50	-2.10	1.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.40	1.60	0.80	inf	1.50	1.60	inf	0.60	1.40	inf	2.10	-0.30	inf	1.60	0.10	0.80
+0.70	-0.50	-0.50	inf	-0.60	0.50	inf	-0.50	0.10	inf	0.40	-3.50	inf	0.50	-3.10	0.50
+2.00	0.80	0.80	inf	0.70	0.80	inf	-0.20	1.50	inf	1.70	-0.30	inf	0.80	0.10	0.00
+2.00	1.90	1.00	inf	2.40	2.80	inf	2.70	1.00	inf	1.80	0.30	inf	2.70	1.80	2.20
+1.90	1.80	0.90	inf	2.20	2.10	inf	1.90	0.90	inf	1.60	-0.80	inf	1.90	0.70	1.00
+0.80	0.70	-0.20	inf	1.10	2.00	inf	1.80	-0.20	inf	0.50	-0.10	inf	1.80	1.40	1.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.80	1.70	0.80	inf	2.10	2.00	inf	1.80	0.80	inf	1.50	-0.90	inf	1.80	0.60	0.90
+2.30	1.60	1.70	inf	2.10	1.90	inf	1.80	1.70	inf	2.10	0.00	inf	1.80	1.50	0.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	1.60	1.70	inf	2.10	1.90	inf	1.80	1.70	inf	2.10	0.00	inf	1.80	1.50	0.90
+0.80	0.70	-0.20	inf	1.10	2.00	inf	1.80	-0.20	inf	0.50	-0.10	inf	1.80	1.40	1.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.30	1.20	0.30	inf	1.70	2.10	inf	2.00	0.30	inf	1.10	-0.40	inf	2.00	1.10	1.50
+1.60	0.50	1.40	inf	0.90	1.80	inf	1.60	1.40	inf	1.30	-2.10	inf	1.60	-0.60	1.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	1.60	1.70	inf	2.10	1.90	inf	1.80	1.70	inf	2.10	0.00	inf	1.80	1.50	0.90
+0.60	-0.50	0.40	inf	0.00	0.80	inf	0.70	0.40	inf	0.40	-3.10	inf	0.70	-1.60	0.60
+1.90	0.80	1.80	inf	1.30	1.10	inf	1.00	1.80	inf	1.70	0.00	inf	1.00	1.60	0.10
+2.80	2.50	1.50	inf	2.60	3.10	inf	3.10	1.50	inf	2.10	1.30	inf	3.10	2.30	2.70
+2.60	2.40	1.40	inf	2.50	2.30	inf	2.30	1.40	inf	1.90	0.20	inf	2.30	1.20	1.50
+1.50	1.30	0.30	inf	1.40	2.20	inf	2.20	0.30	inf	0.80	0.90	inf	2.20	1.90	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	2.30	1.30	inf	2.40	2.20	inf	2.20	1.30	inf	1.80	0.10	inf	2.20	1.10	1.40
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.50	1.30	0.30	inf	1.40	2.20	inf	2.20	0.30	inf	0.80	0.90	inf	2.20	1.90	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.80	0.80	inf	1.90	2.40	inf	2.40	0.80	inf	1.40	0.70	inf	2.40	1.60	2.00
+2.30	1.10	1.90	inf	1.20	2.00	inf	2.00	1.90	inf	1.60	-1.10	inf	2.00	-0.10	2.00
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.30	0.10	0.90	inf	0.20	1.00	inf	1.00	0.90	inf	0.70	-2.10	inf	1.00	-1.10	1.10
+2.70	1.40	2.20	inf	1.50	1.40	inf	1.40	2.20	inf	2.00	1.10	inf	1.40	2.00	0.60
+2.80	2.30	1.70	inf	2.80	3.40	inf	3.40	1.70	inf	2.10	1.00	inf	3.10	2.20	2.90
+2.60	2.20	1.60	inf	2.60	2.60	inf	2.60	1.60	inf	2.00	-0.20	inf	2.30	1.10	1.80
+1.50	1.10	0.50	inf	1.50	2.50	inf	2.50	0.50	inf	0.90	0.50	inf	2.20	1.80	2.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	2.10	1.50	inf	2.50	2.50	inf	2.50	1.50	inf	1.90	-0.30	inf	2.20	1.00	1.70
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.50	1.10	0.50	inf	1.50	2.50	inf	2.50	0.50	inf	0.90	0.50	inf	2.20	1.80	2.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.60	1.00	inf	2.10	2.70	inf	2.70	1.00	inf	1.40	0.30	inf	2.40	1.50	2.20
+2.30	0.90	2.10	inf	1.30	2.30	inf	2.30	2.10	inf	1.70	-1.50	inf	2.00	-0.20	2.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.30	-0.10	1.10	inf	0.30	1.30	inf	1.30	1.10	inf	0.70	-2.50	inf	1.00	-1.20	1.30
+2.70	1.20	2.40	inf	1.70	1.70	inf	1.70	2.40	inf	2.00	0.70	inf	1.40	1.90	0.80
+2.80	2.50	1.50	inf	2.60	3.10	inf	3.10	1.50	inf	2.10	1.30	inf	3.10	2.30	2.70
+2.60	2.40	1.40	inf	2.50	2.30	inf	2.30	1.40	inf	1.90	0.20	inf	2.30	1.20	1.50
+1.50	1.30	0.30	inf	1.40	2.20	inf	2.20	0.30	inf	0.80	0.90	inf	2.20	1.90	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.50	2.30	1.30	inf	2.40	2.20	inf	2.20	1.30	inf	1.80	0.10	inf	2.20	1.10	1.40
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.50	1.30	0.30	inf	1.40	2.20	inf	2.20	0.30	inf	0.80	0.90	inf	2.20	1.90	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.80	0.80	inf	1.90	2.40	inf	2.40	0.80	inf	1.40	0.70	inf	2.40	1.60	2.00
+2.30	1.10	1.90	inf	1.20	2.00	inf	2.00	1.90	inf	1.60	-1.10	inf	2.00	-0.10	2.00
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.30	0.10	0.90	inf	0.20	1.00	inf	1.00	0.90	inf	0.70	-2.10	inf	1.00	-1.10	1.10
+2.70	1.40	2.20	inf	1.50	1.40	inf	1.40	2.20	inf	2.00	1.10	inf	1.40	2.00	0.60
+2.80	2.30	1.70	inf	2.80	3.40	inf	3.40	1.70	inf	2.10	1.00	inf	3.10	2.20	2.90
+2.80	2.30	1.70	inf	2.80	2.80	inf	2.80	1.70	inf	2.10	0.00	inf	2.50	1.20	1.90
+1.70	1.30	0.70	inf	1.70	2.70	inf	2.70	0.70	inf	1.10	0.70	inf	2.40	2.00	2.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	1.90	1.30	inf	2.30	2.30	inf	2.30	1.30	inf	1.70	-0.50	inf	2.00	0.80	1.50
+3.40	2.30	2.70	inf	2.80	2.80	inf	2.80	2.70	inf	2.70	1.00	inf	2.50	2.20	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.70	1.30	0.70	inf	1.70	2.70	inf	2.70	0.70	inf	1.10	0.70	inf	2.40	2.00	2.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.70	1.10	inf	2.10	2.70	inf	2.70	1.10	inf	1.50	0.30	inf	2.40	1.60	2.30
+2.20	0.80	2.00	inf	1.20	2.20	inf	2.20	2.00	inf	1.60	-1.60	inf	1.90	-0.30	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.40	2.30	2.70	inf	2.80	2.80	inf	2.80	2.70	inf	2.70	1.00	inf	2.50	2.20	1.90
+1.00	-0.50	0.70	inf	0.00	1.00	inf	1.00	0.70	inf	0.30	-2.90	inf	0.70	-1.60	0.90
+2.90	1.50	2.70	inf	1.90	1.90	inf	1.90	2.70	inf	2.30	0.90	inf	1.60	2.20	1.10
+2.10	1.90	0.10	inf	1.80	2.50	inf	1.50	0.70	inf	1.80	0.00	inf	2.50	0.40	2.10
+2.10	1.90	0.10	inf	1.80	1.90	inf	0.90	0.70	inf	1.80	-1.00	inf	1.90	-0.60	1.10
+1.10	0.80	-0.90	inf	0.80	1.80	inf	0.90	-0.30	inf	0.70	-0.30	inf	1.90	0.10	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.70	1.40	-0.30	inf	1.40	1.40	inf	0.40	0.30	inf	1.30	-1.50	inf	1.50	-1.10	0.70
+2.70	1.90	1.10	inf	1.80	1.90	inf	0.90	1.70	inf	2.40	0.00	inf	1.90	0.40	1.10
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.40	1.60	0.80	inf	1.50	1.60	inf	0.60	1.40	inf	2.10	-0.30	inf	1.60	0.10	0.80
+1.10	0.80	-0.90	inf	0.80	1.80	inf	0.90	-0.30	inf	0.70	-0.30	inf	1.90	0.10	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.50	1.20	-0.50	inf	1.20	1.80	inf	0.80	0.10	inf	1.10	-0.70	inf	1.90	-0.30	1.50
+1.60	0.30	0.40	inf	0.30	1.30	inf	0.40	1.00	inf	1.20	-2.60	inf	1.40	-2.20	1.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.70	1.90	1.10	inf	1.80	1.90	inf	0.90	1.70	inf	2.40	0.00	inf	1.90	0.40	1.10
+0.30	-0.90	-0.90	inf	-1.00	0.10	inf	-0.90	-0.30	inf	0.00	-3.90	inf	0.10	-3.50	0.10
+2.30	1.00	1.10	inf	1.00	1.00	inf	0.00	1.70	inf	1.90	-0.10	inf	1.10	0.30	0.30
+2.00	1.90	1.00	inf	2.40	2.80	inf	2.70	1.00	inf	1.80	0.30	inf	2.70	1.80	2.20
+2.00	1.90	1.00	inf	2.40	2.20	inf	2.10	1.00	inf	1.80	-0.70	inf	2.10	0.80	1.20
+1.00	0.90	0.00	inf	1.30	2.20	inf	2.00	0.00	inf	0.70	0.10	inf	2.00	1.60	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.60	1.50	0.60	inf	1.90	1.80	inf	1.60	0.60	inf	1.30	-1.10	inf	1.60	0.40	0.70
+2.60	1.90	2.00	inf	2.40	2.20	inf	2.10	2.00	inf	2.40	0.30	inf	2.10	1.80	1.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	1.60	1.70	inf	2.10	1.90	inf	1.80	1.70	inf	2.10	0.00	inf	1.80	1.50	0.90
+1.00	0.90	0.00	inf	1.30	2.20	inf	2.00	0.00	inf	0.70	0.10	inf	2.00	1.60	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+1.40	1.30	0.40	inf	1.70	2.20	inf	2.00	0.40	inf	1.10	-0.30	inf	2.00	1.20	1.50
+1.50	0.40	1.30	inf	0.80	1.70	inf	1.50	1.30	inf	1.20	-2.20	inf	1.50	-0.70	1.50
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.60	1.90	2.00	inf	2.40	2.20	inf	2.10	2.00	inf	2.40	0.30	inf	2.10	1.80	1.20
+0.20	-0.90	0.00	inf	-0.40	0.40	inf	0.30	0.00	inf	0.00	-3.50	inf	0.30	-2.00	0.20
+2.20	1.10	2.00	inf	1.50	1.40	inf	1.20	2.00	inf	1.90	0.30	inf	1.20	1.80	0.30
+2.80	2.50	1.50	inf	2.60	3.10	inf	3.10	1.50	inf	2.10	1.30	inf	3.10	2.30	2.70
+2.80	2.50	1.50	inf	2.60	2.50	inf	2.50	1.50	inf	2.10	0.30	inf	2.50	1.30	1.70
+1.70	1.50	0.50	inf	1.60	2.40	inf	2.40	0.50	inf	1.00	1.10	inf	2.40	2.10	2.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	2.10	1.10	inf	2.20	2.00	inf	2.00	1.10	inf	1.60	-0.10	inf	2.00	0.90	1.20
+3.40	2.50	2.50	inf	2.60	2.50	inf	2.50	2.50	inf	2.70	1.30	inf	2.50	2.30	1.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.70	1.50	0.50	inf	1.60	2.40	inf	2.40	0.50	inf	1.00	1.10	inf	2.40	2.10	2.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.90	0.90	inf	2.00	2.40	inf	2.40	0.90	inf	1.40	0.70	inf	2.40	1.70	2.00
+2.20	1.00	1.80	inf	1.10	1.90	inf	1.90	1.80	inf	1.50	-1.20	inf	1.90	-0.20	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.40	2.50	2.50	inf	2.60	2.50	inf	2.50	2.50	inf	2.70	1.30	inf	2.50	2.30	1.70
+1.00	-0.30	0.50	inf	-0.20	0.70	inf	0.70	0.50	inf	0.30	-2.50	inf	0.70	-1.50	0.70
+2.90	1.70	2.50	inf	1.80	1.60	inf	1.60	2.50	inf	2.20	1.30	inf	1.60	2.30	0.80
+2.80	2.30	1.70	inf	2.80	3.40	inf	3.40	1.70	inf	2.10	1.00	inf	3.10	2.20	2.90
+2.80	2.30	1.70	inf	2.80	2.80	inf	2.80	1.70	inf	2.10	0.00	inf	2.50	1.20	1.90
+1.70	1.30	0.70	inf	1.70	2.70	inf	2.70	0.70	inf	1.10	0.70	inf	2.40	2.00	2.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	1.90	1.30	inf	2.30	2.30	inf	2.30	1.30	inf	1.70	-0.50	inf	2.00	0.80	1.50
+3.40	2.30	2.70	inf	2.80	2.80	inf	2.80	2.70	inf	2.70	1.00	inf	2.50	2.20	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.00	2.40	inf	2.50	2.50	inf	2.50	2.40	inf	2.40	0.70	inf	2.20	1.90	1.60
+1.70	1.30	0.70	inf	1.70	2.70	inf	2.70	0.70	inf	1.10	0.70	inf	2.40	2.00	2.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.70	1.10	inf	2.10	2.70	inf	2.70	1.10	inf	1.50	0.30	inf	2.40	1.60	2.30
+2.20	0.80	2.00	inf	1.20	2.20	inf	2.20	2.00	inf	1.60	-1.60	inf	1.90	-0.30	2.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.40	2.30	2.70	inf	2.80	2.80	inf	2.80	2.70	inf	2.70	1.00	inf	2.50	2.20	1.90
+1.00	-0.50	0.70	inf	0.00	1.00	inf	1.00	0.70	inf	0.30	-2.90	inf	0.70	-1.60	0.90
+2.90	1.50	2.70	inf	1.90	1.90	inf	1.90	2.70	inf	2.30	0.90	inf	1.60	2.20	1.10
+2.80	2.50	1.50	inf	2.60	3.10	inf	3.10	1.50	inf	2.10	1.30	inf	3.10	2.30	2.70
+2.80	2.50	1.50	inf	2.60	2.50	inf	2.50	1.50	inf	2.10	0.30	inf	2.50	1.30	1.70
+1.70	1.50	0.50	inf	1.60	2.40	inf	2.40	0.50	inf	1.00	1.10	inf	2.40	2.10	2.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.30	2.10	1.10	inf	2.20	2.00	inf	2.00	1.10	inf	1.60	-0.10	inf	2.00	0.90	1.20
+3.40	2.50	2.50	inf	2.60	2.50	inf	2.50	2.50	inf	2.70	1.30	inf	2.50	2.30	1.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.10	2.20	2.20	inf	2.30	2.20	inf	2.20	2.20	inf	2.40	1.00	inf	2.20	2.00	1.40
+1.70	1.50	0.50	inf	1.60	2.40	inf	2.40	0.50	inf	1.00	1.10	inf	2.40	2.10	2.40
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+2.10	1.90	0.90	inf	2.00	2.40	inf	2.40	0.90	inf	1.40	0.70	inf	2.40	1.70	2.00
+2.20	1.00	1.80	inf	1.10	1.90	inf	1.90	1.80	inf	1.50	-1.20	inf	1.90	-0.20	1.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf
+3.40	2.50	2.50	inf	2.60	2.50	inf	2.50	2.50	inf	2.70	1.30	inf	2.50	2.30	1.70
+1.00	-0.30	0.50	inf	-0.20	0.70	inf	0.70	0.50	inf	0.30	-2.50	inf	0.70	-1.50	0.70
+2.90	1.70	2.50	inf	1.80	1.60	inf	1.60	2.50	inf	2.20	1.30	inf	1.60	2.30	0.80
diff --git a/gtfold-mfe/data/UNAParams/stack.DAT b/gtfold-mfe/data/UNAParams/stack.DAT
new file mode 100644
index 0000000..e7cc9f4
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/stack.DAT
@@ -0,0 +1,16 @@
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-2.20	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-2.10	inf	-0.60
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-1.10	inf	-1.40	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-2.10	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-3.30	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	-2.40	inf	-1.40	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-2.10	inf	-2.10	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	-2.40	inf	inf	inf	inf	inf	inf	inf	-1.30
+inf	inf	inf	inf	inf	inf	-3.40	inf	inf	inf	inf	inf	inf	inf	-2.50	inf
+inf	inf	inf	inf	inf	-3.30	inf	-1.50	inf	inf	inf	inf	inf	-2.10	inf	inf
+inf	inf	inf	inf	-2.20	inf	-2.50	inf	inf	inf	inf	inf	-1.40	inf	inf	inf
+inf	inf	inf	-1.30	inf	inf	inf	inf	inf	inf	inf	-1.00	inf	inf	inf	inf
+inf	inf	-2.40	inf	inf	inf	inf	inf	inf	inf	-1.50	inf	inf	inf	inf	inf
+inf	-2.10	inf	-1.00	inf	inf	inf	inf	inf	-1.40	inf	inf	inf	inf	inf	inf
+-0.90	inf	-1.30	inf	inf	inf	inf	inf	-0.60	inf	inf	inf	inf	inf	inf	inf
diff --git a/gtfold-mfe/data/UNAParams/tloop.DAT b/gtfold-mfe/data/UNAParams/tloop.DAT
new file mode 100644
index 0000000..6de62b1
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/tloop.DAT
@@ -0,0 +1,30 @@
+AGAAAU	-2.00
+AGCAAU	-1.50
+AGUAAU	-1.50
+AGUGAU	-1.50
+CGAAAG	-3.00
+CGAAGG	-2.50
+CGAGAG	-2.00
+CGCAAG	-3.00
+CGCGAG	-2.50
+CGGAAG	-3.00
+CGGGAG	-1.50
+CGUAAG	-2.00
+CGUGAG	-3.00
+CUAACG	-2.00
+CUACGG	-2.50
+CUUCGG	-3.00
+GGAAAC	-3.00
+GGAAGC	-1.50
+GGAGAC	-3.00
+GGCAAC	-2.50
+GGCGAC	-1.50
+GGGAAC	-1.50
+GGGAGC	-1.50
+GGGGAC	-3.00
+GGUGAC	-3.00
+GUGAAC	-1.50
+UGAAAA	-1.50
+UGAAAG	-2.00
+UGAGAG	-2.50
+UGGAAA	-1.50
diff --git a/gtfold-mfe/data/UNAParams/triloop.DAT b/gtfold-mfe/data/UNAParams/triloop.DAT
new file mode 100644
index 0000000..e69de29
diff --git a/gtfold-mfe/data/UNAParams/tstacke.DAT b/gtfold-mfe/data/UNAParams/tstacke.DAT
new file mode 100644
index 0000000..342f641
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/tstacke.DAT
@@ -0,0 +1,16 @@
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	-1.00	-0.80	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.60	-0.70	inf	-0.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	inf	-0.80	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	inf	-0.80
+inf	inf	inf	inf	inf	inf	inf	inf	-1.50	-1.50	-1.40	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.00	-1.10	inf	-0.80	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.40	inf	-1.60	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	-1.40	inf	-1.20	inf	inf	inf	inf
+inf	inf	inf	inf	-1.10	-1.50	-1.30	inf	inf	inf	inf	inf	-0.30	-1.00	-0.80	inf
+inf	inf	inf	inf	-1.10	-0.70	inf	-0.50	inf	inf	inf	inf	-0.60	-0.70	inf	-0.70
+inf	inf	inf	inf	-1.60	inf	-1.40	inf	inf	inf	inf	inf	-0.60	inf	-0.80	inf
+inf	inf	inf	inf	inf	-1.00	inf	-0.70	inf	inf	inf	inf	inf	-0.80	inf	-0.80
+-1.00	-0.80	-1.10	inf	inf	inf	inf	inf	-1.00	-0.80	-1.10	inf	inf	inf	inf	inf
+-0.70	-0.60	inf	-0.50	inf	inf	inf	inf	-0.70	-0.60	inf	-0.50	inf	inf	inf	inf
+-1.10	inf	-1.20	inf	inf	inf	inf	inf	-0.50	inf	-0.80	-0.80	inf	inf	inf	inf
+inf	-0.60	inf	-0.50	inf	inf	inf	inf	inf	-0.60	-1.10	-0.50	inf	inf	inf	inf
diff --git a/gtfold-mfe/data/UNAParams/tstackh.DAT b/gtfold-mfe/data/UNAParams/tstackh.DAT
new file mode 100644
index 0000000..5c64e84
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/tstackh.DAT
@@ -0,0 +1,16 @@
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.30	-0.50	-0.30	-0.30
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.10	-0.20	-1.50	-0.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-1.10	-1.20	-0.20	0.20
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.30	-0.30	-0.60	-1.10
+inf	inf	inf	inf	inf	inf	inf	inf	-1.50	-1.50	-1.40	-1.80	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.00	-0.90	-2.90	-0.80	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-2.20	-2.00	-1.60	-1.10	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.70	-1.40	-1.80	-2.00	inf	inf	inf	inf
+inf	inf	inf	inf	-1.10	-1.50	-1.30	-2.10	inf	inf	inf	inf	0.20	-0.50	-0.30	-0.30
+inf	inf	inf	inf	-1.10	-0.70	-2.40	-0.50	inf	inf	inf	inf	-0.10	-0.20	-1.50	-0.20
+inf	inf	inf	inf	-2.40	-2.90	-1.40	-1.20	inf	inf	inf	inf	-0.90	-1.10	-0.30	0.00
+inf	inf	inf	inf	-1.90	-1.00	-2.20	-1.50	inf	inf	inf	inf	-0.30	-0.30	-0.40	-1.10
+-0.50	-0.30	-0.60	-0.50	inf	inf	inf	inf	-0.50	-0.30	-0.60	-0.50	inf	inf	inf	inf
+-0.20	-0.10	-1.20	-0.00	inf	inf	inf	inf	-0.20	-0.10	-1.70	0.00	inf	inf	inf	inf
+-1.40	-1.20	-0.70	-0.20	inf	inf	inf	inf	-0.80	-1.20	-0.30	-0.70	inf	inf	inf	inf
+-0.30	-0.10	-0.50	-0.80	inf	inf	inf	inf	-0.60	-0.10	-0.60	-0.80	inf	inf	inf	inf
diff --git a/gtfold-mfe/data/UNAParams/tstacki.DAT b/gtfold-mfe/data/UNAParams/tstacki.DAT
new file mode 100644
index 0000000..d03ca87
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/tstacki.DAT
@@ -0,0 +1,16 @@
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	0.70	0.70	-0.40	0.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	0.70	0.70	0.70	0.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.40	0.70	0.70	0.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	0.70	0.70	0.70	0.00
+inf	inf	inf	inf	inf	inf	inf	inf	-0.00	-0.00	-1.10	-0.00	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-0.00	-0.00	-0.00	-0.00	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.10	-0.00	-0.00	-0.00	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-0.00	-0.00	-0.00	-0.70	inf	inf	inf	inf
+inf	inf	inf	inf	-0.00	-0.00	-1.10	-0.00	inf	inf	inf	inf	0.70	0.70	-0.40	0.70
+inf	inf	inf	inf	-0.00	-0.00	-0.00	-0.00	inf	inf	inf	inf	0.70	0.70	0.70	0.70
+inf	inf	inf	inf	-1.10	-0.00	-0.00	-0.00	inf	inf	inf	inf	-0.40	0.70	0.70	0.70
+inf	inf	inf	inf	-0.00	-0.00	-0.00	-0.70	inf	inf	inf	inf	0.70	0.70	0.70	0.00
+0.70	0.70	-0.40	0.70	inf	inf	inf	inf	0.70	0.70	-0.40	0.70	inf	inf	inf	inf
+0.70	0.70	0.70	0.70	inf	inf	inf	inf	0.70	0.70	0.70	0.70	inf	inf	inf	inf
+-0.40	0.70	0.70	0.70	inf	inf	inf	inf	-0.40	0.70	0.70	0.70	inf	inf	inf	inf
+0.70	0.70	0.70	0.00	inf	inf	inf	inf	0.70	0.70	0.70	0.00	inf	inf	inf	inf
diff --git a/gtfold-mfe/data/UNAParams/tstacki23.DAT b/gtfold-mfe/data/UNAParams/tstacki23.DAT
new file mode 100644
index 0000000..1d11362
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/tstacki23.DAT
@@ -0,0 +1,16 @@
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	1.85	1.85	0.75	1.85
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	1.85	1.85	1.85	1.85
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	0.75	1.85	1.85	1.85
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	1.85	1.85	1.85	1.15
+inf	inf	inf	inf	inf	inf	inf	inf	1.15	1.15	0.05	1.15	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	1.15	1.15	1.15	1.15	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	0.05	1.15	1.15	1.15	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	1.15	1.15	1.15	0.45	inf	inf	inf	inf
+inf	inf	inf	inf	1.15	1.15	0.05	1.15	inf	inf	inf	inf	1.85	1.85	0.75	1.85
+inf	inf	inf	inf	1.15	1.15	1.15	1.15	inf	inf	inf	inf	1.85	1.85	1.85	1.85
+inf	inf	inf	inf	0.05	1.15	1.15	1.15	inf	inf	inf	inf	0.75	1.85	1.85	1.85
+inf	inf	inf	inf	1.15	1.15	1.15	0.45	inf	inf	inf	inf	1.85	1.85	1.85	1.15
+1.85	1.85	0.75	1.85	inf	inf	inf	inf	1.85	1.85	0.75	1.85	inf	inf	inf	inf
+1.85	1.85	1.85	1.85	inf	inf	inf	inf	1.85	1.85	1.85	1.85	inf	inf	inf	inf
+0.75	1.85	1.85	1.85	inf	inf	inf	inf	0.75	1.85	1.85	1.85	inf	inf	inf	inf
+1.85	1.85	1.85	1.15	inf	inf	inf	inf	1.85	1.85	1.85	1.15	inf	inf	inf	inf
diff --git a/gtfold-mfe/data/UNAParams/tstackm.DAT b/gtfold-mfe/data/UNAParams/tstackm.DAT
new file mode 100644
index 0000000..ee473db
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/tstackm.DAT
@@ -0,0 +1,16 @@
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	-1.00	-0.80	-0.90
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.60	-0.70	-2.20	-0.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	-2.10	-0.80	-0.80
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-1.10	-0.80	-1.10	-0.80
+inf	inf	inf	inf	inf	inf	inf	inf	-1.70	-1.70	-1.70	-1.70	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.00	-1.10	-3.30	-0.80	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.70	-2.40	-1.70	-1.70	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.60	-1.40	-1.60	-1.20	inf	inf	inf	inf
+inf	inf	inf	inf	-1.10	-1.50	-1.30	-1.90	inf	inf	inf	inf	-0.80	-1.00	-0.80	-1.30
+inf	inf	inf	inf	-1.10	-0.70	-3.40	-0.50	inf	inf	inf	inf	-0.60	-0.70	-2.50	-0.70
+inf	inf	inf	inf	-1.60	-3.30	-1.40	-1.30	inf	inf	inf	inf	-0.80	-2.10	-0.80	-0.80
+inf	inf	inf	inf	-1.70	-1.00	-2.00	-0.70	inf	inf	inf	inf	-1.40	-0.80	1.30	-0.80
+-1.00	-0.80	-1.10	-1.30	inf	inf	inf	inf	-1.00	-0.80	-1.10	-1.00	inf	inf	inf	inf
+-0.70	-0.60	-2.40	-0.50	inf	inf	inf	inf	-0.70	-0.60	-1.50	-0.50	inf	inf	inf	inf
+-1.10	-2.10	-1.20	-1.00	inf	inf	inf	inf	-0.70	-1.40	-0.80	0.30	inf	inf	inf	inf
+-0.90	-0.60	-1.40	-0.50	inf	inf	inf	inf	-0.50	-0.60	-0.50	-0.50	inf	inf	inf	inf

From b41b45940c9cb1d5eb67af47bf1865ff97eefdad Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 23 Jun 2011 14:25:35 -0400
Subject: [PATCH 167/282] changes to seperate unamode(--unamode), terminal
 mismatch(-m)

---
 gtfold-mfe/include/algorithms.h |  2 +-
 gtfold-mfe/include/options.h    |  1 +
 gtfold-mfe/include/traceback.h  |  2 +-
 gtfold-mfe/src/algorithms.c     | 12 ++++++------
 gtfold-mfe/src/loader.cc        | 14 +++++++++++---
 gtfold-mfe/src/main.cc          |  6 +++---
 gtfold-mfe/src/options.cc       | 16 +++++++++++++++-
 gtfold-mfe/src/traceback.c      | 21 +++++++++++----------
 8 files changed, 49 insertions(+), 25 deletions(-)

diff --git a/gtfold-mfe/include/algorithms.h b/gtfold-mfe/include/algorithms.h
index 9b3dee0..d37a205 100644
--- a/gtfold-mfe/include/algorithms.h
+++ b/gtfold-mfe/include/algorithms.h
@@ -23,7 +23,7 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
-	int calculate(int len, int nThreads, int t_mismatch);
+	int calculate(int len, int nThreads, int unamode ,int t_mismatch);
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 46b3a3a..24217bf 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -20,6 +20,7 @@ extern bool VERBOSE;
 extern bool SHAPE_ENABLED;
 extern bool PARAM_DIR;
 extern bool T_MISMATCH;
+extern bool UNAMODE;
 
 extern string seqfile;
 extern string constraintsFile;
diff --git a/gtfold-mfe/include/traceback.h b/gtfold-mfe/include/traceback.h
index 47a4f19..f250058 100644
--- a/gtfold-mfe/include/traceback.h
+++ b/gtfold-mfe/include/traceback.h
@@ -26,7 +26,7 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
-	void trace(int len, int vbose, int t_mismatch);
+	void trace(int len, int vv, int mode, int mismatch);
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index c428607..b61aa1e 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -120,7 +120,7 @@ int calcVBI2(int i, int j, int  len) {
 	return energy;
 }
 
-int calculate(int len, int nThreads, int t_mismatch) { 
+int calculate(int len, int nThreads, int unamode, int mismatch) { 
 	int b, i, j;
 #ifdef _OPENMP
 	if (nThreads>0) omp_set_num_threads(nThreads);
@@ -132,7 +132,7 @@ int calculate(int len, int nThreads, int t_mismatch) {
 #endif
 
 	initializeMatrix(len);
-	if (t_mismatch) {
+	if (unamode) {
 		prefilter(len,2,2);
 	}
 
@@ -149,7 +149,7 @@ int calculate(int len, int nThreads, int t_mismatch) {
 				int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack
 
 				// Internal Loop BEGIN
-				if (t_mismatch) 
+				if (unamode) 
 					VBI(i,j) = calcVBI1(i,j);
 				else
 					VBI(i,j) = calcVBI(i,j);
@@ -166,7 +166,7 @@ int calculate(int len, int nThreads, int t_mismatch) {
 				VMij = MIN(VMij, (VMidj + d5 +Ec)) ;
 				VMij = MIN(VMij, (VMijd + d3 +Ec));
 
-				if (t_mismatch) {
+				if (unamode || mismatch) {
 					VMij = MIN(VMij, (VMidjd + Estackm(i,j) + 2*Ec));
 				} else {
 					VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec));
@@ -195,7 +195,7 @@ int calculate(int len, int nThreads, int t_mismatch) {
 			newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
 			newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
 
-			if (t_mismatch) {
+			if (unamode || mismatch) {
 				if (i<j-TURN-2)
 					newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; 
 			}
@@ -217,7 +217,7 @@ int calculate(int len, int nThreads, int t_mismatch) {
 			Wim1 = MIN(0, W[i-1]); 
 			Wij = V(i, j) + auPenalty(i, j) + Wim1;
 		
-			if (t_mismatch) {
+			if (unamode || mismatch) {
 				Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Estacke(j-1,i+1) + Wim1:Widjd;
 			} else {
 				Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:Widjd;
diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 66e0ff0..1c25d6a 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -80,7 +80,7 @@ int init;
 int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
 float prelog;
 
-void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int t_mismatch=0) {
+void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode=0, int mismatch=0) {
 	if (!userdatalogic) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
@@ -102,14 +102,22 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int
 	initTstkiValues("tstacki.DAT", EN_DATADIR);
 	initTloopValues("tloop.DAT", EN_DATADIR);
 
-	if (t_mismatch) {
+	if (unamode) {
 		initInt21Values("asint1x2.DAT", EN_DATADIR);
 		initInt22Values("sint4.DAT", EN_DATADIR);
 		initInt11Values("sint2.DAT", EN_DATADIR);
 		initTstkmValues("tstackm.DAT", EN_DATADIR);
 		initTstkeValues("tstacke.DAT", EN_DATADIR);
 		initTstk23Values("tstacki23.DAT", EN_DATADIR);
-	} else {
+	} else if (mismatch) {
+		initTstkmValues("tstackm.DAT", EN_DATADIR);
+		initTstkeValues("tstacke.DAT", EN_DATADIR);
+		initInt21Values("int21.DAT", EN_DATADIR);
+		initInt22Values("int22.DAT", EN_DATADIR);
+		initInt11Values("int11.DAT", EN_DATADIR);
+		
+	}	
+	else {
 		initInt21Values("int21.DAT", EN_DATADIR);
 		initInt22Values("int22.DAT", EN_DATADIR);
 		initInt11Values("int11.DAT", EN_DATADIR);
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 7f11741..42478a5 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -220,7 +220,7 @@ int main(int argc, char** argv) {
 	}
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
-	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, T_MISMATCH);
+	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, T_MISMATCH);
 
 	printRunConfiguration(seq);
 	
@@ -230,7 +230,7 @@ int main(int argc, char** argv) {
 	fflush(stdout);
 
 	t1 = get_seconds();
-	energy = calculate(seq.length(), nThreads, T_MISMATCH);
+	energy = calculate(seq.length(), nThreads, UNAMODE, T_MISMATCH);
 	t1 = get_seconds() - t1;
 	
 	printf("Done.\n\n");
@@ -262,7 +262,7 @@ int main(int argc, char** argv) {
 	}
 	
 	t1 = get_seconds();
-	trace(seq.length(), VERBOSE, T_MISMATCH);
+	trace(seq.length(), VERBOSE, UNAMODE, T_MISMATCH);
 	t1 = get_seconds() - t1;
 
 	printf("\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index a37ee9a..2155a83 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -15,6 +15,7 @@ bool CONS_ENABLED = false;
 bool VERBOSE = false;
 bool SHAPE_ENABLED = false;
 bool T_MISMATCH = false;
+bool UNAMODE = false;
 
 string seqfile = "";
 string constraintsFile = "";
@@ -42,10 +43,11 @@ void help() {
     printf("   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n");
     printf("                        limit is given, base pairs can be over any distance\n");
     printf("   -p  --paramdir DIR   Path to directory from where parameters are to be read\n");
-    printf("   -m   			    enable terminal mismatch calculations\n");
+    printf("   -m   		Enable terminal mismatch calculations\n");
    	printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
     printf("   -t, --threads num    Limit number of threads used\n");
+    printf("   --unamode DIR	Enable UNAfold mode. Path to directory containing UNAfold parameters\n");
 
     printf("\n");
     printf("   -h, --help           Output help (this message) and exit\n");
@@ -104,6 +106,14 @@ void parse_options(int argc, char** argv) {
 					help();
 			} else if (strcmp(argv[i], "-m") == 0) {
                 T_MISMATCH = true;
+			} else if (strcmp(argv[i], "--unamode") == 0) {
+				if(i < argc) {
+					paramDir = argv[++i];
+					UNAMODE = true;
+					PARAM_DIR = true;
+				}
+				else
+					help();
 			}
 		   	else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
 				if(i < argc)
@@ -171,6 +181,10 @@ void printRunConfiguration(string seq) {
 	bool standardRun = true;
 
 	printf("Run Configuration:\n");
+	if (UNAMODE == true) {
+		printf("- running in unamode\n");
+		standardRun = false;
+	}
 
 	if (NOISOLATE == true) {
 		printf("- preventing isolated base pairs\n");
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index e4357d7..1a9511f 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -33,12 +33,14 @@
 int verbose = -1;
 int total_en = 0;
 int total_ex = 0;
-int t_mismatch = 0;
+int unamode = 0;
 
-void trace(int len, int vbose, int t_mismatch_) {
+void trace(int len, int vv, int mode, int mismatch) {
 	int i;
-	verbose = vbose;
-	t_mismatch = t_mismatch_;
+	verbose = vv;
+	unamode = mode;
+	if (mismatch) unamode = 1;
+
 	for (i = 0; i < len+1; i++)
 		structure[i] = 0;
 
@@ -74,7 +76,7 @@ void traceW(int j) {
 		Widjd = Wijd =  Widj = INFINITY_;
 		Wij = V(i,j) + auPenalty(i, j) + wim1;
 		
-		if (t_mismatch) {
+		if (unamode) {
 			Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Estacke(j-1,i+1) + wim1;
 		}
 		else {
@@ -94,7 +96,7 @@ void traceW(int j) {
 			traceV(i, j);
 			if (flag ) traceW(i - 1);
 			break;
-		} else if ((W[j] == Widjd && t_mismatch && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
+		} else if ((W[j] == Widjd && unamode && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
 			done = 1;
 			if (verbose == 1) 
 				printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Estacke(j-1,i+1))/100.00);
@@ -148,9 +150,8 @@ int traceV(int i, int j) {
 	if (j-i < TURN)  return INFINITY_;
 
 	a = canHairpin(i,j)?eH(i, j):INFINITY_;
-	// TODO 
-	// if (eS(i, j) == 0) b = INFINITY_;
 	b = canStack(i,j)?eS(i, j) + V(i + 1, j - 1):INFINITY_;
+	// if (eS(i, j) == 0) b = INFINITY_;
 	c = canStack(i,j)?VBI(i,j):INFINITY_;
 	d = canStack(i,j)?VM(i,j):INFINITY_;
 	
@@ -228,7 +229,7 @@ int traceVM(int i, int j) {
 	done = 0;
 	int VMij = VM(i,j);
 
-	if (t_mismatch && i<j-TURN-2) {
+	if (unamode && i<j-TURN-2) {
 		for (h = i + 3; h <= j - 2 && !done; h++) { 
 			A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i,j) + Estackm(i,j);
 			if (A_temp == VMij && canSS(i+1) && canSS(j-1)) {
@@ -330,7 +331,7 @@ int traceWM(int i, int j) {
 				structure[i + 1] = j - 1;
 				structure[j - 1] = i + 1;
 			}
-		   	else if (WM(i,j) == V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1) && t_mismatch) {
+		   	else if (WM(i,j) == V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1) && unamode) {
 				done = 1;
 				eWM += traceV(i + 1, j - 1);
 				structure[i + 1] = j - 1;

From bcfe0058497d73298ac6fe5c8fdcea175404d41f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 23 Jun 2011 14:26:37 -0400
Subject: [PATCH 168/282] changes to seperate unamode(--unamode), terminal
 mismatch(-m)

---
 gtfold-mfe/include/loader.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h
index c7eff12..41d7c6b 100644
--- a/gtfold-mfe/include/loader.h
+++ b/gtfold-mfe/include/loader.h
@@ -25,7 +25,7 @@
 #include "constants.h"
 #include "data.h"
 
-void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int t_mismatch);
+void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode,int t_mismatch);
 
 int initStackValues(const std::string& fileName, const std::string& dirPath);
 int initMiscloopValues(const std::string& fileName, const std::string& dirPath);

From 69a7bc85632899a3b466add2000541e7cedaa407 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 23 Jun 2011 14:38:40 -0400
Subject: [PATCH 169/282] adding file

---
 gtfold-mfe/data/Turner99/tstacke.DAT | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 gtfold-mfe/data/Turner99/tstacke.DAT

diff --git a/gtfold-mfe/data/Turner99/tstacke.DAT b/gtfold-mfe/data/Turner99/tstacke.DAT
new file mode 100644
index 0000000..342f641
--- /dev/null
+++ b/gtfold-mfe/data/Turner99/tstacke.DAT
@@ -0,0 +1,16 @@
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	-1.00	-0.80	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.60	-0.70	inf	-0.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	inf	-0.80	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	inf	-0.80
+inf	inf	inf	inf	inf	inf	inf	inf	-1.50	-1.50	-1.40	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.00	-1.10	inf	-0.80	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.40	inf	-1.60	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	-1.40	inf	-1.20	inf	inf	inf	inf
+inf	inf	inf	inf	-1.10	-1.50	-1.30	inf	inf	inf	inf	inf	-0.30	-1.00	-0.80	inf
+inf	inf	inf	inf	-1.10	-0.70	inf	-0.50	inf	inf	inf	inf	-0.60	-0.70	inf	-0.70
+inf	inf	inf	inf	-1.60	inf	-1.40	inf	inf	inf	inf	inf	-0.60	inf	-0.80	inf
+inf	inf	inf	inf	inf	-1.00	inf	-0.70	inf	inf	inf	inf	inf	-0.80	inf	-0.80
+-1.00	-0.80	-1.10	inf	inf	inf	inf	inf	-1.00	-0.80	-1.10	inf	inf	inf	inf	inf
+-0.70	-0.60	inf	-0.50	inf	inf	inf	inf	-0.70	-0.60	inf	-0.50	inf	inf	inf	inf
+-1.10	inf	-1.20	inf	inf	inf	inf	inf	-0.50	inf	-0.80	-0.80	inf	inf	inf	inf
+inf	-0.60	inf	-0.50	inf	inf	inf	inf	inf	-0.60	-1.10	-0.50	inf	inf	inf	inf

From 4117ca866687fd68f6e7971e6e0b47189f4768bd Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Thu, 23 Jun 2011 14:39:44 -0400
Subject: [PATCH 170/282] added print statement

---
 gtfold-mfe/src/options.cc | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 2155a83..a9a3cb0 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -182,7 +182,11 @@ void printRunConfiguration(string seq) {
 
 	printf("Run Configuration:\n");
 	if (UNAMODE == true) {
-		printf("- running in unamode\n");
+		printf("+ running in unamode\n");
+		standardRun = false;
+	}
+	if (T_MISMATCH == true) {
+		printf("+ enabled terminal mismatch calculations\n");
 		standardRun = false;
 	}
 

From 4d4789689b70f7dbaadd2aaf2a0c0545db69091c Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Fri, 24 Jun 2011 12:30:32 -0400
Subject: [PATCH 171/282] added entry tstacke; removed sint2, sint4

---
 gtfold-mfe/data/Turner99/Makefile.am | 3 +--
 gtfold-mfe/data/Turner99/Makefile.in | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/data/Turner99/Makefile.am b/gtfold-mfe/data/Turner99/Makefile.am
index c8cf6c6..4390f87 100644
--- a/gtfold-mfe/data/Turner99/Makefile.am
+++ b/gtfold-mfe/data/Turner99/Makefile.am
@@ -10,11 +10,10 @@ gtfold_data_DATA = \
 	int11.DAT\
 	int21.DAT\
 	int22.DAT\
-	sint2.DAT\
-	sint4.DAT\
 	tloop.DAT\
 	tstackh.DAT\
 	tstacki.DAT\
+	tstacke.DAT\
 	tstackm.DAT
 
 
diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in
index 084882b..d21f2af 100644
--- a/gtfold-mfe/data/Turner99/Makefile.in
+++ b/gtfold-mfe/data/Turner99/Makefile.in
@@ -182,11 +182,10 @@ gtfold_data_DATA = \
 	int11.DAT\
 	int21.DAT\
 	int22.DAT\
-	sint2.DAT\
-	sint4.DAT\
 	tloop.DAT\
 	tstackh.DAT\
 	tstacki.DAT\
+	tstacke.DAT\
 	tstackm.DAT
 
 EXTRA_DIST = $(gtfold_data_DATA)

From bd2db4003e93b1f077ed059ec4d4ddafba37f237 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Fri, 24 Jun 2011 12:31:57 -0400
Subject: [PATCH 172/282] added Makefiles under UNAParams

---
 gtfold-mfe/data/UNAParams/Makefile.am |  24 ++
 gtfold-mfe/data/UNAParams/Makefile.in | 400 ++++++++++++++++++++++++++
 2 files changed, 424 insertions(+)
 create mode 100644 gtfold-mfe/data/UNAParams/Makefile.am
 create mode 100644 gtfold-mfe/data/UNAParams/Makefile.in

diff --git a/gtfold-mfe/data/UNAParams/Makefile.am b/gtfold-mfe/data/UNAParams/Makefile.am
new file mode 100644
index 0000000..640c6c6
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/Makefile.am
@@ -0,0 +1,24 @@
+## Process this file with automake to produce Makefile.in
+
+gtfold_datadir = $(datadir)/@PACKAGE@/UNAParams
+
+gtfold_data_DATA = \
+	stack.DAT\
+	miscloop.DAT\
+	dangle.DAT\
+	loop.DAT\
+	asint1x2.DAT\
+	sint2.DAT\
+	sint4.DAT\
+	tloop.DAT\
+	tstackh.DAT\
+	tstacki.DAT\
+	tstackm.DAT\
+	tstacke.DAT\
+	tstacki23.DAT
+
+
+EXTRA_DIST = $(gtfold_data_DATA)
+
+CLEANFILES = *~
+
diff --git a/gtfold-mfe/data/UNAParams/Makefile.in b/gtfold-mfe/data/UNAParams/Makefile.in
new file mode 100644
index 0000000..fa1fe8e
--- /dev/null
+++ b/gtfold-mfe/data/UNAParams/Makefile.in
@@ -0,0 +1,400 @@
+# Makefile.in generated by automake 1.11 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+target_triplet = @target@
+subdir = data/UNAParams
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/gtfold_config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
+DATA = $(gtfold_data_DATA)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMTAR = @AMTAR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CXX = @CXX@
+CXXDEPMODE = @CXXDEPMODE@
+CXXFLAGS = @CXXFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+GREP = @GREP@
+INSTALL = @INSTALL@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+MKDIR_P = @MKDIR_P@
+OBJEXT = @OBJEXT@
+OPENMP_CFLAGS = @OPENMP_CFLAGS@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+VERSION = @VERSION@
+abs_builddir = @abs_builddir@
+abs_srcdir = @abs_srcdir@
+abs_top_builddir = @abs_top_builddir@
+abs_top_srcdir = @abs_top_srcdir@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_CXX = @ac_ct_CXX@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+builddir = @builddir@
+datadir = @datadir@
+datarootdir = @datarootdir@
+docdir = @docdir@
+dvidir = @dvidir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+htmldir = @htmldir@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localedir = @localedir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+pdfdir = @pdfdir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+psdir = @psdir@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+srcdir = @srcdir@
+sysconfdir = @sysconfdir@
+target = @target@
+target_alias = @target_alias@
+target_cpu = @target_cpu@
+target_os = @target_os@
+target_vendor = @target_vendor@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+gtfold_datadir = $(datadir)/@PACKAGE@/UNAParams
+gtfold_data_DATA = \
+	stack.DAT\
+	miscloop.DAT\
+	dangle.DAT\
+	loop.DAT\
+	asint1x2.DAT\
+	sint2.DAT\
+	sint4.DAT\
+	tloop.DAT\
+	tstackh.DAT\
+	tstacki.DAT\
+	tstackm.DAT\
+	tstacke.DAT\
+	tstacki23.DAT
+
+EXTRA_DIST = $(gtfold_data_DATA)
+CLEANFILES = *~
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/UNAParams/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu data/UNAParams/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-gtfold_dataDATA: $(gtfold_data_DATA)
+	@$(NORMAL_INSTALL)
+	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
+	done
+
+uninstall-gtfold_dataDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(DATA)
+installdirs:
+	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am: install-gtfold_dataDATA
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-gtfold_dataDATA
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+	distclean-generic distdir dvi dvi-am html html-am info info-am \
+	install install-am install-data install-data-am install-dvi \
+	install-dvi-am install-exec install-exec-am \
+	install-gtfold_dataDATA install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+	pdf-am ps ps-am uninstall uninstall-am \
+	uninstall-gtfold_dataDATA
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:

From 89d7ef3d08996a6ffd96bee227d11f0970c11b04 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Fri, 24 Jun 2011 12:33:36 -0400
Subject: [PATCH 173/282] added entry UNAParams

---
 gtfold-mfe/data/Makefile.am | 2 +-
 gtfold-mfe/data/Makefile.in | 9 ++++-----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/gtfold-mfe/data/Makefile.am b/gtfold-mfe/data/Makefile.am
index d9d1d43..b6af86e 100644
--- a/gtfold-mfe/data/Makefile.am
+++ b/gtfold-mfe/data/Makefile.am
@@ -1,2 +1,2 @@
-SUBDIRS = Turner04 Turner99 Andronescu
+SUBDIRS = UNAParams Turner04 Turner99 Andronescu 
 
diff --git a/gtfold-mfe/data/Makefile.in b/gtfold-mfe/data/Makefile.in
index 20b49f3..f591147 100644
--- a/gtfold-mfe/data/Makefile.in
+++ b/gtfold-mfe/data/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# Makefile.in generated by automake 1.11 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
@@ -128,7 +128,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 SET_MAKE = @SET_MAKE@
@@ -190,7 +189,7 @@ target_vendor = @target_vendor@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-SUBDIRS = Turner04 Turner99 Andronescu
+SUBDIRS = UNAParams Turner04 Turner99 Andronescu 
 all: all-recursive
 
 .SUFFIXES:
@@ -232,7 +231,7 @@ $(am__aclocal_m4_deps):
 #     (which will cause the Makefiles to be regenerated when you run `make');
 # (2) otherwise, pass the desired values on the `make' command line.
 $(RECURSIVE_TARGETS):
-	@fail= failcom='exit 1'; \
+	@failcom='exit 1'; \
 	for f in x $$MAKEFLAGS; do \
 	  case $$f in \
 	    *=* | --[!k]*);; \
@@ -257,7 +256,7 @@ $(RECURSIVE_TARGETS):
 	fi; test -z "$$fail"
 
 $(RECURSIVE_CLEAN_TARGETS):
-	@fail= failcom='exit 1'; \
+	@failcom='exit 1'; \
 	for f in x $$MAKEFLAGS; do \
 	  case $$f in \
 	    *=* | --[!k]*);; \

From f06c44fd26142141f0e8784f742dd97730922ee0 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Fri, 24 Jun 2011 12:39:29 -0400
Subject: [PATCH 174/282] added entry UNAParams

---
 gtfold-mfe/configure    | 4340 ++++++++++++++++++++++++---------------
 gtfold-mfe/configure.in |    6 +-
 2 files changed, 2653 insertions(+), 1693 deletions(-)

diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure
index 679f8a1..37e6205 100755
--- a/gtfold-mfe/configure
+++ b/gtfold-mfe/configure
@@ -1,22 +1,18 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.67 for gtfold 1.18.
-#
+# Generated by GNU Autoconf 2.63 for gtfold 2.0.
 #
 # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
-# Foundation, Inc.
-#
-#
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
 # This configure script is free software; the Free Software Foundation
 # gives unlimited permission to copy, distribute and modify it.
-## -------------------- ##
-## M4sh Initialization. ##
-## -------------------- ##
+## --------------------- ##
+## M4sh Initialization.  ##
+## --------------------- ##
 
 # Be more Bourne compatible
 DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
   emulate sh
   NULLCMD=:
   # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
@@ -24,15 +20,23 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
   alias -g '${1+"$@"}'='"$@"'
   setopt NO_GLOB_SUBST
 else
-  case `(set -o) 2>/dev/null` in #(
-  *posix*) :
-    set -o posix ;; #(
-  *) :
-     ;;
+  case `(set -o) 2>/dev/null` in
+  *posix*) set -o posix ;;
 esac
+
 fi
 
 
+
+
+# PATH needs CR
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
 as_nl='
 '
 export as_nl
@@ -40,13 +44,7 @@ export as_nl
 as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
 as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
 as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-# Prefer a ksh shell builtin over an external printf program on Solaris,
-# but without wasting forks for bash or zsh.
-if test -z "$BASH_VERSION$ZSH_VERSION" \
-    && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
-  as_echo='print -r --'
-  as_echo_n='print -rn --'
-elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
   as_echo='printf %s\n'
   as_echo_n='printf %s'
 else
@@ -57,7 +55,7 @@ else
     as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
     as_echo_n_body='eval
       arg=$1;
-      case $arg in #(
+      case $arg in
       *"$as_nl"*)
 	expr "X$arg" : "X\\(.*\\)$as_nl";
 	arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
@@ -80,6 +78,13 @@ if test "${PATH_SEPARATOR+set}" != set; then
   }
 fi
 
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+  as_unset=unset
+else
+  as_unset=false
+fi
+
 
 # IFS
 # We need space, tab and new line, in precisely that order.  Quoting is
@@ -89,15 +94,15 @@ fi
 IFS=" ""	$as_nl"
 
 # Find who we are.  Look in the path if we contain no directory separator.
-case $0 in #((
+case $0 in
   *[\\/]* ) as_myself=$0 ;;
   *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
 for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
-  done
+  test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+done
 IFS=$as_save_IFS
 
      ;;
@@ -109,16 +114,12 @@ if test "x$as_myself" = x; then
 fi
 if test ! -f "$as_myself"; then
   $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
-  exit 1
+  { (exit 1); exit 1; }
 fi
 
-# Unset variables that we do not need and which cause bugs (e.g. in
-# pre-3.0 UWIN ksh).  But do not cause bugs in bash 2.01; the "|| exit 1"
-# suppresses any "Segmentation fault" message there.  '((' could
-# trigger a bug in pdksh 5.2.14.
-for as_var in BASH_ENV ENV MAIL MAILPATH
-do eval test x\${$as_var+set} = xset \
-  && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+# Work around bugs in pre-3.0 UWIN ksh.
+for as_var in ENV MAIL MAILPATH
+do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
 done
 PS1='$ '
 PS2='> '
@@ -130,299 +131,330 @@ export LC_ALL
 LANGUAGE=C
 export LANGUAGE
 
+# Required to use basename.
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+   test "X`expr 00001 : '.*\(...\)'`" = X001; then
+  as_expr=expr
+else
+  as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+  as_basename=basename
+else
+  as_basename=false
+fi
+
+
+# Name of the executable.
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+	 X"$0" : 'X\(//\)$' \| \
+	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+    sed '/^.*\/\([^/][^/]*\)\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\/\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\/\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+
 # CDPATH.
-(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+$as_unset CDPATH
+
 
 if test "x$CONFIG_SHELL" = x; then
-  as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
-  emulate sh
-  NULLCMD=:
-  # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
-  # is contrary to our usage.  Disable this feature.
-  alias -g '\${1+\"\$@\"}'='\"\$@\"'
-  setopt NO_GLOB_SUBST
+  if (eval ":") 2>/dev/null; then
+  as_have_required=yes
 else
-  case \`(set -o) 2>/dev/null\` in #(
-  *posix*) :
-    set -o posix ;; #(
-  *) :
-     ;;
-esac
+  as_have_required=no
 fi
-"
-  as_required="as_fn_return () { (exit \$1); }
-as_fn_success () { as_fn_return 0; }
-as_fn_failure () { as_fn_return 1; }
-as_fn_ret_success () { return 0; }
-as_fn_ret_failure () { return 1; }
+
+  if test $as_have_required = yes &&	 (eval ":
+(as_func_return () {
+  (exit \$1)
+}
+as_func_success () {
+  as_func_return 0
+}
+as_func_failure () {
+  as_func_return 1
+}
+as_func_ret_success () {
+  return 0
+}
+as_func_ret_failure () {
+  return 1
+}
 
 exitcode=0
-as_fn_success || { exitcode=1; echo as_fn_success failed.; }
-as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
-as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
-as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
-if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
-
-else
-  exitcode=1; echo positional parameters were not saved.
-fi
-test x\$exitcode = x0 || exit 1"
-  as_suggested="  as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
-  as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
-  eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
-  test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
-test \$(( 1 + 1 )) = 2 || exit 1"
-  if (eval "$as_required") 2>/dev/null; then :
-  as_have_required=yes
+if as_func_success; then
+  :
 else
-  as_have_required=no
+  exitcode=1
+  echo as_func_success failed.
 fi
-  if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
 
+if as_func_failure; then
+  exitcode=1
+  echo as_func_failure succeeded.
+fi
+
+if as_func_ret_success; then
+  :
 else
-  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-as_found=false
+  exitcode=1
+  echo as_func_ret_success failed.
+fi
+
+if as_func_ret_failure; then
+  exitcode=1
+  echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
+  :
+else
+  exitcode=1
+  echo positional parameters were not saved.
+fi
+
+test \$exitcode = 0) || { (exit 1); exit 1; }
+
+(
+  as_lineno_1=\$LINENO
+  as_lineno_2=\$LINENO
+  test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
+  test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
+") 2> /dev/null; then
+  :
+else
+  as_candidate_shells=
+    as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
 for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-  as_found=:
-  case $as_dir in #(
+  case $as_dir in
 	 /*)
 	   for as_base in sh bash ksh sh5; do
-	     # Try only shells that exist, to save several forks.
-	     as_shell=$as_dir/$as_base
-	     if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
-		    { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
-  CONFIG_SHELL=$as_shell as_have_required=yes
-		   if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
-  break 2
-fi
-fi
+	     as_candidate_shells="$as_candidate_shells $as_dir/$as_base"
 	   done;;
        esac
-  as_found=false
 done
-$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
-	      { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
-  CONFIG_SHELL=$SHELL as_have_required=yes
-fi; }
 IFS=$as_save_IFS
 
 
-      if test "x$CONFIG_SHELL" != x; then :
-  # We cannot yet assume a decent shell, so we have to provide a
-	# neutralization value for shells without unset; and this also
-	# works around shells that cannot unset nonexistent variables.
-	BASH_ENV=/dev/null
-	ENV=/dev/null
-	(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
-	export CONFIG_SHELL
-	exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
-fi
+      for as_shell in $as_candidate_shells $SHELL; do
+	 # Try only shells that exist, to save several forks.
+	 if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+		{ ("$as_shell") 2> /dev/null <<\_ASEOF
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+  emulate sh
+  NULLCMD=:
+  # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+  # is contrary to our usage.  Disable this feature.
+  alias -g '${1+"$@"}'='"$@"'
+  setopt NO_GLOB_SUBST
+else
+  case `(set -o) 2>/dev/null` in
+  *posix*) set -o posix ;;
+esac
 
-    if test x$as_have_required = xno; then :
-  $as_echo "$0: This script requires a shell more modern than all"
-  $as_echo "$0: the shells that I found on your system."
-  if test x${ZSH_VERSION+set} = xset ; then
-    $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
-    $as_echo "$0: be upgraded to zsh 4.3.4 or later."
-  else
-    $as_echo "$0: Please tell bug-autoconf@gnu.org about your system,
-$0: including any error possibly output before this
-$0: message. Then install a modern shell, or manually run
-$0: the script under such a shell if you do have one."
-  fi
-  exit 1
-fi
 fi
+
+
+:
+_ASEOF
+}; then
+  CONFIG_SHELL=$as_shell
+	       as_have_required=yes
+	       if { "$as_shell" 2> /dev/null <<\_ASEOF
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+  emulate sh
+  NULLCMD=:
+  # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+  # is contrary to our usage.  Disable this feature.
+  alias -g '${1+"$@"}'='"$@"'
+  setopt NO_GLOB_SUBST
+else
+  case `(set -o) 2>/dev/null` in
+  *posix*) set -o posix ;;
+esac
+
 fi
-SHELL=${CONFIG_SHELL-/bin/sh}
-export SHELL
-# Unset more variables known to interfere with behavior of common tools.
-CLICOLOR_FORCE= GREP_OPTIONS=
-unset CLICOLOR_FORCE GREP_OPTIONS
 
-## --------------------- ##
-## M4sh Shell Functions. ##
-## --------------------- ##
-# as_fn_unset VAR
-# ---------------
-# Portably unset VAR.
-as_fn_unset ()
-{
-  { eval $1=; unset $1;}
+
+:
+(as_func_return () {
+  (exit $1)
+}
+as_func_success () {
+  as_func_return 0
+}
+as_func_failure () {
+  as_func_return 1
+}
+as_func_ret_success () {
+  return 0
+}
+as_func_ret_failure () {
+  return 1
 }
-as_unset=as_fn_unset
 
-# as_fn_set_status STATUS
-# -----------------------
-# Set $? to STATUS, without forking.
-as_fn_set_status ()
-{
-  return $1
-} # as_fn_set_status
+exitcode=0
+if as_func_success; then
+  :
+else
+  exitcode=1
+  echo as_func_success failed.
+fi
 
-# as_fn_exit STATUS
-# -----------------
-# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
-as_fn_exit ()
-{
-  set +e
-  as_fn_set_status $1
-  exit $1
-} # as_fn_exit
-
-# as_fn_mkdir_p
-# -------------
-# Create "$as_dir" as a directory, including parents if necessary.
-as_fn_mkdir_p ()
-{
+if as_func_failure; then
+  exitcode=1
+  echo as_func_failure succeeded.
+fi
 
-  case $as_dir in #(
-  -*) as_dir=./$as_dir;;
-  esac
-  test -d "$as_dir" || eval $as_mkdir_p || {
-    as_dirs=
-    while :; do
-      case $as_dir in #(
-      *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
-      *) as_qdir=$as_dir;;
-      esac
-      as_dirs="'$as_qdir' $as_dirs"
-      as_dir=`$as_dirname -- "$as_dir" ||
-$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-	 X"$as_dir" : 'X\(//\)[^/]' \| \
-	 X"$as_dir" : 'X\(//\)$' \| \
-	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$as_dir" |
-    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)[^/].*/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\).*/{
-	    s//\1/
-	    q
-	  }
-	  s/.*/./; q'`
-      test -d "$as_dir" && break
-    done
-    test -z "$as_dirs" || eval "mkdir $as_dirs"
-  } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
-
-
-} # as_fn_mkdir_p
-# as_fn_append VAR VALUE
-# ----------------------
-# Append the text in VALUE to the end of the definition contained in VAR. Take
-# advantage of any shell optimizations that allow amortized linear growth over
-# repeated appends, instead of the typical quadratic growth present in naive
-# implementations.
-if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
-  eval 'as_fn_append ()
-  {
-    eval $1+=\$2
-  }'
+if as_func_ret_success; then
+  :
 else
-  as_fn_append ()
-  {
-    eval $1=\$$1\$2
-  }
-fi # as_fn_append
-
-# as_fn_arith ARG...
-# ------------------
-# Perform arithmetic evaluation on the ARGs, and store the result in the
-# global $as_val. Take advantage of shells that can avoid forks. The arguments
-# must be portable across $(()) and expr.
-if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
-  eval 'as_fn_arith ()
-  {
-    as_val=$(( $* ))
-  }'
+  exitcode=1
+  echo as_func_ret_success failed.
+fi
+
+if as_func_ret_failure; then
+  exitcode=1
+  echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = "$1" ); then
+  :
 else
-  as_fn_arith ()
-  {
-    as_val=`expr "$@" || test $? -eq 1`
-  }
-fi # as_fn_arith
+  exitcode=1
+  echo positional parameters were not saved.
+fi
 
+test $exitcode = 0) || { (exit 1); exit 1; }
 
-# as_fn_error STATUS ERROR [LINENO LOG_FD]
-# ----------------------------------------
-# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
-# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-# script with STATUS, using 1 if that was 0.
-as_fn_error ()
-{
-  as_status=$1; test $as_status -eq 0 && as_status=1
-  if test "$4"; then
-    as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-    $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
-  fi
-  $as_echo "$as_me: error: $2" >&2
-  as_fn_exit $as_status
-} # as_fn_error
+(
+  as_lineno_1=$LINENO
+  as_lineno_2=$LINENO
+  test "x$as_lineno_1" != "x$as_lineno_2" &&
+  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }
 
-if expr a : '\(a\)' >/dev/null 2>&1 &&
-   test "X`expr 00001 : '.*\(...\)'`" = X001; then
-  as_expr=expr
+_ASEOF
+}; then
+  break
+fi
+
+fi
+
+      done
+
+      if test "x$CONFIG_SHELL" != x; then
+  for as_var in BASH_ENV ENV
+	do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+	done
+	export CONFIG_SHELL
+	exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
+fi
+
+
+    if test $as_have_required = no; then
+  echo This script requires a shell more modern than all the
+      echo shells that I found on your system.  Please install a
+      echo modern shell, or manually run the script under such a
+      echo shell if you do have one.
+      { (exit 1); exit 1; }
+fi
+
+
+fi
+
+fi
+
+
+
+(eval "as_func_return () {
+  (exit \$1)
+}
+as_func_success () {
+  as_func_return 0
+}
+as_func_failure () {
+  as_func_return 1
+}
+as_func_ret_success () {
+  return 0
+}
+as_func_ret_failure () {
+  return 1
+}
+
+exitcode=0
+if as_func_success; then
+  :
 else
-  as_expr=false
+  exitcode=1
+  echo as_func_success failed.
 fi
 
-if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
-  as_basename=basename
+if as_func_failure; then
+  exitcode=1
+  echo as_func_failure succeeded.
+fi
+
+if as_func_ret_success; then
+  :
 else
-  as_basename=false
+  exitcode=1
+  echo as_func_ret_success failed.
 fi
 
-if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
-  as_dirname=dirname
+if as_func_ret_failure; then
+  exitcode=1
+  echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
+  :
 else
-  as_dirname=false
+  exitcode=1
+  echo positional parameters were not saved.
 fi
 
-as_me=`$as_basename -- "$0" ||
-$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
-	 X"$0" : 'X\(//\)$' \| \
-	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X/"$0" |
-    sed '/^.*\/\([^/][^/]*\)\/*$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\/\(\/\/\)$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\/\(\/\).*/{
-	    s//\1/
-	    q
-	  }
-	  s/.*/./; q'`
+test \$exitcode = 0") || {
+  echo No shell found that supports shell functions.
+  echo Please tell bug-autoconf@gnu.org about your system,
+  echo including any error possibly output before this message.
+  echo This can help us improve future autoconf versions.
+  echo Configuration will now proceed without shell functions.
+}
 
-# Avoid depending upon Character Ranges.
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-as_cr_digits='0123456789'
-as_cr_alnum=$as_cr_Letters$as_cr_digits
 
 
-  as_lineno_1=$LINENO as_lineno_1a=$LINENO
-  as_lineno_2=$LINENO as_lineno_2a=$LINENO
-  eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
-  test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
-  # Blame Lee E. McMahon (1931-1989) for sed's syntax.  :-)
+  as_lineno_1=$LINENO
+  as_lineno_2=$LINENO
+  test "x$as_lineno_1" != "x$as_lineno_2" &&
+  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
+
+  # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
+  # uniformly replaced by the line number.  The first 'sed' inserts a
+  # line-number line after each line using $LINENO; the second 'sed'
+  # does the real work.  The second script uses 'N' to pair each
+  # line-number line with the line containing $LINENO, and appends
+  # trailing '-' during substitution so that $LINENO is not a special
+  # case at line end.
+  # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+  # scripts with optimization help from Paolo Bonzini.  Blame Lee
+  # E. McMahon (1931-1989) for sed's syntax.  :-)
   sed -n '
     p
     /[$]LINENO/=
@@ -439,7 +471,8 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits
       s/-\n.*//
     ' >$as_me.lineno &&
   chmod +x "$as_me.lineno" ||
-    { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+    { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
+   { (exit 1); exit 1; }; }
 
   # Don't try to exec as it changes $[0], causing all sort of problems
   # (the dirname of $[0] is not the place where we might find the
@@ -449,18 +482,29 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits
   exit
 }
 
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+  as_dirname=dirname
+else
+  as_dirname=false
+fi
+
 ECHO_C= ECHO_N= ECHO_T=
-case `echo -n x` in #(((((
+case `echo -n x` in
 -n*)
-  case `echo 'xy\c'` in
+  case `echo 'x\c'` in
   *c*) ECHO_T='	';;	# ECHO_T is single tab character.
-  xy)  ECHO_C='\c';;
-  *)   echo `echo ksh88 bug on AIX 6.1` > /dev/null
-       ECHO_T='	';;
+  *)   ECHO_C='\c';;
   esac;;
 *)
   ECHO_N='-n';;
 esac
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+   test "X`expr 00001 : '.*\(...\)'`" = X001; then
+  as_expr=expr
+else
+  as_expr=false
+fi
 
 rm -f conf$$ conf$$.exe conf$$.file
 if test -d conf$$.dir; then
@@ -490,7 +534,7 @@ rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
 rmdir conf$$.dir 2>/dev/null
 
 if mkdir -p . 2>/dev/null; then
-  as_mkdir_p='mkdir -p "$as_dir"'
+  as_mkdir_p=:
 else
   test -d ./-p && rmdir ./-p
   as_mkdir_p=false
@@ -509,10 +553,10 @@ else
       if test -d "$1"; then
 	test -d "$1/.";
       else
-	case $1 in #(
+	case $1 in
 	-*)set "./$1";;
 	esac;
-	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
 	???[sx]*):;;*)false;;esac;fi
     '\'' sh
   '
@@ -526,11 +570,11 @@ as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
 as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
 
 
-test -n "$DJDIR" || exec 7<&0 </dev/null
-exec 6>&1
+
+exec 7<&0 </dev/null 6>&1
 
 # Name of the host.
-# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
+# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
 # so uname gets run too.
 ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
 
@@ -545,14 +589,14 @@ cross_compiling=no
 subdirs=
 MFLAGS=
 MAKEFLAGS=
+SHELL=${CONFIG_SHELL-/bin/sh}
 
 # Identity of this package.
 PACKAGE_NAME='gtfold'
 PACKAGE_TARNAME='gtfold'
-PACKAGE_VERSION='1.18'
-PACKAGE_STRING='gtfold 1.18'
+PACKAGE_VERSION='2.0'
+PACKAGE_STRING='gtfold 2.0'
 PACKAGE_BUGREPORT=''
-PACKAGE_URL=''
 
 ac_unique_file="README"
 # Factoring default headers for most tests.
@@ -688,7 +732,6 @@ bindir
 program_transform_name
 prefix
 exec_prefix
-PACKAGE_URL
 PACKAGE_BUGREPORT
 PACKAGE_STRING
 PACKAGE_VERSION
@@ -778,9 +821,8 @@ do
   fi
 
   case $ac_option in
-  *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
-  *=)   ac_optarg= ;;
-  *)    ac_optarg=yes ;;
+  *=*)	ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+  *)	ac_optarg=yes ;;
   esac
 
   # Accept the important Cygnus configure options, so we can diagnose typos.
@@ -825,7 +867,8 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error $? "invalid feature name: $ac_useropt"
+      { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2
+   { (exit 1); exit 1; }; }
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -851,7 +894,8 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error $? "invalid feature name: $ac_useropt"
+      { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2
+   { (exit 1); exit 1; }; }
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -1055,7 +1099,8 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error $? "invalid package name: $ac_useropt"
+      { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2
+   { (exit 1); exit 1; }; }
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -1071,7 +1116,8 @@ do
     ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
     # Reject names that are not valid shell variable names.
     expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
-      as_fn_error $? "invalid package name: $ac_useropt"
+      { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2
+   { (exit 1); exit 1; }; }
     ac_useropt_orig=$ac_useropt
     ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
     case $ac_user_opts in
@@ -1101,17 +1147,17 @@ do
   | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
     x_libraries=$ac_optarg ;;
 
-  -*) as_fn_error $? "unrecognized option: \`$ac_option'
-Try \`$0 --help' for more information"
+  -*) { $as_echo "$as_me: error: unrecognized option: $ac_option
+Try \`$0 --help' for more information." >&2
+   { (exit 1); exit 1; }; }
     ;;
 
   *=*)
     ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
     # Reject names that are not valid shell variable names.
-    case $ac_envvar in #(
-      '' | [0-9]* | *[!_$as_cr_alnum]* )
-      as_fn_error $? "invalid variable name: \`$ac_envvar'" ;;
-    esac
+    expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null &&
+      { $as_echo "$as_me: error: invalid variable name: $ac_envvar" >&2
+   { (exit 1); exit 1; }; }
     eval $ac_envvar=\$ac_optarg
     export $ac_envvar ;;
 
@@ -1128,13 +1174,15 @@ done
 
 if test -n "$ac_prev"; then
   ac_option=--`echo $ac_prev | sed 's/_/-/g'`
-  as_fn_error $? "missing argument to $ac_option"
+  { $as_echo "$as_me: error: missing argument to $ac_option" >&2
+   { (exit 1); exit 1; }; }
 fi
 
 if test -n "$ac_unrecognized_opts"; then
   case $enable_option_checking in
     no) ;;
-    fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;;
+    fatal) { $as_echo "$as_me: error: unrecognized options: $ac_unrecognized_opts" >&2
+   { (exit 1); exit 1; }; } ;;
     *)     $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;;
   esac
 fi
@@ -1157,7 +1205,8 @@ do
     [\\/$]* | ?:[\\/]* )  continue;;
     NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
   esac
-  as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val"
+  { $as_echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2
+   { (exit 1); exit 1; }; }
 done
 
 # There might be people who depend on the old broken behavior: `$host'
@@ -1171,8 +1220,8 @@ target=$target_alias
 if test "x$host_alias" != x; then
   if test "x$build_alias" = x; then
     cross_compiling=maybe
-    $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host.
-    If a cross compiler is detected then cross compile mode will be used" >&2
+    $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
+    If a cross compiler is detected then cross compile mode will be used." >&2
   elif test "x$build_alias" != "x$host_alias"; then
     cross_compiling=yes
   fi
@@ -1187,9 +1236,11 @@ test "$silent" = yes && exec 6>/dev/null
 ac_pwd=`pwd` && test -n "$ac_pwd" &&
 ac_ls_di=`ls -di .` &&
 ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
-  as_fn_error $? "working directory cannot be determined"
+  { $as_echo "$as_me: error: working directory cannot be determined" >&2
+   { (exit 1); exit 1; }; }
 test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
-  as_fn_error $? "pwd does not report name of working directory"
+  { $as_echo "$as_me: error: pwd does not report name of working directory" >&2
+   { (exit 1); exit 1; }; }
 
 
 # Find the source files, if location was not specified.
@@ -1228,11 +1279,13 @@ else
 fi
 if test ! -r "$srcdir/$ac_unique_file"; then
   test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
-  as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
+  { $as_echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2
+   { (exit 1); exit 1; }; }
 fi
 ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
 ac_abs_confdir=`(
-	cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
+	cd "$srcdir" && test -r "./$ac_unique_file" || { $as_echo "$as_me: error: $ac_msg" >&2
+   { (exit 1); exit 1; }; }
 	pwd)`
 # When building in place, set srcdir=.
 if test "$ac_abs_confdir" = "$ac_pwd"; then
@@ -1258,7 +1311,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures gtfold 1.18 to adapt to many kinds of systems.
+\`configure' configures gtfold 2.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1272,7 +1325,7 @@ Configuration:
       --help=short        display options specific to this package
       --help=recursive    display the short help of all the included packages
   -V, --version           display version information and exit
-  -q, --quiet, --silent   do not print \`checking ...' messages
+  -q, --quiet, --silent   do not print \`checking...' messages
       --cache-file=FILE   cache test results in FILE [disabled]
   -C, --config-cache      alias for \`--cache-file=config.cache'
   -n, --no-create         do not create output files
@@ -1329,7 +1382,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of gtfold 1.18:";;
+     short | recursive ) echo "Configuration of gtfold 2.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1349,537 +1402,93 @@ Some influential environment variables:
   LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
               nonstandard directory <lib dir>
   LIBS        libraries to pass to the linker, e.g. -l<library>
-  CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
+  CPPFLAGS    C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
               you have headers in a nonstandard directory <include dir>
-  CXX         C++ compiler command
-  CXXFLAGS    C++ compiler flags
-  CPP         C preprocessor
-
-Use these variables to override the choices made by `configure' or to help
-it to find libraries and programs with nonstandard names/locations.
-
-Report bugs to the package provider.
-_ACEOF
-ac_status=$?
-fi
-
-if test "$ac_init_help" = "recursive"; then
-  # If there are subdirs, report their specific --help.
-  for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
-    test -d "$ac_dir" ||
-      { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } ||
-      continue
-    ac_builddir=.
-
-case "$ac_dir" in
-.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
-*)
-  ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
-  # A ".." for each directory in $ac_dir_suffix.
-  ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
-  case $ac_top_builddir_sub in
-  "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
-  *)  ac_top_build_prefix=$ac_top_builddir_sub/ ;;
-  esac ;;
-esac
-ac_abs_top_builddir=$ac_pwd
-ac_abs_builddir=$ac_pwd$ac_dir_suffix
-# for backward compatibility:
-ac_top_builddir=$ac_top_build_prefix
-
-case $srcdir in
-  .)  # We are building in place.
-    ac_srcdir=.
-    ac_top_srcdir=$ac_top_builddir_sub
-    ac_abs_top_srcdir=$ac_pwd ;;
-  [\\/]* | ?:[\\/]* )  # Absolute name.
-    ac_srcdir=$srcdir$ac_dir_suffix;
-    ac_top_srcdir=$srcdir
-    ac_abs_top_srcdir=$srcdir ;;
-  *) # Relative name.
-    ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
-    ac_top_srcdir=$ac_top_build_prefix$srcdir
-    ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
-esac
-ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
-
-    cd "$ac_dir" || { ac_status=$?; continue; }
-    # Check for guested configure.
-    if test -f "$ac_srcdir/configure.gnu"; then
-      echo &&
-      $SHELL "$ac_srcdir/configure.gnu" --help=recursive
-    elif test -f "$ac_srcdir/configure"; then
-      echo &&
-      $SHELL "$ac_srcdir/configure" --help=recursive
-    else
-      $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
-    fi || ac_status=$?
-    cd "$ac_pwd" || { ac_status=$?; break; }
-  done
-fi
-
-test -n "$ac_init_help" && exit $ac_status
-if $ac_init_version; then
-  cat <<\_ACEOF
-gtfold configure 1.18
-generated by GNU Autoconf 2.67
-
-Copyright (C) 2010 Free Software Foundation, Inc.
-This configure script is free software; the Free Software Foundation
-gives unlimited permission to copy, distribute and modify it.
-_ACEOF
-  exit
-fi
-
-## ------------------------ ##
-## Autoconf initialization. ##
-## ------------------------ ##
-
-# ac_fn_c_try_compile LINENO
-# --------------------------
-# Try to compile conftest.$ac_ext, and return whether this succeeded.
-ac_fn_c_try_compile ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  rm -f conftest.$ac_objext
-  if { { ac_try="$ac_compile"
-case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_compile") 2>conftest.err
-  ac_status=$?
-  if test -s conftest.err; then
-    grep -v '^ *+' conftest.err >conftest.er1
-    cat conftest.er1 >&5
-    mv -f conftest.er1 conftest.err
-  fi
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; } && {
-	 test -z "$ac_c_werror_flag" ||
-	 test ! -s conftest.err
-       } && test -s conftest.$ac_objext; then :
-  ac_retval=0
-else
-  $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-	ac_retval=1
-fi
-  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-  as_fn_set_status $ac_retval
-
-} # ac_fn_c_try_compile
-
-# ac_fn_cxx_try_compile LINENO
-# ----------------------------
-# Try to compile conftest.$ac_ext, and return whether this succeeded.
-ac_fn_cxx_try_compile ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  rm -f conftest.$ac_objext
-  if { { ac_try="$ac_compile"
-case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_compile") 2>conftest.err
-  ac_status=$?
-  if test -s conftest.err; then
-    grep -v '^ *+' conftest.err >conftest.er1
-    cat conftest.er1 >&5
-    mv -f conftest.er1 conftest.err
-  fi
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; } && {
-	 test -z "$ac_cxx_werror_flag" ||
-	 test ! -s conftest.err
-       } && test -s conftest.$ac_objext; then :
-  ac_retval=0
-else
-  $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-	ac_retval=1
-fi
-  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-  as_fn_set_status $ac_retval
-
-} # ac_fn_cxx_try_compile
-
-# ac_fn_c_try_link LINENO
-# -----------------------
-# Try to link conftest.$ac_ext, and return whether this succeeded.
-ac_fn_c_try_link ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  rm -f conftest.$ac_objext conftest$ac_exeext
-  if { { ac_try="$ac_link"
-case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_link") 2>conftest.err
-  ac_status=$?
-  if test -s conftest.err; then
-    grep -v '^ *+' conftest.err >conftest.er1
-    cat conftest.er1 >&5
-    mv -f conftest.er1 conftest.err
-  fi
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; } && {
-	 test -z "$ac_c_werror_flag" ||
-	 test ! -s conftest.err
-       } && test -s conftest$ac_exeext && {
-	 test "$cross_compiling" = yes ||
-	 $as_test_x conftest$ac_exeext
-       }; then :
-  ac_retval=0
-else
-  $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-	ac_retval=1
-fi
-  # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
-  # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
-  # interfere with the next link command; also delete a directory that is
-  # left behind by Apple's compiler.  We do this before executing the actions.
-  rm -rf conftest.dSYM conftest_ipa8_conftest.oo
-  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-  as_fn_set_status $ac_retval
-
-} # ac_fn_c_try_link
-
-# ac_fn_c_try_cpp LINENO
-# ----------------------
-# Try to preprocess conftest.$ac_ext, and return whether this succeeded.
-ac_fn_c_try_cpp ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  if { { ac_try="$ac_cpp conftest.$ac_ext"
-case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err
-  ac_status=$?
-  if test -s conftest.err; then
-    grep -v '^ *+' conftest.err >conftest.er1
-    cat conftest.er1 >&5
-    mv -f conftest.er1 conftest.err
-  fi
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; } > conftest.i && {
-	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
-	 test ! -s conftest.err
-       }; then :
-  ac_retval=0
-else
-  $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-    ac_retval=1
-fi
-  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-  as_fn_set_status $ac_retval
-
-} # ac_fn_c_try_cpp
-
-# ac_fn_c_try_run LINENO
-# ----------------------
-# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes
-# that executables *can* be run.
-ac_fn_c_try_run ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  if { { ac_try="$ac_link"
-case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_link") 2>&5
-  ac_status=$?
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; } && { ac_try='./conftest$ac_exeext'
-  { { case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_try") 2>&5
-  ac_status=$?
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; }; }; then :
-  ac_retval=0
-else
-  $as_echo "$as_me: program exited with status $ac_status" >&5
-       $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-       ac_retval=$ac_status
-fi
-  rm -rf conftest.dSYM conftest_ipa8_conftest.oo
-  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-  as_fn_set_status $ac_retval
-
-} # ac_fn_c_try_run
-
-# ac_fn_c_check_header_mongrel LINENO HEADER VAR INCLUDES
-# -------------------------------------------------------
-# Tests whether HEADER exists, giving a warning if it cannot be compiled using
-# the include files in INCLUDES and setting the cache variable VAR
-# accordingly.
-ac_fn_c_check_header_mongrel ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  if eval "test \"\${$3+set}\"" = set; then :
-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-$as_echo_n "checking for $2... " >&6; }
-if eval "test \"\${$3+set}\"" = set; then :
-  $as_echo_n "(cached) " >&6
-fi
-eval ac_res=\$$3
-	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-else
-  # Is the header compilable?
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5
-$as_echo_n "checking $2 usability... " >&6; }
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-$4
-#include <$2>
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
-  ac_header_compiler=yes
-else
-  ac_header_compiler=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5
-$as_echo "$ac_header_compiler" >&6; }
-
-# Is the header present?
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5
-$as_echo_n "checking $2 presence... " >&6; }
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#include <$2>
-_ACEOF
-if ac_fn_c_try_cpp "$LINENO"; then :
-  ac_header_preproc=yes
-else
-  ac_header_preproc=no
-fi
-rm -f conftest.err conftest.i conftest.$ac_ext
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
-$as_echo "$ac_header_preproc" >&6; }
-
-# So?  What about this header?
-case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in #((
-  yes:no: )
-    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5
-$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;}
-    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
-$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
-    ;;
-  no:yes:* )
-    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5
-$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;}
-    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2:     check for missing prerequisite headers?" >&5
-$as_echo "$as_me: WARNING: $2:     check for missing prerequisite headers?" >&2;}
-    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5
-$as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
-    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2:     section \"Present But Cannot Be Compiled\"" >&5
-$as_echo "$as_me: WARNING: $2:     section \"Present But Cannot Be Compiled\"" >&2;}
-    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
-$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
-    ;;
-esac
-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-$as_echo_n "checking for $2... " >&6; }
-if eval "test \"\${$3+set}\"" = set; then :
-  $as_echo_n "(cached) " >&6
-else
-  eval "$3=\$ac_header_compiler"
-fi
-eval ac_res=\$$3
-	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-fi
-  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-
-} # ac_fn_c_check_header_mongrel
-
-# ac_fn_c_check_header_compile LINENO HEADER VAR INCLUDES
-# -------------------------------------------------------
-# Tests whether HEADER exists and can be compiled using the include files in
-# INCLUDES, setting the cache variable VAR accordingly.
-ac_fn_c_check_header_compile ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-$as_echo_n "checking for $2... " >&6; }
-if eval "test \"\${$3+set}\"" = set; then :
-  $as_echo_n "(cached) " >&6
-else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-$4
-#include <$2>
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
-  eval "$3=yes"
-else
-  eval "$3=no"
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-eval ac_res=\$$3
-	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+  CXX         C++ compiler command
+  CXXFLAGS    C++ compiler flags
+  CPP         C preprocessor
 
-} # ac_fn_c_check_header_compile
+Use these variables to override the choices made by `configure' or to help
+it to find libraries and programs with nonstandard names/locations.
 
-# ac_fn_c_check_type LINENO TYPE VAR INCLUDES
-# -------------------------------------------
-# Tests whether TYPE exists after having included INCLUDES, setting cache
-# variable VAR accordingly.
-ac_fn_c_check_type ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-$as_echo_n "checking for $2... " >&6; }
-if eval "test \"\${$3+set}\"" = set; then :
-  $as_echo_n "(cached) " >&6
-else
-  eval "$3=no"
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-$4
-int
-main ()
-{
-if (sizeof ($2))
-	 return 0;
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-$4
-int
-main ()
-{
-if (sizeof (($2)))
-	    return 0;
-  ;
-  return 0;
-}
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
-
-else
-  eval "$3=yes"
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_status=$?
 fi
-eval ac_res=\$$3
-	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-
-} # ac_fn_c_check_type
 
-# ac_fn_c_check_func LINENO FUNC VAR
-# ----------------------------------
-# Tests whether FUNC exists, setting the cache variable VAR accordingly
-ac_fn_c_check_func ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-$as_echo_n "checking for $2... " >&6; }
-if eval "test \"\${$3+set}\"" = set; then :
-  $as_echo_n "(cached) " >&6
-else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
-   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
-#define $2 innocuous_$2
+if test "$ac_init_help" = "recursive"; then
+  # If there are subdirs, report their specific --help.
+  for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
+    test -d "$ac_dir" ||
+      { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } ||
+      continue
+    ac_builddir=.
 
-/* System header to define __stub macros and hopefully few prototypes,
-    which can conflict with char $2 (); below.
-    Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
-    <limits.h> exists even on freestanding compilers.  */
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+  ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+  # A ".." for each directory in $ac_dir_suffix.
+  ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+  case $ac_top_builddir_sub in
+  "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+  *)  ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+  esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
 
-#ifdef __STDC__
-# include <limits.h>
-#else
-# include <assert.h>
-#endif
+case $srcdir in
+  .)  # We are building in place.
+    ac_srcdir=.
+    ac_top_srcdir=$ac_top_builddir_sub
+    ac_abs_top_srcdir=$ac_pwd ;;
+  [\\/]* | ?:[\\/]* )  # Absolute name.
+    ac_srcdir=$srcdir$ac_dir_suffix;
+    ac_top_srcdir=$srcdir
+    ac_abs_top_srcdir=$srcdir ;;
+  *) # Relative name.
+    ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+    ac_top_srcdir=$ac_top_build_prefix$srcdir
+    ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
 
-#undef $2
+    cd "$ac_dir" || { ac_status=$?; continue; }
+    # Check for guested configure.
+    if test -f "$ac_srcdir/configure.gnu"; then
+      echo &&
+      $SHELL "$ac_srcdir/configure.gnu" --help=recursive
+    elif test -f "$ac_srcdir/configure"; then
+      echo &&
+      $SHELL "$ac_srcdir/configure" --help=recursive
+    else
+      $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
+    fi || ac_status=$?
+    cd "$ac_pwd" || { ac_status=$?; break; }
+  done
+fi
 
-/* Override any GCC internal prototype to avoid an error.
-   Use char because int might match the return type of a GCC
-   builtin and then its argument prototype would still apply.  */
-#ifdef __cplusplus
-extern "C"
-#endif
-char $2 ();
-/* The GNU C library defines this for functions which it implements
-    to always fail with ENOSYS.  Some functions are actually named
-    something starting with __ and the normal name is an alias.  */
-#if defined __stub_$2 || defined __stub___$2
-choke me
-#endif
+test -n "$ac_init_help" && exit $ac_status
+if $ac_init_version; then
+  cat <<\_ACEOF
+gtfold configure 2.0
+generated by GNU Autoconf 2.63
 
-int
-main ()
-{
-return $2 ();
-  ;
-  return 0;
-}
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
 _ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
-  eval "$3=yes"
-else
-  eval "$3=no"
-fi
-rm -f core conftest.err conftest.$ac_objext \
-    conftest$ac_exeext conftest.$ac_ext
+  exit
 fi
-eval ac_res=\$$3
-	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-  eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
-
-} # ac_fn_c_check_func
 cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by gtfold $as_me 1.18, which was
-generated by GNU Autoconf 2.67.  Invocation command line was
+It was created by gtfold $as_me 2.0, which was
+generated by GNU Autoconf 2.63.  Invocation command line was
 
   $ $0 $@
 
@@ -1915,8 +1524,8 @@ for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    $as_echo "PATH: $as_dir"
-  done
+  $as_echo "PATH: $as_dir"
+done
 IFS=$as_save_IFS
 
 } >&5
@@ -1953,9 +1562,9 @@ do
       ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
     esac
     case $ac_pass in
-    1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
+    1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;;
     2)
-      as_fn_append ac_configure_args1 " '$ac_arg'"
+      ac_configure_args1="$ac_configure_args1 '$ac_arg'"
       if test $ac_must_keep_next = true; then
 	ac_must_keep_next=false # Got value, back to normal.
       else
@@ -1971,13 +1580,13 @@ do
 	  -* ) ac_must_keep_next=true ;;
 	esac
       fi
-      as_fn_append ac_configure_args " '$ac_arg'"
+      ac_configure_args="$ac_configure_args '$ac_arg'"
       ;;
     esac
   done
 done
-{ ac_configure_args0=; unset ac_configure_args0;}
-{ ac_configure_args1=; unset ac_configure_args1;}
+$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; }
+$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; }
 
 # When interrupted or exit'd, cleanup temporary files, and complete
 # config.log.  We remove comments because anyway the quotes in there
@@ -1989,9 +1598,11 @@ trap 'exit_status=$?
   {
     echo
 
-    $as_echo "## ---------------- ##
+    cat <<\_ASBOX
+## ---------------- ##
 ## Cache variables. ##
-## ---------------- ##"
+## ---------------- ##
+_ASBOX
     echo
     # The following way of writing the cache mishandles newlines in values,
 (
@@ -2000,13 +1611,13 @@ trap 'exit_status=$?
     case $ac_val in #(
     *${as_nl}*)
       case $ac_var in #(
-      *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+      *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5
 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
       esac
       case $ac_var in #(
       _ | IFS | as_nl) ;; #(
       BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
-      *) { eval $ac_var=; unset $ac_var;} ;;
+      *) $as_unset $ac_var ;;
       esac ;;
     esac
   done
@@ -2025,9 +1636,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
 )
     echo
 
-    $as_echo "## ----------------- ##
+    cat <<\_ASBOX
+## ----------------- ##
 ## Output variables. ##
-## ----------------- ##"
+## ----------------- ##
+_ASBOX
     echo
     for ac_var in $ac_subst_vars
     do
@@ -2040,9 +1653,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
     echo
 
     if test -n "$ac_subst_files"; then
-      $as_echo "## ------------------- ##
+      cat <<\_ASBOX
+## ------------------- ##
 ## File substitutions. ##
-## ------------------- ##"
+## ------------------- ##
+_ASBOX
       echo
       for ac_var in $ac_subst_files
       do
@@ -2056,9 +1671,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
     fi
 
     if test -s confdefs.h; then
-      $as_echo "## ----------- ##
+      cat <<\_ASBOX
+## ----------- ##
 ## confdefs.h. ##
-## ----------- ##"
+## ----------- ##
+_ASBOX
       echo
       cat confdefs.h
       echo
@@ -2072,39 +1689,37 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
     exit $exit_status
 ' 0
 for ac_signal in 1 2 13 15; do
-  trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
+  trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal
 done
 ac_signal=0
 
 # confdefs.h avoids OS command line length limits that DEFS can exceed.
 rm -f -r conftest* confdefs.h
 
-$as_echo "/* confdefs.h */" > confdefs.h
-
 # Predefined preprocessor variables.
 
 cat >>confdefs.h <<_ACEOF
 #define PACKAGE_NAME "$PACKAGE_NAME"
 _ACEOF
 
+
 cat >>confdefs.h <<_ACEOF
 #define PACKAGE_TARNAME "$PACKAGE_TARNAME"
 _ACEOF
 
+
 cat >>confdefs.h <<_ACEOF
 #define PACKAGE_VERSION "$PACKAGE_VERSION"
 _ACEOF
 
+
 cat >>confdefs.h <<_ACEOF
 #define PACKAGE_STRING "$PACKAGE_STRING"
 _ACEOF
 
-cat >>confdefs.h <<_ACEOF
-#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
-_ACEOF
 
 cat >>confdefs.h <<_ACEOF
-#define PACKAGE_URL "$PACKAGE_URL"
+#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
 _ACEOF
 
 
@@ -2113,12 +1728,7 @@ _ACEOF
 ac_site_file1=NONE
 ac_site_file2=NONE
 if test -n "$CONFIG_SITE"; then
-  # We do not want a PATH search for config.site.
-  case $CONFIG_SITE in #((
-    -*)  ac_site_file1=./$CONFIG_SITE;;
-    */*) ac_site_file1=$CONFIG_SITE;;
-    *)   ac_site_file1=./$CONFIG_SITE;;
-  esac
+  ac_site_file1=$CONFIG_SITE
 elif test "x$prefix" != xNONE; then
   ac_site_file1=$prefix/share/config.site
   ac_site_file2=$prefix/etc/config.site
@@ -2129,23 +1739,19 @@ fi
 for ac_site_file in "$ac_site_file1" "$ac_site_file2"
 do
   test "x$ac_site_file" = xNONE && continue
-  if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
-    { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
+  if test -r "$ac_site_file"; then
+    { $as_echo "$as_me:$LINENO: loading site script $ac_site_file" >&5
 $as_echo "$as_me: loading site script $ac_site_file" >&6;}
     sed 's/^/| /' "$ac_site_file" >&5
-    . "$ac_site_file" \
-      || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "failed to load site script $ac_site_file
-See \`config.log' for more details" "$LINENO" 5 ; }
+    . "$ac_site_file"
   fi
 done
 
 if test -r "$cache_file"; then
-  # Some versions of bash will fail to source /dev/null (special files
-  # actually), so we avoid doing that.  DJGPP emulates it as a regular file.
-  if test /dev/null != "$cache_file" && test -f "$cache_file"; then
-    { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
+  # Some versions of bash will fail to source /dev/null (special
+  # files actually), so we avoid doing that.
+  if test -f "$cache_file"; then
+    { $as_echo "$as_me:$LINENO: loading cache $cache_file" >&5
 $as_echo "$as_me: loading cache $cache_file" >&6;}
     case $cache_file in
       [\\/]* | ?:[\\/]* ) . "$cache_file";;
@@ -2153,7 +1759,7 @@ $as_echo "$as_me: loading cache $cache_file" >&6;}
     esac
   fi
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
+  { $as_echo "$as_me:$LINENO: creating cache $cache_file" >&5
 $as_echo "$as_me: creating cache $cache_file" >&6;}
   >$cache_file
 fi
@@ -2168,11 +1774,11 @@ for ac_var in $ac_precious_vars; do
   eval ac_new_val=\$ac_env_${ac_var}_value
   case $ac_old_set,$ac_new_set in
     set,)
-      { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+      { $as_echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
 $as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
       ac_cache_corrupted=: ;;
     ,set)
-      { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
+      { $as_echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5
 $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
       ac_cache_corrupted=: ;;
     ,);;
@@ -2182,17 +1788,17 @@ $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
 	ac_old_val_w=`echo x $ac_old_val`
 	ac_new_val_w=`echo x $ac_new_val`
 	if test "$ac_old_val_w" != "$ac_new_val_w"; then
-	  { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
+	  { $as_echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5
 $as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
 	  ac_cache_corrupted=:
 	else
-	  { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+	  { $as_echo "$as_me:$LINENO: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
 $as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
 	  eval $ac_var=\$ac_old_val
 	fi
-	{ $as_echo "$as_me:${as_lineno-$LINENO}:   former value:  \`$ac_old_val'" >&5
+	{ $as_echo "$as_me:$LINENO:   former value:  \`$ac_old_val'" >&5
 $as_echo "$as_me:   former value:  \`$ac_old_val'" >&2;}
-	{ $as_echo "$as_me:${as_lineno-$LINENO}:   current value: \`$ac_new_val'" >&5
+	{ $as_echo "$as_me:$LINENO:   current value: \`$ac_new_val'" >&5
 $as_echo "$as_me:   current value: \`$ac_new_val'" >&2;}
       fi;;
   esac
@@ -2204,20 +1810,43 @@ $as_echo "$as_me:   current value: \`$ac_new_val'" >&2;}
     esac
     case " $ac_configure_args " in
       *" '$ac_arg' "*) ;; # Avoid dups.  Use of quotes ensures accuracy.
-      *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+      *) ac_configure_args="$ac_configure_args '$ac_arg'" ;;
     esac
   fi
 done
 if $ac_cache_corrupted; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+  { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-  { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+  { $as_echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5
 $as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
-  as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5
+$as_echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;}
+   { (exit 1); exit 1; }; }
 fi
-## -------------------- ##
-## Main body of script. ##
-## -------------------- ##
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 
 ac_ext=c
 ac_cpp='$CPP $CPPFLAGS'
@@ -2249,7 +1878,9 @@ for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
   fi
 done
 if test -z "$ac_aux_dir"; then
-  as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&5
+$as_echo "$as_me: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&2;}
+   { (exit 1); exit 1; }; }
 fi
 
 # These three variables are undocumented and unsupported,
@@ -2263,27 +1894,35 @@ ac_configure="$SHELL $ac_aux_dir/configure"  # Please don't use this var.
 
 # Make sure we can run config.sub.
 $SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
-  as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: cannot run $SHELL $ac_aux_dir/config.sub" >&5
+$as_echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;}
+   { (exit 1); exit 1; }; }
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
+{ $as_echo "$as_me:$LINENO: checking build system type" >&5
 $as_echo_n "checking build system type... " >&6; }
-if test "${ac_cv_build+set}" = set; then :
+if test "${ac_cv_build+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   ac_build_alias=$build_alias
 test "x$ac_build_alias" = x &&
   ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
 test "x$ac_build_alias" = x &&
-  as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5
+$as_echo "$as_me: error: cannot guess build type; you must specify one" >&2;}
+   { (exit 1); exit 1; }; }
 ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
-  as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5
+$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;}
+   { (exit 1); exit 1; }; }
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_build" >&5
 $as_echo "$ac_cv_build" >&6; }
 case $ac_cv_build in
 *-*-*) ;;
-*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;;
+*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical build" >&5
+$as_echo "$as_me: error: invalid value of canonical build" >&2;}
+   { (exit 1); exit 1; }; };;
 esac
 build=$ac_cv_build
 ac_save_IFS=$IFS; IFS='-'
@@ -2299,24 +1938,28 @@ IFS=$ac_save_IFS
 case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
 
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5
+{ $as_echo "$as_me:$LINENO: checking host system type" >&5
 $as_echo_n "checking host system type... " >&6; }
-if test "${ac_cv_host+set}" = set; then :
+if test "${ac_cv_host+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test "x$host_alias" = x; then
   ac_cv_host=$ac_cv_build
 else
   ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
-    as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
+    { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5
+$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;}
+   { (exit 1); exit 1; }; }
 fi
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_host" >&5
 $as_echo "$ac_cv_host" >&6; }
 case $ac_cv_host in
 *-*-*) ;;
-*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;;
+*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical host" >&5
+$as_echo "$as_me: error: invalid value of canonical host" >&2;}
+   { (exit 1); exit 1; }; };;
 esac
 host=$ac_cv_host
 ac_save_IFS=$IFS; IFS='-'
@@ -2332,24 +1975,28 @@ IFS=$ac_save_IFS
 case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
 
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking target system type" >&5
+{ $as_echo "$as_me:$LINENO: checking target system type" >&5
 $as_echo_n "checking target system type... " >&6; }
-if test "${ac_cv_target+set}" = set; then :
+if test "${ac_cv_target+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test "x$target_alias" = x; then
   ac_cv_target=$ac_cv_host
 else
   ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` ||
-    as_fn_error $? "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5
+    { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&5
+$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&2;}
+   { (exit 1); exit 1; }; }
 fi
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_target" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_target" >&5
 $as_echo "$ac_cv_target" >&6; }
 case $ac_cv_target in
 *-*-*) ;;
-*) as_fn_error $? "invalid value of canonical target" "$LINENO" 5 ;;
+*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical target" >&5
+$as_echo "$as_me: error: invalid value of canonical target" >&2;}
+   { (exit 1); exit 1; }; };;
 esac
 target=$ac_cv_target
 ac_save_IFS=$IFS; IFS='-'
@@ -2388,10 +2035,10 @@ am__api_version='1.11'
 # OS/2's system install, which has a completely different semantic
 # ./install, which can be erroneously created by make from ./install.sh.
 # Reject install programs that cannot install multiple files.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
+{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
 $as_echo_n "checking for a BSD-compatible install... " >&6; }
 if test -z "$INSTALL"; then
-if test "${ac_cv_path_install+set}" = set; then :
+if test "${ac_cv_path_install+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
@@ -2399,11 +2046,11 @@ for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    # Account for people who put trailing slashes in PATH elements.
-case $as_dir/ in #((
-  ./ | .// | /[cC]/* | \
+  # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in
+  ./ | .// | /cC/* | \
   /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
-  ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
+  ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
   /usr/ucb/* ) ;;
   *)
     # OSF1 and SCO ODT 3.0 have their own names for install.
@@ -2440,7 +2087,7 @@ case $as_dir/ in #((
     ;;
 esac
 
-  done
+done
 IFS=$as_save_IFS
 
 rm -rf conftest.one conftest.two conftest.dir
@@ -2456,7 +2103,7 @@ fi
     INSTALL=$ac_install_sh
   fi
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
+{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5
 $as_echo "$INSTALL" >&6; }
 
 # Use test -z because SunOS4 sh mishandles braces in ${var-val}.
@@ -2467,7 +2114,7 @@ test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
 
 test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
+{ $as_echo "$as_me:$LINENO: checking whether build environment is sane" >&5
 $as_echo_n "checking whether build environment is sane... " >&6; }
 # Just in case
 sleep 1
@@ -2478,11 +2125,15 @@ am_lf='
 '
 case `pwd` in
   *[\\\"\#\$\&\'\`$am_lf]*)
-    as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;;
+    { { $as_echo "$as_me:$LINENO: error: unsafe absolute working directory name" >&5
+$as_echo "$as_me: error: unsafe absolute working directory name" >&2;}
+   { (exit 1); exit 1; }; };;
 esac
 case $srcdir in
   *[\\\"\#\$\&\'\`$am_lf\ \	]*)
-    as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;;
+    { { $as_echo "$as_me:$LINENO: error: unsafe srcdir value: \`$srcdir'" >&5
+$as_echo "$as_me: error: unsafe srcdir value: \`$srcdir'" >&2;}
+   { (exit 1); exit 1; }; };;
 esac
 
 # Do `set' in a subshell so we don't clobber the current shell's
@@ -2504,8 +2155,11 @@ if (
       # if, for instance, CONFIG_SHELL is bash and it inherits a
       # broken ls alias from the environment.  This has actually
       # happened.  Such a system could not be considered "sane".
-      as_fn_error $? "ls -t appears to fail.  Make sure there is not a broken
-alias in your environment" "$LINENO" 5
+      { { $as_echo "$as_me:$LINENO: error: ls -t appears to fail.  Make sure there is not a broken
+alias in your environment" >&5
+$as_echo "$as_me: error: ls -t appears to fail.  Make sure there is not a broken
+alias in your environment" >&2;}
+   { (exit 1); exit 1; }; }
    fi
 
    test "$2" = conftest.file
@@ -2514,10 +2168,13 @@ then
    # Ok.
    :
 else
-   as_fn_error $? "newly created file is older than distributed files!
-Check your system clock" "$LINENO" 5
+   { { $as_echo "$as_me:$LINENO: error: newly created file is older than distributed files!
+Check your system clock" >&5
+$as_echo "$as_me: error: newly created file is older than distributed files!
+Check your system clock" >&2;}
+   { (exit 1); exit 1; }; }
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+{ $as_echo "$as_me:$LINENO: result: yes" >&5
 $as_echo "yes" >&6; }
 test "$program_prefix" != NONE &&
   program_transform_name="s&^&$program_prefix&;$program_transform_name"
@@ -2545,7 +2202,7 @@ if eval "$MISSING --run true"; then
   am_missing_run="$MISSING --run "
 else
   am_missing_run=
-  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
+  { $as_echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5
 $as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
 fi
 
@@ -2566,9 +2223,9 @@ if test "$cross_compiling" != no; then
   if test -n "$ac_tool_prefix"; then
   # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
 set dummy ${ac_tool_prefix}strip; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_STRIP+set}" = set; then :
+if test "${ac_cv_prog_STRIP+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test -n "$STRIP"; then
@@ -2579,24 +2236,24 @@ for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    for ac_exec_ext in '' $ac_executable_extensions; do
+  for ac_exec_ext in '' $ac_executable_extensions; do
   if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
     ac_cv_prog_STRIP="${ac_tool_prefix}strip"
-    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
   fi
 done
-  done
+done
 IFS=$as_save_IFS
 
 fi
 fi
 STRIP=$ac_cv_prog_STRIP
 if test -n "$STRIP"; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+  { $as_echo "$as_me:$LINENO: result: $STRIP" >&5
 $as_echo "$STRIP" >&6; }
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  { $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
 fi
 
@@ -2606,9 +2263,9 @@ if test -z "$ac_cv_prog_STRIP"; then
   ac_ct_STRIP=$STRIP
   # Extract the first word of "strip", so it can be a program name with args.
 set dummy strip; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then :
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test -n "$ac_ct_STRIP"; then
@@ -2619,24 +2276,24 @@ for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    for ac_exec_ext in '' $ac_executable_extensions; do
+  for ac_exec_ext in '' $ac_executable_extensions; do
   if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
     ac_cv_prog_ac_ct_STRIP="strip"
-    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
   fi
 done
-  done
+done
 IFS=$as_save_IFS
 
 fi
 fi
 ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
 if test -n "$ac_ct_STRIP"; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+  { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5
 $as_echo "$ac_ct_STRIP" >&6; }
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  { $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
 fi
 
@@ -2645,7 +2302,7 @@ fi
   else
     case $cross_compiling:$ac_tool_warned in
 yes:)
-{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
 ac_tool_warned=yes ;;
 esac
@@ -2658,10 +2315,10 @@ fi
 fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
+{ $as_echo "$as_me:$LINENO: checking for a thread-safe mkdir -p" >&5
 $as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
 if test -z "$MKDIR_P"; then
-  if test "${ac_cv_path_mkdir+set}" = set; then :
+  if test "${ac_cv_path_mkdir+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
@@ -2669,7 +2326,7 @@ for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    for ac_prog in mkdir gmkdir; do
+  for ac_prog in mkdir gmkdir; do
 	 for ac_exec_ext in '' $ac_executable_extensions; do
 	   { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
 	   case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
@@ -2681,12 +2338,11 @@ do
 	   esac
 	 done
        done
-  done
+done
 IFS=$as_save_IFS
 
 fi
 
-  test -d ./--version && rmdir ./--version
   if test "${ac_cv_path_mkdir+set}" = set; then
     MKDIR_P="$ac_cv_path_mkdir -p"
   else
@@ -2694,10 +2350,11 @@ fi
     # value for MKDIR_P within a source directory, because that will
     # break other packages using the cache if that directory is
     # removed, or if the value is a relative name.
+    test -d ./--version && rmdir ./--version
     MKDIR_P="$ac_install_sh -d"
   fi
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
+{ $as_echo "$as_me:$LINENO: result: $MKDIR_P" >&5
 $as_echo "$MKDIR_P" >&6; }
 
 mkdir_p="$MKDIR_P"
@@ -2710,9 +2367,9 @@ for ac_prog in gawk mawk nawk awk
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
 set dummy $ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_AWK+set}" = set; then :
+if test "${ac_cv_prog_AWK+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test -n "$AWK"; then
@@ -2723,24 +2380,24 @@ for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    for ac_exec_ext in '' $ac_executable_extensions; do
+  for ac_exec_ext in '' $ac_executable_extensions; do
   if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
     ac_cv_prog_AWK="$ac_prog"
-    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
   fi
 done
-  done
+done
 IFS=$as_save_IFS
 
 fi
 fi
 AWK=$ac_cv_prog_AWK
 if test -n "$AWK"; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+  { $as_echo "$as_me:$LINENO: result: $AWK" >&5
 $as_echo "$AWK" >&6; }
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  { $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
 fi
 
@@ -2748,11 +2405,11 @@ fi
   test -n "$AWK" && break
 done
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
 $as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
 set x ${MAKE-make}
 ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
-if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then :
+if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then
   $as_echo_n "(cached) " >&6
 else
   cat >conftest.make <<\_ACEOF
@@ -2760,7 +2417,7 @@ SHELL = /bin/sh
 all:
 	@echo '@@@%%%=$(MAKE)=@@@%%%'
 _ACEOF
-# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
 case `${MAKE-make} -f conftest.make 2>/dev/null` in
   *@@@%%%=?*=@@@%%%*)
     eval ac_cv_prog_make_${ac_make}_set=yes;;
@@ -2770,11 +2427,11 @@ esac
 rm -f conftest.make
 fi
 if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+  { $as_echo "$as_me:$LINENO: result: yes" >&5
 $as_echo "yes" >&6; }
   SET_MAKE=
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  { $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
   SET_MAKE="MAKE=${MAKE-make}"
 fi
@@ -2794,7 +2451,9 @@ if test "`cd $srcdir && pwd`" != "`pwd`"; then
   am__isrc=' -I$(srcdir)'
   # test to see if srcdir already configured
   if test -f $srcdir/config.status; then
-    as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+    { { $as_echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5
+$as_echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;}
+   { (exit 1); exit 1; }; }
   fi
 fi
 
@@ -2810,7 +2469,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='gtfold'
- VERSION='1.18'
+ VERSION='2.0'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -2852,11 +2511,13 @@ am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
 
 
 # Check whether --enable-64bit was given.
-if test "${enable_64bit+set}" = set; then :
+if test "${enable_64bit+set}" = set; then
   enableval=$enable_64bit; case "${enableval}" in
     "" | y | ye | yes) gtfold_cv_enable_64bit=yes ;;
     n | no) gtfold_cv_enable_64bit=no ;;
-    *) as_fn_error $? "bad value ${enableval} for --enable-64bit" "$LINENO" 5  ;;
+    *) { { $as_echo "$as_me:$LINENO: error: bad value ${enableval} for --enable-64bit" >&5
+$as_echo "$as_me: error: bad value ${enableval} for --enable-64bit" >&2;}
+   { (exit 1); exit 1; }; } ;;
   esac
 else
   gtfold_cv_enable_64bit=no
@@ -2887,9 +2548,9 @@ if test -n "$ac_tool_prefix"; then
   do
     # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
 set dummy $ac_tool_prefix$ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_CC+set}" = set; then :
+if test "${ac_cv_prog_CC+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test -n "$CC"; then
@@ -2900,24 +2561,24 @@ for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    for ac_exec_ext in '' $ac_executable_extensions; do
+  for ac_exec_ext in '' $ac_executable_extensions; do
   if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
     ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
-    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
   fi
 done
-  done
+done
 IFS=$as_save_IFS
 
 fi
 fi
 CC=$ac_cv_prog_CC
 if test -n "$CC"; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+  { $as_echo "$as_me:$LINENO: result: $CC" >&5
 $as_echo "$CC" >&6; }
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  { $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
 fi
 
@@ -2931,9 +2592,9 @@ if test -z "$CC"; then
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
 set dummy $ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test -n "$ac_ct_CC"; then
@@ -2944,24 +2605,24 @@ for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    for ac_exec_ext in '' $ac_executable_extensions; do
+  for ac_exec_ext in '' $ac_executable_extensions; do
   if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
     ac_cv_prog_ac_ct_CC="$ac_prog"
-    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
   fi
 done
-  done
+done
 IFS=$as_save_IFS
 
 fi
 fi
 ac_ct_CC=$ac_cv_prog_ac_ct_CC
 if test -n "$ac_ct_CC"; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+  { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
 $as_echo "$ac_ct_CC" >&6; }
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  { $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
 fi
 
@@ -2974,7 +2635,7 @@ done
   else
     case $cross_compiling:$ac_tool_warned in
 yes:)
-{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
 ac_tool_warned=yes ;;
 esac
@@ -2983,37 +2644,57 @@ esac
 fi
 
 
-test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "no acceptable C compiler found in \$PATH
-See \`config.log' for more details" "$LINENO" 5 ; }
+{ { $as_echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }; }
 
 # Provide some information about the compiler.
-$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+$as_echo "$as_me:$LINENO: checking for C compiler version" >&5
 set X $ac_compile
 ac_compiler=$2
-for ac_option in --version -v -V -qversion; do
-  { { ac_try="$ac_compiler $ac_option >&5"
+{ (ac_try="$ac_compiler --version >&5"
 case "(($ac_try" in
   *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
   *) ac_try_echo=$ac_try;;
 esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compiler --version >&5") 2>&5
   ac_status=$?
-  if test -s conftest.err; then
-    sed '10a\
-... rest of stderr output deleted ...
-         10q' conftest.err >conftest.er1
-    cat conftest.er1 >&5
-  fi
-  rm -f conftest.er1 conftest.err
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; }
-done
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compiler -v >&5") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compiler -V >&5") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
 
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -3029,8 +2710,8 @@ ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
 # Try to create an executable without -o first, disregard a.out.
 # It will help us diagnose broken compilers, and finding out an intuition
 # of exeext.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
-$as_echo_n "checking whether the C compiler works... " >&6; }
+{ $as_echo "$as_me:$LINENO: checking for C compiler default output file name" >&5
+$as_echo_n "checking for C compiler default output file name... " >&6; }
 ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
 
 # The possible output files:
@@ -3046,17 +2727,17 @@ do
 done
 rm -f $ac_rmfiles
 
-if { { ac_try="$ac_link_default"
+if { (ac_try="$ac_link_default"
 case "(($ac_try" in
   *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
   *) ac_try_echo=$ac_try;;
 esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
   (eval "$ac_link_default") 2>&5
   ac_status=$?
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; }; then :
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
   # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
 # So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
 # in a Makefile.  We should not override ac_cv_exeext if it was cached,
@@ -3073,7 +2754,7 @@ do
 	# certainly right.
 	break;;
     *.* )
-	if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+        if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
 	then :; else
 	   ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
 	fi
@@ -3092,132 +2773,124 @@ test "$ac_cv_exeext" = no && ac_cv_exeext=
 else
   ac_file=''
 fi
-if test -z "$ac_file"; then :
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
 
-{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error 77 "C compiler cannot create executables
-See \`config.log' for more details" "$LINENO" 5 ; }
-else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
-$as_echo_n "checking for C compiler default output file name... " >&6; }
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_file" >&5
 $as_echo "$ac_file" >&6; }
-ac_exeext=$ac_cv_exeext
+if test -z "$ac_file"; then
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
 
-rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
-ac_clean_files=$ac_clean_files_save
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
-$as_echo_n "checking for suffix of executables... " >&6; }
-if { { ac_try="$ac_link"
-case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_link") 2>&5
-  ac_status=$?
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; }; then :
-  # If both `conftest.exe' and `conftest' are `present' (well, observable)
-# catch `conftest.exe'.  For instance with Cygwin, `ls conftest' will
-# work properly (i.e., refer to `conftest.exe'), while it won't with
-# `rm'.
-for ac_file in conftest.exe conftest conftest.*; do
-  test -f "$ac_file" || continue
-  case $ac_file in
-    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
-    *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
-	  break;;
-    * ) break;;
-  esac
-done
-else
-  { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "cannot compute suffix of executables: cannot compile and link
-See \`config.log' for more details" "$LINENO" 5 ; }
+{ { $as_echo "$as_me:$LINENO: error: C compiler cannot create executables
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: C compiler cannot create executables
+See \`config.log' for more details." >&2;}
+   { (exit 77); exit 77; }; }; }
 fi
-rm -f conftest conftest$ac_cv_exeext
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
-$as_echo "$ac_cv_exeext" >&6; }
 
-rm -f conftest.$ac_ext
-EXEEXT=$ac_cv_exeext
-ac_exeext=$EXEEXT
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#include <stdio.h>
-int
-main ()
-{
-FILE *f = fopen ("conftest.out", "w");
- return ferror (f) || fclose (f) != 0;
+ac_exeext=$ac_cv_exeext
 
-  ;
-  return 0;
-}
-_ACEOF
-ac_clean_files="$ac_clean_files conftest.out"
 # Check that the compiler produces executables we can run.  If not, either
 # the compiler is broken, or we cross compile.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
-$as_echo_n "checking whether we are cross compiling... " >&6; }
+{ $as_echo "$as_me:$LINENO: checking whether the C compiler works" >&5
+$as_echo_n "checking whether the C compiler works... " >&6; }
+# FIXME: These cross compiler hacks should be removed for Autoconf 3.0
+# If not cross compiling, check that we can run a simple program.
 if test "$cross_compiling" != yes; then
-  { { ac_try="$ac_link"
-case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_link") 2>&5
-  ac_status=$?
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; }
-  if { ac_try='./conftest$ac_cv_exeext'
-  { { case "(($ac_try" in
+  if { ac_try='./$ac_file'
+  { (case "(($ac_try" in
   *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
   *) ac_try_echo=$ac_try;;
 esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
   (eval "$ac_try") 2>&5
   ac_status=$?
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; }; }; then
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
     cross_compiling=no
   else
     if test "$cross_compiling" = maybe; then
 	cross_compiling=yes
     else
-	{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+	{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "cannot run C compiled programs.
+{ { $as_echo "$as_me:$LINENO: error: cannot run C compiled programs.
 If you meant to cross compile, use \`--host'.
-See \`config.log' for more details" "$LINENO" 5 ; }
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }; }
     fi
   fi
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
-$as_echo "$cross_compiling" >&6; }
+{ $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
 
-rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
 ac_clean_files=$ac_clean_files_save
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
+# Check that the compiler produces executables we can run.  If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:$LINENO: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+{ $as_echo "$as_me:$LINENO: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+{ $as_echo "$as_me:$LINENO: checking for suffix of executables" >&5
+$as_echo_n "checking for suffix of executables... " >&6; }
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
+  # If both `conftest.exe' and `conftest' are `present' (well, observable)
+# catch `conftest.exe'.  For instance with Cygwin, `ls conftest' will
+# work properly (i.e., refer to `conftest.exe'), while it won't with
+# `rm'.
+for ac_file in conftest.exe conftest conftest.*; do
+  test -f "$ac_file" || continue
+  case $ac_file in
+    *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+    *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+	  break;;
+    * ) break;;
+  esac
+done
+else
+  { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }; }
+fi
+
+rm -f conftest$ac_cv_exeext
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5
+$as_echo "$ac_cv_exeext" >&6; }
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+{ $as_echo "$as_me:$LINENO: checking for suffix of object files" >&5
 $as_echo_n "checking for suffix of object files... " >&6; }
-if test "${ac_cv_objext+set}" = set; then :
+if test "${ac_cv_objext+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -3229,17 +2902,17 @@ main ()
 }
 _ACEOF
 rm -f conftest.o conftest.obj
-if { { ac_try="$ac_compile"
+if { (ac_try="$ac_compile"
 case "(($ac_try" in
   *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
   *) ac_try_echo=$ac_try;;
 esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
   (eval "$ac_compile") 2>&5
   ac_status=$?
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; }; then :
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; then
   for ac_file in conftest.o conftest.obj conftest.*; do
   test -f "$ac_file" || continue;
   case $ac_file in
@@ -3252,23 +2925,31 @@ else
   $as_echo "$as_me: failed program was:" >&5
 sed 's/^/| /' conftest.$ac_ext >&5
 
-{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "cannot compute suffix of object files: cannot compile
-See \`config.log' for more details" "$LINENO" 5 ; }
+{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }; }
 fi
+
 rm -f conftest.$ac_cv_objext conftest.$ac_ext
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_objext" >&5
 $as_echo "$ac_cv_objext" >&6; }
 OBJEXT=$ac_cv_objext
 ac_objext=$OBJEXT
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5
 $as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
-if test "${ac_cv_c_compiler_gnu+set}" = set; then :
+if test "${ac_cv_c_compiler_gnu+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -3282,16 +2963,37 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_compiler_gnu=yes
 else
-  ac_compiler_gnu=no
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_compiler_gnu=no
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 ac_cv_c_compiler_gnu=$ac_compiler_gnu
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5
 $as_echo "$ac_cv_c_compiler_gnu" >&6; }
 if test $ac_compiler_gnu = yes; then
   GCC=yes
@@ -3300,16 +3002,20 @@ else
 fi
 ac_test_CFLAGS=${CFLAGS+set}
 ac_save_CFLAGS=$CFLAGS
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5
 $as_echo_n "checking whether $CC accepts -g... " >&6; }
-if test "${ac_cv_prog_cc_g+set}" = set; then :
+if test "${ac_cv_prog_cc_g+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   ac_save_c_werror_flag=$ac_c_werror_flag
    ac_c_werror_flag=yes
    ac_cv_prog_cc_g=no
    CFLAGS="-g"
-   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+   cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -3320,11 +3026,35 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_cv_prog_cc_g=yes
 else
-  CFLAGS=""
-      cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	CFLAGS=""
+      cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -3335,12 +3065,36 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
-
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  :
 else
-  ac_c_werror_flag=$ac_save_c_werror_flag
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_c_werror_flag=$ac_save_c_werror_flag
 	 CFLAGS="-g"
-	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+	 cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -3351,17 +3105,42 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_cv_prog_cc_g=yes
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
    ac_c_werror_flag=$ac_save_c_werror_flag
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5
 $as_echo "$ac_cv_prog_cc_g" >&6; }
 if test "$ac_test_CFLAGS" = set; then
   CFLAGS=$ac_save_CFLAGS
@@ -3378,14 +3157,18 @@ else
     CFLAGS=
   fi
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5
 $as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
-if test "${ac_cv_prog_cc_c89+set}" = set; then :
+if test "${ac_cv_prog_cc_c89+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   ac_cv_prog_cc_c89=no
 ac_save_CC=$CC
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #include <stdarg.h>
 #include <stdio.h>
@@ -3442,9 +3225,32 @@ for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
 	-Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
 do
   CC="$ac_save_CC $ac_arg"
-  if ac_fn_c_try_compile "$LINENO"; then :
+  rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_cv_prog_cc_c89=$ac_arg
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
 fi
+
 rm -f core conftest.err conftest.$ac_objext
   test "x$ac_cv_prog_cc_c89" != "xno" && break
 done
@@ -3455,19 +3261,17 @@ fi
 # AC_CACHE_VAL
 case "x$ac_cv_prog_cc_c89" in
   x)
-    { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+    { $as_echo "$as_me:$LINENO: result: none needed" >&5
 $as_echo "none needed" >&6; } ;;
   xno)
-    { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+    { $as_echo "$as_me:$LINENO: result: unsupported" >&5
 $as_echo "unsupported" >&6; } ;;
   *)
     CC="$CC $ac_cv_prog_cc_c89"
-    { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+    { $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5
 $as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
 esac
-if test "x$ac_cv_prog_cc_c89" != xno; then :
 
-fi
 
 ac_ext=c
 ac_cpp='$CPP $CPPFLAGS'
@@ -3486,7 +3290,7 @@ am__doit:
 .PHONY: am__doit
 END
 # If we don't find an include directive, just comment out the code.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
+{ $as_echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5
 $as_echo_n "checking for style of include used by $am_make... " >&6; }
 am__include="#"
 am__quote=
@@ -3514,12 +3318,12 @@ if test "$am__include" = "#"; then
 fi
 
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
+{ $as_echo "$as_me:$LINENO: result: $_am_result" >&5
 $as_echo "$_am_result" >&6; }
 rm -f confinc confmf
 
 # Check whether --enable-dependency-tracking was given.
-if test "${enable_dependency_tracking+set}" = set; then :
+if test "${enable_dependency_tracking+set}" = set; then
   enableval=$enable_dependency_tracking;
 fi
 
@@ -3539,9 +3343,9 @@ fi
 
 depcc="$CC"   am_compiler_list=
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
 $as_echo_n "checking dependency style of $depcc... " >&6; }
-if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then :
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
@@ -3649,7 +3453,7 @@ else
 fi
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+{ $as_echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5
 $as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
 CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
 
@@ -3678,9 +3482,9 @@ if test -z "$CXX"; then
   do
     # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
 set dummy $ac_tool_prefix$ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_CXX+set}" = set; then :
+if test "${ac_cv_prog_CXX+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test -n "$CXX"; then
@@ -3691,24 +3495,24 @@ for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    for ac_exec_ext in '' $ac_executable_extensions; do
+  for ac_exec_ext in '' $ac_executable_extensions; do
   if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
     ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
-    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
   fi
 done
-  done
+done
 IFS=$as_save_IFS
 
 fi
 fi
 CXX=$ac_cv_prog_CXX
 if test -n "$CXX"; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+  { $as_echo "$as_me:$LINENO: result: $CXX" >&5
 $as_echo "$CXX" >&6; }
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  { $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
 fi
 
@@ -3722,9 +3526,9 @@ if test -z "$CXX"; then
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
 set dummy $ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then :
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test -n "$ac_ct_CXX"; then
@@ -3735,24 +3539,24 @@ for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    for ac_exec_ext in '' $ac_executable_extensions; do
+  for ac_exec_ext in '' $ac_executable_extensions; do
   if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
     ac_cv_prog_ac_ct_CXX="$ac_prog"
-    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
   fi
 done
-  done
+done
 IFS=$as_save_IFS
 
 fi
 fi
 ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
 if test -n "$ac_ct_CXX"; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+  { $as_echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5
 $as_echo "$ac_ct_CXX" >&6; }
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  { $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
 fi
 
@@ -3765,7 +3569,7 @@ done
   else
     case $cross_compiling:$ac_tool_warned in
 yes:)
-{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
 ac_tool_warned=yes ;;
 esac
@@ -3776,36 +3580,53 @@ fi
   fi
 fi
 # Provide some information about the compiler.
-$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+$as_echo "$as_me:$LINENO: checking for C++ compiler version" >&5
 set X $ac_compile
 ac_compiler=$2
-for ac_option in --version -v -V -qversion; do
-  { { ac_try="$ac_compiler $ac_option >&5"
+{ (ac_try="$ac_compiler --version >&5"
 case "(($ac_try" in
   *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
   *) ac_try_echo=$ac_try;;
 esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compiler --version >&5") 2>&5
   ac_status=$?
-  if test -s conftest.err; then
-    sed '10a\
-... rest of stderr output deleted ...
-         10q' conftest.err >conftest.er1
-    cat conftest.er1 >&5
-  fi
-  rm -f conftest.er1 conftest.err
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; }
-done
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compiler -v >&5") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compiler -V >&5") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
+{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5
 $as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
-if test "${ac_cv_cxx_compiler_gnu+set}" = set; then :
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -3819,16 +3640,37 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_compiler_gnu=yes
 else
-  ac_compiler_gnu=no
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_compiler_gnu=no
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5
 $as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
 if test $ac_compiler_gnu = yes; then
   GXX=yes
@@ -3837,16 +3679,20 @@ else
 fi
 ac_test_CXXFLAGS=${CXXFLAGS+set}
 ac_save_CXXFLAGS=$CXXFLAGS
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
+{ $as_echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5
 $as_echo_n "checking whether $CXX accepts -g... " >&6; }
-if test "${ac_cv_prog_cxx_g+set}" = set; then :
+if test "${ac_cv_prog_cxx_g+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   ac_save_cxx_werror_flag=$ac_cxx_werror_flag
    ac_cxx_werror_flag=yes
    ac_cv_prog_cxx_g=no
    CXXFLAGS="-g"
-   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+   cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -3857,11 +3703,35 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_cv_prog_cxx_g=yes
 else
-  CXXFLAGS=""
-      cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	CXXFLAGS=""
+      cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -3872,12 +3742,36 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
-
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  :
 else
-  ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cxx_werror_flag=$ac_save_cxx_werror_flag
 	 CXXFLAGS="-g"
-	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+	 cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -3888,17 +3782,42 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_cv_prog_cxx_g=yes
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
    ac_cxx_werror_flag=$ac_save_cxx_werror_flag
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5
 $as_echo "$ac_cv_prog_cxx_g" >&6; }
 if test "$ac_test_CXXFLAGS" = set; then
   CXXFLAGS=$ac_save_CXXFLAGS
@@ -3923,9 +3842,9 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 depcc="$CXX"  am_compiler_list=
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
 $as_echo_n "checking dependency style of $depcc... " >&6; }
-if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then :
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
@@ -4033,7 +3952,7 @@ else
 fi
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5
+{ $as_echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5
 $as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
 CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
 
@@ -4048,25 +3967,116 @@ else
 fi
 
 
-#AC_PROG_LIBTOOL
+#AC_PROG_LIBTOOL
+# Find a good install program.  We prefer a C program (faster),
+# so one script is as good as another.  But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if test "${ac_cv_path_install+set}" = set; then
+  $as_echo_n "(cached) " >&6
+else
+  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in
+  ./ | .// | /cC/* | \
+  /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+  ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
+  /usr/ucb/* ) ;;
+  *)
+    # OSF1 and SCO ODT 3.0 have their own names for install.
+    # Don't use installbsd from OSF since it installs stuff as root
+    # by default.
+    for ac_prog in ginstall scoinst install; do
+      for ac_exec_ext in '' $ac_executable_extensions; do
+	if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+	  if test $ac_prog = install &&
+	    grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+	    # AIX install.  It has an incompatible calling convention.
+	    :
+	  elif test $ac_prog = install &&
+	    grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+	    # program-specific install script used by HP pwplus--don't use.
+	    :
+	  else
+	    rm -rf conftest.one conftest.two conftest.dir
+	    echo one > conftest.one
+	    echo two > conftest.two
+	    mkdir conftest.dir
+	    if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+	      test -s conftest.one && test -s conftest.two &&
+	      test -s conftest.dir/conftest.one &&
+	      test -s conftest.dir/conftest.two
+	    then
+	      ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+	      break 3
+	    fi
+	  fi
+	fi
+      done
+    done
+    ;;
+esac
+
+done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+  if test "${ac_cv_path_install+set}" = set; then
+    INSTALL=$ac_cv_path_install
+  else
+    # As a last resort, use the slow shell script.  Don't cache a
+    # value for INSTALL within a source directory, because that will
+    # break other packages using the cache if that directory is
+    # removed, or if the value is a relative name.
+    INSTALL=$ac_install_sh
+  fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
 
 
 
 
   OPENMP_CFLAGS=
   # Check whether --enable-openmp was given.
-if test "${enable_openmp+set}" = set; then :
+if test "${enable_openmp+set}" = set; then
   enableval=$enable_openmp;
 fi
 
   if test "$enable_openmp" != no; then
-    { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to support OpenMP" >&5
+    { $as_echo "$as_me:$LINENO: checking for $CC option to support OpenMP" >&5
 $as_echo_n "checking for $CC option to support OpenMP... " >&6; }
-if test "${ac_cv_prog_c_openmp+set}" = set; then :
+if test "${ac_cv_prog_c_openmp+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
+  cat >conftest.$ac_ext <<_ACEOF
 
 #ifndef _OPENMP
  choke me
@@ -4075,15 +4085,37 @@ else
 int main () { return omp_get_num_threads (); }
 
 _ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 $as_test_x conftest$ac_exeext
+       }; then
   ac_cv_prog_c_openmp='none needed'
 else
-  ac_cv_prog_c_openmp='unsupported'
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_prog_c_openmp='unsupported'
 	  	  	  	  	  	  	  	  	  	  	  	  	  for ac_option in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
 	    ac_save_CFLAGS=$CFLAGS
 	    CFLAGS="$CFLAGS $ac_option"
-	    cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
+	    cat >conftest.$ac_ext <<_ACEOF
 
 #ifndef _OPENMP
  choke me
@@ -4092,27 +4124,56 @@ else
 int main () { return omp_get_num_threads (); }
 
 _ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 $as_test_x conftest$ac_exeext
+       }; then
   ac_cv_prog_c_openmp=$ac_option
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
 fi
-rm -f core conftest.err conftest.$ac_objext \
-    conftest$ac_exeext conftest.$ac_ext
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
 	    CFLAGS=$ac_save_CFLAGS
 	    if test "$ac_cv_prog_c_openmp" != unsupported; then
 	      break
 	    fi
 	  done
 fi
-rm -f core conftest.err conftest.$ac_objext \
-    conftest$ac_exeext conftest.$ac_ext
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_c_openmp" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_c_openmp" >&5
 $as_echo "$ac_cv_prog_c_openmp" >&6; }
     case $ac_cv_prog_c_openmp in #(
       "none needed" | unsupported)
-	;; #(
+        ;; #(
       *)
-	OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;;
+        OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;;
     esac
   fi
 
@@ -4120,14 +4181,18 @@ $as_echo "$ac_cv_prog_c_openmp" >&6; }
 
 #AC_DEFINE([_RAND],[],[RNG library to use])
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for log2 in -lm" >&5
+{ $as_echo "$as_me:$LINENO: checking for log2 in -lm" >&5
 $as_echo_n "checking for log2 in -lm... " >&6; }
-if test "${ac_cv_lib_m_log2+set}" = set; then :
+if test "${ac_cv_lib_m_log2+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
 LIBS="-lm  $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 /* Override any GCC internal prototype to avoid an error.
@@ -4145,20 +4210,47 @@ return log2 ();
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 $as_test_x conftest$ac_exeext
+       }; then
   ac_cv_lib_m_log2=yes
 else
-  ac_cv_lib_m_log2=no
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_m_log2=no
 fi
-rm -f core conftest.err conftest.$ac_objext \
-    conftest$ac_exeext conftest.$ac_ext
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
 LIBS=$ac_check_lib_save_LIBS
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_log2" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_m_log2" >&5
 $as_echo "$ac_cv_lib_m_log2" >&6; }
-if test "x$ac_cv_lib_m_log2" = x""yes; then :
+if test "x$ac_cv_lib_m_log2" = x""yes; then
 
-$as_echo "#define HAVE_LOG2 /**/" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_LOG2 /**/
+_ACEOF
 
 fi
 
@@ -4168,14 +4260,14 @@ ac_cpp='$CPP $CPPFLAGS'
 ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
 ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5
+{ $as_echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5
 $as_echo_n "checking how to run the C preprocessor... " >&6; }
 # On Suns, sometimes $CPP names a directory.
 if test -n "$CPP" && test -d "$CPP"; then
   CPP=
 fi
 if test -z "$CPP"; then
-  if test "${ac_cv_prog_CPP+set}" = set; then :
+  if test "${ac_cv_prog_CPP+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
       # Double quotes because CPP needs to be expanded
@@ -4190,7 +4282,11 @@ do
   # <limits.h> exists even on freestanding compilers.
   # On the NeXT, cc -E runs the code through the compiler's parser,
   # not just through cpp. "Syntax error" is here to catch this case.
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #ifdef __STDC__
 # include <limits.h>
@@ -4199,34 +4295,78 @@ do
 #endif
 		     Syntax error
 _ACEOF
-if ac_fn_c_try_cpp "$LINENO"; then :
-
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  :
 else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
   # Broken: fails on valid input.
 continue
 fi
-rm -f conftest.err conftest.i conftest.$ac_ext
+
+rm -f conftest.err conftest.$ac_ext
 
   # OK, works on sane cases.  Now check whether nonexistent headers
   # can be detected and how.
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #include <ac_nonexistent.h>
 _ACEOF
-if ac_fn_c_try_cpp "$LINENO"; then :
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
   # Broken: success on invalid input.
 continue
 else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
   # Passes both tests.
 ac_preproc_ok=:
 break
 fi
-rm -f conftest.err conftest.i conftest.$ac_ext
+
+rm -f conftest.err conftest.$ac_ext
 
 done
 # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
-rm -f conftest.i conftest.err conftest.$ac_ext
-if $ac_preproc_ok; then :
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
   break
 fi
 
@@ -4238,7 +4378,7 @@ fi
 else
   ac_cv_prog_CPP=$CPP
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5
+{ $as_echo "$as_me:$LINENO: result: $CPP" >&5
 $as_echo "$CPP" >&6; }
 ac_preproc_ok=false
 for ac_c_preproc_warn_flag in '' yes
@@ -4249,7 +4389,11 @@ do
   # <limits.h> exists even on freestanding compilers.
   # On the NeXT, cc -E runs the code through the compiler's parser,
   # not just through cpp. "Syntax error" is here to catch this case.
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #ifdef __STDC__
 # include <limits.h>
@@ -4258,40 +4402,87 @@ do
 #endif
 		     Syntax error
 _ACEOF
-if ac_fn_c_try_cpp "$LINENO"; then :
-
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  :
 else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
   # Broken: fails on valid input.
 continue
 fi
-rm -f conftest.err conftest.i conftest.$ac_ext
+
+rm -f conftest.err conftest.$ac_ext
 
   # OK, works on sane cases.  Now check whether nonexistent headers
   # can be detected and how.
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #include <ac_nonexistent.h>
 _ACEOF
-if ac_fn_c_try_cpp "$LINENO"; then :
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
   # Broken: success on invalid input.
 continue
 else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
   # Passes both tests.
 ac_preproc_ok=:
 break
 fi
-rm -f conftest.err conftest.i conftest.$ac_ext
+
+rm -f conftest.err conftest.$ac_ext
 
 done
 # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
-rm -f conftest.i conftest.err conftest.$ac_ext
-if $ac_preproc_ok; then :
-
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+  :
 else
-  { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+  { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "C preprocessor \"$CPP\" fails sanity check
-See \`config.log' for more details" "$LINENO" 5 ; }
+{ { $as_echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&2;}
+   { (exit 1); exit 1; }; }; }
 fi
 
 ac_ext=c
@@ -4301,9 +4492,9 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
+{ $as_echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5
 $as_echo_n "checking for grep that handles long lines and -e... " >&6; }
-if test "${ac_cv_path_GREP+set}" = set; then :
+if test "${ac_cv_path_GREP+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if test -z "$GREP"; then
@@ -4314,7 +4505,7 @@ for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    for ac_prog in grep ggrep; do
+  for ac_prog in grep ggrep; do
     for ac_exec_ext in '' $ac_executable_extensions; do
       ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
       { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
@@ -4334,7 +4525,7 @@ case `"$ac_path_GREP" --version 2>&1` in
     $as_echo 'GREP' >> "conftest.nl"
     "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
     diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
-    as_fn_arith $ac_count + 1 && ac_count=$as_val
+    ac_count=`expr $ac_count + 1`
     if test $ac_count -gt ${ac_path_GREP_max-0}; then
       # Best one so far, save it but keep looking for a better one
       ac_cv_path_GREP="$ac_path_GREP"
@@ -4349,24 +4540,26 @@ esac
       $ac_path_GREP_found && break 3
     done
   done
-  done
+done
 IFS=$as_save_IFS
   if test -z "$ac_cv_path_GREP"; then
-    as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+    { { $as_echo "$as_me:$LINENO: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
+$as_echo "$as_me: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
+   { (exit 1); exit 1; }; }
   fi
 else
   ac_cv_path_GREP=$GREP
 fi
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5
 $as_echo "$ac_cv_path_GREP" >&6; }
  GREP="$ac_cv_path_GREP"
 
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
+{ $as_echo "$as_me:$LINENO: checking for egrep" >&5
 $as_echo_n "checking for egrep... " >&6; }
-if test "${ac_cv_path_EGREP+set}" = set; then :
+if test "${ac_cv_path_EGREP+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
@@ -4380,7 +4573,7 @@ for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    for ac_prog in egrep; do
+  for ac_prog in egrep; do
     for ac_exec_ext in '' $ac_executable_extensions; do
       ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
       { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
@@ -4400,7 +4593,7 @@ case `"$ac_path_EGREP" --version 2>&1` in
     $as_echo 'EGREP' >> "conftest.nl"
     "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
     diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
-    as_fn_arith $ac_count + 1 && ac_count=$as_val
+    ac_count=`expr $ac_count + 1`
     if test $ac_count -gt ${ac_path_EGREP_max-0}; then
       # Best one so far, save it but keep looking for a better one
       ac_cv_path_EGREP="$ac_path_EGREP"
@@ -4415,10 +4608,12 @@ esac
       $ac_path_EGREP_found && break 3
     done
   done
-  done
+done
 IFS=$as_save_IFS
   if test -z "$ac_cv_path_EGREP"; then
-    as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+    { { $as_echo "$as_me:$LINENO: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
+$as_echo "$as_me: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
+   { (exit 1); exit 1; }; }
   fi
 else
   ac_cv_path_EGREP=$EGREP
@@ -4426,17 +4621,21 @@ fi
 
    fi
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5
 $as_echo "$ac_cv_path_EGREP" >&6; }
  EGREP="$ac_cv_path_EGREP"
 
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
+{ $as_echo "$as_me:$LINENO: checking for ANSI C header files" >&5
 $as_echo_n "checking for ANSI C header files... " >&6; }
-if test "${ac_cv_header_stdc+set}" = set; then :
+if test "${ac_cv_header_stdc+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #include <stdlib.h>
 #include <stdarg.h>
@@ -4451,23 +4650,48 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_cv_header_stdc=yes
 else
-  ac_cv_header_stdc=no
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_header_stdc=no
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 
 if test $ac_cv_header_stdc = yes; then
   # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #include <string.h>
 
 _ACEOF
 if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
-  $EGREP "memchr" >/dev/null 2>&1; then :
-
+  $EGREP "memchr" >/dev/null 2>&1; then
+  :
 else
   ac_cv_header_stdc=no
 fi
@@ -4477,14 +4701,18 @@ fi
 
 if test $ac_cv_header_stdc = yes; then
   # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #include <stdlib.h>
 
 _ACEOF
 if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
-  $EGREP "free" >/dev/null 2>&1; then :
-
+  $EGREP "free" >/dev/null 2>&1; then
+  :
 else
   ac_cv_header_stdc=no
 fi
@@ -4494,10 +4722,14 @@ fi
 
 if test $ac_cv_header_stdc = yes; then
   # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
-  if test "$cross_compiling" = yes; then :
+  if test "$cross_compiling" = yes; then
   :
 else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #include <ctype.h>
 #include <stdlib.h>
@@ -4524,49 +4756,269 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_run "$LINENO"; then :
-
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+  { (case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); }; }; then
+  :
 else
-  ac_cv_header_stdc=no
+  $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_header_stdc=no
 fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
-  conftest.$ac_objext conftest.beam conftest.$ac_ext
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
 fi
 
+
 fi
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5
 $as_echo "$ac_cv_header_stdc" >&6; }
 if test $ac_cv_header_stdc = yes; then
 
-$as_echo "#define STDC_HEADERS 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define STDC_HEADERS 1
+_ACEOF
 
 fi
 
 #AC_CHECK_HEADERS(sys/resource.h)
 #AC_CHECK_HEADERS(getopt.h)
 # On IRIX 5.3, sys/types and inttypes.h are conflicting.
+
+
+
+
+
+
+
+
+
 for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
 		  inttypes.h stdint.h unistd.h
-do :
-  as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
-"
-if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  $as_echo_n "(cached) " >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  eval "$as_ac_Header=yes"
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	eval "$as_ac_Header=no"
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+		 $as_echo "$as_val"'`
+	       { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_Header'}
+		 $as_echo "$as_val"'`
+   if test "x$as_val" = x""yes; then
   cat >>confdefs.h <<_ACEOF
 #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
 _ACEOF
 
 fi
-
-done
-
-
-for ac_header in stdlib.h string.h sys/time.h
-do :
-  as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
-if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+
+done
+
+
+
+
+
+for ac_header in stdlib.h string.h sys/time.h
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  $as_echo_n "(cached) " >&6
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+		 $as_echo "$as_val"'`
+	       { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+  # Is the header compilable?
+{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5
+$as_echo_n "checking $ac_header usability... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_header_compiler=yes
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5
+$as_echo_n "checking $ac_header presence... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <$ac_header>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  ac_header_preproc=yes
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So?  What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+  yes:no: )
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+    ac_header_preproc=yes
+    ;;
+  no:yes:* )
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header:     check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $ac_header:     check for missing prerequisite headers?" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header:     section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $ac_header:     section \"Present But Cannot Be Compiled\"" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+
+    ;;
+esac
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  $as_echo_n "(cached) " >&6
+else
+  eval "$as_ac_Header=\$ac_header_preproc"
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+		 $as_echo "$as_val"'`
+	       { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+
+fi
+as_val=`eval 'as_val=${'$as_ac_Header'}
+		 $as_echo "$as_val"'`
+   if test "x$as_val" = x""yes; then
   cat >>confdefs.h <<_ACEOF
 #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
 _ACEOF
@@ -4576,12 +5028,16 @@ fi
 done
 
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5
+{ $as_echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5
 $as_echo_n "checking for an ANSI C-conforming const... " >&6; }
-if test "${ac_cv_c_const+set}" = set; then :
+if test "${ac_cv_c_const+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -4641,29 +5097,56 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_cv_c_const=yes
 else
-  ac_cv_c_const=no
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_c_const=no
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5
 $as_echo "$ac_cv_c_const" >&6; }
 if test $ac_cv_c_const = no; then
 
-$as_echo "#define const /**/" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define const /**/
+_ACEOF
 
 fi
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5
+{ $as_echo "$as_me:$LINENO: checking for inline" >&5
 $as_echo_n "checking for inline... " >&6; }
-if test "${ac_cv_c_inline+set}" = set; then :
+if test "${ac_cv_c_inline+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   ac_cv_c_inline=no
 for ac_kw in inline __inline__ __inline; do
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #ifndef __cplusplus
 typedef int foo_t;
@@ -4672,17 +5155,41 @@ $ac_kw foo_t foo () {return 0; }
 #endif
 
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_cv_c_inline=$ac_kw
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
   test "$ac_cv_c_inline" != no && break
 done
 
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5
 $as_echo "$ac_cv_c_inline" >&6; }
 
+
 case $ac_cv_c_inline in
   inline | yes) ;;
   *)
@@ -4698,9 +5205,102 @@ _ACEOF
     ;;
 esac
 
-ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default"
-if test "x$ac_cv_type_size_t" = x""yes; then :
+{ $as_echo "$as_me:$LINENO: checking for size_t" >&5
+$as_echo_n "checking for size_t... " >&6; }
+if test "${ac_cv_type_size_t+set}" = set; then
+  $as_echo_n "(cached) " >&6
+else
+  ac_cv_type_size_t=no
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+int
+main ()
+{
+if (sizeof (size_t))
+       return 0;
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+int
+main ()
+{
+if (sizeof ((size_t)))
+	  return 0;
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  :
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_type_size_t=yes
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
 
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_size_t" >&5
+$as_echo "$ac_cv_type_size_t" >&6; }
+if test "x$ac_cv_type_size_t" = x""yes; then
+  :
 else
 
 cat >>confdefs.h <<_ACEOF
@@ -4709,12 +5309,16 @@ _ACEOF
 
 fi
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether time.h and sys/time.h may both be included" >&5
+{ $as_echo "$as_me:$LINENO: checking whether time.h and sys/time.h may both be included" >&5
 $as_echo_n "checking whether time.h and sys/time.h may both be included... " >&6; }
-if test "${ac_cv_header_time+set}" = set; then :
+if test "${ac_cv_header_time+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #include <sys/types.h>
 #include <sys/time.h>
@@ -4729,27 +5333,54 @@ return 0;
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_cv_header_time=yes
 else
-  ac_cv_header_time=no
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_header_time=no
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_time" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_time" >&5
 $as_echo "$ac_cv_header_time" >&6; }
 if test $ac_cv_header_time = yes; then
 
-$as_echo "#define TIME_WITH_SYS_TIME 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define TIME_WITH_SYS_TIME 1
+_ACEOF
 
 fi
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether struct tm is in sys/time.h or time.h" >&5
+{ $as_echo "$as_me:$LINENO: checking whether struct tm is in sys/time.h or time.h" >&5
 $as_echo_n "checking whether struct tm is in sys/time.h or time.h... " >&6; }
-if test "${ac_cv_struct_tm+set}" = set; then :
+if test "${ac_cv_struct_tm+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 #include <sys/types.h>
 #include <time.h>
@@ -4764,18 +5395,41 @@ struct tm tm;
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
   ac_cv_struct_tm=time.h
 else
-  ac_cv_struct_tm=sys/time.h
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_struct_tm=sys/time.h
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_struct_tm" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_struct_tm" >&5
 $as_echo "$ac_cv_struct_tm" >&6; }
 if test $ac_cv_struct_tm = sys/time.h; then
 
-$as_echo "#define TM_IN_SYS_TIME 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define TM_IN_SYS_TIME 1
+_ACEOF
 
 fi
 
@@ -4799,9 +5453,13 @@ fi
 
 
 If Sun cc is present, define appropriate compiler flags
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun C compiler" >&5
+{ $as_echo "$as_me:$LINENO: checking for Sun C compiler" >&5
 $as_echo_n "checking for Sun C compiler... " >&6; }
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -4815,22 +5473,47 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  { $as_echo "$as_me:$LINENO: result: yes" >&5
 $as_echo "yes" >&6; }
                     gtfold_cv_check_sunpro_cc=yes
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	{ $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
                     gtfold_cv_check_sunpro_cc=no
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 
 if test "$gtfold_cv_check_sunpro_cc" == "yes";
 then
-	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun C compiler architecture target" >&5
+	{ $as_echo "$as_me:$LINENO: checking for Sun C compiler architecture target" >&5
 $as_echo_n "checking for Sun C compiler architecture target... " >&6; }
-	cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+	cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -4844,15 +5527,36 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  { $as_echo "$as_me:$LINENO: result: yes" >&5
 $as_echo "yes" >&6; }
                     gtfold_cv_check_sun_sparc=yes
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	{ $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
                     gtfold_cv_check_sun_sparc=no
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
 fi
 
@@ -4860,9 +5564,13 @@ if test "$gtfold_cv_check_sunpro_cc" == "yes";
 then
 	if test "$gtfold_cv_check_sun_sparc" == "yes";
 	then
-		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun sparc v9 architecture" >&5
+		{ $as_echo "$as_me:$LINENO: checking for Sun sparc v9 architecture" >&5
 $as_echo_n "checking for Sun sparc v9 architecture... " >&6; }
-		cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+		cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 int
@@ -4876,15 +5584,36 @@ main ()
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  { $as_echo "$as_me:$LINENO: result: yes" >&5
 $as_echo "yes" >&6; }
 				    gtfold_cv_check_sun_sparcv9=yes
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	{ $as_echo "$as_me:$LINENO: result: no" >&5
 $as_echo "no" >&6; }
 				    gtfold_cv_check_sun_sparcv9=no
 fi
+
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
         fi
 fi
@@ -4907,14 +5636,18 @@ fi
 
 if test "$enable_openmp" != 'no'; then
    if test "x${GCC}" = "xyes"; then
-      { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GOMP_parallel_start in -lomp" >&5
+      { $as_echo "$as_me:$LINENO: checking for GOMP_parallel_start in -lomp" >&5
 $as_echo_n "checking for GOMP_parallel_start in -lomp... " >&6; }
-if test "${ac_cv_lib_omp_GOMP_parallel_start+set}" = set; then :
+if test "${ac_cv_lib_omp_GOMP_parallel_start+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
 LIBS="-lomp  $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 /* Override any GCC internal prototype to avoid an error.
@@ -4932,29 +5665,58 @@ return GOMP_parallel_start ();
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 $as_test_x conftest$ac_exeext
+       }; then
   ac_cv_lib_omp_GOMP_parallel_start=yes
 else
-  ac_cv_lib_omp_GOMP_parallel_start=no
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_omp_GOMP_parallel_start=no
 fi
-rm -f core conftest.err conftest.$ac_objext \
-    conftest$ac_exeext conftest.$ac_ext
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
 LIBS=$ac_check_lib_save_LIBS
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_omp_GOMP_parallel_start" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_omp_GOMP_parallel_start" >&5
 $as_echo "$ac_cv_lib_omp_GOMP_parallel_start" >&6; }
-if test "x$ac_cv_lib_omp_GOMP_parallel_start" = x""yes; then :
+if test "x$ac_cv_lib_omp_GOMP_parallel_start" = x""yes; then
   LIB_OMP="-lgomp"
 fi
 
-      { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GOMP_parallel_start in -lgomp" >&5
+      { $as_echo "$as_me:$LINENO: checking for GOMP_parallel_start in -lgomp" >&5
 $as_echo_n "checking for GOMP_parallel_start in -lgomp... " >&6; }
-if test "${ac_cv_lib_gomp_GOMP_parallel_start+set}" = set; then :
+if test "${ac_cv_lib_gomp_GOMP_parallel_start+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
 LIBS="-lgomp  $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 /* Override any GCC internal prototype to avoid an error.
@@ -4972,30 +5734,59 @@ return GOMP_parallel_start ();
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 $as_test_x conftest$ac_exeext
+       }; then
   ac_cv_lib_gomp_GOMP_parallel_start=yes
 else
-  ac_cv_lib_gomp_GOMP_parallel_start=no
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_gomp_GOMP_parallel_start=no
 fi
-rm -f core conftest.err conftest.$ac_objext \
-    conftest$ac_exeext conftest.$ac_ext
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
 LIBS=$ac_check_lib_save_LIBS
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_gomp_GOMP_parallel_start" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_gomp_GOMP_parallel_start" >&5
 $as_echo "$ac_cv_lib_gomp_GOMP_parallel_start" >&6; }
-if test "x$ac_cv_lib_gomp_GOMP_parallel_start" = x""yes; then :
+if test "x$ac_cv_lib_gomp_GOMP_parallel_start" = x""yes; then
   GOMP_LIBS="-lgomp"
 fi
 
    else
-      { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sunw_mp_register_warn in -lmtsk" >&5
+      { $as_echo "$as_me:$LINENO: checking for sunw_mp_register_warn in -lmtsk" >&5
 $as_echo_n "checking for sunw_mp_register_warn in -lmtsk... " >&6; }
-if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then :
+if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
 LIBS="-lmtsk  $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 /* Override any GCC internal prototype to avoid an error.
@@ -5013,29 +5804,58 @@ return sunw_mp_register_warn ();
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 $as_test_x conftest$ac_exeext
+       }; then
   ac_cv_lib_mtsk_sunw_mp_register_warn=yes
 else
-  ac_cv_lib_mtsk_sunw_mp_register_warn=no
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_mtsk_sunw_mp_register_warn=no
 fi
-rm -f core conftest.err conftest.$ac_objext \
-    conftest$ac_exeext conftest.$ac_ext
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
 LIBS=$ac_check_lib_save_LIBS
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5
 $as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; }
-if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then :
+if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then
   LIB_OMP="-lmtsk"
 fi
 
-      { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sunw_mp_register_warn in -lmtsk" >&5
+      { $as_echo "$as_me:$LINENO: checking for sunw_mp_register_warn in -lmtsk" >&5
 $as_echo_n "checking for sunw_mp_register_warn in -lmtsk... " >&6; }
-if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then :
+if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
 LIBS="-lmtsk  $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 
 /* Override any GCC internal prototype to avoid an error.
@@ -5044,40 +5864,156 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 #ifdef __cplusplus
 extern "C"
 #endif
-char sunw_mp_register_warn ();
+char sunw_mp_register_warn ();
+int
+main ()
+{
+return sunw_mp_register_warn ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 $as_test_x conftest$ac_exeext
+       }; then
+  ac_cv_lib_mtsk_sunw_mp_register_warn=yes
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_mtsk_sunw_mp_register_warn=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5
+$as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; }
+if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then
+  GOMP_LIBS="-lmtsk"
+fi
+
+   fi
+   LIBS="$GOMP_LIBS $LIBS"
+fi
+
+
+
+
+
+for ac_func in floor gettimeofday pow
+do
+as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5
+$as_echo_n "checking for $ac_func... " >&6; }
+if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then
+  $as_echo_n "(cached) " >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+    which can conflict with char $ac_func (); below.
+    Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+    <limits.h> exists even on freestanding compilers.  */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+    to always fail with ENOSYS.  Some functions are actually named
+    something starting with __ and the normal name is an alias.  */
+#if defined __stub_$ac_func || defined __stub___$ac_func
+choke me
+#endif
+
 int
 main ()
 {
-return sunw_mp_register_warn ();
+return $ac_func ();
   ;
   return 0;
 }
 _ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
-  ac_cv_lib_mtsk_sunw_mp_register_warn=yes
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 $as_test_x conftest$ac_exeext
+       }; then
+  eval "$as_ac_var=yes"
 else
-  ac_cv_lib_mtsk_sunw_mp_register_warn=no
-fi
-rm -f core conftest.err conftest.$ac_objext \
-    conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5
-$as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; }
-if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then :
-  GOMP_LIBS="-lmtsk"
-fi
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
 
-   fi
-   LIBS="$GOMP_LIBS $LIBS"
+	eval "$as_ac_var=no"
 fi
 
-
-for ac_func in floor gettimeofday pow
-do :
-  as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
-if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_var'}
+		 $as_echo "$as_val"'`
+	       { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_var'}
+		 $as_echo "$as_val"'`
+   if test "x$as_val" = x""yes; then
   cat >>confdefs.h <<_ACEOF
 #define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
 _ACEOF
@@ -5087,12 +6023,14 @@ done
 
 
 # Check whether --enable-debug was given.
-if test "${enable_debug+set}" = set; then :
+if test "${enable_debug+set}" = set; then
   enableval=$enable_debug; case "${enableval}" in
     "" | y | ye | yes) debug=true;
 		       CFLAGS=$(echo $CFLAGS -g | sed -e 's/-O\|-O2\|-O3//g') ;;
     n | no) debug=false ;;
-    *) as_fn_error $? "bad value ${enableval} for --enable-debug" "$LINENO" 5  ;;
+    *) { { $as_echo "$as_me:$LINENO: error: bad value ${enableval} for --enable-debug" >&5
+$as_echo "$as_me: error: bad value ${enableval} for --enable-debug" >&2;}
+   { (exit 1); exit 1; }; } ;;
   esac
 else
   debug=false
@@ -5109,7 +6047,7 @@ fi
 
 ac_config_files="$ac_config_files Makefile src/Makefile data/Makefile include/Makefile"
 
-ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile"
+ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile"
 
 
 cat >confcache <<\_ACEOF
@@ -5139,13 +6077,13 @@ _ACEOF
     case $ac_val in #(
     *${as_nl}*)
       case $ac_var in #(
-      *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+      *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5
 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
       esac
       case $ac_var in #(
       _ | IFS | as_nl) ;; #(
       BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
-      *) { eval $ac_var=; unset $ac_var;} ;;
+      *) $as_unset $ac_var ;;
       esac ;;
     esac
   done
@@ -5153,8 +6091,8 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
   (set) 2>&1 |
     case $as_nl`(ac_space=' '; set) 2>&1` in #(
     *${as_nl}ac_space=\ *)
-      # `set' does not quote correctly, so add quotes: double-quote
-      # substitution turns \\\\ into \\, and sed turns \\ into \.
+      # `set' does not quote correctly, so add quotes (double-quote
+      # substitution turns \\\\ into \\, and sed turns \\ into \).
       sed -n \
 	"s/'/'\\\\''/g;
 	  s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
@@ -5177,11 +6115,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
 if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
   if test -w "$cache_file"; then
     test "x$cache_file" != "x/dev/null" &&
-      { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+      { $as_echo "$as_me:$LINENO: updating cache $cache_file" >&5
 $as_echo "$as_me: updating cache $cache_file" >&6;}
     cat confcache >$cache_file
   else
-    { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+    { $as_echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5
 $as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
   fi
 fi
@@ -5195,15 +6133,14 @@ DEFS=-DHAVE_CONFIG_H
 
 ac_libobjs=
 ac_ltlibobjs=
-U=
 for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
   # 1. Remove the extension, and $U if already installed.
   ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
   ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
   # 2. Prepend LIBOBJDIR.  When used with automake>=1.10 LIBOBJDIR
   #    will be set to the directory where LIBOBJS objects are built.
-  as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
-  as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+  ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+  ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo'
 done
 LIBOBJS=$ac_libobjs
 
@@ -5219,30 +6156,41 @@ else
 fi
 
 if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
-  as_fn_error $? "conditional \"AMDEP\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+   { (exit 1); exit 1; }; }
 fi
 if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
-  as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+   { (exit 1); exit 1; }; }
 fi
 if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
-  as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+   { (exit 1); exit 1; }; }
 fi
 if test -z "${GTFOLD_DEBUG_TRUE}" && test -z "${GTFOLD_DEBUG_FALSE}"; then
-  as_fn_error $? "conditional \"GTFOLD_DEBUG\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: conditional \"GTFOLD_DEBUG\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"GTFOLD_DEBUG\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+   { (exit 1); exit 1; }; }
 fi
 
 : ${CONFIG_STATUS=./config.status}
 ac_write_fail=0
 ac_clean_files_save=$ac_clean_files
 ac_clean_files="$ac_clean_files $CONFIG_STATUS"
-{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+{ $as_echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5
 $as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
-as_write_fail=0
-cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+cat >$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 #! $SHELL
 # Generated by $as_me.
 # Run this file to recreate the current configuration.
@@ -5252,18 +6200,17 @@ cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
 debug=false
 ac_cs_recheck=false
 ac_cs_silent=false
-
 SHELL=\${CONFIG_SHELL-$SHELL}
-export SHELL
-_ASEOF
-cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
-## -------------------- ##
-## M4sh Initialization. ##
-## -------------------- ##
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+## --------------------- ##
+## M4sh Initialization.  ##
+## --------------------- ##
 
 # Be more Bourne compatible
 DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
   emulate sh
   NULLCMD=:
   # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
@@ -5271,15 +6218,23 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
   alias -g '${1+"$@"}'='"$@"'
   setopt NO_GLOB_SUBST
 else
-  case `(set -o) 2>/dev/null` in #(
-  *posix*) :
-    set -o posix ;; #(
-  *) :
-     ;;
+  case `(set -o) 2>/dev/null` in
+  *posix*) set -o posix ;;
 esac
+
 fi
 
 
+
+
+# PATH needs CR
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
 as_nl='
 '
 export as_nl
@@ -5287,13 +6242,7 @@ export as_nl
 as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
 as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
 as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-# Prefer a ksh shell builtin over an external printf program on Solaris,
-# but without wasting forks for bash or zsh.
-if test -z "$BASH_VERSION$ZSH_VERSION" \
-    && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
-  as_echo='print -r --'
-  as_echo_n='print -rn --'
-elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
   as_echo='printf %s\n'
   as_echo_n='printf %s'
 else
@@ -5304,7 +6253,7 @@ else
     as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
     as_echo_n_body='eval
       arg=$1;
-      case $arg in #(
+      case $arg in
       *"$as_nl"*)
 	expr "X$arg" : "X\\(.*\\)$as_nl";
 	arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
@@ -5327,6 +6276,13 @@ if test "${PATH_SEPARATOR+set}" != set; then
   }
 fi
 
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+  as_unset=unset
+else
+  as_unset=false
+fi
+
 
 # IFS
 # We need space, tab and new line, in precisely that order.  Quoting is
@@ -5336,15 +6292,15 @@ fi
 IFS=" ""	$as_nl"
 
 # Find who we are.  Look in the path if we contain no directory separator.
-case $0 in #((
+case $0 in
   *[\\/]* ) as_myself=$0 ;;
   *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
 for as_dir in $PATH
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
-    test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
-  done
+  test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+done
 IFS=$as_save_IFS
 
      ;;
@@ -5356,16 +6312,12 @@ if test "x$as_myself" = x; then
 fi
 if test ! -f "$as_myself"; then
   $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
-  exit 1
+  { (exit 1); exit 1; }
 fi
 
-# Unset variables that we do not need and which cause bugs (e.g. in
-# pre-3.0 UWIN ksh).  But do not cause bugs in bash 2.01; the "|| exit 1"
-# suppresses any "Segmentation fault" message there.  '((' could
-# trigger a bug in pdksh 5.2.14.
-for as_var in BASH_ENV ENV MAIL MAILPATH
-do eval test x\${$as_var+set} = xset \
-  && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+# Work around bugs in pre-3.0 UWIN ksh.
+for as_var in ENV MAIL MAILPATH
+do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
 done
 PS1='$ '
 PS2='> '
@@ -5377,89 +6329,7 @@ export LC_ALL
 LANGUAGE=C
 export LANGUAGE
 
-# CDPATH.
-(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
-
-
-# as_fn_error STATUS ERROR [LINENO LOG_FD]
-# ----------------------------------------
-# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
-# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-# script with STATUS, using 1 if that was 0.
-as_fn_error ()
-{
-  as_status=$1; test $as_status -eq 0 && as_status=1
-  if test "$4"; then
-    as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-    $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
-  fi
-  $as_echo "$as_me: error: $2" >&2
-  as_fn_exit $as_status
-} # as_fn_error
-
-
-# as_fn_set_status STATUS
-# -----------------------
-# Set $? to STATUS, without forking.
-as_fn_set_status ()
-{
-  return $1
-} # as_fn_set_status
-
-# as_fn_exit STATUS
-# -----------------
-# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
-as_fn_exit ()
-{
-  set +e
-  as_fn_set_status $1
-  exit $1
-} # as_fn_exit
-
-# as_fn_unset VAR
-# ---------------
-# Portably unset VAR.
-as_fn_unset ()
-{
-  { eval $1=; unset $1;}
-}
-as_unset=as_fn_unset
-# as_fn_append VAR VALUE
-# ----------------------
-# Append the text in VALUE to the end of the definition contained in VAR. Take
-# advantage of any shell optimizations that allow amortized linear growth over
-# repeated appends, instead of the typical quadratic growth present in naive
-# implementations.
-if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
-  eval 'as_fn_append ()
-  {
-    eval $1+=\$2
-  }'
-else
-  as_fn_append ()
-  {
-    eval $1=\$$1\$2
-  }
-fi # as_fn_append
-
-# as_fn_arith ARG...
-# ------------------
-# Perform arithmetic evaluation on the ARGs, and store the result in the
-# global $as_val. Take advantage of shells that can avoid forks. The arguments
-# must be portable across $(()) and expr.
-if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
-  eval 'as_fn_arith ()
-  {
-    as_val=$(( $* ))
-  }'
-else
-  as_fn_arith ()
-  {
-    as_val=`expr "$@" || test $? -eq 1`
-  }
-fi # as_fn_arith
-
-
+# Required to use basename.
 if expr a : '\(a\)' >/dev/null 2>&1 &&
    test "X`expr 00001 : '.*\(...\)'`" = X001; then
   as_expr=expr
@@ -5473,12 +6343,8 @@ else
   as_basename=false
 fi
 
-if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
-  as_dirname=dirname
-else
-  as_dirname=false
-fi
 
+# Name of the executable.
 as_me=`$as_basename -- "$0" ||
 $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
 	 X"$0" : 'X\(//\)$' \| \
@@ -5498,25 +6364,76 @@ $as_echo X/"$0" |
 	  }
 	  s/.*/./; q'`
 
-# Avoid depending upon Character Ranges.
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-as_cr_digits='0123456789'
-as_cr_alnum=$as_cr_Letters$as_cr_digits
+# CDPATH.
+$as_unset CDPATH
+
+
+
+  as_lineno_1=$LINENO
+  as_lineno_2=$LINENO
+  test "x$as_lineno_1" != "x$as_lineno_2" &&
+  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
+
+  # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
+  # uniformly replaced by the line number.  The first 'sed' inserts a
+  # line-number line after each line using $LINENO; the second 'sed'
+  # does the real work.  The second script uses 'N' to pair each
+  # line-number line with the line containing $LINENO, and appends
+  # trailing '-' during substitution so that $LINENO is not a special
+  # case at line end.
+  # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+  # scripts with optimization help from Paolo Bonzini.  Blame Lee
+  # E. McMahon (1931-1989) for sed's syntax.  :-)
+  sed -n '
+    p
+    /[$]LINENO/=
+  ' <$as_myself |
+    sed '
+      s/[$]LINENO.*/&-/
+      t lineno
+      b
+      :lineno
+      N
+      :loop
+      s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+      t loop
+      s/-\n.*//
+    ' >$as_me.lineno &&
+  chmod +x "$as_me.lineno" ||
+    { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
+   { (exit 1); exit 1; }; }
+
+  # Don't try to exec as it changes $[0], causing all sort of problems
+  # (the dirname of $[0] is not the place where we might find the
+  # original and so on.  Autoconf is especially sensitive to this).
+  . "./$as_me.lineno"
+  # Exit status is that of the last command.
+  exit
+}
+
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+  as_dirname=dirname
+else
+  as_dirname=false
+fi
 
 ECHO_C= ECHO_N= ECHO_T=
-case `echo -n x` in #(((((
+case `echo -n x` in
 -n*)
-  case `echo 'xy\c'` in
+  case `echo 'x\c'` in
   *c*) ECHO_T='	';;	# ECHO_T is single tab character.
-  xy)  ECHO_C='\c';;
-  *)   echo `echo ksh88 bug on AIX 6.1` > /dev/null
-       ECHO_T='	';;
+  *)   ECHO_C='\c';;
   esac;;
 *)
   ECHO_N='-n';;
 esac
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+   test "X`expr 00001 : '.*\(...\)'`" = X001; then
+  as_expr=expr
+else
+  as_expr=false
+fi
 
 rm -f conf$$ conf$$.exe conf$$.file
 if test -d conf$$.dir; then
@@ -5545,56 +6462,8 @@ fi
 rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
 rmdir conf$$.dir 2>/dev/null
 
-
-# as_fn_mkdir_p
-# -------------
-# Create "$as_dir" as a directory, including parents if necessary.
-as_fn_mkdir_p ()
-{
-
-  case $as_dir in #(
-  -*) as_dir=./$as_dir;;
-  esac
-  test -d "$as_dir" || eval $as_mkdir_p || {
-    as_dirs=
-    while :; do
-      case $as_dir in #(
-      *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
-      *) as_qdir=$as_dir;;
-      esac
-      as_dirs="'$as_qdir' $as_dirs"
-      as_dir=`$as_dirname -- "$as_dir" ||
-$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-	 X"$as_dir" : 'X\(//\)[^/]' \| \
-	 X"$as_dir" : 'X\(//\)$' \| \
-	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$as_dir" |
-    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)[^/].*/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\).*/{
-	    s//\1/
-	    q
-	  }
-	  s/.*/./; q'`
-      test -d "$as_dir" && break
-    done
-    test -z "$as_dirs" || eval "mkdir $as_dirs"
-  } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
-
-
-} # as_fn_mkdir_p
 if mkdir -p . 2>/dev/null; then
-  as_mkdir_p='mkdir -p "$as_dir"'
+  as_mkdir_p=:
 else
   test -d ./-p && rmdir ./-p
   as_mkdir_p=false
@@ -5613,10 +6482,10 @@ else
       if test -d "$1"; then
 	test -d "$1/.";
       else
-	case $1 in #(
+	case $1 in
 	-*)set "./$1";;
 	esac;
-	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
+	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
 	???[sx]*):;;*)false;;esac;fi
     '\'' sh
   '
@@ -5631,19 +6500,13 @@ as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
 
 
 exec 6>&1
-## ----------------------------------- ##
-## Main body of $CONFIG_STATUS script. ##
-## ----------------------------------- ##
-_ASEOF
-test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
 
-cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-# Save the log message, to keep $0 and so on meaningful, and to
+# Save the log message, to keep $[0] and so on meaningful, and to
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by gtfold $as_me 1.18, which was
-generated by GNU Autoconf 2.67.  Invocation command line was
+This file was extended by gtfold $as_me 2.0, which was
+generated by GNU Autoconf 2.63.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
   CONFIG_HEADERS  = $CONFIG_HEADERS
@@ -5675,15 +6538,13 @@ _ACEOF
 
 cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 ac_cs_usage="\
-\`$as_me' instantiates files and other configuration actions
-from templates according to the current configuration.  Unless the files
-and actions are specified as TAGs, all are instantiated by default.
+\`$as_me' instantiates files from templates according to the
+current configuration.
 
-Usage: $0 [OPTION]... [TAG]...
+Usage: $0 [OPTION]... [FILE]...
 
   -h, --help       print this help, then exit
   -V, --version    print version number and configuration settings, then exit
-      --config     print configuration, then exit
   -q, --quiet, --silent
                    do not print progress messages
   -d, --debug      don't remove temporary files
@@ -5702,17 +6563,16 @@ $config_headers
 Configuration commands:
 $config_commands
 
-Report bugs to the package provider."
+Report bugs to <bug-autoconf@gnu.org>."
 
 _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-gtfold config.status 1.18
-configured by $0, generated by GNU Autoconf 2.67,
-  with options \\"\$ac_cs_config\\"
+gtfold config.status 2.0
+configured by $0, generated by GNU Autoconf 2.63,
+  with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
 
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2008 Free Software Foundation, Inc.
 This config.status script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it."
 
@@ -5730,16 +6590,11 @@ ac_need_defaults=:
 while test $# != 0
 do
   case $1 in
-  --*=?*)
+  --*=*)
     ac_option=`expr "X$1" : 'X\([^=]*\)='`
     ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
     ac_shift=:
     ;;
-  --*=)
-    ac_option=`expr "X$1" : 'X\([^=]*\)='`
-    ac_optarg=
-    ac_shift=:
-    ;;
   *)
     ac_option=$1
     ac_optarg=$2
@@ -5753,29 +6608,27 @@ do
     ac_cs_recheck=: ;;
   --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
     $as_echo "$ac_cs_version"; exit ;;
-  --config | --confi | --conf | --con | --co | --c )
-    $as_echo "$ac_cs_config"; exit ;;
   --debug | --debu | --deb | --de | --d | -d )
     debug=: ;;
   --file | --fil | --fi | --f )
     $ac_shift
     case $ac_optarg in
     *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
-    '') as_fn_error $? "missing file argument" ;;
     esac
-    as_fn_append CONFIG_FILES " '$ac_optarg'"
+    CONFIG_FILES="$CONFIG_FILES '$ac_optarg'"
     ac_need_defaults=false;;
   --header | --heade | --head | --hea )
     $ac_shift
     case $ac_optarg in
     *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
     esac
-    as_fn_append CONFIG_HEADERS " '$ac_optarg'"
+    CONFIG_HEADERS="$CONFIG_HEADERS '$ac_optarg'"
     ac_need_defaults=false;;
   --he | --h)
     # Conflict between --help and --header
-    as_fn_error $? "ambiguous option: \`$1'
-Try \`$0 --help' for more information.";;
+    { $as_echo "$as_me: error: ambiguous option: $1
+Try \`$0 --help' for more information." >&2
+   { (exit 1); exit 1; }; };;
   --help | --hel | -h )
     $as_echo "$ac_cs_usage"; exit ;;
   -q | -quiet | --quiet | --quie | --qui | --qu | --q \
@@ -5783,10 +6636,11 @@ Try \`$0 --help' for more information.";;
     ac_cs_silent=: ;;
 
   # This is an error.
-  -*) as_fn_error $? "unrecognized option: \`$1'
-Try \`$0 --help' for more information." ;;
+  -*) { $as_echo "$as_me: error: unrecognized option: $1
+Try \`$0 --help' for more information." >&2
+   { (exit 1); exit 1; }; } ;;
 
-  *) as_fn_append ac_config_targets " $1"
+  *) ac_config_targets="$ac_config_targets $1"
      ac_need_defaults=false ;;
 
   esac
@@ -5846,8 +6700,11 @@ do
     "data/Turner99/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner99/Makefile" ;;
     "data/Turner04/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner04/Makefile" ;;
     "data/Andronescu/Makefile") CONFIG_FILES="$CONFIG_FILES data/Andronescu/Makefile" ;;
+    "data/UNAParams/Makefile") CONFIG_FILES="$CONFIG_FILES data/UNAParams/Makefile" ;;
 
-  *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;;
+  *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
+$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
+   { (exit 1); exit 1; }; };;
   esac
 done
 
@@ -5874,7 +6731,7 @@ $debug ||
   trap 'exit_status=$?
   { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
 ' 0
-  trap 'as_fn_exit 1' 1 2 13 15
+  trap '{ (exit 1); exit 1; }' 1 2 13 15
 }
 # Create a (secure) tmp directory for tmp files.
 
@@ -5885,7 +6742,11 @@ $debug ||
 {
   tmp=./conf$$-$RANDOM
   (umask 077 && mkdir "$tmp")
-} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
+} ||
+{
+   $as_echo "$as_me: cannot create a temporary directory in ." >&2
+   { (exit 1); exit 1; }
+}
 
 # Set up the scripts for CONFIG_FILES section.
 # No need to generate them if there are no CONFIG_FILES.
@@ -5893,13 +6754,7 @@ $debug ||
 if test -n "$CONFIG_FILES"; then
 
 
-ac_cr=`echo X | tr X '\015'`
-# On cygwin, bash can eat \r inside `` if the user requested igncr.
-# But we know of no other shell where ac_cr would be empty at this
-# point, so we can use a bashism as a fallback.
-if test "x$ac_cr" = x; then
-  eval ac_cr=\$\'\\r\'
-fi
+ac_cr='
'
 ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
 if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
   ac_cs_awk_cr='\\r'
@@ -5916,18 +6771,24 @@ _ACEOF
   echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
   echo "_ACEOF"
 } >conf$$subs.sh ||
-  as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
-ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+  { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+   { (exit 1); exit 1; }; }
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'`
 ac_delim='%!_!# '
 for ac_last_try in false false false false false :; do
   . ./conf$$subs.sh ||
-    as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+    { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+   { (exit 1); exit 1; }; }
 
   ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
   if test $ac_delim_n = $ac_delim_num; then
     break
   elif $ac_last_try; then
-    as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+    { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+   { (exit 1); exit 1; }; }
   else
     ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
   fi
@@ -5949,7 +6810,7 @@ s/'"$ac_delim"'$//
 t delim
 :nl
 h
-s/\(.\{148\}\)..*/\1/
+s/\(.\{148\}\).*/\1/
 t more1
 s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
 p
@@ -5963,7 +6824,7 @@ s/.\{148\}//
 t nl
 :delim
 h
-s/\(.\{148\}\)..*/\1/
+s/\(.\{148\}\).*/\1/
 t more2
 s/["\\]/\\&/g; s/^/"/; s/$/"/
 p
@@ -6016,28 +6877,22 @@ if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
 else
   cat
 fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
-  || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+  || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5
+$as_echo "$as_me: error: could not setup config files machinery" >&2;}
+   { (exit 1); exit 1; }; }
 _ACEOF
 
-# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
-# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# VPATH may cause trouble with some makes, so we remove $(srcdir),
+# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and
 # trailing colons and then remove the whole line if VPATH becomes empty
 # (actually we leave an empty line to preserve line numbers).
 if test "x$srcdir" = x.; then
-  ac_vpsub='/^[	 ]*VPATH[	 ]*=[	 ]*/{
-h
-s///
-s/^/:/
-s/[	 ]*$/:/
-s/:\$(srcdir):/:/g
-s/:\${srcdir}:/:/g
-s/:@srcdir@:/:/g
-s/^:*//
+  ac_vpsub='/^[	 ]*VPATH[	 ]*=/{
+s/:*\$(srcdir):*/:/
+s/:*\${srcdir}:*/:/
+s/:*@srcdir@:*/:/
+s/^\([^=]*=[	 ]*\):*/\1/
 s/:*$//
-x
-s/\(=[	 ]*\).*/\1/
-G
-s/\n//
 s/^[^=]*=[	 ]*$//
 }'
 fi
@@ -6065,7 +6920,9 @@ for ac_last_try in false false :; do
   if test -z "$ac_t"; then
     break
   elif $ac_last_try; then
-    as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
+    { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_HEADERS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_HEADERS" >&2;}
+   { (exit 1); exit 1; }; }
   else
     ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
   fi
@@ -6150,7 +7007,9 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 _ACAWK
 _ACEOF
 cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-  as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: could not setup config headers machinery" >&5
+$as_echo "$as_me: error: could not setup config headers machinery" >&2;}
+   { (exit 1); exit 1; }; }
 fi # test -n "$CONFIG_HEADERS"
 
 
@@ -6163,7 +7022,9 @@ do
   esac
   case $ac_mode$ac_tag in
   :[FHL]*:*);;
-  :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;;
+  :L* | :C*:*) { { $as_echo "$as_me:$LINENO: error: invalid tag $ac_tag" >&5
+$as_echo "$as_me: error: invalid tag $ac_tag" >&2;}
+   { (exit 1); exit 1; }; };;
   :[FH]-) ac_tag=-:-;;
   :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
   esac
@@ -6191,10 +7052,12 @@ do
 	   [\\/$]*) false;;
 	   *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
 	   esac ||
-	   as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;;
+	   { { $as_echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5
+$as_echo "$as_me: error: cannot find input file: $ac_f" >&2;}
+   { (exit 1); exit 1; }; };;
       esac
       case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
-      as_fn_append ac_file_inputs " '$ac_f'"
+      ac_file_inputs="$ac_file_inputs '$ac_f'"
     done
 
     # Let's still pretend it is `configure' which instantiates (i.e., don't
@@ -6205,7 +7068,7 @@ do
 	`' by configure.'
     if test x"$ac_file" != x-; then
       configure_input="$ac_file.  $configure_input"
-      { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+      { $as_echo "$as_me:$LINENO: creating $ac_file" >&5
 $as_echo "$as_me: creating $ac_file" >&6;}
     fi
     # Neutralize special characters interpreted by sed in replacement strings.
@@ -6218,7 +7081,9 @@ $as_echo "$as_me: creating $ac_file" >&6;}
 
     case $ac_tag in
     *:-:* | *:-) cat >"$tmp/stdin" \
-      || as_fn_error $? "could not create $ac_file" "$LINENO" 5  ;;
+      || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+   { (exit 1); exit 1; }; } ;;
     esac
     ;;
   esac
@@ -6246,7 +7111,47 @@ $as_echo X"$ac_file" |
 	    q
 	  }
 	  s/.*/./; q'`
-  as_dir="$ac_dir"; as_fn_mkdir_p
+  { as_dir="$ac_dir"
+  case $as_dir in #(
+  -*) as_dir=./$as_dir;;
+  esac
+  test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
+    as_dirs=
+    while :; do
+      case $as_dir in #(
+      *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+      *) as_qdir=$as_dir;;
+      esac
+      as_dirs="'$as_qdir' $as_dirs"
+      as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	 X"$as_dir" : 'X\(//\)[^/]' \| \
+	 X"$as_dir" : 'X\(//\)$' \| \
+	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)[^/].*/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+      test -d "$as_dir" && break
+    done
+    test -z "$as_dirs" || eval "mkdir $as_dirs"
+  } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
+$as_echo "$as_me: error: cannot create directory $as_dir" >&2;}
+   { (exit 1); exit 1; }; }; }
   ac_builddir=.
 
 case "$ac_dir" in
@@ -6303,6 +7208,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # If the template does not know about datarootdir, expand it.
 # FIXME: This hack should be removed a few years after 2.60.
 ac_datarootdir_hack=; ac_datarootdir_seen=
+
 ac_sed_dataroot='
 /datarootdir/ {
   p
@@ -6312,11 +7218,12 @@ ac_sed_dataroot='
 /@docdir@/p
 /@infodir@/p
 /@localedir@/p
-/@mandir@/p'
+/@mandir@/p
+'
 case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
 *datarootdir*) ac_datarootdir_seen=yes;;
 *@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
-  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+  { $as_echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
 $as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
 _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
@@ -6326,7 +7233,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
   s&@infodir@&$infodir&g
   s&@localedir@&$localedir&g
   s&@mandir@&$mandir&g
-  s&\\\${datarootdir}&$datarootdir&g' ;;
+    s&\\\${datarootdir}&$datarootdir&g' ;;
 esac
 _ACEOF
 
@@ -6355,22 +7262,26 @@ s&@MKDIR_P@&$ac_MKDIR_P&;t t
 $ac_datarootdir_hack
 "
 eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \
-  || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+  || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+   { (exit 1); exit 1; }; }
 
 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
   { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
   { ac_out=`sed -n '/^[	 ]*datarootdir[	 ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
-  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined.  Please make sure it is defined" >&5
+  { $as_echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined.  Please make sure it is defined." >&5
 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined.  Please make sure it is defined" >&2;}
+which seems to be undefined.  Please make sure it is defined." >&2;}
 
   rm -f "$tmp/stdin"
   case $ac_file in
   -) cat "$tmp/out" && rm -f "$tmp/out";;
   *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
   esac \
-  || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+  || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+   { (exit 1); exit 1; }; }
  ;;
   :H)
   #
@@ -6381,19 +7292,25 @@ which seems to be undefined.  Please make sure it is defined" >&2;}
       $as_echo "/* $configure_input  */" \
       && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs"
     } >"$tmp/config.h" \
-      || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+      || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+   { (exit 1); exit 1; }; }
     if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then
-      { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
+      { $as_echo "$as_me:$LINENO: $ac_file is unchanged" >&5
 $as_echo "$as_me: $ac_file is unchanged" >&6;}
     else
       rm -f "$ac_file"
       mv "$tmp/config.h" "$ac_file" \
-	|| as_fn_error $? "could not create $ac_file" "$LINENO" 5
+	|| { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+   { (exit 1); exit 1; }; }
     fi
   else
     $as_echo "/* $configure_input  */" \
       && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \
-      || as_fn_error $? "could not create -" "$LINENO" 5
+      || { { $as_echo "$as_me:$LINENO: error: could not create -" >&5
+$as_echo "$as_me: error: could not create -" >&2;}
+   { (exit 1); exit 1; }; }
   fi
 # Compute "$ac_file"'s index in $config_headers.
 _am_arg="$ac_file"
@@ -6431,7 +7348,7 @@ $as_echo X"$_am_arg" |
 	  s/.*/./; q'`/stamp-h$_am_stamp_count
  ;;
 
-  :C)  { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+  :C)  { $as_echo "$as_me:$LINENO: executing $ac_file commands" >&5
 $as_echo "$as_me: executing $ac_file commands" >&6;}
  ;;
   esac
@@ -6526,7 +7443,47 @@ $as_echo X"$file" |
 	    q
 	  }
 	  s/.*/./; q'`
-      as_dir=$dirpart/$fdir; as_fn_mkdir_p
+      { as_dir=$dirpart/$fdir
+  case $as_dir in #(
+  -*) as_dir=./$as_dir;;
+  esac
+  test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
+    as_dirs=
+    while :; do
+      case $as_dir in #(
+      *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+      *) as_qdir=$as_dir;;
+      esac
+      as_dirs="'$as_qdir' $as_dirs"
+      as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	 X"$as_dir" : 'X\(//\)[^/]' \| \
+	 X"$as_dir" : 'X\(//\)$' \| \
+	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)[^/].*/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\/\)$/{
+	    s//\1/
+	    q
+	  }
+	  /^X\(\/\).*/{
+	    s//\1/
+	    q
+	  }
+	  s/.*/./; q'`
+      test -d "$as_dir" && break
+    done
+    test -z "$as_dirs" || eval "mkdir $as_dirs"
+  } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
+$as_echo "$as_me: error: cannot create directory $as_dir" >&2;}
+   { (exit 1); exit 1; }; }; }
       # echo "creating $dirpart/$file"
       echo '# dummy' > "$dirpart/$file"
     done
@@ -6538,12 +7495,15 @@ $as_echo X"$file" |
 done # for ac_tag
 
 
-as_fn_exit 0
+{ (exit 0); exit 0; }
 _ACEOF
+chmod +x $CONFIG_STATUS
 ac_clean_files=$ac_clean_files_save
 
 test $ac_write_fail = 0 ||
-  as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+  { { $as_echo "$as_me:$LINENO: error: write failure creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: write failure creating $CONFIG_STATUS" >&2;}
+   { (exit 1); exit 1; }; }
 
 
 # configure is writing to config.log, and then calls config.status.
@@ -6564,10 +7524,10 @@ if test "$no_create" != yes; then
   exec 5>>config.log
   # Use ||, not &&, to avoid exiting from the if with $? = 1, which
   # would make configure fail if this is the last instruction.
-  $ac_cs_success || as_fn_exit 1
+  $ac_cs_success || { (exit 1); exit 1; }
 fi
 if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+  { $as_echo "$as_me:$LINENO: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
 $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
 fi
 
diff --git a/gtfold-mfe/configure.in b/gtfold-mfe/configure.in
index ef1ddde..e4e1755 100644
--- a/gtfold-mfe/configure.in
+++ b/gtfold-mfe/configure.in
@@ -2,10 +2,10 @@ dnl Process this file with autoconf to produce a configure script.
 
 dnl AC_PREREQ([2.67])
 dnl AC 2.62 needed for OpenMP
-AC_PREREQ([2.67])
+AC_PREREQ([2.63])
 
 dnl AC_INIT (package, version, [bug-report-email], [tarname])
-AC_INIT([gtfold],[1.18])
+AC_INIT([gtfold],[2.0])
 
 dnl check for this file's existence to make sure that the directory
 dnl specified by --srcdir is the right one
@@ -178,7 +178,7 @@ AM_CONDITIONAL(GTFOLD_DEBUG, test x$debug = xtrue)
 
 dnl Create makefiles and other configuration files
 AC_CONFIG_FILES([Makefile src/Makefile data/Makefile include/Makefile])
-AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile])
+AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile])
 
 dnl Generate `config.status' and launch it
 AC_OUTPUT

From d9170d0601fcfdc1fee27aac89fafb450354c48e Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Fri, 24 Jun 2011 12:50:16 -0400
Subject: [PATCH 175/282] delete these auto generated file

---
 gtfold-mfe/data/Andronescu/Makefile | 399 --------------------------
 gtfold-mfe/data/Turner04/Makefile   | 405 ---------------------------
 gtfold-mfe/data/Turner99/Makefile   | 420 ----------------------------
 gtfold-mfe/include/Makefile         | 388 -------------------------
 4 files changed, 1612 deletions(-)
 delete mode 100644 gtfold-mfe/data/Andronescu/Makefile
 delete mode 100644 gtfold-mfe/data/Turner04/Makefile
 delete mode 100644 gtfold-mfe/data/Turner99/Makefile
 delete mode 100644 gtfold-mfe/include/Makefile

diff --git a/gtfold-mfe/data/Andronescu/Makefile b/gtfold-mfe/data/Andronescu/Makefile
deleted file mode 100644
index 8dc0b5c..0000000
--- a/gtfold-mfe/data/Andronescu/Makefile
+++ /dev/null
@@ -1,399 +0,0 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
-# data/Andronescu/Makefile.  Generated from Makefile.in by configure.
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-
-
-
-pkgdatadir = $(datadir)/gtfold
-pkgincludedir = $(includedir)/gtfold
-pkglibdir = $(libdir)/gtfold
-pkglibexecdir = $(libexecdir)/gtfold
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = x86_64-unknown-linux-gnu
-host_triplet = x86_64-unknown-linux-gnu
-target_triplet = x86_64-unknown-linux-gnu
-subdir = data/Andronescu
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-am__vpath_adj = case $$p in \
-    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-    *) f=$$p;; \
-  esac;
-am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-am__install_max = 40
-am__nobase_strip_setup = \
-  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-am__nobase_strip = \
-  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-am__nobase_list = $(am__nobase_strip_setup); \
-  for p in $$list; do echo "$$p $$p"; done | \
-  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-    if (++n[$$2] == $(am__install_max)) \
-      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-    END { for (dir in files) print dir, files[dir] }'
-am__base_list = \
-  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
-DATA = $(gtfold_data_DATA)
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = mawk
-CC = gcc
-CCDEPMODE = depmode=gcc3
-CFLAGS = -g -O2 -Wall
-CPP = gcc -E
-CPPFLAGS = 
-CXX = g++
-CXXDEPMODE = depmode=gcc3
-CXXFLAGS = -g -O2 -Wall
-CYGPATH_W = echo
-DEFS = -DHAVE_CONFIG_H
-DEPDIR = .deps
-ECHO_C = 
-ECHO_N = -n
-ECHO_T = 
-EGREP = /bin/grep -E
-EXEEXT = 
-GREP = /bin/grep
-INSTALL = /usr/bin/install -c
-INSTALL_DATA = ${INSTALL} -m 644
-INSTALL_PROGRAM = ${INSTALL}
-INSTALL_SCRIPT = ${INSTALL}
-INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
-LDFLAGS = 
-LIBOBJS = 
-LIBS = -lgomp 
-LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
-MKDIR_P = /bin/mkdir -p
-OBJEXT = o
-OPENMP_CFLAGS = -fopenmp
-PACKAGE = gtfold
-PACKAGE_BUGREPORT = 
-PACKAGE_NAME = gtfold
-PACKAGE_STRING = gtfold 1.18
-PACKAGE_TARNAME = gtfold
-PACKAGE_URL = 
-PACKAGE_VERSION = 1.18
-PATH_SEPARATOR = :
-SET_MAKE = 
-SHELL = /bin/bash
-STRIP = 
-VERSION = 1.18
-abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data/Andronescu
-abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data/Andronescu
-abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
-abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
-ac_ct_CC = gcc
-ac_ct_CXX = g++
-am__include = include
-am__leading_dot = .
-am__quote = 
-am__tar = ${AMTAR} chof - "$$tardir"
-am__untar = ${AMTAR} xf -
-bindir = ${exec_prefix}/bin
-build = x86_64-unknown-linux-gnu
-build_alias = 
-build_cpu = x86_64
-build_os = linux-gnu
-build_vendor = unknown
-builddir = .
-datadir = ${datarootdir}
-datarootdir = ${prefix}/share
-docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
-dvidir = ${docdir}
-exec_prefix = ${prefix}
-host = x86_64-unknown-linux-gnu
-host_alias = 
-host_cpu = x86_64
-host_os = linux-gnu
-host_vendor = unknown
-htmldir = ${docdir}
-includedir = ${prefix}/include
-infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
-libdir = ${exec_prefix}/lib
-libexecdir = ${exec_prefix}/libexec
-localedir = ${datarootdir}/locale
-localstatedir = ${prefix}/var
-mandir = ${datarootdir}/man
-mkdir_p = /bin/mkdir -p
-oldincludedir = /usr/include
-pdfdir = ${docdir}
-prefix = /usr/local
-program_transform_name = s,x,x,
-psdir = ${docdir}
-sbindir = ${exec_prefix}/sbin
-sharedstatedir = ${prefix}/com
-srcdir = .
-sysconfdir = ${prefix}/etc
-target = x86_64-unknown-linux-gnu
-target_alias = 
-target_cpu = x86_64
-target_os = linux-gnu
-target_vendor = unknown
-top_build_prefix = ../../
-top_builddir = ../..
-top_srcdir = ../..
-gtfold_datadir = $(datadir)/gtfold/Andronescu
-gtfold_data_DATA = \
-	stack.dat\
-	miscloop.dat\
-	dangle.dat\
-	loop.dat\
-	int11.dat\
-	int21.dat\
-	int22.dat\
-	tloop.dat\
-	triloop.dat\
-	tstackh.dat\
-	tstacki.dat
-
-EXTRA_DIST = $(gtfold_data_DATA)
-CLEANFILES = *~
-all: all-am
-
-.SUFFIXES:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Andronescu/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu data/Andronescu/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-install-gtfold_dataDATA: $(gtfold_data_DATA)
-	@$(NORMAL_INSTALL)
-	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	for p in $$list; do \
-	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-	  echo "$$d$$p"; \
-	done | $(am__base_list) | \
-	while read files; do \
-	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
-	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
-	done
-
-uninstall-gtfold_dataDATA:
-	@$(NORMAL_UNINSTALL)
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-	test -n "$$files" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
-tags: TAGS
-TAGS:
-
-ctags: CTAGS
-CTAGS:
-
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-am
-all-am: Makefile $(DATA)
-installdirs:
-	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
-	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-	done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-am
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am: install-gtfold_dataDATA
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-gtfold_dataDATA
-
-.MAKE: install-am install-strip
-
-.PHONY: all all-am check check-am clean clean-generic distclean \
-	distclean-generic distdir dvi dvi-am html html-am info info-am \
-	install install-am install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am \
-	install-gtfold_dataDATA install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am uninstall uninstall-am \
-	uninstall-gtfold_dataDATA
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/gtfold-mfe/data/Turner04/Makefile b/gtfold-mfe/data/Turner04/Makefile
deleted file mode 100644
index 65f56b2..0000000
--- a/gtfold-mfe/data/Turner04/Makefile
+++ /dev/null
@@ -1,405 +0,0 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
-# data/Turner04/Makefile.  Generated from Makefile.in by configure.
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-
-
-
-pkgdatadir = $(datadir)/gtfold
-pkgincludedir = $(includedir)/gtfold
-pkglibdir = $(libdir)/gtfold
-pkglibexecdir = $(libexecdir)/gtfold
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = x86_64-unknown-linux-gnu
-host_triplet = x86_64-unknown-linux-gnu
-target_triplet = x86_64-unknown-linux-gnu
-subdir = data/Turner04
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-am__vpath_adj = case $$p in \
-    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-    *) f=$$p;; \
-  esac;
-am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-am__install_max = 40
-am__nobase_strip_setup = \
-  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-am__nobase_strip = \
-  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-am__nobase_list = $(am__nobase_strip_setup); \
-  for p in $$list; do echo "$$p $$p"; done | \
-  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-    if (++n[$$2] == $(am__install_max)) \
-      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-    END { for (dir in files) print dir, files[dir] }'
-am__base_list = \
-  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
-DATA = $(gtfold_data_DATA)
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = mawk
-CC = gcc
-CCDEPMODE = depmode=gcc3
-CFLAGS = -g -O2 -Wall
-CPP = gcc -E
-CPPFLAGS = 
-CXX = g++
-CXXDEPMODE = depmode=gcc3
-CXXFLAGS = -g -O2 -Wall
-CYGPATH_W = echo
-DEFS = -DHAVE_CONFIG_H
-DEPDIR = .deps
-ECHO_C = 
-ECHO_N = -n
-ECHO_T = 
-EGREP = /bin/grep -E
-EXEEXT = 
-GREP = /bin/grep
-INSTALL = /usr/bin/install -c
-INSTALL_DATA = ${INSTALL} -m 644
-INSTALL_PROGRAM = ${INSTALL}
-INSTALL_SCRIPT = ${INSTALL}
-INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
-LDFLAGS = 
-LIBOBJS = 
-LIBS = -lgomp 
-LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
-MKDIR_P = /bin/mkdir -p
-OBJEXT = o
-OPENMP_CFLAGS = -fopenmp
-PACKAGE = gtfold
-PACKAGE_BUGREPORT = 
-PACKAGE_NAME = gtfold
-PACKAGE_STRING = gtfold 1.18
-PACKAGE_TARNAME = gtfold
-PACKAGE_URL = 
-PACKAGE_VERSION = 1.18
-PATH_SEPARATOR = :
-SET_MAKE = 
-SHELL = /bin/bash
-STRIP = 
-VERSION = 1.18
-abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner04
-abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner04
-abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
-abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
-ac_ct_CC = gcc
-ac_ct_CXX = g++
-am__include = include
-am__leading_dot = .
-am__quote = 
-am__tar = ${AMTAR} chof - "$$tardir"
-am__untar = ${AMTAR} xf -
-bindir = ${exec_prefix}/bin
-build = x86_64-unknown-linux-gnu
-build_alias = 
-build_cpu = x86_64
-build_os = linux-gnu
-build_vendor = unknown
-builddir = .
-datadir = ${datarootdir}
-datarootdir = ${prefix}/share
-docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
-dvidir = ${docdir}
-exec_prefix = ${prefix}
-host = x86_64-unknown-linux-gnu
-host_alias = 
-host_cpu = x86_64
-host_os = linux-gnu
-host_vendor = unknown
-htmldir = ${docdir}
-includedir = ${prefix}/include
-infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
-libdir = ${exec_prefix}/lib
-libexecdir = ${exec_prefix}/libexec
-localedir = ${datarootdir}/locale
-localstatedir = ${prefix}/var
-mandir = ${datarootdir}/man
-mkdir_p = /bin/mkdir -p
-oldincludedir = /usr/include
-pdfdir = ${docdir}
-prefix = /usr/local
-program_transform_name = s,x,x,
-psdir = ${docdir}
-sbindir = ${exec_prefix}/sbin
-sharedstatedir = ${prefix}/com
-srcdir = .
-sysconfdir = ${prefix}/etc
-target = x86_64-unknown-linux-gnu
-target_alias = 
-target_cpu = x86_64
-target_os = linux-gnu
-target_vendor = unknown
-top_build_prefix = ../../
-top_builddir = ../..
-top_srcdir = ../..
-gtfold_datadir = $(datadir)/gtfold/Turner04
-gtfold_data_DATA = \
-	stack.dat\
-	miscloop.dat\
-	dangle.dat\
-	loop.dat\
-	coaxial.dat\
-	coaxstack.dat\
-	hexaloop.dat\
-	int11.dat\
-	int21.dat\
-	int22.dat\
-	tloop.dat\
-	triloop.dat\
-	tstack.dat\
-	tstackcoax.dat\
-	tstackh.dat\
-	tstacki.dat\
-	tstackm.dat
-
-EXTRA_DIST = $(gtfold_data_DATA)
-CLEANFILES = *~
-all: all-am
-
-.SUFFIXES:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Turner04/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu data/Turner04/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-install-gtfold_dataDATA: $(gtfold_data_DATA)
-	@$(NORMAL_INSTALL)
-	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	for p in $$list; do \
-	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-	  echo "$$d$$p"; \
-	done | $(am__base_list) | \
-	while read files; do \
-	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
-	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
-	done
-
-uninstall-gtfold_dataDATA:
-	@$(NORMAL_UNINSTALL)
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-	test -n "$$files" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
-tags: TAGS
-TAGS:
-
-ctags: CTAGS
-CTAGS:
-
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-am
-all-am: Makefile $(DATA)
-installdirs:
-	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
-	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-	done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-am
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am: install-gtfold_dataDATA
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-gtfold_dataDATA
-
-.MAKE: install-am install-strip
-
-.PHONY: all all-am check check-am clean clean-generic distclean \
-	distclean-generic distdir dvi dvi-am html html-am info info-am \
-	install install-am install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am \
-	install-gtfold_dataDATA install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am uninstall uninstall-am \
-	uninstall-gtfold_dataDATA
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/gtfold-mfe/data/Turner99/Makefile b/gtfold-mfe/data/Turner99/Makefile
deleted file mode 100644
index abc7da4..0000000
--- a/gtfold-mfe/data/Turner99/Makefile
+++ /dev/null
@@ -1,420 +0,0 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
-# data/Turner99/Makefile.  Generated from Makefile.in by configure.
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-
-
-
-pkgdatadir = $(datadir)/gtfold
-pkgincludedir = $(includedir)/gtfold
-pkglibdir = $(libdir)/gtfold
-pkglibexecdir = $(libexecdir)/gtfold
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = x86_64-unknown-linux-gnu
-host_triplet = x86_64-unknown-linux-gnu
-target_triplet = x86_64-unknown-linux-gnu
-subdir = data/Turner99
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-am__vpath_adj = case $$p in \
-    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-    *) f=$$p;; \
-  esac;
-am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-am__install_max = 40
-am__nobase_strip_setup = \
-  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-am__nobase_strip = \
-  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-am__nobase_list = $(am__nobase_strip_setup); \
-  for p in $$list; do echo "$$p $$p"; done | \
-  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-    if (++n[$$2] == $(am__install_max)) \
-      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-    END { for (dir in files) print dir, files[dir] }'
-am__base_list = \
-  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
-DATA = $(gtfold_data_DATA)
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = mawk
-CC = gcc
-CCDEPMODE = depmode=gcc3
-CFLAGS = -g -O2 -Wall
-CPP = gcc -E
-CPPFLAGS = 
-CXX = g++
-CXXDEPMODE = depmode=gcc3
-CXXFLAGS = -g -O2 -Wall
-CYGPATH_W = echo
-DEFS = -DHAVE_CONFIG_H
-DEPDIR = .deps
-ECHO_C = 
-ECHO_N = -n
-ECHO_T = 
-EGREP = /bin/grep -E
-EXEEXT = 
-GREP = /bin/grep
-INSTALL = /usr/bin/install -c
-INSTALL_DATA = ${INSTALL} -m 644
-INSTALL_PROGRAM = ${INSTALL}
-INSTALL_SCRIPT = ${INSTALL}
-INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
-LDFLAGS = 
-LIBOBJS = 
-LIBS = -lgomp 
-LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
-MKDIR_P = /bin/mkdir -p
-OBJEXT = o
-OPENMP_CFLAGS = -fopenmp
-PACKAGE = gtfold
-PACKAGE_BUGREPORT = 
-PACKAGE_NAME = gtfold
-PACKAGE_STRING = gtfold 1.18
-PACKAGE_TARNAME = gtfold
-PACKAGE_URL = 
-PACKAGE_VERSION = 1.18
-PATH_SEPARATOR = :
-SET_MAKE = 
-SHELL = /bin/bash
-STRIP = 
-VERSION = 1.18
-abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner99
-abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner99
-abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
-abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
-ac_ct_CC = gcc
-ac_ct_CXX = g++
-am__include = include
-am__leading_dot = .
-am__quote = 
-am__tar = ${AMTAR} chof - "$$tardir"
-am__untar = ${AMTAR} xf -
-bindir = ${exec_prefix}/bin
-build = x86_64-unknown-linux-gnu
-build_alias = 
-build_cpu = x86_64
-build_os = linux-gnu
-build_vendor = unknown
-builddir = .
-datadir = ${datarootdir}
-datarootdir = ${prefix}/share
-docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
-dvidir = ${docdir}
-exec_prefix = ${prefix}
-host = x86_64-unknown-linux-gnu
-host_alias = 
-host_cpu = x86_64
-host_os = linux-gnu
-host_vendor = unknown
-htmldir = ${docdir}
-includedir = ${prefix}/include
-infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
-libdir = ${exec_prefix}/lib
-libexecdir = ${exec_prefix}/libexec
-localedir = ${datarootdir}/locale
-localstatedir = ${prefix}/var
-mandir = ${datarootdir}/man
-mkdir_p = /bin/mkdir -p
-oldincludedir = /usr/include
-pdfdir = ${docdir}
-prefix = /usr/local
-program_transform_name = s,x,x,
-psdir = ${docdir}
-sbindir = ${exec_prefix}/sbin
-sharedstatedir = ${prefix}/com
-srcdir = .
-sysconfdir = ${prefix}/etc
-target = x86_64-unknown-linux-gnu
-target_alias = 
-target_cpu = x86_64
-target_os = linux-gnu
-target_vendor = unknown
-top_build_prefix = ../../
-top_builddir = ../..
-top_srcdir = ../..
-gtfold_datadir = $(datadir)/gtfold/Turner99
-gtfold_data_DATA = \
-	stack.DAT\
-	miscloop.DAT\
-	dangle.DAT\
-	loop.DAT\
-	int11.DAT\
-	int21.DAT\
-	int22.DAT\
-	sint2.DAT\
-	sint4.DAT\
-	tloop.DAT\
-	tstackh.DAT\
-	tstacki.DAT\
-	tstackm.DAT\
-	stack.dat\
-	miscloop.dat\
-	dangle.dat\
-	loop.dat\
-	asint1x2.dat\
-	coaxial.dat\
-	coaxstack.dat\
-	int11.dat\
-	int21.dat\
-	int22.dat\
-	sint2.dat\
-	sint4.dat\
-	tloop.dat\
-	triloop.dat\
-	tstack.dat\
-	tstackcoax.dat\
-	tstackh.dat\
-	tstacki.dat\
-	tstackm.dat
-
-EXTRA_DIST = $(gtfold_data_DATA)
-CLEANFILES = *~
-all: all-am
-
-.SUFFIXES:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Turner99/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu data/Turner99/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-install-gtfold_dataDATA: $(gtfold_data_DATA)
-	@$(NORMAL_INSTALL)
-	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	for p in $$list; do \
-	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-	  echo "$$d$$p"; \
-	done | $(am__base_list) | \
-	while read files; do \
-	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
-	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
-	done
-
-uninstall-gtfold_dataDATA:
-	@$(NORMAL_UNINSTALL)
-	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
-	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-	test -n "$$files" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
-tags: TAGS
-TAGS:
-
-ctags: CTAGS
-CTAGS:
-
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-am
-all-am: Makefile $(DATA)
-installdirs:
-	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
-	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-	done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-am
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am: install-gtfold_dataDATA
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-gtfold_dataDATA
-
-.MAKE: install-am install-strip
-
-.PHONY: all all-am check check-am clean clean-generic distclean \
-	distclean-generic distdir dvi dvi-am html html-am info info-am \
-	install install-am install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am \
-	install-gtfold_dataDATA install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am uninstall uninstall-am \
-	uninstall-gtfold_dataDATA
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/gtfold-mfe/include/Makefile b/gtfold-mfe/include/Makefile
deleted file mode 100644
index 596ed80..0000000
--- a/gtfold-mfe/include/Makefile
+++ /dev/null
@@ -1,388 +0,0 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
-# include/Makefile.  Generated from Makefile.in by configure.
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-
-
-
-pkgdatadir = $(datadir)/gtfold
-pkgincludedir = $(includedir)/gtfold
-pkglibdir = $(libdir)/gtfold
-pkglibexecdir = $(libexecdir)/gtfold
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = x86_64-unknown-linux-gnu
-host_triplet = x86_64-unknown-linux-gnu
-target_triplet = x86_64-unknown-linux-gnu
-subdir = include
-DIST_COMMON = $(noinst_HEADERS) $(srcdir)/Makefile.am \
-	$(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-HEADERS = $(noinst_HEADERS)
-ETAGS = etags
-CTAGS = ctags
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = mawk
-CC = gcc
-CCDEPMODE = depmode=gcc3
-CFLAGS = -g -O2 -Wall
-CPP = gcc -E
-CPPFLAGS = 
-CXX = g++
-CXXDEPMODE = depmode=gcc3
-CXXFLAGS = -g -O2 -Wall
-CYGPATH_W = echo
-DEFS = -DHAVE_CONFIG_H
-DEPDIR = .deps
-ECHO_C = 
-ECHO_N = -n
-ECHO_T = 
-EGREP = /bin/grep -E
-EXEEXT = 
-GREP = /bin/grep
-INSTALL = /usr/bin/install -c
-INSTALL_DATA = ${INSTALL} -m 644
-INSTALL_PROGRAM = ${INSTALL}
-INSTALL_SCRIPT = ${INSTALL}
-INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
-LDFLAGS = 
-LIBOBJS = 
-LIBS = -lgomp 
-LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
-MKDIR_P = /bin/mkdir -p
-OBJEXT = o
-OPENMP_CFLAGS = -fopenmp
-PACKAGE = gtfold
-PACKAGE_BUGREPORT = 
-PACKAGE_NAME = gtfold
-PACKAGE_STRING = gtfold 1.18
-PACKAGE_TARNAME = gtfold
-PACKAGE_URL = 
-PACKAGE_VERSION = 1.18
-PATH_SEPARATOR = :
-SET_MAKE = 
-SHELL = /bin/bash
-STRIP = 
-VERSION = 1.18
-abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/include
-abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/include
-abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
-abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
-ac_ct_CC = gcc
-ac_ct_CXX = g++
-am__include = include
-am__leading_dot = .
-am__quote = 
-am__tar = ${AMTAR} chof - "$$tardir"
-am__untar = ${AMTAR} xf -
-bindir = ${exec_prefix}/bin
-build = x86_64-unknown-linux-gnu
-build_alias = 
-build_cpu = x86_64
-build_os = linux-gnu
-build_vendor = unknown
-builddir = .
-datadir = ${datarootdir}
-datarootdir = ${prefix}/share
-docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
-dvidir = ${docdir}
-exec_prefix = ${prefix}
-host = x86_64-unknown-linux-gnu
-host_alias = 
-host_cpu = x86_64
-host_os = linux-gnu
-host_vendor = unknown
-htmldir = ${docdir}
-includedir = ${prefix}/include
-infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
-libdir = ${exec_prefix}/lib
-libexecdir = ${exec_prefix}/libexec
-localedir = ${datarootdir}/locale
-localstatedir = ${prefix}/var
-mandir = ${datarootdir}/man
-mkdir_p = /bin/mkdir -p
-oldincludedir = /usr/include
-pdfdir = ${docdir}
-prefix = /usr/local
-program_transform_name = s,x,x,
-psdir = ${docdir}
-sbindir = ${exec_prefix}/sbin
-sharedstatedir = ${prefix}/com
-srcdir = .
-sysconfdir = ${prefix}/etc
-target = x86_64-unknown-linux-gnu
-target_alias = 
-target_cpu = x86_64
-target_os = linux-gnu
-target_vendor = unknown
-top_build_prefix = ../
-top_builddir = ..
-top_srcdir = ..
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h
-CLEANFILES = *~
-all: all-am
-
-.SUFFIXES:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu include/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu include/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	mkid -fID $$unique
-tags: TAGS
-
-TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	set x; \
-	here=`pwd`; \
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	shift; \
-	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-	  test -n "$$unique" || unique=$$empty_fix; \
-	  if test $$# -gt 0; then \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      "$$@" $$unique; \
-	  else \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      $$unique; \
-	  fi; \
-	fi
-ctags: CTAGS
-CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	test -z "$(CTAGS_ARGS)$$unique" \
-	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$unique
-
-GTAGS:
-	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && $(am__cd) $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) "$$here"
-
-distclean-tags:
-	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-am
-all-am: Makefile $(HEADERS)
-installdirs:
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-am
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-am
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic distclean-tags
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am:
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am:
-
-.MAKE: install-am install-strip
-
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
-	ctags distclean distclean-generic distclean-tags distdir dvi \
-	dvi-am html html-am info info-am install install-am \
-	install-data install-data-am install-dvi install-dvi-am \
-	install-exec install-exec-am install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am tags uninstall uninstall-am
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:

From 43a71ff2dd4990cff517262dae328cf323ed749c Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Fri, 24 Jun 2011 12:51:34 -0400
Subject: [PATCH 176/282] delete these auto generated file

---
 gtfold-mfe/Makefile      | 753 ---------------------------------------
 gtfold-mfe/data/Makefile | 536 ----------------------------
 2 files changed, 1289 deletions(-)
 delete mode 100644 gtfold-mfe/Makefile
 delete mode 100644 gtfold-mfe/data/Makefile

diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile
deleted file mode 100644
index cdd52e6..0000000
--- a/gtfold-mfe/Makefile
+++ /dev/null
@@ -1,753 +0,0 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
-# Makefile.  Generated from Makefile.in by configure.
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-
-
-
-pkgdatadir = $(datadir)/gtfold
-pkgincludedir = $(includedir)/gtfold
-pkglibdir = $(libdir)/gtfold
-pkglibexecdir = $(libexecdir)/gtfold
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = x86_64-unknown-linux-gnu
-host_triplet = x86_64-unknown-linux-gnu
-target_triplet = x86_64-unknown-linux-gnu
-subdir = .
-DIST_COMMON = README $(am__configure_deps) $(include_HEADERS) \
-	$(srcdir)/Makefile.am $(srcdir)/Makefile.in \
-	$(srcdir)/gtfold_config.h.in $(top_srcdir)/configure AUTHORS \
-	COPYING ChangeLog INSTALL NEWS TODO config.guess config.sub \
-	depcomp install-sh missing
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
- configure.lineno config.status.lineno
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
-	html-recursive info-recursive install-data-recursive \
-	install-dvi-recursive install-exec-recursive \
-	install-html-recursive install-info-recursive \
-	install-pdf-recursive install-ps-recursive install-recursive \
-	installcheck-recursive installdirs-recursive pdf-recursive \
-	ps-recursive uninstall-recursive
-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-am__vpath_adj = case $$p in \
-    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-    *) f=$$p;; \
-  esac;
-am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-am__install_max = 40
-am__nobase_strip_setup = \
-  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-am__nobase_strip = \
-  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-am__nobase_list = $(am__nobase_strip_setup); \
-  for p in $$list; do echo "$$p $$p"; done | \
-  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-    if (++n[$$2] == $(am__install_max)) \
-      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-    END { for (dir in files) print dir, files[dir] }'
-am__base_list = \
-  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__installdirs = "$(DESTDIR)$(includedir)"
-HEADERS = $(include_HEADERS)
-RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
-  distclean-recursive maintainer-clean-recursive
-AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-	$(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
-	distdir dist dist-all distcheck
-ETAGS = etags
-CTAGS = ctags
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-distdir = $(PACKAGE)-$(VERSION)
-top_distdir = $(distdir)
-am__remove_distdir = \
-  { test ! -d "$(distdir)" \
-    || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
-         && rm -fr "$(distdir)"; }; }
-am__relativize = \
-  dir0=`pwd`; \
-  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
-  sed_rest='s,^[^/]*/*,,'; \
-  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
-  sed_butlast='s,/*[^/]*$$,,'; \
-  while test -n "$$dir1"; do \
-    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
-    if test "$$first" != "."; then \
-      if test "$$first" = ".."; then \
-        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
-        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
-      else \
-        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
-        if test "$$first2" = "$$first"; then \
-          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
-        else \
-          dir2="../$$dir2"; \
-        fi; \
-        dir0="$$dir0"/"$$first"; \
-      fi; \
-    fi; \
-    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
-  done; \
-  reldir="$$dir2"
-DIST_ARCHIVES = $(distdir).tar.gz
-GZIP_ENV = --best
-distuninstallcheck_listfiles = find . -type f -print
-distcleancheck_listfiles = find . -type f -print
-ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = mawk
-CC = gcc
-CCDEPMODE = depmode=gcc3
-CFLAGS = -g -O2 -Wall
-CPP = gcc -E
-CPPFLAGS = 
-CXX = g++
-CXXDEPMODE = depmode=gcc3
-CXXFLAGS = -g -O2 -Wall
-CYGPATH_W = echo
-DEFS = -DHAVE_CONFIG_H
-DEPDIR = .deps
-ECHO_C = 
-ECHO_N = -n
-ECHO_T = 
-EGREP = /bin/grep -E
-EXEEXT = 
-GREP = /bin/grep
-INSTALL = /usr/bin/install -c
-INSTALL_DATA = ${INSTALL} -m 644
-INSTALL_PROGRAM = ${INSTALL}
-INSTALL_SCRIPT = ${INSTALL}
-INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
-LDFLAGS = 
-LIBOBJS = 
-LIBS = -lgomp 
-LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
-MKDIR_P = /bin/mkdir -p
-OBJEXT = o
-OPENMP_CFLAGS = -fopenmp
-PACKAGE = gtfold
-PACKAGE_BUGREPORT = 
-PACKAGE_NAME = gtfold
-PACKAGE_STRING = gtfold 1.18
-PACKAGE_TARNAME = gtfold
-PACKAGE_URL = 
-PACKAGE_VERSION = 1.18
-PATH_SEPARATOR = :
-SET_MAKE = 
-SHELL = /bin/bash
-STRIP = 
-VERSION = 1.18
-abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe
-abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
-abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
-abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
-ac_ct_CC = gcc
-ac_ct_CXX = g++
-am__include = include
-am__leading_dot = .
-am__quote = 
-am__tar = ${AMTAR} chof - "$$tardir"
-am__untar = ${AMTAR} xf -
-bindir = ${exec_prefix}/bin
-build = x86_64-unknown-linux-gnu
-build_alias = 
-build_cpu = x86_64
-build_os = linux-gnu
-build_vendor = unknown
-builddir = .
-datadir = ${datarootdir}
-datarootdir = ${prefix}/share
-docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
-dvidir = ${docdir}
-exec_prefix = ${prefix}
-host = x86_64-unknown-linux-gnu
-host_alias = 
-host_cpu = x86_64
-host_os = linux-gnu
-host_vendor = unknown
-htmldir = ${docdir}
-includedir = ${prefix}/include
-infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
-libdir = ${exec_prefix}/lib
-libexecdir = ${exec_prefix}/libexec
-localedir = ${datarootdir}/locale
-localstatedir = ${prefix}/var
-mandir = ${datarootdir}/man
-mkdir_p = /bin/mkdir -p
-oldincludedir = /usr/include
-pdfdir = ${docdir}
-prefix = /usr/local
-program_transform_name = s,x,x,
-psdir = ${docdir}
-sbindir = ${exec_prefix}/sbin
-sharedstatedir = ${prefix}/com
-srcdir = .
-sysconfdir = ${prefix}/etc
-target = x86_64-unknown-linux-gnu
-target_alias = 
-target_cpu = x86_64
-target_os = linux-gnu
-target_vendor = unknown
-top_build_prefix = 
-top_builddir = .
-top_srcdir = .
-SUBDIRS = src include data
-DIST_SUBDIRS = src include data
-include_HEADERS = gtfold_config.h
-CLEANFILES = *~
-MAINTAINERCLEANDIRS = autom4te.cache
-# MAINTAINERCLEANFILES = libtool gtfold_config.h.in
-MAINTAINERCLEANFILES = gtfold_config.h gtfold_config.h.in
-EXTRA_DIST = autogen.sh
-all: gtfold_config.h
-	$(MAKE) $(AM_MAKEFLAGS) all-recursive
-
-.SUFFIXES:
-am--refresh:
-	@:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      echo ' cd $(srcdir) && $(AUTOMAKE) --gnu'; \
-	      $(am__cd) $(srcdir) && $(AUTOMAKE) --gnu \
-		&& exit 0; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    echo ' $(SHELL) ./config.status'; \
-	    $(SHELL) ./config.status;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	$(SHELL) ./config.status --recheck
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	$(am__cd) $(srcdir) && $(AUTOCONF)
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	$(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
-$(am__aclocal_m4_deps):
-
-gtfold_config.h: stamp-h1
-	@if test ! -f $@; then \
-	  rm -f stamp-h1; \
-	  $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
-	else :; fi
-
-stamp-h1: $(srcdir)/gtfold_config.h.in $(top_builddir)/config.status
-	@rm -f stamp-h1
-	cd $(top_builddir) && $(SHELL) ./config.status gtfold_config.h
-$(srcdir)/gtfold_config.h.in:  $(am__configure_deps) 
-	($(am__cd) $(top_srcdir) && $(AUTOHEADER))
-	rm -f stamp-h1
-	touch $@
-
-distclean-hdr:
-	-rm -f gtfold_config.h stamp-h1
-install-includeHEADERS: $(include_HEADERS)
-	@$(NORMAL_INSTALL)
-	test -z "$(includedir)" || $(MKDIR_P) "$(DESTDIR)$(includedir)"
-	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
-	for p in $$list; do \
-	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-	  echo "$$d$$p"; \
-	done | $(am__base_list) | \
-	while read files; do \
-	  echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(includedir)'"; \
-	  $(INSTALL_HEADER) $$files "$(DESTDIR)$(includedir)" || exit $$?; \
-	done
-
-uninstall-includeHEADERS:
-	@$(NORMAL_UNINSTALL)
-	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
-	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-	test -n "$$files" || exit 0; \
-	echo " ( cd '$(DESTDIR)$(includedir)' && rm -f" $$files ")"; \
-	cd "$(DESTDIR)$(includedir)" && rm -f $$files
-
-# This directory's subdirectories are mostly independent; you can cd
-# into them and run `make' without going through this Makefile.
-# To change the values of `make' variables: instead of editing Makefiles,
-# (1) if the variable is set in `config.status', edit `config.status'
-#     (which will cause the Makefiles to be regenerated when you run `make');
-# (2) otherwise, pass the desired values on the `make' command line.
-$(RECURSIVE_TARGETS):
-	@fail= failcom='exit 1'; \
-	for f in x $$MAKEFLAGS; do \
-	  case $$f in \
-	    *=* | --[!k]*);; \
-	    *k*) failcom='fail=yes';; \
-	  esac; \
-	done; \
-	dot_seen=no; \
-	target=`echo $@ | sed s/-recursive//`; \
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  echo "Making $$target in $$subdir"; \
-	  if test "$$subdir" = "."; then \
-	    dot_seen=yes; \
-	    local_target="$$target-am"; \
-	  else \
-	    local_target="$$target"; \
-	  fi; \
-	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-	  || eval $$failcom; \
-	done; \
-	if test "$$dot_seen" = "no"; then \
-	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
-	fi; test -z "$$fail"
-
-$(RECURSIVE_CLEAN_TARGETS):
-	@fail= failcom='exit 1'; \
-	for f in x $$MAKEFLAGS; do \
-	  case $$f in \
-	    *=* | --[!k]*);; \
-	    *k*) failcom='fail=yes';; \
-	  esac; \
-	done; \
-	dot_seen=no; \
-	case "$@" in \
-	  distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
-	  *) list='$(SUBDIRS)' ;; \
-	esac; \
-	rev=''; for subdir in $$list; do \
-	  if test "$$subdir" = "."; then :; else \
-	    rev="$$subdir $$rev"; \
-	  fi; \
-	done; \
-	rev="$$rev ."; \
-	target=`echo $@ | sed s/-recursive//`; \
-	for subdir in $$rev; do \
-	  echo "Making $$target in $$subdir"; \
-	  if test "$$subdir" = "."; then \
-	    local_target="$$target-am"; \
-	  else \
-	    local_target="$$target"; \
-	  fi; \
-	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-	  || eval $$failcom; \
-	done && test -z "$$fail"
-tags-recursive:
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-	done
-ctags-recursive:
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
-	done
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	mkid -fID $$unique
-tags: TAGS
-
-TAGS: tags-recursive $(HEADERS) $(SOURCES) gtfold_config.h.in $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	set x; \
-	here=`pwd`; \
-	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
-	  include_option=--etags-include; \
-	  empty_fix=.; \
-	else \
-	  include_option=--include; \
-	  empty_fix=; \
-	fi; \
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    test ! -f $$subdir/TAGS || \
-	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
-	  fi; \
-	done; \
-	list='$(SOURCES) $(HEADERS) gtfold_config.h.in $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	shift; \
-	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-	  test -n "$$unique" || unique=$$empty_fix; \
-	  if test $$# -gt 0; then \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      "$$@" $$unique; \
-	  else \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      $$unique; \
-	  fi; \
-	fi
-ctags: CTAGS
-CTAGS: ctags-recursive $(HEADERS) $(SOURCES) gtfold_config.h.in $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	list='$(SOURCES) $(HEADERS) gtfold_config.h.in $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	test -z "$(CTAGS_ARGS)$$unique" \
-	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$unique
-
-GTAGS:
-	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && $(am__cd) $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) "$$here"
-
-distclean-tags:
-	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
-distdir: $(DISTFILES)
-	$(am__remove_distdir)
-	test -d "$(distdir)" || mkdir "$(distdir)"
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    test -d "$(distdir)/$$subdir" \
-	    || $(MKDIR_P) "$(distdir)/$$subdir" \
-	    || exit 1; \
-	  fi; \
-	done
-	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
-	    $(am__relativize); \
-	    new_distdir=$$reldir; \
-	    dir1=$$subdir; dir2="$(top_distdir)"; \
-	    $(am__relativize); \
-	    new_top_distdir=$$reldir; \
-	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
-	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
-	    ($(am__cd) $$subdir && \
-	      $(MAKE) $(AM_MAKEFLAGS) \
-	        top_distdir="$$new_top_distdir" \
-	        distdir="$$new_distdir" \
-		am__remove_distdir=: \
-		am__skip_length_check=: \
-		am__skip_mode_fix=: \
-	        distdir) \
-	      || exit 1; \
-	  fi; \
-	done
-	-test -n "$(am__skip_mode_fix)" \
-	|| find "$(distdir)" -type d ! -perm -755 \
-		-exec chmod u+rwx,go+rx {} \; -o \
-	  ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
-	  ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
-	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
-	|| chmod -R a+r "$(distdir)"
-dist-gzip: distdir
-	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
-	$(am__remove_distdir)
-
-dist-bzip2: distdir
-	tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2
-	$(am__remove_distdir)
-
-dist-lzma: distdir
-	tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma
-	$(am__remove_distdir)
-
-dist-xz: distdir
-	tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz
-	$(am__remove_distdir)
-
-dist-tarZ: distdir
-	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
-	$(am__remove_distdir)
-
-dist-shar: distdir
-	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
-	$(am__remove_distdir)
-
-dist-zip: distdir
-	-rm -f $(distdir).zip
-	zip -rq $(distdir).zip $(distdir)
-	$(am__remove_distdir)
-
-dist dist-all: distdir
-	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
-	$(am__remove_distdir)
-
-# This target untars the dist file and tries a VPATH configuration.  Then
-# it guarantees that the distribution is self-contained by making another
-# tarfile.
-distcheck: dist
-	case '$(DIST_ARCHIVES)' in \
-	*.tar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
-	*.tar.bz2*) \
-	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
-	*.tar.lzma*) \
-	  lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\
-	*.tar.xz*) \
-	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
-	*.tar.Z*) \
-	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
-	*.shar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
-	*.zip*) \
-	  unzip $(distdir).zip ;;\
-	esac
-	chmod -R a-w $(distdir); chmod a+w $(distdir)
-	mkdir $(distdir)/_build
-	mkdir $(distdir)/_inst
-	chmod a-w $(distdir)
-	test -d $(distdir)/_build || exit 0; \
-	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
-	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
-	  && am__cwd=`pwd` \
-	  && $(am__cd) $(distdir)/_build \
-	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
-	    $(DISTCHECK_CONFIGURE_FLAGS) \
-	  && $(MAKE) $(AM_MAKEFLAGS) \
-	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
-	  && $(MAKE) $(AM_MAKEFLAGS) check \
-	  && $(MAKE) $(AM_MAKEFLAGS) install \
-	  && $(MAKE) $(AM_MAKEFLAGS) installcheck \
-	  && $(MAKE) $(AM_MAKEFLAGS) uninstall \
-	  && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
-	        distuninstallcheck \
-	  && chmod -R a-w "$$dc_install_base" \
-	  && ({ \
-	       (cd ../.. && umask 077 && mkdir "$$dc_destdir") \
-	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
-	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
-	       && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
-	            distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
-	      } || { rm -rf "$$dc_destdir"; exit 1; }) \
-	  && rm -rf "$$dc_destdir" \
-	  && $(MAKE) $(AM_MAKEFLAGS) dist \
-	  && rm -rf $(DIST_ARCHIVES) \
-	  && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
-	  && cd "$$am__cwd" \
-	  || exit 1
-	$(am__remove_distdir)
-	@(echo "$(distdir) archives ready for distribution: "; \
-	  list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
-	  sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
-distuninstallcheck:
-	@$(am__cd) '$(distuninstallcheck_dir)' \
-	&& test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
-	   || { echo "ERROR: files left after uninstall:" ; \
-	        if test -n "$(DESTDIR)"; then \
-	          echo "  (check DESTDIR support)"; \
-	        fi ; \
-	        $(distuninstallcheck_listfiles) ; \
-	        exit 1; } >&2
-distcleancheck: distclean
-	@if test '$(srcdir)' = . ; then \
-	  echo "ERROR: distcleancheck can only run from a VPATH build" ; \
-	  exit 1 ; \
-	fi
-	@test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
-	  || { echo "ERROR: files left in build directory after distclean:" ; \
-	       $(distcleancheck_listfiles) ; \
-	       exit 1; } >&2
-check-am: all-am
-check: check-recursive
-all-am: Makefile $(HEADERS) gtfold_config.h
-installdirs: installdirs-recursive
-installdirs-am:
-	for dir in "$(DESTDIR)$(includedir)"; do \
-	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-	done
-install: install-recursive
-install-exec: install-exec-recursive
-install-data: install-data-recursive
-uninstall: uninstall-recursive
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-recursive
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-	-test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
-clean: clean-recursive
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-recursive
-	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic distclean-hdr distclean-tags
-
-dvi: dvi-recursive
-
-dvi-am:
-
-html: html-recursive
-
-html-am:
-
-info: info-recursive
-
-info-am:
-
-install-data-am: install-includeHEADERS
-
-install-dvi: install-dvi-recursive
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-recursive
-
-install-html-am:
-
-install-info: install-info-recursive
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-recursive
-
-install-pdf-am:
-
-install-ps: install-ps-recursive
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-recursive
-	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
-	-rm -rf $(top_srcdir)/autom4te.cache
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-recursive
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-recursive
-
-pdf-am:
-
-ps: ps-recursive
-
-ps-am:
-
-uninstall-am: uninstall-includeHEADERS
-
-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
-	ctags-recursive install-am install-strip tags-recursive
-
-.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-	all all-am am--refresh check check-am clean clean-generic \
-	ctags ctags-recursive dist dist-all dist-bzip2 dist-gzip \
-	dist-lzma dist-shar dist-tarZ dist-xz dist-zip distcheck \
-	distclean distclean-generic distclean-hdr distclean-tags \
-	distcleancheck distdir distuninstallcheck dvi dvi-am html \
-	html-am info info-am install install-am install-data \
-	install-data-am install-dvi install-dvi-am install-exec \
-	install-exec-am install-html install-html-am \
-	install-includeHEADERS install-info install-info-am \
-	install-man install-pdf install-pdf-am install-ps \
-	install-ps-am install-strip installcheck installcheck-am \
-	installdirs installdirs-am maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am \
-	uninstall-includeHEADERS
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/gtfold-mfe/data/Makefile b/gtfold-mfe/data/Makefile
deleted file mode 100644
index 654058c..0000000
--- a/gtfold-mfe/data/Makefile
+++ /dev/null
@@ -1,536 +0,0 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
-# data/Makefile.  Generated from Makefile.in by configure.
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-
-
-pkgdatadir = $(datadir)/gtfold
-pkgincludedir = $(includedir)/gtfold
-pkglibdir = $(libdir)/gtfold
-pkglibexecdir = $(libexecdir)/gtfold
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = x86_64-unknown-linux-gnu
-host_triplet = x86_64-unknown-linux-gnu
-target_triplet = x86_64-unknown-linux-gnu
-subdir = data
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/gtfold_config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-SOURCES =
-DIST_SOURCES =
-RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
-	html-recursive info-recursive install-data-recursive \
-	install-dvi-recursive install-exec-recursive \
-	install-html-recursive install-info-recursive \
-	install-pdf-recursive install-ps-recursive install-recursive \
-	installcheck-recursive installdirs-recursive pdf-recursive \
-	ps-recursive uninstall-recursive
-RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
-  distclean-recursive maintainer-clean-recursive
-AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-	$(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
-	distdir
-ETAGS = etags
-CTAGS = ctags
-DIST_SUBDIRS = $(SUBDIRS)
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-am__relativize = \
-  dir0=`pwd`; \
-  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
-  sed_rest='s,^[^/]*/*,,'; \
-  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
-  sed_butlast='s,/*[^/]*$$,,'; \
-  while test -n "$$dir1"; do \
-    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
-    if test "$$first" != "."; then \
-      if test "$$first" = ".."; then \
-        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
-        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
-      else \
-        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
-        if test "$$first2" = "$$first"; then \
-          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
-        else \
-          dir2="../$$dir2"; \
-        fi; \
-        dir0="$$dir0"/"$$first"; \
-      fi; \
-    fi; \
-    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
-  done; \
-  reldir="$$dir2"
-ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11
-AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar
-AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf
-AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader
-AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11
-AWK = mawk
-CC = gcc
-CCDEPMODE = depmode=gcc3
-CFLAGS = -g -O2 -Wall
-CPP = gcc -E
-CPPFLAGS = 
-CXX = g++
-CXXDEPMODE = depmode=gcc3
-CXXFLAGS = -g -O2 -Wall
-CYGPATH_W = echo
-DEFS = -DHAVE_CONFIG_H
-DEPDIR = .deps
-ECHO_C = 
-ECHO_N = -n
-ECHO_T = 
-EGREP = /bin/grep -E
-EXEEXT = 
-GREP = /bin/grep
-INSTALL = /usr/bin/install -c
-INSTALL_DATA = ${INSTALL} -m 644
-INSTALL_PROGRAM = ${INSTALL}
-INSTALL_SCRIPT = ${INSTALL}
-INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
-LDFLAGS = 
-LIBOBJS = 
-LIBS = -lgomp 
-LTLIBOBJS = 
-MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo
-MKDIR_P = /bin/mkdir -p
-OBJEXT = o
-OPENMP_CFLAGS = -fopenmp
-PACKAGE = gtfold
-PACKAGE_BUGREPORT = 
-PACKAGE_NAME = gtfold
-PACKAGE_STRING = gtfold 1.18
-PACKAGE_TARNAME = gtfold
-PACKAGE_URL = 
-PACKAGE_VERSION = 1.18
-PATH_SEPARATOR = :
-SET_MAKE = 
-SHELL = /bin/bash
-STRIP = 
-VERSION = 1.18
-abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data
-abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data
-abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe
-abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe
-ac_ct_CC = gcc
-ac_ct_CXX = g++
-am__include = include
-am__leading_dot = .
-am__quote = 
-am__tar = ${AMTAR} chof - "$$tardir"
-am__untar = ${AMTAR} xf -
-bindir = ${exec_prefix}/bin
-build = x86_64-unknown-linux-gnu
-build_alias = 
-build_cpu = x86_64
-build_os = linux-gnu
-build_vendor = unknown
-builddir = .
-datadir = ${datarootdir}
-datarootdir = ${prefix}/share
-docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
-dvidir = ${docdir}
-exec_prefix = ${prefix}
-host = x86_64-unknown-linux-gnu
-host_alias = 
-host_cpu = x86_64
-host_os = linux-gnu
-host_vendor = unknown
-htmldir = ${docdir}
-includedir = ${prefix}/include
-infodir = ${datarootdir}/info
-install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh
-libdir = ${exec_prefix}/lib
-libexecdir = ${exec_prefix}/libexec
-localedir = ${datarootdir}/locale
-localstatedir = ${prefix}/var
-mandir = ${datarootdir}/man
-mkdir_p = /bin/mkdir -p
-oldincludedir = /usr/include
-pdfdir = ${docdir}
-prefix = /usr/local
-program_transform_name = s,x,x,
-psdir = ${docdir}
-sbindir = ${exec_prefix}/sbin
-sharedstatedir = ${prefix}/com
-srcdir = .
-sysconfdir = ${prefix}/etc
-target = x86_64-unknown-linux-gnu
-target_alias = 
-target_cpu = x86_64
-target_os = linux-gnu
-target_vendor = unknown
-top_build_prefix = ../
-top_builddir = ..
-top_srcdir = ..
-SUBDIRS = Turner04 Turner99 Andronescu
-all: all-recursive
-
-.SUFFIXES:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
-	@for dep in $?; do \
-	  case '$(am__configure_deps)' in \
-	    *$$dep*) \
-	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
-	        && { if test -f $@; then exit 0; else break; fi; }; \
-	      exit 1;; \
-	  esac; \
-	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Makefile'; \
-	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu data/Makefile
-.PRECIOUS: Makefile
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
-	@case '$?' in \
-	  *config.status*) \
-	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
-	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
-	esac;
-
-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-
-$(top_srcdir)/configure:  $(am__configure_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
-	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
-$(am__aclocal_m4_deps):
-
-# This directory's subdirectories are mostly independent; you can cd
-# into them and run `make' without going through this Makefile.
-# To change the values of `make' variables: instead of editing Makefiles,
-# (1) if the variable is set in `config.status', edit `config.status'
-#     (which will cause the Makefiles to be regenerated when you run `make');
-# (2) otherwise, pass the desired values on the `make' command line.
-$(RECURSIVE_TARGETS):
-	@fail= failcom='exit 1'; \
-	for f in x $$MAKEFLAGS; do \
-	  case $$f in \
-	    *=* | --[!k]*);; \
-	    *k*) failcom='fail=yes';; \
-	  esac; \
-	done; \
-	dot_seen=no; \
-	target=`echo $@ | sed s/-recursive//`; \
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  echo "Making $$target in $$subdir"; \
-	  if test "$$subdir" = "."; then \
-	    dot_seen=yes; \
-	    local_target="$$target-am"; \
-	  else \
-	    local_target="$$target"; \
-	  fi; \
-	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-	  || eval $$failcom; \
-	done; \
-	if test "$$dot_seen" = "no"; then \
-	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
-	fi; test -z "$$fail"
-
-$(RECURSIVE_CLEAN_TARGETS):
-	@fail= failcom='exit 1'; \
-	for f in x $$MAKEFLAGS; do \
-	  case $$f in \
-	    *=* | --[!k]*);; \
-	    *k*) failcom='fail=yes';; \
-	  esac; \
-	done; \
-	dot_seen=no; \
-	case "$@" in \
-	  distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
-	  *) list='$(SUBDIRS)' ;; \
-	esac; \
-	rev=''; for subdir in $$list; do \
-	  if test "$$subdir" = "."; then :; else \
-	    rev="$$subdir $$rev"; \
-	  fi; \
-	done; \
-	rev="$$rev ."; \
-	target=`echo $@ | sed s/-recursive//`; \
-	for subdir in $$rev; do \
-	  echo "Making $$target in $$subdir"; \
-	  if test "$$subdir" = "."; then \
-	    local_target="$$target-am"; \
-	  else \
-	    local_target="$$target"; \
-	  fi; \
-	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
-	  || eval $$failcom; \
-	done && test -z "$$fail"
-tags-recursive:
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
-	done
-ctags-recursive:
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
-	done
-
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	mkid -fID $$unique
-tags: TAGS
-
-TAGS: tags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	set x; \
-	here=`pwd`; \
-	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
-	  include_option=--etags-include; \
-	  empty_fix=.; \
-	else \
-	  include_option=--include; \
-	  empty_fix=; \
-	fi; \
-	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    test ! -f $$subdir/TAGS || \
-	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
-	  fi; \
-	done; \
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	shift; \
-	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-	  test -n "$$unique" || unique=$$empty_fix; \
-	  if test $$# -gt 0; then \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      "$$@" $$unique; \
-	  else \
-	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	      $$unique; \
-	  fi; \
-	fi
-ctags: CTAGS
-CTAGS: ctags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	test -z "$(CTAGS_ARGS)$$unique" \
-	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$unique
-
-GTAGS:
-	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && $(am__cd) $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) "$$here"
-
-distclean-tags:
-	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-
-distdir: $(DISTFILES)
-	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-	list='$(DISTFILES)'; \
-	  dist_files=`for file in $$list; do echo $$file; done | \
-	  sed -e "s|^$$srcdirstrip/||;t" \
-	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-	case $$dist_files in \
-	  */*) $(MKDIR_P) `echo "$$dist_files" | \
-			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-			   sort -u` ;; \
-	esac; \
-	for file in $$dist_files; do \
-	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-	  if test -d $$d/$$file; then \
-	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d "$(distdir)/$$file"; then \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-	    fi; \
-	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-	  else \
-	    test -f "$(distdir)/$$file" \
-	    || cp -p $$d/$$file "$(distdir)/$$file" \
-	    || exit 1; \
-	  fi; \
-	done
-	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    test -d "$(distdir)/$$subdir" \
-	    || $(MKDIR_P) "$(distdir)/$$subdir" \
-	    || exit 1; \
-	  fi; \
-	done
-	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
-	  if test "$$subdir" = .; then :; else \
-	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
-	    $(am__relativize); \
-	    new_distdir=$$reldir; \
-	    dir1=$$subdir; dir2="$(top_distdir)"; \
-	    $(am__relativize); \
-	    new_top_distdir=$$reldir; \
-	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
-	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
-	    ($(am__cd) $$subdir && \
-	      $(MAKE) $(AM_MAKEFLAGS) \
-	        top_distdir="$$new_top_distdir" \
-	        distdir="$$new_distdir" \
-		am__remove_distdir=: \
-		am__skip_length_check=: \
-		am__skip_mode_fix=: \
-	        distdir) \
-	      || exit 1; \
-	  fi; \
-	done
-check-am: all-am
-check: check-recursive
-all-am: Makefile
-installdirs: installdirs-recursive
-installdirs-am:
-install: install-recursive
-install-exec: install-exec-recursive
-install-data: install-data-recursive
-uninstall: uninstall-recursive
-
-install-am: all-am
-	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-
-installcheck: installcheck-recursive
-install-strip:
-	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	  `test -z '$(STRIP)' || \
-	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-mostlyclean-generic:
-
-clean-generic:
-
-distclean-generic:
-	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-
-maintainer-clean-generic:
-	@echo "This command is intended for maintainers to use"
-	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-recursive
-
-clean-am: clean-generic mostlyclean-am
-
-distclean: distclean-recursive
-	-rm -f Makefile
-distclean-am: clean-am distclean-generic distclean-tags
-
-dvi: dvi-recursive
-
-dvi-am:
-
-html: html-recursive
-
-html-am:
-
-info: info-recursive
-
-info-am:
-
-install-data-am:
-
-install-dvi: install-dvi-recursive
-
-install-dvi-am:
-
-install-exec-am:
-
-install-html: install-html-recursive
-
-install-html-am:
-
-install-info: install-info-recursive
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-recursive
-
-install-pdf-am:
-
-install-ps: install-ps-recursive
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-recursive
-	-rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-recursive
-
-mostlyclean-am: mostlyclean-generic
-
-pdf: pdf-recursive
-
-pdf-am:
-
-ps: ps-recursive
-
-ps-am:
-
-uninstall-am:
-
-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
-	install-am install-strip tags-recursive
-
-.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-	all all-am check check-am clean clean-generic ctags \
-	ctags-recursive distclean distclean-generic distclean-tags \
-	distdir dvi dvi-am html html-am info info-am install \
-	install-am install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am install-html \
-	install-html-am install-info install-info-am install-man \
-	install-pdf install-pdf-am install-ps install-ps-am \
-	install-strip installcheck installcheck-am installdirs \
-	installdirs-am maintainer-clean maintainer-clean-generic \
-	mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \
-	tags-recursive uninstall uninstall-am
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:

From 82bf3ec970552f6d346f85962ae63fe1a492bb94 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Fri, 24 Jun 2011 12:53:01 -0400
Subject: [PATCH 177/282] deleted unwanted files

---
 gtfold-mfe/src/.deps/algorithms.Po       | 139 -------
 gtfold-mfe/src/.deps/constraints.Po      | 373 -------------------
 gtfold-mfe/src/.deps/energy.Po           | 124 -------
 gtfold-mfe/src/.deps/global.Po           |  93 -----
 gtfold-mfe/src/.deps/loader.Po           | 370 -------------------
 gtfold-mfe/src/.deps/main.Po             | 440 -----------------------
 gtfold-mfe/src/.deps/options.Po          | 262 --------------
 gtfold-mfe/src/.deps/shapereader.Po      | 358 ------------------
 gtfold-mfe/src/.deps/subopt_traceback.Po | 346 ------------------
 gtfold-mfe/src/.deps/traceback.Po        | 134 -------
 gtfold-mfe/src/.deps/utils.Po            | 217 -----------
 11 files changed, 2856 deletions(-)
 delete mode 100644 gtfold-mfe/src/.deps/algorithms.Po
 delete mode 100644 gtfold-mfe/src/.deps/constraints.Po
 delete mode 100644 gtfold-mfe/src/.deps/energy.Po
 delete mode 100644 gtfold-mfe/src/.deps/global.Po
 delete mode 100644 gtfold-mfe/src/.deps/loader.Po
 delete mode 100644 gtfold-mfe/src/.deps/main.Po
 delete mode 100644 gtfold-mfe/src/.deps/options.Po
 delete mode 100644 gtfold-mfe/src/.deps/shapereader.Po
 delete mode 100644 gtfold-mfe/src/.deps/subopt_traceback.Po
 delete mode 100644 gtfold-mfe/src/.deps/traceback.Po
 delete mode 100644 gtfold-mfe/src/.deps/utils.Po

diff --git a/gtfold-mfe/src/.deps/algorithms.Po b/gtfold-mfe/src/.deps/algorithms.Po
deleted file mode 100644
index d5d1ad2..0000000
--- a/gtfold-mfe/src/.deps/algorithms.Po
+++ /dev/null
@@ -1,139 +0,0 @@
-algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \
- /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
- /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
- /usr/include/gnu/stubs-64.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/bits/types.h /usr/include/bits/typesizes.h \
- /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \
- /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
- /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
- /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
- /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
- /usr/include/time.h /usr/include/bits/time.h /usr/include/xlocale.h \
- /usr/include/sys/time.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/stdlib.h /usr/include/bits/waitflags.h \
- /usr/include/bits/waitstatus.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/types.h /usr/include/sys/sysmacros.h \
- /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
- /usr/include/bits/stdlib.h /usr/include/assert.h ../include/constants.h \
- ../include/utils.h ../include/constants.h ../include/energy.h \
- ../include/data.h ../include/global.h ../include/algorithms.h \
- ../include/constraints.h ../include/shapereader.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/omp.h
-
-/usr/include/stdio.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/wchar.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/bits/stdio.h:
-
-/usr/include/bits/stdio2.h:
-
-/usr/include/math.h:
-
-/usr/include/bits/huge_val.h:
-
-/usr/include/bits/huge_valf.h:
-
-/usr/include/bits/huge_vall.h:
-
-/usr/include/bits/inf.h:
-
-/usr/include/bits/nan.h:
-
-/usr/include/bits/mathdef.h:
-
-/usr/include/bits/mathcalls.h:
-
-/usr/include/bits/mathinline.h:
-
-/usr/include/time.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/xlocale.h:
-
-/usr/include/sys/time.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/stdlib.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/alloca.h:
-
-/usr/include/bits/stdlib.h:
-
-/usr/include/assert.h:
-
-../include/constants.h:
-
-../include/utils.h:
-
-../include/constants.h:
-
-../include/energy.h:
-
-../include/data.h:
-
-../include/global.h:
-
-../include/algorithms.h:
-
-../include/constraints.h:
-
-../include/shapereader.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/omp.h:
diff --git a/gtfold-mfe/src/.deps/constraints.Po b/gtfold-mfe/src/.deps/constraints.Po
deleted file mode 100644
index 891773e..0000000
--- a/gtfold-mfe/src/.deps/constraints.Po
+++ /dev/null
@@ -1,373 +0,0 @@
-constraints.o: constraints.cc /usr/include/stdlib.h \
- /usr/include/features.h /usr/include/bits/predefs.h \
- /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
- /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/xlocale.h \
- /usr/include/sys/types.h /usr/include/bits/types.h \
- /usr/include/bits/typesizes.h /usr/include/time.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
- /usr/include/bits/sigset.h /usr/include/bits/time.h \
- /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
- /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/string.h \
- /usr/include/bits/string3.h /usr/include/stdio.h /usr/include/libio.h \
- /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/c++/4.5/iostream \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \
- /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \
- /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \
- /usr/include/c++/4.5/cstddef /usr/include/bits/wchar.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \
- /usr/include/c++/4.5/bits/char_traits.h \
- /usr/include/c++/4.5/bits/stl_algobase.h \
- /usr/include/c++/4.5/bits/functexcept.h \
- /usr/include/c++/4.5/exception_defines.h \
- /usr/include/c++/4.5/bits/cpp_type_traits.h \
- /usr/include/c++/4.5/ext/type_traits.h \
- /usr/include/c++/4.5/ext/numeric_traits.h \
- /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
- /usr/include/c++/4.5/bits/concept_check.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.5/bits/stl_iterator.h \
- /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.5/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \
- /usr/include/ctype.h /usr/include/c++/4.5/bits/ios_base.h \
- /usr/include/c++/4.5/ext/atomicity.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
- /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
- /usr/include/bits/setjmp.h /usr/include/unistd.h \
- /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
- /usr/include/bits/confname.h /usr/include/getopt.h \
- /usr/include/bits/unistd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \
- /usr/include/c++/4.5/bits/allocator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
- /usr/include/c++/4.5/bits/ostream_insert.h \
- /usr/include/c++/4.5/cxxabi-forced.h \
- /usr/include/c++/4.5/bits/stl_function.h \
- /usr/include/c++/4.5/backward/binders.h \
- /usr/include/c++/4.5/bits/basic_string.h \
- /usr/include/c++/4.5/initializer_list \
- /usr/include/c++/4.5/bits/basic_string.tcc \
- /usr/include/c++/4.5/bits/locale_classes.tcc \
- /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \
- /usr/include/c++/4.5/bits/basic_ios.h \
- /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \
- /usr/include/wctype.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \
- /usr/include/c++/4.5/bits/streambuf_iterator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \
- /usr/include/c++/4.5/bits/locale_facets.tcc \
- /usr/include/c++/4.5/bits/basic_ios.tcc \
- /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \
- /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \
- /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \
- /usr/include/c++/4.5/bits/fstream.tcc /usr/include/c++/4.5/vector \
- /usr/include/c++/4.5/bits/stl_construct.h \
- /usr/include/c++/4.5/bits/stl_uninitialized.h \
- /usr/include/c++/4.5/bits/stl_vector.h \
- /usr/include/c++/4.5/bits/stl_bvector.h \
- /usr/include/c++/4.5/bits/vector.tcc /usr/include/c++/4.5/algorithm \
- /usr/include/c++/4.5/utility /usr/include/c++/4.5/bits/stl_relops.h \
- /usr/include/c++/4.5/bits/stl_algo.h /usr/include/c++/4.5/cstdlib \
- /usr/include/c++/4.5/bits/algorithmfwd.h \
- /usr/include/c++/4.5/bits/stl_heap.h \
- /usr/include/c++/4.5/bits/stl_tempbuf.h ../include/global.h \
- ../include/constants.h ../include/options.h /usr/include/c++/4.5/cstring \
- ../include/constraints.h
-
-/usr/include/stdlib.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/xlocale.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/time.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/alloca.h:
-
-/usr/include/bits/stdlib.h:
-
-/usr/include/string.h:
-
-/usr/include/bits/string3.h:
-
-/usr/include/stdio.h:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/wchar.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/bits/stdio.h:
-
-/usr/include/bits/stdio2.h:
-
-/usr/include/c++/4.5/iostream:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
-
-/usr/include/c++/4.5/ostream:
-
-/usr/include/c++/4.5/ios:
-
-/usr/include/c++/4.5/iosfwd:
-
-/usr/include/c++/4.5/bits/stringfwd.h:
-
-/usr/include/c++/4.5/bits/postypes.h:
-
-/usr/include/c++/4.5/cwchar:
-
-/usr/include/c++/4.5/cstddef:
-
-/usr/include/bits/wchar.h:
-
-/usr/include/bits/wchar2.h:
-
-/usr/include/c++/4.5/exception:
-
-/usr/include/c++/4.5/bits/char_traits.h:
-
-/usr/include/c++/4.5/bits/stl_algobase.h:
-
-/usr/include/c++/4.5/bits/functexcept.h:
-
-/usr/include/c++/4.5/exception_defines.h:
-
-/usr/include/c++/4.5/bits/cpp_type_traits.h:
-
-/usr/include/c++/4.5/ext/type_traits.h:
-
-/usr/include/c++/4.5/ext/numeric_traits.h:
-
-/usr/include/c++/4.5/bits/stl_pair.h:
-
-/usr/include/c++/4.5/bits/move.h:
-
-/usr/include/c++/4.5/bits/concept_check.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
-
-/usr/include/c++/4.5/bits/stl_iterator.h:
-
-/usr/include/c++/4.5/debug/debug.h:
-
-/usr/include/c++/4.5/bits/localefwd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
-
-/usr/include/c++/4.5/clocale:
-
-/usr/include/locale.h:
-
-/usr/include/bits/locale.h:
-
-/usr/include/c++/4.5/cctype:
-
-/usr/include/ctype.h:
-
-/usr/include/c++/4.5/bits/ios_base.h:
-
-/usr/include/c++/4.5/ext/atomicity.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
-
-/usr/include/pthread.h:
-
-/usr/include/sched.h:
-
-/usr/include/bits/sched.h:
-
-/usr/include/bits/setjmp.h:
-
-/usr/include/unistd.h:
-
-/usr/include/bits/posix_opt.h:
-
-/usr/include/bits/environments.h:
-
-/usr/include/bits/confname.h:
-
-/usr/include/getopt.h:
-
-/usr/include/bits/unistd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.5/bits/locale_classes.h:
-
-/usr/include/c++/4.5/string:
-
-/usr/include/c++/4.5/bits/allocator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
-
-/usr/include/c++/4.5/ext/new_allocator.h:
-
-/usr/include/c++/4.5/new:
-
-/usr/include/c++/4.5/bits/ostream_insert.h:
-
-/usr/include/c++/4.5/cxxabi-forced.h:
-
-/usr/include/c++/4.5/bits/stl_function.h:
-
-/usr/include/c++/4.5/backward/binders.h:
-
-/usr/include/c++/4.5/bits/basic_string.h:
-
-/usr/include/c++/4.5/initializer_list:
-
-/usr/include/c++/4.5/bits/basic_string.tcc:
-
-/usr/include/c++/4.5/bits/locale_classes.tcc:
-
-/usr/include/c++/4.5/streambuf:
-
-/usr/include/c++/4.5/bits/streambuf.tcc:
-
-/usr/include/c++/4.5/bits/basic_ios.h:
-
-/usr/include/c++/4.5/bits/locale_facets.h:
-
-/usr/include/c++/4.5/cwctype:
-
-/usr/include/wctype.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h:
-
-/usr/include/c++/4.5/bits/streambuf_iterator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h:
-
-/usr/include/c++/4.5/bits/locale_facets.tcc:
-
-/usr/include/c++/4.5/bits/basic_ios.tcc:
-
-/usr/include/c++/4.5/bits/ostream.tcc:
-
-/usr/include/c++/4.5/istream:
-
-/usr/include/c++/4.5/bits/istream.tcc:
-
-/usr/include/c++/4.5/fstream:
-
-/usr/include/c++/4.5/bits/codecvt.h:
-
-/usr/include/c++/4.5/cstdio:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h:
-
-/usr/include/c++/4.5/bits/fstream.tcc:
-
-/usr/include/c++/4.5/vector:
-
-/usr/include/c++/4.5/bits/stl_construct.h:
-
-/usr/include/c++/4.5/bits/stl_uninitialized.h:
-
-/usr/include/c++/4.5/bits/stl_vector.h:
-
-/usr/include/c++/4.5/bits/stl_bvector.h:
-
-/usr/include/c++/4.5/bits/vector.tcc:
-
-/usr/include/c++/4.5/algorithm:
-
-/usr/include/c++/4.5/utility:
-
-/usr/include/c++/4.5/bits/stl_relops.h:
-
-/usr/include/c++/4.5/bits/stl_algo.h:
-
-/usr/include/c++/4.5/cstdlib:
-
-/usr/include/c++/4.5/bits/algorithmfwd.h:
-
-/usr/include/c++/4.5/bits/stl_heap.h:
-
-/usr/include/c++/4.5/bits/stl_tempbuf.h:
-
-../include/global.h:
-
-../include/constants.h:
-
-../include/options.h:
-
-/usr/include/c++/4.5/cstring:
-
-../include/constraints.h:
diff --git a/gtfold-mfe/src/.deps/energy.Po b/gtfold-mfe/src/.deps/energy.Po
deleted file mode 100644
index 1ddcb82..0000000
--- a/gtfold-mfe/src/.deps/energy.Po
+++ /dev/null
@@ -1,124 +0,0 @@
-energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \
- /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
- /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
- /usr/include/gnu/stubs-64.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/types.h \
- /usr/include/bits/types.h /usr/include/bits/typesizes.h \
- /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
- /usr/include/bits/sigset.h /usr/include/bits/time.h \
- /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
- /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/stdio.h \
- /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \
- /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
- /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
- /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
- /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
- ../include/energy.h ../include/data.h ../include/constants.h \
- ../include/utils.h ../include/global.h ../include/constants.h \
- ../include/shapereader.h
-
-/usr/include/stdlib.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/time.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/alloca.h:
-
-/usr/include/bits/stdlib.h:
-
-/usr/include/stdio.h:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/wchar.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/bits/stdio.h:
-
-/usr/include/bits/stdio2.h:
-
-/usr/include/math.h:
-
-/usr/include/bits/huge_val.h:
-
-/usr/include/bits/huge_valf.h:
-
-/usr/include/bits/huge_vall.h:
-
-/usr/include/bits/inf.h:
-
-/usr/include/bits/nan.h:
-
-/usr/include/bits/mathdef.h:
-
-/usr/include/bits/mathcalls.h:
-
-/usr/include/bits/mathinline.h:
-
-../include/energy.h:
-
-../include/data.h:
-
-../include/constants.h:
-
-../include/utils.h:
-
-../include/global.h:
-
-../include/constants.h:
-
-../include/shapereader.h:
diff --git a/gtfold-mfe/src/.deps/global.Po b/gtfold-mfe/src/.deps/global.Po
deleted file mode 100644
index 58728cf..0000000
--- a/gtfold-mfe/src/.deps/global.Po
+++ /dev/null
@@ -1,93 +0,0 @@
-global.o: global.c /usr/include/stdio.h /usr/include/features.h \
- /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
- /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
- /usr/include/gnu/stubs-64.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/bits/types.h /usr/include/bits/typesizes.h \
- /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/stdlib.h /usr/include/bits/waitflags.h \
- /usr/include/bits/waitstatus.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
- /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
- /usr/include/bits/stdlib.h ../include/global.h ../include/constants.h \
- ../include/constraints.h
-
-/usr/include/stdio.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/wchar.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/bits/stdio.h:
-
-/usr/include/bits/stdio2.h:
-
-/usr/include/stdlib.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/time.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/alloca.h:
-
-/usr/include/bits/stdlib.h:
-
-../include/global.h:
-
-../include/constants.h:
-
-../include/constraints.h:
diff --git a/gtfold-mfe/src/.deps/loader.Po b/gtfold-mfe/src/.deps/loader.Po
deleted file mode 100644
index 926b316..0000000
--- a/gtfold-mfe/src/.deps/loader.Po
+++ /dev/null
@@ -1,370 +0,0 @@
-loader.o: loader.cc /usr/include/c++/4.5/iostream \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
- /usr/include/features.h /usr/include/bits/predefs.h \
- /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
- /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \
- /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \
- /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \
- /usr/include/c++/4.5/cstddef \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/wchar.h /usr/include/stdio.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/wchar.h /usr/include/xlocale.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \
- /usr/include/c++/4.5/bits/char_traits.h \
- /usr/include/c++/4.5/bits/stl_algobase.h \
- /usr/include/c++/4.5/bits/functexcept.h \
- /usr/include/c++/4.5/exception_defines.h \
- /usr/include/c++/4.5/bits/cpp_type_traits.h \
- /usr/include/c++/4.5/ext/type_traits.h \
- /usr/include/c++/4.5/ext/numeric_traits.h \
- /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
- /usr/include/c++/4.5/bits/concept_check.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.5/bits/stl_iterator.h \
- /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.5/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \
- /usr/include/ctype.h /usr/include/bits/types.h \
- /usr/include/bits/typesizes.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/c++/4.5/bits/ios_base.h \
- /usr/include/c++/4.5/ext/atomicity.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
- /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h \
- /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
- /usr/include/unistd.h /usr/include/bits/posix_opt.h \
- /usr/include/bits/environments.h /usr/include/bits/confname.h \
- /usr/include/getopt.h /usr/include/bits/unistd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \
- /usr/include/c++/4.5/bits/allocator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
- /usr/include/c++/4.5/bits/ostream_insert.h \
- /usr/include/c++/4.5/cxxabi-forced.h \
- /usr/include/c++/4.5/bits/stl_function.h \
- /usr/include/c++/4.5/backward/binders.h \
- /usr/include/c++/4.5/bits/basic_string.h \
- /usr/include/c++/4.5/initializer_list \
- /usr/include/c++/4.5/bits/basic_string.tcc \
- /usr/include/c++/4.5/bits/locale_classes.tcc \
- /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \
- /usr/include/c++/4.5/bits/basic_ios.h \
- /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \
- /usr/include/wctype.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \
- /usr/include/c++/4.5/bits/streambuf_iterator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \
- /usr/include/c++/4.5/bits/locale_facets.tcc \
- /usr/include/c++/4.5/bits/basic_ios.tcc \
- /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \
- /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \
- /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \
- /usr/include/libio.h /usr/include/_G_config.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \
- /usr/include/c++/4.5/bits/fstream.tcc /usr/include/c++/4.5/sstream \
- /usr/include/c++/4.5/bits/sstream.tcc /usr/include/math.h \
- /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
- /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
- /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
- /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
- /usr/include/c++/4.5/cstring /usr/include/string.h \
- /usr/include/bits/string3.h /usr/include/stdlib.h \
- /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
- /usr/include/sys/types.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/sys/sysmacros.h /usr/include/alloca.h \
- /usr/include/bits/stdlib.h ../include/data.h ../include/constants.h \
- ../include/utils.h ../include/constants.h ../include/global.h \
- ../include/loader.h ../include/data.h
-
-/usr/include/c++/4.5/iostream:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
-
-/usr/include/c++/4.5/ostream:
-
-/usr/include/c++/4.5/ios:
-
-/usr/include/c++/4.5/iosfwd:
-
-/usr/include/c++/4.5/bits/stringfwd.h:
-
-/usr/include/c++/4.5/bits/postypes.h:
-
-/usr/include/c++/4.5/cwchar:
-
-/usr/include/c++/4.5/cstddef:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/wchar.h:
-
-/usr/include/stdio.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/wchar.h:
-
-/usr/include/xlocale.h:
-
-/usr/include/bits/wchar2.h:
-
-/usr/include/c++/4.5/exception:
-
-/usr/include/c++/4.5/bits/char_traits.h:
-
-/usr/include/c++/4.5/bits/stl_algobase.h:
-
-/usr/include/c++/4.5/bits/functexcept.h:
-
-/usr/include/c++/4.5/exception_defines.h:
-
-/usr/include/c++/4.5/bits/cpp_type_traits.h:
-
-/usr/include/c++/4.5/ext/type_traits.h:
-
-/usr/include/c++/4.5/ext/numeric_traits.h:
-
-/usr/include/c++/4.5/bits/stl_pair.h:
-
-/usr/include/c++/4.5/bits/move.h:
-
-/usr/include/c++/4.5/bits/concept_check.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
-
-/usr/include/c++/4.5/bits/stl_iterator.h:
-
-/usr/include/c++/4.5/debug/debug.h:
-
-/usr/include/c++/4.5/bits/localefwd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
-
-/usr/include/c++/4.5/clocale:
-
-/usr/include/locale.h:
-
-/usr/include/bits/locale.h:
-
-/usr/include/c++/4.5/cctype:
-
-/usr/include/ctype.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/c++/4.5/bits/ios_base.h:
-
-/usr/include/c++/4.5/ext/atomicity.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
-
-/usr/include/pthread.h:
-
-/usr/include/sched.h:
-
-/usr/include/time.h:
-
-/usr/include/bits/sched.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/bits/setjmp.h:
-
-/usr/include/unistd.h:
-
-/usr/include/bits/posix_opt.h:
-
-/usr/include/bits/environments.h:
-
-/usr/include/bits/confname.h:
-
-/usr/include/getopt.h:
-
-/usr/include/bits/unistd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.5/bits/locale_classes.h:
-
-/usr/include/c++/4.5/string:
-
-/usr/include/c++/4.5/bits/allocator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
-
-/usr/include/c++/4.5/ext/new_allocator.h:
-
-/usr/include/c++/4.5/new:
-
-/usr/include/c++/4.5/bits/ostream_insert.h:
-
-/usr/include/c++/4.5/cxxabi-forced.h:
-
-/usr/include/c++/4.5/bits/stl_function.h:
-
-/usr/include/c++/4.5/backward/binders.h:
-
-/usr/include/c++/4.5/bits/basic_string.h:
-
-/usr/include/c++/4.5/initializer_list:
-
-/usr/include/c++/4.5/bits/basic_string.tcc:
-
-/usr/include/c++/4.5/bits/locale_classes.tcc:
-
-/usr/include/c++/4.5/streambuf:
-
-/usr/include/c++/4.5/bits/streambuf.tcc:
-
-/usr/include/c++/4.5/bits/basic_ios.h:
-
-/usr/include/c++/4.5/bits/locale_facets.h:
-
-/usr/include/c++/4.5/cwctype:
-
-/usr/include/wctype.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h:
-
-/usr/include/c++/4.5/bits/streambuf_iterator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h:
-
-/usr/include/c++/4.5/bits/locale_facets.tcc:
-
-/usr/include/c++/4.5/bits/basic_ios.tcc:
-
-/usr/include/c++/4.5/bits/ostream.tcc:
-
-/usr/include/c++/4.5/istream:
-
-/usr/include/c++/4.5/bits/istream.tcc:
-
-/usr/include/c++/4.5/fstream:
-
-/usr/include/c++/4.5/bits/codecvt.h:
-
-/usr/include/c++/4.5/cstdio:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/bits/stdio.h:
-
-/usr/include/bits/stdio2.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h:
-
-/usr/include/c++/4.5/bits/fstream.tcc:
-
-/usr/include/c++/4.5/sstream:
-
-/usr/include/c++/4.5/bits/sstream.tcc:
-
-/usr/include/math.h:
-
-/usr/include/bits/huge_val.h:
-
-/usr/include/bits/huge_valf.h:
-
-/usr/include/bits/huge_vall.h:
-
-/usr/include/bits/inf.h:
-
-/usr/include/bits/nan.h:
-
-/usr/include/bits/mathdef.h:
-
-/usr/include/bits/mathcalls.h:
-
-/usr/include/bits/mathinline.h:
-
-/usr/include/c++/4.5/cstring:
-
-/usr/include/string.h:
-
-/usr/include/bits/string3.h:
-
-/usr/include/stdlib.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/alloca.h:
-
-/usr/include/bits/stdlib.h:
-
-../include/data.h:
-
-../include/constants.h:
-
-../include/utils.h:
-
-../include/constants.h:
-
-../include/global.h:
-
-../include/loader.h:
-
-../include/data.h:
diff --git a/gtfold-mfe/src/.deps/main.Po b/gtfold-mfe/src/.deps/main.Po
deleted file mode 100644
index 64c9b68..0000000
--- a/gtfold-mfe/src/.deps/main.Po
+++ /dev/null
@@ -1,440 +0,0 @@
-main.o: main.cc /usr/include/c++/4.5/iostream \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
- /usr/include/features.h /usr/include/bits/predefs.h \
- /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
- /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \
- /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \
- /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \
- /usr/include/c++/4.5/cstddef \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/wchar.h /usr/include/stdio.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/wchar.h /usr/include/xlocale.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \
- /usr/include/c++/4.5/bits/char_traits.h \
- /usr/include/c++/4.5/bits/stl_algobase.h \
- /usr/include/c++/4.5/bits/functexcept.h \
- /usr/include/c++/4.5/exception_defines.h \
- /usr/include/c++/4.5/bits/cpp_type_traits.h \
- /usr/include/c++/4.5/ext/type_traits.h \
- /usr/include/c++/4.5/ext/numeric_traits.h \
- /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
- /usr/include/c++/4.5/bits/concept_check.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.5/bits/stl_iterator.h \
- /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.5/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \
- /usr/include/ctype.h /usr/include/bits/types.h \
- /usr/include/bits/typesizes.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/c++/4.5/bits/ios_base.h \
- /usr/include/c++/4.5/ext/atomicity.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
- /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h \
- /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
- /usr/include/unistd.h /usr/include/bits/posix_opt.h \
- /usr/include/bits/environments.h /usr/include/bits/confname.h \
- /usr/include/getopt.h /usr/include/bits/unistd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \
- /usr/include/c++/4.5/bits/allocator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
- /usr/include/c++/4.5/bits/ostream_insert.h \
- /usr/include/c++/4.5/cxxabi-forced.h \
- /usr/include/c++/4.5/bits/stl_function.h \
- /usr/include/c++/4.5/backward/binders.h \
- /usr/include/c++/4.5/bits/basic_string.h \
- /usr/include/c++/4.5/initializer_list \
- /usr/include/c++/4.5/bits/basic_string.tcc \
- /usr/include/c++/4.5/bits/locale_classes.tcc \
- /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \
- /usr/include/c++/4.5/bits/basic_ios.h \
- /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \
- /usr/include/wctype.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \
- /usr/include/c++/4.5/bits/streambuf_iterator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \
- /usr/include/c++/4.5/bits/locale_facets.tcc \
- /usr/include/c++/4.5/bits/basic_ios.tcc \
- /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \
- /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/iomanip \
- /usr/include/c++/4.5/fstream /usr/include/c++/4.5/bits/codecvt.h \
- /usr/include/c++/4.5/cstdio /usr/include/libio.h \
- /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \
- /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
- /usr/include/bits/stdio2.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \
- /usr/include/c++/4.5/bits/fstream.tcc /usr/include/math.h \
- /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
- /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
- /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
- /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
- /usr/include/sys/time.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/c++/4.5/sstream /usr/include/c++/4.5/bits/sstream.tcc \
- /usr/include/stdlib.h /usr/include/bits/waitflags.h \
- /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
- /usr/include/sys/sysmacros.h /usr/include/alloca.h \
- /usr/include/bits/stdlib.h /usr/include/string.h \
- /usr/include/bits/string3.h ../include/main.h \
- /usr/include/c++/4.5/vector /usr/include/c++/4.5/bits/stl_construct.h \
- /usr/include/c++/4.5/bits/stl_uninitialized.h \
- /usr/include/c++/4.5/bits/stl_vector.h \
- /usr/include/c++/4.5/bits/stl_bvector.h \
- /usr/include/c++/4.5/bits/vector.tcc ../include/constants.h \
- ../include/utils.h ../include/loader.h ../include/data.h \
- ../include/options.h /usr/include/c++/4.5/cstring ../include/global.h \
- ../include/energy.h ../include/algorithms.h \
- ../include/algorithms-partition.h ../include/partition-dangle.h \
- ../include/constraints.h ../include/traceback.h \
- ../include/subopt_traceback.h /usr/include/c++/4.5/cassert \
- /usr/include/assert.h /usr/include/c++/4.5/stack \
- /usr/include/c++/4.5/deque /usr/include/c++/4.5/bits/stl_deque.h \
- /usr/include/c++/4.5/bits/deque.tcc \
- /usr/include/c++/4.5/bits/stl_stack.h /usr/include/c++/4.5/map \
- /usr/include/c++/4.5/bits/stl_tree.h /usr/include/c++/4.5/bits/stl_map.h \
- /usr/include/c++/4.5/bits/stl_multimap.h ../include/shapereader.h
-
-/usr/include/c++/4.5/iostream:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
-
-/usr/include/c++/4.5/ostream:
-
-/usr/include/c++/4.5/ios:
-
-/usr/include/c++/4.5/iosfwd:
-
-/usr/include/c++/4.5/bits/stringfwd.h:
-
-/usr/include/c++/4.5/bits/postypes.h:
-
-/usr/include/c++/4.5/cwchar:
-
-/usr/include/c++/4.5/cstddef:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/wchar.h:
-
-/usr/include/stdio.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/wchar.h:
-
-/usr/include/xlocale.h:
-
-/usr/include/bits/wchar2.h:
-
-/usr/include/c++/4.5/exception:
-
-/usr/include/c++/4.5/bits/char_traits.h:
-
-/usr/include/c++/4.5/bits/stl_algobase.h:
-
-/usr/include/c++/4.5/bits/functexcept.h:
-
-/usr/include/c++/4.5/exception_defines.h:
-
-/usr/include/c++/4.5/bits/cpp_type_traits.h:
-
-/usr/include/c++/4.5/ext/type_traits.h:
-
-/usr/include/c++/4.5/ext/numeric_traits.h:
-
-/usr/include/c++/4.5/bits/stl_pair.h:
-
-/usr/include/c++/4.5/bits/move.h:
-
-/usr/include/c++/4.5/bits/concept_check.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
-
-/usr/include/c++/4.5/bits/stl_iterator.h:
-
-/usr/include/c++/4.5/debug/debug.h:
-
-/usr/include/c++/4.5/bits/localefwd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
-
-/usr/include/c++/4.5/clocale:
-
-/usr/include/locale.h:
-
-/usr/include/bits/locale.h:
-
-/usr/include/c++/4.5/cctype:
-
-/usr/include/ctype.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/c++/4.5/bits/ios_base.h:
-
-/usr/include/c++/4.5/ext/atomicity.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
-
-/usr/include/pthread.h:
-
-/usr/include/sched.h:
-
-/usr/include/time.h:
-
-/usr/include/bits/sched.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/bits/setjmp.h:
-
-/usr/include/unistd.h:
-
-/usr/include/bits/posix_opt.h:
-
-/usr/include/bits/environments.h:
-
-/usr/include/bits/confname.h:
-
-/usr/include/getopt.h:
-
-/usr/include/bits/unistd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.5/bits/locale_classes.h:
-
-/usr/include/c++/4.5/string:
-
-/usr/include/c++/4.5/bits/allocator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
-
-/usr/include/c++/4.5/ext/new_allocator.h:
-
-/usr/include/c++/4.5/new:
-
-/usr/include/c++/4.5/bits/ostream_insert.h:
-
-/usr/include/c++/4.5/cxxabi-forced.h:
-
-/usr/include/c++/4.5/bits/stl_function.h:
-
-/usr/include/c++/4.5/backward/binders.h:
-
-/usr/include/c++/4.5/bits/basic_string.h:
-
-/usr/include/c++/4.5/initializer_list:
-
-/usr/include/c++/4.5/bits/basic_string.tcc:
-
-/usr/include/c++/4.5/bits/locale_classes.tcc:
-
-/usr/include/c++/4.5/streambuf:
-
-/usr/include/c++/4.5/bits/streambuf.tcc:
-
-/usr/include/c++/4.5/bits/basic_ios.h:
-
-/usr/include/c++/4.5/bits/locale_facets.h:
-
-/usr/include/c++/4.5/cwctype:
-
-/usr/include/wctype.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h:
-
-/usr/include/c++/4.5/bits/streambuf_iterator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h:
-
-/usr/include/c++/4.5/bits/locale_facets.tcc:
-
-/usr/include/c++/4.5/bits/basic_ios.tcc:
-
-/usr/include/c++/4.5/bits/ostream.tcc:
-
-/usr/include/c++/4.5/istream:
-
-/usr/include/c++/4.5/bits/istream.tcc:
-
-/usr/include/c++/4.5/iomanip:
-
-/usr/include/c++/4.5/fstream:
-
-/usr/include/c++/4.5/bits/codecvt.h:
-
-/usr/include/c++/4.5/cstdio:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/bits/stdio.h:
-
-/usr/include/bits/stdio2.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h:
-
-/usr/include/c++/4.5/bits/fstream.tcc:
-
-/usr/include/math.h:
-
-/usr/include/bits/huge_val.h:
-
-/usr/include/bits/huge_valf.h:
-
-/usr/include/bits/huge_vall.h:
-
-/usr/include/bits/inf.h:
-
-/usr/include/bits/nan.h:
-
-/usr/include/bits/mathdef.h:
-
-/usr/include/bits/mathcalls.h:
-
-/usr/include/bits/mathinline.h:
-
-/usr/include/sys/time.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/c++/4.5/sstream:
-
-/usr/include/c++/4.5/bits/sstream.tcc:
-
-/usr/include/stdlib.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/alloca.h:
-
-/usr/include/bits/stdlib.h:
-
-/usr/include/string.h:
-
-/usr/include/bits/string3.h:
-
-../include/main.h:
-
-/usr/include/c++/4.5/vector:
-
-/usr/include/c++/4.5/bits/stl_construct.h:
-
-/usr/include/c++/4.5/bits/stl_uninitialized.h:
-
-/usr/include/c++/4.5/bits/stl_vector.h:
-
-/usr/include/c++/4.5/bits/stl_bvector.h:
-
-/usr/include/c++/4.5/bits/vector.tcc:
-
-../include/constants.h:
-
-../include/utils.h:
-
-../include/loader.h:
-
-../include/data.h:
-
-../include/options.h:
-
-/usr/include/c++/4.5/cstring:
-
-../include/global.h:
-
-../include/energy.h:
-
-../include/algorithms.h:
-
-../include/algorithms-partition.h:
-
-../include/partition-dangle.h:
-
-../include/constraints.h:
-
-../include/traceback.h:
-
-../include/subopt_traceback.h:
-
-/usr/include/c++/4.5/cassert:
-
-/usr/include/assert.h:
-
-/usr/include/c++/4.5/stack:
-
-/usr/include/c++/4.5/deque:
-
-/usr/include/c++/4.5/bits/stl_deque.h:
-
-/usr/include/c++/4.5/bits/deque.tcc:
-
-/usr/include/c++/4.5/bits/stl_stack.h:
-
-/usr/include/c++/4.5/map:
-
-/usr/include/c++/4.5/bits/stl_tree.h:
-
-/usr/include/c++/4.5/bits/stl_map.h:
-
-/usr/include/c++/4.5/bits/stl_multimap.h:
-
-../include/shapereader.h:
diff --git a/gtfold-mfe/src/.deps/options.Po b/gtfold-mfe/src/.deps/options.Po
deleted file mode 100644
index 7d4de3a..0000000
--- a/gtfold-mfe/src/.deps/options.Po
+++ /dev/null
@@ -1,262 +0,0 @@
-options.o: options.cc ../include/loader.h /usr/include/c++/4.5/string \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
- /usr/include/features.h /usr/include/bits/predefs.h \
- /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
- /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.5/bits/stringfwd.h \
- /usr/include/c++/4.5/bits/char_traits.h \
- /usr/include/c++/4.5/bits/stl_algobase.h /usr/include/c++/4.5/cstddef \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/c++/4.5/bits/functexcept.h \
- /usr/include/c++/4.5/exception_defines.h \
- /usr/include/c++/4.5/bits/cpp_type_traits.h \
- /usr/include/c++/4.5/ext/type_traits.h \
- /usr/include/c++/4.5/ext/numeric_traits.h \
- /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
- /usr/include/c++/4.5/bits/concept_check.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.5/bits/stl_iterator.h \
- /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/postypes.h \
- /usr/include/c++/4.5/cwchar /usr/include/wchar.h /usr/include/stdio.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/wchar.h /usr/include/xlocale.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.5/bits/allocator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
- /usr/include/c++/4.5/exception /usr/include/c++/4.5/bits/localefwd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.5/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.5/iosfwd \
- /usr/include/c++/4.5/cctype /usr/include/ctype.h \
- /usr/include/bits/types.h /usr/include/bits/typesizes.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ostream_insert.h \
- /usr/include/c++/4.5/cxxabi-forced.h \
- /usr/include/c++/4.5/bits/stl_function.h \
- /usr/include/c++/4.5/backward/binders.h \
- /usr/include/c++/4.5/bits/basic_string.h \
- /usr/include/c++/4.5/ext/atomicity.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
- /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h \
- /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
- /usr/include/unistd.h /usr/include/bits/posix_opt.h \
- /usr/include/bits/environments.h /usr/include/bits/confname.h \
- /usr/include/getopt.h /usr/include/bits/unistd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.5/initializer_list \
- /usr/include/c++/4.5/bits/basic_string.tcc ../include/constants.h \
- ../include/data.h ../include/options.h /usr/include/stdlib.h \
- /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
- /usr/include/sys/types.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/sys/sysmacros.h /usr/include/alloca.h \
- /usr/include/bits/stdlib.h /usr/include/c++/4.5/cstring \
- /usr/include/string.h /usr/include/bits/string3.h /usr/include/libio.h \
- /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \
- /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
- /usr/include/bits/stdio2.h
-
-../include/loader.h:
-
-/usr/include/c++/4.5/string:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
-
-/usr/include/c++/4.5/bits/stringfwd.h:
-
-/usr/include/c++/4.5/bits/char_traits.h:
-
-/usr/include/c++/4.5/bits/stl_algobase.h:
-
-/usr/include/c++/4.5/cstddef:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/c++/4.5/bits/functexcept.h:
-
-/usr/include/c++/4.5/exception_defines.h:
-
-/usr/include/c++/4.5/bits/cpp_type_traits.h:
-
-/usr/include/c++/4.5/ext/type_traits.h:
-
-/usr/include/c++/4.5/ext/numeric_traits.h:
-
-/usr/include/c++/4.5/bits/stl_pair.h:
-
-/usr/include/c++/4.5/bits/move.h:
-
-/usr/include/c++/4.5/bits/concept_check.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
-
-/usr/include/c++/4.5/bits/stl_iterator.h:
-
-/usr/include/c++/4.5/debug/debug.h:
-
-/usr/include/c++/4.5/bits/postypes.h:
-
-/usr/include/c++/4.5/cwchar:
-
-/usr/include/wchar.h:
-
-/usr/include/stdio.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/wchar.h:
-
-/usr/include/xlocale.h:
-
-/usr/include/bits/wchar2.h:
-
-/usr/include/c++/4.5/bits/allocator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
-
-/usr/include/c++/4.5/ext/new_allocator.h:
-
-/usr/include/c++/4.5/new:
-
-/usr/include/c++/4.5/exception:
-
-/usr/include/c++/4.5/bits/localefwd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
-
-/usr/include/c++/4.5/clocale:
-
-/usr/include/locale.h:
-
-/usr/include/bits/locale.h:
-
-/usr/include/c++/4.5/iosfwd:
-
-/usr/include/c++/4.5/cctype:
-
-/usr/include/ctype.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/c++/4.5/bits/ostream_insert.h:
-
-/usr/include/c++/4.5/cxxabi-forced.h:
-
-/usr/include/c++/4.5/bits/stl_function.h:
-
-/usr/include/c++/4.5/backward/binders.h:
-
-/usr/include/c++/4.5/bits/basic_string.h:
-
-/usr/include/c++/4.5/ext/atomicity.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
-
-/usr/include/pthread.h:
-
-/usr/include/sched.h:
-
-/usr/include/time.h:
-
-/usr/include/bits/sched.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/bits/setjmp.h:
-
-/usr/include/unistd.h:
-
-/usr/include/bits/posix_opt.h:
-
-/usr/include/bits/environments.h:
-
-/usr/include/bits/confname.h:
-
-/usr/include/getopt.h:
-
-/usr/include/bits/unistd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.5/initializer_list:
-
-/usr/include/c++/4.5/bits/basic_string.tcc:
-
-../include/constants.h:
-
-../include/data.h:
-
-../include/options.h:
-
-/usr/include/stdlib.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/alloca.h:
-
-/usr/include/bits/stdlib.h:
-
-/usr/include/c++/4.5/cstring:
-
-/usr/include/string.h:
-
-/usr/include/bits/string3.h:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/bits/stdio.h:
-
-/usr/include/bits/stdio2.h:
diff --git a/gtfold-mfe/src/.deps/shapereader.Po b/gtfold-mfe/src/.deps/shapereader.Po
deleted file mode 100644
index aa9b3a0..0000000
--- a/gtfold-mfe/src/.deps/shapereader.Po
+++ /dev/null
@@ -1,358 +0,0 @@
-shapereader.o: shapereader.cc /usr/include/c++/4.5/iostream \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
- /usr/include/features.h /usr/include/bits/predefs.h \
- /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
- /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \
- /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \
- /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \
- /usr/include/c++/4.5/cstddef \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/wchar.h /usr/include/stdio.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/wchar.h /usr/include/xlocale.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \
- /usr/include/c++/4.5/bits/char_traits.h \
- /usr/include/c++/4.5/bits/stl_algobase.h \
- /usr/include/c++/4.5/bits/functexcept.h \
- /usr/include/c++/4.5/exception_defines.h \
- /usr/include/c++/4.5/bits/cpp_type_traits.h \
- /usr/include/c++/4.5/ext/type_traits.h \
- /usr/include/c++/4.5/ext/numeric_traits.h \
- /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
- /usr/include/c++/4.5/bits/concept_check.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.5/bits/stl_iterator.h \
- /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.5/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \
- /usr/include/ctype.h /usr/include/bits/types.h \
- /usr/include/bits/typesizes.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/c++/4.5/bits/ios_base.h \
- /usr/include/c++/4.5/ext/atomicity.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
- /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h \
- /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
- /usr/include/unistd.h /usr/include/bits/posix_opt.h \
- /usr/include/bits/environments.h /usr/include/bits/confname.h \
- /usr/include/getopt.h /usr/include/bits/unistd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \
- /usr/include/c++/4.5/bits/allocator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
- /usr/include/c++/4.5/bits/ostream_insert.h \
- /usr/include/c++/4.5/cxxabi-forced.h \
- /usr/include/c++/4.5/bits/stl_function.h \
- /usr/include/c++/4.5/backward/binders.h \
- /usr/include/c++/4.5/bits/basic_string.h \
- /usr/include/c++/4.5/initializer_list \
- /usr/include/c++/4.5/bits/basic_string.tcc \
- /usr/include/c++/4.5/bits/locale_classes.tcc \
- /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \
- /usr/include/c++/4.5/bits/basic_ios.h \
- /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \
- /usr/include/wctype.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \
- /usr/include/c++/4.5/bits/streambuf_iterator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \
- /usr/include/c++/4.5/bits/locale_facets.tcc \
- /usr/include/c++/4.5/bits/basic_ios.tcc \
- /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \
- /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \
- /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \
- /usr/include/libio.h /usr/include/_G_config.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \
- /usr/include/c++/4.5/bits/fstream.tcc /usr/include/string.h \
- /usr/include/bits/string3.h /usr/include/stdlib.h \
- /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
- /usr/include/sys/types.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/sys/sysmacros.h /usr/include/alloca.h \
- /usr/include/bits/stdlib.h /usr/include/math.h \
- /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
- /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
- /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
- /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
- ../include/shapereader.h ../include/global.h ../include/constants.h \
- ../include/options.h /usr/include/c++/4.5/cstring
-
-/usr/include/c++/4.5/iostream:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
-
-/usr/include/c++/4.5/ostream:
-
-/usr/include/c++/4.5/ios:
-
-/usr/include/c++/4.5/iosfwd:
-
-/usr/include/c++/4.5/bits/stringfwd.h:
-
-/usr/include/c++/4.5/bits/postypes.h:
-
-/usr/include/c++/4.5/cwchar:
-
-/usr/include/c++/4.5/cstddef:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/wchar.h:
-
-/usr/include/stdio.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/wchar.h:
-
-/usr/include/xlocale.h:
-
-/usr/include/bits/wchar2.h:
-
-/usr/include/c++/4.5/exception:
-
-/usr/include/c++/4.5/bits/char_traits.h:
-
-/usr/include/c++/4.5/bits/stl_algobase.h:
-
-/usr/include/c++/4.5/bits/functexcept.h:
-
-/usr/include/c++/4.5/exception_defines.h:
-
-/usr/include/c++/4.5/bits/cpp_type_traits.h:
-
-/usr/include/c++/4.5/ext/type_traits.h:
-
-/usr/include/c++/4.5/ext/numeric_traits.h:
-
-/usr/include/c++/4.5/bits/stl_pair.h:
-
-/usr/include/c++/4.5/bits/move.h:
-
-/usr/include/c++/4.5/bits/concept_check.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
-
-/usr/include/c++/4.5/bits/stl_iterator.h:
-
-/usr/include/c++/4.5/debug/debug.h:
-
-/usr/include/c++/4.5/bits/localefwd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
-
-/usr/include/c++/4.5/clocale:
-
-/usr/include/locale.h:
-
-/usr/include/bits/locale.h:
-
-/usr/include/c++/4.5/cctype:
-
-/usr/include/ctype.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/c++/4.5/bits/ios_base.h:
-
-/usr/include/c++/4.5/ext/atomicity.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
-
-/usr/include/pthread.h:
-
-/usr/include/sched.h:
-
-/usr/include/time.h:
-
-/usr/include/bits/sched.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/bits/setjmp.h:
-
-/usr/include/unistd.h:
-
-/usr/include/bits/posix_opt.h:
-
-/usr/include/bits/environments.h:
-
-/usr/include/bits/confname.h:
-
-/usr/include/getopt.h:
-
-/usr/include/bits/unistd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.5/bits/locale_classes.h:
-
-/usr/include/c++/4.5/string:
-
-/usr/include/c++/4.5/bits/allocator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
-
-/usr/include/c++/4.5/ext/new_allocator.h:
-
-/usr/include/c++/4.5/new:
-
-/usr/include/c++/4.5/bits/ostream_insert.h:
-
-/usr/include/c++/4.5/cxxabi-forced.h:
-
-/usr/include/c++/4.5/bits/stl_function.h:
-
-/usr/include/c++/4.5/backward/binders.h:
-
-/usr/include/c++/4.5/bits/basic_string.h:
-
-/usr/include/c++/4.5/initializer_list:
-
-/usr/include/c++/4.5/bits/basic_string.tcc:
-
-/usr/include/c++/4.5/bits/locale_classes.tcc:
-
-/usr/include/c++/4.5/streambuf:
-
-/usr/include/c++/4.5/bits/streambuf.tcc:
-
-/usr/include/c++/4.5/bits/basic_ios.h:
-
-/usr/include/c++/4.5/bits/locale_facets.h:
-
-/usr/include/c++/4.5/cwctype:
-
-/usr/include/wctype.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h:
-
-/usr/include/c++/4.5/bits/streambuf_iterator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h:
-
-/usr/include/c++/4.5/bits/locale_facets.tcc:
-
-/usr/include/c++/4.5/bits/basic_ios.tcc:
-
-/usr/include/c++/4.5/bits/ostream.tcc:
-
-/usr/include/c++/4.5/istream:
-
-/usr/include/c++/4.5/bits/istream.tcc:
-
-/usr/include/c++/4.5/fstream:
-
-/usr/include/c++/4.5/bits/codecvt.h:
-
-/usr/include/c++/4.5/cstdio:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/bits/stdio.h:
-
-/usr/include/bits/stdio2.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h:
-
-/usr/include/c++/4.5/bits/fstream.tcc:
-
-/usr/include/string.h:
-
-/usr/include/bits/string3.h:
-
-/usr/include/stdlib.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/alloca.h:
-
-/usr/include/bits/stdlib.h:
-
-/usr/include/math.h:
-
-/usr/include/bits/huge_val.h:
-
-/usr/include/bits/huge_valf.h:
-
-/usr/include/bits/huge_vall.h:
-
-/usr/include/bits/inf.h:
-
-/usr/include/bits/nan.h:
-
-/usr/include/bits/mathdef.h:
-
-/usr/include/bits/mathcalls.h:
-
-/usr/include/bits/mathinline.h:
-
-../include/shapereader.h:
-
-../include/global.h:
-
-../include/constants.h:
-
-../include/options.h:
-
-/usr/include/c++/4.5/cstring:
diff --git a/gtfold-mfe/src/.deps/subopt_traceback.Po b/gtfold-mfe/src/.deps/subopt_traceback.Po
deleted file mode 100644
index 6dac6fe..0000000
--- a/gtfold-mfe/src/.deps/subopt_traceback.Po
+++ /dev/null
@@ -1,346 +0,0 @@
-subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.5/cstdio \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
- /usr/include/features.h /usr/include/bits/predefs.h \
- /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
- /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.5/cstddef \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/stdio.h /usr/include/bits/types.h \
- /usr/include/bits/typesizes.h /usr/include/libio.h \
- /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- ../include/constants.h ../include/energy.h ../include/data.h \
- ../include/constants.h ../include/utils.h ../include/global.h \
- ../include/subopt_traceback.h /usr/include/c++/4.5/cassert \
- /usr/include/assert.h /usr/include/c++/4.5/iostream \
- /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \
- /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \
- /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \
- /usr/include/bits/wchar.h /usr/include/xlocale.h \
- /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \
- /usr/include/c++/4.5/bits/char_traits.h \
- /usr/include/c++/4.5/bits/stl_algobase.h \
- /usr/include/c++/4.5/bits/functexcept.h \
- /usr/include/c++/4.5/exception_defines.h \
- /usr/include/c++/4.5/bits/cpp_type_traits.h \
- /usr/include/c++/4.5/ext/type_traits.h \
- /usr/include/c++/4.5/ext/numeric_traits.h \
- /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
- /usr/include/c++/4.5/bits/concept_check.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.5/bits/stl_iterator.h \
- /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.5/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \
- /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ios_base.h \
- /usr/include/c++/4.5/ext/atomicity.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
- /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h \
- /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
- /usr/include/unistd.h /usr/include/bits/posix_opt.h \
- /usr/include/bits/environments.h /usr/include/bits/confname.h \
- /usr/include/getopt.h /usr/include/bits/unistd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \
- /usr/include/c++/4.5/bits/allocator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
- /usr/include/c++/4.5/bits/ostream_insert.h \
- /usr/include/c++/4.5/cxxabi-forced.h \
- /usr/include/c++/4.5/bits/stl_function.h \
- /usr/include/c++/4.5/backward/binders.h \
- /usr/include/c++/4.5/bits/basic_string.h \
- /usr/include/c++/4.5/initializer_list \
- /usr/include/c++/4.5/bits/basic_string.tcc \
- /usr/include/c++/4.5/bits/locale_classes.tcc \
- /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \
- /usr/include/c++/4.5/bits/basic_ios.h \
- /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \
- /usr/include/wctype.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \
- /usr/include/c++/4.5/bits/streambuf_iterator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \
- /usr/include/c++/4.5/bits/locale_facets.tcc \
- /usr/include/c++/4.5/bits/basic_ios.tcc \
- /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \
- /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/sstream \
- /usr/include/c++/4.5/bits/sstream.tcc /usr/include/c++/4.5/stack \
- /usr/include/c++/4.5/deque /usr/include/c++/4.5/bits/stl_construct.h \
- /usr/include/c++/4.5/bits/stl_uninitialized.h \
- /usr/include/c++/4.5/bits/stl_deque.h \
- /usr/include/c++/4.5/bits/deque.tcc \
- /usr/include/c++/4.5/bits/stl_stack.h /usr/include/c++/4.5/map \
- /usr/include/c++/4.5/bits/stl_tree.h /usr/include/c++/4.5/bits/stl_map.h \
- /usr/include/c++/4.5/bits/stl_multimap.h /usr/include/c++/4.5/vector \
- /usr/include/c++/4.5/bits/stl_vector.h \
- /usr/include/c++/4.5/bits/stl_bvector.h \
- /usr/include/c++/4.5/bits/vector.tcc
-
-/usr/include/c++/4.5/cstdio:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
-
-/usr/include/c++/4.5/cstddef:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/stdio.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/wchar.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/bits/stdio.h:
-
-/usr/include/bits/stdio2.h:
-
-../include/constants.h:
-
-../include/energy.h:
-
-../include/data.h:
-
-../include/constants.h:
-
-../include/utils.h:
-
-../include/global.h:
-
-../include/subopt_traceback.h:
-
-/usr/include/c++/4.5/cassert:
-
-/usr/include/assert.h:
-
-/usr/include/c++/4.5/iostream:
-
-/usr/include/c++/4.5/ostream:
-
-/usr/include/c++/4.5/ios:
-
-/usr/include/c++/4.5/iosfwd:
-
-/usr/include/c++/4.5/bits/stringfwd.h:
-
-/usr/include/c++/4.5/bits/postypes.h:
-
-/usr/include/c++/4.5/cwchar:
-
-/usr/include/bits/wchar.h:
-
-/usr/include/xlocale.h:
-
-/usr/include/bits/wchar2.h:
-
-/usr/include/c++/4.5/exception:
-
-/usr/include/c++/4.5/bits/char_traits.h:
-
-/usr/include/c++/4.5/bits/stl_algobase.h:
-
-/usr/include/c++/4.5/bits/functexcept.h:
-
-/usr/include/c++/4.5/exception_defines.h:
-
-/usr/include/c++/4.5/bits/cpp_type_traits.h:
-
-/usr/include/c++/4.5/ext/type_traits.h:
-
-/usr/include/c++/4.5/ext/numeric_traits.h:
-
-/usr/include/c++/4.5/bits/stl_pair.h:
-
-/usr/include/c++/4.5/bits/move.h:
-
-/usr/include/c++/4.5/bits/concept_check.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
-
-/usr/include/c++/4.5/bits/stl_iterator.h:
-
-/usr/include/c++/4.5/debug/debug.h:
-
-/usr/include/c++/4.5/bits/localefwd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
-
-/usr/include/c++/4.5/clocale:
-
-/usr/include/locale.h:
-
-/usr/include/bits/locale.h:
-
-/usr/include/c++/4.5/cctype:
-
-/usr/include/ctype.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/c++/4.5/bits/ios_base.h:
-
-/usr/include/c++/4.5/ext/atomicity.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
-
-/usr/include/pthread.h:
-
-/usr/include/sched.h:
-
-/usr/include/time.h:
-
-/usr/include/bits/sched.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/bits/setjmp.h:
-
-/usr/include/unistd.h:
-
-/usr/include/bits/posix_opt.h:
-
-/usr/include/bits/environments.h:
-
-/usr/include/bits/confname.h:
-
-/usr/include/getopt.h:
-
-/usr/include/bits/unistd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.5/bits/locale_classes.h:
-
-/usr/include/c++/4.5/string:
-
-/usr/include/c++/4.5/bits/allocator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
-
-/usr/include/c++/4.5/ext/new_allocator.h:
-
-/usr/include/c++/4.5/new:
-
-/usr/include/c++/4.5/bits/ostream_insert.h:
-
-/usr/include/c++/4.5/cxxabi-forced.h:
-
-/usr/include/c++/4.5/bits/stl_function.h:
-
-/usr/include/c++/4.5/backward/binders.h:
-
-/usr/include/c++/4.5/bits/basic_string.h:
-
-/usr/include/c++/4.5/initializer_list:
-
-/usr/include/c++/4.5/bits/basic_string.tcc:
-
-/usr/include/c++/4.5/bits/locale_classes.tcc:
-
-/usr/include/c++/4.5/streambuf:
-
-/usr/include/c++/4.5/bits/streambuf.tcc:
-
-/usr/include/c++/4.5/bits/basic_ios.h:
-
-/usr/include/c++/4.5/bits/locale_facets.h:
-
-/usr/include/c++/4.5/cwctype:
-
-/usr/include/wctype.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h:
-
-/usr/include/c++/4.5/bits/streambuf_iterator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h:
-
-/usr/include/c++/4.5/bits/locale_facets.tcc:
-
-/usr/include/c++/4.5/bits/basic_ios.tcc:
-
-/usr/include/c++/4.5/bits/ostream.tcc:
-
-/usr/include/c++/4.5/istream:
-
-/usr/include/c++/4.5/bits/istream.tcc:
-
-/usr/include/c++/4.5/sstream:
-
-/usr/include/c++/4.5/bits/sstream.tcc:
-
-/usr/include/c++/4.5/stack:
-
-/usr/include/c++/4.5/deque:
-
-/usr/include/c++/4.5/bits/stl_construct.h:
-
-/usr/include/c++/4.5/bits/stl_uninitialized.h:
-
-/usr/include/c++/4.5/bits/stl_deque.h:
-
-/usr/include/c++/4.5/bits/deque.tcc:
-
-/usr/include/c++/4.5/bits/stl_stack.h:
-
-/usr/include/c++/4.5/map:
-
-/usr/include/c++/4.5/bits/stl_tree.h:
-
-/usr/include/c++/4.5/bits/stl_map.h:
-
-/usr/include/c++/4.5/bits/stl_multimap.h:
-
-/usr/include/c++/4.5/vector:
-
-/usr/include/c++/4.5/bits/stl_vector.h:
-
-/usr/include/c++/4.5/bits/stl_bvector.h:
-
-/usr/include/c++/4.5/bits/vector.tcc:
diff --git a/gtfold-mfe/src/.deps/traceback.Po b/gtfold-mfe/src/.deps/traceback.Po
deleted file mode 100644
index 28cf049..0000000
--- a/gtfold-mfe/src/.deps/traceback.Po
+++ /dev/null
@@ -1,134 +0,0 @@
-traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \
- /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
- /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
- /usr/include/gnu/stubs-64.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/bits/types.h /usr/include/bits/typesizes.h \
- /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \
- /usr/include/stdlib.h /usr/include/bits/waitflags.h \
- /usr/include/bits/waitstatus.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
- /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
- /usr/include/bits/stdlib.h /usr/include/math.h \
- /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
- /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
- /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
- /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
- /usr/include/assert.h ../include/data.h ../include/constants.h \
- ../include/constants.h ../include/constraints.h ../include/energy.h \
- ../include/data.h ../include/global.h ../include/traceback.h \
- ../include/utils.h ../include/shapereader.h
-
-/usr/include/stdio.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/wchar.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/bits/stdio.h:
-
-/usr/include/bits/stdio2.h:
-
-/usr/include/stdlib.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/time.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/alloca.h:
-
-/usr/include/bits/stdlib.h:
-
-/usr/include/math.h:
-
-/usr/include/bits/huge_val.h:
-
-/usr/include/bits/huge_valf.h:
-
-/usr/include/bits/huge_vall.h:
-
-/usr/include/bits/inf.h:
-
-/usr/include/bits/nan.h:
-
-/usr/include/bits/mathdef.h:
-
-/usr/include/bits/mathcalls.h:
-
-/usr/include/bits/mathinline.h:
-
-/usr/include/assert.h:
-
-../include/data.h:
-
-../include/constants.h:
-
-../include/constants.h:
-
-../include/constraints.h:
-
-../include/energy.h:
-
-../include/data.h:
-
-../include/global.h:
-
-../include/traceback.h:
-
-../include/utils.h:
-
-../include/shapereader.h:
diff --git a/gtfold-mfe/src/.deps/utils.Po b/gtfold-mfe/src/.deps/utils.Po
deleted file mode 100644
index d92a43a..0000000
--- a/gtfold-mfe/src/.deps/utils.Po
+++ /dev/null
@@ -1,217 +0,0 @@
-utils.o: utils.cc ../include/utils.h ../include/constants.h \
- /usr/include/string.h /usr/include/features.h \
- /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \
- /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
- /usr/include/gnu/stubs-64.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \
- /usr/include/xlocale.h /usr/include/bits/string3.h \
- /usr/include/c++/4.5/string \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \
- /usr/include/c++/4.5/bits/stringfwd.h \
- /usr/include/c++/4.5/bits/char_traits.h \
- /usr/include/c++/4.5/bits/stl_algobase.h /usr/include/c++/4.5/cstddef \
- /usr/include/c++/4.5/bits/functexcept.h \
- /usr/include/c++/4.5/exception_defines.h \
- /usr/include/c++/4.5/bits/cpp_type_traits.h \
- /usr/include/c++/4.5/ext/type_traits.h \
- /usr/include/c++/4.5/ext/numeric_traits.h \
- /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \
- /usr/include/c++/4.5/bits/concept_check.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_types.h \
- /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \
- /usr/include/c++/4.5/bits/stl_iterator.h \
- /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/postypes.h \
- /usr/include/c++/4.5/cwchar /usr/include/wchar.h /usr/include/stdio.h \
- /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \
- /usr/include/bits/wchar.h /usr/include/bits/wchar2.h \
- /usr/include/c++/4.5/bits/allocator.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \
- /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \
- /usr/include/c++/4.5/exception /usr/include/c++/4.5/bits/localefwd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \
- /usr/include/c++/4.5/clocale /usr/include/locale.h \
- /usr/include/bits/locale.h /usr/include/c++/4.5/iosfwd \
- /usr/include/c++/4.5/cctype /usr/include/ctype.h \
- /usr/include/bits/types.h /usr/include/bits/typesizes.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ostream_insert.h \
- /usr/include/c++/4.5/cxxabi-forced.h \
- /usr/include/c++/4.5/bits/stl_function.h \
- /usr/include/c++/4.5/backward/binders.h \
- /usr/include/c++/4.5/bits/basic_string.h \
- /usr/include/c++/4.5/ext/atomicity.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \
- /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h \
- /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
- /usr/include/unistd.h /usr/include/bits/posix_opt.h \
- /usr/include/bits/environments.h /usr/include/bits/confname.h \
- /usr/include/getopt.h /usr/include/bits/unistd.h \
- /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \
- /usr/include/c++/4.5/initializer_list \
- /usr/include/c++/4.5/bits/basic_string.tcc
-
-../include/utils.h:
-
-../include/constants.h:
-
-/usr/include/string.h:
-
-/usr/include/features.h:
-
-/usr/include/bits/predefs.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-64.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h:
-
-/usr/include/xlocale.h:
-
-/usr/include/bits/string3.h:
-
-/usr/include/c++/4.5/string:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h:
-
-/usr/include/c++/4.5/bits/stringfwd.h:
-
-/usr/include/c++/4.5/bits/char_traits.h:
-
-/usr/include/c++/4.5/bits/stl_algobase.h:
-
-/usr/include/c++/4.5/cstddef:
-
-/usr/include/c++/4.5/bits/functexcept.h:
-
-/usr/include/c++/4.5/exception_defines.h:
-
-/usr/include/c++/4.5/bits/cpp_type_traits.h:
-
-/usr/include/c++/4.5/ext/type_traits.h:
-
-/usr/include/c++/4.5/ext/numeric_traits.h:
-
-/usr/include/c++/4.5/bits/stl_pair.h:
-
-/usr/include/c++/4.5/bits/move.h:
-
-/usr/include/c++/4.5/bits/concept_check.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_types.h:
-
-/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h:
-
-/usr/include/c++/4.5/bits/stl_iterator.h:
-
-/usr/include/c++/4.5/debug/debug.h:
-
-/usr/include/c++/4.5/bits/postypes.h:
-
-/usr/include/c++/4.5/cwchar:
-
-/usr/include/wchar.h:
-
-/usr/include/stdio.h:
-
-/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h:
-
-/usr/include/bits/wchar.h:
-
-/usr/include/bits/wchar2.h:
-
-/usr/include/c++/4.5/bits/allocator.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h:
-
-/usr/include/c++/4.5/ext/new_allocator.h:
-
-/usr/include/c++/4.5/new:
-
-/usr/include/c++/4.5/exception:
-
-/usr/include/c++/4.5/bits/localefwd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h:
-
-/usr/include/c++/4.5/clocale:
-
-/usr/include/locale.h:
-
-/usr/include/bits/locale.h:
-
-/usr/include/c++/4.5/iosfwd:
-
-/usr/include/c++/4.5/cctype:
-
-/usr/include/ctype.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/bits/byteswap.h:
-
-/usr/include/c++/4.5/bits/ostream_insert.h:
-
-/usr/include/c++/4.5/cxxabi-forced.h:
-
-/usr/include/c++/4.5/bits/stl_function.h:
-
-/usr/include/c++/4.5/backward/binders.h:
-
-/usr/include/c++/4.5/bits/basic_string.h:
-
-/usr/include/c++/4.5/ext/atomicity.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h:
-
-/usr/include/pthread.h:
-
-/usr/include/sched.h:
-
-/usr/include/time.h:
-
-/usr/include/bits/sched.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/bits/setjmp.h:
-
-/usr/include/unistd.h:
-
-/usr/include/bits/posix_opt.h:
-
-/usr/include/bits/environments.h:
-
-/usr/include/bits/confname.h:
-
-/usr/include/getopt.h:
-
-/usr/include/bits/unistd.h:
-
-/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.5/initializer_list:
-
-/usr/include/c++/4.5/bits/basic_string.tcc:

From ae599b41e34f9caf258a729b2444bb2505f17ed7 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@castor.cc.gt.atl.ga.us>
Date: Fri, 24 Jun 2011 14:41:23 -0400
Subject: [PATCH 178/282] added prefilter option, rectified unamode option

---
 gtfold-mfe/include/algorithms.h |  2 +-
 gtfold-mfe/include/global.h     |  8 ++++++++
 gtfold-mfe/include/options.h    |  3 +++
 gtfold-mfe/src/algorithms.c     | 16 +++++++--------
 gtfold-mfe/src/global.c         |  8 ++++++++
 gtfold-mfe/src/loader.cc        | 12 ++++++++---
 gtfold-mfe/src/main.cc          | 11 ++++++++--
 gtfold-mfe/src/options.cc       | 36 ++++++++++++++++++++++++---------
 8 files changed, 72 insertions(+), 24 deletions(-)

diff --git a/gtfold-mfe/include/algorithms.h b/gtfold-mfe/include/algorithms.h
index d37a205..1f0f1df 100644
--- a/gtfold-mfe/include/algorithms.h
+++ b/gtfold-mfe/include/algorithms.h
@@ -23,7 +23,7 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
-	int calculate(int len, int nThreads, int unamode ,int t_mismatch);
+	int calculate(int len);//, int nThreads, int unamode ,int t_mismatch);
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h
index fe2d9df..1bdc31e 100644
--- a/gtfold-mfe/include/global.h
+++ b/gtfold-mfe/include/global.h
@@ -7,6 +7,14 @@ extern unsigned char *RNA;
 extern int *structure; 
 extern int* constraints;
 
+extern int g_nthreads;
+extern int g_unamode;
+extern int g_mismatch;
+extern int g_verbose;
+extern int g_prefilter_mode;
+extern int g_prefilter1;
+extern int g_prefilter2;
+
 extern unsigned int chPairKey;
 
 // The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). 
diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 24217bf..58db1a8 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -30,6 +30,9 @@ extern string paramDir;
 
 extern float suboptDelta;
 extern int nThreads;
+extern bool b_prefilter;
+extern int prefilter1;
+extern int prefilter2;
 
 extern bool LIMIT_DISTANCE;
 extern int contactDistance;
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index b61aa1e..a0fe2ae 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -120,10 +120,10 @@ int calcVBI2(int i, int j, int  len) {
 	return energy;
 }
 
-int calculate(int len, int nThreads, int unamode, int mismatch) { 
+int calculate(int len) { //, int nThreads, int unamode, int mismatch) { 
 	int b, i, j;
 #ifdef _OPENMP
-	if (nThreads>0) omp_set_num_threads(nThreads);
+	if (g_nthreads > 0) omp_set_num_threads(g_nthreads);
 #endif
 #ifdef _OPENMP
 #pragma omp parallel
@@ -132,8 +132,8 @@ int calculate(int len, int nThreads, int unamode, int mismatch) {
 #endif
 
 	initializeMatrix(len);
-	if (unamode) {
-		prefilter(len,2,2);
+	if (g_unamode || g_prefilter_mode) {
+		prefilter(len,g_prefilter1,g_prefilter2);
 	}
 
 	for (b = TURN+1; b <= len-1; b++) {
@@ -149,7 +149,7 @@ int calculate(int len, int nThreads, int unamode, int mismatch) {
 				int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack
 
 				// Internal Loop BEGIN
-				if (unamode) 
+				if (g_unamode) 
 					VBI(i,j) = calcVBI1(i,j);
 				else
 					VBI(i,j) = calcVBI(i,j);
@@ -166,7 +166,7 @@ int calculate(int len, int nThreads, int unamode, int mismatch) {
 				VMij = MIN(VMij, (VMidj + d5 +Ec)) ;
 				VMij = MIN(VMij, (VMijd + d3 +Ec));
 
-				if (unamode || mismatch) {
+				if (g_unamode || g_mismatch) {
 					VMij = MIN(VMij, (VMidjd + Estackm(i,j) + 2*Ec));
 				} else {
 					VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec));
@@ -195,7 +195,7 @@ int calculate(int len, int nThreads, int unamode, int mismatch) {
 			newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
 			newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
 
-			if (unamode || mismatch) {
+			if (g_unamode || g_mismatch) {
 				if (i<j-TURN-2)
 					newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; 
 			}
@@ -217,7 +217,7 @@ int calculate(int len, int nThreads, int unamode, int mismatch) {
 			Wim1 = MIN(0, W[i-1]); 
 			Wij = V(i, j) + auPenalty(i, j) + Wim1;
 		
-			if (unamode || mismatch) {
+			if (g_unamode || g_mismatch) {
 				Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Estacke(j-1,i+1) + Wim1:Widjd;
 			} else {
 				Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:Widjd;
diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c
index a83c475..1a64fe7 100644
--- a/gtfold-mfe/src/global.c
+++ b/gtfold-mfe/src/global.c
@@ -8,6 +8,14 @@ unsigned char *RNA;
 int *structure; 
 unsigned int chPairKey;
 
+int g_nthreads;
+int g_unamode;
+int g_mismatch;
+int g_verbose;
+int g_prefilter_mode;
+int g_prefilter1;
+int g_prefilter2;
+
 void init_global_params(int len) {
 	RNA = (unsigned char *) malloc((len+1)* sizeof(unsigned char));
 	if (RNA == NULL) {
diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 1c25d6a..9144c07 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -80,11 +80,17 @@ int init;
 int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
 float prelog;
 
-void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode=0, int mismatch=0) {
-	if (!userdatalogic) {
+void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode = 0, int mismatch = 0) {
+	
+	if (!userdatalogic && unamode) {
+		EN_DATADIR.assign(xstr(DATADIR));
+		EN_DATADIR += "/";
+		EN_DATADIR += "UNAParams";
+	}
+    else if (!userdatalogic) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
-		EN_DATADIR += userdatadir;
+		EN_DATADIR += "Turner99";
 	} else {
 		EN_DATADIR.assign(userdatadir);
 	}
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 42478a5..893e468 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -70,7 +70,14 @@ void init_fold(string seq) {
 	if (SHAPE_ENABLED) {
 		readSHAPEarray(shapeFile.c_str(),len);
 	}
-
+	
+	g_nthreads = nThreads;
+	g_unamode  = UNAMODE;
+	g_mismatch = T_MISMATCH;
+	g_verbose  = VERBOSE;
+	g_prefilter_mode  = b_prefilter;
+	g_prefilter1  = prefilter1;
+	g_prefilter2  = prefilter2;
 }
 
 void free_fold(int len) {
@@ -230,7 +237,7 @@ int main(int argc, char** argv) {
 	fflush(stdout);
 
 	t1 = get_seconds();
-	energy = calculate(seq.length(), nThreads, UNAMODE, T_MISMATCH);
+	energy = calculate(seq.length()) ; //, nThreads, UNAMODE, T_MISMATCH);
 	t1 = get_seconds() - t1;
 	
 	printf("Done.\n\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index a9a3cb0..8c2c224 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -1,12 +1,12 @@
 #include "loader.h"
 #include "options.h"
 
+#include <sstream>
+
 using namespace std;
 
 bool ILSA;
 bool NOISOLATE;
-//bool USERDATA;
-//bool PARAMS;
 bool PARAM_DIR = false;
 bool LIMIT_DISTANCE;
 bool BPP_ENABLED;
@@ -16,13 +16,16 @@ bool VERBOSE = false;
 bool SHAPE_ENABLED = false;
 bool T_MISMATCH = false;
 bool UNAMODE = false;
+bool b_prefilter = false;
 
 string seqfile = "";
 string constraintsFile = "";
 string outputFile = "";
 string shapeFile = "";
-string paramDir = "Turner99"; // default value
+string paramDir; // default value
 
+int prefilter1=2;
+int prefilter2=2;
 
 float suboptDelta = 0.0;
 int nThreads = -1;
@@ -47,7 +50,8 @@ void help() {
    	printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
     printf("   -t, --threads num    Limit number of threads used\n");
-    printf("   --unamode DIR	Enable UNAfold mode. Path to directory containing UNAfold parameters\n");
+    printf("   --unamode 	Enable UNAfold mode. \n");
+    printf("   --prefilter value1,value2 Sets the prefilter mode similar to UNAfold\n");
 
     printf("\n");
     printf("   -h, --help           Output help (this message) and exit\n");
@@ -105,14 +109,22 @@ void parse_options(int argc, char** argv) {
 				else
 					help();
 			} else if (strcmp(argv[i], "-m") == 0) {
-                T_MISMATCH = true;
+				T_MISMATCH = true;
 			} else if (strcmp(argv[i], "--unamode") == 0) {
+				UNAMODE = true;
+			} else if (strcmp(argv[i], "--prefilter") == 0) {
 				if(i < argc) {
-					paramDir = argv[++i];
-					UNAMODE = true;
-					PARAM_DIR = true;
-				}
-				else
+					int value1 = -1, value2 = -1;
+					std::stringstream ss;
+					ss << argv[++i];
+					sscanf(ss.str().c_str(),"%d,%d", &value1, &value2);
+					if (value1 < 0 || value2 < 0) {
+						help();
+					}
+					b_prefilter =true;
+					prefilter1 = value1;
+					prefilter2 = value2;
+				} else 
 					help();
 			}
 		   	else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
@@ -189,6 +201,10 @@ void printRunConfiguration(string seq) {
 		printf("+ enabled terminal mismatch calculations\n");
 		standardRun = false;
 	}
+	if (b_prefilter == true) {
+		printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2);
+		standardRun = false;
+	}
 
 	if (NOISOLATE == true) {
 		printf("- preventing isolated base pairs\n");

From f3c2db0339a3afd46150c6dd95e875952ae8c789 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 24 Jun 2011 14:57:39 -0400
Subject: [PATCH 179/282] removed unwanted print statement

---
 gtfold-mfe/src/energy.c | 2 --
 1 file changed, 2 deletions(-)

diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 616ad48..bc71d37 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -192,7 +192,6 @@ inline int eL1(int i, int j, int ip, int jp) {
 		}
 		else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */
 			energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]];
-			if (i==1 && j==22) printf("2x2 loop at %d %d %d\n", i,j, energy);
 		} else if (size1 == 1 && size2 == 2) {
 			energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]];
 		} else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */
@@ -264,7 +263,6 @@ inline int eL(int i, int j, int ip, int jp) {
 		}
 		else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */
 			energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]];
-			if (i==1 && j==22) printf("2x2 loop at %d %d %d\n", i,j, energy);
 		} else if (size1 == 1 && size2 == 2) {
 			energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]];
 		} else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */

From d768553d1212f85e3dc776d2835cbb81f6b31a89 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 24 Jun 2011 15:04:27 -0400
Subject: [PATCH 180/282] added check for prefilter inputs

---
 gtfold-mfe/src/options.cc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 8c2c224..a7b9ca8 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -118,7 +118,8 @@ void parse_options(int argc, char** argv) {
 					std::stringstream ss;
 					ss << argv[++i];
 					sscanf(ss.str().c_str(),"%d,%d", &value1, &value2);
-					if (value1 < 0 || value2 < 0) {
+					if (value1 <= 0 || value2 <= 0) {
+						printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
 						help();
 					}
 					b_prefilter =true;

From 69869ccfb4e76b2ffef83bb5f11d6d13a88db663 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 24 Jun 2011 15:39:18 -0400
Subject: [PATCH 181/282] fixed formatting problem in help message

---
 gtfold-mfe/src/options.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index a7b9ca8..212fe3b 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -50,8 +50,8 @@ void help() {
    	printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
     printf("   -t, --threads num    Limit number of threads used\n");
-    printf("   --unamode 	Enable UNAfold mode. \n");
-    printf("   --prefilter value1,value2 Sets the prefilter mode similar to UNAfold\n");
+    printf("   --unamode 		Enable UNAfold mode. \n");
+    printf("   --prefilter 		value1,value2 Sets the prefilter mode similar to UNAfold\n");
 
     printf("\n");
     printf("   -h, --help           Output help (this message) and exit\n");

From 54a21b8fc6a066da4017ac0e1d65fb8ab6c14fd7 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 24 Jun 2011 16:22:38 -0400
Subject: [PATCH 182/282] added newline after Total

---
 gtfold-mfe/src/algorithms-partition.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c
index 1492a8e..a914ddd 100644
--- a/gtfold-mfe/src/algorithms-partition.c
+++ b/gtfold-mfe/src/algorithms-partition.c
@@ -119,7 +119,7 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) {
             }
         }
     }
-	printf("Total partition number: %f", Q[1][len]);
+	printf("Total partition number: %f\n", Q[1][len]);
 }
 
 /**

From fcb3e207d5eaa2b8fce32bf65b6d07724da049a5 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 27 Jun 2011 16:25:33 -0400
Subject: [PATCH 183/282] added prefix and workdir option, fixed -d option

---
 gtfold-mfe/include/algorithms-partition.h |  2 +-
 gtfold-mfe/include/options.h              |  3 ++
 gtfold-mfe/src/algorithms-partition.c     | 11 ++--
 gtfold-mfe/src/main.cc                    | 21 +++-----
 gtfold-mfe/src/options.cc                 | 61 +++++++++++++++++------
 5 files changed, 64 insertions(+), 34 deletions(-)

diff --git a/gtfold-mfe/include/algorithms-partition.h b/gtfold-mfe/include/algorithms-partition.h
index ef55266..3bfb26d 100644
--- a/gtfold-mfe/include/algorithms-partition.h
+++ b/gtfold-mfe/include/algorithms-partition.h
@@ -15,7 +15,7 @@ typedef struct _pFuncData {
 */
 void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM);
 void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, double**P);
-void printBasePairProbabilities(int n, int *structure, double **P);
+void printBasePairProbabilities(int n, int *structure, double **P, const char* bppfile);
 
 double probabilityUnpaired(int length, int i, double **P);
 
diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 58db1a8..4d4dbf1 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -25,7 +25,10 @@ extern bool UNAMODE;
 extern string seqfile;
 extern string constraintsFile;
 extern string shapeFile;
+extern string outputDir;
 extern string outputFile;
+extern string bppOutFile;
+extern string suboptFile;
 extern string paramDir;
 
 extern float suboptDelta;
diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c
index a914ddd..fa3b9b8 100644
--- a/gtfold-mfe/src/algorithms-partition.c
+++ b/gtfold-mfe/src/algorithms-partition.c
@@ -199,16 +199,21 @@ void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM,
  *                  unpaired.
  * @param P Partition function array
  */
-void printBasePairProbabilities(int n, int *structure, double **P) {
+void printBasePairProbabilities(int n, int *structure, double **P, const char* outfile) {
+    FILE* outp = fopen(outfile,"w");
+	if (outp == NULL) {
+		fprintf(stderr, "printBasePairProbabilities() : Cannot open %s",outfile);	
+	}	
 
     int i;
     for(i=1; i<=n; ++i) {
         int j = structure[i];
         if(j)
-            printf("%d-%d pair\tPr: %f\n", i, j, P[MIN(i,j)][MAX(i,j)]);
+            fprintf(outp, "%d-%d pair\tPr: %f\n", i, j, P[MIN(i,j)][MAX(i,j)]);
         else
-            printf("%d unpaired\tPr: %f\n", i, probabilityUnpaired(n, i, P));
+            fprintf(outp, "%d unpaired\tPr: %f\n", i, probabilityUnpaired(n, i, P));
     }
+	fclose(outp);
 }
 
 /**
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 893e468..52172cd 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -250,20 +250,11 @@ int main(int argc, char** argv) {
 		t1 = get_seconds();
 		ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta);
 		t1 = get_seconds() - t1;
-		printf("Subopt traceback running time: %9.6f seconds\n\n", t1);
+		printf("\n");
+		printf("Subopt traceback running time: %9.6f seconds\n", t1);
 		
-		string suboptfile;
-		suboptfile	+= seqfile;
-		if(suboptfile.find("/") != string::npos) {
-			size_t pos = suboptfile.find_last_of("/");
-			suboptfile.erase(0,pos+1);
-		}
-		if(suboptfile.find(".") != string::npos)
-			suboptfile.erase(suboptfile.rfind("."));
-		suboptfile += ".ss";	
-		
-		printf("Suboptimal structures saved in %s\n", suboptfile.c_str());
-		save_subopt_file(suboptfile, subopt_data, seq, energy);	
+		printf("Subopt structures saved in %s\n", suboptFile.c_str());
+		save_subopt_file(suboptFile, subopt_data, seq, energy);	
 		free_fold(seq.length());
 		exit(0);
 	}
@@ -301,6 +292,7 @@ int main(int argc, char** argv) {
 	}
 
 	if(BPP_ENABLED){
+		printf("\n");
 		printf("Calculating partition function\n");
 		double ** Q,  **QM, **QB, **P;
 		Q = mallocTwoD(seq.length() + 1, seq.length() + 1);
@@ -311,7 +303,8 @@ int main(int argc, char** argv) {
 	
 		fill_partition_fn_arrays(seq.length(), Q, QB, QM);
 		fillBasePairProbabilities(seq.length(), Q, QB, QM, P);
-		printBasePairProbabilities(seq.length(), structure, P);
+		printBasePairProbabilities(seq.length(), structure, P, bppOutFile.c_str());
+		printf("Saved BPP output in %s\n",bppOutFile.c_str());
 
 		freeTwoD(Q, seq.length() + 1, seq.length() + 1);
 		freeTwoD(QM, seq.length() + 1, seq.length() + 1);
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 212fe3b..6dad154 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -20,7 +20,11 @@ bool b_prefilter = false;
 
 string seqfile = "";
 string constraintsFile = "";
+string outputPrefix = "";
 string outputFile = "";
+string suboptFile = "";
+string bppOutFile = "";
+string outputDir = "";
 string shapeFile = "";
 string paramDir; // default value
 
@@ -48,10 +52,11 @@ void help() {
     printf("   -p  --paramdir DIR   Path to directory from where parameters are to be read\n");
     printf("   -m   		Enable terminal mismatch calculations\n");
    	printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
-    printf("   -o, --output FILE    Output to FILE (default output is to a .ct extension)\n");
+    printf("   -o, --output NAME    Name output files with prefix\n");
+    printf("   -w, --workDir DIR    Path to directory for output files\n");
     printf("   -t, --threads num    Limit number of threads used\n");
     printf("   --unamode 		Enable UNAfold mode. \n");
-    printf("   --prefilter 		value1,value2 Sets the prefilter mode similar to UNAfold\n");
+    printf("   --prefilter value1,value2 \n\t\t\tSets the prefilter mode similar to UNAfold\n");
 
     printf("\n");
     printf("   -h, --help           Output help (this message) and exit\n");
@@ -89,20 +94,30 @@ void parse_options(int argc, char** argv) {
 					help();
 			} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-d") == 0) {
 				if(i < argc){
-					LIMIT_DISTANCE = true;
 					contactDistance = atoi(argv[++i]);
+					stringstream ss;
+					ss << contactDistance;
+					if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
+						LIMIT_DISTANCE = true;
+					else
+						help();
 				}
 				else
 					help();
 			} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
 				NOISOLATE = true;
-			} else if(strcmp(argv[i], "--output") == 0 || strcmp(argv[i], "-o") == 0) {
+			} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
+				if(i < argc)
+					outputPrefix = argv[++i];
+				else
+					help();
+			} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
 				if(i < argc)
-					outputFile = argv[++i];
+					outputDir = argv[++i];
 				else
 					help();
 			} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
-				if(i < argc) {
+					if(i < argc) {
 					paramDir = argv[++i];
 					PARAM_DIR = true;
 				}
@@ -122,7 +137,7 @@ void parse_options(int argc, char** argv) {
 						printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
 						help();
 					}
-					b_prefilter =true;
+					b_prefilter = true;
 					prefilter1 = value1;
 					prefilter2 = value2;
 				} else 
@@ -165,24 +180,36 @@ void parse_options(int argc, char** argv) {
 	}
 
 	// If no output file specified, create one
-	if(outputFile.empty()) {
-
+	if(outputPrefix.empty()) {
 		// base it off the input file
-		outputFile += seqfile;
+		outputPrefix += seqfile;
 		
 		size_t pos;
 		// extract file name from the path
-		if ((pos=outputFile.find_last_of('/')) > 0) {
-			outputFile = outputFile.substr(pos+1);
+		if ((pos=outputPrefix.find_last_of('/')) > 0) {
+			outputPrefix = outputPrefix.substr(pos+1);
 		}
 
 		// and if an extension exists, remove it ...
-		if(outputFile.find(".") != string::npos)
-			outputFile.erase(outputFile.rfind("."));
+		if(outputPrefix.find(".") != string::npos)
+			outputPrefix.erase(outputPrefix.rfind("."));
+	 }
 
-		// ... and append the .ct
-		outputFile += ".ct";
+	// If output dir specified
+	if (!outputDir.empty()) {
+		outputFile += outputDir;
+		suboptFile += outputDir;
+		bppOutFile += outputDir;
 	}
+	// ... and append the .ct
+	outputFile += outputPrefix;
+	outputFile += ".ct";
+
+	suboptFile += outputPrefix;	
+	suboptFile += "_ss.txt";	
+
+	bppOutFile += outputPrefix;	
+	bppOutFile += "_bpp.txt";	
 }
 
 /**
@@ -227,11 +254,13 @@ void printRunConfiguration(string seq) {
 
 	if (BPP_ENABLED == true) {
 		printf("+ calculating base pair probabilities\n");
+		printf("+ BPP output file: %s\n", bppOutFile.c_str());
 		standardRun = false;
 	}
 
 	if (SUBOPT_ENABLED) {
 		printf("+ calculating suboptimal structures within %f kcal/mol of MFE\n", suboptDelta);
+		printf("+ suboptimal structures file: %s\n", suboptFile.c_str());
 		standardRun = false;
 	}
 

From 43b8ec5913c7ca17c829a2ac42c91d324ea9a784 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 27 Jun 2011 17:26:32 -0400
Subject: [PATCH 184/282] added Vienna energy params

---
 gtfold-mfe/configure                   |   3 +-
 gtfold-mfe/configure.in                |   2 +-
 gtfold-mfe/data/Makefile.am            |   2 +-
 gtfold-mfe/data/Makefile.in            |   2 +-
 gtfold-mfe/data/RNAParams/Makefile.am  |  23 +
 gtfold-mfe/data/RNAParams/Makefile.in  | 399 +++++++++++++++++
 gtfold-mfe/data/RNAParams/dangle.DAT   |   8 +
 gtfold-mfe/data/RNAParams/int11.DAT    |  24 ++
 gtfold-mfe/data/RNAParams/int21.DAT    |  96 +++++
 gtfold-mfe/data/RNAParams/int22.DAT    | 576 +++++++++++++++++++++++++
 gtfold-mfe/data/RNAParams/loop.DAT     |  30 ++
 gtfold-mfe/data/RNAParams/miscloop.DAT |  12 +
 gtfold-mfe/data/RNAParams/sint2.DAT    |  24 ++
 gtfold-mfe/data/RNAParams/sint4.DAT    | 576 +++++++++++++++++++++++++
 gtfold-mfe/data/RNAParams/stack.DAT    |  16 +
 gtfold-mfe/data/RNAParams/tloop.DAT    |  30 ++
 gtfold-mfe/data/RNAParams/tstacke.DAT  |  16 +
 gtfold-mfe/data/RNAParams/tstackh.DAT  |  16 +
 gtfold-mfe/data/RNAParams/tstacki.DAT  |  16 +
 gtfold-mfe/data/RNAParams/tstackm.DAT  |  16 +
 20 files changed, 1883 insertions(+), 4 deletions(-)
 create mode 100644 gtfold-mfe/data/RNAParams/Makefile.am
 create mode 100644 gtfold-mfe/data/RNAParams/Makefile.in
 create mode 100644 gtfold-mfe/data/RNAParams/dangle.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/int11.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/int21.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/int22.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/loop.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/miscloop.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/sint2.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/sint4.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/stack.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/tloop.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/tstacke.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/tstackh.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/tstacki.DAT
 create mode 100644 gtfold-mfe/data/RNAParams/tstackm.DAT

diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure
index 37e6205..c0dc675 100755
--- a/gtfold-mfe/configure
+++ b/gtfold-mfe/configure
@@ -6047,7 +6047,7 @@ fi
 
 ac_config_files="$ac_config_files Makefile src/Makefile data/Makefile include/Makefile"
 
-ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile"
+ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile data/RNAParams/Makefile"
 
 
 cat >confcache <<\_ACEOF
@@ -6701,6 +6701,7 @@ do
     "data/Turner04/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner04/Makefile" ;;
     "data/Andronescu/Makefile") CONFIG_FILES="$CONFIG_FILES data/Andronescu/Makefile" ;;
     "data/UNAParams/Makefile") CONFIG_FILES="$CONFIG_FILES data/UNAParams/Makefile" ;;
+    "data/RNAParams/Makefile") CONFIG_FILES="$CONFIG_FILES data/RNAParams/Makefile" ;;
 
   *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
 $as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
diff --git a/gtfold-mfe/configure.in b/gtfold-mfe/configure.in
index e4e1755..03441fc 100644
--- a/gtfold-mfe/configure.in
+++ b/gtfold-mfe/configure.in
@@ -178,7 +178,7 @@ AM_CONDITIONAL(GTFOLD_DEBUG, test x$debug = xtrue)
 
 dnl Create makefiles and other configuration files
 AC_CONFIG_FILES([Makefile src/Makefile data/Makefile include/Makefile])
-AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile])
+AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile data/RNAParams/Makefile])
 
 dnl Generate `config.status' and launch it
 AC_OUTPUT
diff --git a/gtfold-mfe/data/Makefile.am b/gtfold-mfe/data/Makefile.am
index b6af86e..001e73e 100644
--- a/gtfold-mfe/data/Makefile.am
+++ b/gtfold-mfe/data/Makefile.am
@@ -1,2 +1,2 @@
-SUBDIRS = UNAParams Turner04 Turner99 Andronescu 
+SUBDIRS = UNAParams RNAParams Turner04 Turner99 Andronescu 
 
diff --git a/gtfold-mfe/data/Makefile.in b/gtfold-mfe/data/Makefile.in
index f591147..a245c3c 100644
--- a/gtfold-mfe/data/Makefile.in
+++ b/gtfold-mfe/data/Makefile.in
@@ -189,7 +189,7 @@ target_vendor = @target_vendor@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-SUBDIRS = UNAParams Turner04 Turner99 Andronescu 
+SUBDIRS = UNAParams RNAParams Turner04 Turner99 Andronescu 
 all: all-recursive
 
 .SUFFIXES:
diff --git a/gtfold-mfe/data/RNAParams/Makefile.am b/gtfold-mfe/data/RNAParams/Makefile.am
new file mode 100644
index 0000000..8655bda
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/Makefile.am
@@ -0,0 +1,23 @@
+## Process this file with automake to produce Makefile.in
+
+gtfold_datadir = $(datadir)/@PACKAGE@/RNAParams
+
+gtfold_data_DATA = \
+	stack.DAT\
+	miscloop.DAT\
+	dangle.DAT\
+	loop.DAT\
+	int11.DAT\
+	int21.DAT\
+	int22.DAT\
+	tloop.DAT\
+	tstackh.DAT\
+	tstacki.DAT\
+	tstacke.DAT\
+	tstackm.DAT
+
+
+EXTRA_DIST = $(gtfold_data_DATA)
+
+CLEANFILES = *~
+
diff --git a/gtfold-mfe/data/RNAParams/Makefile.in b/gtfold-mfe/data/RNAParams/Makefile.in
new file mode 100644
index 0000000..6f1691d
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/Makefile.in
@@ -0,0 +1,399 @@
+# Makefile.in generated by automake 1.11 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+target_triplet = @target@
+subdir = data/RNAParams
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/gtfold_config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+SOURCES =
+DIST_SOURCES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__installdirs = "$(DESTDIR)$(gtfold_datadir)"
+DATA = $(gtfold_data_DATA)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMTAR = @AMTAR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CXX = @CXX@
+CXXDEPMODE = @CXXDEPMODE@
+CXXFLAGS = @CXXFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+GREP = @GREP@
+INSTALL = @INSTALL@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+MKDIR_P = @MKDIR_P@
+OBJEXT = @OBJEXT@
+OPENMP_CFLAGS = @OPENMP_CFLAGS@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+VERSION = @VERSION@
+abs_builddir = @abs_builddir@
+abs_srcdir = @abs_srcdir@
+abs_top_builddir = @abs_top_builddir@
+abs_top_srcdir = @abs_top_srcdir@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_CXX = @ac_ct_CXX@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+builddir = @builddir@
+datadir = @datadir@
+datarootdir = @datarootdir@
+docdir = @docdir@
+dvidir = @dvidir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+htmldir = @htmldir@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localedir = @localedir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+pdfdir = @pdfdir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+psdir = @psdir@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+srcdir = @srcdir@
+sysconfdir = @sysconfdir@
+target = @target@
+target_alias = @target_alias@
+target_cpu = @target_cpu@
+target_os = @target_os@
+target_vendor = @target_vendor@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+gtfold_datadir = $(datadir)/@PACKAGE@/RNAParams
+gtfold_data_DATA = \
+	stack.DAT\
+	miscloop.DAT\
+	dangle.DAT\
+	loop.DAT\
+	int11.DAT\
+	int21.DAT\
+	int22.DAT\
+	tloop.DAT\
+	tstackh.DAT\
+	tstacki.DAT\
+	tstacke.DAT\
+	tstackm.DAT
+
+EXTRA_DIST = $(gtfold_data_DATA)
+CLEANFILES = *~
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/RNAParams/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu data/RNAParams/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-gtfold_dataDATA: $(gtfold_data_DATA)
+	@$(NORMAL_INSTALL)
+	test -z "$(gtfold_datadir)" || $(MKDIR_P) "$(DESTDIR)$(gtfold_datadir)"
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gtfold_datadir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(gtfold_datadir)" || exit $$?; \
+	done
+
+uninstall-gtfold_dataDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(gtfold_data_DATA)'; test -n "$(gtfold_datadir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(gtfold_datadir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(gtfold_datadir)" && rm -f $$files
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(DATA)
+installdirs:
+	for dir in "$(DESTDIR)$(gtfold_datadir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+	-test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am: install-gtfold_dataDATA
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-gtfold_dataDATA
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+	distclean-generic distdir dvi dvi-am html html-am info info-am \
+	install install-am install-data install-data-am install-dvi \
+	install-dvi-am install-exec install-exec-am \
+	install-gtfold_dataDATA install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+	pdf-am ps ps-am uninstall uninstall-am \
+	uninstall-gtfold_dataDATA
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/gtfold-mfe/data/RNAParams/dangle.DAT b/gtfold-mfe/data/RNAParams/dangle.DAT
new file mode 100644
index 0000000..9fb7c28
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/dangle.DAT
@@ -0,0 +1,8 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.80	-0.50	-0.80	-0.60
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.70	-0.80	-1.70	-1.20	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-1.10	-0.40	-1.30	-0.60	inf 	inf 	inf 	inf	-0.80	-0.50	-0.80	-0.60
+-0.70	-0.10	-0.70	-0.10	inf 	inf 	inf 	inf	-0.70	-0.10	-0.70	-0.10	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.30	-0.10	-0.20	-0.20
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.20	-0.30	-0.0	-0.0	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-0.50	-0.30	-0.20	-0.10	inf 	inf 	inf 	inf	-0.30	-0.10	-0.20	-0.20
+-0.30	-0.30	-0.40	-0.20	inf 	inf 	inf 	inf	-0.30	-0.30	-0.40	-0.20	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/RNAParams/int11.DAT b/gtfold-mfe/data/RNAParams/int11.DAT
new file mode 100644
index 0000000..96eabfd
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/int11.DAT
@@ -0,0 +1,24 @@
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.50	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.20	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.10	1.10	1.10	1.10	0.40	-0.40	0.40	0.40	1.10	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.30	0.50	0.40	0.50	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	-0.10	0.40	-1.70	0.40	0.40	0.40	-1.40	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.00	0.40	-0.30	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.80	0.40	0.40	0.40	0.40	0.30	-0.10	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	0.40	-0.40	0.50	0.40	0.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	0.40	0.40	-2.10	0.40	0.40	0.40	-1.70	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	-0.70	0.40	0.50	0.40	-0.30	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.80	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.50	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
diff --git a/gtfold-mfe/data/RNAParams/int21.DAT b/gtfold-mfe/data/RNAParams/int21.DAT
new file mode 100644
index 0000000..0dfe3c4
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/int21.DAT
@@ -0,0 +1,96 @@
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.20	3.00	2.40	4.80	2.30	2.20	1.10	4.00	2.40	2.20	1.60	4.00	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80
+3.10	3.00	4.80	3.00	2.30	2.20	4.00	2.20	2.30	2.20	4.00	2.20	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00
+2.50	4.80	1.60	4.80	1.70	4.00	0.80	4.00	1.70	4.00	0.80	4.00	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+2.90	2.50	2.40	4.80	2.10	1.70	1.60	4.00	2.10	1.70	1.60	4.00	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80
+3.00	3.30	4.80	3.00	2.20	2.50	4.00	2.20	2.20	2.50	4.00	2.20	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	3.00	4.80	2.10	4.00	2.20	4.00	1.50	4.00	2.20	4.00	1.30	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10
+1.80	1.40	1.20	4.80	0.80	0.60	0.40	4.00	1.00	0.60	0.40	4.00	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+1.60	4.80	3.00	4.80	0.80	4.00	2.20	4.00	0.80	4.00	2.20	4.00	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+3.30	2.70	4.80	3.00	2.50	1.90	4.00	2.20	2.50	1.90	4.00	2.20	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	2.50	4.80	2.00	4.00	1.70	4.00	1.20	4.00	1.70	4.00	1.20	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00
+3.20	3.00	2.40	4.80	2.40	2.20	1.60	4.00	2.50	2.20	2.10	4.00	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80
+3.10	3.00	4.80	3.00	2.30	2.20	4.00	2.20	2.30	2.20	4.00	2.20	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00
+2.50	4.80	1.60	4.80	1.70	4.00	0.80	4.00	1.70	4.00	0.80	4.00	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+2.90	2.50	2.40	4.80	2.10	1.70	1.60	4.00	2.10	1.70	1.60	4.00	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80
+3.00	3.30	4.80	3.00	2.20	2.50	4.00	2.20	2.20	2.50	4.00	2.20	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	3.00	4.80	2.10	4.00	2.20	4.00	1.30	4.00	2.20	4.00	1.20	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10
+1.80	1.40	1.20	4.80	1.00	0.60	0.40	4.00	1.20	0.60	0.40	4.00	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+1.60	4.80	3.00	4.80	0.80	4.00	2.20	4.00	0.80	4.00	2.20	4.00	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+3.30	2.70	4.80	3.00	2.50	1.90	4.00	2.20	2.50	1.90	4.00	2.20	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00
+4.80	4.80	4.80	4.80	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.00	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80
+4.80	2.50	4.80	2.00	4.00	1.70	4.00	1.20	4.00	1.70	4.00	1.20	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
+3.90	3.70	3.10	5.50	3.20	3.00	2.40	4.80	3.20	3.00	2.40	4.80	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50	3.90	3.70	3.10	5.50
+3.80	3.70	5.50	3.70	3.10	3.00	4.80	3.00	3.10	3.00	4.80	3.00	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70	3.80	3.70	5.50	3.70
+3.20	5.50	2.30	5.50	2.50	4.80	1.60	4.80	2.50	4.80	1.60	4.80	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50	3.20	5.50	2.30	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+3.60	3.20	3.10	5.50	2.90	2.50	2.40	4.80	2.90	2.50	2.40	4.80	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50	3.60	3.20	3.10	5.50
+3.70	4.00	5.50	3.70	3.00	3.30	4.80	3.00	3.00	3.30	4.80	3.00	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70	3.70	4.00	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.70	5.50	2.80	4.80	3.00	4.80	2.10	4.80	3.00	4.80	2.10	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80	5.50	3.70	5.50	2.80
+2.50	2.10	1.90	5.50	1.80	1.40	1.20	4.80	1.80	1.40	1.20	4.80	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50	2.50	2.10	1.90	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+2.30	5.50	3.70	5.50	1.60	4.80	3.00	4.80	1.60	4.80	3.00	4.80	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50	2.30	5.50	3.70	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+4.00	3.40	5.50	3.70	3.30	2.70	4.80	3.00	3.30	2.70	4.80	3.00	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70	4.00	3.40	5.50	3.70
+5.50	5.50	5.50	5.50	4.80	4.80	4.80	4.80	4.80	4.80	4.80	4.80	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50	5.50
+5.50	3.20	5.50	2.70	4.80	2.50	4.80	2.00	4.80	2.50	4.80	2.00	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70	5.50	3.20	5.50	2.70
diff --git a/gtfold-mfe/data/RNAParams/int22.DAT b/gtfold-mfe/data/RNAParams/int22.DAT
new file mode 100644
index 0000000..9691143
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/int22.DAT
@@ -0,0 +1,576 @@
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
+  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
+  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
+  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
+  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
+  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
+  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
+  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
+  0.50  1.10 -0.30  2.00  1.10  1.70  2.00  0.70  0.40  2.00  1.00  0.10  2.00  1.80 -0.50  1.50 
+  0.60  1.50  0.10  2.00  1.10  1.50  2.00  0.50  0.50  2.00  1.40 -0.70  2.00  1.50 -0.60  0.00 
+  0.00 -0.70 -1.60  2.00 -1.00 -0.60  2.00  0.20 -0.70  2.00  0.00 -0.80  2.00  1.20 -0.60  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.00 -0.70  2.00  1.00  1.00  2.00  0.00  0.70  2.00  0.90 -1.90  2.00  1.10 -1.50 -0.20 
+  2.20  1.30  0.70  2.00  1.90  1.30  2.00  0.30  0.70  2.00  1.80 -0.30  2.00  1.40 -0.20 -0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.00  1.20  0.40  2.00  1.10  1.20  2.00  1.70  1.00  2.00  1.70 -0.70  2.00  1.20 -0.30  0.20 
+ -0.20 -0.40 -1.70  2.00  0.70  1.10  2.00  0.20 -0.50  2.00  0.00 -0.90  2.00  1.20 -1.30  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
+  0.90  0.00  0.30  2.00 -0.10  1.00  2.00  0.00  0.60  2.00  0.90 -3.00  2.00  1.00 -2.40  0.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.00  1.20  0.40  2.00  1.10  1.20  2.00  0.20  0.50  2.00  1.70 -0.70  2.00  1.20 -0.10  0.40 
+ -0.10 -1.60 -1.60  2.00 -1.60 -0.60  2.00 -1.60 -0.60  2.00 -0.70 -4.40  2.00 -0.50 -4.10 -1.00 
+  1.40  0.30  0.50  2.00  0.30  0.30  2.00  0.10  1.40  2.00  1.20 -1.00  2.00  0.30  0.10  0.60 
+  1.30  1.20  0.30  2.00  1.60  2.10  2.00  1.90  0.30  2.00  1.00 -0.40  2.00  1.90  1.10  1.40 
+  1.60  1.50  0.60  2.00  2.00  1.80  2.00  1.70  0.60  2.00  1.40 -1.10  2.00  1.70  0.40  0.80 
+  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.20  1.10  0.20  2.00  1.50  1.40  2.00  1.20  0.20  2.00  0.90 -1.50  2.00  1.20  0.00  0.30 
+  2.10  1.40  1.50  2.00  1.80  1.70  2.00  1.50  1.50  2.00  1.80 -0.20  2.00  1.50  1.30  0.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
+  0.30  0.20 -0.70  2.00  0.60  1.50  2.00  1.30 -0.70  2.00  0.00 -0.60  2.00  1.30  0.90  1.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
+  1.10  0.00  0.90  2.00  0.40  1.30  2.00  1.10  0.90  2.00  0.90 -2.60  2.00  1.10 -1.10  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.20  1.30  2.00  1.70  1.50  2.00  1.40  1.30  2.00  1.70 -0.40  2.00  1.40  1.10  0.50 
+ -0.40 -1.50 -0.60  2.00 -1.10 -0.20  2.00 -0.40 -0.60  2.00 -0.70 -4.20  2.00 -0.40 -2.60 -0.50 
+  1.40  0.30  1.30  2.00  0.80  0.60  2.00  0.50  1.30  2.00  1.20 -0.50  2.00  0.50  1.10 -0.40 
+  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
+  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
+  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
+  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
+  2.00  1.60  1.00  2.00  2.00  2.60  2.00  2.60  1.00  2.00  1.40  0.20  2.00  2.30  1.50  2.20 
+  2.40  1.90  1.30  2.00  2.40  2.40  2.00  2.40  1.30  2.00  1.70 -0.40  2.00  2.10  0.80  1.50 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.50  0.90  2.00  1.90  1.90  2.00  1.90  0.90  2.00  1.30 -0.90  2.00  1.60  0.40  1.10 
+  2.80  1.80  2.20  2.00  2.20  2.20  2.00  2.20  2.20  2.00  2.20  0.40  2.00  1.90  1.70  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  1.00  0.60  0.00  2.00  1.00  2.00  2.00  2.00  0.00  2.00  0.40  0.00  2.00  1.70  1.30  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  1.80  0.40  1.60  2.00  0.80  1.80  2.00  1.80  1.60  2.00  1.20 -2.00  2.00  1.50 -0.70  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.60  2.00  2.00  2.10  2.10  2.00  2.10  2.00  2.00  2.00  0.30  2.00  1.80  1.50  1.20 
+  0.30 -1.10  0.10  2.00 -0.70  0.30  2.00  0.30  0.10  2.00 -0.30 -3.50  2.00  0.00 -2.20  0.30 
+  2.20  0.70  1.90  2.00  1.20  1.20  2.00  1.20  1.90  2.00  1.50  0.20  2.00  0.90  1.50  0.30 
+  2.00  1.80  0.80  2.00  1.90  2.30  2.00  2.30  0.80  2.00  1.30  0.60  2.00  2.30  1.60  1.90 
+  2.40  2.10  1.10  2.00  2.20  2.10  2.00  2.10  1.10  2.00  1.70  0.00  2.00  2.10  0.90  1.30 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.70  0.70  2.00  1.80  1.60  2.00  1.60  0.70  2.00  1.20 -0.50  2.00  1.60  0.50  0.80 
+  2.80  2.00  2.00  2.00  2.10  1.90  2.00  1.90  2.00  2.00  2.10  0.80  2.00  1.90  1.80  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  1.00  0.80 -0.20  2.00  0.90  1.70  2.00  1.70 -0.20  2.00  0.30  0.40  2.00  1.70  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  1.80  0.60  1.40  2.00  0.70  1.50  2.00  1.50  1.40  2.00  1.10 -1.60  2.00  1.50 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.80  1.80  2.00  1.90  1.80  2.00  1.80  1.80  2.00  2.00  0.70  2.00  1.80  1.60  1.00 
+  0.30 -0.90 -0.10  2.00 -0.80  0.00  2.00  0.00 -0.10  2.00 -0.40 -3.10  2.00  0.00 -2.10  0.00 
+  2.20  0.90  1.80  2.00  1.00  0.90  2.00  0.90  1.80  2.00  1.50  0.60  2.00  0.90  1.60  0.10 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
+  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
+  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
+  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
+  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
+  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.20  0.90 -0.80  2.00  0.90  0.90  2.00  0.00 -0.20  2.00  0.80 -2.00  2.00  1.00 -1.60  0.20 
+  0.10 -0.10 -1.90  2.00 -0.20  0.90  2.00 -0.10 -1.30  2.00 -0.20 -1.30  2.00  0.90 -0.90  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.20  1.00 -0.80  2.00  0.90  1.00  2.00  0.00 -0.10  2.00  0.90 -1.90  2.00  1.00 -1.50  0.20 
+  1.80  1.00  0.20  2.00  0.90  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.00 -0.50  0.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.00  0.30  2.00  1.00  1.00  2.00  0.00  0.90  2.00  1.50 -0.90  2.00  1.10 -0.50  0.30 
+ -0.50 -0.80 -2.60  2.00 -0.80  0.20  2.00 -0.80 -1.90  2.00 -0.90 -1.90  2.00  0.30 -1.50  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  0.90 -0.90  2.00  0.80  1.50  2.00  0.50 -0.20  2.00  0.80 -1.00  2.00  1.50 -0.60  1.10 
+ -0.30 -1.50 -1.50  2.00 -1.60 -0.50  2.00 -1.50 -0.90  2.00 -0.60 -4.50  2.00 -0.50 -4.10 -0.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  0.80  0.00 -0.80  2.00  0.00  0.00  2.00 -1.00 -0.10  2.00  0.50 -1.90  2.00  0.00 -1.50 -0.70 
+ -0.70 -1.90 -1.90  2.00 -2.00 -0.90  2.00 -1.90 -1.30  2.00 -1.00 -4.90  2.00 -0.90 -4.50 -0.90 
+  1.50  0.20  0.30  2.00  0.20  0.20  2.00 -0.70  0.90  2.00  1.10 -0.90  2.00  0.30 -0.50 -0.50 
+  0.50  1.30 -0.20  2.00  0.60  2.20  2.00  2.00  0.00  2.00  1.10 -0.10  2.00  2.00  0.90  1.40 
+  1.10  1.00  0.70  2.00  1.10  1.90  2.00  1.10 -1.00  2.00  0.80 -1.60  2.00  1.10 -0.10  0.30 
+  0.40  0.70 -0.50  2.00  0.50  0.70  2.00  0.50 -0.70  2.00 -0.20 -0.60  2.00  1.00  0.60  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.10  1.00 -0.40  2.00  1.50  1.30  2.00  1.20 -0.70  2.00  0.90 -1.60  2.00  1.20  0.00  0.30 
+  1.70  1.00  1.10  2.00  1.50  1.30  2.00  1.20 -0.60  2.00  1.50 -0.60  2.00  1.20  1.00  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.10  1.20  2.00  1.50  1.40  2.00  1.20  1.20  2.00  1.50 -0.50  2.00  1.20  1.00  0.30 
+ -0.30 -0.70 -1.70  2.00  0.10  0.70  2.00  0.40 -1.60  2.00 -0.90 -1.60  2.00  0.40  0.30  0.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.00  0.90  0.00  2.00  1.40  1.80  2.00  1.70  0.00  2.00  0.80 -0.70  2.00  1.70  0.90  1.20 
+ -0.50 -1.50 -1.30  2.00 -0.60 -0.20  2.00 -0.10 -0.60  2.00 -0.60 -4.10  2.00 -0.30 -2.40  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  0.70  0.00  0.20  2.00  0.50  0.30  2.00  0.20  0.20  2.00  0.50 -1.60  2.00  1.70  0.00  0.10 
+  0.10 -1.90 -0.90  2.00 -0.70 -0.30  2.00 -0.70 -0.80  2.00 -1.00 -4.40  2.00 -0.70 -3.00 -1.00 
+  1.50 -0.20  0.90  2.00  0.00 -0.10  2.00  0.40  0.90  2.00  1.10 -1.00  2.00  0.20  0.60  0.60 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
+  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
+  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
+  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
+  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
+  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  1.80  1.40  0.80  2.00  1.80  1.80  2.00  1.80  0.80  2.00  1.20 -1.00  2.00  1.50  0.30  1.00 
+  0.70  0.30 -0.30  2.00  0.70  1.70  2.00  1.70 -0.30  2.00  0.10 -0.30  2.00  1.40  1.00  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.40  0.80  2.00  1.90  1.90  2.00  1.90  0.80  2.00  1.20 -0.90  2.00  1.60  0.30  1.00 
+  2.50  1.40  1.80  2.00  1.90  1.90  2.00  1.90  1.80  2.00  1.80  0.10  2.00  1.60  1.30  1.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.50  1.90  2.00  1.90  1.90  2.00  1.90  1.90  2.00  1.90  0.10  2.00  1.60  1.40  1.10 
+  0.10 -0.30 -0.90  2.00  0.10  1.10  2.00  1.10 -0.90  2.00 -0.50 -0.90  2.00  0.80  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.30  0.70  2.00  1.80  2.40  2.00  2.40  0.70  2.00  1.10  0.00  2.00  2.10  1.20  1.90 
+  0.40 -1.10  0.10  2.00 -0.60  0.40  2.00  0.40  0.10  2.00 -0.30 -3.50  2.00  0.10 -2.20  0.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.40  0.90  2.00  0.90  0.90  2.00  0.90  0.90  2.00  0.80 -0.90  2.00  0.60  0.40  0.00 
+  0.00 -1.50 -0.30  2.00 -1.00  0.00  2.00  0.00 -0.30  2.00 -0.70 -3.90  2.00 -0.30 -2.60 -0.10 
+  2.10  0.70  1.90  2.00  1.10  1.10  2.00  1.10  1.90  2.00  1.50  0.10  2.00  0.80  1.40  0.30 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  1.80  1.60  0.60  2.00  1.70  1.50  2.00  1.50  0.60  2.00  1.10 -0.60  2.00  1.50  0.40  0.70 
+  0.70  0.50 -0.50  2.00  0.60  1.40  2.00  1.40 -0.50  2.00  0.00  0.10  2.00  1.40  1.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60  0.60  2.00  1.70  1.60  2.00  1.60  0.60  2.00  1.20 -0.50  2.00  1.60  0.40  0.80 
+  2.50  1.60  1.60  2.00  1.70  1.60  2.00  1.60  1.60  2.00  1.80  0.50  2.00  1.60  1.40  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  1.70  1.70  2.00  1.80  1.60  2.00  1.60  1.70  2.00  1.80  0.50  2.00  1.60  1.50  0.80 
+  0.10 -0.10 -1.10  2.00  0.00  0.80  2.00  0.80 -1.10  2.00 -0.60 -0.50  2.00  0.80  0.50  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.50  0.50  2.00  1.60  2.10  2.00  2.10  0.50  2.00  1.10  0.40  2.00  2.10  1.30  1.70 
+  0.40 -0.90 -0.10  2.00 -0.80  0.10  2.00  0.10 -0.10  2.00 -0.30 -3.10  2.00  0.10 -2.10  0.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  0.60  0.70  2.00  0.70  0.60  2.00  0.60  0.70  2.00  0.80 -0.50  2.00  0.60  0.50 -0.20 
+  0.00 -1.30 -0.50  2.00 -1.20 -0.30  2.00 -0.30 -0.50  2.00 -0.70 -3.50  2.00 -0.30 -2.50 -0.30 
+  2.10  0.90  1.70  2.00  1.00  0.80  2.00  0.80  1.70  2.00  1.40  0.50  2.00  0.80  1.50  0.00 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
+  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
+  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
+  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.00  1.70  0.00  2.00  1.70  1.70  2.00  0.70  0.60  2.00  1.60 -1.20  2.00  1.80 -0.80  1.00 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.90  1.60 -0.10  2.00  1.60  1.60  2.00  0.60  0.50  2.00  1.50 -1.30  2.00  1.70 -0.90  0.90 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.90  0.60 -1.10  2.00  0.60  1.60  2.00  0.70 -0.50  2.00  0.50 -0.50  2.00  1.70 -0.10  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.20 -0.60  2.00  1.10  1.80  2.00  0.80  0.00  2.00  1.10 -0.70  2.00  1.80 -0.30  1.40 
+  1.70  0.40  0.50  2.00  0.40  1.40  2.00  0.50  1.10  2.00  1.30 -2.50  2.00  1.50 -2.10  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  0.70 -0.50 -0.50  2.00 -0.60  0.50  2.00 -0.50  0.10  2.00  0.40 -3.50  2.00  0.50 -3.10  0.50 
+  2.00  0.80  0.80  2.00  0.70  0.80  2.00 -0.20  1.50  2.00  1.70 -0.30  2.00  0.80  0.10  0.00 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  1.90  1.80  0.90  2.00  2.20  2.10  2.00  1.90  0.90  2.00  1.60 -0.80  2.00  1.90  0.70  1.00 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.80  1.70  0.80  2.00  2.10  2.00  2.00  1.80  0.80  2.00  1.50 -0.90  2.00  1.80  0.60  0.90 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.80  0.70 -0.20  2.00  1.10  2.00  2.00  1.80 -0.20  2.00  0.50 -0.10  2.00  1.80  1.40  1.80 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.30  1.20  0.30  2.00  1.70  2.10  2.00  2.00  0.30  2.00  1.10 -0.40  2.00  2.00  1.10  1.50 
+  1.60  0.50  1.40  2.00  0.90  1.80  2.00  1.60  1.40  2.00  1.30 -2.10  2.00  1.60 -0.60  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  0.60 -0.50  0.40  2.00  0.00  0.80  2.00  0.70  0.40  2.00  0.40 -3.10  2.00  0.70 -1.60  0.60 
+  1.90  0.80  1.80  2.00  1.30  1.10  2.00  1.00  1.80  2.00  1.70  0.00  2.00  1.00  1.60  0.10 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.60  2.20  1.60  2.00  2.60  2.60  2.00  2.60  1.60  2.00  2.00 -0.20  2.00  2.30  1.10  1.80 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.10  1.50  2.00  2.50  2.50  2.00  2.50  1.50  2.00  1.90 -0.30  2.00  2.20  1.00  1.70 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.50  1.10  0.50  2.00  1.50  2.50  2.00  2.50  0.50  2.00  0.90  0.50  2.00  2.20  1.80  2.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.60  1.00  2.00  2.10  2.70  2.00  2.70  1.00  2.00  1.40  0.30  2.00  2.40  1.50  2.20 
+  2.30  0.90  2.10  2.00  1.30  2.30  2.00  2.30  2.10  2.00  1.70 -1.50  2.00  2.00 -0.20  2.30 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.30 -0.10  1.10  2.00  0.30  1.30  2.00  1.30  1.10  2.00  0.70 -2.50  2.00  1.00 -1.20  1.30 
+  2.70  1.20  2.40  2.00  1.70  1.70  2.00  1.70  2.40  2.00  2.00  0.70  2.00  1.40  1.90  0.80 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.60  2.40  1.40  2.00  2.50  2.30  2.00  2.30  1.40  2.00  1.90  0.20  2.00  2.30  1.20  1.50 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.50  2.30  1.30  2.00  2.40  2.20  2.00  2.20  1.30  2.00  1.80  0.10  2.00  2.20  1.10  1.40 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.50  1.30  0.30  2.00  1.40  2.20  2.00  2.20  0.30  2.00  0.80  0.90  2.00  2.20  1.90  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.80  0.80  2.00  1.90  2.40  2.00  2.40  0.80  2.00  1.40  0.70  2.00  2.40  1.60  2.00 
+  2.30  1.10  1.90  2.00  1.20  2.00  2.00  2.00  1.90  2.00  1.60 -1.10  2.00  2.00 -0.10  2.00 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.30  0.10  0.90  2.00  0.20  1.00  2.00  1.00  0.90  2.00  0.70 -2.10  2.00  1.00 -1.10  1.10 
+  2.70  1.40  2.20  2.00  1.50  1.40  2.00  1.40  2.20  2.00  2.00  1.10  2.00  1.40  2.00  0.60 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+  2.10  1.90  0.10  2.00  1.80  2.50  2.00  1.50  0.70  2.00  1.80  0.00  2.00  2.50  0.40  2.10 
+  2.10  1.90  0.10  2.00  1.80  1.90  2.00  0.90  0.70  2.00  1.80 -1.00  2.00  1.90 -0.60  1.10 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.70  1.40 -0.30  2.00  1.40  1.40  2.00  0.40  0.30  2.00  1.30 -1.50  2.00  1.50 -1.10  0.70 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.40  1.60  0.80  2.00  1.50  1.60  2.00  0.60  1.40  2.00  2.10 -0.30  2.00  1.60  0.10  0.80 
+  1.10  0.80 -0.90  2.00  0.80  1.80  2.00  0.90 -0.30  2.00  0.70 -0.30  2.00  1.90  0.10  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.50  1.20 -0.50  2.00  1.20  1.80  2.00  0.80  0.10  2.00  1.10 -0.70  2.00  1.90 -0.30  1.50 
+  1.60  0.30  0.40  2.00  0.30  1.30  2.00  0.40  1.00  2.00  1.20 -2.60  2.00  1.40 -2.20  1.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.70  1.90  1.10  2.00  1.80  1.90  2.00  0.90  1.70  2.00  2.40  0.00  2.00  1.90  0.40  1.10 
+  0.30 -0.90 -0.90  2.00 -1.00  0.10  2.00 -0.90 -0.30  2.00  0.00 -3.90  2.00  0.10 -3.50  0.10 
+  2.30  1.00  1.10  2.00  1.00  1.00  2.00  0.00  1.70  2.00  1.90 -0.10  2.00  1.10  0.30  0.30 
+  2.00  1.90  1.00  2.00  2.40  2.80  2.00  2.70  1.00  2.00  1.80  0.30  2.00  2.70  1.80  2.20 
+  2.00  1.90  1.00  2.00  2.40  2.20  2.00  2.10  1.00  2.00  1.80 -0.70  2.00  2.10  0.80  1.20 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.60  1.50  0.60  2.00  1.90  1.80  2.00  1.60  0.60  2.00  1.30 -1.10  2.00  1.60  0.40  0.70 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.60  1.70  2.00  2.10  1.90  2.00  1.80  1.70  2.00  2.10  0.00  2.00  1.80  1.50  0.90 
+  1.00  0.90  0.00  2.00  1.30  2.20  2.00  2.00  0.00  2.00  0.70  0.10  2.00  2.00  1.60  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  1.40  1.30  0.40  2.00  1.70  2.20  2.00  2.00  0.40  2.00  1.10 -0.30  2.00  2.00  1.20  1.50 
+  1.50  0.40  1.30  2.00  0.80  1.70  2.00  1.50  1.30  2.00  1.20 -2.20  2.00  1.50 -0.70  1.50 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.60  1.90  2.00  2.00  2.40  2.20  2.00  2.10  2.00  2.00  2.40  0.30  2.00  2.10  1.80  1.20 
+  0.20 -0.90  0.00  2.00 -0.40  0.40  2.00  0.30  0.00  2.00  0.00 -3.50  2.00  0.30 -2.00  0.20 
+  2.20  1.10  2.00  2.00  1.50  1.40  2.00  1.20  2.00  2.00  1.90  0.30  2.00  1.20  1.80  0.30 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80 
+  2.80  2.30  1.70  2.00  2.80  3.40  2.00  3.40  1.70  2.00  2.10  1.00  2.00  3.10  2.20  2.90 
+  2.80  2.30  1.70  2.00  2.80  2.80  2.00  2.80  1.70  2.00  2.10  0.00  2.00  2.50  1.20  1.90 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  1.90  1.30  2.00  2.30  2.30  2.00  2.30  1.30  2.00  1.70 -0.50  2.00  2.00  0.80  1.50 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.00  2.40  2.00  2.50  2.50  2.00  2.50  2.40  2.00  2.40  0.70  2.00  2.20  1.90  1.60 
+  1.70  1.30  0.70  2.00  1.70  2.70  2.00  2.70  0.70  2.00  1.10  0.70  2.00  2.40  2.00  2.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.70  1.10  2.00  2.10  2.70  2.00  2.70  1.10  2.00  1.50  0.30  2.00  2.40  1.60  2.30 
+  2.20  0.80  2.00  2.00  1.20  2.20  2.00  2.20  2.00  2.00  1.60 -1.60  2.00  1.90 -0.30  2.20 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.30  2.70  2.00  2.80  2.80  2.00  2.80  2.70  2.00  2.70  1.00  2.00  2.50  2.20  1.90 
+  1.00 -0.50  0.70  2.00  0.00  1.00  2.00  1.00  0.70  2.00  0.30 -2.90  2.00  0.70 -1.60  0.90 
+  2.90  1.50  2.70  2.00  1.90  1.90  2.00  1.90  2.70  2.00  2.30  0.90  2.00  1.60  2.20  1.10 
+  2.80  2.50  1.50  2.00  2.60  3.10  2.00  3.10  1.50  2.00  2.10  1.30  2.00  3.10  2.30  2.70 
+  2.80  2.50  1.50  2.00  2.60  2.50  2.00  2.50  1.50  2.00  2.10  0.30  2.00  2.50  1.30  1.70 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.30  2.10  1.10  2.00  2.20  2.00  2.00  2.00  1.10  2.00  1.60 -0.10  2.00  2.00  0.90  1.20 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.10  2.20  2.20  2.00  2.30  2.20  2.00  2.20  2.20  2.00  2.40  1.00  2.00  2.20  2.00  1.40 
+  1.70  1.50  0.50  2.00  1.60  2.40  2.00  2.40  0.50  2.00  1.00  1.10  2.00  2.40  2.10  2.40 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  2.10  1.90  0.90  2.00  2.00  2.40  2.00  2.40  0.90  2.00  1.40  0.70  2.00  2.40  1.70  2.00 
+  2.20  1.00  1.80  2.00  1.10  1.90  2.00  1.90  1.80  2.00  1.50 -1.20  2.00  1.90 -0.20  1.90 
+  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00 
+  3.40  2.50  2.50  2.00  2.60  2.50  2.00  2.50  2.50  2.00  2.70  1.30  2.00  2.50  2.30  1.70 
+  1.00 -0.30  0.50  2.00 -0.20  0.70  2.00  0.70  0.50  2.00  0.30 -2.50  2.00  0.70 -1.50  0.70 
+  2.90  1.70  2.50  2.00  1.80  1.60  2.00  1.60  2.50  2.00  2.20  1.30  2.00  1.60  2.30  0.80
diff --git a/gtfold-mfe/data/RNAParams/loop.DAT b/gtfold-mfe/data/RNAParams/loop.DAT
new file mode 100644
index 0000000..98c1285
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/loop.DAT
@@ -0,0 +1,30 @@
+1	inf		3.80	inf
+2	4.10	2.80	inf
+3	5.10	3.20	5.70
+4	1.70	3.60	5.60
+5	1.80	4.00	5.60
+6	2.00	4.40	5.40
+7	2.20	4.59	5.90
+8	2.30	4.70	5.60
+9	2.40	4.80	6.40
+10	2.50	4.90	6.50
+11	2.60	5.00	6.60
+12	2.70	5.10	6.70
+13	2.78	5.19	6.78
+14	2.86	5.27	6.86
+15	2.94	5.34	6.94
+16	3.01	5.41	7.01
+17	3.07	5.48	7.07
+18	3.13	5.54	7.13
+19	3.19	5.60	7.19
+20	3.25	5.65	7.25
+21	3.30	5.71	7.30
+22	3.35	5.76	7.35
+23	3.40	5.80	7.40
+24	3.45	5.85	7.44
+25	3.49	5.89	7.49
+26	3.53	5.94	7.53
+27	3.57	5.98	7.57
+28	3.61	6.02	7.61
+29	3.65	6.05	7.65
+30	3.69	6.09	7.69
diff --git a/gtfold-mfe/data/RNAParams/miscloop.DAT b/gtfold-mfe/data/RNAParams/miscloop.DAT
new file mode 100644
index 0000000..3c000a5
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/miscloop.DAT
@@ -0,0 +1,12 @@
+1.079
+3.00
+.50	.50	.50	.50
+3.40	.00	.40
+10.10	-0.30	-0.30
+0.50
+0.0
+0.30
+1.60
+1.40
+4.10
+0
diff --git a/gtfold-mfe/data/RNAParams/sint2.DAT b/gtfold-mfe/data/RNAParams/sint2.DAT
new file mode 100644
index 0000000..96eabfd
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/sint2.DAT
@@ -0,0 +1,24 @@
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.50	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.20	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.10	1.10	1.10	1.10	0.40	-0.40	0.40	0.40	1.10	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.30	0.50	0.40	0.50	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	-0.10	0.40	-1.70	0.40	0.40	0.40	-1.40	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.00	0.40	-0.30	0.40	0.40	0.40	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.80	0.40	0.40	0.40	0.40	0.30	-0.10	0.40	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	0.40	-0.40	0.50	0.40	0.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.10	1.10	-1.00	1.10	0.40	0.40	-2.10	0.40	0.40	0.40	-1.70	0.40	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10
+1.10	1.10	1.10	1.10	0.40	0.40	0.40	-0.70	0.40	0.50	0.40	-0.30	1.10	1.10	1.10	1.00	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.80	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.50	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
+1.70	1.70	-0.40	1.70	1.10	1.10	-1.00	1.10	1.10	1.10	-1.00	1.10	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70	1.70	1.70	-0.40	1.70
+1.70	1.70	1.70	1.70	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.10	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70	1.70
diff --git a/gtfold-mfe/data/RNAParams/sint4.DAT b/gtfold-mfe/data/RNAParams/sint4.DAT
new file mode 100644
index 0000000..c878345
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/sint4.DAT
@@ -0,0 +1,576 @@
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.00	1.70	0.00	2.00	1.70	1.70	2.00	0.70	0.60	2.00	1.60	-1.20	2.00	1.80	-0.80	1.00
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	-0.10	2.00	1.60	1.60	2.00	0.60	0.50	2.00	1.50	-1.30	2.00	1.70	-0.90	0.90
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.20	-0.60	2.00	1.10	1.80	2.00	0.80	0.00	2.00	1.10	-0.70	2.00	1.80	-0.30	1.40
+1.70	0.40	0.50	2.00	0.40	1.40	2.00	0.50	1.10	2.00	1.30	-2.50	2.00	1.50	-2.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.70	-0.50	-0.50	2.00	-0.60	0.50	2.00	-0.50	0.10	2.00	0.40	-3.50	2.00	0.50	-3.10	0.50
+2.00	0.80	0.80	2.00	0.70	0.80	2.00	-0.20	1.50	2.00	1.70	-0.30	2.00	0.80	0.10	0.00
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+1.90	1.80	0.90	2.00	2.20	2.10	2.00	1.90	0.90	2.00	1.60	-0.80	2.00	1.90	0.70	1.00
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.70	0.80	2.00	2.10	2.00	2.00	1.80	0.80	2.00	1.50	-0.90	2.00	1.80	0.60	0.90
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.30	1.20	0.30	2.00	1.70	2.10	2.00	2.00	0.30	2.00	1.10	-0.40	2.00	2.00	1.10	1.50
+1.60	0.50	1.40	2.00	0.90	1.80	2.00	1.60	1.40	2.00	1.30	-2.10	2.00	1.60	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.60	-0.50	0.40	2.00	0.00	0.80	2.00	0.70	0.40	2.00	0.40	-3.10	2.00	0.70	-1.60	0.60
+1.90	0.80	1.80	2.00	1.30	1.10	2.00	1.00	1.80	2.00	1.70	0.00	2.00	1.00	1.60	0.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.00	1.60	1.00	2.00	2.00	2.60	2.00	2.60	1.00	2.00	1.40	0.20	2.00	2.30	1.50	2.20
+2.40	1.90	1.30	2.00	2.40	2.40	2.00	2.40	1.30	2.00	1.70	-0.40	2.00	2.10	0.80	1.50
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.50	0.90	2.00	1.90	1.90	2.00	1.90	0.90	2.00	1.30	-0.90	2.00	1.60	0.40	1.10
+2.80	1.80	2.20	2.00	2.20	2.20	2.00	2.20	2.20	2.00	2.20	0.40	2.00	1.90	1.70	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+1.80	0.40	1.60	2.00	0.80	1.80	2.00	1.80	1.60	2.00	1.20	-2.00	2.00	1.50	-0.70	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+0.30	-1.10	0.10	2.00	-0.70	0.30	2.00	0.30	0.10	2.00	-0.30	-3.50	2.00	0.00	-2.20	0.30
+2.20	0.70	1.90	2.00	1.20	1.20	2.00	1.20	1.90	2.00	1.50	0.20	2.00	0.90	1.50	0.30
+0.50	1.10	-0.30	2.00	1.10	1.70	2.00	0.70	0.40	2.00	1.00	0.10	2.00	1.80	-0.50	1.50
+0.60	1.50	0.10	2.00	1.10	1.50	2.00	0.50	0.50	2.00	1.40	-0.70	2.00	1.50	-0.60	0.00
+0.00	-0.70	-1.60	2.00	-1.00	-0.60	2.00	0.20	-0.70	2.00	0.00	-0.80	2.00	1.20	-0.60	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.30	1.00	-0.70	2.00	1.00	1.00	2.00	0.00	0.70	2.00	0.90	-1.90	2.00	1.10	-1.50	-0.20
+2.20	1.30	0.70	2.00	1.90	1.30	2.00	0.30	0.70	2.00	1.80	-0.30	2.00	1.40	-0.20	-0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.00	1.20	0.40	2.00	1.10	1.20	2.00	1.70	1.00	2.00	1.70	-0.70	2.00	1.20	-0.30	0.20
+-0.20	-0.40	-1.70	2.00	0.70	1.10	2.00	0.20	-0.50	2.00	0.00	-0.90	2.00	1.20	-1.30	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.10	0.90	-0.90	2.00	0.80	1.50	2.00	0.50	-0.20	2.00	0.80	-1.00	2.00	1.50	-0.60	1.10
+0.90	0.00	0.30	2.00	-0.10	1.00	2.00	0.00	0.60	2.00	0.90	-3.00	2.00	1.00	-2.40	0.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.00	1.20	0.40	2.00	1.10	1.20	2.00	0.20	0.50	2.00	1.70	-0.70	2.00	1.20	-0.10	0.40
+-0.10	-1.60	-1.60	2.00	-1.60	-0.60	2.00	-1.60	-0.60	2.00	-0.70	-4.40	2.00	-0.50	-4.10	-1.00
+1.40	0.30	0.50	2.00	0.30	0.30	2.00	0.10	1.40	2.00	1.20	-1.00	2.00	0.30	0.10	0.60
+1.30	1.20	0.30	2.00	1.60	2.10	2.00	1.90	0.30	2.00	1.00	-0.40	2.00	1.90	1.10	1.40
+1.60	1.50	0.60	2.00	2.00	1.80	2.00	1.70	0.60	2.00	1.40	-1.10	2.00	1.70	0.40	0.80
+0.30	0.20	-0.70	2.00	0.60	1.50	2.00	1.30	-0.70	2.00	0.00	-0.60	2.00	1.30	0.90	1.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.20	1.10	0.20	2.00	1.50	1.40	2.00	1.20	0.20	2.00	0.90	-1.50	2.00	1.20	0.00	0.30
+2.10	1.40	1.50	2.00	1.80	1.70	2.00	1.50	1.50	2.00	1.80	-0.20	2.00	1.50	1.30	0.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.20	1.30	2.00	1.70	1.50	2.00	1.40	1.30	2.00	1.70	-0.40	2.00	1.40	1.10	0.50
+0.30	0.20	-0.70	2.00	0.60	1.50	2.00	1.30	-0.70	2.00	0.00	-0.60	2.00	1.30	0.90	1.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.00	0.90	0.00	2.00	1.40	1.80	2.00	1.70	0.00	2.00	0.80	-0.70	2.00	1.70	0.90	1.20
+1.10	0.00	0.90	2.00	0.40	1.30	2.00	1.10	0.90	2.00	0.90	-2.60	2.00	1.10	-1.10	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.20	1.30	2.00	1.70	1.50	2.00	1.40	1.30	2.00	1.70	-0.40	2.00	1.40	1.10	0.50
+-0.40	-1.50	-0.60	2.00	-1.10	-0.20	2.00	-0.40	-0.60	2.00	-0.70	-4.20	2.00	-0.40	-2.60	-0.50
+1.40	0.30	1.30	2.00	0.80	0.60	2.00	0.50	1.30	2.00	1.20	-0.50	2.00	0.50	1.10	-0.40
+2.00	1.80	0.80	2.00	1.90	2.30	2.00	2.30	0.80	2.00	1.30	0.60	2.00	2.30	1.60	1.90
+2.40	2.10	1.10	2.00	2.20	2.10	2.00	2.10	1.10	2.00	1.70	0.00	2.00	2.10	0.90	1.30
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.70	0.70	2.00	1.80	1.60	2.00	1.60	0.70	2.00	1.20	-0.50	2.00	1.60	0.50	0.80
+2.80	2.00	2.00	2.00	2.10	1.90	2.00	1.90	2.00	2.00	2.10	0.80	2.00	1.90	1.80	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+1.80	0.60	1.40	2.00	0.70	1.50	2.00	1.50	1.40	2.00	1.10	-1.60	2.00	1.50	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+0.30	-0.90	-0.10	2.00	-0.80	0.00	2.00	0.00	-0.10	2.00	-0.40	-3.10	2.00	0.00	-2.10	0.00
+2.20	0.90	1.80	2.00	1.00	0.90	2.00	0.90	1.80	2.00	1.50	0.60	2.00	0.90	1.60	0.10
+2.00	1.60	1.00	2.00	2.00	2.60	2.00	2.60	1.00	2.00	1.40	0.20	2.00	2.30	1.50	2.20
+2.40	1.90	1.30	2.00	2.40	2.40	2.00	2.40	1.30	2.00	1.70	-0.40	2.00	2.10	0.80	1.50
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.50	0.90	2.00	1.90	1.90	2.00	1.90	0.90	2.00	1.30	-0.90	2.00	1.60	0.40	1.10
+2.80	1.80	2.20	2.00	2.20	2.20	2.00	2.20	2.20	2.00	2.20	0.40	2.00	1.90	1.70	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+1.00	0.60	0.00	2.00	1.00	2.00	2.00	2.00	0.00	2.00	0.40	0.00	2.00	1.70	1.30	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+1.80	0.40	1.60	2.00	0.80	1.80	2.00	1.80	1.60	2.00	1.20	-2.00	2.00	1.50	-0.70	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.60	2.00	2.00	2.10	2.10	2.00	2.10	2.00	2.00	2.00	0.30	2.00	1.80	1.50	1.20
+0.30	-1.10	0.10	2.00	-0.70	0.30	2.00	0.30	0.10	2.00	-0.30	-3.50	2.00	0.00	-2.20	0.30
+2.20	0.70	1.90	2.00	1.20	1.20	2.00	1.20	1.90	2.00	1.50	0.20	2.00	0.90	1.50	0.30
+2.00	1.80	0.80	2.00	1.90	2.30	2.00	2.30	0.80	2.00	1.30	0.60	2.00	2.30	1.60	1.90
+2.40	2.10	1.10	2.00	2.20	2.10	2.00	2.10	1.10	2.00	1.70	0.00	2.00	2.10	0.90	1.30
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.70	0.70	2.00	1.80	1.60	2.00	1.60	0.70	2.00	1.20	-0.50	2.00	1.60	0.50	0.80
+2.80	2.00	2.00	2.00	2.10	1.90	2.00	1.90	2.00	2.00	2.10	0.80	2.00	1.90	1.80	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+1.00	0.80	-0.20	2.00	0.90	1.70	2.00	1.70	-0.20	2.00	0.30	0.40	2.00	1.70	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+1.80	0.60	1.40	2.00	0.70	1.50	2.00	1.50	1.40	2.00	1.10	-1.60	2.00	1.50	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.80	1.80	2.00	1.90	1.80	2.00	1.80	1.80	2.00	2.00	0.70	2.00	1.80	1.60	1.00
+0.30	-0.90	-0.10	2.00	-0.80	0.00	2.00	0.00	-0.10	2.00	-0.40	-3.10	2.00	0.00	-2.10	0.00
+2.20	0.90	1.80	2.00	1.00	0.90	2.00	0.90	1.80	2.00	1.50	0.60	2.00	0.90	1.60	0.10
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+1.80	1.40	0.80	2.00	1.80	1.80	2.00	1.80	0.80	2.00	1.20	-1.00	2.00	1.50	0.30	1.00
+0.70	0.30	-0.30	2.00	0.70	1.70	2.00	1.70	-0.30	2.00	0.10	-0.30	2.00	1.40	1.00	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.40	0.80	2.00	1.90	1.90	2.00	1.90	0.80	2.00	1.20	-0.90	2.00	1.60	0.30	1.00
+2.50	1.40	1.80	2.00	1.90	1.90	2.00	1.90	1.80	2.00	1.80	0.10	2.00	1.60	1.30	1.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.50	1.90	2.00	1.90	1.90	2.00	1.90	1.90	2.00	1.90	0.10	2.00	1.60	1.40	1.10
+0.10	-0.30	-0.90	2.00	0.10	1.10	2.00	1.10	-0.90	2.00	-0.50	-0.90	2.00	0.80	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+0.40	-1.10	0.10	2.00	-0.60	0.40	2.00	0.40	0.10	2.00	-0.30	-3.50	2.00	0.10	-2.20	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.40	0.90	2.00	0.90	0.90	2.00	0.90	0.90	2.00	0.80	-0.90	2.00	0.60	0.40	0.00
+0.00	-1.50	-0.30	2.00	-1.00	0.00	2.00	0.00	-0.30	2.00	-0.70	-3.90	2.00	-0.30	-2.60	-0.10
+2.10	0.70	1.90	2.00	1.10	1.10	2.00	1.10	1.90	2.00	1.50	0.10	2.00	0.80	1.40	0.30
+1.50	1.20	-0.50	2.00	1.20	1.80	2.00	0.80	0.10	2.00	1.10	-0.70	2.00	1.90	-0.30	1.50
+1.20	0.90	-0.80	2.00	0.90	0.90	2.00	0.00	-0.20	2.00	0.80	-2.00	2.00	1.00	-1.60	0.20
+0.10	-0.10	-1.90	2.00	-0.20	0.90	2.00	-0.10	-1.30	2.00	-0.20	-1.30	2.00	0.90	-0.90	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.20	1.00	-0.80	2.00	0.90	1.00	2.00	0.00	-0.10	2.00	0.90	-1.90	2.00	1.00	-1.50	0.20
+1.80	1.00	0.20	2.00	0.90	1.00	2.00	0.00	0.90	2.00	1.50	-0.90	2.00	1.00	-0.50	0.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.00	0.30	2.00	1.00	1.00	2.00	0.00	0.90	2.00	1.50	-0.90	2.00	1.10	-0.50	0.30
+-0.50	-0.80	-2.60	2.00	-0.80	0.20	2.00	-0.80	-1.90	2.00	-0.90	-1.90	2.00	0.30	-1.50	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.10	0.90	-0.90	2.00	0.80	1.50	2.00	0.50	-0.20	2.00	0.80	-1.00	2.00	1.50	-0.60	1.10
+-0.30	-1.50	-1.50	2.00	-1.60	-0.50	2.00	-1.50	-0.90	2.00	-0.60	-4.50	2.00	-0.50	-4.10	-0.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+0.80	0.00	-0.80	2.00	0.00	0.00	2.00	-1.00	-0.10	2.00	0.50	-1.90	2.00	0.00	-1.50	-0.70
+-0.70	-1.90	-1.90	2.00	-2.00	-0.90	2.00	-1.90	-1.30	2.00	-1.00	-4.90	2.00	-0.90	-4.50	-0.90
+1.50	0.20	0.30	2.00	0.20	0.20	2.00	-0.70	0.90	2.00	1.10	-0.90	2.00	0.30	-0.50	-0.50
+0.50	1.30	-0.20	2.00	0.60	2.20	2.00	2.00	0.00	2.00	1.10	-0.10	2.00	2.00	0.90	1.40
+1.10	1.00	0.70	2.00	1.10	1.90	2.00	1.10	-1.00	2.00	0.80	-1.60	2.00	1.10	-0.10	0.30
+0.40	0.70	-0.50	2.00	0.50	0.70	2.00	0.50	-0.70	2.00	-0.20	-0.60	2.00	1.00	0.60	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.10	1.00	-0.40	2.00	1.50	1.30	2.00	1.20	-0.70	2.00	0.90	-1.60	2.00	1.20	0.00	0.30
+1.70	1.00	1.10	2.00	1.50	1.30	2.00	1.20	-0.60	2.00	1.50	-0.60	2.00	1.20	1.00	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.10	1.20	2.00	1.50	1.40	2.00	1.20	1.20	2.00	1.50	-0.50	2.00	1.20	1.00	0.30
+-0.30	-0.70	-1.70	2.00	0.10	0.70	2.00	0.40	-1.60	2.00	-0.90	-1.60	2.00	0.40	0.30	0.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.00	0.90	0.00	2.00	1.40	1.80	2.00	1.70	0.00	2.00	0.80	-0.70	2.00	1.70	0.90	1.20
+-0.50	-1.50	-1.30	2.00	-0.60	-0.20	2.00	-0.10	-0.60	2.00	-0.60	-4.10	2.00	-0.30	-2.40	0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+0.70	0.00	0.20	2.00	0.50	0.30	2.00	0.20	0.20	2.00	0.50	-1.60	2.00	1.70	0.00	0.10
+0.10	-1.90	-0.90	2.00	-0.70	-0.30	2.00	-0.70	-0.80	2.00	-1.00	-4.40	2.00	-0.70	-3.00	-1.00
+1.50	-0.20	0.90	2.00	0.00	-0.10	2.00	0.40	0.90	2.00	1.10	-1.00	2.00	0.20	0.60	0.60
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+1.80	1.60	0.60	2.00	1.70	1.50	2.00	1.50	0.60	2.00	1.10	-0.60	2.00	1.50	0.40	0.70
+0.70	0.50	-0.50	2.00	0.60	1.40	2.00	1.40	-0.50	2.00	0.00	0.10	2.00	1.40	1.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	0.60	2.00	1.70	1.60	2.00	1.60	0.60	2.00	1.20	-0.50	2.00	1.60	0.40	0.80
+2.50	1.60	1.60	2.00	1.70	1.60	2.00	1.60	1.60	2.00	1.80	0.50	2.00	1.60	1.40	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.70	1.70	2.00	1.80	1.60	2.00	1.60	1.70	2.00	1.80	0.50	2.00	1.60	1.50	0.80
+0.10	-0.10	-1.10	2.00	0.00	0.80	2.00	0.80	-1.10	2.00	-0.60	-0.50	2.00	0.80	0.50	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+0.40	-0.90	-0.10	2.00	-0.80	0.10	2.00	0.10	-0.10	2.00	-0.30	-3.10	2.00	0.10	-2.10	0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.60	0.70	2.00	0.70	0.60	2.00	0.60	0.70	2.00	0.80	-0.50	2.00	0.60	0.50	-0.20
+0.00	-1.30	-0.50	2.00	-1.20	-0.30	2.00	-0.30	-0.50	2.00	-0.70	-3.50	2.00	-0.30	-2.50	-0.30
+2.10	0.90	1.70	2.00	1.00	0.80	2.00	0.80	1.70	2.00	1.40	0.50	2.00	0.80	1.50	0.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+1.80	1.40	0.80	2.00	1.80	1.80	2.00	1.80	0.80	2.00	1.20	-1.00	2.00	1.50	0.30	1.00
+0.70	0.30	-0.30	2.00	0.70	1.70	2.00	1.70	-0.30	2.00	0.10	-0.30	2.00	1.40	1.00	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.40	0.80	2.00	1.90	1.90	2.00	1.90	0.80	2.00	1.20	-0.90	2.00	1.60	0.30	1.00
+2.50	1.40	1.80	2.00	1.90	1.90	2.00	1.90	1.80	2.00	1.80	0.10	2.00	1.60	1.30	1.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.50	1.90	2.00	1.90	1.90	2.00	1.90	1.90	2.00	1.90	0.10	2.00	1.60	1.40	1.10
+0.10	-0.30	-0.90	2.00	0.10	1.10	2.00	1.10	-0.90	2.00	-0.50	-0.90	2.00	0.80	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.30	0.70	2.00	1.80	2.40	2.00	2.40	0.70	2.00	1.10	0.00	2.00	2.10	1.20	1.90
+0.40	-1.10	0.10	2.00	-0.60	0.40	2.00	0.40	0.10	2.00	-0.30	-3.50	2.00	0.10	-2.20	0.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.40	0.90	2.00	0.90	0.90	2.00	0.90	0.90	2.00	0.80	-0.90	2.00	0.60	0.40	0.00
+0.00	-1.50	-0.30	2.00	-1.00	0.00	2.00	0.00	-0.30	2.00	-0.70	-3.90	2.00	-0.30	-2.60	-0.10
+2.10	0.70	1.90	2.00	1.10	1.10	2.00	1.10	1.90	2.00	1.50	0.10	2.00	0.80	1.40	0.30
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+1.80	1.60	0.60	2.00	1.70	1.50	2.00	1.50	0.60	2.00	1.10	-0.60	2.00	1.50	0.40	0.70
+0.70	0.50	-0.50	2.00	0.60	1.40	2.00	1.40	-0.50	2.00	0.00	0.10	2.00	1.40	1.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	0.60	2.00	1.70	1.60	2.00	1.60	0.60	2.00	1.20	-0.50	2.00	1.60	0.40	0.80
+2.50	1.60	1.60	2.00	1.70	1.60	2.00	1.60	1.60	2.00	1.80	0.50	2.00	1.60	1.40	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	1.70	1.70	2.00	1.80	1.60	2.00	1.60	1.70	2.00	1.80	0.50	2.00	1.60	1.50	0.80
+0.10	-0.10	-1.10	2.00	0.00	0.80	2.00	0.80	-1.10	2.00	-0.60	-0.50	2.00	0.80	0.50	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.50	0.50	2.00	1.60	2.10	2.00	2.10	0.50	2.00	1.10	0.40	2.00	2.10	1.30	1.70
+0.40	-0.90	-0.10	2.00	-0.80	0.10	2.00	0.10	-0.10	2.00	-0.30	-3.10	2.00	0.10	-2.10	0.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	0.60	0.70	2.00	0.70	0.60	2.00	0.60	0.70	2.00	0.80	-0.50	2.00	0.60	0.50	-0.20
+0.00	-1.30	-0.50	2.00	-1.20	-0.30	2.00	-0.30	-0.50	2.00	-0.70	-3.50	2.00	-0.30	-2.50	-0.30
+2.10	0.90	1.70	2.00	1.00	0.80	2.00	0.80	1.70	2.00	1.40	0.50	2.00	0.80	1.50	0.00
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.10	1.90	0.10	2.00	1.80	1.90	2.00	0.90	0.70	2.00	1.80	-1.00	2.00	1.90	-0.60	1.10
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.70	1.40	-0.30	2.00	1.40	1.40	2.00	0.40	0.30	2.00	1.30	-1.50	2.00	1.50	-1.10	0.70
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	1.20	-0.50	2.00	1.20	1.80	2.00	0.80	0.10	2.00	1.10	-0.70	2.00	1.90	-0.30	1.50
+1.60	0.30	0.40	2.00	0.30	1.30	2.00	0.40	1.00	2.00	1.20	-2.60	2.00	1.40	-2.20	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+0.30	-0.90	-0.90	2.00	-1.00	0.10	2.00	-0.90	-0.30	2.00	0.00	-3.90	2.00	0.10	-3.50	0.10
+2.30	1.00	1.10	2.00	1.00	1.00	2.00	0.00	1.70	2.00	1.90	-0.10	2.00	1.10	0.30	0.30
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+2.00	1.90	1.00	2.00	2.40	2.20	2.00	2.10	1.00	2.00	1.80	-0.70	2.00	2.10	0.80	1.20
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.60	1.50	0.60	2.00	1.90	1.80	2.00	1.60	0.60	2.00	1.30	-1.10	2.00	1.60	0.40	0.70
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.30	0.40	2.00	1.70	2.20	2.00	2.00	0.40	2.00	1.10	-0.30	2.00	2.00	1.20	1.50
+1.50	0.40	1.30	2.00	0.80	1.70	2.00	1.50	1.30	2.00	1.20	-2.20	2.00	1.50	-0.70	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+0.20	-0.90	0.00	2.00	-0.40	0.40	2.00	0.30	0.00	2.00	0.00	-3.50	2.00	0.30	-2.00	0.20
+2.20	1.10	2.00	2.00	1.50	1.40	2.00	1.20	2.00	2.00	1.90	0.30	2.00	1.20	1.80	0.30
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.00	1.70	0.00	2.00	1.70	1.70	2.00	0.70	0.60	2.00	1.60	-1.20	2.00	1.80	-0.80	1.00
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.90	1.60	-0.10	2.00	1.60	1.60	2.00	0.60	0.50	2.00	1.50	-1.30	2.00	1.70	-0.90	0.90
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.90	0.60	-1.10	2.00	0.60	1.60	2.00	0.70	-0.50	2.00	0.50	-0.50	2.00	1.70	-0.10	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.20	-0.60	2.00	1.10	1.80	2.00	0.80	0.00	2.00	1.10	-0.70	2.00	1.80	-0.30	1.40
+1.70	0.40	0.50	2.00	0.40	1.40	2.00	0.50	1.10	2.00	1.30	-2.50	2.00	1.50	-2.10	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+0.70	-0.50	-0.50	2.00	-0.60	0.50	2.00	-0.50	0.10	2.00	0.40	-3.50	2.00	0.50	-3.10	0.50
+2.00	0.80	0.80	2.00	0.70	0.80	2.00	-0.20	1.50	2.00	1.70	-0.30	2.00	0.80	0.10	0.00
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+1.90	1.80	0.90	2.00	2.20	2.10	2.00	1.90	0.90	2.00	1.60	-0.80	2.00	1.90	0.70	1.00
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.80	1.70	0.80	2.00	2.10	2.00	2.00	1.80	0.80	2.00	1.50	-0.90	2.00	1.80	0.60	0.90
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.80	0.70	-0.20	2.00	1.10	2.00	2.00	1.80	-0.20	2.00	0.50	-0.10	2.00	1.80	1.40	1.80
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.30	1.20	0.30	2.00	1.70	2.10	2.00	2.00	0.30	2.00	1.10	-0.40	2.00	2.00	1.10	1.50
+1.60	0.50	1.40	2.00	0.90	1.80	2.00	1.60	1.40	2.00	1.30	-2.10	2.00	1.60	-0.60	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+0.60	-0.50	0.40	2.00	0.00	0.80	2.00	0.70	0.40	2.00	0.40	-3.10	2.00	0.70	-1.60	0.60
+1.90	0.80	1.80	2.00	1.30	1.10	2.00	1.00	1.80	2.00	1.70	0.00	2.00	1.00	1.60	0.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.60	2.20	1.60	2.00	2.60	2.60	2.00	2.60	1.60	2.00	2.00	-0.20	2.00	2.30	1.10	1.80
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.10	1.50	2.00	2.50	2.50	2.00	2.50	1.50	2.00	1.90	-0.30	2.00	2.20	1.00	1.70
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.50	1.10	0.50	2.00	1.50	2.50	2.00	2.50	0.50	2.00	0.90	0.50	2.00	2.20	1.80	2.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.60	1.00	2.00	2.10	2.70	2.00	2.70	1.00	2.00	1.40	0.30	2.00	2.40	1.50	2.20
+2.30	0.90	2.10	2.00	1.30	2.30	2.00	2.30	2.10	2.00	1.70	-1.50	2.00	2.00	-0.20	2.30
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.30	-0.10	1.10	2.00	0.30	1.30	2.00	1.30	1.10	2.00	0.70	-2.50	2.00	1.00	-1.20	1.30
+2.70	1.20	2.40	2.00	1.70	1.70	2.00	1.70	2.40	2.00	2.00	0.70	2.00	1.40	1.90	0.80
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.60	2.40	1.40	2.00	2.50	2.30	2.00	2.30	1.40	2.00	1.90	0.20	2.00	2.30	1.20	1.50
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.50	2.30	1.30	2.00	2.40	2.20	2.00	2.20	1.30	2.00	1.80	0.10	2.00	2.20	1.10	1.40
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.50	1.30	0.30	2.00	1.40	2.20	2.00	2.20	0.30	2.00	0.80	0.90	2.00	2.20	1.90	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.80	0.80	2.00	1.90	2.40	2.00	2.40	0.80	2.00	1.40	0.70	2.00	2.40	1.60	2.00
+2.30	1.10	1.90	2.00	1.20	2.00	2.00	2.00	1.90	2.00	1.60	-1.10	2.00	2.00	-0.10	2.00
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.30	0.10	0.90	2.00	0.20	1.00	2.00	1.00	0.90	2.00	0.70	-2.10	2.00	1.00	-1.10	1.10
+2.70	1.40	2.20	2.00	1.50	1.40	2.00	1.40	2.20	2.00	2.00	1.10	2.00	1.40	2.00	0.60
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.10	1.90	0.10	2.00	1.80	2.50	2.00	1.50	0.70	2.00	1.80	0.00	2.00	2.50	0.40	2.10
+2.10	1.90	0.10	2.00	1.80	1.90	2.00	0.90	0.70	2.00	1.80	-1.00	2.00	1.90	-0.60	1.10
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.70	1.40	-0.30	2.00	1.40	1.40	2.00	0.40	0.30	2.00	1.30	-1.50	2.00	1.50	-1.10	0.70
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.40	1.60	0.80	2.00	1.50	1.60	2.00	0.60	1.40	2.00	2.10	-0.30	2.00	1.60	0.10	0.80
+1.10	0.80	-0.90	2.00	0.80	1.80	2.00	0.90	-0.30	2.00	0.70	-0.30	2.00	1.90	0.10	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.50	1.20	-0.50	2.00	1.20	1.80	2.00	0.80	0.10	2.00	1.10	-0.70	2.00	1.90	-0.30	1.50
+1.60	0.30	0.40	2.00	0.30	1.30	2.00	0.40	1.00	2.00	1.20	-2.60	2.00	1.40	-2.20	1.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.70	1.90	1.10	2.00	1.80	1.90	2.00	0.90	1.70	2.00	2.40	0.00	2.00	1.90	0.40	1.10
+0.30	-0.90	-0.90	2.00	-1.00	0.10	2.00	-0.90	-0.30	2.00	0.00	-3.90	2.00	0.10	-3.50	0.10
+2.30	1.00	1.10	2.00	1.00	1.00	2.00	0.00	1.70	2.00	1.90	-0.10	2.00	1.10	0.30	0.30
+2.00	1.90	1.00	2.00	2.40	2.80	2.00	2.70	1.00	2.00	1.80	0.30	2.00	2.70	1.80	2.20
+2.00	1.90	1.00	2.00	2.40	2.20	2.00	2.10	1.00	2.00	1.80	-0.70	2.00	2.10	0.80	1.20
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.60	1.50	0.60	2.00	1.90	1.80	2.00	1.60	0.60	2.00	1.30	-1.10	2.00	1.60	0.40	0.70
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.60	1.70	2.00	2.10	1.90	2.00	1.80	1.70	2.00	2.10	0.00	2.00	1.80	1.50	0.90
+1.00	0.90	0.00	2.00	1.30	2.20	2.00	2.00	0.00	2.00	0.70	0.10	2.00	2.00	1.60	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+1.40	1.30	0.40	2.00	1.70	2.20	2.00	2.00	0.40	2.00	1.10	-0.30	2.00	2.00	1.20	1.50
+1.50	0.40	1.30	2.00	0.80	1.70	2.00	1.50	1.30	2.00	1.20	-2.20	2.00	1.50	-0.70	1.50
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.60	1.90	2.00	2.00	2.40	2.20	2.00	2.10	2.00	2.00	2.40	0.30	2.00	2.10	1.80	1.20
+0.20	-0.90	0.00	2.00	-0.40	0.40	2.00	0.30	0.00	2.00	0.00	-3.50	2.00	0.30	-2.00	0.20
+2.20	1.10	2.00	2.00	1.50	1.40	2.00	1.20	2.00	2.00	1.90	0.30	2.00	1.20	1.80	0.30
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
+2.80	2.30	1.70	2.00	2.80	3.40	2.00	3.40	1.70	2.00	2.10	1.00	2.00	3.10	2.20	2.90
+2.80	2.30	1.70	2.00	2.80	2.80	2.00	2.80	1.70	2.00	2.10	0.00	2.00	2.50	1.20	1.90
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	1.90	1.30	2.00	2.30	2.30	2.00	2.30	1.30	2.00	1.70	-0.50	2.00	2.00	0.80	1.50
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.00	2.40	2.00	2.50	2.50	2.00	2.50	2.40	2.00	2.40	0.70	2.00	2.20	1.90	1.60
+1.70	1.30	0.70	2.00	1.70	2.70	2.00	2.70	0.70	2.00	1.10	0.70	2.00	2.40	2.00	2.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.70	1.10	2.00	2.10	2.70	2.00	2.70	1.10	2.00	1.50	0.30	2.00	2.40	1.60	2.30
+2.20	0.80	2.00	2.00	1.20	2.20	2.00	2.20	2.00	2.00	1.60	-1.60	2.00	1.90	-0.30	2.20
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.30	2.70	2.00	2.80	2.80	2.00	2.80	2.70	2.00	2.70	1.00	2.00	2.50	2.20	1.90
+1.00	-0.50	0.70	2.00	0.00	1.00	2.00	1.00	0.70	2.00	0.30	-2.90	2.00	0.70	-1.60	0.90
+2.90	1.50	2.70	2.00	1.90	1.90	2.00	1.90	2.70	2.00	2.30	0.90	2.00	1.60	2.20	1.10
+2.80	2.50	1.50	2.00	2.60	3.10	2.00	3.10	1.50	2.00	2.10	1.30	2.00	3.10	2.30	2.70
+2.80	2.50	1.50	2.00	2.60	2.50	2.00	2.50	1.50	2.00	2.10	0.30	2.00	2.50	1.30	1.70
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.30	2.10	1.10	2.00	2.20	2.00	2.00	2.00	1.10	2.00	1.60	-0.10	2.00	2.00	0.90	1.20
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.10	2.20	2.20	2.00	2.30	2.20	2.00	2.20	2.20	2.00	2.40	1.00	2.00	2.20	2.00	1.40
+1.70	1.50	0.50	2.00	1.60	2.40	2.00	2.40	0.50	2.00	1.00	1.10	2.00	2.40	2.10	2.40
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+2.10	1.90	0.90	2.00	2.00	2.40	2.00	2.40	0.90	2.00	1.40	0.70	2.00	2.40	1.70	2.00
+2.20	1.00	1.80	2.00	1.10	1.90	2.00	1.90	1.80	2.00	1.50	-1.20	2.00	1.90	-0.20	1.90
+2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00	2.00
+3.40	2.50	2.50	2.00	2.60	2.50	2.00	2.50	2.50	2.00	2.70	1.30	2.00	2.50	2.30	1.70
+1.00	-0.30	0.50	2.00	-0.20	0.70	2.00	0.70	0.50	2.00	0.30	-2.50	2.00	0.70	-1.50	0.70
+2.90	1.70	2.50	2.00	1.80	1.60	2.00	1.60	2.50	2.00	2.20	1.30	2.00	1.60	2.30	0.80
diff --git a/gtfold-mfe/data/RNAParams/stack.DAT b/gtfold-mfe/data/RNAParams/stack.DAT
new file mode 100644
index 0000000..04a6889
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/stack.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.90
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.20	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.10	inf	-0.60
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.10	inf	-1.40	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.10	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-3.30	inf 	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.40	inf	-1.40	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.10	inf	-2.10	inf 	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.40	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.30
+inf 	inf 	inf 	inf 	inf 	inf	-3.40	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.50	inf
+inf 	inf 	inf 	inf 	inf	-3.30	inf	-1.50	inf 	inf 	inf 	inf 	inf	-2.10	inf	-0.50
+inf 	inf 	inf 	inf	-2.20	inf	-2.50	inf 	inf 	inf 	inf 	inf	-1.40	inf	1.30	inf
+inf 	inf 	inf	-1.30	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.00	inf 	inf 	inf 	inf
+inf 	inf	-2.40	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.50	inf 	inf 	inf 	inf 	inf
+inf	-2.10	inf	-1.00	inf 	inf 	inf 	inf 	inf	-1.40	inf	0.30	inf 	inf 	inf 	inf
+-0.90	inf	-1.30	inf 	inf 	inf 	inf 	inf	-0.60	inf	-0.50	inf 	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/RNAParams/tloop.DAT b/gtfold-mfe/data/RNAParams/tloop.DAT
new file mode 100644
index 0000000..dda2750
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/tloop.DAT
@@ -0,0 +1,30 @@
+GGGGAC	-3.00
+GGUGAC	-3.00
+CGAAAG	-3.00
+GGAGAC	-3.00
+CGCAAG	-3.00
+GGAAAC	-3.00
+CGGAAG	-3.00
+CUUCGG	-3.00
+CGUGAG	-3.00
+CGAAGG	-2.50
+CUACGG	-2.50
+GGCAAC	-2.50
+CGCGAG	-2.50
+UGAGAG	-2.50
+CGAGAG	-2.00
+AGAAAU	-2.00
+CGUAAG	-2.00
+CUAACG	-2.00
+UGAAAG	-2.00
+GGAAGC	-1.50
+GGGAAC	-1.50
+UGAAAA	-1.50
+AGCAAU	-1.50
+AGUAAU	-1.50
+CGGGAG	-1.50
+AGUGAU	-1.50
+GGCGAC	-1.50
+GGGAGC	-1.50
+GUGAAC	-1.50
+UGGAAA	-1.50
diff --git a/gtfold-mfe/data/RNAParams/tstacke.DAT b/gtfold-mfe/data/RNAParams/tstacke.DAT
new file mode 100644
index 0000000..342f641
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/tstacke.DAT
@@ -0,0 +1,16 @@
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	-1.00	-0.80	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.60	-0.70	inf	-0.70
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	inf	-0.80	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	inf	-0.80	inf	-0.80
+inf	inf	inf	inf	inf	inf	inf	inf	-1.50	-1.50	-1.40	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.00	-1.10	inf	-0.80	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	-1.40	inf	-1.60	inf	inf	inf	inf	inf
+inf	inf	inf	inf	inf	inf	inf	inf	inf	-1.40	inf	-1.20	inf	inf	inf	inf
+inf	inf	inf	inf	-1.10	-1.50	-1.30	inf	inf	inf	inf	inf	-0.30	-1.00	-0.80	inf
+inf	inf	inf	inf	-1.10	-0.70	inf	-0.50	inf	inf	inf	inf	-0.60	-0.70	inf	-0.70
+inf	inf	inf	inf	-1.60	inf	-1.40	inf	inf	inf	inf	inf	-0.60	inf	-0.80	inf
+inf	inf	inf	inf	inf	-1.00	inf	-0.70	inf	inf	inf	inf	inf	-0.80	inf	-0.80
+-1.00	-0.80	-1.10	inf	inf	inf	inf	inf	-1.00	-0.80	-1.10	inf	inf	inf	inf	inf
+-0.70	-0.60	inf	-0.50	inf	inf	inf	inf	-0.70	-0.60	inf	-0.50	inf	inf	inf	inf
+-1.10	inf	-1.20	inf	inf	inf	inf	inf	-0.50	inf	-0.80	-0.80	inf	inf	inf	inf
+inf	-0.60	inf	-0.50	inf	inf	inf	inf	inf	-0.60	-1.10	-0.50	inf	inf	inf	inf
diff --git a/gtfold-mfe/data/RNAParams/tstackh.DAT b/gtfold-mfe/data/RNAParams/tstackh.DAT
new file mode 100644
index 0000000..7648650
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/tstackh.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.30	-0.50	-0.30	-0.30
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.10	-0.20	-1.50	-0.20
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.10	-1.20	-0.20	0.20
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.30	-0.30	-0.60	-1.10
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.50	-1.50	-1.40	-1.80	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.00	-0.90	-2.90	-0.80	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-2.20	-2.00	-1.60	-1.10	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.70	-1.40	-1.80	-2.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-1.10	-1.50	-1.30	-2.10	inf 	inf 	inf 	inf	0.20	-0.50	-0.30	-0.30
+inf 	inf 	inf 	inf	-1.10	-0.70	-2.40	-0.50	inf 	inf 	inf 	inf	-0.10	-0.20	-1.50	-0.20
+inf 	inf 	inf 	inf	-2.40	-2.90	-1.40	-1.20	inf 	inf 	inf 	inf	-0.90	-1.10	-0.30	0.00
+inf 	inf 	inf 	inf	-1.90	-1.00	-2.20	-1.50	inf 	inf 	inf 	inf	-0.30	-0.30	-0.40	-1.10
+-0.50	-0.30	-0.60	-0.50	inf 	inf 	inf 	inf	-0.50	-0.30	-0.60	-0.50	inf 	inf 	inf 	inf
+-0.20	-0.10	-1.20	-0.00	inf 	inf 	inf 	inf	-0.20	-0.10	-1.70	0.00	inf 	inf 	inf 	inf
+-1.40	-1.20	-0.70	-0.20	inf 	inf 	inf 	inf	-0.80	-1.20	-0.30	-0.70	inf 	inf 	inf 	inf
+-0.30	-0.10	-0.50	-0.80	inf 	inf 	inf 	inf	-0.60	-0.10	-0.60	-0.80	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/RNAParams/tstacki.DAT b/gtfold-mfe/data/RNAParams/tstacki.DAT
new file mode 100644
index 0000000..dd7b5da
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/tstacki.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	0.70	0.70	-0.40	0.70
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.70
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.40	0.70	0.70	0.70
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.00
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.00	-0.00	-1.10	-0.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-1.10	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf 	inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.70	inf 	inf 	inf 	inf
+inf 	inf 	inf 	inf	-0.00	-0.00	-1.10	-0.00	inf 	inf 	inf 	inf	0.70	0.70	-0.40	0.70
+inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.70
+inf 	inf 	inf 	inf	-1.10	-0.00	-0.00	-0.00	inf 	inf 	inf 	inf	-0.40	0.70	0.70	0.70
+inf 	inf 	inf 	inf	-0.00	-0.00	-0.00	-0.70	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.00
+0.70	0.70	-0.40	0.70	inf 	inf 	inf 	inf	0.70	0.70	-0.40	0.70	inf 	inf 	inf 	inf
+0.70	0.70	0.70	0.70	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.70	inf 	inf 	inf 	inf
+-0.40	0.70	0.70	0.70	inf 	inf 	inf 	inf	-0.40	0.70	0.70	0.70	inf 	inf 	inf 	inf
+0.70	0.70	0.70	0.00	inf 	inf 	inf 	inf	0.70	0.70	0.70	0.00	inf 	inf 	inf 	inf
diff --git a/gtfold-mfe/data/RNAParams/tstackm.DAT b/gtfold-mfe/data/RNAParams/tstackm.DAT
new file mode 100644
index 0000000..b850f80
--- /dev/null
+++ b/gtfold-mfe/data/RNAParams/tstackm.DAT
@@ -0,0 +1,16 @@
+inf 	inf 	inf	-1.00	inf 	inf 	inf	-1.00	inf 	inf 	inf	-2.20	-0.80	-1.00	-0.80	-0.90
+inf 	inf	-1.50	inf 	inf 	inf	-1.50	inf 	inf 	inf	-2.70	inf	-0.60	-0.70	-2.20	-0.70
+inf	-1.50	inf	-1.00	inf	-1.50	inf	-1.00	inf	-2.70	inf	-2.20	-0.80	-2.10	-0.80	-0.80
+-1.00	inf	-1.50	inf	-1.00	inf	-1.50	inf	-2.20	inf	-2.70	inf	-1.10	-0.80	-1.10	-0.80
+inf 	inf 	inf	-1.00	inf 	inf 	inf	-1.00	-1.70	-1.70	-1.70	-1.70	inf 	inf 	inf	-1.00
+inf 	inf	-1.50	inf 	inf 	inf	-1.50	inf	-1.00	-1.10	-3.30	-0.80	inf 	inf	-1.50	inf
+inf	-1.50	inf	-1.00	inf	-1.50	inf	-1.00	-1.70	-2.40	-1.70	-1.70	inf	-1.50	inf	-1.00
+-1.00	inf	-1.50	inf	-1.00	inf	-1.50	inf	-1.60	-1.40	-1.60	-1.20	-1.00	inf	-1.50	inf
+inf 	inf 	inf	-2.20	-1.10	-1.50	-1.30	-1.90	inf 	inf 	inf	-1.00	-0.80	-1.00	-0.80	-1.30
+inf 	inf	-2.70	inf	-1.10	-0.70	-3.40	-0.50	inf 	inf	-1.50	inf	-0.60	-0.70	-2.50	-0.70
+inf	-2.70	inf	-2.20	-1.60	-3.30	-1.40	-1.30	inf	-1.50	inf	-1.00	-0.80	-2.10	-0.80	-0.80
+-2.20	inf	-2.70	inf	-1.70	-1.00	-2.00	-0.70	-1.00	inf	-1.50	inf	-1.40	-0.80	1.30	-0.80
+-1.00	-0.80	-1.10	-1.30	inf 	inf 	inf	-1.00	-1.00	-0.80	-1.10	-1.00	inf 	inf 	inf	-2.00
+-0.70	-0.60	-2.40	-0.50	inf 	inf	-1.50	inf	-0.70	-0.60	-1.50	-0.50	inf 	inf	-2.50	inf
+-1.10	-2.10	-1.20	-1.00	inf	-1.50	inf	-1.00	-0.70	-1.40	-0.80	0.30	inf	-2.50	inf	-2.00
+-0.90	-0.60	-1.40	-0.50	-1.00	inf	-1.50	inf	-0.50	-0.60	-0.50	-0.50	-2.00	inf	-2.50	inf

From 2e9862ac86e70b59b62ce1e0d8fcaab57b7238c1 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 27 Jun 2011 17:27:38 -0400
Subject: [PATCH 185/282] changes for --rnafold option

---
 gtfold-mfe/include/loader.h  |  2 +-
 gtfold-mfe/include/options.h |  1 +
 gtfold-mfe/src/loader.cc     | 10 ++++++++--
 gtfold-mfe/src/main.cc       |  5 +++--
 gtfold-mfe/src/options.cc    |  3 +++
 5 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h
index 41d7c6b..1bac05c 100644
--- a/gtfold-mfe/include/loader.h
+++ b/gtfold-mfe/include/loader.h
@@ -25,7 +25,7 @@
 #include "constants.h"
 #include "data.h"
 
-void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode,int t_mismatch);
+void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode, int rnamode, int t_mismatch);
 
 int initStackValues(const std::string& fileName, const std::string& dirPath);
 int initMiscloopValues(const std::string& fileName, const std::string& dirPath);
diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 4d4dbf1..7c0cdbc 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -21,6 +21,7 @@ extern bool SHAPE_ENABLED;
 extern bool PARAM_DIR;
 extern bool T_MISMATCH;
 extern bool UNAMODE;
+extern bool RNAMODE;
 
 extern string seqfile;
 extern string constraintsFile;
diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 9144c07..0ab17e3 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -80,14 +80,20 @@ int init;
 int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
 float prelog;
 
-void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode = 0, int mismatch = 0) {
+void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, 
+				int unamode = 0, int rnamode = 0, int mismatch = 0) {
 	
 	if (!userdatalogic && unamode) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
 		EN_DATADIR += "UNAParams";
+		printf("readThermodynamicParameters() %d %s\n",unamode, EN_DATADIR.c_str());
+	}else if (!userdatalogic && rnamode) {
+		EN_DATADIR.assign(xstr(DATADIR));
+		EN_DATADIR += "/";
+		EN_DATADIR += "RNAParams";
 	}
-    else if (!userdatalogic) {
+    	else if (!userdatalogic) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
 		EN_DATADIR += "Turner99";
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 52172cd..5a7f707 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -226,10 +226,11 @@ int main(int argc, char** argv) {
 		exit(-1);
 	}
 	
+	printRunConfiguration(seq);
+	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
-	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, T_MISMATCH);
+	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
 
-	printRunConfiguration(seq);
 	
 	init_fold(seq);
 
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 6dad154..77dabb8 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -16,6 +16,7 @@ bool VERBOSE = false;
 bool SHAPE_ENABLED = false;
 bool T_MISMATCH = false;
 bool UNAMODE = false;
+bool RNAMODE = false;
 bool b_prefilter = false;
 
 string seqfile = "";
@@ -127,6 +128,8 @@ void parse_options(int argc, char** argv) {
 				T_MISMATCH = true;
 			} else if (strcmp(argv[i], "--unamode") == 0) {
 				UNAMODE = true;
+			} else if (strcmp(argv[i], "--rnafold") == 0) {
+				RNAMODE = true;
 			} else if (strcmp(argv[i], "--prefilter") == 0) {
 				if(i < argc) {
 					int value1 = -1, value2 = -1;

From 8d711d36102ae88c429096c740b4d54f09a7c934 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 27 Jun 2011 18:03:36 -0400
Subject: [PATCH 186/282] fixed issue 17

---
 gtfold-mfe/src/main.cc     | 13 +++++++------
 gtfold-mfe/src/traceback.c |  2 +-
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 5a7f707..280ed9e 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -243,10 +243,13 @@ int main(int argc, char** argv) {
 	
 	printf("Done.\n\n");
 	printf("Results:\n");
-	printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00);
+	if (energy >= MAXENG)	
+		printf("- Minimum Free Energy: %12.4f kcal/mol\n", 0.00);
+	else
+		printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00);
 	printf("- MFE runtime: %9.6f seconds\n", t1);
-	
-	
+
+
 	if (SUBOPT_ENABLED) {	
 		t1 = get_seconds();
 		ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta);
@@ -263,17 +266,15 @@ int main(int argc, char** argv) {
 	t1 = get_seconds();
 	trace(seq.length(), VERBOSE, UNAMODE, T_MISMATCH);
 	t1 = get_seconds() - t1;
-
+	
 	printf("\n");
 	print_sequence(seq.length());
 	print_structure(seq.length());
 	if (CONS_ENABLED)
 		print_constraints(seq.length());
 
-
 	if (SHAPE_ENABLED && VERBOSE)
 		print_shapeArray(seq.length());
-	
 
 	save_ct_file(outputFile, seq, energy);
 	printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str());
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 1a9511f..6cea549 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -45,7 +45,7 @@ void trace(int len, int vv, int mode, int mismatch) {
 		structure[i] = 0;
 
 	if (W[len] >= MAXENG) {
-		printf("\n No Structure ");
+		printf("- No Structure \n");
 		return;
 	}
 

From f9305506acf16fe2fa86523b4aa228e27bacd7aa Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 29 Jun 2011 16:32:07 -0400
Subject: [PATCH 187/282] - changed --unamode to --unafold, - removed a debug
 statement

---
 gtfold-mfe/src/loader.cc  | 1 -
 gtfold-mfe/src/options.cc | 7 ++++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 0ab17e3..8ec31df 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -87,7 +87,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic,
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
 		EN_DATADIR += "UNAParams";
-		printf("readThermodynamicParameters() %d %s\n",unamode, EN_DATADIR.c_str());
 	}else if (!userdatalogic && rnamode) {
 		EN_DATADIR.assign(xstr(DATADIR));
 		EN_DATADIR += "/";
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 77dabb8..a690bc1 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -56,8 +56,9 @@ void help() {
     printf("   -o, --output NAME    Name output files with prefix\n");
     printf("   -w, --workDir DIR    Path to directory for output files\n");
     printf("   -t, --threads num    Limit number of threads used\n");
-    printf("   --unamode 		Enable UNAfold mode. \n");
-    printf("   --prefilter value1,value2 \n\t\t\tSets the prefilter mode similar to UNAfold\n");
+    printf("   --unafold 		Run as UNAFOLD default mode (version 3.8). \n");
+    printf("   --prefilter num1,num2 \n\t\t\tSets the prefilter mode similar to UNAfold\n");
+    printf("   --rnafold 		Run as RNAFOLD default mode (version 1.8.5). \n");
 
     printf("\n");
     printf("   -h, --help           Output help (this message) and exit\n");
@@ -126,7 +127,7 @@ void parse_options(int argc, char** argv) {
 					help();
 			} else if (strcmp(argv[i], "-m") == 0) {
 				T_MISMATCH = true;
-			} else if (strcmp(argv[i], "--unamode") == 0) {
+			} else if (strcmp(argv[i], "--unafold") == 0) {
 				UNAMODE = true;
 			} else if (strcmp(argv[i], "--rnafold") == 0) {
 				RNAMODE = true;

From 07ed2e69c852a2edbd7c235757b88ad365535d2f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 8 Jul 2011 12:46:52 -0400
Subject: [PATCH 188/282] added d2 option

---
 gtfold-mfe/include/global.h    |   1 +
 gtfold-mfe/include/options.h   |   1 +
 gtfold-mfe/include/traceback.h |   3 +-
 gtfold-mfe/src/algorithms.c    | 300 ++++++++++++++---------
 gtfold-mfe/src/global.c        |   1 +
 gtfold-mfe/src/main.cc         |  10 +-
 gtfold-mfe/src/options.cc      |  28 ++-
 gtfold-mfe/src/traceback.c     | 430 +++++++++++++++++----------------
 8 files changed, 435 insertions(+), 339 deletions(-)

diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h
index 1bdc31e..c452b2a 100644
--- a/gtfold-mfe/include/global.h
+++ b/gtfold-mfe/include/global.h
@@ -9,6 +9,7 @@ extern int* constraints;
 
 extern int g_nthreads;
 extern int g_unamode;
+extern int g_dangles;
 extern int g_mismatch;
 extern int g_verbose;
 extern int g_prefilter_mode;
diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 7c0cdbc..44de1ce 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -37,6 +37,7 @@ extern int nThreads;
 extern bool b_prefilter;
 extern int prefilter1;
 extern int prefilter2;
+extern int dangles;
 
 extern bool LIMIT_DISTANCE;
 extern int contactDistance;
diff --git a/gtfold-mfe/include/traceback.h b/gtfold-mfe/include/traceback.h
index f250058..ff654f4 100644
--- a/gtfold-mfe/include/traceback.h
+++ b/gtfold-mfe/include/traceback.h
@@ -26,7 +26,7 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
-	void trace(int len, int vv, int mode, int mismatch);
+	void trace(int len); //, int vv, int mode, int mismatch);
 #ifdef __cplusplus
 }
 #endif
@@ -36,5 +36,6 @@ int traceV(int i, int j);
 int traceVM(int i, int j);
 int traceVBI(int i, int j);
 int traceWM(int i, int j);
+int traceWMPrime(int i, int j);
 
 #endif
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index a0fe2ae..79425a5 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -30,7 +30,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
 #include "omp.h"
 #endif
 
-//#define DEBUG 1
+#define DEBUG 1
 
 void initializeMatrix(int len) {
 	int i, j;
@@ -120,134 +120,200 @@ int calcVBI2(int i, int j, int  len) {
 	return energy;
 }
 
-int calculate(int len) { //, int nThreads, int unamode, int mismatch) { 
-	int b, i, j;
+int calculate(int len) { 
+								int b, i, j;
 #ifdef _OPENMP
-	if (g_nthreads > 0) omp_set_num_threads(g_nthreads);
+								if (g_nthreads > 0) omp_set_num_threads(g_nthreads);
 #endif
+
 #ifdef _OPENMP
 #pragma omp parallel
 #pragma omp master
-	fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
+								fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
 #endif
 
-	initializeMatrix(len);
-	if (g_unamode || g_prefilter_mode) {
-		prefilter(len,g_prefilter1,g_prefilter2);
-	}
-
-	for (b = TURN+1; b <= len-1; b++) {
+								initializeMatrix(len);
+								if (g_unamode || g_prefilter_mode) {
+																prefilter(len,g_prefilter1,g_prefilter2);
+								}
+								
+								for (b = TURN+1; b <= len-1; b++) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
 #endif
-		for (i = 1; i <= len - b; i++) {
-			j = i + b;
-			int newWM = INFINITY_; 
-			
-			if (PP[i][j]==1) {
-				int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
-				int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack
-
-				// Internal Loop BEGIN
-				if (g_unamode) 
-					VBI(i,j) = calcVBI1(i,j);
-				else
-					VBI(i,j) = calcVBI(i,j);
-				// Internal Loop END
-
-				// Multi Loop BEGIN
-				int VMij =  WMPrime[i+1][j-1]; 
-				int VMidj = WMPrime[i+2][j-1]; 
-				int VMijd = WMPrime[i+1][j-2]; 
-				int VMidjd = WMPrime[i+2][j-2]; 
-
-				int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
-				int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
-				VMij = MIN(VMij, (VMidj + d5 +Ec)) ;
-				VMij = MIN(VMij, (VMijd + d3 +Ec));
-
-				if (g_unamode || g_mismatch) {
-					VMij = MIN(VMij, (VMidjd + Estackm(i,j) + 2*Ec));
-				} else {
-					VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec));
-				}
-
-				VMij = VMij + Ea + Eb + auPenalty(i,j);
-				VM(i,j) = canStack(i,j)?VMij:INFINITY_;
-				// Multi Loop END
-
-				V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j));
-			}
-			else V(i,j) = INFINITY_;
-
-			int h; 
-			for (h = i+TURN+1 ; h <= j-TURN-2; h++) {
-				// Added auxillary storage WMPrime to speedup multiloop calculations
-				WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); 
-				//newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM;
-			}
-			
-			//ZS: This sum corresponds to when i,j are NOT paired with each other.
-			//So we need to make sure only terms where i,j aren't pairing are considered. 
-			newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM;
-			
-			newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
-			newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
-			newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
-
-			if (g_unamode || g_mismatch) {
-				if (i<j-TURN-2)
-					newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; 
-			}
-			else {
-				newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; //i,j dangle
-			}
-
-			newWM = canSS(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; //i dangle
-			newWM = canSS(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; //j dangle
-			WMU(i,j) = WML(i,j) = newWM;
-		}
-	}
-
-	for (j = TURN+2; j <= len; j++) {
-		int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
-		Wj = INFINITY_;
-		for (i = 1; i < j-TURN; i++) {
-			Wij = Widjd = Wijd = Widj = INFINITY_;
-			Wim1 = MIN(0, W[i-1]); 
-			Wij = V(i, j) + auPenalty(i, j) + Wim1;
-		
-			if (g_unamode || g_mismatch) {
-				Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Estacke(j-1,i+1) + Wim1:Widjd;
-			} else {
-				Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:Widjd;
-			}
-			
-			Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd;
-			Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj;
-			Wj = MIN(MIN4(Wij, Widjd, Wijd, Widj), Wj); 
-		}
-		W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj;
-	}
+																for (i = 1; i <= len - b; i++) {
+																								j = i + b;
+
+																								if (PP[i][j] == 1) {
+																																int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
+																																int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack
+
+																																// Internal Loop BEGIN
+																																if (g_unamode) 
+																																								VBI(i,j) = calcVBI1(i,j);
+																																else
+																																								VBI(i,j) = calcVBI(i,j);
+																																// Internal Loop END
+
+																																// Multi Loop BEGIN
+																																int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
+																																int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
+
+																																if (g_unamode || g_mismatch) { // unamode, terminal mismatch
+																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb);
+																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-1] + d5 + auPenalty(i,j) + Ea + Eb + Ec);
+																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-2] + d3 + auPenalty(i,j) + Ea + Eb + Ec);
+																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-2] + Estackm(i,j) + auPenalty(i,j) + Ea + Eb + 2*Ec);
+																																} else if (g_dangles == 2) { // -d2
+																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + d3 + d5 + auPenalty(i,j) + Ea + Eb);
+																																} else if (g_dangles == 0) { // -d0
+																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb);
+																																}	else { // default 
+																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb);
+																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-1] + d5 + auPenalty(i,j) + Ea + Eb + Ec);
+																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-2] + d3 + auPenalty(i,j) + Ea + Eb + Ec);
+																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-2] + d3 + d5 + auPenalty(i,j) + Ea + Eb + 2*Ec);
+																																}
+																																VM(i,j) = canStack(i,j)?VM(i,j):INFINITY_;
+																																// Multi Loop END
+
+																																V(i,j) = MIN4(  eh,
+																																																es,
+																																																VBI(i,j),
+																																																VM(i,j));
+																								}
+																								else {
+																																V(i,j) = INFINITY_;
+																								}
+
+																								// Added auxillary storage WMPrime to speedup multiloop calculations
+																								int h;
+																								for (h = i+TURN+1 ; h <= j-TURN-2; h++) {
+																																WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); 
+																								}
+
+																								// WM begin
+																								int newWM = INFINITY_; 
+																								
+																								//ZS: This sum corresponds to when i,j are NOT paired with each other.
+																								//So we need to make sure only terms where i,j aren't pairing are considered. 
+																								newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM;
+
+																								if (g_unamode || g_mismatch) { // unamode
+																																newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
+																																newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
+																																newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
+																																if (i<j-TURN-2)
+																																								newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; 
+																								} else if (g_dangles == 2) {
+																																int energy = V(i,j) + auPenalty(i,j) + Eb;
+																																energy += (i==1)?Ed3(j,i,len):Ed3(j,i,i-1);
+																																/*if (j<len)*/ energy += Ed5(j,i,j+1);
+																																newWM = (canSS(i)&&canSS(j))?MIN(energy, newWM):newWM; //i,j dangle
+																								} else if (g_dangles == 0) {
+																																newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
+																								} else { // default
+																																newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
+																																newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
+																																newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
+																																newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; //i,j dangle
+																								}
+																								newWM = canSS(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; //i dangle
+																								newWM = canSS(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; //j dangle
+
+																								WMU(i,j) = WML(i,j) = newWM;
+																								// WM end
+																}
+								}
+						
+								for (j = TURN+2; j <= len; j++) {
+																int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
+																Wj = INFINITY_;
+																for (i = 1; i < j-TURN; i++) {
+																								Wij = Widjd = Wijd = Widj = INFINITY_;
+																								Wim1 = MIN(0, W[i-1]); 
+
+																								if (g_unamode || g_mismatch) { // unafold option
+																																Wij = V(i, j) + auPenalty(i, j) + Wim1;
+																																Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj;
+																																Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd;
+																																Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Estacke(j-1,i+1) + Wim1:Widjd;
+																																Wij = MIN4(Wij, Widjd, Wijd, Widj);
+																								} else if (g_dangles == 2) { // -d2 option
+																																int energy = V(i,j) +	 auPenalty(i,j) + Wim1;
+																																if (i>1) energy +=  Ed3(j,i,i-1);
+																																if (j<len) energy += Ed5(j,i,j+1);
+																																Widjd = (canSS(i)&&canSS(j))? energy:Widjd;
+																																Wij = MIN(Wij, Widjd);
+																								}	else if (g_dangles == 0) { // -d0 option
+																																Wij = V(i, j) + auPenalty(i, j) + Wim1;
+																								} else { // default
+																																Wij = V(i, j) + auPenalty(i, j) + Wim1;
+																																Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:INFINITY_;
+																																Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:INFINITY_;
+																																Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:INFINITY_;
+																																Wij = MIN4(Wij, Widjd, Wijd, Widj);
+																								}
+
+																								Wj = MIN(Wj,Wij); 
+																}
+																W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj;
+								}
 
 #ifdef DEBUG
-	FILE* file = fopen("VM.txt", "w");
-	int ii, jj;
-	for (ii = 1; ii <= len; ++ii) {    
-		for (jj = 1; jj <= len; ++jj) {
-			fprintf(file, "%d %d %d\n",ii,jj,VM(ii,jj));
-		}
-	}    
-	fclose(file);
+								FILE* file = fopen("VBI.txt", "w");
+								int ii, jj;
+								for (ii = 1; ii <= len; ++ii) {    
+																for (jj = len; jj > ii; --jj) {
+																								fprintf(file, "%d %d %d\n",ii,jj,VBI(ii,jj));
+																}
+								}    
+								fclose(file);
+
+								file = fopen("Eh.txt", "w");
+								for (ii = 1; ii <= len; ++ii) {    
+																for (jj = len; jj > ii; --jj) {
+																				int eh = INFINITY_;
+																			 if (PP[ii][jj])	eh = eH(ii,jj);
+																				fprintf(file, "%d %d %d\n",ii,jj,eh>=INFINITY_?INFINITY_:eh);
+																}
+								}    
+								fclose(file);
 	
- 	file = fopen("WM.txt", "w");
-	for (ii = 1; ii <= len; ++ii) {    
-		for (jj = 1; jj <= len; ++jj) {
-			fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj));
-		}
-	}    
-	fclose(file);
+								file = fopen("Es.txt", "w");
+								for (ii = 1; ii <= len; ++ii) {    
+																for (jj = len; jj > ii; --jj) {
+																				int es = INFINITY_;
+																				if (PP[ii][jj] && PP[ii+1][jj-1]) es = eS(ii,jj);
+																				fprintf(file, "%d %d %d\n",ii,jj,es>=INFINITY_?INFINITY_:es);
+																}
+								}    
+								fclose(file);
+															
+								file = fopen("BP.txt", "w");
+								for (ii = 1; ii <= len; ++ii) {    
+																for (jj = len; jj > ii; --jj) {
+																								fprintf(file, "%d %d %d\n",ii,jj,PP[ii][jj]);
+																}
+								}    
+								fclose(file);
+
+								file = fopen("VM.txt", "w");
+								for (ii = 1; ii <= len; ++ii) {    
+																for (jj = len; jj > ii; --jj) {
+																								fprintf(file, "%d %d %d\n",ii,jj,VM(ii,jj));
+																}
+								}    
+								fclose(file);
+
+								file = fopen("WM.txt", "w");
+								for (ii = 1; ii <= len; ++ii) {    
+																for (jj = len; jj > ii; --jj) {
+																								fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj));
+																}
+								}    
+								fclose(file);
 #endif
-	
-	return W[len];
+
+								return W[len];
 }
diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c
index 1a64fe7..1c2d45b 100644
--- a/gtfold-mfe/src/global.c
+++ b/gtfold-mfe/src/global.c
@@ -9,6 +9,7 @@ int *structure;
 unsigned int chPairKey;
 
 int g_nthreads;
+int g_dangles;
 int g_unamode;
 int g_mismatch;
 int g_verbose;
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 280ed9e..23e8380 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -78,6 +78,7 @@ void init_fold(string seq) {
 	g_prefilter_mode  = b_prefilter;
 	g_prefilter1  = prefilter1;
 	g_prefilter2  = prefilter2;
+	g_dangles = dangles;
 }
 
 void free_fold(int len) {
@@ -226,19 +227,18 @@ int main(int argc, char** argv) {
 		exit(-1);
 	}
 	
-	printRunConfiguration(seq);
-	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
 	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
 
-	
 	init_fold(seq);
+	
+	printRunConfiguration(seq);
 
 	printf("\nComputing minimum free energy structure...\n");
 	fflush(stdout);
 
 	t1 = get_seconds();
-	energy = calculate(seq.length()) ; //, nThreads, UNAMODE, T_MISMATCH);
+	energy = calculate(seq.length()) ; 
 	t1 = get_seconds() - t1;
 	
 	printf("Done.\n\n");
@@ -264,7 +264,7 @@ int main(int argc, char** argv) {
 	}
 	
 	t1 = get_seconds();
-	trace(seq.length(), VERBOSE, UNAMODE, T_MISMATCH);
+	trace(seq.length()); //, VERBOSE, UNAMODE, T_MISMATCH);
 	t1 = get_seconds() - t1;
 	
 	printf("\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index a690bc1..e60c8b7 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -29,6 +29,7 @@ string outputDir = "";
 string shapeFile = "";
 string paramDir; // default value
 
+int dangles=-1;
 int prefilter1=2;
 int prefilter2=2;
 
@@ -52,6 +53,7 @@ void help() {
     printf("                        limit is given, base pairs can be over any distance\n");
     printf("   -p  --paramdir DIR   Path to directory from where parameters are to be read\n");
     printf("   -m   		Enable terminal mismatch calculations\n");
+    printf("   -d2   		Enable d2 calculations\n");
    	printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output NAME    Name output files with prefix\n");
     printf("   -w, --workDir DIR    Path to directory for output files\n");
@@ -109,16 +111,19 @@ void parse_options(int argc, char** argv) {
 			} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
 				NOISOLATE = true;
 			} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
-				if(i < argc)
+				if(i < argc) {
 					outputPrefix = argv[++i];
+				}
 				else
 					help();
 			} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
-				if(i < argc)
+				if(i < argc) {
 					outputDir = argv[++i];
+				}
 				else
 					help();
-			} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+			} 
+			else if (strcmp(argv[i], "--paramdir")== 0 || strcmp(argv[i], "-p") == 0) {
 					if(i < argc) {
 					paramDir = argv[++i];
 					PARAM_DIR = true;
@@ -127,6 +132,10 @@ void parse_options(int argc, char** argv) {
 					help();
 			} else if (strcmp(argv[i], "-m") == 0) {
 				T_MISMATCH = true;
+			} else if (strcmp(argv[i], "-d2") == 0) {
+				dangles = 2;
+			} else if (strcmp(argv[i], "-d0") == 0) {
+				dangles = 0;
 			} else if (strcmp(argv[i], "--unafold") == 0) {
 				UNAMODE = true;
 			} else if (strcmp(argv[i], "--rnafold") == 0) {
@@ -202,8 +211,11 @@ void parse_options(int argc, char** argv) {
 	// If output dir specified
 	if (!outputDir.empty()) {
 		outputFile += outputDir;
+		outputFile += "/";
 		suboptFile += outputDir;
+		suboptFile += "/";
 		bppOutFile += outputDir;
+		bppOutFile += "/";
 	}
 	// ... and append the .ct
 	outputFile += outputPrefix;
@@ -225,8 +237,16 @@ void printRunConfiguration(string seq) {
 	bool standardRun = true;
 
 	printf("Run Configuration:\n");
+		if (RNAMODE == true) {
+		printf("+ running in rnafold mode\n");
+		standardRun = false;
+	}
 	if (UNAMODE == true) {
-		printf("+ running in unamode\n");
+		printf("+ running in unafold mode\n");
+		standardRun = false;
+	}
+	if (dangles == 2) {
+		printf("+ running in -d2 mode\n");
 		standardRun = false;
 	}
 	if (T_MISMATCH == true) {
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 6cea549..508ed8f 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -30,20 +30,16 @@
 #include "utils.h"
 #include "shapereader.h"
 
-int verbose = -1;
 int total_en = 0;
 int total_ex = 0;
-int unamode = 0;
+int length = 0;
 
-void trace(int len, int vv, int mode, int mismatch) {
+void trace(int len) { 
+	printf("traceback()\n");
 	int i;
-	verbose = vv;
-	unamode = mode;
-	if (mismatch) unamode = 1;
-
-	for (i = 0; i < len+1; i++)
-		structure[i] = 0;
+	for (i = 0; i <= len; i++) structure[i] = 0;
 
+	length = len;
 	if (W[len] >= MAXENG) {
 		printf("- No Structure \n");
 		return;
@@ -58,14 +54,11 @@ void trace(int len, int vv, int mode, int mismatch) {
 }
 
 void traceW(int j) {
-	int done, i, Wj;
-	int wim1, flag, Widjd, Wijd, Widj, Wij;
-	Wj = INFINITY_;
-	flag = 1;
-	done = 0; 
+	int done = 0, i;
+	int wim1, flag = 1 ;
+	
+	assert(!(j == 0 || j == 1)); 
 	
-	if (j == 0 || j == 1) return;
-
 	for (i = 1; i < j && !done; i++) {
 		if (j-i < TURN) continue;
 
@@ -73,74 +66,95 @@ void traceW(int j) {
 		flag = 1;
 		if ( wim1 != W[i-1] && canSSregion(0,i)) flag = 0;
 
-		Widjd = Wijd =  Widj = INFINITY_;
-		Wij = V(i,j) + auPenalty(i, j) + wim1;
-		
-		if (unamode) {
-			Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Estacke(j-1,i+1) + wim1;
-		}
-		else {
-			Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1;
-		}
-
-		Wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
-		Widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
-
-		if ((W[j] == Wij && canStack(i,j)) || forcePair(i,j)) { 
-			done = 1;
-			if (verbose == 1) 
-				printf("i %5d j %5d ExtLoop   %12.2f\n", i, j, auPenalty(i, j)/100.00);
-			total_ex += auPenalty(i, j);
-			structure[i] = j;
-			structure[j] = i;
-			traceV(i, j);
-			if (flag ) traceW(i - 1);
-			break;
-		} else if ((W[j] == Widjd && unamode && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
-			done = 1;
-			if (verbose == 1) 
-				printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Estacke(j-1,i+1))/100.00);
-			total_ex += (auPenalty(i+1, j-1) + Estacke(j-1,i+1));
-			structure[i + 1] = j - 1;
-			structure[j - 1] = i + 1;
-			traceV(i + 1, j - 1);
-			if (flag ) traceW(i - 1);
-			break;
-		}
-	   	else if ((W[j] == Widjd && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
-			done = 1;
-			if (verbose == 1) 
-				printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
-			total_ex += (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
-			structure[i + 1] = j - 1;
-			structure[j - 1] = i + 1;
-			traceV(i + 1, j - 1);
-			if (flag ) traceW(i - 1);
-			break;
-		} else if ((W[j] == Wijd && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) { 	
-			done = 1;
-			if (verbose == 1) 
-				printf("i %5d j %5d ExtLoop   %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
-			total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
-			structure[i] = j - 1;
-			structure[j - 1] = i;
-			traceV(i, j - 1);
-			if (flag ) traceW(i - 1);
-			break;
-		} else if ((W[j] == Widj && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){
-			done = 1;
-			if (verbose == 1) 
-				printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
-			total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
-			structure[i + 1] = j;
-			structure[j] = i + 1;
-			traceV(i + 1, j);
-			if (flag ) traceW(i - 1);
-			break;
+		if (g_unamode||g_mismatch) {
+			if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) { 
+							done = 1;
+							if (g_verbose == 1) printf("i %5d j %5d ExtLoop   %12.2f\n", i, j, auPenalty(i, j)/100.00);
+							total_ex += auPenalty(i, j);
+							traceV(i, j);
+							if (flag ) traceW(i - 1);
+							break;
+			} else if ((W[j] ==  V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1 && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) { 	
+							done = 1;
+							if (g_verbose == 1) printf("i %5d j %5d ExtLoop   %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
+							total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
+							traceV(i, j - 1);
+							if (flag ) traceW(i - 1);
+							break;
+			} else if ((W[j] == V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1 && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){
+							done = 1;
+							if (g_verbose == 1) printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
+							total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
+							traceV(i + 1, j);
+							if (flag ) traceW(i - 1);
+							break;
+			} else if ((W[j] == V(i+1,j-1) + auPenalty(i+1, j-1) + Estacke(j-1,i+1) + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
+							done = 1;
+							if (g_verbose == 1) printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Estacke(j-1,i+1))/100.00);
+							total_ex += (auPenalty(i+1, j-1) + Estacke(j-1,i+1));
+							traceV(i + 1, j - 1);
+							if (flag ) traceW(i - 1);
+							break;
+			}
+		} else if (g_dangles == 2) {
+				int e_dangles = 0;
+				if (i>1) e_dangles +=  Ed3(j,i,i-1);
+				if (j<length) e_dangles += Ed5(j,i,j+1);
+				if ((W[j] == V(i,j) + auPenalty(i, j) + e_dangles + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
+												done = 1;
+												if (g_verbose == 1) printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i, j) + e_dangles)/100.00);
+												total_ex += (auPenalty(i, j) + e_dangles);
+												traceV(i, j);
+												if (flag ) traceW(i - 1);
+												break;
+				} 
+		}	else if (g_dangles == 0) {
+			if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) { 
+							done = 1;
+							if (g_verbose == 1) printf("i %5d j %5d ExtLoop   %12.2f\n", i, j, auPenalty(i, j)/100.00);
+							total_ex += auPenalty(i, j);
+							traceV(i, j);
+							if (flag ) traceW(i - 1);
+							break;
+			}
+		} else { // default
+			if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) { 
+							done = 1;
+							if (g_verbose == 1) printf("i %5d j %5d ExtLoop   %12.2f\n", i, j, auPenalty(i, j)/100.00);
+							total_ex += auPenalty(i, j);
+							traceV(i, j);
+							if (flag ) traceW(i - 1);
+							break;
+			} else if ((W[j] ==  V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1 && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) { 	
+							done = 1;
+							if (g_verbose == 1) printf("i %5d j %5d ExtLoop   %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
+							total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
+							traceV(i, j - 1);
+							if (flag ) traceW(i - 1);
+							break;
+			} else if ((W[j] == V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1 && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){
+							done = 1;
+							if (g_verbose == 1) printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
+							total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
+							traceV(i + 1, j);
+							if (flag ) traceW(i - 1);
+							break;
+			} else if ((W[j] == V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { 
+							done = 1;
+							if (g_verbose == 1) printf("i %5d j %5d ExtLoop   %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
+							total_ex += (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
+							traceV(i + 1, j - 1);
+							if (flag ) traceW(i - 1);
+							break;
+			} 
 		}
 	}
 		
 	if (W[j] == W[j - 1] && !done) traceW(j-1);
+ 
+	//if (!done) {
+	//	fprintf(stderr, "ERROR: W(%d) could not be traced\n", j);
+	//}
 
 	return;
 }
@@ -151,34 +165,29 @@ int traceV(int i, int j) {
 
 	a = canHairpin(i,j)?eH(i, j):INFINITY_;
 	b = canStack(i,j)?eS(i, j) + V(i + 1, j - 1):INFINITY_;
-	// if (eS(i, j) == 0) b = INFINITY_;
 	c = canStack(i,j)?VBI(i,j):INFINITY_;
 	d = canStack(i,j)?VM(i,j):INFINITY_;
 	
 	Vij = V(i,j);
+	structure[i] = j;
+	structure[j] = i;
 
 	if (Vij == a ) { 
-		if (verbose == 1) 
-			printf("i %5d j %5d Hairpin   %12.2f\n", i, j, eH(i, j)/100.00);
+		if (g_verbose == 1) printf("i %5d j %5d Hairpin   %12.2f\n", i, j, eH(i, j)/100.00);
 		total_en += eH(i,j);
 		return Vij;
 	} else if (Vij == b) { 
-		if (verbose == 1) 
-			printf("i %5d j %5d Stack     %12.2f\n", i, j, eS(i, j)/100.00);
+		if (g_verbose == 1) printf("i %5d j %5d Stack     %12.2f\n", i, j, eS(i, j)/100.00);
 		total_en += eS(i,j);
-		structure[i + 1] = j - 1;
-		structure[j - 1] = i + 1;
 		traceV(i + 1, j - 1);
 		return Vij;
 	} else if (Vij == c) { 
-		if (verbose == 1) 
-			printf("i %5d j %5d IntLoop  ", i, j);
+		if (g_verbose == 1) printf("i %5d j %5d IntLoop  ", i, j);
 		traceVBI(i, j);
 		return Vij;
 	} else if (Vij == d) { 
 		int eVM = traceVM(i, j);
-		if (verbose ==1) 
-			printf("i %5d j %5d MultiLoop %12.2f\n", i, j, (Vij-eVM)/100.0);
+		if (g_verbose ==1) printf("i %5d j %5d MultiLoop %12.2f\n", i, j, (Vij-eVM)/100.0);
 		total_en += (Vij-eVM);
 		return Vij;
 	}
@@ -187,9 +196,8 @@ int traceV(int i, int j) {
 }
 
 int traceVBI(int i, int j) {
-	
-	int VBIij_temp;
-	int ip, jp, el, v;
+	int VBIij;
+	int ip, jp;
 	int ifinal, jfinal;
 
 	ifinal = 0;
@@ -197,157 +205,155 @@ int traceVBI(int i, int j) {
 
 	for (ip = i + 1; ip < j - 1; ip++) {
 		for (jp = ip + 1; jp < j; jp++) {
-			el = eL(i, j, ip, jp);
-			v = V(ip, jp);
-			VBIij_temp = el + v;
-			if (VBIij_temp == VBI(i,j) || forcePair(ip,jp)){
+			VBIij = eL(i, j, ip, jp)+ V(ip,jp);
+			if (VBIij == VBI(i,j) || forcePair(ip,jp)){
 				ifinal = ip;
 				jfinal = jp;
 				break;
 			}
 		}
-		if (jp != j)
-			break;
+		if (jp != j) break;
 	}
 
-	structure[ifinal] = jfinal;
-	structure[jfinal] = ifinal;
-	if (verbose==1) 
-		printf(" %12.2f\n", eL(i, j, ifinal, jfinal)/100.00);
+	if (g_verbose==1) printf(" %12.2f\n", eL(i, j, ifinal, jfinal)/100.00);
 	total_en += eL(i, j, ifinal, jfinal);
 
-	int eVI = traceV(ifinal, jfinal);
-	return eVI ;
+	return traceV(ifinal, jfinal);
 }
 
 int traceVM(int i, int j) {
-	int done;
-	int h;
-	int A_temp;
+	int done = 0;
 	int eVM = 0;
 
-	done = 0;
-	int VMij = VM(i,j);
-
-	if (unamode && i<j-TURN-2) {
-		for (h = i + 3; h <= j - 2 && !done; h++) { 
-			A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i,j) + Estackm(i,j);
-			if (A_temp == VMij && canSS(i+1) && canSS(j-1)) {
-				done = 1;
-				eVM += traceWM(i + 2, h - 1);
-				eVM += traceWM(h, j - 2);
-				break;
-			}
+	if (g_unamode||g_mismatch) {
+		if (VM(i,j) == WMPrime[i+1][j - 1] + Ea + Eb + auPenalty(i, j) ) {
+			done = 1;
+			eVM += traceWMPrime(i + 1, j - 1);
+		} else if (VM(i,j) == WMPrime[i + 2][j - 1] + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ec && canSS(i+1) ) {
+			done = 1;
+			eVM += traceWMPrime(i + 2, j - 1);
 		}
-	}
-	else {
-		for (h = i + 3; h <= j - 2 && !done; h++) { 
-			A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1);
-			if (A_temp == VMij && canSS(i+1) && canSS(j-1)) {
-				done = 1;
-				eVM += traceWM(i + 2, h - 1);
-				eVM += traceWM(h, j - 2);
-				break;
-			}
+		else if ( VM(i,j) == WMPrime[i + 1][j - 2] + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1) + Ec && canSS(j-1)) {
+			done = 1;
+			eVM += traceWMPrime(i + 1, j - 2);
 		}
-	}
-
-	for (h = i + 2; h <= j - 1 && !done; h++) {
-		A_temp = WM(i+1,h-1) + WM(h,j - 1) + Ea + Eb + auPenalty(i, j);
-		if (A_temp == VMij) { 
+		else if (V(i,j) == WMPrime[i + 2][j - 2] + Ea + Eb + auPenalty(i,j) + Estackm(i,j) + 2*Ec && canSS(i+1) && canSS(j-1) ) {
 			done = 1;
-			eVM += traceWM(i + 1, h - 1);
-			eVM += traceWM(h, j - 1);
-			break;
+			eVM += traceWMPrime(i + 2, j - 2);
 		}
-	}
-
-	for (h = i + 3; h <= j - 1 && !done; h++) {
-		A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1); 
-		if (A_temp == VMij && canSS(i+1) ) {
+	} else if (g_dangles == 2) {
+		if (V(i,j) ==  WMPrime[i + 1][j - 1] + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1) && canSS(i+1) && canSS(j-1) ) {
 			done = 1;
-			eVM += traceWM(i + 2, h - 1);
-			eVM += traceWM(h, j - 1);
-			break;
+			eVM += traceWMPrime(i + 1, j - 1);
 		}
-	}
-
-	for (h = i + 2; h <= j - 2 && !done; h++) { 
-		A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1);
-		if (A_temp == VMij && canSS(j-1)) {
+	}	else if (g_dangles == 0) {
+		if (VM(i,j) == WMPrime[i+1][j - 1] + Ea + Eb + auPenalty(i, j) ) {
 			done = 1;
-			eVM += traceWM(i + 1, h - 1);
-			eVM += traceWM(h, j - 2);
-			break;
+			eVM += traceWMPrime(i + 1, j - 1);
 		}
+	} else {
+		if (VM(i,j) == WMPrime[i+1][j - 1] + Ea + Eb + auPenalty(i, j) ) {
+			done = 1;
+			eVM += traceWMPrime(i + 1, j - 1);
+		} else if (VM(i,j) == WMPrime[i + 2][j - 1] + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ec && canSS(i+1) ) {
+			done = 1;
+			eVM += traceWMPrime(i + 2, j - 1);
+		}
+		else if ( VM(i,j) == WMPrime[i + 1][j - 2] + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1) + Ec && canSS(j-1)) {
+			done = 1;
+			eVM += traceWMPrime(i + 1, j - 2);
+		} else if (V(i,j) ==  WMPrime[i + 2][j - 2] + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1) + 2*Ec && canSS(i+1) && canSS(j-1) ) {
+			done = 1;
+			eVM += traceWMPrime(i + 2, j - 2);
+		}
+	}
+	if(!done) { 
+		fprintf(stderr, "ERROR: VM(%d,%d) could not be traced\n", i,j);
 	}
 
-		return eVM;
+	return eVM;
 }
 
-int traceWM(int i, int j) {
+int traceWMPrime(int i, int j) {
+	int done=0, h, energy=0;
+	
+	for (h = i; h < j && !done; h++) {
+			if (WM(i,h) + WM(h + 1,j) == WMPrime(i,j)) {
+				energy += traceWM(i, h);
+				energy += traceWM(h + 1, j);
+				done = 1;
+		 	  break;
+		}
+	}
+	return energy;
+}
 
-	int done;
-	int h1, h;
-	int eWM = 0; 
+int traceWM(int i, int j) {
+	assert(i < j);
+	int done=0, eWM=0;
 
-	done = 0;
-	h1 = 0;
+	if (!done && WM(i,j) == WMPrime[i][j]) {
+			eWM += traceWMPrime(i,j);
+			done = 1;
+	}
 
-	if (i >= j)
-		return 0;
-	else {
-		for (h = i; h < j && !done; h++) {
-			int aa = WM(i,h) + WM(h + 1,j); 
-			if (aa == WM(i,j)) {
-				done = 1;
-				h1 = h;
-				break;
-			}
+	if (!done){
+		if (g_unamode||g_mismatch) {
+						if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) { 
+										eWM += traceV(i, j);
+										done = 1;
+						} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) &&  canStack(i+1,j)) { 
+										eWM += traceV(i + 1, j);
+										done = 1;
+						} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec && canSS(j) && canStack(i,j-1)) { 
+										done = 1;
+										eWM += traceV(i, j - 1);
+						} else if (WM(i,j) == V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) {
+										done = 1;
+										eWM += traceV(i + 1, j - 1);
+						}
+		} else if (g_dangles == 2) {
+						int energy = V(i,j) + auPenalty(i, j) + Eb;				
+						energy += (i==1)?Ed3(j,i,length):Ed3(j,i,i-1);
+						/*if (j<len)*/ energy += Ed5(j,i,j+1);
+						if (WM(i,j) ==  energy && canSS(i) && canSS(j) && canStack(i+1,j-1)) { 
+										eWM += traceV(i, j);
+										done = 1;
+						}
+		} else if (g_dangles == 0) {
+						if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) { 
+										eWM += traceV(i, j);
+										done = 1;
+						}
+		} else  {
+						if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) { 
+										eWM += traceV(i, j);
+										done = 1;
+						} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) &&  canStack(i+1,j)) { 
+										eWM += traceV(i + 1, j);
+										done = 1;
+						} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec && canSS(j) && canStack(i,j-1)) { 
+										eWM += traceV(i, j - 1);
+										done = 1;
+						} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) { 
+										eWM += traceV(i + 1, j - 1);
+										done = 1;
+						}
 		}
-		if (h1 != 0) {
-			eWM += traceWM(i, h);
-			eWM += traceWM(h + 1, j);
-			done = 1;
-		} else {
-			if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) { 
-				structure[i] = j;
-				structure[j] = i;
-				eWM += traceV(i, j);
-				done = 1;
-			} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) &&  canStack(i+1,j)) { 
-				eWM += traceV(i + 1, j);
-				structure[i + 1] = j;
-				structure[j] = i + 1;
-				done = 1;
-			} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) +  Eb + Ec && canSS(j) && canStack(i,j-1)) { 
-				done = 1;
-				eWM += traceV(i, j - 1);
-				structure[i] = j - 1;
-				structure[j - 1] = i;
-			} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) { 
-				done = 1;
-				eWM += traceV(i + 1, j - 1);
-				structure[i + 1] = j - 1;
-				structure[j - 1] = i + 1;
-			}
-		   	else if (WM(i,j) == V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1) && unamode) {
-				done = 1;
-				eWM += traceV(i + 1, j - 1);
-				structure[i + 1] = j - 1;
-				structure[j - 1] = i + 1;
-			}
-			else if (WM(i,j) == WM(i + 1,j) + Ec && canSS(i)) { 
-				done = 1;
-				eWM += traceWM(i + 1, j);
-			} else if (WM(i,j) == WM(i,j - 1) + Ec && canSS(j)) { 
-				done = 1;
-				eWM += traceWM(i, j - 1);
-			}
+	}
+	
+	if (!done){
+		if (WM(i,j) == WM(i + 1,j) + Ec && canSS(i)) { 
+							done = 1;
+							eWM += traceWM(i + 1, j);
+		} else if (WM(i,j) == WM(i,j - 1) + Ec && canSS(j)) { 
+							done = 1;
+							eWM += traceWM(i, j - 1);
 		}
 	}
+
 	if(!done) { 
-		fprintf(stderr, "ERROR: WM(%d,%d) could not be traced!\n", i,j);
+		fprintf(stderr, "ERROR: WM(%d,%d) could not be traced\n", i,j);
 	}
 	return eWM;
 }

From 21abfb5919e4b8b7341c3273f30b664414ad42ab Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 8 Jul 2011 12:48:53 -0400
Subject: [PATCH 189/282] changed parameters for RNAfold mode

---
 gtfold-mfe/data/RNAParams/miscloop.DAT | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/data/RNAParams/miscloop.DAT b/gtfold-mfe/data/RNAParams/miscloop.DAT
index 3c000a5..69847f3 100644
--- a/gtfold-mfe/data/RNAParams/miscloop.DAT
+++ b/gtfold-mfe/data/RNAParams/miscloop.DAT
@@ -5,8 +5,8 @@
 10.10	-0.30	-0.30
 0.50
 0.0
-0.30
-1.60
-1.40
+0.0
+0.0
+0.0
 4.10
 0

From 9b11ef9650daff6cea3779bed9ba8f74cf7b80e5 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 8 Jul 2011 12:55:01 -0400
Subject: [PATCH 190/282] removed debug mode

---
 gtfold-mfe/src/algorithms.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 79425a5..bdf40c4 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -30,7 +30,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
 #include "omp.h"
 #endif
 
-#define DEBUG 1
+//#define DEBUG 1
 
 void initializeMatrix(int len) {
 	int i, j;

From 544254c80324c560f2cf0a8bff0a86a0375c29c2 Mon Sep 17 00:00:00 2001
From: Shel Swenson <shelswenson@gmail.com>
Date: Fri, 8 Jul 2011 15:28:20 -0400
Subject: [PATCH 191/282] Edited descriptions of --help message

---
 gtfold-mfe/src/options.cc | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index a690bc1..ec828de 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -48,17 +48,17 @@ void help() {
     printf("   -c, --constraints FILE\n");
     printf("                        Load constraints from FILE.  See Constraint syntax below\n");
 
-    printf("   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n");
+    printf("   -d, --limitCD INT    Set a maximum base pair contact distance to INT. If no\n");
     printf("                        limit is given, base pairs can be over any distance\n");
-    printf("   -p  --paramdir DIR   Path to directory from where parameters are to be read\n");
-    printf("   -m   		Enable terminal mismatch calculations\n");
-   	printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
-    printf("   -o, --output NAME    Name output files with prefix\n");
-    printf("   -w, --workDir DIR    Path to directory for output files\n");
-    printf("   -t, --threads num    Limit number of threads used\n");
-    printf("   --unafold 		Run as UNAFOLD default mode (version 3.8). \n");
-    printf("   --prefilter num1,num2 \n\t\t\tSets the prefilter mode similar to UNAfold\n");
-    printf("   --rnafold 		Run as RNAFOLD default mode (version 1.8.5). \n");
+    printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
+    printf("   -m                   Enable terminal mismatch calculations\n");
+    printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
+    printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
+    printf("   -w, --workDir DIR    Path of directory where output files will be written\n");
+    printf("   -t, --threads INT    Limit number of threads used to INT\n");
+    printf("   --unafold            Run as UNAfold default mode (version 3.8)\n");
+    printf("   --prefilter INT,INT  Sets the prefilter mode similar to UNAfold\n");
+    printf("   --rnafold            Run as RNAfold default mode (ViennaPackage version 1.8.5)\n");
 
     printf("\n");
     printf("   -h, --help           Output help (this message) and exit\n");
@@ -68,7 +68,7 @@ void help() {
     printf("   --bpp                Calculate base pair probabilities\n");
     printf("   --subopt range       Calculate suboptimal structures within 'range' kcal/mol\n");
     printf("                        of the mfe\n");
-    printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE");      
+    printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE\n");      
 
     printf("\nConstraint syntax:\n");
     printf("\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n");

From f79902585d266ace2437440907cc08e89624b302 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 8 Jul 2011 15:44:40 -0400
Subject: [PATCH 192/282] merged Shel's changes

---
 gtfold-mfe/src/options.cc | 32 ++++++++++++++------------------
 1 file changed, 14 insertions(+), 18 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index e60c8b7..7238419 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -49,18 +49,17 @@ void help() {
     printf("   -c, --constraints FILE\n");
     printf("                        Load constraints from FILE.  See Constraint syntax below\n");
 
-    printf("   -d, --limitCD num    Set a maximum base pair contact distance to num. If no\n");
+    printf("   -d, --limitCD INT    Set a maximum base pair contact distance to INT. If no\n");
     printf("                        limit is given, base pairs can be over any distance\n");
-    printf("   -p  --paramdir DIR   Path to directory from where parameters are to be read\n");
-    printf("   -m   		Enable terminal mismatch calculations\n");
-    printf("   -d2   		Enable d2 calculations\n");
-   	printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
-    printf("   -o, --output NAME    Name output files with prefix\n");
-    printf("   -w, --workDir DIR    Path to directory for output files\n");
-    printf("   -t, --threads num    Limit number of threads used\n");
-    printf("   --unafold 		Run as UNAFOLD default mode (version 3.8). \n");
-    printf("   --prefilter num1,num2 \n\t\t\tSets the prefilter mode similar to UNAfold\n");
-    printf("   --rnafold 		Run as RNAFOLD default mode (version 1.8.5). \n");
+    printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
+    printf("   -m                   Enable terminal mismatch calculations\n");
+    printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
+    printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
+    printf("   -w, --workDir DIR    Path of directory where output files will be written\n");
+    printf("   -t, --threads INT    Limit number of threads used to INT\n");
+    printf("   --unafold            Run as UNAfold default mode (version 3.8)\n");
+    printf("   --prefilter INT,INT  Sets the prefilter mode similar to UNAfold\n");
+    printf("   --rnafold            Run as RNAfold default mode (ViennaPackage version 1.8.5)\n");
 
     printf("\n");
     printf("   -h, --help           Output help (this message) and exit\n");
@@ -70,7 +69,7 @@ void help() {
     printf("   --bpp                Calculate base pair probabilities\n");
     printf("   --subopt range       Calculate suboptimal structures within 'range' kcal/mol\n");
     printf("                        of the mfe\n");
-    printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE");      
+    printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE\n");      
 
     printf("\nConstraint syntax:\n");
     printf("\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n");
@@ -111,19 +110,16 @@ void parse_options(int argc, char** argv) {
 			} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
 				NOISOLATE = true;
 			} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
-				if(i < argc) {
+				if(i < argc)
 					outputPrefix = argv[++i];
-				}
 				else
 					help();
 			} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
-				if(i < argc) {
+				if(i < argc)
 					outputDir = argv[++i];
-				}
 				else
 					help();
-			} 
-			else if (strcmp(argv[i], "--paramdir")== 0 || strcmp(argv[i], "-p") == 0) {
+			} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
 					if(i < argc) {
 					paramDir = argv[++i];
 					PARAM_DIR = true;

From 7f6c3c618927f8ac8a520167f4d4cbb467198dfa Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 11 Jul 2011 12:50:37 -0400
Subject: [PATCH 193/282] removed debug statement

---
 gtfold-mfe/src/traceback.c | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 508ed8f..35c7c29 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -35,7 +35,6 @@ int total_ex = 0;
 int length = 0;
 
 void trace(int len) { 
-	printf("traceback()\n");
 	int i;
 	for (i = 0; i <= len; i++) structure[i] = 0;
 

From 6cbc69ebea0603cfd752452143115a6c51689088 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 11 Jul 2011 12:51:46 -0400
Subject: [PATCH 194/282] added options for dangles, mismatch

---
 gtfold-mfe/src/main.cc    | 12 ++++++++++++
 gtfold-mfe/src/options.cc | 30 ++++++++++++++++++------------
 2 files changed, 30 insertions(+), 12 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 23e8380..9e76e49 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -43,6 +43,8 @@
 #include "subopt_traceback.h"
 #include "shapereader.h"
 
+//#define DEBUG 1
+
 using namespace std;
 
 double get_seconds() {
@@ -79,6 +81,16 @@ void init_fold(string seq) {
 	g_prefilter1  = prefilter1;
 	g_prefilter2  = prefilter2;
 	g_dangles = dangles;
+
+#ifdef DEBUG
+	printf("g_nthreads = %d\n", g_nthreads);
+	printf("g_unamode = %d\n", g_unamode);
+	printf("g_mismatch = %d\n", g_mismatch);
+	printf("g_prefilter_mode = %d\n", g_prefilter_mode);
+	printf("g_dangles = %d\n", g_dangles);
+
+#endif
+
 }
 
 void free_fold(int len) {
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 7238419..9282c22 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -49,10 +49,10 @@ void help() {
     printf("   -c, --constraints FILE\n");
     printf("                        Load constraints from FILE.  See Constraint syntax below\n");
 
-    printf("   -d, --limitCD INT    Set a maximum base pair contact distance to INT. If no\n");
+    printf("   -l, --limitCD INT    Set a maximum base pair contact distance to INT. If no\n");
     printf("                        limit is given, base pairs can be over any distance\n");
     printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
-    printf("   -m                   Enable terminal mismatch calculations\n");
+    printf("   -m  --mismatch       Enable terminal mismatch calculations\n");
     printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
     printf("   -w, --workDir DIR    Path of directory where output files will be written\n");
@@ -95,7 +95,7 @@ void parse_options(int argc, char** argv) {
 				}
 				else
 					help();
-			} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-d") == 0) {
+			} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
 				if(i < argc){
 					contactDistance = atoi(argv[++i]);
 					stringstream ss;
@@ -126,16 +126,22 @@ void parse_options(int argc, char** argv) {
 				}
 				else
 					help();
-			} else if (strcmp(argv[i], "-m") == 0) {
-				T_MISMATCH = true;
-			} else if (strcmp(argv[i], "-d2") == 0) {
-				dangles = 2;
-			} else if (strcmp(argv[i], "-d0") == 0) {
-				dangles = 0;
+			} else if (strcmp(argv[i], "--dangles") == 0 || strcmp(argv[i], "-d") == 0) {
+						if(i < argc) {
+									dangles = atoi(argv[++i]);
+									if (!(dangles == 0 || dangles == 1 || dangles == 2))
+											help();
+						} else
+								 help();
+			} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
+					if (!(dangles == 0 || dangles == 1 || dangles == 2))
+													T_MISMATCH = true;
 			} else if (strcmp(argv[i], "--unafold") == 0) {
 				UNAMODE = true;
+				dangles = -1;
 			} else if (strcmp(argv[i], "--rnafold") == 0) {
 				RNAMODE = true;
+				dangles = 1;
 			} else if (strcmp(argv[i], "--prefilter") == 0) {
 				if(i < argc) {
 					int value1 = -1, value2 = -1;
@@ -233,7 +239,7 @@ void printRunConfiguration(string seq) {
 	bool standardRun = true;
 
 	printf("Run Configuration:\n");
-		if (RNAMODE == true) {
+	if (RNAMODE == true) {
 		printf("+ running in rnafold mode\n");
 		standardRun = false;
 	}
@@ -241,8 +247,8 @@ void printRunConfiguration(string seq) {
 		printf("+ running in unafold mode\n");
 		standardRun = false;
 	}
-	if (dangles == 2) {
-		printf("+ running in -d2 mode\n");
+	if (dangles >= 0 && !RNAMODE) {
+		printf("+ running in dangles %d mode\n", dangles);
 		standardRun = false;
 	}
 	if (T_MISMATCH == true) {

From 3f2effa02f6f28e75b3da1ebb965612fd9a60bff Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 11 Jul 2011 12:59:29 -0400
Subject: [PATCH 195/282] enabled precedence of -d over -m optiom

---
 gtfold-mfe/src/options.cc | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 9282c22..8a7e138 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -129,19 +129,20 @@ void parse_options(int argc, char** argv) {
 			} else if (strcmp(argv[i], "--dangles") == 0 || strcmp(argv[i], "-d") == 0) {
 						if(i < argc) {
 									dangles = atoi(argv[++i]);
-									if (!(dangles == 0 || dangles == 1 || dangles == 2))
-											help();
+									if (!(dangles == 0 || dangles == 1 || dangles == 2)) help();
+									T_MISMATCH = false;
 						} else
 								 help();
 			} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
-					if (!(dangles == 0 || dangles == 1 || dangles == 2))
-													T_MISMATCH = true;
+					if (!(dangles == 0 || dangles == 1 || dangles == 2)) T_MISMATCH = true;
 			} else if (strcmp(argv[i], "--unafold") == 0) {
 				UNAMODE = true;
 				dangles = -1;
+				T_MISMATCH = false;
 			} else if (strcmp(argv[i], "--rnafold") == 0) {
 				RNAMODE = true;
 				dangles = 1;
+				T_MISMATCH = false;
 			} else if (strcmp(argv[i], "--prefilter") == 0) {
 				if(i < argc) {
 					int value1 = -1, value2 = -1;

From 57e86f4c414ef050b9886a9ad9e6c6a44e5ed91c Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 11 Jul 2011 13:14:22 -0400
Subject: [PATCH 196/282] options.cc

---
 gtfold-mfe/src/options.cc | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 8a7e138..cd16136 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -127,21 +127,32 @@ void parse_options(int argc, char** argv) {
 				else
 					help();
 			} else if (strcmp(argv[i], "--dangles") == 0 || strcmp(argv[i], "-d") == 0) {
+											std::string cmd = argv[i];
 						if(i < argc) {
 									dangles = atoi(argv[++i]);
-									if (!(dangles == 0 || dangles == 1 || dangles == 2)) help();
-									T_MISMATCH = false;
+									if (!(dangles == 0 || dangles == 2)) {
+																dangles = -1;
+																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
+									} else {
+																T_MISMATCH = false;
+									}
 						} else
 								 help();
 			} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
-					if (!(dangles == 0 || dangles == 1 || dangles == 2)) T_MISMATCH = true;
+											std::string cmd = argv[i];
+					if (!(dangles == 0 ||  dangles == 2)) 
+													T_MISMATCH = true;
+					else {
+													printf("Ignoring %s option\n", cmd.c_str());
+													T_MISMATCH = false;
+					}
 			} else if (strcmp(argv[i], "--unafold") == 0) {
 				UNAMODE = true;
 				dangles = -1;
 				T_MISMATCH = false;
 			} else if (strcmp(argv[i], "--rnafold") == 0) {
 				RNAMODE = true;
-				dangles = 1;
+				//dangles = 1;
 				T_MISMATCH = false;
 			} else if (strcmp(argv[i], "--prefilter") == 0) {
 				if(i < argc) {

From e8c7d3e288459b649b7a4208481e67bae067a0dd Mon Sep 17 00:00:00 2001
From: Shel Swenson <shelswenson@gmail.com>
Date: Mon, 11 Jul 2011 16:26:17 -0400
Subject: [PATCH 197/282] Edited descriptions of --help message

---
 gtfold-mfe/src/options.cc | 28 ++++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index cd16136..7a2f446 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -48,22 +48,24 @@ void help() {
     printf("OPTIONS\n");
     printf("   -c, --constraints FILE\n");
     printf("                        Load constraints from FILE.  See Constraint syntax below\n");
-
+    printf("   -d, --dangle INT     Allow only one treatment of dangleing end energies in \n");
+    printf("                        mulit- and external loops (INT=0,2) see below for details\n");
+    printf("   -h, --help           Output help (this message) and exit\n");
     printf("   -l, --limitCD INT    Set a maximum base pair contact distance to INT. If no\n");
     printf("                        limit is given, base pairs can be over any distance\n");
-    printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
     printf("   -m  --mismatch       Enable terminal mismatch calculations\n");
-    printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
+//    printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
-    printf("   -w, --workDir DIR    Path of directory where output files will be written\n");
+    printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
     printf("   -t, --threads INT    Limit number of threads used to INT\n");
-    printf("   --unafold            Run as UNAfold default mode (version 3.8)\n");
-    printf("   --prefilter INT,INT  Sets the prefilter mode similar to UNAfold\n");
+    printf("   -v, --verbose        Run in verbose mode\n");
+    printf("   -w, --workDir DIR    Path of directory where output files will be written\n");
+    printf("   --prefilter INT      Prohibits any basepair which does not have appropriate\n");
+    printf("                        neighboring nucleotides such that it could be part of\n");
+    printf("                        a helix of length INT\n");
     printf("   --rnafold            Run as RNAfold default mode (ViennaPackage version 1.8.5)\n");
+    printf("   --unafold            Run as UNAfold default mode (version 3.8)\n");
 
-    printf("\n");
-    printf("   -h, --help           Output help (this message) and exit\n");
-    printf("   -v, --verbose        Run in verbose mode\n");
 
     printf("\nBETA OPTIONS\n");
     printf("   --bpp                Calculate base pair probabilities\n");
@@ -75,6 +77,12 @@ void help() {
     printf("\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n");
     printf("\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n");
     printf("\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
+
+    printf("\nDangle:\n");
+    printf("\tINT=0 ignores dangling end energies (mostly for debugging).\n");
+    printf("\tINT=2 dangling end energies are added for nucleotieds on either\n");
+    printf("\tside of each branch in multi-loops and external loops.\n");
+    printf("\tAll other values for INT are ignored.\n");
     exit(-1);
 }
 
@@ -126,7 +134,7 @@ void parse_options(int argc, char** argv) {
 				}
 				else
 					help();
-			} else if (strcmp(argv[i], "--dangles") == 0 || strcmp(argv[i], "-d") == 0) {
+			} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
 											std::string cmd = argv[i];
 						if(i < argc) {
 									dangles = atoi(argv[++i]);

From 7959d2f46303b79a9af0fe784dd3b78cf5ac7d77 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 11 Jul 2011 17:32:31 -0400
Subject: [PATCH 198/282] fixed commandline options

---
 gtfold-mfe/src/main.cc    |  39 ++++-
 gtfold-mfe/src/options.cc | 321 ++++++++++++++++++--------------------
 2 files changed, 192 insertions(+), 168 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 9e76e49..86aee90 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -72,7 +72,41 @@ void init_fold(string seq) {
 	if (SHAPE_ENABLED) {
 		readSHAPEarray(shapeFile.c_str(),len);
 	}
+
+	if (UNAMODE) {
+									if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n");
+									if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n");
+									if (dangles == 0 || dangles == 2) 
+																	printf("Ignoring -d option, using --unafold\n");
+									if (b_prefilter == 1) 
+																	printf("Ignoring --prefilter option, using --unafold\n");
+									T_MISMATCH = false;
+									PARAM_DIR = false;
+									dangles = -1;
+									b_prefilter = false;
+	}
 	
+	if (RNAMODE) {
+									if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n");
+									if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n");
+									if (dangles == 0 || dangles == 2) 
+																	printf("Ignoring -d option, using --rnafold\n");
+									if (b_prefilter == 1) 
+																	printf("Ignoring --prefilter option, using --rnafold\n");
+									T_MISMATCH = false;
+									PARAM_DIR = false;
+									dangles = -1;
+									b_prefilter = false;
+	}
+
+	if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) {
+									if (T_MISMATCH) printf("Ignoring -m option, using -d option\n");
+									T_MISMATCH = false;
+	} else {
+									if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n");	
+									dangles = -1;
+	}
+
 	g_nthreads = nThreads;
 	g_unamode  = UNAMODE;
 	g_mismatch = T_MISMATCH;
@@ -82,7 +116,7 @@ void init_fold(string seq) {
 	g_prefilter2  = prefilter2;
 	g_dangles = dangles;
 
-#ifdef DEBUG
+	#ifdef DEBUG
 	printf("g_nthreads = %d\n", g_nthreads);
 	printf("g_unamode = %d\n", g_unamode);
 	printf("g_mismatch = %d\n", g_mismatch);
@@ -238,12 +272,11 @@ int main(int argc, char** argv) {
 		printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
 		exit(-1);
 	}
+	init_fold(seq);
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
 	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
 
-	init_fold(seq);
-	
 	printRunConfiguration(seq);
 
 	printf("\nComputing minimum free energy structure...\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index cd16136..191fb5d 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -48,22 +48,24 @@ void help() {
     printf("OPTIONS\n");
     printf("   -c, --constraints FILE\n");
     printf("                        Load constraints from FILE.  See Constraint syntax below\n");
-
+    printf("   -d, --dangle INT     Allow only one treatment of dangleing end energies in \n");
+    printf("                        mulit- and external loops (INT=0,2) see below for details\n");
+    printf("   -h, --help           Output help (this message) and exit\n");
     printf("   -l, --limitCD INT    Set a maximum base pair contact distance to INT. If no\n");
     printf("                        limit is given, base pairs can be over any distance\n");
-    printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
     printf("   -m  --mismatch       Enable terminal mismatch calculations\n");
-    printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
+//    printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
     printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
-    printf("   -w, --workDir DIR    Path of directory where output files will be written\n");
+    printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
     printf("   -t, --threads INT    Limit number of threads used to INT\n");
-    printf("   --unafold            Run as UNAfold default mode (version 3.8)\n");
-    printf("   --prefilter INT,INT  Sets the prefilter mode similar to UNAfold\n");
+    printf("   -v, --verbose        Run in verbose mode\n");
+    printf("   -w, --workDir DIR    Path of directory where output files will be written\n");
+    printf("   --prefilter INT      Prohibits any basepair which does not have appropriate\n");
+    printf("                        neighboring nucleotides such that it could be part of\n");
+    printf("                        a helix of length INT\n");
     printf("   --rnafold            Run as RNAfold default mode (ViennaPackage version 1.8.5)\n");
+    printf("   --unafold            Run as UNAfold default mode (version 3.8)\n");
 
-    printf("\n");
-    printf("   -h, --help           Output help (this message) and exit\n");
-    printf("   -v, --verbose        Run in verbose mode\n");
 
     printf("\nBETA OPTIONS\n");
     printf("   --bpp                Calculate base pair probabilities\n");
@@ -75,6 +77,12 @@ void help() {
     printf("\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n");
     printf("\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n");
     printf("\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
+
+    printf("\nDangle:\n");
+    printf("\tINT=0 ignores dangling end energies (mostly for debugging).\n");
+    printf("\tINT=2 dangling end energies are added for nucleotieds on either\n");
+    printf("\tside of each branch in multi-loops and external loops.\n");
+    printf("\tAll other values for INT are ignored.\n");
     exit(-1);
 }
 
@@ -82,164 +90,148 @@ void help() {
  * Parse the options from argc and argv and save them into global state.
  */
 void parse_options(int argc, char** argv) {
-	int i;
+								int i;
 
-	for(i=1; i<argc; i++) {
-		if(argv[i][0] == '-') {
-			if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
-				help();
-			} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
-				if(i < argc) {
-					constraintsFile = argv[++i];
-					CONS_ENABLED = true;
-				}
-				else
-					help();
-			} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
-				if(i < argc){
-					contactDistance = atoi(argv[++i]);
-					stringstream ss;
-					ss << contactDistance;
-					if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
-						LIMIT_DISTANCE = true;
-					else
-						help();
-				}
-				else
-					help();
-			} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
-				NOISOLATE = true;
-			} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
-				if(i < argc)
-					outputPrefix = argv[++i];
-				else
-					help();
-			} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
-				if(i < argc)
-					outputDir = argv[++i];
-				else
-					help();
-			} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
-					if(i < argc) {
-					paramDir = argv[++i];
-					PARAM_DIR = true;
-				}
-				else
-					help();
-			} else if (strcmp(argv[i], "--dangles") == 0 || strcmp(argv[i], "-d") == 0) {
-											std::string cmd = argv[i];
-						if(i < argc) {
-									dangles = atoi(argv[++i]);
-									if (!(dangles == 0 || dangles == 2)) {
-																dangles = -1;
-																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
-									} else {
-																T_MISMATCH = false;
-									}
-						} else
-								 help();
-			} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
-											std::string cmd = argv[i];
-					if (!(dangles == 0 ||  dangles == 2)) 
-													T_MISMATCH = true;
-					else {
-													printf("Ignoring %s option\n", cmd.c_str());
-													T_MISMATCH = false;
-					}
-			} else if (strcmp(argv[i], "--unafold") == 0) {
-				UNAMODE = true;
-				dangles = -1;
-				T_MISMATCH = false;
-			} else if (strcmp(argv[i], "--rnafold") == 0) {
-				RNAMODE = true;
-				//dangles = 1;
-				T_MISMATCH = false;
-			} else if (strcmp(argv[i], "--prefilter") == 0) {
-				if(i < argc) {
-					int value1 = -1, value2 = -1;
-					std::stringstream ss;
-					ss << argv[++i];
-					sscanf(ss.str().c_str(),"%d,%d", &value1, &value2);
-					if (value1 <= 0 || value2 <= 0) {
-						printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
-						help();
-					}
-					b_prefilter = true;
-					prefilter1 = value1;
-					prefilter2 = value2;
-				} else 
-					help();
-			}
-		   	else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
-				if(i < argc)
-					nThreads = atoi(argv[++i]);
-				else
-					help();	
-			} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
-                VERBOSE = true;
-			}
-			else if(strcmp(argv[i], "--bpp") == 0) {
-				BPP_ENABLED = true;
-			} else if(strcmp(argv[i], "--subopt") == 0) {
-				SUBOPT_ENABLED = true;
-				if(i < argc)
-					suboptDelta = atof(argv[++i]);
-				else
-					help();
-			}
-			else if (strcmp(argv[i], "--useSHAPE") == 0){
-				if( i < argc){
-					shapeFile = argv[++i];
-					SHAPE_ENABLED = true;
-				}
-				else
-					help();
-			}				
-		} else {
-			seqfile = argv[i];
-		}
-	}
+								for(i=1; i<argc; i++) {
+																if(argv[i][0] == '-') {
+																								if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
+																																help();
+																								} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
+																																if(i < argc) {
+																																								constraintsFile = argv[++i];
+																																								CONS_ENABLED = true;
+																																}
+																																else
+																																								help();
+																								} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
+																																if(i < argc){
+																																								contactDistance = atoi(argv[++i]);
+																																								stringstream ss;
+																																								ss << contactDistance;
+																																								if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
+																																																LIMIT_DISTANCE = true;
+																																								else
+																																																help();
+																																}
+																																else
+																																								help();
+																								} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
+																																NOISOLATE = true;
+																								} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
+																																if(i < argc)
+																																								outputPrefix = argv[++i];
+																																else
+																																								help();
+																								} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
+																																if(i < argc)
+																																								outputDir = argv[++i];
+																																else
+																																								help();
+																								} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+																																if(i < argc) {
+																																								paramDir = argv[++i];
+																																								PARAM_DIR = true;
+																																}
+																																else
+																																								help();
+																								} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
+																																std::string cmd = argv[i];
+																																if(i < argc) {
+																																								dangles = atoi(argv[++i]);
+																																								if (!(dangles == 0 || dangles == 2)) {
+																																																dangles = -1;
+																																																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
+																																								} 
+																																} else
+																																								help();
+																								} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
+																																T_MISMATCH = true;
+																								} else if (strcmp(argv[i], "--unafold") == 0) {
+																																UNAMODE = true;
+																								} else if (strcmp(argv[i], "--rnafold") == 0) {
+																																RNAMODE = true;
+																								} else if (strcmp(argv[i], "--prefilter") == 0) {
+																																if(i < argc) {
+																																								prefilter1 = atoi(argv[++i]);
+																																								if (prefilter1 <= 0 ) {
+																																																printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
+																																																help();
+																																								}
+																																								b_prefilter = true;
+																																								prefilter2 = prefilter1;
+																																} else 
+																																								help();
+																								}
+																								else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
+																																if(i < argc)
+																																								nThreads = atoi(argv[++i]);
+																																else
+																																								help();	
+																								} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
+																																VERBOSE = true;
+																								}
+																								else if(strcmp(argv[i], "--bpp") == 0) {
+																																BPP_ENABLED = true;
+																								} else if(strcmp(argv[i], "--subopt") == 0) {
+																																SUBOPT_ENABLED = true;
+																																if(i < argc)
+																																								suboptDelta = atof(argv[++i]);
+																																else
+																																								help();
+																								}
+																								else if (strcmp(argv[i], "--useSHAPE") == 0){
+																																if( i < argc){
+																																								shapeFile = argv[++i];
+																																								SHAPE_ENABLED = true;
+																																}
+																																else
+																																								help();
+																								}				
+																} else {
+																								seqfile = argv[i];
+																}
+								}
 
-	// Must have an input file specified
-	if(seqfile.empty()) {
-		help();
-		printf("Missing input file.\n");
-	}
+								// Must have an input file specified
+								if(seqfile.empty()) {
+																help();
+																printf("Missing input file.\n");
+								}
 
-	// If no output file specified, create one
-	if(outputPrefix.empty()) {
-		// base it off the input file
-		outputPrefix += seqfile;
-		
-		size_t pos;
-		// extract file name from the path
-		if ((pos=outputPrefix.find_last_of('/')) > 0) {
-			outputPrefix = outputPrefix.substr(pos+1);
-		}
+								// If no output file specified, create one
+								if(outputPrefix.empty()) {
+																// base it off the input file
+																outputPrefix += seqfile;
 
-		// and if an extension exists, remove it ...
-		if(outputPrefix.find(".") != string::npos)
-			outputPrefix.erase(outputPrefix.rfind("."));
-	 }
+																size_t pos;
+																// extract file name from the path
+																if ((pos=outputPrefix.find_last_of('/')) > 0) {
+																								outputPrefix = outputPrefix.substr(pos+1);
+																}
 
-	// If output dir specified
-	if (!outputDir.empty()) {
-		outputFile += outputDir;
-		outputFile += "/";
-		suboptFile += outputDir;
-		suboptFile += "/";
-		bppOutFile += outputDir;
-		bppOutFile += "/";
-	}
-	// ... and append the .ct
-	outputFile += outputPrefix;
-	outputFile += ".ct";
+																// and if an extension exists, remove it ...
+																if(outputPrefix.find(".") != string::npos)
+																								outputPrefix.erase(outputPrefix.rfind("."));
+								}
 
-	suboptFile += outputPrefix;	
-	suboptFile += "_ss.txt";	
+								// If output dir specified
+								if (!outputDir.empty()) {
+																outputFile += outputDir;
+																outputFile += "/";
+																suboptFile += outputDir;
+																suboptFile += "/";
+																bppOutFile += outputDir;
+																bppOutFile += "/";
+								}
+								// ... and append the .ct
+								outputFile += outputPrefix;
+								outputFile += ".ct";
 
-	bppOutFile += outputPrefix;	
-	bppOutFile += "_bpp.txt";	
+								suboptFile += outputPrefix;	
+								suboptFile += "_ss.txt";	
+
+								bppOutFile += outputPrefix;	
+								bppOutFile += "_bpp.txt";	
 }
 
 /**
@@ -254,15 +246,15 @@ void printRunConfiguration(string seq) {
 	if (RNAMODE == true) {
 		printf("+ running in rnafold mode\n");
 		standardRun = false;
-	}
+	} 
 	if (UNAMODE == true) {
 		printf("+ running in unafold mode\n");
 		standardRun = false;
 	}
-	if (dangles >= 0 && !RNAMODE) {
-		printf("+ running in dangles %d mode\n", dangles);
+	if (dangles == 0 || dangles == 2) {
+		printf("+ running in dangle %d mode\n", dangles);
 		standardRun = false;
-	}
+	} 
 	if (T_MISMATCH == true) {
 		printf("+ enabled terminal mismatch calculations\n");
 		standardRun = false;
@@ -271,7 +263,6 @@ void printRunConfiguration(string seq) {
 		printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2);
 		standardRun = false;
 	}
-
 	if (NOISOLATE == true) {
 		printf("- preventing isolated base pairs\n");
 		standardRun = false;

From 93972e5372cbab03c46fef5b99a100636245031f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Mon, 11 Jul 2011 17:36:16 -0400
Subject: [PATCH 199/282] fixed a print statement

---
 gtfold-mfe/src/options.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 191fb5d..6886f65 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -260,7 +260,7 @@ void printRunConfiguration(string seq) {
 		standardRun = false;
 	}
 	if (b_prefilter == true) {
-		printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2);
+		printf("+ running with prefilter value = %d\n",prefilter1);
 		standardRun = false;
 	}
 	if (NOISOLATE == true) {

From 63fbc244a6315d204de8826fa14a12130bd09fca Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 12:47:02 -0400
Subject: [PATCH 200/282] merged changes

---
 gtfold-mfe/src/main.cc    |  39 +----
 gtfold-mfe/src/options.cc | 297 ++++++++++++++++++++------------------
 2 files changed, 160 insertions(+), 176 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 86aee90..9e76e49 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -72,41 +72,7 @@ void init_fold(string seq) {
 	if (SHAPE_ENABLED) {
 		readSHAPEarray(shapeFile.c_str(),len);
 	}
-
-	if (UNAMODE) {
-									if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n");
-									if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n");
-									if (dangles == 0 || dangles == 2) 
-																	printf("Ignoring -d option, using --unafold\n");
-									if (b_prefilter == 1) 
-																	printf("Ignoring --prefilter option, using --unafold\n");
-									T_MISMATCH = false;
-									PARAM_DIR = false;
-									dangles = -1;
-									b_prefilter = false;
-	}
 	
-	if (RNAMODE) {
-									if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n");
-									if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n");
-									if (dangles == 0 || dangles == 2) 
-																	printf("Ignoring -d option, using --rnafold\n");
-									if (b_prefilter == 1) 
-																	printf("Ignoring --prefilter option, using --rnafold\n");
-									T_MISMATCH = false;
-									PARAM_DIR = false;
-									dangles = -1;
-									b_prefilter = false;
-	}
-
-	if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) {
-									if (T_MISMATCH) printf("Ignoring -m option, using -d option\n");
-									T_MISMATCH = false;
-	} else {
-									if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n");	
-									dangles = -1;
-	}
-
 	g_nthreads = nThreads;
 	g_unamode  = UNAMODE;
 	g_mismatch = T_MISMATCH;
@@ -116,7 +82,7 @@ void init_fold(string seq) {
 	g_prefilter2  = prefilter2;
 	g_dangles = dangles;
 
-	#ifdef DEBUG
+#ifdef DEBUG
 	printf("g_nthreads = %d\n", g_nthreads);
 	printf("g_unamode = %d\n", g_unamode);
 	printf("g_mismatch = %d\n", g_mismatch);
@@ -272,11 +238,12 @@ int main(int argc, char** argv) {
 		printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
 		exit(-1);
 	}
-	init_fold(seq);
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
 	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
 
+	init_fold(seq);
+	
 	printRunConfiguration(seq);
 
 	printf("\nComputing minimum free energy structure...\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 6886f65..7a2f446 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -90,148 +90,164 @@ void help() {
  * Parse the options from argc and argv and save them into global state.
  */
 void parse_options(int argc, char** argv) {
-								int i;
+	int i;
 
-								for(i=1; i<argc; i++) {
-																if(argv[i][0] == '-') {
-																								if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
-																																help();
-																								} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
-																																if(i < argc) {
-																																								constraintsFile = argv[++i];
-																																								CONS_ENABLED = true;
-																																}
-																																else
-																																								help();
-																								} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
-																																if(i < argc){
-																																								contactDistance = atoi(argv[++i]);
-																																								stringstream ss;
-																																								ss << contactDistance;
-																																								if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
-																																																LIMIT_DISTANCE = true;
-																																								else
-																																																help();
-																																}
-																																else
-																																								help();
-																								} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
-																																NOISOLATE = true;
-																								} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
-																																if(i < argc)
-																																								outputPrefix = argv[++i];
-																																else
-																																								help();
-																								} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
-																																if(i < argc)
-																																								outputDir = argv[++i];
-																																else
-																																								help();
-																								} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
-																																if(i < argc) {
-																																								paramDir = argv[++i];
-																																								PARAM_DIR = true;
-																																}
-																																else
-																																								help();
-																								} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
-																																std::string cmd = argv[i];
-																																if(i < argc) {
-																																								dangles = atoi(argv[++i]);
-																																								if (!(dangles == 0 || dangles == 2)) {
-																																																dangles = -1;
-																																																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
-																																								} 
-																																} else
-																																								help();
-																								} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
-																																T_MISMATCH = true;
-																								} else if (strcmp(argv[i], "--unafold") == 0) {
-																																UNAMODE = true;
-																								} else if (strcmp(argv[i], "--rnafold") == 0) {
-																																RNAMODE = true;
-																								} else if (strcmp(argv[i], "--prefilter") == 0) {
-																																if(i < argc) {
-																																								prefilter1 = atoi(argv[++i]);
-																																								if (prefilter1 <= 0 ) {
-																																																printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
-																																																help();
-																																								}
-																																								b_prefilter = true;
-																																								prefilter2 = prefilter1;
-																																} else 
-																																								help();
-																								}
-																								else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
-																																if(i < argc)
-																																								nThreads = atoi(argv[++i]);
-																																else
-																																								help();	
-																								} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
-																																VERBOSE = true;
-																								}
-																								else if(strcmp(argv[i], "--bpp") == 0) {
-																																BPP_ENABLED = true;
-																								} else if(strcmp(argv[i], "--subopt") == 0) {
-																																SUBOPT_ENABLED = true;
-																																if(i < argc)
-																																								suboptDelta = atof(argv[++i]);
-																																else
-																																								help();
-																								}
-																								else if (strcmp(argv[i], "--useSHAPE") == 0){
-																																if( i < argc){
-																																								shapeFile = argv[++i];
-																																								SHAPE_ENABLED = true;
-																																}
-																																else
-																																								help();
-																								}				
-																} else {
-																								seqfile = argv[i];
-																}
-								}
-
-								// Must have an input file specified
-								if(seqfile.empty()) {
-																help();
-																printf("Missing input file.\n");
-								}
+	for(i=1; i<argc; i++) {
+		if(argv[i][0] == '-') {
+			if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
+				help();
+			} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
+				if(i < argc) {
+					constraintsFile = argv[++i];
+					CONS_ENABLED = true;
+				}
+				else
+					help();
+			} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
+				if(i < argc){
+					contactDistance = atoi(argv[++i]);
+					stringstream ss;
+					ss << contactDistance;
+					if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
+						LIMIT_DISTANCE = true;
+					else
+						help();
+				}
+				else
+					help();
+			} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
+				NOISOLATE = true;
+			} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
+				if(i < argc)
+					outputPrefix = argv[++i];
+				else
+					help();
+			} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
+				if(i < argc)
+					outputDir = argv[++i];
+				else
+					help();
+			} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+					if(i < argc) {
+					paramDir = argv[++i];
+					PARAM_DIR = true;
+				}
+				else
+					help();
+			} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
+											std::string cmd = argv[i];
+						if(i < argc) {
+									dangles = atoi(argv[++i]);
+									if (!(dangles == 0 || dangles == 2)) {
+																dangles = -1;
+																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
+									} else {
+																T_MISMATCH = false;
+									}
+						} else
+								 help();
+			} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
+											std::string cmd = argv[i];
+					if (!(dangles == 0 ||  dangles == 2)) 
+													T_MISMATCH = true;
+					else {
+													printf("Ignoring %s option\n", cmd.c_str());
+													T_MISMATCH = false;
+					}
+			} else if (strcmp(argv[i], "--unafold") == 0) {
+				UNAMODE = true;
+				dangles = -1;
+				T_MISMATCH = false;
+			} else if (strcmp(argv[i], "--rnafold") == 0) {
+				RNAMODE = true;
+				//dangles = 1;
+				T_MISMATCH = false;
+			} else if (strcmp(argv[i], "--prefilter") == 0) {
+				if(i < argc) {
+					int value1 = -1, value2 = -1;
+					std::stringstream ss;
+					ss << argv[++i];
+					sscanf(ss.str().c_str(),"%d,%d", &value1, &value2);
+					if (value1 <= 0 || value2 <= 0) {
+						printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
+						help();
+					}
+					b_prefilter = true;
+					prefilter1 = value1;
+					prefilter2 = value2;
+				} else 
+					help();
+			}
+		   	else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
+				if(i < argc)
+					nThreads = atoi(argv[++i]);
+				else
+					help();	
+			} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
+                VERBOSE = true;
+			}
+			else if(strcmp(argv[i], "--bpp") == 0) {
+				BPP_ENABLED = true;
+			} else if(strcmp(argv[i], "--subopt") == 0) {
+				SUBOPT_ENABLED = true;
+				if(i < argc)
+					suboptDelta = atof(argv[++i]);
+				else
+					help();
+			}
+			else if (strcmp(argv[i], "--useSHAPE") == 0){
+				if( i < argc){
+					shapeFile = argv[++i];
+					SHAPE_ENABLED = true;
+				}
+				else
+					help();
+			}				
+		} else {
+			seqfile = argv[i];
+		}
+	}
 
-								// If no output file specified, create one
-								if(outputPrefix.empty()) {
-																// base it off the input file
-																outputPrefix += seqfile;
+	// Must have an input file specified
+	if(seqfile.empty()) {
+		help();
+		printf("Missing input file.\n");
+	}
 
-																size_t pos;
-																// extract file name from the path
-																if ((pos=outputPrefix.find_last_of('/')) > 0) {
-																								outputPrefix = outputPrefix.substr(pos+1);
-																}
+	// If no output file specified, create one
+	if(outputPrefix.empty()) {
+		// base it off the input file
+		outputPrefix += seqfile;
+		
+		size_t pos;
+		// extract file name from the path
+		if ((pos=outputPrefix.find_last_of('/')) > 0) {
+			outputPrefix = outputPrefix.substr(pos+1);
+		}
 
-																// and if an extension exists, remove it ...
-																if(outputPrefix.find(".") != string::npos)
-																								outputPrefix.erase(outputPrefix.rfind("."));
-								}
+		// and if an extension exists, remove it ...
+		if(outputPrefix.find(".") != string::npos)
+			outputPrefix.erase(outputPrefix.rfind("."));
+	 }
 
-								// If output dir specified
-								if (!outputDir.empty()) {
-																outputFile += outputDir;
-																outputFile += "/";
-																suboptFile += outputDir;
-																suboptFile += "/";
-																bppOutFile += outputDir;
-																bppOutFile += "/";
-								}
-								// ... and append the .ct
-								outputFile += outputPrefix;
-								outputFile += ".ct";
+	// If output dir specified
+	if (!outputDir.empty()) {
+		outputFile += outputDir;
+		outputFile += "/";
+		suboptFile += outputDir;
+		suboptFile += "/";
+		bppOutFile += outputDir;
+		bppOutFile += "/";
+	}
+	// ... and append the .ct
+	outputFile += outputPrefix;
+	outputFile += ".ct";
 
-								suboptFile += outputPrefix;	
-								suboptFile += "_ss.txt";	
+	suboptFile += outputPrefix;	
+	suboptFile += "_ss.txt";	
 
-								bppOutFile += outputPrefix;	
-								bppOutFile += "_bpp.txt";	
+	bppOutFile += outputPrefix;	
+	bppOutFile += "_bpp.txt";	
 }
 
 /**
@@ -246,23 +262,24 @@ void printRunConfiguration(string seq) {
 	if (RNAMODE == true) {
 		printf("+ running in rnafold mode\n");
 		standardRun = false;
-	} 
+	}
 	if (UNAMODE == true) {
 		printf("+ running in unafold mode\n");
 		standardRun = false;
 	}
-	if (dangles == 0 || dangles == 2) {
-		printf("+ running in dangle %d mode\n", dangles);
+	if (dangles >= 0 && !RNAMODE) {
+		printf("+ running in dangles %d mode\n", dangles);
 		standardRun = false;
-	} 
+	}
 	if (T_MISMATCH == true) {
 		printf("+ enabled terminal mismatch calculations\n");
 		standardRun = false;
 	}
 	if (b_prefilter == true) {
-		printf("+ running with prefilter value = %d\n",prefilter1);
+		printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2);
 		standardRun = false;
 	}
+
 	if (NOISOLATE == true) {
 		printf("- preventing isolated base pairs\n");
 		standardRun = false;

From 3249482366ecfa4104a3cc90bece6b8724d2326b Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 12:49:48 -0400
Subject: [PATCH 201/282] fixed commanline options

---
 gtfold-mfe/src/main.cc    |  39 ++++-
 gtfold-mfe/src/options.cc | 297 ++++++++++++++++++--------------------
 2 files changed, 176 insertions(+), 160 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 9e76e49..86aee90 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -72,7 +72,41 @@ void init_fold(string seq) {
 	if (SHAPE_ENABLED) {
 		readSHAPEarray(shapeFile.c_str(),len);
 	}
+
+	if (UNAMODE) {
+									if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n");
+									if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n");
+									if (dangles == 0 || dangles == 2) 
+																	printf("Ignoring -d option, using --unafold\n");
+									if (b_prefilter == 1) 
+																	printf("Ignoring --prefilter option, using --unafold\n");
+									T_MISMATCH = false;
+									PARAM_DIR = false;
+									dangles = -1;
+									b_prefilter = false;
+	}
 	
+	if (RNAMODE) {
+									if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n");
+									if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n");
+									if (dangles == 0 || dangles == 2) 
+																	printf("Ignoring -d option, using --rnafold\n");
+									if (b_prefilter == 1) 
+																	printf("Ignoring --prefilter option, using --rnafold\n");
+									T_MISMATCH = false;
+									PARAM_DIR = false;
+									dangles = -1;
+									b_prefilter = false;
+	}
+
+	if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) {
+									if (T_MISMATCH) printf("Ignoring -m option, using -d option\n");
+									T_MISMATCH = false;
+	} else {
+									if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n");	
+									dangles = -1;
+	}
+
 	g_nthreads = nThreads;
 	g_unamode  = UNAMODE;
 	g_mismatch = T_MISMATCH;
@@ -82,7 +116,7 @@ void init_fold(string seq) {
 	g_prefilter2  = prefilter2;
 	g_dangles = dangles;
 
-#ifdef DEBUG
+	#ifdef DEBUG
 	printf("g_nthreads = %d\n", g_nthreads);
 	printf("g_unamode = %d\n", g_unamode);
 	printf("g_mismatch = %d\n", g_mismatch);
@@ -238,12 +272,11 @@ int main(int argc, char** argv) {
 		printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
 		exit(-1);
 	}
+	init_fold(seq);
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
 	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
 
-	init_fold(seq);
-	
 	printRunConfiguration(seq);
 
 	printf("\nComputing minimum free energy structure...\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 7a2f446..6886f65 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -90,164 +90,148 @@ void help() {
  * Parse the options from argc and argv and save them into global state.
  */
 void parse_options(int argc, char** argv) {
-	int i;
+								int i;
 
-	for(i=1; i<argc; i++) {
-		if(argv[i][0] == '-') {
-			if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
-				help();
-			} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
-				if(i < argc) {
-					constraintsFile = argv[++i];
-					CONS_ENABLED = true;
-				}
-				else
-					help();
-			} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
-				if(i < argc){
-					contactDistance = atoi(argv[++i]);
-					stringstream ss;
-					ss << contactDistance;
-					if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
-						LIMIT_DISTANCE = true;
-					else
-						help();
-				}
-				else
-					help();
-			} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
-				NOISOLATE = true;
-			} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
-				if(i < argc)
-					outputPrefix = argv[++i];
-				else
-					help();
-			} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
-				if(i < argc)
-					outputDir = argv[++i];
-				else
-					help();
-			} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
-					if(i < argc) {
-					paramDir = argv[++i];
-					PARAM_DIR = true;
-				}
-				else
-					help();
-			} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
-											std::string cmd = argv[i];
-						if(i < argc) {
-									dangles = atoi(argv[++i]);
-									if (!(dangles == 0 || dangles == 2)) {
-																dangles = -1;
-																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
-									} else {
-																T_MISMATCH = false;
-									}
-						} else
-								 help();
-			} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
-											std::string cmd = argv[i];
-					if (!(dangles == 0 ||  dangles == 2)) 
-													T_MISMATCH = true;
-					else {
-													printf("Ignoring %s option\n", cmd.c_str());
-													T_MISMATCH = false;
-					}
-			} else if (strcmp(argv[i], "--unafold") == 0) {
-				UNAMODE = true;
-				dangles = -1;
-				T_MISMATCH = false;
-			} else if (strcmp(argv[i], "--rnafold") == 0) {
-				RNAMODE = true;
-				//dangles = 1;
-				T_MISMATCH = false;
-			} else if (strcmp(argv[i], "--prefilter") == 0) {
-				if(i < argc) {
-					int value1 = -1, value2 = -1;
-					std::stringstream ss;
-					ss << argv[++i];
-					sscanf(ss.str().c_str(),"%d,%d", &value1, &value2);
-					if (value1 <= 0 || value2 <= 0) {
-						printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
-						help();
-					}
-					b_prefilter = true;
-					prefilter1 = value1;
-					prefilter2 = value2;
-				} else 
-					help();
-			}
-		   	else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
-				if(i < argc)
-					nThreads = atoi(argv[++i]);
-				else
-					help();	
-			} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
-                VERBOSE = true;
-			}
-			else if(strcmp(argv[i], "--bpp") == 0) {
-				BPP_ENABLED = true;
-			} else if(strcmp(argv[i], "--subopt") == 0) {
-				SUBOPT_ENABLED = true;
-				if(i < argc)
-					suboptDelta = atof(argv[++i]);
-				else
-					help();
-			}
-			else if (strcmp(argv[i], "--useSHAPE") == 0){
-				if( i < argc){
-					shapeFile = argv[++i];
-					SHAPE_ENABLED = true;
-				}
-				else
-					help();
-			}				
-		} else {
-			seqfile = argv[i];
-		}
-	}
+								for(i=1; i<argc; i++) {
+																if(argv[i][0] == '-') {
+																								if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
+																																help();
+																								} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
+																																if(i < argc) {
+																																								constraintsFile = argv[++i];
+																																								CONS_ENABLED = true;
+																																}
+																																else
+																																								help();
+																								} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
+																																if(i < argc){
+																																								contactDistance = atoi(argv[++i]);
+																																								stringstream ss;
+																																								ss << contactDistance;
+																																								if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
+																																																LIMIT_DISTANCE = true;
+																																								else
+																																																help();
+																																}
+																																else
+																																								help();
+																								} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
+																																NOISOLATE = true;
+																								} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
+																																if(i < argc)
+																																								outputPrefix = argv[++i];
+																																else
+																																								help();
+																								} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
+																																if(i < argc)
+																																								outputDir = argv[++i];
+																																else
+																																								help();
+																								} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+																																if(i < argc) {
+																																								paramDir = argv[++i];
+																																								PARAM_DIR = true;
+																																}
+																																else
+																																								help();
+																								} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
+																																std::string cmd = argv[i];
+																																if(i < argc) {
+																																								dangles = atoi(argv[++i]);
+																																								if (!(dangles == 0 || dangles == 2)) {
+																																																dangles = -1;
+																																																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
+																																								} 
+																																} else
+																																								help();
+																								} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
+																																T_MISMATCH = true;
+																								} else if (strcmp(argv[i], "--unafold") == 0) {
+																																UNAMODE = true;
+																								} else if (strcmp(argv[i], "--rnafold") == 0) {
+																																RNAMODE = true;
+																								} else if (strcmp(argv[i], "--prefilter") == 0) {
+																																if(i < argc) {
+																																								prefilter1 = atoi(argv[++i]);
+																																								if (prefilter1 <= 0 ) {
+																																																printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
+																																																help();
+																																								}
+																																								b_prefilter = true;
+																																								prefilter2 = prefilter1;
+																																} else 
+																																								help();
+																								}
+																								else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
+																																if(i < argc)
+																																								nThreads = atoi(argv[++i]);
+																																else
+																																								help();	
+																								} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
+																																VERBOSE = true;
+																								}
+																								else if(strcmp(argv[i], "--bpp") == 0) {
+																																BPP_ENABLED = true;
+																								} else if(strcmp(argv[i], "--subopt") == 0) {
+																																SUBOPT_ENABLED = true;
+																																if(i < argc)
+																																								suboptDelta = atof(argv[++i]);
+																																else
+																																								help();
+																								}
+																								else if (strcmp(argv[i], "--useSHAPE") == 0){
+																																if( i < argc){
+																																								shapeFile = argv[++i];
+																																								SHAPE_ENABLED = true;
+																																}
+																																else
+																																								help();
+																								}				
+																} else {
+																								seqfile = argv[i];
+																}
+								}
 
-	// Must have an input file specified
-	if(seqfile.empty()) {
-		help();
-		printf("Missing input file.\n");
-	}
+								// Must have an input file specified
+								if(seqfile.empty()) {
+																help();
+																printf("Missing input file.\n");
+								}
 
-	// If no output file specified, create one
-	if(outputPrefix.empty()) {
-		// base it off the input file
-		outputPrefix += seqfile;
-		
-		size_t pos;
-		// extract file name from the path
-		if ((pos=outputPrefix.find_last_of('/')) > 0) {
-			outputPrefix = outputPrefix.substr(pos+1);
-		}
+								// If no output file specified, create one
+								if(outputPrefix.empty()) {
+																// base it off the input file
+																outputPrefix += seqfile;
 
-		// and if an extension exists, remove it ...
-		if(outputPrefix.find(".") != string::npos)
-			outputPrefix.erase(outputPrefix.rfind("."));
-	 }
+																size_t pos;
+																// extract file name from the path
+																if ((pos=outputPrefix.find_last_of('/')) > 0) {
+																								outputPrefix = outputPrefix.substr(pos+1);
+																}
 
-	// If output dir specified
-	if (!outputDir.empty()) {
-		outputFile += outputDir;
-		outputFile += "/";
-		suboptFile += outputDir;
-		suboptFile += "/";
-		bppOutFile += outputDir;
-		bppOutFile += "/";
-	}
-	// ... and append the .ct
-	outputFile += outputPrefix;
-	outputFile += ".ct";
+																// and if an extension exists, remove it ...
+																if(outputPrefix.find(".") != string::npos)
+																								outputPrefix.erase(outputPrefix.rfind("."));
+								}
+
+								// If output dir specified
+								if (!outputDir.empty()) {
+																outputFile += outputDir;
+																outputFile += "/";
+																suboptFile += outputDir;
+																suboptFile += "/";
+																bppOutFile += outputDir;
+																bppOutFile += "/";
+								}
+								// ... and append the .ct
+								outputFile += outputPrefix;
+								outputFile += ".ct";
 
-	suboptFile += outputPrefix;	
-	suboptFile += "_ss.txt";	
+								suboptFile += outputPrefix;	
+								suboptFile += "_ss.txt";	
 
-	bppOutFile += outputPrefix;	
-	bppOutFile += "_bpp.txt";	
+								bppOutFile += outputPrefix;	
+								bppOutFile += "_bpp.txt";	
 }
 
 /**
@@ -262,24 +246,23 @@ void printRunConfiguration(string seq) {
 	if (RNAMODE == true) {
 		printf("+ running in rnafold mode\n");
 		standardRun = false;
-	}
+	} 
 	if (UNAMODE == true) {
 		printf("+ running in unafold mode\n");
 		standardRun = false;
 	}
-	if (dangles >= 0 && !RNAMODE) {
-		printf("+ running in dangles %d mode\n", dangles);
+	if (dangles == 0 || dangles == 2) {
+		printf("+ running in dangle %d mode\n", dangles);
 		standardRun = false;
-	}
+	} 
 	if (T_MISMATCH == true) {
 		printf("+ enabled terminal mismatch calculations\n");
 		standardRun = false;
 	}
 	if (b_prefilter == true) {
-		printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2);
+		printf("+ running with prefilter value = %d\n",prefilter1);
 		standardRun = false;
 	}
-
 	if (NOISOLATE == true) {
 		printf("- preventing isolated base pairs\n");
 		standardRun = false;

From 58bc5a2605f11298c59430eb8328134a409bf48b Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 12:53:22 -0400
Subject: [PATCH 202/282] merged changes

---
 gtfold-mfe/src/main.cc    |  39 +----
 gtfold-mfe/src/options.cc | 297 ++++++++++++++++++++------------------
 2 files changed, 160 insertions(+), 176 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 86aee90..9e76e49 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -72,41 +72,7 @@ void init_fold(string seq) {
 	if (SHAPE_ENABLED) {
 		readSHAPEarray(shapeFile.c_str(),len);
 	}
-
-	if (UNAMODE) {
-									if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n");
-									if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n");
-									if (dangles == 0 || dangles == 2) 
-																	printf("Ignoring -d option, using --unafold\n");
-									if (b_prefilter == 1) 
-																	printf("Ignoring --prefilter option, using --unafold\n");
-									T_MISMATCH = false;
-									PARAM_DIR = false;
-									dangles = -1;
-									b_prefilter = false;
-	}
 	
-	if (RNAMODE) {
-									if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n");
-									if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n");
-									if (dangles == 0 || dangles == 2) 
-																	printf("Ignoring -d option, using --rnafold\n");
-									if (b_prefilter == 1) 
-																	printf("Ignoring --prefilter option, using --rnafold\n");
-									T_MISMATCH = false;
-									PARAM_DIR = false;
-									dangles = -1;
-									b_prefilter = false;
-	}
-
-	if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) {
-									if (T_MISMATCH) printf("Ignoring -m option, using -d option\n");
-									T_MISMATCH = false;
-	} else {
-									if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n");	
-									dangles = -1;
-	}
-
 	g_nthreads = nThreads;
 	g_unamode  = UNAMODE;
 	g_mismatch = T_MISMATCH;
@@ -116,7 +82,7 @@ void init_fold(string seq) {
 	g_prefilter2  = prefilter2;
 	g_dangles = dangles;
 
-	#ifdef DEBUG
+#ifdef DEBUG
 	printf("g_nthreads = %d\n", g_nthreads);
 	printf("g_unamode = %d\n", g_unamode);
 	printf("g_mismatch = %d\n", g_mismatch);
@@ -272,11 +238,12 @@ int main(int argc, char** argv) {
 		printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
 		exit(-1);
 	}
-	init_fold(seq);
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
 	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
 
+	init_fold(seq);
+	
 	printRunConfiguration(seq);
 
 	printf("\nComputing minimum free energy structure...\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 6886f65..7a2f446 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -90,148 +90,164 @@ void help() {
  * Parse the options from argc and argv and save them into global state.
  */
 void parse_options(int argc, char** argv) {
-								int i;
+	int i;
 
-								for(i=1; i<argc; i++) {
-																if(argv[i][0] == '-') {
-																								if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
-																																help();
-																								} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
-																																if(i < argc) {
-																																								constraintsFile = argv[++i];
-																																								CONS_ENABLED = true;
-																																}
-																																else
-																																								help();
-																								} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
-																																if(i < argc){
-																																								contactDistance = atoi(argv[++i]);
-																																								stringstream ss;
-																																								ss << contactDistance;
-																																								if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
-																																																LIMIT_DISTANCE = true;
-																																								else
-																																																help();
-																																}
-																																else
-																																								help();
-																								} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
-																																NOISOLATE = true;
-																								} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
-																																if(i < argc)
-																																								outputPrefix = argv[++i];
-																																else
-																																								help();
-																								} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
-																																if(i < argc)
-																																								outputDir = argv[++i];
-																																else
-																																								help();
-																								} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
-																																if(i < argc) {
-																																								paramDir = argv[++i];
-																																								PARAM_DIR = true;
-																																}
-																																else
-																																								help();
-																								} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
-																																std::string cmd = argv[i];
-																																if(i < argc) {
-																																								dangles = atoi(argv[++i]);
-																																								if (!(dangles == 0 || dangles == 2)) {
-																																																dangles = -1;
-																																																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
-																																								} 
-																																} else
-																																								help();
-																								} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
-																																T_MISMATCH = true;
-																								} else if (strcmp(argv[i], "--unafold") == 0) {
-																																UNAMODE = true;
-																								} else if (strcmp(argv[i], "--rnafold") == 0) {
-																																RNAMODE = true;
-																								} else if (strcmp(argv[i], "--prefilter") == 0) {
-																																if(i < argc) {
-																																								prefilter1 = atoi(argv[++i]);
-																																								if (prefilter1 <= 0 ) {
-																																																printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
-																																																help();
-																																								}
-																																								b_prefilter = true;
-																																								prefilter2 = prefilter1;
-																																} else 
-																																								help();
-																								}
-																								else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
-																																if(i < argc)
-																																								nThreads = atoi(argv[++i]);
-																																else
-																																								help();	
-																								} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
-																																VERBOSE = true;
-																								}
-																								else if(strcmp(argv[i], "--bpp") == 0) {
-																																BPP_ENABLED = true;
-																								} else if(strcmp(argv[i], "--subopt") == 0) {
-																																SUBOPT_ENABLED = true;
-																																if(i < argc)
-																																								suboptDelta = atof(argv[++i]);
-																																else
-																																								help();
-																								}
-																								else if (strcmp(argv[i], "--useSHAPE") == 0){
-																																if( i < argc){
-																																								shapeFile = argv[++i];
-																																								SHAPE_ENABLED = true;
-																																}
-																																else
-																																								help();
-																								}				
-																} else {
-																								seqfile = argv[i];
-																}
-								}
-
-								// Must have an input file specified
-								if(seqfile.empty()) {
-																help();
-																printf("Missing input file.\n");
-								}
+	for(i=1; i<argc; i++) {
+		if(argv[i][0] == '-') {
+			if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
+				help();
+			} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
+				if(i < argc) {
+					constraintsFile = argv[++i];
+					CONS_ENABLED = true;
+				}
+				else
+					help();
+			} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
+				if(i < argc){
+					contactDistance = atoi(argv[++i]);
+					stringstream ss;
+					ss << contactDistance;
+					if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
+						LIMIT_DISTANCE = true;
+					else
+						help();
+				}
+				else
+					help();
+			} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
+				NOISOLATE = true;
+			} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
+				if(i < argc)
+					outputPrefix = argv[++i];
+				else
+					help();
+			} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
+				if(i < argc)
+					outputDir = argv[++i];
+				else
+					help();
+			} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+					if(i < argc) {
+					paramDir = argv[++i];
+					PARAM_DIR = true;
+				}
+				else
+					help();
+			} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
+											std::string cmd = argv[i];
+						if(i < argc) {
+									dangles = atoi(argv[++i]);
+									if (!(dangles == 0 || dangles == 2)) {
+																dangles = -1;
+																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
+									} else {
+																T_MISMATCH = false;
+									}
+						} else
+								 help();
+			} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
+											std::string cmd = argv[i];
+					if (!(dangles == 0 ||  dangles == 2)) 
+													T_MISMATCH = true;
+					else {
+													printf("Ignoring %s option\n", cmd.c_str());
+													T_MISMATCH = false;
+					}
+			} else if (strcmp(argv[i], "--unafold") == 0) {
+				UNAMODE = true;
+				dangles = -1;
+				T_MISMATCH = false;
+			} else if (strcmp(argv[i], "--rnafold") == 0) {
+				RNAMODE = true;
+				//dangles = 1;
+				T_MISMATCH = false;
+			} else if (strcmp(argv[i], "--prefilter") == 0) {
+				if(i < argc) {
+					int value1 = -1, value2 = -1;
+					std::stringstream ss;
+					ss << argv[++i];
+					sscanf(ss.str().c_str(),"%d,%d", &value1, &value2);
+					if (value1 <= 0 || value2 <= 0) {
+						printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
+						help();
+					}
+					b_prefilter = true;
+					prefilter1 = value1;
+					prefilter2 = value2;
+				} else 
+					help();
+			}
+		   	else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
+				if(i < argc)
+					nThreads = atoi(argv[++i]);
+				else
+					help();	
+			} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
+                VERBOSE = true;
+			}
+			else if(strcmp(argv[i], "--bpp") == 0) {
+				BPP_ENABLED = true;
+			} else if(strcmp(argv[i], "--subopt") == 0) {
+				SUBOPT_ENABLED = true;
+				if(i < argc)
+					suboptDelta = atof(argv[++i]);
+				else
+					help();
+			}
+			else if (strcmp(argv[i], "--useSHAPE") == 0){
+				if( i < argc){
+					shapeFile = argv[++i];
+					SHAPE_ENABLED = true;
+				}
+				else
+					help();
+			}				
+		} else {
+			seqfile = argv[i];
+		}
+	}
 
-								// If no output file specified, create one
-								if(outputPrefix.empty()) {
-																// base it off the input file
-																outputPrefix += seqfile;
+	// Must have an input file specified
+	if(seqfile.empty()) {
+		help();
+		printf("Missing input file.\n");
+	}
 
-																size_t pos;
-																// extract file name from the path
-																if ((pos=outputPrefix.find_last_of('/')) > 0) {
-																								outputPrefix = outputPrefix.substr(pos+1);
-																}
+	// If no output file specified, create one
+	if(outputPrefix.empty()) {
+		// base it off the input file
+		outputPrefix += seqfile;
+		
+		size_t pos;
+		// extract file name from the path
+		if ((pos=outputPrefix.find_last_of('/')) > 0) {
+			outputPrefix = outputPrefix.substr(pos+1);
+		}
 
-																// and if an extension exists, remove it ...
-																if(outputPrefix.find(".") != string::npos)
-																								outputPrefix.erase(outputPrefix.rfind("."));
-								}
+		// and if an extension exists, remove it ...
+		if(outputPrefix.find(".") != string::npos)
+			outputPrefix.erase(outputPrefix.rfind("."));
+	 }
 
-								// If output dir specified
-								if (!outputDir.empty()) {
-																outputFile += outputDir;
-																outputFile += "/";
-																suboptFile += outputDir;
-																suboptFile += "/";
-																bppOutFile += outputDir;
-																bppOutFile += "/";
-								}
-								// ... and append the .ct
-								outputFile += outputPrefix;
-								outputFile += ".ct";
+	// If output dir specified
+	if (!outputDir.empty()) {
+		outputFile += outputDir;
+		outputFile += "/";
+		suboptFile += outputDir;
+		suboptFile += "/";
+		bppOutFile += outputDir;
+		bppOutFile += "/";
+	}
+	// ... and append the .ct
+	outputFile += outputPrefix;
+	outputFile += ".ct";
 
-								suboptFile += outputPrefix;	
-								suboptFile += "_ss.txt";	
+	suboptFile += outputPrefix;	
+	suboptFile += "_ss.txt";	
 
-								bppOutFile += outputPrefix;	
-								bppOutFile += "_bpp.txt";	
+	bppOutFile += outputPrefix;	
+	bppOutFile += "_bpp.txt";	
 }
 
 /**
@@ -246,23 +262,24 @@ void printRunConfiguration(string seq) {
 	if (RNAMODE == true) {
 		printf("+ running in rnafold mode\n");
 		standardRun = false;
-	} 
+	}
 	if (UNAMODE == true) {
 		printf("+ running in unafold mode\n");
 		standardRun = false;
 	}
-	if (dangles == 0 || dangles == 2) {
-		printf("+ running in dangle %d mode\n", dangles);
+	if (dangles >= 0 && !RNAMODE) {
+		printf("+ running in dangles %d mode\n", dangles);
 		standardRun = false;
-	} 
+	}
 	if (T_MISMATCH == true) {
 		printf("+ enabled terminal mismatch calculations\n");
 		standardRun = false;
 	}
 	if (b_prefilter == true) {
-		printf("+ running with prefilter value = %d\n",prefilter1);
+		printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2);
 		standardRun = false;
 	}
+
 	if (NOISOLATE == true) {
 		printf("- preventing isolated base pairs\n");
 		standardRun = false;

From 6b6b7badbb12bd0fa43828cadc13ab8697cbf732 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 12:54:43 -0400
Subject: [PATCH 203/282] fixed commanline options

---
 gtfold-mfe/src/main.cc    |  39 ++++-
 gtfold-mfe/src/options.cc | 297 ++++++++++++++++++--------------------
 2 files changed, 176 insertions(+), 160 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 9e76e49..86aee90 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -72,7 +72,41 @@ void init_fold(string seq) {
 	if (SHAPE_ENABLED) {
 		readSHAPEarray(shapeFile.c_str(),len);
 	}
+
+	if (UNAMODE) {
+									if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n");
+									if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n");
+									if (dangles == 0 || dangles == 2) 
+																	printf("Ignoring -d option, using --unafold\n");
+									if (b_prefilter == 1) 
+																	printf("Ignoring --prefilter option, using --unafold\n");
+									T_MISMATCH = false;
+									PARAM_DIR = false;
+									dangles = -1;
+									b_prefilter = false;
+	}
 	
+	if (RNAMODE) {
+									if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n");
+									if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n");
+									if (dangles == 0 || dangles == 2) 
+																	printf("Ignoring -d option, using --rnafold\n");
+									if (b_prefilter == 1) 
+																	printf("Ignoring --prefilter option, using --rnafold\n");
+									T_MISMATCH = false;
+									PARAM_DIR = false;
+									dangles = -1;
+									b_prefilter = false;
+	}
+
+	if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) {
+									if (T_MISMATCH) printf("Ignoring -m option, using -d option\n");
+									T_MISMATCH = false;
+	} else {
+									if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n");	
+									dangles = -1;
+	}
+
 	g_nthreads = nThreads;
 	g_unamode  = UNAMODE;
 	g_mismatch = T_MISMATCH;
@@ -82,7 +116,7 @@ void init_fold(string seq) {
 	g_prefilter2  = prefilter2;
 	g_dangles = dangles;
 
-#ifdef DEBUG
+	#ifdef DEBUG
 	printf("g_nthreads = %d\n", g_nthreads);
 	printf("g_unamode = %d\n", g_unamode);
 	printf("g_mismatch = %d\n", g_mismatch);
@@ -238,12 +272,11 @@ int main(int argc, char** argv) {
 		printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
 		exit(-1);
 	}
+	init_fold(seq);
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
 	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
 
-	init_fold(seq);
-	
 	printRunConfiguration(seq);
 
 	printf("\nComputing minimum free energy structure...\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 7a2f446..6886f65 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -90,164 +90,148 @@ void help() {
  * Parse the options from argc and argv and save them into global state.
  */
 void parse_options(int argc, char** argv) {
-	int i;
+								int i;
 
-	for(i=1; i<argc; i++) {
-		if(argv[i][0] == '-') {
-			if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
-				help();
-			} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
-				if(i < argc) {
-					constraintsFile = argv[++i];
-					CONS_ENABLED = true;
-				}
-				else
-					help();
-			} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
-				if(i < argc){
-					contactDistance = atoi(argv[++i]);
-					stringstream ss;
-					ss << contactDistance;
-					if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
-						LIMIT_DISTANCE = true;
-					else
-						help();
-				}
-				else
-					help();
-			} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
-				NOISOLATE = true;
-			} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
-				if(i < argc)
-					outputPrefix = argv[++i];
-				else
-					help();
-			} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
-				if(i < argc)
-					outputDir = argv[++i];
-				else
-					help();
-			} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
-					if(i < argc) {
-					paramDir = argv[++i];
-					PARAM_DIR = true;
-				}
-				else
-					help();
-			} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
-											std::string cmd = argv[i];
-						if(i < argc) {
-									dangles = atoi(argv[++i]);
-									if (!(dangles == 0 || dangles == 2)) {
-																dangles = -1;
-																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
-									} else {
-																T_MISMATCH = false;
-									}
-						} else
-								 help();
-			} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
-											std::string cmd = argv[i];
-					if (!(dangles == 0 ||  dangles == 2)) 
-													T_MISMATCH = true;
-					else {
-													printf("Ignoring %s option\n", cmd.c_str());
-													T_MISMATCH = false;
-					}
-			} else if (strcmp(argv[i], "--unafold") == 0) {
-				UNAMODE = true;
-				dangles = -1;
-				T_MISMATCH = false;
-			} else if (strcmp(argv[i], "--rnafold") == 0) {
-				RNAMODE = true;
-				//dangles = 1;
-				T_MISMATCH = false;
-			} else if (strcmp(argv[i], "--prefilter") == 0) {
-				if(i < argc) {
-					int value1 = -1, value2 = -1;
-					std::stringstream ss;
-					ss << argv[++i];
-					sscanf(ss.str().c_str(),"%d,%d", &value1, &value2);
-					if (value1 <= 0 || value2 <= 0) {
-						printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
-						help();
-					}
-					b_prefilter = true;
-					prefilter1 = value1;
-					prefilter2 = value2;
-				} else 
-					help();
-			}
-		   	else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
-				if(i < argc)
-					nThreads = atoi(argv[++i]);
-				else
-					help();	
-			} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
-                VERBOSE = true;
-			}
-			else if(strcmp(argv[i], "--bpp") == 0) {
-				BPP_ENABLED = true;
-			} else if(strcmp(argv[i], "--subopt") == 0) {
-				SUBOPT_ENABLED = true;
-				if(i < argc)
-					suboptDelta = atof(argv[++i]);
-				else
-					help();
-			}
-			else if (strcmp(argv[i], "--useSHAPE") == 0){
-				if( i < argc){
-					shapeFile = argv[++i];
-					SHAPE_ENABLED = true;
-				}
-				else
-					help();
-			}				
-		} else {
-			seqfile = argv[i];
-		}
-	}
+								for(i=1; i<argc; i++) {
+																if(argv[i][0] == '-') {
+																								if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
+																																help();
+																								} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
+																																if(i < argc) {
+																																								constraintsFile = argv[++i];
+																																								CONS_ENABLED = true;
+																																}
+																																else
+																																								help();
+																								} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
+																																if(i < argc){
+																																								contactDistance = atoi(argv[++i]);
+																																								stringstream ss;
+																																								ss << contactDistance;
+																																								if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
+																																																LIMIT_DISTANCE = true;
+																																								else
+																																																help();
+																																}
+																																else
+																																								help();
+																								} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
+																																NOISOLATE = true;
+																								} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
+																																if(i < argc)
+																																								outputPrefix = argv[++i];
+																																else
+																																								help();
+																								} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
+																																if(i < argc)
+																																								outputDir = argv[++i];
+																																else
+																																								help();
+																								} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+																																if(i < argc) {
+																																								paramDir = argv[++i];
+																																								PARAM_DIR = true;
+																																}
+																																else
+																																								help();
+																								} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
+																																std::string cmd = argv[i];
+																																if(i < argc) {
+																																								dangles = atoi(argv[++i]);
+																																								if (!(dangles == 0 || dangles == 2)) {
+																																																dangles = -1;
+																																																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
+																																								} 
+																																} else
+																																								help();
+																								} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
+																																T_MISMATCH = true;
+																								} else if (strcmp(argv[i], "--unafold") == 0) {
+																																UNAMODE = true;
+																								} else if (strcmp(argv[i], "--rnafold") == 0) {
+																																RNAMODE = true;
+																								} else if (strcmp(argv[i], "--prefilter") == 0) {
+																																if(i < argc) {
+																																								prefilter1 = atoi(argv[++i]);
+																																								if (prefilter1 <= 0 ) {
+																																																printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
+																																																help();
+																																								}
+																																								b_prefilter = true;
+																																								prefilter2 = prefilter1;
+																																} else 
+																																								help();
+																								}
+																								else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
+																																if(i < argc)
+																																								nThreads = atoi(argv[++i]);
+																																else
+																																								help();	
+																								} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
+																																VERBOSE = true;
+																								}
+																								else if(strcmp(argv[i], "--bpp") == 0) {
+																																BPP_ENABLED = true;
+																								} else if(strcmp(argv[i], "--subopt") == 0) {
+																																SUBOPT_ENABLED = true;
+																																if(i < argc)
+																																								suboptDelta = atof(argv[++i]);
+																																else
+																																								help();
+																								}
+																								else if (strcmp(argv[i], "--useSHAPE") == 0){
+																																if( i < argc){
+																																								shapeFile = argv[++i];
+																																								SHAPE_ENABLED = true;
+																																}
+																																else
+																																								help();
+																								}				
+																} else {
+																								seqfile = argv[i];
+																}
+								}
 
-	// Must have an input file specified
-	if(seqfile.empty()) {
-		help();
-		printf("Missing input file.\n");
-	}
+								// Must have an input file specified
+								if(seqfile.empty()) {
+																help();
+																printf("Missing input file.\n");
+								}
 
-	// If no output file specified, create one
-	if(outputPrefix.empty()) {
-		// base it off the input file
-		outputPrefix += seqfile;
-		
-		size_t pos;
-		// extract file name from the path
-		if ((pos=outputPrefix.find_last_of('/')) > 0) {
-			outputPrefix = outputPrefix.substr(pos+1);
-		}
+								// If no output file specified, create one
+								if(outputPrefix.empty()) {
+																// base it off the input file
+																outputPrefix += seqfile;
 
-		// and if an extension exists, remove it ...
-		if(outputPrefix.find(".") != string::npos)
-			outputPrefix.erase(outputPrefix.rfind("."));
-	 }
+																size_t pos;
+																// extract file name from the path
+																if ((pos=outputPrefix.find_last_of('/')) > 0) {
+																								outputPrefix = outputPrefix.substr(pos+1);
+																}
 
-	// If output dir specified
-	if (!outputDir.empty()) {
-		outputFile += outputDir;
-		outputFile += "/";
-		suboptFile += outputDir;
-		suboptFile += "/";
-		bppOutFile += outputDir;
-		bppOutFile += "/";
-	}
-	// ... and append the .ct
-	outputFile += outputPrefix;
-	outputFile += ".ct";
+																// and if an extension exists, remove it ...
+																if(outputPrefix.find(".") != string::npos)
+																								outputPrefix.erase(outputPrefix.rfind("."));
+								}
+
+								// If output dir specified
+								if (!outputDir.empty()) {
+																outputFile += outputDir;
+																outputFile += "/";
+																suboptFile += outputDir;
+																suboptFile += "/";
+																bppOutFile += outputDir;
+																bppOutFile += "/";
+								}
+								// ... and append the .ct
+								outputFile += outputPrefix;
+								outputFile += ".ct";
 
-	suboptFile += outputPrefix;	
-	suboptFile += "_ss.txt";	
+								suboptFile += outputPrefix;	
+								suboptFile += "_ss.txt";	
 
-	bppOutFile += outputPrefix;	
-	bppOutFile += "_bpp.txt";	
+								bppOutFile += outputPrefix;	
+								bppOutFile += "_bpp.txt";	
 }
 
 /**
@@ -262,24 +246,23 @@ void printRunConfiguration(string seq) {
 	if (RNAMODE == true) {
 		printf("+ running in rnafold mode\n");
 		standardRun = false;
-	}
+	} 
 	if (UNAMODE == true) {
 		printf("+ running in unafold mode\n");
 		standardRun = false;
 	}
-	if (dangles >= 0 && !RNAMODE) {
-		printf("+ running in dangles %d mode\n", dangles);
+	if (dangles == 0 || dangles == 2) {
+		printf("+ running in dangle %d mode\n", dangles);
 		standardRun = false;
-	}
+	} 
 	if (T_MISMATCH == true) {
 		printf("+ enabled terminal mismatch calculations\n");
 		standardRun = false;
 	}
 	if (b_prefilter == true) {
-		printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2);
+		printf("+ running with prefilter value = %d\n",prefilter1);
 		standardRun = false;
 	}
-
 	if (NOISOLATE == true) {
 		printf("- preventing isolated base pairs\n");
 		standardRun = false;

From ef1b79b0e8cdce6d1cfb026f2e3ce87df595392a Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 13:27:09 -0400
Subject: [PATCH 204/282] fixed minor issue

---
 gtfold-mfe/configure    | 2 +-
 gtfold-mfe/configure.in | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure
index c0dc675..e4e3fd1 100755
--- a/gtfold-mfe/configure
+++ b/gtfold-mfe/configure
@@ -5452,7 +5452,7 @@ if test "x$GXX" = "xyes"; then
 fi
 
 
-If Sun cc is present, define appropriate compiler flags
+#If Sun cc is present, define appropriate compiler flags
 { $as_echo "$as_me:$LINENO: checking for Sun C compiler" >&5
 $as_echo_n "checking for Sun C compiler... " >&6; }
 cat >conftest.$ac_ext <<_ACEOF
diff --git a/gtfold-mfe/configure.in b/gtfold-mfe/configure.in
index 03441fc..0643019 100644
--- a/gtfold-mfe/configure.in
+++ b/gtfold-mfe/configure.in
@@ -99,7 +99,7 @@ fi
 dnl This is an example how to check for compiler characteristics that
 dnl are not a part of the standard Autoconf tests:
 
-If Sun cc is present, define appropriate compiler flags  
+#If Sun cc is present, define appropriate compiler flags  
 AC_MSG_CHECKING(for Sun C compiler)
 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __SUNPRO_C
                     #include "error: this is not a Sun C compiler."

From 4bfd1f85ce99dca3d48320bade2114f513fcdc93 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 13:28:04 -0400
Subject: [PATCH 205/282] added  new features list

---
 README            | 13 ++++++++++++-
 gtfold-mfe/README | 13 ++++++++++++-
 2 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/README b/README
index 34a28f1..3741de6 100644
--- a/README
+++ b/README
@@ -110,4 +110,15 @@ Version History:
 1.16 20 May 2010  Fixed another nasty bug with prohibited constraints handling.
             Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure.
             Some documentation added.
-                    
+2.0 11 July 2011                      
+   								 Optimized the code to enable faster multiloop calculations 
+												Added -d, --dangle to allow treatment of dangling end energies based on user input 
+												Added -m  --mismatch to enable terminal mismatch calculations
+												Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name 
+												Added -p  --paramdir to allow user to provide custom parameters		
+												Added -t, --threads to limit number of threads used
+												Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides 
+												such that it could be part of a helix of length INT
+   									Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5)
+												Added --unafold to run GTfold in UNAfold default mode (version 3.8)
+												Added beta options --subopt, --bpp, --useShape
diff --git a/gtfold-mfe/README b/gtfold-mfe/README
index 34a28f1..3741de6 100644
--- a/gtfold-mfe/README
+++ b/gtfold-mfe/README
@@ -110,4 +110,15 @@ Version History:
 1.16 20 May 2010  Fixed another nasty bug with prohibited constraints handling.
             Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure.
             Some documentation added.
-                    
+2.0 11 July 2011                      
+   								 Optimized the code to enable faster multiloop calculations 
+												Added -d, --dangle to allow treatment of dangling end energies based on user input 
+												Added -m  --mismatch to enable terminal mismatch calculations
+												Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name 
+												Added -p  --paramdir to allow user to provide custom parameters		
+												Added -t, --threads to limit number of threads used
+												Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides 
+												such that it could be part of a helix of length INT
+   									Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5)
+												Added --unafold to run GTfold in UNAfold default mode (version 3.8)
+												Added beta options --subopt, --bpp, --useShape

From 951612c2f739de63d4e4c2634731d9b141564bfa Mon Sep 17 00:00:00 2001
From: Shel Swenson <shelswenson@gmail.com>
Date: Tue, 12 Jul 2011 14:01:29 -0400
Subject: [PATCH 206/282] updated copyright information

---
 gtfold-mfe/src/main.cc | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 86aee90..32cc9ad 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -1,6 +1,7 @@
 /*
  GTfold: compute minimum free energy of RNA secondary structure
- Copyright (C) 2008  David A. Bader
+ Copyright (C) 2007-2011  David A. Bader, Christine E. Heitsch, 
+ and Steve C. Harvey
  http://www.cc.gatech.edu/~bader
 
  This program is free software: you can redistribute it and/or modify
@@ -215,7 +216,7 @@ bool encodeSequence(string seq) {
 
 void print_header() {
 	printf("GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n");
-	printf("(c) 2007-2011  D.A. Bader, S. Mallidi, A. Mathuriya, C.E. Heitsch, S.C. Harvey\n");
+	printf("(c) 2007-2011  D.A. Bader, C.E. Heitsch, S.C. Harvey\n");
 	printf("Georgia Institute of Technology\n\n");
 }
 

From 6c7bdb50ed28b05b6922eea8c068f50c8b352b79 Mon Sep 17 00:00:00 2001
From: Shel Swenson <shelswenson@gmail.com>
Date: Tue, 12 Jul 2011 14:45:31 -0400
Subject: [PATCH 207/282] corrected spelling errors in help message

---
 gtfold-mfe/src/options.cc | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 6886f65..b31d789 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -48,8 +48,8 @@ void help() {
     printf("OPTIONS\n");
     printf("   -c, --constraints FILE\n");
     printf("                        Load constraints from FILE.  See Constraint syntax below\n");
-    printf("   -d, --dangle INT     Allow only one treatment of dangleing end energies in \n");
-    printf("                        mulit- and external loops (INT=0,2) see below for details\n");
+    printf("   -d, --dangle INT     Allow only one treatment of dangling end energies in \n");
+    printf("                        multi- and external loops (INT=0,2) see below for details\n");
     printf("   -h, --help           Output help (this message) and exit\n");
     printf("   -l, --limitCD INT    Set a maximum base pair contact distance to INT. If no\n");
     printf("                        limit is given, base pairs can be over any distance\n");
@@ -80,7 +80,7 @@ void help() {
 
     printf("\nDangle:\n");
     printf("\tINT=0 ignores dangling end energies (mostly for debugging).\n");
-    printf("\tINT=2 dangling end energies are added for nucleotieds on either\n");
+    printf("\tINT=2 dangling end energies are added for nucleotides on either\n");
     printf("\tside of each branch in multi-loops and external loops.\n");
     printf("\tAll other values for INT are ignored.\n");
     exit(-1);

From 01c1ecbcd7b02e71944a18ada38f23c65a240409 Mon Sep 17 00:00:00 2001
From: Shel Swenson <shelswenson@gmail.com>
Date: Tue, 12 Jul 2011 16:41:33 -0400
Subject: [PATCH 208/282] updated copyright info in README's and autor list in
 AUTHORS

---
 README             | 48 ++++++++++++++++++++++++++++++----------------
 gtfold-mfe/AUTHORS |  1 +
 gtfold-mfe/README  | 48 ++++++++++++++++++++++++++++++----------------
 3 files changed, 63 insertions(+), 34 deletions(-)

diff --git a/README b/README
index 3741de6..56622c2 100644
--- a/README
+++ b/README
@@ -1,14 +1,23 @@
 GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction
 
-(C) 2007-2010, David A. Bader
-               Amrita Mathuriya
+(C) 2007-2011, David A. Bader
                 College of Computing, Georgia Institute of Technology
                Christine E. Heitsch
                 School of Mathematics, Georgia Institute of Technology
                Stephen C. Harvey
                 School of Biology, Georgia Institute of Technology
-               Sainath Mallidi
-                College of Computing, Georgia Institute of Technology
+               And various contributing authors
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 The prediction of the correct secondary structures of large RNAs is
 one of the unsolved challenges of computational molecular biology.
@@ -28,8 +37,11 @@ DBI-04-20513. Additionally, the research of Christine E. Heitsch,
 Ph.D., is supported in part by a Career Award at the Scientific
 Interface (CASI) from the Burroughs Wellcome Fund (BWF). 
 
-Additional contributors to GTfold's implementation include Georgia
-Tech visiting students Gregory Nou, Sonny Hernandez, and Manoj Soni.
+Additional contributors to GTfold's implementation include 
+Georgia Tech graduate students Sainath Mallidi, Amrita Mathuriya, 
+and Prashant Gaurav, undergraduates Joshua Anderson and Andrew Ash
+and visiting students Gregory Nou, Sonny Hernandez, Manoj Soni,
+and Zsuzsanna Sukosd.
 
 INSTALLATION -
 Please execute the following commands
@@ -111,14 +123,16 @@ Version History:
             Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure.
             Some documentation added.
 2.0 11 July 2011                      
-   								 Optimized the code to enable faster multiloop calculations 
-												Added -d, --dangle to allow treatment of dangling end energies based on user input 
-												Added -m  --mismatch to enable terminal mismatch calculations
-												Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name 
-												Added -p  --paramdir to allow user to provide custom parameters		
-												Added -t, --threads to limit number of threads used
-												Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides 
-												such that it could be part of a helix of length INT
-   									Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5)
-												Added --unafold to run GTfold in UNAfold default mode (version 3.8)
-												Added beta options --subopt, --bpp, --useShape
+            Optimized the code to enable faster multiloop calculations 
+            Added -d, --dangle to allow treatment of dangling end energies based on user input 
+            Added -m  --mismatch to enable terminal mismatch calculations
+            Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name 
+            Added -p  --paramdir to allow user to provide custom parameters		
+            Added -t, --threads to limit number of threads used
+            Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides 
+                    such that it could be part of a helix of length INT
+            Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5)
+            Added --unafold to run GTfold in UNAfold default mode (version 3.8)
+            Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE 
+            Added --bpp (Beta only) which outputs basepair probabilities based on the partiaiton function 
+            Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data
diff --git a/gtfold-mfe/AUTHORS b/gtfold-mfe/AUTHORS
index 0f01d3b..0e9ed76 100644
--- a/gtfold-mfe/AUTHORS
+++ b/gtfold-mfe/AUTHORS
@@ -4,4 +4,5 @@ Amrita Mathuriya <amathuriya3@gatech.edu> August 2007 - January 2009
 Sainath Mallidi <sainath@gatech.edu> August 2009 - December 2010
 Josh Anderson <janderson3@gatech.edu> August 2010 - May 2011
 Andrew Ash <andrew.ash@gatech.edu> August 2010 - May 2011
+Zsuzsanna Sukosd <sz@mb.au.dk> February 2011 - June 2011 
 Prashant Gaurav <pgaurav3@gatech.edu> August 2010 - 
diff --git a/gtfold-mfe/README b/gtfold-mfe/README
index 3741de6..56622c2 100644
--- a/gtfold-mfe/README
+++ b/gtfold-mfe/README
@@ -1,14 +1,23 @@
 GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction
 
-(C) 2007-2010, David A. Bader
-               Amrita Mathuriya
+(C) 2007-2011, David A. Bader
                 College of Computing, Georgia Institute of Technology
                Christine E. Heitsch
                 School of Mathematics, Georgia Institute of Technology
                Stephen C. Harvey
                 School of Biology, Georgia Institute of Technology
-               Sainath Mallidi
-                College of Computing, Georgia Institute of Technology
+               And various contributing authors
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 The prediction of the correct secondary structures of large RNAs is
 one of the unsolved challenges of computational molecular biology.
@@ -28,8 +37,11 @@ DBI-04-20513. Additionally, the research of Christine E. Heitsch,
 Ph.D., is supported in part by a Career Award at the Scientific
 Interface (CASI) from the Burroughs Wellcome Fund (BWF). 
 
-Additional contributors to GTfold's implementation include Georgia
-Tech visiting students Gregory Nou, Sonny Hernandez, and Manoj Soni.
+Additional contributors to GTfold's implementation include 
+Georgia Tech graduate students Sainath Mallidi, Amrita Mathuriya, 
+and Prashant Gaurav, undergraduates Joshua Anderson and Andrew Ash
+and visiting students Gregory Nou, Sonny Hernandez, Manoj Soni,
+and Zsuzsanna Sukosd.
 
 INSTALLATION -
 Please execute the following commands
@@ -111,14 +123,16 @@ Version History:
             Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure.
             Some documentation added.
 2.0 11 July 2011                      
-   								 Optimized the code to enable faster multiloop calculations 
-												Added -d, --dangle to allow treatment of dangling end energies based on user input 
-												Added -m  --mismatch to enable terminal mismatch calculations
-												Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name 
-												Added -p  --paramdir to allow user to provide custom parameters		
-												Added -t, --threads to limit number of threads used
-												Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides 
-												such that it could be part of a helix of length INT
-   									Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5)
-												Added --unafold to run GTfold in UNAfold default mode (version 3.8)
-												Added beta options --subopt, --bpp, --useShape
+            Optimized the code to enable faster multiloop calculations 
+            Added -d, --dangle to allow treatment of dangling end energies based on user input 
+            Added -m  --mismatch to enable terminal mismatch calculations
+            Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name 
+            Added -p  --paramdir to allow user to provide custom parameters		
+            Added -t, --threads to limit number of threads used
+            Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides 
+                    such that it could be part of a helix of length INT
+            Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5)
+            Added --unafold to run GTfold in UNAfold default mode (version 3.8)
+            Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE 
+            Added --bpp (Beta only) which outputs basepair probabilities based on the partiaiton function 
+            Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data

From 3b6010e3187489a7fa04a80a3b789c0c302cc42f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 16:56:51 -0400
Subject: [PATCH 209/282] added new header files

---
 gtfold-mfe/include/Makefile.am | 3 +--
 gtfold-mfe/include/Makefile.in | 5 ++---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am
index a03865e..5a61bdd 100644
--- a/gtfold-mfe/include/Makefile.am
+++ b/gtfold-mfe/include/Makefile.am
@@ -1,3 +1,2 @@
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h
-
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h global.h options.h random-sample.h subopt_traceback.h constraints.h energy.h shapereader.h utils.h
 CLEANFILES = *~
diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in
index 44a1859..607786e 100644
--- a/gtfold-mfe/include/Makefile.in
+++ b/gtfold-mfe/include/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# Makefile.in generated by automake 1.11 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
@@ -93,7 +93,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 SET_MAKE = @SET_MAKE@
@@ -155,7 +154,7 @@ target_vendor = @target_vendor@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h
+noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h global.h options.h random-sample.h subopt_traceback.h constraints.h energy.h shapereader.h utils.h
 CLEANFILES = *~
 all: all-am
 

From c45defaea509bb30513ce46eda9060d4af64e407 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 16:57:54 -0400
Subject: [PATCH 210/282] removed TODO file

---
 gtfold-mfe/TODO | 7 -------
 1 file changed, 7 deletions(-)
 delete mode 100644 gtfold-mfe/TODO

diff --git a/gtfold-mfe/TODO b/gtfold-mfe/TODO
deleted file mode 100644
index 366385a..0000000
--- a/gtfold-mfe/TODO
+++ /dev/null
@@ -1,7 +0,0 @@
-Make single-letter options work
-
-Partition Function
-==================
-
- - fast inner loops optimization
- - factor in dangling energies

From e09900940c1523b7e358ff041731ef786f4dd62a Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 17:16:54 -0400
Subject: [PATCH 211/282] removed TODO NEWS

---
 gtfold-mfe/Makefile.in | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/gtfold-mfe/Makefile.in b/gtfold-mfe/Makefile.in
index 61df044..da3d87e 100644
--- a/gtfold-mfe/Makefile.in
+++ b/gtfold-mfe/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# Makefile.in generated by automake 1.11 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
@@ -39,7 +39,7 @@ subdir = .
 DIST_COMMON = README $(am__configure_deps) $(include_HEADERS) \
 	$(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(srcdir)/gtfold_config.h.in $(top_srcdir)/configure AUTHORS \
-	COPYING ChangeLog INSTALL NEWS TODO config.guess config.sub \
+	COPYING ChangeLog INSTALL NEWS config.guess config.sub \
 	depcomp install-sh missing
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/configure.in
@@ -167,7 +167,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 SET_MAKE = @SET_MAKE@
@@ -320,7 +319,7 @@ uninstall-includeHEADERS:
 #     (which will cause the Makefiles to be regenerated when you run `make');
 # (2) otherwise, pass the desired values on the `make' command line.
 $(RECURSIVE_TARGETS):
-	@fail= failcom='exit 1'; \
+	@failcom='exit 1'; \
 	for f in x $$MAKEFLAGS; do \
 	  case $$f in \
 	    *=* | --[!k]*);; \
@@ -345,7 +344,7 @@ $(RECURSIVE_TARGETS):
 	fi; test -z "$$fail"
 
 $(RECURSIVE_CLEAN_TARGETS):
-	@fail= failcom='exit 1'; \
+	@failcom='exit 1'; \
 	for f in x $$MAKEFLAGS; do \
 	  case $$f in \
 	    *=* | --[!k]*);; \
@@ -509,8 +508,7 @@ distdir: $(DISTFILES)
 	  fi; \
 	done
 	-test -n "$(am__skip_mode_fix)" \
-	|| find "$(distdir)" -type d ! -perm -755 \
-		-exec chmod u+rwx,go+rx {} \; -o \
+	|| find "$(distdir)" -type d ! -perm -777 -exec chmod a+rwx {} \; -o \
 	  ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
 	  ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
 	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
@@ -554,17 +552,17 @@ dist dist-all: distdir
 distcheck: dist
 	case '$(DIST_ARCHIVES)' in \
 	*.tar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
+	  GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
-	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
+	  bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\
 	*.tar.lzma*) \
-	  lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\
+	  unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\
 	*.tar.xz*) \
 	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
 	*.tar.Z*) \
 	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
 	*.shar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
+	  GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	esac

From bbe5f6d75be54d93308a7bc2734aa06e7c42eb11 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 17:17:50 -0400
Subject: [PATCH 212/282] removing NEWS

---
 gtfold-mfe/NEWS | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 gtfold-mfe/NEWS

diff --git a/gtfold-mfe/NEWS b/gtfold-mfe/NEWS
deleted file mode 100644
index e69de29..0000000

From b68b49a30edeac2a927803a8757ff743df2d1e88 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 12 Jul 2011 17:22:10 -0400
Subject: [PATCH 213/282] removing NEWS

---
 gtfold-mfe/Makefile.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/Makefile.in b/gtfold-mfe/Makefile.in
index da3d87e..5f77d42 100644
--- a/gtfold-mfe/Makefile.in
+++ b/gtfold-mfe/Makefile.in
@@ -39,7 +39,7 @@ subdir = .
 DIST_COMMON = README $(am__configure_deps) $(include_HEADERS) \
 	$(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(srcdir)/gtfold_config.h.in $(top_srcdir)/configure AUTHORS \
-	COPYING ChangeLog INSTALL NEWS config.guess config.sub \
+	COPYING ChangeLog INSTALL config.guess config.sub \
 	depcomp install-sh missing
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/configure.in

From d8014e13df65de87d3f7065b0fa0fd054a0cf4d0 Mon Sep 17 00:00:00 2001
From: Shel Swenson <shelswenson@gmail.com>
Date: Wed, 20 Jul 2011 08:30:06 -0400
Subject: [PATCH 214/282] clarified help message

---
 gtfold-mfe/src/options.cc | 45 ++++++++++++++++++++-------------------
 1 file changed, 23 insertions(+), 22 deletions(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index b31d789..5ef3802 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -43,44 +43,45 @@ int contactDistance = -1;
 void help() {
     printf("Usage: gtfold [OPTION]... FILE\n\n");
 
-    printf("  FILE is an RNA sequence file.  Single line or FASTA formats are accepted.\n\n");
+    printf("   FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n");
 
     printf("OPTIONS\n");
     printf("   -c, --constraints FILE\n");
-    printf("                        Load constraints from FILE.  See Constraint syntax below\n");
-    printf("   -d, --dangle INT     Allow only one treatment of dangling end energies in \n");
-    printf("                        multi- and external loops (INT=0,2) see below for details\n");
-    printf("   -h, --help           Output help (this message) and exit\n");
+    printf("                        Load constraints from FILE.  See Constraint syntax below.\n");
+    printf("   -d, --dangle INT     Restricts treatment of dangling energies (INT=0,2),\n"); 
+    printf("                        see below for details.\n");
+    printf("   -h, --help           Output help (this message) and exit.\n");
     printf("   -l, --limitCD INT    Set a maximum base pair contact distance to INT. If no\n");
-    printf("                        limit is given, base pairs can be over any distance\n");
+    printf("                        limit is given, base pairs can be over any distance.\n");
     printf("   -m  --mismatch       Enable terminal mismatch calculations\n");
-//    printf("   -n, --noisolate      Prevent isolated base pairs from forming\n");
+//    printf("   -n, --noisolate      Prevent isolated base pairs from forming.\n");
     printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
     printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
-    printf("   -t, --threads INT    Limit number of threads used to INT\n");
-    printf("   -v, --verbose        Run in verbose mode\n");
-    printf("   -w, --workDir DIR    Path of directory where output files will be written\n");
+    printf("   -t, --threads INT    Limit number of threads used to INT.\n");
+    printf("   -v, --verbose        Run in verbose mode (includes loop-by-loop energy decomposition\n");
+    printf("                        and confirmation of constraints satisfied).\n");
+    printf("   -w, --workdir DIR    Path of directory where output files will be written.\n");
     printf("   --prefilter INT      Prohibits any basepair which does not have appropriate\n");
     printf("                        neighboring nucleotides such that it could be part of\n");
-    printf("                        a helix of length INT\n");
-    printf("   --rnafold            Run as RNAfold default mode (ViennaPackage version 1.8.5)\n");
-    printf("   --unafold            Run as UNAfold default mode (version 3.8)\n");
-
+    printf("                        a helix of length INT.\n");
+    printf("   --rnafold            Run as RNAfold default mode (ViennaPackage version 1.8.5).\n");
+    printf("   --unafold            Run as UNAfold default mode (version 3.8), subject to traceback\n");
+    printf("                        implementation.\n");
 
     printf("\nBETA OPTIONS\n");
-    printf("   --bpp                Calculate base pair probabilities\n");
-    printf("   --subopt range       Calculate suboptimal structures within 'range' kcal/mol\n");
-    printf("                        of the mfe\n");
-    printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE\n");      
+    printf("   --bpp                Calculate base pair probabilities.\n");
+    printf("   --subopt NUM         Calculate suboptimal structures within NUM kcal/mol\n");
+    printf("                        of the MFE.\n");
+    printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE.\n");      
 
     printf("\nConstraint syntax:\n");
-    printf("\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n");
-    printf("\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n");
+    printf("\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n");
+    printf("\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n");
     printf("\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
 
     printf("\nDangle:\n");
-    printf("\tINT=0 ignores dangling end energies (mostly for debugging).\n");
-    printf("\tINT=2 dangling end energies are added for nucleotides on either\n");
+    printf("\tINT=0 ignores dangling energies (mostly for debugging).\n");
+    printf("\tINT=2 dangling energies are added for nucleotides on either\n");
     printf("\tside of each branch in multi-loops and external loops.\n");
     printf("\tAll other values for INT are ignored.\n");
     exit(-1);

From 4e11ae59062a8a66a56b94a587aa4e1426cc7ee2 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 20 Jul 2011 12:12:46 -0400
Subject: [PATCH 215/282] enable -d 2 when subopt is invoked

---
 gtfold-mfe/src/main.cc    | 5 ++++-
 gtfold-mfe/src/options.cc | 1 +
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 32cc9ad..4b016de 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -276,7 +276,10 @@ int main(int argc, char** argv) {
 	init_fold(seq);
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
-	readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
+	if (SUBOPT_ENABLED) 
+									readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, 1, T_MISMATCH);
+	else
+									readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
 
 	printRunConfiguration(seq);
 
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 5ef3802..d893af6 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -175,6 +175,7 @@ void parse_options(int argc, char** argv) {
 																																BPP_ENABLED = true;
 																								} else if(strcmp(argv[i], "--subopt") == 0) {
 																																SUBOPT_ENABLED = true;
+																																dangles = 2;
 																																if(i < argc)
 																																								suboptDelta = atof(argv[++i]);
 																																else

From 4656b8bc34f81f29768a83e054fdf7da21b73411 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 20 Jul 2011 12:13:33 -0400
Subject: [PATCH 216/282] new subopt algorithm using -d 2 mode

---
 gtfold-mfe/include/subopt_traceback.h |   6 +-
 gtfold-mfe/src/subopt_traceback.cc    | 547 +++++++++-----------------
 2 files changed, 186 insertions(+), 367 deletions(-)

diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h
index cccf44e..fd819b6 100644
--- a/gtfold-mfe/include/subopt_traceback.h
+++ b/gtfold-mfe/include/subopt_traceback.h
@@ -30,7 +30,7 @@
 #include <map>
 #include <vector>
 
-enum label {lW=0, lV, lVBI, lVM, lWM};
+enum label {lW=0, lV, lVBI, lVM, lWM, lWMPrime};
 extern const char* lstr[]; 
 
 struct segment 
@@ -221,6 +221,8 @@ void traceV(int i, int j, ps_t & ps, ps_stack_t & gs);
 void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs);
 void traceW(int i, int j, ps_t & ps, ps_stack_t & gs);
 void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs);
-void traceWM(ps_t& ps, ps_map_t& filter);
+void traceWM(int i, int j, ps_t &  ps, ps_stack_t & gs);
+void traceWMPrime(int i, int j, ps_t &  ps, ps_stack_t & gs);
+//void traceWM(ps_t& ps, ps_map_t& filter);
 
 #endif
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index d5e4729..ccaa4a1 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -28,388 +28,205 @@
 #include "global.h"
 #include "subopt_traceback.h"
 
-const char* lstr[] = {"W", "V", "VBI", "VM", "WM"};
-
-void (*trace_func[5]) (int i, int j, ps_t& ps, ps_stack_t& gs);
-int delta = 0;
-int mfe = INFINITY_;
-
-void print_stack(ps_stack_t temp)
-{	
-	std::cout << "{\n";
-	while (!temp.empty())
-	{
-		ps_t ps = temp.top();
-		temp.pop();
-		ps.print();
-		std::cout << '\n' ;
-	}	
-	std::cout << "}\n";
+#define DEBUG 1
+
+const char* lstr[] = {"W", "V", "VBI", "VM", "WM", "WMPrime"};
+
+void (*trace_func[6]) (int i, int j, ps_t& ps, ps_stack_t& gs);
+static int delta = 0;
+static int mfe = INFINITY_;
+static int length = -1;
+static int gflag = 0;
+
+void process(ss_map_t& subopt_data, int len) {
+								int count = 0 ;
+								ps_stack_t gstack;
+
+								// initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} 
+								ps_t first(0, len);
+								first.push(segment(1, len, lW, W[len]));	
+								gstack.push(first); // initialize the partial structure stacka
+
+								while (1) {
+																if (gstack.empty()) break; // exit
+																ps_t ps = gstack.top();
+																gstack.pop(); 
+
+																if (ps.empty()) {
+																								count++;
+																								subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
+																								continue;
+																}	
+																else {
+																								segment smt = ps.top();
+																								ps.pop();
+																								
+																								gflag = 0;
+																								if (smt.j_ - smt.i_ > TURN) {
+																																(*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack);
+																								}
+																								
+																								// discarded current segment, using remaining ones
+																								if (!gflag) {
+																																ps_t ps1(ps);
+																																gstack.push(ps1);
+																								}
+																}
+								}
+								
+#ifdef DEBUG 
+								printf("# SS = %d\n", count);
+#endif
 }
 
-void process(ss_map_t& subopt_data, int len)
-{
-	int count = 0 ;
-	ps_stack_t gstack;
-
-	// initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} 
-	ps_t first(0, len);
-	first.push(segment(1, len, lW, W[len]));	
-	gstack.push(first); // initialize the partial structure stacka
+ss_map_t subopt_traceback(int len, int _delta) {
+								trace_func[0] = traceW;
+								trace_func[1] = traceV;
+								/* trace_func[2] = traceVBI;*/
+								trace_func[3] = traceVM;
+								trace_func[4] = traceWM;
+								trace_func[5] = traceWMPrime;
 
-	while (1)
-	{
-		if (gstack.empty()) break; // exit
+								mfe = W[len];
+								delta = _delta;
+								length = len;
 
-		ps_t ps = gstack.top();
-		gstack.pop(); 
+								ss_map_t subopt_data;
+								process(subopt_data, len);
 
-		if (ps.empty()) 
-		{
-			//std::cout << ps.str << ' ' << ps.ae_/100.0 << std::endl;
-			ss_map_t::iterator it = subopt_data.find(ps.str); 
-			if ( it == subopt_data.end())
-			{
-				subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
-				count++;
-			} 
-			else 
-			{
-				int energy = it->second;
-				if (ps.ae_ < energy && (ps.ae_ >= mfe && ps.ae_ <= mfe + delta)) {
-					subopt_data[it->first] = ps.ae_;					
-				}		
-			}
-			continue;
-		}	
-		else
-		{
-			segment smt = ps.top();
-			ps.pop();
-			size_t s1 = gstack.size();
-
-			if (smt.j_ - smt.i_ >= TURN)
-			{
-				(*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack);
-			}
-			
-			// discard this segment, use remaining ones
-			if (gstack.size() == s1 && ps.total() <= mfe + delta)
-			{
-				ps_t ps1(ps);
-				gstack.push(ps1);
-			}
-		}
-	}
+								return subopt_data;
 }
 
-ss_map_t subopt_traceback(int len, int _delta)
-{
-	trace_func[0] = traceW;
-	trace_func[1] = traceV;
-	trace_func[3] = traceVM;
-
-	mfe = W[len];
-	delta = _delta;
-
-	ss_map_t subopt_data;
-	process(subopt_data, len);
-
-	return subopt_data;
+void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) {
+								// Hairpin Loop
+								if (eH(i,j) + ps.total()  <= mfe + delta) {
+																ps_t ps1(ps); 
+																ps1.accumulate(eH(i,j));
+																ps1.update(i, j, '(', ')');
+																push_to_gstack(gstack, ps1);
+								}
+
+								// Stack
+								if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) {
+																ps_t ps1(ps);
+																ps1.push(segment(i+1, j-1, lV, V(i+1, j-1)));
+																ps1.accumulate(eS(i,j));
+																ps1.update(i, j , '(', ')');
+																push_to_gstack(gstack, ps1);
+								}
+
+								// Internal Loop
+								if (VBI(i,j) + ps.total() <= mfe + delta) {
+																traceVBI(i,j,ps,gstack);
+								}
+
+								// Multiloop
+								if ( VM(i,j) + ps.total() <= mfe + delta) {
+																ps_t ps1(ps);
+																ps1.push(segment(i, j, lVM, VM(i,j)));
+																ps1.update(i, j, '(', ')');
+																push_to_gstack(gstack, ps1);
+								}
 }
 
-void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack)
-{
-	// Hairpin Loop
-	if (eH(i,j) + ps.total()  <= mfe + delta )
-	{
-		//std::cout << "Hairpin " << i  << ' ' << j << std::endl;
-		ps_t ps1(ps); 
-		ps1.accumulate(eH(i,j));
-		ps1.update(i, j, '(', ')');
-		push_to_gstack(gstack, ps1);
-	}
-
-	// Stack
-	if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta)
-	{
-		//	std::cout << "Stack " << i  << ' ' << j << std::endl;
-		ps_t ps1(ps);
-		ps1.push(segment(i+1, j-1, lV, V(i+1, j-1)));
-		ps1.accumulate(eS(i,j));
-		ps1.update(i, j , '(', ')');
-		push_to_gstack(gstack, ps1);
-	}
-
-	// Internal Loop
-	if (VBI(i,j) + ps.total() <= mfe + delta )
-	{
-		//std::cout << "Internal " << i  << ' ' << j << std::endl;
-		//ps_t ps1(ps);
-		//ps1.push(segment(i, j, lVBI, VBI(i,j)));
-		//ps1.update(i, j, 'i', 'i');
-		//push_to_gstack(gstack, ps1);
-		traceVBI(i,j,ps,gstack);
-	}
-
-	// Multiloop
-	if ( VM(i,j) + ps.total() <= mfe + delta )
-	{
-		//std::cout << "Multi " << i  << ' ' << j << std::endl;
-		ps_t ps1(ps);
-		ps1.push(segment(i, j, lVM, VM(i,j)));
-		ps1.update(i, j, '(', ')');
-		push_to_gstack(gstack, ps1);
-	}
-
+void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) {
+								int p,q;
+
+								for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
+																int minq = j-i+p-MAXLOOP-2;
+																if (minq < p+1+TURN) minq = p+1+TURN;
+																int maxq = (p==(i+1))?(j-2):(j-1);
+																for (q = minq; q <= maxq; q++) {
+																								if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta) {
+																																ps_t ps1(ps);
+																																ps1.push(segment(p, q, lV, V(p, q)));
+																																ps1.update(i, j , '(', ')');
+																																ps1.accumulate(eL(i, j, p, q));
+																																push_to_gstack(gstack, ps1);
+																								}
+																}
+								}
 }
 
-void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack)
-{
-	int p,q;
-	for (p = i+1; p < MIN(j-2-TURN, i+MAXLOOP+1); ++p)
-	{
-		int minq = j-i+p-MAXLOOP-2;
-		if (minq < p+1+TURN) minq = p+1+TURN;
-		int maxq = (p==(i+1))?(j-2):(j-1);
-
-		for (q = minq; q <= maxq; q++) 
-		{
-			if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta && PP[p][q] == 1)
-			{
-				ps_t ps1(ps);
-				ps1.update(i, j, '(', ')');
-				ps1.push(segment(p, q, lV, V(p, q)));
-				ps1.accumulate(eL(i, j, p, q));
-				push_to_gstack(gstack, ps1);
-			}
-		}
-	}
+void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack) {
+								for (int i = 1; i < j-TURN; ++i) {
+																int wim1 =  MIN(0, W[i-1]);
+																int d3 = (i>1)?Ed3(j,i,i-1):0;
+																int d5 = (j<length)?Ed5(j,i,j+1):0;
+																
+																int Wij = V(i,j) + auPenalty(i, j) + d3 + d5 + wim1;
+																if (Wij + ps.total() <= mfe + delta ) {
+																								ps_t ps1(ps);
+																								ps1.push(segment(i, j, lV, V(i,j)));
+																								if (wim1 == W[i-1]) ps1.push(segment(1, i-1, lW, W[i-1]));
+																								ps1.accumulate(auPenalty(i, j) + d3 + d5);
+																								push_to_gstack(gstack, ps1);
+																}
+								}
+
+								if (W[j-1] + ps.total() <= mfe + delta) {
+																ps_t ps1(ps);
+																ps1.push(segment(1, j-1, lW, V(1,j-1)));
+																push_to_gstack(gstack, ps1);
+								}
 }
-
-void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack)
-{
-	for (int i = 1; i < j-TURN; ++i)
-	{
-		int wim1 =  MIN(0, W[i-1]);
-
-		int wij = V(i,j) + auPenalty(i, j) + wim1;
-		if (wij + ps.total() <= mfe + delta )
-		{
-			ps_t ps1(ps);
-			ps1.push(segment(i, j, lV, V(i,j)));
-			if (wim1 <= 0 && i > 1) ps1.push(segment(1, i-1, lW, W[i-1]));
-			ps1.accumulate(auPenalty(i, j));
-			push_to_gstack(gstack, ps1);
-		}		
-		
-		
-		int wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1;
-		if (wijd + ps.total() <= mfe + delta )
-		{
-			ps_t ps3(ps);
-			ps3.push(segment(i, j-1, lV, V(i, j-1)));
-			if (wim1 <= 0 && i > 1)	ps3.push(segment(1, i-1, lW, W[i-1]));
-			ps3.accumulate(auPenalty(i,j-1) + Ed5(j-1,i,j)); 
-			push_to_gstack(gstack, ps3);
-		}	
-
-		int widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1;
-		if (widj + ps.total() <= mfe + delta )
-		{
-			ps_t ps4(ps);
-			ps4.push(segment(i+1, j, lV, V(i+1,j)));
-			if (wim1 <= 0 && i > 1) ps4.push(segment(1, i-1, lW, W[i-1]));
-			ps4.accumulate(auPenalty(i+1, j) + Ed3(j,i+1,i));
-			push_to_gstack(gstack, ps4);
-		}
-
-		int widjd = V(i+1, j-1) + auPenalty(i+1,j-1) + Ed3(j-1, i+1, i) + Ed5(j-1, i+1, j) + wim1;
-		if (widjd + ps.total() <= mfe + delta )
-		{
-			ps_t ps2(ps);
-			ps2.push(segment(i+1, j-1, lV, V(i+1,j-1)));
-			if (wim1 <= 0 && i > 1) ps2.push(segment(1, i-1, lW, W[i-1]));
-			ps2.accumulate(auPenalty(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
-			push_to_gstack(gstack, ps2);
-		}
-	} 
-
-	if (W[j-1] + ps.total() <= mfe + delta )
-	{
-		ps_t ps1(ps);
-		ps1.push(segment(1, j-1, lW, W[j-1]));
-		push_to_gstack(gstack, ps1);
-	}	
+								
+void traceWM(int i, int j, ps_t& ps, ps_stack_t& gstack) {
+								int d3 = (i==1)?Ed3(j,i,length):Ed3(j,i,i-1);
+								int d5 = Ed5(j,i,j+1);
+								
+								if (V(i,j) + auPenalty(i, j) + Eb + d3 + d5 + ps.total() <= mfe + delta) {
+																ps_t ps_new(ps);
+																ps_new.accumulate(auPenalty(i, j) + Eb + d3 + d5);
+																ps_new.push(segment(i,j, lV, V(i,j)));
+																push_to_gstack(gstack, ps_new);
+								}
+								
+								if (WMPrime[i][j] + ps.total() <= mfe + delta) {
+																ps_t ps_new(ps);
+																ps_new.push(segment(i,j, lWMPrime, WMPrime[i][j]));
+																push_to_gstack(gstack, ps_new);
+								}
+								
+								if (WM(i+1,j) + Ec + ps.total() <= mfe + delta) {
+																ps_t ps_new(ps);
+																ps_new.accumulate(Ec);
+																ps_new.push(segment(i+1,j, lWM, WM(i+1,j)));
+																push_to_gstack(gstack, ps_new);
+								}
+								
+								if (WM(i,j-1) + Ec + ps.total() <= mfe + delta) {
+																ps_t ps_new(ps);
+																ps_new.accumulate(Ec);
+																ps_new.push(segment(i,j-1, lWM, WM(i,j-1)));
+																push_to_gstack(gstack, ps_new);
+								}
 }
 
-void traceWM(ps_t& ps, ps_map_t& filter)
-{
-	ps_stack_t wm_stack;
-	wm_stack.push(ps);
-
-	while (!wm_stack.empty())
-	{
-		ps_t pss = wm_stack.top();
-		wm_stack.pop();
-
-		// check if all segments in pss are Vs
-		if (pss.empty()) 
-		{
-			std::string key = pss.str;
-			while (!pss.empty_v())
-			{
-				segment ss = pss.top_v();
-				pss.pop_v();
-
-				pss.push(ss);
-				key[ss.i_-1] = '*'; key[ss.j_-1] = '*';
-			}
-			filter.insert(std::pair<std::string, ps_t>(key, pss));
-			continue;
-		}
-
-		segment wm_seg = pss.top();
-		pss.pop();
-
-		int i1 = wm_seg.i_; int j1 = wm_seg.j_;
-
-		if (wm_seg.label_ == lV)
-		{
-			ps_t ps1(pss);
-			ps1.push_v(wm_seg);
-			wm_stack.push(ps1);
-			continue;
-		}
-		int h = i1; int k = j1;
-
-		int wmij = V(h,k) + auPenalty(h,k) + Eb;
-		if (pss.total() + wmij <= mfe + delta )
-		{
-			ps_t ps1(pss);
-			ps1.push_v(segment(h,k,lV, V(h,k)));
-			ps1.accumulate(auPenalty(h,k) + Eb);
-			wm_stack.push(ps1);
-		}
-
-		int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+ Ec ;
-		if (pss.total() + wmijd <= mfe + delta )
-		{
-			ps_t ps1(pss);
-			ps1.push_v(segment(h,k-1,lV, V(h,k-1)));
-			ps1.accumulate(Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+Ec);
-			wm_stack.push(ps1);
-		}
-
-		int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + Eb+Ec ;
-		if (pss.total() + wmidj <= mfe + delta )
-		{
-			ps_t ps1(pss);
-			ps1.push_v(segment(h+1, k, lV, V(h+1,k)));
-			ps1.accumulate(Ed3(k,h+1,h) + auPenalty(h+1,k) +Eb+Ec);
-			wm_stack.push(ps1);
-		}
-
-		int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) +  auPenalty(h+1,k-1) +Eb+ 2*Ec ;
-		if (pss.total() + wmidjd <= mfe + delta )
-		{
-			ps_t ps1(pss);
-			ps1.push_v(segment(h+1, k-1, lV, V(h+1,k-1)));
-			ps1.accumulate(Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec);
-			wm_stack.push(ps1);
-		}
-
-
-		if (pss.total() + WM(i1,j1-1)  + Ec  <= mfe + delta )
-		{
-			ps_t ps1(pss);
-			ps1.push(segment(i1,j1-1, lWM, WM(i1,j1-1)));		
-			ps1.accumulate(Ec);
-			wm_stack.push(ps1);
-		}
-
-		if (pss.total() + WM[i1+1][j1] + Ec <= mfe + delta )
-		{
-			ps_t ps1(pss);
-			ps1.push(segment(i1+1,j1, lWM, WM(i1+1,j1)));		
-			ps1.accumulate(Ec);
-			wm_stack.push(ps1);
-		}
-
-		for (int h = i1+1; h <= j1-1; ++h)
-		{	
-			if (WM(i1,h) + WM(h+1,j1) + pss.total() <= mfe + delta )
-			{
-				ps_t ps1(pss);
-				ps1.push(segment(i1, h, lWM, WM(i1,h)));
-				ps1.push(segment(h+1, j1, lWM, WM(h+1,j1)));
-				wm_stack.push(ps1);
-			}
-		}
-	}
+void traceWMPrime(int i, int j, ps_t& ps, ps_stack_t& gstack) {
+								for (int h = i+TURN+1 ; h <= j-TURN-2; h++) {
+																if (WM(i,h-1) + WM(h,j) + ps.total() <= mfe + delta) {
+																								ps_t ps_new(ps);
+																								ps_new.push(segment(i,h-1, lWM, WM(i,h-1)));
+																								ps_new.push(segment(h,j, lWM, WM(h,j)));
+																								push_to_gstack(gstack, ps_new);
+																}
+								}
 }
 
-void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack)
-{
-	std::map<std::string, ps_t> filter;
-	int h;	
-
-	for (h = i+1; h <= j-1; ++h)
-	{
-		int dG;
-		int d5 = Ed5(i,j,i+1);
-		int d3 = Ed3(i,j,j-1);
-		int common = auPenalty(i,j) + Ea + Eb;
-
-		dG = common + WM[i+1][h-1] + WM[h][j-1];
-		if (dG + ps.total()  <= mfe + delta )
-		{
-			ps_t ps1(ps);
-			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));
-			ps1.push(segment(h, j-1, lWM, WM[h][j-1]));
-			ps1.accumulate(common) ; 
-			traceWM(ps1, filter);
-		}
-
-		dG =  common + WM[i+2][h-1] + WM[h][j-1] + d5 + Ec;
-		if (dG + ps.total()  <= mfe + delta )
-		{
-			ps_t ps1(ps);
-			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
-			ps1.push(segment(h, j-1, lWM, WM[h][j-1]));	
-			ps1.accumulate(common + d5 + Ec);
-			traceWM(ps1, filter);
-		}
-
-		dG = common + WM[i+1][h-1] + WM[h][j-2] + d3 + Ec;
-		if (dG + ps.total()  <= mfe + delta )
-		{
-			ps_t ps1(ps);	
-			ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1]));	
-			ps1.push(segment(h, j-2, lWM, WM[h][j-2]));	
-			ps1.accumulate(common + d3 + Ec);
-			traceWM(ps1, filter);
-		}
-
-		dG = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*Ec;
-		if (dG + ps.total()  <= mfe + delta )
-		{ 	
-			ps_t ps1(ps);	
-			ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1]));	
-			ps1.push(segment(h, j-2, lWM, WM[h][j-2]));	
-			ps1.accumulate(common + d3 + d5 + 2*Ec) ;
-			traceWM(ps1, filter);
-		}
-	}
+void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) {
+								int d3 = Ed3(i,j,j-1);
+								int d5 = Ed5(i,j,i+1);
 
-	ps_map_t::iterator it ;
-	for (it = filter.begin(); it != filter.end(); ++it)
-	{
-		push_to_gstack(gstack, it->second);
-	}
+								if (WMPrime[i+1][j-1] + Ea + Eb + auPenalty(i, j) + d3 + d5 + ps.total() <= mfe + delta) {
+																ps_t ps_new(ps);
+																ps_new.accumulate(Ea + Eb + auPenalty(i, j) + d3 + d5); 
+																ps_new.push(segment(i+1,j-1, lWMPrime,WMPrime[i+1][j-1] ));
+																push_to_gstack(gstack, ps_new);
+								}
 }
 
-void push_to_gstack(ps_stack_t& gstack , const ps_t& v)
-{
-	gstack.push(v);
+void push_to_gstack(ps_stack_t& gstack , const ps_t& v) {
+								gflag = 1;
+								gstack.push(v);
 }

From 462278d215babb250be4b2d39920b9cd0dadce2c Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 20 Jul 2011 12:16:37 -0400
Subject: [PATCH 217/282] removed debug statement

---
 gtfold-mfe/src/subopt_traceback.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index ccaa4a1..2d3d9ed 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -28,7 +28,7 @@
 #include "global.h"
 #include "subopt_traceback.h"
 
-#define DEBUG 1
+//#define DEBUG 1
 
 const char* lstr[] = {"W", "V", "VBI", "VM", "WM", "WMPrime"};
 

From 88591d68d2e08b3217b06a8cc41f4dc99a6a73ed Mon Sep 17 00:00:00 2001
From: Shel Swenson <shelswenson@gmail.com>
Date: Wed, 20 Jul 2011 12:28:07 -0400
Subject: [PATCH 218/282] clarified help message

---
 gtfold-mfe/src/options.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index d893af6..831bf5d 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -71,7 +71,7 @@ void help() {
     printf("\nBETA OPTIONS\n");
     printf("   --bpp                Calculate base pair probabilities.\n");
     printf("   --subopt NUM         Calculate suboptimal structures within NUM kcal/mol\n");
-    printf("                        of the MFE.\n");
+    printf("                        of the MFE. (Uses -d 2 treatment of dangling energies.)\n");
     printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE.\n");      
 
     printf("\nConstraint syntax:\n");

From 71817d1c43c35f0996d1fc8a4711bdd23c952514 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 20 Jul 2011 12:35:21 -0400
Subject: [PATCH 219/282] added NEWS

---
 gtfold-mfe/NEWS | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 gtfold-mfe/NEWS

diff --git a/gtfold-mfe/NEWS b/gtfold-mfe/NEWS
new file mode 100644
index 0000000..e69de29

From dc12e6a3ffd0b291ec4b3219899809b161e38994 Mon Sep 17 00:00:00 2001
From: Shel Swenson <shelswenson@gmail.com>
Date: Wed, 20 Jul 2011 13:19:23 -0400
Subject: [PATCH 220/282] fixed typos and spelling errors in README

---
 README            | 5 +++--
 gtfold-mfe/README | 5 +++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/README b/README
index 56622c2..0034999 100644
--- a/README
+++ b/README
@@ -126,13 +126,14 @@ Version History:
             Optimized the code to enable faster multiloop calculations 
             Added -d, --dangle to allow treatment of dangling end energies based on user input 
             Added -m  --mismatch to enable terminal mismatch calculations
-            Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name 
+            Added -o, --output, , -w --workdir options to allow to write output files/directories with desired name 
             Added -p  --paramdir to allow user to provide custom parameters		
             Added -t, --threads to limit number of threads used
+            Added -v, --verbose to print loop-by-loop energy decomposition and confirm that constraints are satisfied
             Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides 
                     such that it could be part of a helix of length INT
             Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5)
             Added --unafold to run GTfold in UNAfold default mode (version 3.8)
             Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE 
-            Added --bpp (Beta only) which outputs basepair probabilities based on the partiaiton function 
+            Added --bpp (Beta only) which outputs basepair probabilities based on the partition function 
             Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data
diff --git a/gtfold-mfe/README b/gtfold-mfe/README
index 56622c2..0034999 100644
--- a/gtfold-mfe/README
+++ b/gtfold-mfe/README
@@ -126,13 +126,14 @@ Version History:
             Optimized the code to enable faster multiloop calculations 
             Added -d, --dangle to allow treatment of dangling end energies based on user input 
             Added -m  --mismatch to enable terminal mismatch calculations
-            Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name 
+            Added -o, --output, , -w --workdir options to allow to write output files/directories with desired name 
             Added -p  --paramdir to allow user to provide custom parameters		
             Added -t, --threads to limit number of threads used
+            Added -v, --verbose to print loop-by-loop energy decomposition and confirm that constraints are satisfied
             Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides 
                     such that it could be part of a helix of length INT
             Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5)
             Added --unafold to run GTfold in UNAfold default mode (version 3.8)
             Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE 
-            Added --bpp (Beta only) which outputs basepair probabilities based on the partiaiton function 
+            Added --bpp (Beta only) which outputs basepair probabilities based on the partition function 
             Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data

From 2170c3f7cd56f3e5c8ad3b813ffdc29801ff07a2 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 21 Jul 2011 16:41:43 -0400
Subject: [PATCH 221/282] added logic to read data from install dir, environ
 dir, current dir

---
 gtfold-mfe/src/loader.cc | 159 ++++++++++++++++++++++++++-------------
 1 file changed, 106 insertions(+), 53 deletions(-)

diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 8ec31df..9af6e97 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -26,6 +26,11 @@
 #include <cstring>
 #include <stdlib.h>
 
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <unistd.h>
+#include <errno.h>
+
 #include "data.h"
 #include "utils.h"
 #include "constants.h"
@@ -80,59 +85,101 @@ int init;
 int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */
 float prelog;
 
-void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, 
-				int unamode = 0, int rnamode = 0, int mismatch = 0) {
-	
-	if (!userdatalogic && unamode) {
-		EN_DATADIR.assign(xstr(DATADIR));
-		EN_DATADIR += "/";
-		EN_DATADIR += "UNAParams";
-	}else if (!userdatalogic && rnamode) {
-		EN_DATADIR.assign(xstr(DATADIR));
-		EN_DATADIR += "/";
-		EN_DATADIR += "RNAParams";
-	}
-    	else if (!userdatalogic) {
-		EN_DATADIR.assign(xstr(DATADIR));
-		EN_DATADIR += "/";
-		EN_DATADIR += "Turner99";
-	} else {
-		EN_DATADIR.assign(userdatadir);
-	}
-
-	//Handle the ending forward slash case
-	if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') {
-		EN_DATADIR += "/";
-	}
-
-	initMiscloopValues("miscloop.DAT", EN_DATADIR);
-	initDangleValues("dangle.DAT", EN_DATADIR);
-	initStackValues("stack.DAT", EN_DATADIR);
-	initLoopValues("loop.DAT", EN_DATADIR);
-	initTstkhValues("tstackh.DAT", EN_DATADIR);
-	initTstkiValues("tstacki.DAT", EN_DATADIR);
-	initTloopValues("tloop.DAT", EN_DATADIR);
-
-	if (unamode) {
-		initInt21Values("asint1x2.DAT", EN_DATADIR);
-		initInt22Values("sint4.DAT", EN_DATADIR);
-		initInt11Values("sint2.DAT", EN_DATADIR);
-		initTstkmValues("tstackm.DAT", EN_DATADIR);
-		initTstkeValues("tstacke.DAT", EN_DATADIR);
-		initTstk23Values("tstacki23.DAT", EN_DATADIR);
-	} else if (mismatch) {
-		initTstkmValues("tstackm.DAT", EN_DATADIR);
-		initTstkeValues("tstacke.DAT", EN_DATADIR);
-		initInt21Values("int21.DAT", EN_DATADIR);
-		initInt22Values("int22.DAT", EN_DATADIR);
-		initInt11Values("int11.DAT", EN_DATADIR);
-		
-	}	
-	else {
-		initInt21Values("int21.DAT", EN_DATADIR);
-		initInt22Values("int22.DAT", EN_DATADIR);
-		initInt11Values("int11.DAT", EN_DATADIR);
-	}
+void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode = 0, int rnamode = 0, int mismatch = 0) {
+								struct stat buf;
+								
+								if (!userdatalogic) {
+																std::string opt1, opt2, opt3;
+																char cwd[1024];
+																bool found = false;
+
+																opt1.assign(xstr(DATADIR));
+																if (getenv("GTDATADIR") != 0)
+																								opt2.assign(getenv("GTDATADIR"));
+																if (getcwd(cwd, sizeof(cwd)) != 0) {
+																								opt3.assign(cwd);
+																								opt3 += "/data";
+																}
+																
+																if (stat(opt1.c_str(), &buf) == 0) {
+																								found = true;
+																								EN_DATADIR.assign(opt1); 
+																							fprintf(stdout,"Checking for default datadir '%s', found.\n", opt1.c_str());
+																} else  {
+																							if (found == false)	fprintf(stdout,"Checking for default datadir '%s', not found.\n", opt1.c_str());
+																}
+
+																if (!found && stat(opt2.c_str(), &buf) == 0) {
+																								found = true;
+																								EN_DATADIR.assign(opt2);
+																								fprintf(stdout,"Checking for environ variable 'GTDATADIR', found \n");
+																} else {
+																							if (found == false)	fprintf(stdout,"Checking for environ variable 'GTDATADIR', not found \n");
+																}
+
+																if (!found && stat(opt3.c_str(), &buf) == 0){
+																								found = true;
+																								EN_DATADIR.assign(opt3);
+																								fprintf(stdout,"Checking under current dir '%s', found.\n", opt3.c_str());
+
+																} else {
+																							if (found == false)	fprintf(stdout,"Checking under current dir '%s', not found.\n", opt3.c_str());
+																}
+
+																EN_DATADIR += "/";
+																if (found == false) {
+																	exit(-1);
+																}	
+
+																if (unamode) {
+																								EN_DATADIR += "UNAParams";
+																}else if (rnamode) {
+																								EN_DATADIR += "RNAParams";
+																} else {
+																								EN_DATADIR += "Turner99";
+																}
+								}
+							 else {
+																EN_DATADIR.assign(userdatadir);
+																if (stat(EN_DATADIR.c_str(), &buf) == -1){
+																								fprintf(stdout,"Checking for parameter files in dir '%s', not found.\n\n", EN_DATADIR.c_str());
+																								exit(-1);		
+																}
+								}
+
+								//Handle the ending forward slash case
+								if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') {
+																EN_DATADIR += "/";
+								}
+
+								initMiscloopValues("miscloop.DAT", EN_DATADIR);
+								initDangleValues("dangle.DAT", EN_DATADIR);
+								initStackValues("stack.DAT", EN_DATADIR);
+								initLoopValues("loop.DAT", EN_DATADIR);
+								initTstkhValues("tstackh.DAT", EN_DATADIR);
+								initTstkiValues("tstacki.DAT", EN_DATADIR);
+								initTloopValues("tloop.DAT", EN_DATADIR);
+
+								if (unamode) {
+																initInt21Values("asint1x2.DAT", EN_DATADIR);
+																initInt22Values("sint4.DAT", EN_DATADIR);
+																initInt11Values("sint2.DAT", EN_DATADIR);
+																initTstkmValues("tstackm.DAT", EN_DATADIR);
+																initTstkeValues("tstacke.DAT", EN_DATADIR);
+																initTstk23Values("tstacki23.DAT", EN_DATADIR);
+								} else if (mismatch) {
+																initTstkmValues("tstackm.DAT", EN_DATADIR);
+																initTstkeValues("tstacke.DAT", EN_DATADIR);
+																initInt21Values("int21.DAT", EN_DATADIR);
+																initInt22Values("int22.DAT", EN_DATADIR);
+																initInt11Values("int11.DAT", EN_DATADIR);
+
+								}	
+								else {
+																initInt21Values("int21.DAT", EN_DATADIR);
+																initInt22Values("int22.DAT", EN_DATADIR);
+																initInt11Values("int11.DAT", EN_DATADIR);
+								}
 }
 
 int initStackValues(const string& fileName, const string& dirPath)  { 
@@ -142,6 +189,12 @@ int initStackValues(const string& fileName, const string& dirPath)  {
 	filePath = dirPath + fileName;
 	cf.open(filePath.c_str(), ios::in);
 
+	if (!cf.good()) {
+		std::cerr << "File open failed - " << filePath << std::endl;
+		cf.close();
+		exit(-1);		
+	}
+
 	for (int i = 0; i < 4; i++) {
 		for (int j = 0; j < 4; j++) {
 			for (int k = 0; k < 4; k++) {

From 5bc618a65e128e954708220ee79ab628b77d90fb Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 21 Jul 2011 16:50:26 -0400
Subject: [PATCH 222/282] renamed environ var to GTFOLDDATADIR

---
 gtfold-mfe/src/loader.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 9af6e97..b39796f 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -94,8 +94,8 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int
 																bool found = false;
 
 																opt1.assign(xstr(DATADIR));
-																if (getenv("GTDATADIR") != 0)
-																								opt2.assign(getenv("GTDATADIR"));
+																if (getenv("GTFOLDDATADIR") != 0)
+																								opt2.assign(getenv("GTFOLDDATADIR"));
 																if (getcwd(cwd, sizeof(cwd)) != 0) {
 																								opt3.assign(cwd);
 																								opt3 += "/data";

From 018827a03d8226c7ca9e6458757c5986b67d49e4 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 21 Jul 2011 16:51:56 -0400
Subject: [PATCH 223/282] renamed environ var to GTFOLDDATADIR

---
 gtfold-mfe/src/loader.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index b39796f..1043dc8 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -112,7 +112,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int
 																if (!found && stat(opt2.c_str(), &buf) == 0) {
 																								found = true;
 																								EN_DATADIR.assign(opt2);
-																								fprintf(stdout,"Checking for environ variable 'GTDATADIR', found \n");
+																								fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', found \n");
 																} else {
 																							if (found == false)	fprintf(stdout,"Checking for environ variable 'GTDATADIR', not found \n");
 																}

From 766e66f5e44a0b75ba84139d636076c55006cadc Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 21 Jul 2011 18:29:59 -0400
Subject: [PATCH 224/282] lookup environ var then install dir

---
 gtfold-mfe/src/loader.cc | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc
index 1043dc8..1c39db9 100644
--- a/gtfold-mfe/src/loader.cc
+++ b/gtfold-mfe/src/loader.cc
@@ -100,8 +100,16 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int
 																								opt3.assign(cwd);
 																								opt3 += "/data";
 																}
-																
-																if (stat(opt1.c_str(), &buf) == 0) {
+	
+																if (stat(opt2.c_str(), &buf) == 0) {
+																								found = true;
+																								EN_DATADIR.assign(opt2);
+																								fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', found \n");
+																} else {
+																							if (found == false)	fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', not found \n");
+																}
+
+																if (!found && stat(opt1.c_str(), &buf) == 0) {
 																								found = true;
 																								EN_DATADIR.assign(opt1); 
 																							fprintf(stdout,"Checking for default datadir '%s', found.\n", opt1.c_str());
@@ -109,14 +117,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int
 																							if (found == false)	fprintf(stdout,"Checking for default datadir '%s', not found.\n", opt1.c_str());
 																}
 
-																if (!found && stat(opt2.c_str(), &buf) == 0) {
-																								found = true;
-																								EN_DATADIR.assign(opt2);
-																								fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', found \n");
-																} else {
-																							if (found == false)	fprintf(stdout,"Checking for environ variable 'GTDATADIR', not found \n");
-																}
-
 																if (!found && stat(opt3.c_str(), &buf) == 0){
 																								found = true;
 																								EN_DATADIR.assign(opt3);

From a8470e37d1bb4b5798bec19af1ffdb2d63f2b246 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 9 Sep 2011 11:04:34 -0400
Subject: [PATCH 225/282] Fixed pseudoknot detection logic in constraint
 pre-processing part of the code.

---
 gtfold-mfe/src/constraints.cc | 408 ++++++++++++++++++----------------
 1 file changed, 214 insertions(+), 194 deletions(-)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 08f67bc..f2ac801 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -5,11 +5,16 @@
 #include <fstream>
 #include <vector>
 #include <algorithm>
+#include <map>
+#include <iterator>
 
 #include "global.h"
 #include "options.h"
 #include "constraints.h"
 
+using std::map;
+using std::pair;
+
 int* BP;
 int* ind;
 
@@ -19,17 +24,17 @@ ZS: Explanation to BP array.
 BP(i,j) for i!=j can have one of the following values: 
 0: Nothing is required about a pair i,j in constraints
 1: Force pairing between i and j. This implies also that
-   any non-nested pairings will be prohibited and any 
-   other pairs i and j would be involved in are also prohibited. 
+any non-nested pairings will be prohibited and any 
+other pairs i and j would be involved in are also prohibited. 
 2: Prohibit pairing between i and j. (Nothing else is done)
 
 BP(i,i) can have one of the following values: 
 0: Nothing is known about position i at all
 3: Position i is forced to be single-stranded. This implies also that
-   any pairs with i will be prohibited. 
+any pairs with i will be prohibited. 
 4: Position i is NOT single-stranded, it is forced to be in a pair. 
 5: Position i is prohibited from pairing with at least one nucleotide. 
-*/
+ */
 
 int** PBP;
 int** FBP;
@@ -37,96 +42,111 @@ int** FBP;
 int nPBP;
 int nFBP;
 
-bool compare_bp(const std::pair<int,int>& o1, 
-			   	const std::pair<int,int>& o2) {
-	return o1.first < o2.first;
-}
-
-
 static int load_constraints(const char* constr_file, int verbose=0) {
-	
+
 
 	fprintf(stdout, "- Running with constraints\n");
 
 
 	std::ifstream cfcons;
 	cfcons.open(constr_file, std::ios::in);
-    if (cfcons == 0) {
-        fprintf(stderr, "Error opening constraint file\n\n");
-        cfcons.close();
-        return -1;
-    }
-
-    char cons[100];
-
-    while (!cfcons.eof()) {
-        cfcons.getline(cons, 100);
-        if (cons[0] == 'F' || cons[0] == 'f') nFBP++;
-        if (cons[0] == 'P' || cons[0] == 'p') nPBP++;
-    }
-    cfcons.close();
-
-    //fprintf(stdout, "Number of Constraints given: %d\n\n", nFBP + nPBP);
-    if (nFBP + nPBP == 0) {
-        fprintf(stderr, "No Constraints found.\n\n");
-        return -1;
-    }
-
-    FBP = (int**) malloc(nFBP*sizeof(int*));
-    PBP = (int**) malloc(nPBP*sizeof(int*));
-
-    int fit = 0, pit = 0, it = 0;
-
-    for (it = 0; it < nFBP; it++) {
-        FBP[it] = (int*) malloc(2* sizeof (int));
-    }
-    for(it=0; it < nPBP; it++) {
-        PBP[it] = (int*)malloc(2*sizeof(int));
-    }
-    cfcons.open(constr_file, std::ios::in);
-
-    while(!cfcons.eof()) {
-        cfcons.getline(cons,100);
-        char *p=strtok(cons, " ");
-        p = strtok(0, " ");
-        if(cons[0]=='F' || cons[0]=='f') {
-            int fit1=0;
-            while(p!=0) {
-                FBP[fit][fit1++] = atoi(p);
-                p = strtok(0, " ");
-            }
-            fit++;
-        }
-        if(cons[0]=='P' || cons[0]=='p') {
-            int pit1=0;
-            while(p!=0) {
-                PBP[pit][pit1++] = atoi(p);
-                p = strtok(0, " ");
-            }
-            pit++;
-        }
-    }
-
-	std::vector<std::pair<int,int> > v_fbp;
+	if (cfcons == 0) {
+		fprintf(stderr, "Error opening constraint file\n\n");
+		cfcons.close();
+		return -1;
+	}
+
+	char cons[100];
+
+	while (!cfcons.eof()) {
+		cfcons.getline(cons, 100);
+		if (cons[0] == 'F' || cons[0] == 'f') nFBP++;
+		if (cons[0] == 'P' || cons[0] == 'p') nPBP++;
+	}
+	cfcons.close();
+
+	//fprintf(stdout, "Number of Constraints given: %d\n\n", nFBP + nPBP);
+	if (nFBP + nPBP == 0) {
+		fprintf(stderr, "No Constraints found.\n\n");
+		return -1;
+	}
+
+	FBP = (int**) malloc(nFBP*sizeof(int*));
+	PBP = (int**) malloc(nPBP*sizeof(int*));
+
+	int fit = 0, pit = 0, it = 0;
+
+	for (it = 0; it < nFBP; it++) {
+		FBP[it] = (int*) malloc(2* sizeof (int));
+	}
+	for(it=0; it < nPBP; it++) {
+		PBP[it] = (int*)malloc(2*sizeof(int));
+	}
+	cfcons.open(constr_file, std::ios::in);
+
+	while(!cfcons.eof()) {
+		cfcons.getline(cons,100);
+		char *p=strtok(cons, " ");
+		p = strtok(0, " ");
+		if(cons[0]=='F' || cons[0]=='f') {
+			int fit1=0;
+			while(p!=0) {
+				FBP[fit][fit1++] = atoi(p);
+				p = strtok(0, " ");
+			}
+			fit++;
+		}
+		if(cons[0]=='P' || cons[0]=='p') {
+			int pit1=0;
+			while(p!=0) {
+				PBP[pit][pit1++] = atoi(p);
+				p = strtok(0, " ");
+			}
+			pit++;
+		}
+	}
+
+	map<int, pair<int,int> > all_bases;
 	for(it=0; it< nFBP; it++) {
-		for(int k=1;k<= FBP[it][2];k++)
-			v_fbp.push_back(std::pair<int,int>(FBP[it][0]+k-1, FBP[it][1]-k+1));
+		for(int k=1;k<= FBP[it][2];k++) {
+			pair<int,int> base_pair(FBP[it][0]+k-1, FBP[it][1]-k+1);
+			pair<map<int,pair<int,int> >::iterator, bool> retVal;
+			retVal = all_bases.insert(pair<int, pair<int,int> >(base_pair.first, base_pair));
+			if (retVal.second == false) {
+				fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n",
+					 base_pair.first, base_pair.first, base_pair.second);
+				exit(1);
+			}
+			retVal = all_bases.insert(pair<int, pair<int,int> >(base_pair.second, base_pair) );
+			if (retVal.second == false) {
+				fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n",
+					 base_pair.first, base_pair.first, base_pair.second);
+				exit(1);
+			}
+		}
 	}
-	
-	if(v_fbp.size()>1){
-		std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
-		for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) {
-			if (v_fbp[ii].second!=0&&v_fbp[ii].second <= v_fbp[ii+1].second
-				&& v_fbp[ii].second >= v_fbp[ii+1].first) {
+
+	vector<pair<int,int> > verify_stack;
+	for (map<int,pair<int,int> >::iterator it = all_bases.begin(); it != all_bases.end(); ++it) {
+
+		pair<int, pair<int,int> > map_element = (*it);
+		int base = map_element.first;
+		pair<int, int> base_pair = map_element.second;
+		if (base_pair.first == base) {
+			verify_stack.push_back(base_pair);
+		} else {
+        		pair<int,int> last_base_pair = verify_stack.back();
+			if (last_base_pair.second == base) {
+				verify_stack.pop_back();
+			}
+			else {
 				fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n");
-				exit(-1);
+				exit(1);
 			}
-			
 		}
 	}
 
-  
-    return 0;
+	return 0;
 }
 
 int init_constraints(const char* constr_file,int length) {
@@ -145,11 +165,11 @@ int init_constraints(const char* constr_file,int length) {
 
 
 	BP = (int*) malloc((((length+1)*(length))/2+1)*sizeof(int));
-	    if (BP == NULL) {
-        	perror("Cannot allocate variable 'constraints'");
-	        exit(-1);
-	    }
-	
+	if (BP == NULL) {
+		perror("Cannot allocate variable 'constraints'");
+		exit(-1);
+	}
+
 	int LLL = length*(length+1)/2 + 1;
 
 
@@ -158,7 +178,7 @@ int init_constraints(const char* constr_file,int length) {
 		BP[i] = 0;
 	}
 
-	
+
 	//ZS: for noncanonical bases (right now this only handles 'N'), force single-stranded. 
 	for(i = 1; i <= length; i++){
 		if(RNA[i]=='N'){
@@ -171,7 +191,7 @@ int init_constraints(const char* constr_file,int length) {
 		}
 	}
 
-	
+
 	//ZS: set prohibited basepairs
 	if(nPBP != 0){
 		int temp;
@@ -189,9 +209,9 @@ int init_constraints(const char* constr_file,int length) {
 				printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
 				continue;
 			}
-		
+
 			for(k = 1; k <= PBP[it][2]; k++){
-				
+
 				BP(PBP[it][0]+k-1, PBP[it][1]-(k-1)) = 2;
 
 				//Mark that these two nucleotides are involved in a prohibited pair (only used for for printing out)
@@ -265,7 +285,7 @@ int init_constraints(const char* constr_file,int length) {
 						BP(FBP[it][0]+k-1,i) = 2;
 						BP(i,FBP[it][1]-(k-1)) = 2;
 					}
-					
+
 
 					//mark that these two nucleotides are involved in a constrained pair
 					//to avoid searching in O(N^2) time
@@ -273,7 +293,7 @@ int init_constraints(const char* constr_file,int length) {
 					BP(FBP[it][1]-(k-1), FBP[it][1]-(k-1))=4;
 					//force pairing 
 					BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1;
-					
+
 				}
 			}
 		}
@@ -285,70 +305,70 @@ int init_constraints(const char* constr_file,int length) {
 int verify_structure(){
 	//ZS: This method returns true if the structure (global.h) is consistent with
 	//the constraints, and false if it is not.
-	
+
 	if(CONS_ENABLED){
-	int errorhappened = 0;
-	int it, k;
-	//Check prohibited constraints
-	if(nPBP != 0){
-		for(it = 0; it < nPBP; it++){
-			if(PBP[it][2] < 1 || PBP[it][1] == 0){
-				//printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
-				continue;
-			}
-			for(k = 1; k <= PBP[it][2]; k++){
-				//correct answer: strcuture(PBP[it][0]+k-1) != structure(PBP[it][1]-(k-1))
-				if(structure[PBP[it][0]+k-1] == PBP[it][1]-(k-1) || structure[PBP[it][1]-(k-1)] == PBP[it][0]+k-1){	
-					errorhappened = 1; 
-					fprintf(stderr, "Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]);
-					break;
+		int errorhappened = 0;
+		int it, k;
+		//Check prohibited constraints
+		if(nPBP != 0){
+			for(it = 0; it < nPBP; it++){
+				if(PBP[it][2] < 1 || PBP[it][1] == 0){
+					//printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
+					continue;
 				}
-			}
-		}	
-	}
-
-	//Check forced constraints
-	if(nFBP != 0){
-		for(it = 0; it<nFBP; it++){
-			if(FBP[it][2] < 1){
-				//printf("Invalid entry (F: %d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
-				continue;
-			}
-
-			for(k = 1; k<=FBP[it][2]; k++){
-				int i1 = FBP[it][0]+k-1;
-				int j1 = FBP[it][1]-k+1;
-				if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){
-					//printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
-					continue;			
+				for(k = 1; k <= PBP[it][2]; k++){
+					//correct answer: strcuture(PBP[it][0]+k-1) != structure(PBP[it][1]-(k-1))
+					if(structure[PBP[it][0]+k-1] == PBP[it][1]-(k-1) || structure[PBP[it][1]-(k-1)] == PBP[it][0]+k-1){	
+						errorhappened = 1; 
+						fprintf(stderr, "Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]);
+						break;
+					}
 				}
-				if(FBP[it][1]!=0&&(j1-i1 < TURN)){
-					//printf("Can't force (%d, %d) to pair (turn too tight) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
+			}	
+		}
+
+		//Check forced constraints
+		if(nFBP != 0){
+			for(it = 0; it<nFBP; it++){
+				if(FBP[it][2] < 1){
+					//printf("Invalid entry (F: %d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
 					continue;
 				}
-				if(FBP[it][1] == 0){
-					//force single-stranded
-					if(structure[FBP[it][0]] != 0){
-						fprintf(stderr, "Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
-						errorhappened = 1;
+
+				for(k = 1; k<=FBP[it][2]; k++){
+					int i1 = FBP[it][0]+k-1;
+					int j1 = FBP[it][1]-k+1;
+					if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){
+						//printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
+						continue;			
 					}
-				}
-				else{
-					if(structure[FBP[it][0]+k-1] != FBP[it][1]-(k-1) || structure[FBP[it][1]-(k-1)] != FBP[it][0]+k-1){
-						fprintf(stderr, "Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
-						errorhappened = 1;
+					if(FBP[it][1]!=0&&(j1-i1 < TURN)){
+						//printf("Can't force (%d, %d) to pair (turn too tight) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
+						continue;
+					}
+					if(FBP[it][1] == 0){
+						//force single-stranded
+						if(structure[FBP[it][0]] != 0){
+							fprintf(stderr, "Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
+							errorhappened = 1;
+						}
+					}
+					else{
+						if(structure[FBP[it][0]+k-1] != FBP[it][1]-(k-1) || structure[FBP[it][1]-(k-1)] != FBP[it][0]+k-1){
+							fprintf(stderr, "Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
+							errorhappened = 1;
+						}
+
 					}
-					
 				}
 			}
 		}
-	}
 		return errorhappened?0:1;
 	}
 	else{
 		return 1;
 	}
-		 
+
 }
 
 
@@ -358,57 +378,57 @@ void free_constraints(int len) {
 
 void print_constraints(int len) {
 
-    int i = 1;
-    int j = 1;
-/*
-
-    printf("Printing constraints \n");
-
-
-    for(j = 1; j<=len; j++){
-	for(i = 1; i<=j; i++){
-		printf("BP(%d,%d)=%d\t", i,j,BP(i,j));
-	}
-	printf("\n\n");
-    }
-
-*/
-    for (i = 1; i <= len; i++) {
-	    switch(BP(i,i)){
-		case 3:
-			//printf("%d: .\n", i);break;
-			printf("x");break;
-		case 4:
-			//printf("%d - ", i);
-			for(j = 1;j<=len;j++){ 
-				if(i<j&&BP(i,j)==1){
-					//printf("%d",j);
-					printf("(");
-				}
-				else if(j<i&&BP(j,i)==1){
-					//printf("%d",j);
-					printf(")");
+	int i = 1;
+	int j = 1;
+	/*
+
+	   printf("Printing constraints \n");
+
+
+	   for(j = 1; j<=len; j++){
+	   for(i = 1; i<=j; i++){
+	   printf("BP(%d,%d)=%d\t", i,j,BP(i,j));
+	   }
+	   printf("\n\n");
+	   }
+
+	 */
+	for (i = 1; i <= len; i++) {
+		switch(BP(i,i)){
+			case 3:
+				//printf("%d: .\n", i);break;
+				printf("x");break;
+			case 4:
+				//printf("%d - ", i);
+				for(j = 1;j<=len;j++){ 
+					if(i<j&&BP(i,j)==1){
+						//printf("%d",j);
+						printf("(");
+					}
+					else if(j<i&&BP(j,i)==1){
+						//printf("%d",j);
+						printf(")");
+					}
 				}
-			}
-			//printf("\n");
-			break;
-		case 5: 
-			//printf("%d P \n", i); break;
-			printf("P");break;
-		case 0:
-			//printf("%d not constrained\n",i);
-			printf(".");
-			break;
-		default:
-			fprintf(stderr,"ERROR in constraint value, debugging info: i=%d, BP(i,i)=%d",i,BP(i,i));break;
-	    }  
-    }
-    printf("\n");
- 
+				//printf("\n");
+				break;
+			case 5: 
+				//printf("%d P \n", i); break;
+				printf("P");break;
+			case 0:
+				//printf("%d not constrained\n",i);
+				printf(".");
+				break;
+			default:
+				fprintf(stderr,"ERROR in constraint value, debugging info: i=%d, BP(i,i)=%d",i,BP(i,i));break;
+		}  
+	}
+	printf("\n");
+
 }
 
 int forcePair(int i, int j) {
-//ZS: this function returns true if the pair i-j is forced.
+	//ZS: this function returns true if the pair i-j is forced.
 	if (CONS_ENABLED) 
 		return BP(i,j)==1;
 	else
@@ -416,7 +436,7 @@ int forcePair(int i, int j) {
 }
 
 int forceSS(int i){
-//ZS: this function returns true if base i is forced to be single-stranded 
+	//ZS: this function returns true if base i is forced to be single-stranded 
 	if(CONS_ENABLED)
 		return BP(i,i)==3;
 	else 
@@ -437,7 +457,7 @@ int forceSSregion(int i, int j){
 }
 
 int canILoop(int i, int j, int p, int q) {
-//ZS: This function returns 1 if internal loop with pairs i,j and p,q is allowed, 0 if not allowed
+	//ZS: This function returns 1 if internal loop with pairs i,j and p,q is allowed, 0 if not allowed
 	if (CONS_ENABLED){
 		//Need to check that i,j and p,q pairs are allowed, 
 		//and single-stranded regions between i,p and q,j are allowed
@@ -457,8 +477,8 @@ int canHairpin(int i, int j) {
 }
 
 int canSSregion(int i, int j){
-//ZS: This function returns 0 if any nucleotide between i and j is forced to pair with something
-//(i and j are NOT included in the check)
+	//ZS: This function returns 0 if any nucleotide between i and j is forced to pair with something
+	//(i and j are NOT included in the check)
 	if(CONS_ENABLED){
 		for(int p = i+1; p<j; p++){
 			if(BP(p,p)==4) return 0;
@@ -478,9 +498,9 @@ int canSS(int i){
 }
 
 int canStack(int i, int j) {
-// ZS: This function returns 1 if an i,j pair is allowed, 0 if not allowed
-// (Unfortunately the more intuitive "canPair" name is already used to mark complementary nucleotides so 
-// I couldn't use that again) 
+	// ZS: This function returns 1 if an i,j pair is allowed, 0 if not allowed
+	// (Unfortunately the more intuitive "canPair" name is already used to mark complementary nucleotides so 
+	// I couldn't use that again) 
 	if (CONS_ENABLED){ 
 		//can't pair if i,j is prohibited, or i or j are forced to be single-stranded
 		if(BP(i,j)==2||BP(i,i)==3||BP(j,j)==3) return 0;

From 8dc69513ef0565f9718b4138950d4277c9670ac5 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 9 Sep 2011 22:07:01 -0400
Subject: [PATCH 226/282] Revert "Fixed pseudoknot detection logic in
 constraint pre-processing part of the code." Looks like I updated an older
 version of the constraints.cc file. Will do a new commit with the latest
 file.

This reverts commit a8470e37d1bb4b5798bec19af1ffdb2d63f2b246.
---
 gtfold-mfe/src/constraints.cc | 408 ++++++++++++++++------------------
 1 file changed, 194 insertions(+), 214 deletions(-)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index f2ac801..08f67bc 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -5,16 +5,11 @@
 #include <fstream>
 #include <vector>
 #include <algorithm>
-#include <map>
-#include <iterator>
 
 #include "global.h"
 #include "options.h"
 #include "constraints.h"
 
-using std::map;
-using std::pair;
-
 int* BP;
 int* ind;
 
@@ -24,17 +19,17 @@ ZS: Explanation to BP array.
 BP(i,j) for i!=j can have one of the following values: 
 0: Nothing is required about a pair i,j in constraints
 1: Force pairing between i and j. This implies also that
-any non-nested pairings will be prohibited and any 
-other pairs i and j would be involved in are also prohibited. 
+   any non-nested pairings will be prohibited and any 
+   other pairs i and j would be involved in are also prohibited. 
 2: Prohibit pairing between i and j. (Nothing else is done)
 
 BP(i,i) can have one of the following values: 
 0: Nothing is known about position i at all
 3: Position i is forced to be single-stranded. This implies also that
-any pairs with i will be prohibited. 
+   any pairs with i will be prohibited. 
 4: Position i is NOT single-stranded, it is forced to be in a pair. 
 5: Position i is prohibited from pairing with at least one nucleotide. 
- */
+*/
 
 int** PBP;
 int** FBP;
@@ -42,111 +37,96 @@ int** FBP;
 int nPBP;
 int nFBP;
 
-static int load_constraints(const char* constr_file, int verbose=0) {
+bool compare_bp(const std::pair<int,int>& o1, 
+			   	const std::pair<int,int>& o2) {
+	return o1.first < o2.first;
+}
 
 
+static int load_constraints(const char* constr_file, int verbose=0) {
+	
+
 	fprintf(stdout, "- Running with constraints\n");
 
 
 	std::ifstream cfcons;
 	cfcons.open(constr_file, std::ios::in);
-	if (cfcons == 0) {
-		fprintf(stderr, "Error opening constraint file\n\n");
-		cfcons.close();
-		return -1;
-	}
-
-	char cons[100];
-
-	while (!cfcons.eof()) {
-		cfcons.getline(cons, 100);
-		if (cons[0] == 'F' || cons[0] == 'f') nFBP++;
-		if (cons[0] == 'P' || cons[0] == 'p') nPBP++;
-	}
-	cfcons.close();
-
-	//fprintf(stdout, "Number of Constraints given: %d\n\n", nFBP + nPBP);
-	if (nFBP + nPBP == 0) {
-		fprintf(stderr, "No Constraints found.\n\n");
-		return -1;
-	}
-
-	FBP = (int**) malloc(nFBP*sizeof(int*));
-	PBP = (int**) malloc(nPBP*sizeof(int*));
-
-	int fit = 0, pit = 0, it = 0;
-
-	for (it = 0; it < nFBP; it++) {
-		FBP[it] = (int*) malloc(2* sizeof (int));
-	}
-	for(it=0; it < nPBP; it++) {
-		PBP[it] = (int*)malloc(2*sizeof(int));
-	}
-	cfcons.open(constr_file, std::ios::in);
-
-	while(!cfcons.eof()) {
-		cfcons.getline(cons,100);
-		char *p=strtok(cons, " ");
-		p = strtok(0, " ");
-		if(cons[0]=='F' || cons[0]=='f') {
-			int fit1=0;
-			while(p!=0) {
-				FBP[fit][fit1++] = atoi(p);
-				p = strtok(0, " ");
-			}
-			fit++;
-		}
-		if(cons[0]=='P' || cons[0]=='p') {
-			int pit1=0;
-			while(p!=0) {
-				PBP[pit][pit1++] = atoi(p);
-				p = strtok(0, " ");
-			}
-			pit++;
-		}
-	}
-
-	map<int, pair<int,int> > all_bases;
+    if (cfcons == 0) {
+        fprintf(stderr, "Error opening constraint file\n\n");
+        cfcons.close();
+        return -1;
+    }
+
+    char cons[100];
+
+    while (!cfcons.eof()) {
+        cfcons.getline(cons, 100);
+        if (cons[0] == 'F' || cons[0] == 'f') nFBP++;
+        if (cons[0] == 'P' || cons[0] == 'p') nPBP++;
+    }
+    cfcons.close();
+
+    //fprintf(stdout, "Number of Constraints given: %d\n\n", nFBP + nPBP);
+    if (nFBP + nPBP == 0) {
+        fprintf(stderr, "No Constraints found.\n\n");
+        return -1;
+    }
+
+    FBP = (int**) malloc(nFBP*sizeof(int*));
+    PBP = (int**) malloc(nPBP*sizeof(int*));
+
+    int fit = 0, pit = 0, it = 0;
+
+    for (it = 0; it < nFBP; it++) {
+        FBP[it] = (int*) malloc(2* sizeof (int));
+    }
+    for(it=0; it < nPBP; it++) {
+        PBP[it] = (int*)malloc(2*sizeof(int));
+    }
+    cfcons.open(constr_file, std::ios::in);
+
+    while(!cfcons.eof()) {
+        cfcons.getline(cons,100);
+        char *p=strtok(cons, " ");
+        p = strtok(0, " ");
+        if(cons[0]=='F' || cons[0]=='f') {
+            int fit1=0;
+            while(p!=0) {
+                FBP[fit][fit1++] = atoi(p);
+                p = strtok(0, " ");
+            }
+            fit++;
+        }
+        if(cons[0]=='P' || cons[0]=='p') {
+            int pit1=0;
+            while(p!=0) {
+                PBP[pit][pit1++] = atoi(p);
+                p = strtok(0, " ");
+            }
+            pit++;
+        }
+    }
+
+	std::vector<std::pair<int,int> > v_fbp;
 	for(it=0; it< nFBP; it++) {
-		for(int k=1;k<= FBP[it][2];k++) {
-			pair<int,int> base_pair(FBP[it][0]+k-1, FBP[it][1]-k+1);
-			pair<map<int,pair<int,int> >::iterator, bool> retVal;
-			retVal = all_bases.insert(pair<int, pair<int,int> >(base_pair.first, base_pair));
-			if (retVal.second == false) {
-				fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n",
-					 base_pair.first, base_pair.first, base_pair.second);
-				exit(1);
-			}
-			retVal = all_bases.insert(pair<int, pair<int,int> >(base_pair.second, base_pair) );
-			if (retVal.second == false) {
-				fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n",
-					 base_pair.first, base_pair.first, base_pair.second);
-				exit(1);
-			}
-		}
+		for(int k=1;k<= FBP[it][2];k++)
+			v_fbp.push_back(std::pair<int,int>(FBP[it][0]+k-1, FBP[it][1]-k+1));
 	}
-
-	vector<pair<int,int> > verify_stack;
-	for (map<int,pair<int,int> >::iterator it = all_bases.begin(); it != all_bases.end(); ++it) {
-
-		pair<int, pair<int,int> > map_element = (*it);
-		int base = map_element.first;
-		pair<int, int> base_pair = map_element.second;
-		if (base_pair.first == base) {
-			verify_stack.push_back(base_pair);
-		} else {
-        		pair<int,int> last_base_pair = verify_stack.back();
-			if (last_base_pair.second == base) {
-				verify_stack.pop_back();
-			}
-			else {
+	
+	if(v_fbp.size()>1){
+		std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
+		for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) {
+			if (v_fbp[ii].second!=0&&v_fbp[ii].second <= v_fbp[ii+1].second
+				&& v_fbp[ii].second >= v_fbp[ii+1].first) {
 				fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n");
-				exit(1);
+				exit(-1);
 			}
+			
 		}
 	}
 
-	return 0;
+  
+    return 0;
 }
 
 int init_constraints(const char* constr_file,int length) {
@@ -165,11 +145,11 @@ int init_constraints(const char* constr_file,int length) {
 
 
 	BP = (int*) malloc((((length+1)*(length))/2+1)*sizeof(int));
-	if (BP == NULL) {
-		perror("Cannot allocate variable 'constraints'");
-		exit(-1);
-	}
-
+	    if (BP == NULL) {
+        	perror("Cannot allocate variable 'constraints'");
+	        exit(-1);
+	    }
+	
 	int LLL = length*(length+1)/2 + 1;
 
 
@@ -178,7 +158,7 @@ int init_constraints(const char* constr_file,int length) {
 		BP[i] = 0;
 	}
 
-
+	
 	//ZS: for noncanonical bases (right now this only handles 'N'), force single-stranded. 
 	for(i = 1; i <= length; i++){
 		if(RNA[i]=='N'){
@@ -191,7 +171,7 @@ int init_constraints(const char* constr_file,int length) {
 		}
 	}
 
-
+	
 	//ZS: set prohibited basepairs
 	if(nPBP != 0){
 		int temp;
@@ -209,9 +189,9 @@ int init_constraints(const char* constr_file,int length) {
 				printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
 				continue;
 			}
-
+		
 			for(k = 1; k <= PBP[it][2]; k++){
-
+				
 				BP(PBP[it][0]+k-1, PBP[it][1]-(k-1)) = 2;
 
 				//Mark that these two nucleotides are involved in a prohibited pair (only used for for printing out)
@@ -285,7 +265,7 @@ int init_constraints(const char* constr_file,int length) {
 						BP(FBP[it][0]+k-1,i) = 2;
 						BP(i,FBP[it][1]-(k-1)) = 2;
 					}
-
+					
 
 					//mark that these two nucleotides are involved in a constrained pair
 					//to avoid searching in O(N^2) time
@@ -293,7 +273,7 @@ int init_constraints(const char* constr_file,int length) {
 					BP(FBP[it][1]-(k-1), FBP[it][1]-(k-1))=4;
 					//force pairing 
 					BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1;
-
+					
 				}
 			}
 		}
@@ -305,70 +285,70 @@ int init_constraints(const char* constr_file,int length) {
 int verify_structure(){
 	//ZS: This method returns true if the structure (global.h) is consistent with
 	//the constraints, and false if it is not.
-
+	
 	if(CONS_ENABLED){
-		int errorhappened = 0;
-		int it, k;
-		//Check prohibited constraints
-		if(nPBP != 0){
-			for(it = 0; it < nPBP; it++){
-				if(PBP[it][2] < 1 || PBP[it][1] == 0){
-					//printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
-					continue;
-				}
-				for(k = 1; k <= PBP[it][2]; k++){
-					//correct answer: strcuture(PBP[it][0]+k-1) != structure(PBP[it][1]-(k-1))
-					if(structure[PBP[it][0]+k-1] == PBP[it][1]-(k-1) || structure[PBP[it][1]-(k-1)] == PBP[it][0]+k-1){	
-						errorhappened = 1; 
-						fprintf(stderr, "Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]);
-						break;
-					}
+	int errorhappened = 0;
+	int it, k;
+	//Check prohibited constraints
+	if(nPBP != 0){
+		for(it = 0; it < nPBP; it++){
+			if(PBP[it][2] < 1 || PBP[it][1] == 0){
+				//printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
+				continue;
+			}
+			for(k = 1; k <= PBP[it][2]; k++){
+				//correct answer: strcuture(PBP[it][0]+k-1) != structure(PBP[it][1]-(k-1))
+				if(structure[PBP[it][0]+k-1] == PBP[it][1]-(k-1) || structure[PBP[it][1]-(k-1)] == PBP[it][0]+k-1){	
+					errorhappened = 1; 
+					fprintf(stderr, "Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]);
+					break;
 				}
-			}	
-		}
+			}
+		}	
+	}
+
+	//Check forced constraints
+	if(nFBP != 0){
+		for(it = 0; it<nFBP; it++){
+			if(FBP[it][2] < 1){
+				//printf("Invalid entry (F: %d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
+				continue;
+			}
 
-		//Check forced constraints
-		if(nFBP != 0){
-			for(it = 0; it<nFBP; it++){
-				if(FBP[it][2] < 1){
-					//printf("Invalid entry (F: %d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
+			for(k = 1; k<=FBP[it][2]; k++){
+				int i1 = FBP[it][0]+k-1;
+				int j1 = FBP[it][1]-k+1;
+				if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){
+					//printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
+					continue;			
+				}
+				if(FBP[it][1]!=0&&(j1-i1 < TURN)){
+					//printf("Can't force (%d, %d) to pair (turn too tight) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
 					continue;
 				}
-
-				for(k = 1; k<=FBP[it][2]; k++){
-					int i1 = FBP[it][0]+k-1;
-					int j1 = FBP[it][1]-k+1;
-					if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){
-						//printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
-						continue;			
-					}
-					if(FBP[it][1]!=0&&(j1-i1 < TURN)){
-						//printf("Can't force (%d, %d) to pair (turn too tight) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
-						continue;
-					}
-					if(FBP[it][1] == 0){
-						//force single-stranded
-						if(structure[FBP[it][0]] != 0){
-							fprintf(stderr, "Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
-							errorhappened = 1;
-						}
+				if(FBP[it][1] == 0){
+					//force single-stranded
+					if(structure[FBP[it][0]] != 0){
+						fprintf(stderr, "Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
+						errorhappened = 1;
 					}
-					else{
-						if(structure[FBP[it][0]+k-1] != FBP[it][1]-(k-1) || structure[FBP[it][1]-(k-1)] != FBP[it][0]+k-1){
-							fprintf(stderr, "Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
-							errorhappened = 1;
-						}
-
+				}
+				else{
+					if(structure[FBP[it][0]+k-1] != FBP[it][1]-(k-1) || structure[FBP[it][1]-(k-1)] != FBP[it][0]+k-1){
+						fprintf(stderr, "Constraint F %d %d %d is not fulfilled.\n",FBP[it][0], FBP[it][1], FBP[it][2]);
+						errorhappened = 1;
 					}
+					
 				}
 			}
 		}
+	}
 		return errorhappened?0:1;
 	}
 	else{
 		return 1;
 	}
-
+		 
 }
 
 
@@ -378,57 +358,57 @@ void free_constraints(int len) {
 
 void print_constraints(int len) {
 
-	int i = 1;
-	int j = 1;
-	/*
-
-	   printf("Printing constraints \n");
-
-
-	   for(j = 1; j<=len; j++){
-	   for(i = 1; i<=j; i++){
-	   printf("BP(%d,%d)=%d\t", i,j,BP(i,j));
-	   }
-	   printf("\n\n");
-	   }
-
-	 */
-	for (i = 1; i <= len; i++) {
-		switch(BP(i,i)){
-			case 3:
-				//printf("%d: .\n", i);break;
-				printf("x");break;
-			case 4:
-				//printf("%d - ", i);
-				for(j = 1;j<=len;j++){ 
-					if(i<j&&BP(i,j)==1){
-						//printf("%d",j);
-						printf("(");
-					}
-					else if(j<i&&BP(j,i)==1){
-						//printf("%d",j);
-						printf(")");
-					}
-				}
-				//printf("\n");
-				break;
-			case 5: 
-				//printf("%d P \n", i); break;
-				printf("P");break;
-			case 0:
-				//printf("%d not constrained\n",i);
-				printf(".");
-				break;
-			default:
-				fprintf(stderr,"ERROR in constraint value, debugging info: i=%d, BP(i,i)=%d",i,BP(i,i));break;
-		}  
-	}
-	printf("\n");
+    int i = 1;
+    int j = 1;
+/*
+
+    printf("Printing constraints \n");
 
+
+    for(j = 1; j<=len; j++){
+	for(i = 1; i<=j; i++){
+		printf("BP(%d,%d)=%d\t", i,j,BP(i,j));
+	}
+	printf("\n\n");
+    }
+
+*/
+    for (i = 1; i <= len; i++) {
+	    switch(BP(i,i)){
+		case 3:
+			//printf("%d: .\n", i);break;
+			printf("x");break;
+		case 4:
+			//printf("%d - ", i);
+			for(j = 1;j<=len;j++){ 
+				if(i<j&&BP(i,j)==1){
+					//printf("%d",j);
+					printf("(");
+				}
+				else if(j<i&&BP(j,i)==1){
+					//printf("%d",j);
+					printf(")");
+				}
+			}
+			//printf("\n");
+			break;
+		case 5: 
+			//printf("%d P \n", i); break;
+			printf("P");break;
+		case 0:
+			//printf("%d not constrained\n",i);
+			printf(".");
+			break;
+		default:
+			fprintf(stderr,"ERROR in constraint value, debugging info: i=%d, BP(i,i)=%d",i,BP(i,i));break;
+	    }  
+    }
+    printf("\n");
+ 
 }
 
 int forcePair(int i, int j) {
-	//ZS: this function returns true if the pair i-j is forced.
+//ZS: this function returns true if the pair i-j is forced.
 	if (CONS_ENABLED) 
 		return BP(i,j)==1;
 	else
@@ -436,7 +416,7 @@ int forcePair(int i, int j) {
 }
 
 int forceSS(int i){
-	//ZS: this function returns true if base i is forced to be single-stranded 
+//ZS: this function returns true if base i is forced to be single-stranded 
 	if(CONS_ENABLED)
 		return BP(i,i)==3;
 	else 
@@ -457,7 +437,7 @@ int forceSSregion(int i, int j){
 }
 
 int canILoop(int i, int j, int p, int q) {
-	//ZS: This function returns 1 if internal loop with pairs i,j and p,q is allowed, 0 if not allowed
+//ZS: This function returns 1 if internal loop with pairs i,j and p,q is allowed, 0 if not allowed
 	if (CONS_ENABLED){
 		//Need to check that i,j and p,q pairs are allowed, 
 		//and single-stranded regions between i,p and q,j are allowed
@@ -477,8 +457,8 @@ int canHairpin(int i, int j) {
 }
 
 int canSSregion(int i, int j){
-	//ZS: This function returns 0 if any nucleotide between i and j is forced to pair with something
-	//(i and j are NOT included in the check)
+//ZS: This function returns 0 if any nucleotide between i and j is forced to pair with something
+//(i and j are NOT included in the check)
 	if(CONS_ENABLED){
 		for(int p = i+1; p<j; p++){
 			if(BP(p,p)==4) return 0;
@@ -498,9 +478,9 @@ int canSS(int i){
 }
 
 int canStack(int i, int j) {
-	// ZS: This function returns 1 if an i,j pair is allowed, 0 if not allowed
-	// (Unfortunately the more intuitive "canPair" name is already used to mark complementary nucleotides so 
-	// I couldn't use that again) 
+// ZS: This function returns 1 if an i,j pair is allowed, 0 if not allowed
+// (Unfortunately the more intuitive "canPair" name is already used to mark complementary nucleotides so 
+// I couldn't use that again) 
 	if (CONS_ENABLED){ 
 		//can't pair if i,j is prohibited, or i or j are forced to be single-stranded
 		if(BP(i,j)==2||BP(i,i)==3||BP(j,j)==3) return 0;

From 6cdf73e50ea7e0b9babbee32e142ce6a3e1f4257 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Sat, 10 Sep 2011 13:49:26 -0400
Subject: [PATCH 227/282] Fix pseudoknot detection code.

---
 gtfold-mfe/src/constraints.cc | 76 +++++++++++++++++++++++++----------
 1 file changed, 55 insertions(+), 21 deletions(-)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 08f67bc..27ec4a7 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -5,6 +5,8 @@
 #include <fstream>
 #include <vector>
 #include <algorithm>
+#include <map>
+#include <iterator>
 
 #include "global.h"
 #include "options.h"
@@ -13,6 +15,8 @@
 int* BP;
 int* ind;
 
+typedef pair<int,int> basepair_t;
+
 /*
 ZS: Explanation to BP array. 
 
@@ -37,13 +41,7 @@ int** FBP;
 int nPBP;
 int nFBP;
 
-bool compare_bp(const std::pair<int,int>& o1, 
-			   	const std::pair<int,int>& o2) {
-	return o1.first < o2.first;
-}
-
-
-static int load_constraints(const char* constr_file, int verbose=0) {
+static int load_constraints(const char* constr_file, int seq_length, int verbose=0) {
 	
 
 	fprintf(stdout, "- Running with constraints\n");
@@ -107,30 +105,66 @@ static int load_constraints(const char* constr_file, int verbose=0) {
         }
     }
 
-	std::vector<std::pair<int,int> > v_fbp;
+	map<int, basepair_t > all_bases;
 	for(it=0; it< nFBP; it++) {
-		for(int k=1;k<= FBP[it][2];k++)
-			v_fbp.push_back(std::pair<int,int>(FBP[it][0]+k-1, FBP[it][1]-k+1));
+		for(int k=1;k<= FBP[it][2];k++) {
+			basepair_t base_pair(FBP[it][0]+k-1, FBP[it][1]-k+1);
+			pair<map<int,basepair_t>::iterator, bool> retVal;
+			retVal = all_bases.insert(pair<int, basepair_t>(base_pair.first, base_pair));
+			if (base_pair.first < 1 || base_pair.first > seq_length) {
+				fprintf(stderr, "\nBase %d from constraint (%d,%d) is out of bounds of the sequence which has length %d \n",
+					base_pair.first, base_pair.first, base_pair.second, seq_length);
+				exit(1);
+			}
+			if (base_pair.second < 1 || base_pair.second > seq_length) {
+				fprintf(stderr, "\nBase %d from constraint (%d,%d) is out of bounds of the sequence which has length %d \n",
+					base_pair.second, base_pair.first, base_pair.second, seq_length);
+				exit(1);
+			}
+			if (base_pair.first >= base_pair.second - TURN) {
+				fprintf(stderr, "\nDistance between bases of base pair (%d,%d) is too small\n",
+					base_pair.first, base_pair.second);
+				exit(1);
+			}
+			if (retVal.second == false) {
+				fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n",
+					 base_pair.first, base_pair.first, base_pair.second);
+				exit(1);
+			}
+			retVal = all_bases.insert(pair<int,basepair_t>(base_pair.second, base_pair) );
+			if (retVal.second == false) {
+				fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n",
+					 base_pair.first, base_pair.first, base_pair.second);
+				exit(1);
+			}
+		}
 	}
-	
-	if(v_fbp.size()>1){
-		std::sort(v_fbp.begin(), v_fbp.end(), compare_bp);
-		for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) {
-			if (v_fbp[ii].second!=0&&v_fbp[ii].second <= v_fbp[ii+1].second
-				&& v_fbp[ii].second >= v_fbp[ii+1].first) {
+
+	vector<basepair_t> verify_stack;
+	for (map<int,basepair_t>::iterator it = all_bases.begin(); it != all_bases.end(); ++it) {
+
+		pair<int,basepair_t> map_element = (*it);
+		int base = map_element.first;
+		basepair_t base_pair = map_element.second;
+		if (base_pair.first == base) {
+			verify_stack.push_back(base_pair);
+		} else {
+        		basepair_t last_base_pair = verify_stack.back();
+			if (last_base_pair.second == base) {
+				verify_stack.pop_back();
+			}
+			else {
 				fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n");
-				exit(-1);
+				exit(1);
 			}
-			
 		}
 	}
 
-  
     return 0;
 }
 
 int init_constraints(const char* constr_file,int length) {
-	load_constraints(constr_file);
+	load_constraints(constr_file, length);
 
 
 	int i,j,it,k;
@@ -177,7 +211,7 @@ int init_constraints(const char* constr_file,int length) {
 		int temp;
 		//Make sure smallest one is first 
 		for(it = 0; it < nPBP; it++){
-			if(PBP[it][0] > PBP[it][1]){
+			if(PBP[it][0] > PBP[it][1] && PBP[it][1] != 0){
 				temp = PBP[it][0];	
 				PBP[it][0] = PBP[it][1];
 				PBP[it][1] = temp;

From e9100f1da3609ebb4a06b2fee31fcb4456861d12 Mon Sep 17 00:00:00 2001
From: Manoj Soni <manoj6891@gmail.com>
Date: Sun, 11 Sep 2011 22:02:19 -0400
Subject: [PATCH 228/282] Corrected constraints code for handling single
 stranded constraints properly

---
 gtfold-mfe/src/constraints.cc | 100 +++++++++++++++++-----------------
 1 file changed, 50 insertions(+), 50 deletions(-)

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index 08f67bc..f6ee6b0 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -177,7 +177,7 @@ int init_constraints(const char* constr_file,int length) {
 		int temp;
 		//Make sure smallest one is first 
 		for(it = 0; it < nPBP; it++){
-			if(PBP[it][0] > PBP[it][1]){
+			if(PBP[it][0] > PBP[it][1] && PBP[it][1]!=0){
 				temp = PBP[it][0];	
 				PBP[it][0] = PBP[it][1];
 				PBP[it][1] = temp;
@@ -185,18 +185,33 @@ int init_constraints(const char* constr_file,int length) {
 		}
 
 		for(it = 0; it < nPBP; it++){
-			if(PBP[it][2] < 1 || PBP[it][1] == 0){
+			if(PBP[it][2] < 1){
 				printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]);
 				continue;
 			}
 		
 			for(k = 1; k <= PBP[it][2]; k++){
 				
-				BP(PBP[it][0]+k-1, PBP[it][1]-(k-1)) = 2;
+				 if(PBP[it][1] == 0){
+                                        //force single-stranded
+                                        BP(PBP[it][0]+k-1, PBP[it][0]+k-1) = 3;
+                                        //prohibit all pairs with that base
+                                        for(i = 1; i<=length; i++){
+                                                if(i<PBP[it][0]+k-1){
+                                                        BP(i, PBP[it][0]+k-1) = 2;
+                                                }
+                                                if(PBP[it][0]+k-1<i){
+                                                        BP(PBP[it][0]+k-1, i) = 2;
+                                                }
+                                        }
+                                }
+				else{
+					BP(PBP[it][0]+k-1, PBP[it][1]-(k-1)) = 2;
 
-				//Mark that these two nucleotides are involved in a prohibited pair (only used for for printing out)
-				BP(PBP[it][0]+k-1,PBP[it][0]+k-1) = 5;
-				BP(PBP[it][1]-(k-1),PBP[it][1]-(k-1)) = 5;
+					//Mark that these two nucleotides are involved in a prohibited pair (only used for for printing out)
+					BP(PBP[it][0]+k-1,PBP[it][0]+k-1) = 5;
+					BP(PBP[it][1]-(k-1),PBP[it][1]-(k-1)) = 5;
+				}
 			}
 		}	
 	}
@@ -207,14 +222,14 @@ int init_constraints(const char* constr_file,int length) {
 		int temp; 
 		//Make sure smallest one is first, UNLESS forcing single-stranded 
 		for(it  = 0; it < nFBP; it++){
-			if(FBP[it][0] > FBP[it][1] && FBP[it][1]!=0){
+			if(FBP[it][0] > FBP[it][1]){
 				temp = FBP[it][0];
 				FBP[it][0] = FBP[it][1];
 				FBP[it][1] = temp; 
 			}
 		}
 		for(it = 0; it<nFBP; it++){
-			if(FBP[it][2] < 1){
+			if(FBP[it][2] < 1 || FBP[it][1] == 0){
 				printf("Invalid entry (F: %d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]);
 				continue;
 			}
@@ -223,58 +238,43 @@ int init_constraints(const char* constr_file,int length) {
 			for(k = 1; k<=FBP[it][2]; k++){
 				int i1 = FBP[it][0]+k-1;
 				int j1 = FBP[it][1]-k+1;
-				if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){
+				if(!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){
 					fprintf(stderr,"Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
 					continue;			
 				}
-				if(FBP[it][1]!=0&&(j1-i1 < TURN)){
+				if((j1-i1 < TURN)){
 					fprintf(stderr,"Can't force (%d, %d) to pair (turn too tight) \n", FBP[it][0]+k-1, FBP[it][1]-k+1);
 					continue;
 				}
-				if(FBP[it][1] == 0){
-					//force single-stranded
-					BP(FBP[it][0]+k-1, FBP[it][0]+k-1) = 3;
-					//prohibit all pairs with that base
-					for(i = 1; i<=length; i++){
-						if(i<FBP[it][0]+k-1){
-							BP(i, FBP[it][0]+k-1) = 2;
-						}
-						if(FBP[it][0]+k-1<i){
-							BP(FBP[it][0]+k-1, i) = 2;
-						}
+				
+				//force pairing
+				BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1;
+				//prohibit all pairs not-nested with respect to this one 
+				//(including the ones which include either of the bases)
+				for(i = 1; i<FBP[it][0]+k-1; i++){
+					for(j = FBP[it][0]+k-1; j<=FBP[it][1]-(k-1); j++){
+						BP(i,j)=2;
 					}
 				}
-				else{
-					//force pairing
-					BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1;
-					//prohibit all pairs not-nested with respect to this one 
-					//(including the ones which include either of the bases)
-					for(i = 1; i<FBP[it][0]+k-1; i++){
-						for(j = FBP[it][0]+k-1; j<=FBP[it][1]-(k-1); j++){
-							BP(i,j)=2;
-						}
-					}
-					for(i = FBP[it][0]+k-1; i<=FBP[it][1]-(k-1); i++){
-						for(j = FBP[it][1]-(k-1)+1; j<=length; j++){
-							BP(i,j)=2;
-						}
-					}
-					//prohibit all remaining pairs with the pairing bases 
-					//(inside enclosed region)
-					for(i = FBP[it][0]+k; i<FBP[it][1]-(k-1); i++){
-						BP(FBP[it][0]+k-1,i) = 2;
-						BP(i,FBP[it][1]-(k-1)) = 2;
+				for(i = FBP[it][0]+k-1; i<=FBP[it][1]-(k-1); i++){
+					for(j = FBP[it][1]-(k-1)+1; j<=length; j++){
+						BP(i,j)=2;
 					}
-					
-
-					//mark that these two nucleotides are involved in a constrained pair
-					//to avoid searching in O(N^2) time
-					BP(FBP[it][0]+k-1, FBP[it][0]+k-1) = 4;
-					BP(FBP[it][1]-(k-1), FBP[it][1]-(k-1))=4;
-					//force pairing 
-					BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1;
-					
 				}
+				//prohibit all remaining pairs with the pairing bases 
+				//(inside enclosed region)
+				for(i = FBP[it][0]+k; i<FBP[it][1]-(k-1); i++){
+					BP(FBP[it][0]+k-1,i) = 2;
+					BP(i,FBP[it][1]-(k-1)) = 2;
+				}
+				
+
+				//mark that these two nucleotides are involved in a constrained pair
+				//to avoid searching in O(N^2) time
+				BP(FBP[it][0]+k-1, FBP[it][0]+k-1) = 4;
+				BP(FBP[it][1]-(k-1), FBP[it][1]-(k-1))=4;
+				//force pairing 
+				BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1;
 			}
 		}
 	}

From 54cfe37819d01b6480440d6aa86e5222a33e3dee Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 14 Sep 2011 11:04:58 -0400
Subject: [PATCH 229/282] adding partitition function header/src files

---
 gtfold-mfe/include/partition-func.h | 31 +++++++++++++++++++++++++
 gtfold-mfe/src/partition-func.c     | 36 +++++++++++++++++++++++++++++
 2 files changed, 67 insertions(+)
 create mode 100644 gtfold-mfe/include/partition-func.h
 create mode 100644 gtfold-mfe/src/partition-func.c

diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h
new file mode 100644
index 0000000..ca2af33
--- /dev/null
+++ b/gtfold-mfe/include/partition-func.h
@@ -0,0 +1,31 @@
+#ifndef _PARTITION_DANGLE_H
+#define _PARTITION_DANGLE_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct partition_struct {
+	double ** u;
+	double ** up;
+	double ** upm;
+	double ** ud;
+	double ** u1d;
+
+	double ** s1;
+	double ** s2;
+	double ** s3;
+	double ** u1;
+
+	int length;
+} partition_t;
+
+extern partition_t partition;
+
+void calculate_partition();
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
new file mode 100644
index 0000000..fe61d0c
--- /dev/null
+++ b/gtfold-mfe/src/partition-func.c
@@ -0,0 +1,36 @@
+#include "partition-func.h"
+
+static void create_partition_arrays();
+static void init_partition_arrays();
+static void fill_partition_arrays();
+static void free_partition_arrays();
+
+static void calc_u(int i, int j);
+static void calc_ud(int i, int j);
+static void calc_up(int i, int j);
+static void calc_upm(int i, int j);
+static void calc_u1(int i, int j);
+static void calc_u1d(int i, int j);
+static void calc_s1(int i, int j);
+static void calc_s2(int i, int j);
+static void calc_s3(int i, int j);
+
+void create_partition_arrays()
+{
+
+}
+
+void init_partition_arrays()
+{
+		
+}
+
+void fill_partition_arrays()
+{
+
+}
+
+void free_partition_arrays()
+{
+
+}

From 17bc05349ede27257f1ed42869776d09244d713d Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 14 Sep 2011 11:14:50 -0400
Subject: [PATCH 230/282] added header energy.h

---
 gtfold-mfe/src/partition-func.c | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index fe61d0c..44de0ea 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -1,4 +1,6 @@
 #include "partition-func.h"
+#include "energy.h"
+
 
 static void create_partition_arrays();
 static void init_partition_arrays();

From 089d8d67459d83cdc28a2539783815ccc6638779 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 14 Sep 2011 11:41:41 -0400
Subject: [PATCH 231/282] added global vars

---
 gtfold-mfe/include/partition-func.h | 26 +++++++++++---------------
 1 file changed, 11 insertions(+), 15 deletions(-)

diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h
index ca2af33..dcbea32 100644
--- a/gtfold-mfe/include/partition-func.h
+++ b/gtfold-mfe/include/partition-func.h
@@ -5,24 +5,20 @@
 extern "C" {
 #endif
 
-typedef struct partition_struct {
-	double ** u;
-	double ** up;
-	double ** upm;
-	double ** ud;
-	double ** u1d;
+extern	double ** u;
+extern	double ** up;
+extern	double ** upm;
+extern	double ** ud;
+extern	double ** u1d;
 
-	double ** s1;
-	double ** s2;
-	double ** s3;
-	double ** u1;
+extern	double ** s1;
+extern	double ** s2;
+extern	double ** s3;
+extern	double ** u1;
 
-	int length;
-} partition_t;
+extern int part_len;
 
-extern partition_t partition;
-
-void calculate_partition();
+void calculate_partition(int len);
 
 #ifdef __cplusplus
 }

From f96b75f866447ca6e40cf3b57d38a12360fd506d Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 16 Sep 2011 10:35:48 -0400
Subject: [PATCH 232/282] integrated partition func

---
 gtfold-mfe/include/options.h        |   1 +
 gtfold-mfe/include/partition-func.h |   4 +
 gtfold-mfe/src/Makefile.am          |   1 +
 gtfold-mfe/src/Makefile.in          |   9 +-
 gtfold-mfe/src/main.cc              |  11 +-
 gtfold-mfe/src/options.cc           | 274 ++++++++++++++--------------
 gtfold-mfe/src/partition-func.c     | 236 +++++++++++++++++++++++-
 7 files changed, 394 insertions(+), 142 deletions(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 44de1ce..5dbebf1 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -22,6 +22,7 @@ extern bool PARAM_DIR;
 extern bool T_MISMATCH;
 extern bool UNAMODE;
 extern bool RNAMODE;
+extern bool CALC_PART_FUNC;
 
 extern string seqfile;
 extern string constraintsFile;
diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h
index dcbea32..9761531 100644
--- a/gtfold-mfe/include/partition-func.h
+++ b/gtfold-mfe/include/partition-func.h
@@ -1,6 +1,9 @@
 #ifndef _PARTITION_DANGLE_H
 #define _PARTITION_DANGLE_H
 
+
+#include <math.h>
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -19,6 +22,7 @@ extern	double ** u1;
 extern int part_len;
 
 void calculate_partition(int len);
+void free_partition();
 
 #ifdef __cplusplus
 }
diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am
index 428951a..c595933 100644
--- a/gtfold-mfe/src/Makefile.am
+++ b/gtfold-mfe/src/Makefile.am
@@ -18,6 +18,7 @@ gtfold_SOURCES = \
 	subopt_traceback.cc\
 	algorithms-partition.c\
 	partition-dangle.c\
+	partition-func.c\
 	random-sample.cc\
 	shapereader.cc
 
diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in
index e8e0471..bad351a 100644
--- a/gtfold-mfe/src/Makefile.in
+++ b/gtfold-mfe/src/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# Makefile.in generated by automake 1.11 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
@@ -52,8 +52,8 @@ am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
 	options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \
 	energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \
 	subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \
-	partition-dangle.$(OBJEXT) random-sample.$(OBJEXT) \
-	shapereader.$(OBJEXT)
+	partition-dangle.$(OBJEXT) partition-func.$(OBJEXT) \
+	random-sample.$(OBJEXT) shapereader.$(OBJEXT)
 gtfold_OBJECTS = $(am_gtfold_OBJECTS)
 gtfold_DEPENDENCIES =
 gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
@@ -117,7 +117,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 SET_MAKE = @SET_MAKE@
@@ -195,6 +194,7 @@ gtfold_SOURCES = \
 	subopt_traceback.cc\
 	algorithms-partition.c\
 	partition-dangle.c\
+	partition-func.c\
 	random-sample.cc\
 	shapereader.cc
 
@@ -291,6 +291,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-func.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/random-sample.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 4b016de..952aba1 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -38,7 +38,7 @@
 #include "energy.h"
 #include "algorithms.h"
 #include "algorithms-partition.h"
-#include "partition-dangle.h"
+#include "partition-func.h"
 #include "constraints.h"
 #include "traceback.h"
 #include "subopt_traceback.h"
@@ -283,6 +283,15 @@ int main(int argc, char** argv) {
 
 	printRunConfiguration(seq);
 
+  if (CALC_PART_FUNC == true)
+  {
+    printf("\nComputing partition function...\n");
+    calculate_partition(seq.length());
+    free_partition();
+    free_fold(seq.length());
+    exit(0);
+  }
+
 	printf("\nComputing minimum free energy structure...\n");
 	fflush(stdout);
 
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 831bf5d..7b4a4ee 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -18,6 +18,7 @@ bool T_MISMATCH = false;
 bool UNAMODE = false;
 bool RNAMODE = false;
 bool b_prefilter = false;
+bool CALC_PART_FUNC = false;
 
 string seqfile = "";
 string constraintsFile = "";
@@ -70,6 +71,7 @@ void help() {
 
     printf("\nBETA OPTIONS\n");
     printf("   --bpp                Calculate base pair probabilities.\n");
+    printf("   --partition          Calculate the partition function.\n");
     printf("   --subopt NUM         Calculate suboptimal structures within NUM kcal/mol\n");
     printf("                        of the MFE. (Uses -d 2 treatment of dangling energies.)\n");
     printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE.\n");      
@@ -91,149 +93,151 @@ void help() {
  * Parse the options from argc and argv and save them into global state.
  */
 void parse_options(int argc, char** argv) {
-								int i;
+  int i;
 
-								for(i=1; i<argc; i++) {
-																if(argv[i][0] == '-') {
-																								if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
-																																help();
-																								} else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
-																																if(i < argc) {
-																																								constraintsFile = argv[++i];
-																																								CONS_ENABLED = true;
-																																}
-																																else
-																																								help();
-																								} else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
-																																if(i < argc){
-																																								contactDistance = atoi(argv[++i]);
-																																								stringstream ss;
-																																								ss << contactDistance;
-																																								if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
-																																																LIMIT_DISTANCE = true;
-																																								else
-																																																help();
-																																}
-																																else
-																																								help();
-																								} else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
-																																NOISOLATE = true;
-																								} else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
-																																if(i < argc)
-																																								outputPrefix = argv[++i];
-																																else
-																																								help();
-																								} else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
-																																if(i < argc)
-																																								outputDir = argv[++i];
-																																else
-																																								help();
-																								} else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
-																																if(i < argc) {
-																																								paramDir = argv[++i];
-																																								PARAM_DIR = true;
-																																}
-																																else
-																																								help();
-																								} else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
-																																std::string cmd = argv[i];
-																																if(i < argc) {
-																																								dangles = atoi(argv[++i]);
-																																								if (!(dangles == 0 || dangles == 2)) {
-																																																dangles = -1;
-																																																printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
-																																								} 
-																																} else
-																																								help();
-																								} else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
-																																T_MISMATCH = true;
-																								} else if (strcmp(argv[i], "--unafold") == 0) {
-																																UNAMODE = true;
-																								} else if (strcmp(argv[i], "--rnafold") == 0) {
-																																RNAMODE = true;
-																								} else if (strcmp(argv[i], "--prefilter") == 0) {
-																																if(i < argc) {
-																																								prefilter1 = atoi(argv[++i]);
-																																								if (prefilter1 <= 0 ) {
-																																																printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
-																																																help();
-																																								}
-																																								b_prefilter = true;
-																																								prefilter2 = prefilter1;
-																																} else 
-																																								help();
-																								}
-																								else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
-																																if(i < argc)
-																																								nThreads = atoi(argv[++i]);
-																																else
-																																								help();	
-																								} else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
-																																VERBOSE = true;
-																								}
-																								else if(strcmp(argv[i], "--bpp") == 0) {
-																																BPP_ENABLED = true;
-																								} else if(strcmp(argv[i], "--subopt") == 0) {
-																																SUBOPT_ENABLED = true;
-																																dangles = 2;
-																																if(i < argc)
-																																								suboptDelta = atof(argv[++i]);
-																																else
-																																								help();
-																								}
-																								else if (strcmp(argv[i], "--useSHAPE") == 0){
-																																if( i < argc){
-																																								shapeFile = argv[++i];
-																																								SHAPE_ENABLED = true;
-																																}
-																																else
-																																								help();
-																								}				
-																} else {
-																								seqfile = argv[i];
-																}
-								}
+  for(i=1; i<argc; i++) {
+    if(argv[i][0] == '-') {
+      if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
+        help();
+      } else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
+        if(i < argc) {
+          constraintsFile = argv[++i];
+          CONS_ENABLED = true;
+        }
+        else
+          help();
+      } else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
+        if(i < argc){
+          contactDistance = atoi(argv[++i]);
+          stringstream ss;
+          ss << contactDistance;
+          if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i]))
+            LIMIT_DISTANCE = true;
+          else
+            help();
+        }
+        else
+          help();
+      } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) {
+        NOISOLATE = true;
+      } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
+        if(i < argc)
+          outputPrefix = argv[++i];
+        else
+          help();
+      } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
+        if(i < argc)
+          outputDir = argv[++i];
+        else
+          help();
+      } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+        if(i < argc) {
+          paramDir = argv[++i];
+          PARAM_DIR = true;
+        }
+        else
+          help();
+      } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
+        std::string cmd = argv[i];
+        if(i < argc) {
+          dangles = atoi(argv[++i]);
+          if (!(dangles == 0 || dangles == 2)) {
+            dangles = -1;
+            printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
+          } 
+        } else
+          help();
+      } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
+        T_MISMATCH = true;
+      } else if (strcmp(argv[i], "--unafold") == 0) {
+        UNAMODE = true;
+      } else if (strcmp(argv[i], "--rnafold") == 0) {
+        RNAMODE = true;
+      } else if (strcmp(argv[i], "--prefilter") == 0) {
+        if(i < argc) {
+          prefilter1 = atoi(argv[++i]);
+          if (prefilter1 <= 0 ) {
+            printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
+            help();
+          }
+          b_prefilter = true;
+          prefilter2 = prefilter1;
+        } else 
+          help();
+      }
+      else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
+        if(i < argc)
+          nThreads = atoi(argv[++i]);
+        else
+          help();	
+      } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
+        VERBOSE = true;
+      }
+      else if(strcmp(argv[i], "--bpp") == 0) {
+        BPP_ENABLED = true;
+      } else if(strcmp(argv[i], "--subopt") == 0) {
+        SUBOPT_ENABLED = true;
+        dangles = 2;
+        if(i < argc)
+          suboptDelta = atof(argv[++i]);
+        else
+          help();
+      } else if (strcmp(argv[i],"--partition") == 0) {
+        CALC_PART_FUNC = true;
+      }
+      else if (strcmp(argv[i], "--useSHAPE") == 0){
+        if( i < argc){
+          shapeFile = argv[++i];
+          SHAPE_ENABLED = true;
+        }
+        else
+          help();
+      }				
+    } else {
+      seqfile = argv[i];
+    }
+  }
 
-								// Must have an input file specified
-								if(seqfile.empty()) {
-																help();
-																printf("Missing input file.\n");
-								}
+  // Must have an input file specified
+  if(seqfile.empty()) {
+    help();
+    printf("Missing input file.\n");
+  }
 
-								// If no output file specified, create one
-								if(outputPrefix.empty()) {
-																// base it off the input file
-																outputPrefix += seqfile;
+  // If no output file specified, create one
+  if(outputPrefix.empty()) {
+    // base it off the input file
+    outputPrefix += seqfile;
 
-																size_t pos;
-																// extract file name from the path
-																if ((pos=outputPrefix.find_last_of('/')) > 0) {
-																								outputPrefix = outputPrefix.substr(pos+1);
-																}
+    size_t pos;
+    // extract file name from the path
+    if ((pos=outputPrefix.find_last_of('/')) > 0) {
+      outputPrefix = outputPrefix.substr(pos+1);
+    }
 
-																// and if an extension exists, remove it ...
-																if(outputPrefix.find(".") != string::npos)
-																								outputPrefix.erase(outputPrefix.rfind("."));
-								}
+    // and if an extension exists, remove it ...
+    if(outputPrefix.find(".") != string::npos)
+      outputPrefix.erase(outputPrefix.rfind("."));
+  }
 
-								// If output dir specified
-								if (!outputDir.empty()) {
-																outputFile += outputDir;
-																outputFile += "/";
-																suboptFile += outputDir;
-																suboptFile += "/";
-																bppOutFile += outputDir;
-																bppOutFile += "/";
-								}
-								// ... and append the .ct
-								outputFile += outputPrefix;
-								outputFile += ".ct";
+  // If output dir specified
+  if (!outputDir.empty()) {
+    outputFile += outputDir;
+    outputFile += "/";
+    suboptFile += outputDir;
+    suboptFile += "/";
+    bppOutFile += outputDir;
+    bppOutFile += "/";
+  }
+  // ... and append the .ct
+  outputFile += outputPrefix;
+  outputFile += ".ct";
 
-								suboptFile += outputPrefix;	
-								suboptFile += "_ss.txt";	
+  suboptFile += outputPrefix;	
+  suboptFile += "_ss.txt";	
 
-								bppOutFile += outputPrefix;	
-								bppOutFile += "_bpp.txt";	
+  bppOutFile += outputPrefix;	
+  bppOutFile += "_bpp.txt";	
 }
 
 /**
diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index 44de0ea..5319eb8 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -1,7 +1,21 @@
 #include "partition-func.h"
 #include "energy.h"
+#include "algorithms-partition.h"
 
 
+double ** u;
+double ** up;
+double ** upm;
+double ** ud;
+double ** u1d;
+
+double ** s1;
+double ** s2;
+double ** s3;
+double ** u1;
+
+int part_len;
+
 static void create_partition_arrays();
 static void init_partition_arrays();
 static void fill_partition_arrays();
@@ -16,23 +30,241 @@ static void calc_u1d(int i, int j);
 static void calc_s1(int i, int j);
 static void calc_s2(int i, int j);
 static void calc_s3(int i, int j);
+static double f(int j, int h, int l);
 
-void create_partition_arrays()
+double f(int j, int h, int l){
+	if(j - 1 == l)
+		return 1;
+	else 
+		return exp(-Ed3(h,l,l+1)/RT);
+}
+
+
+void calculate_partition(int len) 
 {
+  part_len = len;
+  create_partition_arrays();
+  init_partition_arrays();
+  fill_partition_arrays();
+}
 
+void free_partition()
+{
+  free_partition_arrays();
 }
 
 void init_partition_arrays()
 {
-		
+  int i, j;							
+  int n = part_len;
+  for(i=1; i<=n-3; ++i){
+    for(j=i; j<=i+3; ++j){
+      u[i][j] = 1;
+      up[i][j] = 0;
+      ud[i][j] = 0;
+      u1[i][j] = 0;
+      u1d[i][j] =0 ;
+      s1[i][j] = 0;
+      s2[i][j] = 0;
+      s3[i][j] = 0;
+    }
+  }	
+  for(i=1; i<=n-4; ++i){
+    s1[i][i+4] = 0;
+    s2[i][i+4] = 0;
+  }
+  for(i=1; i<n; ++i){
+    u[i+1][i] = 1;
+    u1[i+1][i] = 0;
+    u1d[i+1][i] = 0;
+  }
+  for(i=1; i<n-1; i++){
+    u1[i+2][i] = 0;
+  }
 }
 
 void fill_partition_arrays()
 {
+  int b,i;
+  int n=part_len;
+  for(b=1; b<n; ++b){
+    for(i=1; i<=n-b; ++i){
+      int j=i+b;
+      calc_s1(i,j);
+      calc_s2(i,j);
+      calc_s3(i,j);
+      calc_u1d(i,j);
+      calc_u1(i,j);
+      calc_upm(i,j);
+      calc_up(i,j);
+      calc_ud(i,j);
+      calc_u(i,j);
+    }
+  }
+}
 
+void calc_s1(int h, int j)
+{
+		int l;						
+		for (l = h; l < j; ++l)
+		{
+				s1[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
+						(exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+
+																				up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))));							
+		}
+}
+
+void calc_s2(int h, int j)
+{
+	int l;							
+	for (l = h; l < j; ++l)
+	{
+			s2[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
+										(exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1]+u1d[l+1][j-1]);							
+	}
+}
+
+void calc_s3(int h, int j)
+{
+  int l;							
+  for (l = h; l < j; ++l)
+  {
+    s3[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
+      (f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + 
+       exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j] + u1d[l+1][j]);
+  }
+}
+
+void create_partition_arrays()
+{
+  int len = part_len + 1;						
+  u = mallocTwoD(len,len);
+  up = mallocTwoD(len,len);
+  upm = mallocTwoD(len,len);
+  ud = mallocTwoD(len,len);
+  u1d = mallocTwoD(len,len);
+  s1 = mallocTwoD(len,len);
+  s2 = mallocTwoD(len,len);
+  s3 = mallocTwoD(len,len);
+  u1 = mallocTwoD(len,len);
 }
 
 void free_partition_arrays()
 {
+  int len = part_len + 1;
+  freeTwoD(u,len,len);
+  freeTwoD(up,len,len);
+  freeTwoD(upm,len,len);
+  freeTwoD(ud,len,len);
+  freeTwoD(u1d,len,len);
+  freeTwoD(s1,len,len);
+  freeTwoD(s2,len,len);
+  freeTwoD(s3,len,len);
+  freeTwoD(u1,len,len);
+}
+
+void calc_upm(int i, int j){
+	double a = Ea, b=Eb, c=Ec;
+	double p_val = 0;
+	int l,h;
+	double quadraticSum = 0;
+	
+	for(l=i+2; l<j; ++l){
+		p_val += (up[i+1][l] * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT) * 
+																		(exp((-1)*(Ed3(i+1,l,l+1)+b)/RT) * u1[l+2][j-1] + u1d[l+1][j-1]));
+	}
+	
+	for(l=i+3; l<j; ++l){
+		p_val += (up[i+2][l]*exp((-1)*(a+2*c+b+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * 
+																		(exp((-1)*(Ed3(i+2,l,l+1)+b)/RT)*u1[l+2][j-1] + u1d[l+1][j-1]));
+	}
+	
+	for(h=i+3; h<j-1; ++h){
+		quadraticSum += (s2[h][j] * exp((-1)*(a+2*c+(h-i-1)*b)/RT));	
+	}
+	quadraticSum *= exp((-1)*Ed3(i,j,i+1)/RT);
+	
+	p_val += quadraticSum;
+	
+	upm[i][j] = p_val;
+}
+
+void calc_u1(int i, int j){
+	double b=Eb, c=Ec;
+	double p_val = u1d[i][j];
+	int h;
+	double quadraticSum = 0;
+	
+	for(h=i+1; h<j; ++h){
+		quadraticSum += (s3[h][j] * exp((-1)*(c+(h-i)*b)/RT));
+	}
+	
+	p_val += quadraticSum;
+	
+	u1[i][j] = p_val;
+}
+
+void calc_u1d(int i, int j){
+	double b=Eb, c=Ec;
+	double p_val = 0;
+	int l;
+
+	for(l=i+1; l<=j; ++l){
+    if (l > part_len-2) continue;
+		p_val += (up[i][l]*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(Ed3(i,l,l+1)+b)/RT)*u1[l+2][j] + u1d[l+1][j]));
+	}
+
+	u1d[l+1][j] = p_val;
+}
+
+void calc_u(int i, int j)
+{
+	int uval = 1;
+ int h;
+	int ctr;
+
+	for (h = i+1; h < j; ++h) {
+		uval = up[h][j] * exp( -(Ed5(h,j,h-1) + auPenalty(h,j)) / RT );
+	}
+
+	uval = uval + ud[i][j];
+
+	for (ctr = i+1; ctr < j-1; ++ctr) {
+		uval = uval + s1[ctr][j];
+	}
+}
+
+void calc_ud(int i, int j)
+{
+	int l;
+
+	for (l = i+1; l < j; ++l) {
+		double val1, val2, val3;
+		val1 = up[i][l];
+		val1 = val1 * exp(-auPenalty(i,l) / RT);
+
+		val2 = u[l+2][j];
+		val2 = val2 * exp(-Ed3(i,l,l+1)/RT);
+
+		val3 = ud[l+1][j];
+		val2 = val2 + up[l+1][j] * exp( -auPenalty(l+1,j) / RT );
+
+		ud[i][j] = ud[i][j] + (val1 * val2);
+	}
+}
+
+void calc_up(int i, int j)
+{
+	double up_val = 0.0;
+ int h,l;
 
+	for (h = i+1; h < j-1; ++h) {
+		for (l = h+1; l < j; ++l) {
+			up_val = up[h][l] * exp(-eL(i,j,h,l)/RT);
+		}
+	}
+	up_val = up_val * exp(-Ed3(i,j,i+1)/RT);
+	up_val = up_val + exp(-eH(i,j)/RT );
+	up_val = up_val + exp(-eS(i,j)/RT ) * up[i+1][j-1];
+	up_val = up_val + upm[i][j];
 }

From a922dc664c0aa5dbd9109354036461d6d6f5e9aa Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 16 Sep 2011 11:21:57 -0400
Subject: [PATCH 233/282] boundary correction

---
 gtfold-mfe/src/partition-func.c | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index 5319eb8..ae5ee53 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -73,12 +73,12 @@ void init_partition_arrays()
     s1[i][i+4] = 0;
     s2[i][i+4] = 0;
   }
-  for(i=1; i<n; ++i){
+  for(i=1; i<=n; ++i){
     u[i+1][i] = 1;
     u1[i+1][i] = 0;
     u1d[i+1][i] = 0;
   }
-  for(i=1; i<n-1; i++){
+  for(i=1; i<=n-1; i++){
     u1[i+2][i] = 0;
   }
 }
@@ -87,18 +87,20 @@ void fill_partition_arrays()
 {
   int b,i;
   int n=part_len;
-  for(b=1; b<n; ++b){
+  for(b=TURN+1; b<n; ++b){
     for(i=1; i<=n-b; ++i){
       int j=i+b;
       calc_s1(i,j);
       calc_s2(i,j);
       calc_s3(i,j);
+      /*
       calc_u1d(i,j);
       calc_u1(i,j);
       calc_upm(i,j);
       calc_up(i,j);
       calc_ud(i,j);
       calc_u(i,j);
+      */
     }
   }
 }
@@ -137,7 +139,7 @@ void calc_s3(int h, int j)
 
 void create_partition_arrays()
 {
-  int len = part_len + 1;						
+  int len = part_len + 2;						
   u = mallocTwoD(len,len);
   up = mallocTwoD(len,len);
   upm = mallocTwoD(len,len);

From 42cb45d8144cd045d97d30bf5536add7c597c5e2 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 16 Sep 2011 11:37:30 -0400
Subject: [PATCH 234/282] more boundary correction

---
 gtfold-mfe/src/partition-func.c | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index ae5ee53..21d96ca 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -90,17 +90,21 @@ void fill_partition_arrays()
   for(b=TURN+1; b<n; ++b){
     for(i=1; i<=n-b; ++i){
       int j=i+b;
+      
+      // Auxillary array
       calc_s1(i,j);
       calc_s2(i,j);
       calc_s3(i,j);
-      /*
-      calc_u1d(i,j);
-      calc_u1(i,j);
+      
+      if (j < n) { // handled boundary condition
+        calc_u1d(i,j);
+        calc_u1(i,j);
+      }
+
       calc_upm(i,j);
       calc_up(i,j);
       calc_ud(i,j);
       calc_u(i,j);
-      */
     }
   }
 }
@@ -212,11 +216,10 @@ void calc_u1d(int i, int j){
 	int l;
 
 	for(l=i+1; l<=j; ++l){
-    if (l > part_len-2) continue;
 		p_val += (up[i][l]*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(Ed3(i,l,l+1)+b)/RT)*u1[l+2][j] + u1d[l+1][j]));
 	}
 
-	u1d[l+1][j] = p_val;
+	u1d[i][j] = p_val;
 }
 
 void calc_u(int i, int j)

From 91e95b88fe8365855504ae5110712d8213bc95c0 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 16 Sep 2011 11:42:28 -0400
Subject: [PATCH 235/282] more boundary correction

---
 gtfold-mfe/src/partition-func.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index 21d96ca..62a56d6 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -157,7 +157,7 @@ void create_partition_arrays()
 
 void free_partition_arrays()
 {
-  int len = part_len + 1;
+  int len = part_len + 2;
   freeTwoD(u,len,len);
   freeTwoD(up,len,len);
   freeTwoD(upm,len,len);

From abcd9f532a8fc2788ea1717d2d16d151d1c580a4 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 16 Sep 2011 17:30:32 -0400
Subject: [PATCH 236/282] more boundary correction

---
 gtfold-mfe/src/partition-func.c | 157 ++++++++++++++++++++++++--------
 1 file changed, 121 insertions(+), 36 deletions(-)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index 62a56d6..e004a74 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -1,7 +1,37 @@
+#include <stdio.h>
 #include "partition-func.h"
 #include "energy.h"
 #include "algorithms-partition.h"
-
+#include "global.h"
+#include "utils.h"
+
+#ifdef _OPENMP 
+#include "omp.h"
+#endif
+
+#define DEBUG_PF 1
+
+#ifdef DEBUG_PF 
+  #undef Ec
+  #undef Eb
+  #undef Ea
+  #define Ec 0
+  #define Eb 0
+  #define Ea 0
+  #define eS StackE
+  #define eH HairE
+  #define eL ILoopE
+  #define Ed3 D3
+  #define Ed5 D5
+  #define auPenalty Etp
+#endif
+
+int StackE(int i, int j) { return 0; }
+int HairE(int i, int j) { return 0; }
+int ILoopE(int i, int j, int ip, int jp) { return 0; }
+int D3(int i, int j, int k) { return 0; } 
+int D5(int i, int j, int k) { return 0; }
+int Etp(int i, int j) { return 0; }
 
 double ** u;
 double ** up;
@@ -42,10 +72,20 @@ double f(int j, int h, int l){
 
 void calculate_partition(int len) 
 {
+  int i, j;
   part_len = len;
   create_partition_arrays();
   init_partition_arrays();
   fill_partition_arrays();
+
+  for (i = 0; i <= part_len+1; ++i) 
+  {
+    for (j = 0; j <= part_len+1; ++j)
+      printf("%0.1f ",u[i][j]);
+    printf("\n");
+  }
+
+  printf("%4.4f\n",u[1][part_len]);
 }
 
 void free_partition()
@@ -53,8 +93,29 @@ void free_partition()
   free_partition_arrays();
 }
 
+void init_part_arrays_zeros(){
+  int i,j,n;
+  n = part_len+1;
+  for(i=0; i<=n; ++i){
+    for(j=0; j<=n; ++j){
+      u[i][j]=0;
+      up[i][j]=0;
+      upm[i][j]=0;
+      ud[i][j]=0;
+      u1d[i][j]=0;
+
+      s1[i][j]=0;
+      s2[i][j]=0;
+      s3[i][j]=0;
+      u1[i][j]=0;
+    }
+  }
+}
+
 void init_partition_arrays()
 {
+  init_part_arrays_zeros();
+
   int i, j;							
   int n = part_len;
   for(i=1; i<=n-3; ++i){
@@ -85,12 +146,12 @@ void init_partition_arrays()
 
 void fill_partition_arrays()
 {
-  int b,i;
+  int b,i,j;
   int n=part_len;
   for(b=TURN+1; b<n; ++b){
     for(i=1; i<=n-b; ++i){
-      int j=i+b;
-      
+      j=i+b;
+         
       // Auxillary array
       calc_s1(i,j);
       calc_s2(i,j);
@@ -103,6 +164,7 @@ void fill_partition_arrays()
 
       calc_upm(i,j);
       calc_up(i,j);
+      
       calc_ud(i,j);
       calc_u(i,j);
     }
@@ -175,24 +237,29 @@ void calc_upm(int i, int j){
 	int l,h;
 	double quadraticSum = 0;
 	
-	for(l=i+2; l<j; ++l){
-		p_val += (up[i+1][l] * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT) * 
-																		(exp((-1)*(Ed3(i+1,l,l+1)+b)/RT) * u1[l+2][j-1] + u1d[l+1][j-1]));
-	}
-	
-	for(l=i+3; l<j; ++l){
-		p_val += (up[i+2][l]*exp((-1)*(a+2*c+b+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * 
-																		(exp((-1)*(Ed3(i+2,l,l+1)+b)/RT)*u1[l+2][j-1] + u1d[l+1][j-1]));
-	}
-	
-	for(h=i+3; h<j-1; ++h){
-		quadraticSum += (s2[h][j] * exp((-1)*(a+2*c+(h-i-1)*b)/RT));	
-	}
-	quadraticSum *= exp((-1)*Ed3(i,j,i+1)/RT);
-	
-	p_val += quadraticSum;
-	
-	upm[i][j] = p_val;
+  if (canPair(RNA[i],RNA[j]) && j-i > TURN)
+  {
+   for(l=i+2; l<j; ++l){
+      p_val += (up[i+1][l] * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT) * 
+          (exp((-1)*(Ed3(i+1,l,l+1)+b)/RT) * u1[l+2][j-1] + u1d[l+1][j-1]));
+    }
+
+    for(l=i+3; l<j; ++l){
+      p_val += (up[i+2][l]*exp((-1)*(a+2*c+b+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * 
+          (exp((-1)*(Ed3(i+2,l,l+1)+b)/RT)*u1[l+2][j-1] + u1d[l+1][j-1]));
+    }
+
+    for(h=i+3; h<j-1; ++h){
+      quadraticSum += (s2[h][j] * exp((-1)*(a+2*c+(h-i-1)*b)/RT));	
+    }
+    quadraticSum *= exp((-1)*Ed3(i,j,i+1)/RT);
+
+    p_val += quadraticSum;
+    upm[i][j] = p_val;
+  }
+  else {
+    upm[i][j] = 0;   
+  }
 }
 
 void calc_u1(int i, int j){
@@ -237,13 +304,16 @@ void calc_u(int i, int j)
 	for (ctr = i+1; ctr < j-1; ++ctr) {
 		uval = uval + s1[ctr][j];
 	}
+	u[i][j] = uval;
 }
 
 void calc_ud(int i, int j)
 {
 	int l;
+  double udij = 0;
 
-	for (l = i+1; l < j; ++l) {
+	for (l = i+1; l < j; ++l) 
+  {
 		double val1, val2, val3;
 		val1 = up[i][l];
 		val1 = val1 * exp(-auPenalty(i,l) / RT);
@@ -252,24 +322,39 @@ void calc_ud(int i, int j)
 		val2 = val2 * exp(-Ed3(i,l,l+1)/RT);
 
 		val3 = ud[l+1][j];
-		val2 = val2 + up[l+1][j] * exp( -auPenalty(l+1,j) / RT );
+		val3 = val3 + up[l+1][j] * exp( -auPenalty(l+1,j) / RT );
 
-		ud[i][j] = ud[i][j] + (val1 * val2);
+		udij += (val1 * (val2 + val3));
 	}
+  ud[i][j]  = udij;
 }
 
 void calc_up(int i, int j)
 {
-	double up_val = 0.0;
- int h,l;
+  double up_val = 0.0;
+  int p,q;
 
-	for (h = i+1; h < j-1; ++h) {
-		for (l = h+1; l < j; ++l) {
-			up_val = up[h][l] * exp(-eL(i,j,h,l)/RT);
-		}
-	}
-	up_val = up_val * exp(-Ed3(i,j,i+1)/RT);
-	up_val = up_val + exp(-eH(i,j)/RT );
-	up_val = up_val + exp(-eS(i,j)/RT ) * up[i+1][j-1];
-	up_val = up_val + upm[i][j];
+  if (canPair(RNA[i],RNA[j]) && j-i > TURN)
+  {
+    for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
+      int minq = j-i+p-MAXLOOP-2;
+      if (minq < p+1+TURN) minq = p+1+TURN;
+      int maxq = (p==(i+1))?(j-2):(j-1);
+
+      for (q = minq; q <= maxq; q++) {
+        if (canPair(p,q)==0) continue;
+        up_val += (up[p][q] * exp(-eL(i,j,p,q)/RT));
+      }
+    }
+
+    up_val = up_val * exp(-Ed3(i,j,i+1)/RT);
+    up_val = up_val + exp(-eH(i,j)/RT );
+    up_val = up_val + exp(-eS(i,j)/RT ) * up[i+1][j-1];
+    up_val = up_val + upm[i][j];
+
+    up[i][j] = up_val;
+  }
+  else  {
+    up[i][j] = 0;   
+  }
 }

From badba13c72b4a9a0f833d81eb2a3dff6b18c5628 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 16 Sep 2011 17:48:05 -0400
Subject: [PATCH 237/282] debug changes

---
 gtfold-mfe/src/partition-func.c | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index e004a74..215b1ba 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -268,7 +268,7 @@ void calc_u1(int i, int j){
 	int h;
 	double quadraticSum = 0;
 	
-	for(h=i+1; h<j; ++h){
+	for(h=i+1; h<=j; ++h){
 		quadraticSum += (s3[h][j] * exp((-1)*(c+(h-i)*b)/RT));
 	}
 	
@@ -292,17 +292,16 @@ void calc_u1d(int i, int j){
 void calc_u(int i, int j)
 {
 	int uval = 1;
- int h;
+  int h;
 	int ctr;
-
-	for (h = i+1; h < j; ++h) {
-		uval = up[h][j] * exp( -(Ed5(h,j,h-1) + auPenalty(h,j)) / RT );
+	uval +=  ud[i][j];
+	
+  for (h = i+1; h < j; ++h) {
+		uval += up[h][j] * exp( -(Ed5(h,j,h-1) + auPenalty(h,j)) / RT );
 	}
 
-	uval = uval + ud[i][j];
-
 	for (ctr = i+1; ctr < j-1; ++ctr) {
-		uval = uval + s1[ctr][j];
+		uval += s1[ctr][j];
 	}
 	u[i][j] = uval;
 }

From dd345900a97ccc861e683aa6c24ca876b59ee968 Mon Sep 17 00:00:00 2001
From: Manoj Soni <manoj6891@gmail.com>
Date: Mon, 26 Sep 2011 23:21:00 -0400
Subject: [PATCH 238/282] Test for single stranded constraint

---
 gtfold-mfe/src/test_ss_constraint.c | 155 ++++++++++++++++++++++++++++
 1 file changed, 155 insertions(+)
 create mode 100644 gtfold-mfe/src/test_ss_constraint.c

diff --git a/gtfold-mfe/src/test_ss_constraint.c b/gtfold-mfe/src/test_ss_constraint.c
new file mode 100644
index 0000000..e3bd2d3
--- /dev/null
+++ b/gtfold-mfe/src/test_ss_constraint.c
@@ -0,0 +1,155 @@
+/*This program is used for testing single stranded constraints. Functions written in this file can be used for other scripts as well
+Author: Manoj Soni
+Email: manoj6891@gmail.com
+*/
+#include<stdio.h>
+#include<stdlib.h>
+#include<string.h>
+//#include<fstream.h>
+#define LENGTH 10
+#define MAX_CONSTRS 10
+
+void executeCommand(char* cmd){
+	printf("Executing command: %s\n", cmd);
+	int returnVal = system(cmd);
+	printf("return value: %d\n", returnVal);
+	if(returnVal != 0){
+		printf("Error: returnVal:%d, Exiting...\n", returnVal);
+		exit(-1);
+	}
+}
+
+char* getToken(char* str, char* sep, int index){
+  char * pch;
+  pch = strtok (str,sep);
+  char* fName = pch;
+  if(index==0) return fName;
+  if(index != -1){
+	printf("Error: index can be only 0 or -1. 0 means first and -1 means last token\n");
+	exit(-1);
+  }
+  while (pch != NULL)
+  {
+    //printf ("%s\n",pch);
+    fName=pch;
+    pch = strtok (NULL, sep);
+  }	
+  printf("%s\n",fName);
+  return fName;
+}
+
+char* getSeqName(char* seqFileName1){
+	char* seqFileName = malloc(200);
+	strcpy(seqFileName,seqFileName1);
+	char* seq = getToken(seqFileName, "/", -1);
+        char* seqName = getToken(seq, ".", 0);
+	printf("seqName: %s\n",seqName);
+	return seqName;
+
+}
+
+void parseCtFileToFindForcedConstraintRegion(char* ctFileName, char* constrs[MAX_CONSTRS]){//printf("Entering parse method\n");
+//ct file contents are
+//dG = -5.8
+//1       C       0       2       12      1
+//2       C       1       3       11      2
+//... ... ...
+//then 1 is pairing with 12, 2 is pairing with 11 .. ?
+//in other words, first column is i and 5th column is j for a pair (i,j)
+  //char* constrs[MAX_CONSTRS];
+  int index=0;
+  FILE* ctFile = fopen(ctFileName, "r");
+  char str[100];
+  int arr[5];
+  char c;
+  fscanf(ctFile, "%[^\n]", str);printf("first line: %s\n",str);
+  int start=-1, end=-1;
+ while(feof(ctFile)==0){
+   fscanf(ctFile, "%d %c %d %d %d %d\n", &arr[0],&c,&arr[1],&arr[2],&arr[3],&arr[4]);
+   if(arr[3]!=0){
+	if(start==-1){ start=arr[0]; end=arr[0];}
+	else end=arr[0];
+	if (start!=-1 && end-start+1 >= LENGTH){
+		//char* ss_constr;
+		char* ss_constr = (char*)malloc(30);//new char[30];
+		sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1));
+		constrs[index++] = ss_constr;
+		printf("constraint is: %s\n",ss_constr);
+		if(index>=MAX_CONSTRS) break;
+		start=-1;
+	}   
+   }
+  else{
+	if(start==-1) continue;
+	//	  char* ss_constr;
+                char* ss_constr = malloc(30);//new char[30];
+               sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1));
+                constrs[index++] = ss_constr;
+                printf("constraint is: %s\n",ss_constr);
+                if(index>=MAX_CONSTRS) break;
+                start=-1;
+
+  }
+  // printf("line is: %d %c %d %d %d %d\n", arr[0],c,arr[1],arr[2],arr[3],arr[4]);
+  }
+  if(index>=MAX_CONSTRS) return ;//constrs;
+  //char* ss_constr;
+  char* ss_constr = malloc(30);//new char[30];
+  if(start!=-1){
+	sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1));
+	printf("constraint is: %s\n",ss_constr);
+	constrs[index++] = ss_constr;
+  }
+  fclose(ctFile);
+  return ;//ss_constr;
+}
+
+char* createConstraintFile(char* constrs[MAX_CONSTRS]){
+	char* constrFileName = "constraints.txt";
+	FILE* constrFile = fopen(constrFileName, "w+");
+	int i;
+	for(i=0; i<MAX_CONSTRS; ++i){
+		if(constrs[i]==NULL)break;
+		fprintf(constrFile, "%s\n", constrs[i]);
+		//rewind(constrFile);
+		printf("writing constraint: %s\n", constrs[i]);
+	}
+	fclose(constrFile);
+
+}
+
+int validateCtFileForSSconstraint(char* ctFileName, char* constrs[MAX_CONSTRS]){
+	return 1;
+}
+int main(int argc, char* argv[]){
+	//ar
+	if(argc < 2 ){
+		printf("Error: argc < 2, Exiting...\n");
+		exit(-1);
+	}
+	char* seqFileName = argv[1];
+	char cmd[200];
+	printf("seqFileName: %s\n", seqFileName);
+	printf("running the program gtfold on this seq without constraints\n");
+	strcat(cmd, "./gtfold ");strcat(cmd, seqFileName);
+	executeCommand(cmd);
+	
+ 	char* seqName = getSeqName(seqFileName);	
+	
+	char* ctFileName = strcat(seqName, ".ct");
+	printf("ctFileName: %s\n", ctFileName);
+	char* constrs[MAX_CONSTRS];
+	parseCtFileToFindForcedConstraintRegion(ctFileName, constrs);
+
+	createConstraintFile(constrs);
+
+	//now run same program with this constraint
+	cmd[0] = '\0';
+	strcat(cmd, "./gtfold -v -c constraints.txt ");strcat(cmd, seqFileName);
+        executeCommand(cmd);	
+	
+	int passed = validateCtFileForSSconstraint(ctFileName, constrs);
+	if(passed==1){
+		printf("Single constraint test passed\n");
+	}
+}

From 20e64c6e78ab1727ebda43c2ea2b0af038d13546 Mon Sep 17 00:00:00 2001
From: Manoj Soni <manoj6891@gmail.com>
Date: Mon, 26 Sep 2011 23:21:10 -0400
Subject: [PATCH 239/282] Test for single stranded constraint

---
 gtfold-mfe/src/test_ss_constraint.pl | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100755 gtfold-mfe/src/test_ss_constraint.pl

diff --git a/gtfold-mfe/src/test_ss_constraint.pl b/gtfold-mfe/src/test_ss_constraint.pl
new file mode 100755
index 0000000..60e7fc6
--- /dev/null
+++ b/gtfold-mfe/src/test_ss_constraint.pl
@@ -0,0 +1,11 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use File::Basename;
+
+die "Usage: ./test_ss_constraint.pl <seq file>" if @ARGV < 1;
+
+my $seqName = $ARGV[0];
+
+system("gcc -o test_ss_constraint test_ss_constraint.c");
+system("./test_ss_constraint $seqName");

From 0ffefa57394c34e0774589bccef51ab43037e063 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 30 Sep 2011 00:15:27 -0400
Subject: [PATCH 240/282] First version of test scripts:

---
 gtfold-mfe/tests/config/root-logger.conf      |  7 ++
 gtfold-mfe/tests/config/test-list.conf        |  1 +
 gtfold-mfe/tests/config/test-params.conf      | 22 +++++
 .../data/16S_sequences/d.16.e.A.ambigua.seq   |  2 +
 .../16S_sequences/d.16.e.A.baicalensis.seq    |  2 +
 .../data/16S_sequences/d.16.e.A.bongranii.seq |  2 +
 .../data/16S_sequences/d.16.e.A.bracteata.seq |  2 +
 .../16S_sequences/d.16.e.A.capitellata.seq    |  2 +
 .../16S_sequences/d.16.e.A.castellanii.seq    |  2 +
 .../16S_sequences/d.16.e.A.connecticus.seq    |  2 +
 .../data/16S_sequences/d.16.e.A.dasyae.seq    |  2 +
 .../data/16S_sequences/d.16.e.A.ferocious.seq |  2 +
 .../data/16S_sequences/d.16.e.A.flavus.seq    |  2 +
 .../data/16S_sequences/d.16.e.A.fundyense.seq |  2 +
 .../data/16S_sequences/d.16.e.A.hermannii.seq |  2 +
 .../data/16S_sequences/d.16.e.A.invadans.seq  |  2 +
 .../data/16S_sequences/d.16.e.A.kariana.seq   |  2 +
 .../16S_sequences/d.16.e.A.khaliulini.seq     |  2 +
 .../16S_sequences/d.16.e.A.macrogynus.seq     |  2 +
 .../data/16S_sequences/d.16.e.A.majus.seq     |  2 +
 .../data/16S_sequences/d.16.e.A.michaelis.seq |  2 +
 .../data/16S_sequences/d.16.e.A.plicata.seq   |  2 +
 .../data/16S_sequences/d.16.e.A.scoticae.seq  |  2 +
 .../data/16S_sequences/d.16.e.A.thaliana.seq  |  2 +
 .../d.16.e.A.verticilliflorum.seq             |  2 +
 .../data/16S_sequences/d.16.e.B.bigemina.seq  |  2 +
 .../data/16S_sequences/d.16.e.B.bovis.seq     |  2 +
 .../data/16S_sequences/d.16.e.B.canis.seq     |  2 +
 .../data/16S_sequences/d.16.e.B.coli.seq      |  2 +
 .../data/16S_sequences/d.16.e.B.emersonii.seq |  2 +
 .../16S_sequences/d.16.e.B.gelatinosum.seq    |  2 +
 .../data/16S_sequences/d.16.e.B.gibsoni.seq   |  2 +
 .../data/16S_sequences/d.16.e.B.hamifera.seq  |  2 +
 .../16S_sequences/d.16.e.B.investiens.seq     |  2 +
 .../16S_sequences/d.16.e.B.macrosporum.seq    |  2 +
 .../16S_sequences/d.16.e.B.mandrillaris.seq   |  2 +
 .../16S_sequences/d.16.e.B.mediterranea.seq   |  2 +
 .../data/16S_sequences/d.16.e.B.microti.1.seq |  2 +
 .../data/16S_sequences/d.16.e.B.microti.2.seq |  2 +
 .../data/16S_sequences/d.16.e.B.microti.3.seq |  2 +
 .../data/16S_sequences/d.16.e.B.microti.4.seq |  2 +
 .../data/16S_sequences/d.16.e.B.microti.5.seq |  2 +
 .../16S_sequences/d.16.e.B.moritziana.seq     |  2 +
 .../data/16S_sequences/d.16.e.B.ostreae.seq   |  2 +
 .../data/16S_sequences/d.16.e.B.pacifica.seq  |  2 +
 .../16S_sequences/d.16.e.B.plumatellae.seq    |  2 +
 .../data/16S_sequences/d.16.e.B.rodhaini.seq  |  2 +
 .../data/16S_sequences/d.16.e.G.vagum.seq     |  2 +
 .../data/16S_sequences/d.16.e.G.vavrai.seq    |  2 +
 .../tests/scripts/Scoregtwithunafold.pm       | 60 ++++++++++++
 gtfold-mfe/tests/scripts/start_test.pm        | 94 +++++++++++++++++++
 gtfold-mfe/tests/scripts/test_utils.pl        | 84 +++++++++++++++++
 52 files changed, 360 insertions(+)
 create mode 100644 gtfold-mfe/tests/config/root-logger.conf
 create mode 100644 gtfold-mfe/tests/config/test-list.conf
 create mode 100644 gtfold-mfe/tests/config/test-params.conf
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq
 create mode 100755 gtfold-mfe/tests/scripts/Scoregtwithunafold.pm
 create mode 100755 gtfold-mfe/tests/scripts/start_test.pm
 create mode 100755 gtfold-mfe/tests/scripts/test_utils.pl

diff --git a/gtfold-mfe/tests/config/root-logger.conf b/gtfold-mfe/tests/config/root-logger.conf
new file mode 100644
index 0000000..7fa2cc7
--- /dev/null
+++ b/gtfold-mfe/tests/config/root-logger.conf
@@ -0,0 +1,7 @@
+#root-logger.conf
+log4perl.rootLogger               = INFO, myFILE
+log4perl.appender.myFILE          = Log::Log4perl::Appender::File
+log4perl.appender.myFILE.filename = ../logs/error_log
+log4perl.appender.myFILE.mode     = append
+log4perl.appender.myFILE.layout   = Log::Log4perl::Layout::PatternLayout
+log4perl.appender.myFILE.layout.ConversionPattern = [%p] (%F line %L) %m%n
diff --git a/gtfold-mfe/tests/config/test-list.conf b/gtfold-mfe/tests/config/test-list.conf
new file mode 100644
index 0000000..b339d8d
--- /dev/null
+++ b/gtfold-mfe/tests/config/test-list.conf
@@ -0,0 +1 @@
+Scoregtwithunafold
diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf
new file mode 100644
index 0000000..2922a50
--- /dev/null
+++ b/gtfold-mfe/tests/config/test-params.conf
@@ -0,0 +1,22 @@
+# Important directory variables
+G_GTFOLD_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/src/
+G_UNAFOLD_DIR=/home/users/rbanga/rna/unafold/install/bin/
+#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/
+G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/
+G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/23S_sequences/
+#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/Other_sequences/
+G_WORK_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/work/
+G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test-list.conf
+
+#Sequence Inclusion Filters
+#G_INCLUDE_SEQUENCES=rad
+#G_INCLUDE_SEQUENCES=d.16.e.B.g*
+#G_INCLUDE_SEQUENCES=d.16.e.B.m*
+#G_INCLUDE_SEQUENCES=d.16.e.B.h*
+G_INCLUDE_SEQUENCES=d.16.e.G.va*
+#G_EXCLUDE_SEQUENCES=d.16.e.A.*
+#G_EXCLUDE_SEQUENCES=d.16.e.B.ma*
+#G_INCLUDE_SEQUENCES=acc1
+#G_INCLUDE_SEQUENCES=a.*j
+#G_INCLUDE_SEQUENCES=a..tb*
+
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq
new file mode 100644
index 0000000..53be3ef
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.ambigua
+NAACCUGGUUGAUCCUGCCAGUAGUGAUACGCUGUCAUUAAGACUAAGCCAUGCAUGUGUAAGUAUAAGAAGUACUCGAGACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAGAUCCGACUUCGGGAGGAUUGUAUUUAUUAGGUUACAAAACCAACCCUCUCUCGGGAGGUUCUUUGGGUGAGUCAUGAUAAGCAUGCGGAUCGCAGGGCUUUACGCCGGCGACGGAUCAUGUAAGUUCCUGCCCUAUCAGCUUCGGAUGGUAGGGUAUUGGCCUACCAUGGCAUUAACGGGUAACGGGAGAUCAGGGUUUGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACGAUAAAUAACAAUGCCGGGCCUUUCUAGGUCUGGCAAUUGGAAUGAGAACGAUGCAAASACCCUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCUGGUGGAGUCGGUCUGUCCUUCACUUGGUGUUGGUACGUGACUGUAUCUCUGCCCUCCUUGGUUGGAUCCAGUGCUGGCAUUUGGUUGUCGGUCUGGGGACGGCCAUCGUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCUUAGGCCUUGAAUACAUUAGCAUGGAAUAAUGAAAUAGGGUUUUGGCACUAUUUCGUUGGUUUGCGCGCCGAAACAAUGAUUAAUAGGGACAGUUUGGGGAUAUUCCUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACGACUGCGAAAGCAUUUAUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACCAUGCCGACUAGGGAUUUGCGGUUGUUCUUGUAGACUCCGUAAGCACCUUAUGAGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGBGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUCCGGUGAAUGAGUUUUCAUUGACCUGGUCUUCUUAGAGGGACUUUCGGUGACUAACCGAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGAUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUCUAGAACCUUGGCCGAGAGGCCUGGGUAAUCUUGUGAACGUGCAUCGUGAUAGGGAUUGAAUAUUGCAAUUAUUAUUCAUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGCGGUCCGUUCCUUUACUGGGAUGUGGCUGUGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq
new file mode 100644
index 0000000..6dbbac3
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.baicalensis
+NAACCUGGUUGAUCCUGCCAGUAGUGAUACGCUGUCAUUAAGGACUAAGCCAUGCAUGUGUAAGUAUAAGAACUUUCGAGACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAGAUCCGACUUCGGGAGGAUCGUAUUUAUUAGGUUACAAAACCAACCCUCUUUCGGGAGGUUCUCUGGGUGAGUCAUGAUAAGCAUGCGGAUCGCACGGCUUUAUGCCGGCGUCGGAUCAGGUAAGUUCCUGCCCCAUCAGCUUCGGAUGGUAGAGUAUUGGCCUACCAUGGCGUUAACGGGUAACGGGAGAUCAGGGUUUGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACGAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACGAUGCAAAUACCCUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCUGGUGGAGUCGGUCUGUCCUUCACUUGGUGUUGGUUCGUGACUGUAUCUCUGCCCUCCUUGGUUGGAGCCAGUGUUGGCAUUCAGUUGUUGGGCUGGGGACAAUCAUCGUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCUUAGGCCUUGAAUACAUUAGCAUGGAAUAAUGAAAUAGGGUUUUGGCACUAUUUUGUUGGUUUGCGCGCCAAAAUAAUGAUUAACAGGGACAGUUUGGGGAUAUUCGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACGACUGCGAAAGCAUUUAUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUUGCGGUUGUUCUUGUAGACUCCGUAAGCACCUUAUGAGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACAGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUCCGGUGAAUGAGUUUUCAUUGACCUGGUCUUCUUAGAGGGACUUUCGGUGACUAACCGAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGAUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUCUAGAACCUUGGCCGUGAGGCCUGGGUAAUCUUAUGAACGUGCAUCGUGCUAGGGAUUGAAUAUUGCAAUUAUUAUUCAUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGGUCCGUUCCUUCAGUGGGAUGUGGCUGUGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq
new file mode 100644
index 0000000..bd0b78d
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.bongranii
+NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAACUCUUUUACUUGAAAACUGCGAACGGCUCAUUAUAUCAGUUAUAGUUUAUUGGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCGAUACCCUUCUGGGGUAGUAUUUAUUAGAUAGAAACCAACCCCUUCGGGGUGAUGUGGUGAUUCAUAAUAAGUUUACGAAUCGCAUGCCUUCGGGCGGCGAUGGAUCUUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGGAAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUGACACAGAGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUGUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUGUGGCUGUUGCGGGAGGCCUGGCACGUGCCAGCGCUCUUCCUGCGACGCCAUCCUUGGGUUGAAAGUGGGUGGCAUUAGGUUGUCGCCUAUGGGAAGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCGUUGAAUAGAUUAGCAUGGAAUAAUAAGAUAGGACCUGGGUACUAUUUUGUUGGUUUGCGUACUUAGGUAAUGAUUAACAGGGACAGUUGGGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGAGUUUCUUUAUGUCUCCGUCAGCACCUUAUGAGAAAUCACAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGUUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGCUUGGUUAGUGAAUCUUCACUGGCUGAAGCUUCUUAGAGGGACGUGCAUUCUAUCAGAUGCAGGAAGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGAGAGGCCUGGGCAAUCUUCUGAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAUUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGGCUAGCUCCCUUCAUUGUGGGUUGGCCGCGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq
new file mode 100644
index 0000000..ddb3562
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.bracteata
+CACCAGGUUGAUUCUGCCUGACACACACGCUCGUCCCAAAGAUUAAGCCAUGCAUGCUUGUGAAGGAAGCGGAACGGCGUACGGCUCAGUAGGACGGACCUAAUCUAUCCAGCACGGGAGGGAUAACCACGGGAAACUGUGGCUAAGACCGGGAUCUGCCGUGCCCUCGGGUGCUGAAGAGCGGCGGUGUGCUGGGCGAGAGUCUGACCUAUUAGCUUGAUGGCGCGGUAAGGGCGGGCCAUGGCGACGAUGGGUGACGGGGAAUCGGGGUUUGAUUCCGGAGAAGGAGGCUGAGAGACGGCUCCUACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCACUCGAGCGGAGGUAGUGACGGGACGUCUAUGGGGAGCUCUUGAUAACUGCGAGGGGCCUCUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGUGUGUGGUGAUUGCUGCAGUUAAAAGGUCCGUAGUCGACGUGUCUGGCGGGGUCUUGAGGUGCGCUCAACGUGCUAGGACCUCCGCGAGUUGCGUUCCGGAGCACUUGGGGGUGAGGGUAUUCCUGCGUGAGAGGUGAAAUUCGGUGAUCGCGGGGGGACCGACGGGGGCGCAGGCGCUCAUCCAGACUGUGUCCUAUGAUCAAGGGCGGAAGCCGUGGUAGCGAAGGUGAUUAGUGACCACUGUAGUCGCGGCCGCAAACGAUGCGUUCCCGCCUGCUGGGCGGAGGGAAACCGAGAGAGCUCUGGGGAUAGUACGAGCGCAAGCCUGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGAGUGGAUCAUGCGGGUUAAUUUGACUCAACGCGGGGCAGCUUACCAGGGCACGCGCGGGUGCGAUCGCGAUGCGAGAUUCUGCGGCGAGUGGUGCAUGGCCGUUUCUAACACGUGGGGUGACCAGUCUGGUUAAGUCCGAUAACGCGUGCCGCCCCGGCCCUGUGCGAAUGGGGGACGACUGCCGACGAGGCAGGGGAAGAGGGGCGAAAACAGGUCCGUAAUGCCCUCCGAAGCCCUGGGCGCCACGCGUGAUACAAUAGCUGCGUCGCGGUUGGGGUCGGGACUGCGGGCUGCGAGGCCAGCACGAACGCGGAAUUCCUAGUAAGCGUGCGUCACCAUUGCGUGCUGAAUGCGUCCCUGUCCUUUGUACACACCGCCCGUCGUUAUUUGAGAUGGUAGUGCGGCCGAGCGGCUGUCCUCGGGCGGCCGCGAGUCCGCCCUGCUAGAUCGAAUACAAGUCGUAACAAGGUAACCANNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq
new file mode 100644
index 0000000..3de621e
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.capitellata
+NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGACUAAGCCAUGCAAGUCUAAGUAUAAAUCUUUUACUUUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUCACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAUACCCUUCUGGGGUAGUAUUUAUUAGAUGGAAACCAACCCCUUCGGGGUGAUGUGGUGAAUCAUAAUAAGCUUGCGGAGYCCGGUGGCGAUGGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGACGGUAAGGUAUUGGCUUACCGUGGCUUUAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCUUGACACAAGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUAUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAACCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUGUGGCGGUUCCUGUGGUCCGAUUUCGGUACUUUCUGGGACUGCCAUCCUUGGGUGGAUCCUGUGUGGCAUUAGGUUGUCGUGCAGGGGAUGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCGUUGAAUAUAUUAGCAUGGAAUAAUGAGAUAGGACCUUGGUACUAUUUUGUUGGUUUGCGCACCGAGGUAAUGAUUAAUAGGGACAGUUGUGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACUAAUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGGUUUCGUUACGUCUCCGUCAGCACCUUAUGAGAAAUCACAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGUCCUUUGAGUGAUUUUCACUGAUUCGGGCUUCUUAGAGGGACGUGCAUUCUAUUAGAUGCAGGAAGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUCCUUGGCCGAGAGGCCUGGGCAAUCUUUUGAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGGAUGGUCCGGUGAAGCCUCGGGAUUGUGACCGGUGCCUUUAUUGGUGUCGGUCGCGAGAACUUGUCUAAACCUUAUCAUCUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq
new file mode 100644
index 0000000..aee7873
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.castellanii
+CGACUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUGUUUAUACGGCGAGACUGCGGAUGGCUCAUUAAAUCAGUUAUAGGUUAUUUGAUGGUCUCUUUUGUCUUUUUUUACCUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCGCAAGGUCCCGAGCGCGGGGGGCGGGGCUUCACGGCCUCGUCCUCGCAUGCGCAGAGGGAUGUAUUUAUUAGGUUAAAAACCAGCAGCCGGCAACGGCUUCAACUCCUGGUGAUUCAUAGUAACUCUUUCGGAUCGCAUUCAUGCCCUCCUUGUGGGGGCGGCGACGAUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUCGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGCGCUCGAUAAGAGUCUUGUAAUUGGAAUGAGUACAAUUUAAACCCCUUAACGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUCUAGGGACGCGCAUUUCAAGCGCCCGUGUCGUCGGGUCAAACCGGCGACUGCGUUGGCGUUGCGGGCUCGGUCCGUCGGUGCCCCACAAAGGGCUACUGGCGUGUCAACCGGCCCGCCCGUCCCCUCCUUCUGGAUUCCCGUUCCUGCUAUUGAGUUAGUGGGGACGUCACAGGGGGCUCAUCGUCGUGCGGCGUCAAAACCGUGGCGGCGGUGGGUCCCUGGGGCCCAGAUCGUUUACCGUGAAAAAAUUAGAGUGUUCAAAGCAGGCAGAUCCAAUUUUCUGCCACCGAAUACAUUAGCAUGGGAUAAUGGAAUAGGACCCUGUCCUCCUAUUUUCAGUUGGUUUUGGCAGCGCGAGGACUAGGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUCUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACCAGCGAUUAGGAGACGUUGAAUACAAAACACCACCAUCGGCGCGGUCGUCCUUGGCGUCGGUCCUUCACGGGGCCGGCGCGAGGGCGGCUUAGCCCGGUGGCACCGGUGAAUGACUCCCCUAGCAGCUUGUGAGAAAUCAUAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAUGCCGCGCUAGCCCGUCCAUCAAAACCCAUGCGUGGCUCACGCGGUCCGCUGCGGGGUGGUGUCACUUCGCGGCGACGUCAUCCCGCCGGCAGGGCCCGGGUCCGUGUGGGCGGUAGGGUUCGGCGUCCGUGCUUCUUAGAGGGACUGCUGCGCGCCUAGCCAGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUUAAUCCAACGAGUCCGCUUCAAUCGAGGCGCGAUGCCGUUGGGGUCAAACCCAACUGCGUCGCUGUCCUCGAUCGCGCCUGGGCCGAUAGGUCCGGGUAAUCUUUGCAAAUUUAAUCGUGCUGGGGAUAGAUCAUUGUAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUCCUCGGAGCCGUGGCCUCUACGCAAUCCGGGCAACCGGGUUGUGAGGUCUCCCCUUUUGGCGGCGAAGUCGAUUGAACCUUACCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUCUCCGUAGGUGAACCUGCGAAAGGAUCAGGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq
new file mode 100644
index 0000000..accfe21
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.connecticus
+CACCAGGUUGAUUCUGCCUGACGUGGACGCUAGCCUUGAAGAUUAAGCCAUGCAAGCUUGUGAAUAUUAUAUAUGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCCAUAUUAUUUAUAACCACGGGAAACUGUGGCUAAGUAUUAGGAUGAGGAUGUGACCUAUCAGCUUGACGGUACGGUAAGUGCGUACCGUGGCUAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAUUAUUAGUGUAUAUGGUGUGUAUAAACAGCACACCGAAGUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAGUAGCGUCUGUGUUUAUUGCUGCGGUUAAAAUGUGCGUAGUCUGGUUAGUGGUCUGGAGUAAAUCUUUUGUAUCUAACAACAGGGUAUUCUAGAGACUUAUACCUUGAGACAGGGAAGAGGCGAUGAUAUUUGGUAGCGAGAGGUGAAAAUCGAUGACCUACCAAGGAGCACCGGAGGCGAAAGCGAUCGCCGAGAACUGUUCUGACGAUCAAGCGCGUGAGCAGGAGUAUCGAAGAGGAUUAGAGACCCACGUAGUUCCUUGCAGUCAACGAUGCCAACGCUGUGGUGGUAUUUACCAUUGCAGAGGCGAAAGCUAGUGUAUGGGCUCCGGGGAUAGUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCCGGGCAGGCAAUUGUCGAGGGAAGCUAUUGUAGCUGAUGAUAUUGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGAGUGAUCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGAGUGGUUGCUUUUGUGACUAGACGGUGUCUGUAAAGACAAGGAAGCGACACCCAAUAACAGGUCUGUGAUGCCCGUAGAUGUCCGGGGCUCCACGCGCACUACAAUGGGUGGUAGUAUUAGUAAAGUGUAGCUAGCCGUAGUUGGGAUUGACAUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACUAACGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGCGGGUGAAGAUGCGAGCAGUCAGGUGAUGGGGAUAAGUGUUUGUGAGUAAUGAAUGCUUGGAACUGUUGCUGGUAAAUGAUUGUGAGUGUAAGAACCCGUGCAGCUAAAUUGGAUGUAAGUCGUAACAAGGUAACCNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq
new file mode 100644
index 0000000..c3ebfab
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.dasyae
+CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGAGGUAACUCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCUCGUAAGAGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUUCUGACACAGAGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGGGCAGCCCGUGCUGUGCGCGUAGUGCGUGCGGCGCUGGGAUGUUCUUUUGUGGAGGGCGGCGCGUCGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGGGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGAGCCGUUACCAUUGUGUAGCUGUUGCUCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAACGGACCAACGGGUGAGGAUGCGCGAAAGCGUUUCCCAAUCCCUAAAUCCGUUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCCUGGCCGCGGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAAN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq
new file mode 100644
index 0000000..4352cb6
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.ferocious
+CACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUUGAAGAUUAAGCCAUGCAAGCCUGUGAAUACUUGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCACNAACCCUAAUAACCACGGUAAACUGUGGCUAAGGUAGUGGAUGAGGAUGUGACCUAUCAGCUUUGUCGGUACGAUAAGUGCGUACCGUGGCUAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAAGUUAUAUUGAGUGAAUAAAAUACACUCAUAAAUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAAUAGCGUCUGUGUUUAUUGCUGCGGUUAAAACGUGCGUAGUCUGGUUUAUAGCCUGAGUUAAAUACGUGUGCUUUAAGCAUGAAGUAUGUCAGGGACUUAGACCUUGGGAUAGGGACGGGGCAAUGAUAUUCGGCAGCGAGAGGUGAAAAUCGAUGACCUGCUGAGGAGCAACAGAGGCGAAAGCGGUUGUCCAGAACUAGUCCGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGGCGAUUAGAGACCGUCGUAGUUCCUAGCAGUAAACGAUGCCAACACUGUGGUGGAAUGUCACUGCAGAAGCGAAAGCUAGUGUGUAGGCUCCGGGGAUAGUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCUGAGGCAGGCUGUUAGUAGGAGAUUGCUUAGCAAGAUACUGCAGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGGGUGACCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGGAUUCUAUUGUAAAAGGUAGAGACGGUGUAUGUAAGUACAAGGAAGCACCACCCAAUAACAAGUCUGUGAUGCCCGUAGAUGUCCAGGGCUCCACGCGCACUACAGUUUAGUGAAGUGUGUGGAGAGUGAUUUGCUAGGUAGUUGGGAUUGAUGUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACCAACGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGUGGGUNAANUCCAUAGCGAGCUUAGCGAGGUAGUGAUUAUGCACGAGUUAGGUUAGUUAUGGAAAGAACCCAUGCAGCUAGAUUGGAUGUAAGUCGUAACAAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq
new file mode 100644
index 0000000..b35efec
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.flavus
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCACUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUACCUUACUACAUGGAUACCUGUGGUAAUUCUAGAGCUAAUACAUGCUAAAAACCUCGACUUCGGAAGGGGUGUAUUUAUUAGAUAAAAAACCAAUGCCCUUCGGGGCUCCUUGGUGAUUCAUAAUAACUUAACGAAUCGCAUGGCCUUGCGCCGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUACUGAUACGGGGCUCUUUUGGGUCUCGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGUCUGGCUGGCCGGUCCGCCUCACCGCGAGUACUGGUCCGGCUGGACCUUUCCUUCUGGGGAACCUCAUGGCCUUCACUGGCUGUGGGGGGAACCAGGACUUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCCUUUGCUCGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGGACCGCCGUAAUGAUUAAUAGGGAUAGUCGGGGGCGUCAGUAUUCAGCUGUCAGAGGUGAAAUUCUUGGAUUUGCUGAAGACUAACUACUGCGAAAGCAUUCGCCAAGGAUGUUUUCAUUAAUCAGGGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGCGGUGUUUCUAUGAUGACCCGCUCGGCACCUUACGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACAAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAAAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUCUUUUGGAUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUCGGCCCUUAAAUAGCCCGGUCCGCGUUUGCGGGCCGCUGGCUUCUUAGGGGGACUAUCGGCUCAAGCCGAUGGAAGUGCGCGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACAGGGCCAGCGAGUACAUCACCUUGGCCGAGAGGUCCGGGUAAUCUUGUUAAACCCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUGCCUAGUAGGCACGAGUCAUCAGCUCGUGCCGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUCGGUGAGGCCUUCGGACUGGCCCAGGAGGGUUGGCAACGACCCCCCAGGGCCGGAAAGUUGGUCAAACCCGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq
new file mode 100644
index 0000000..cd73918
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.fundyense
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUCAAUUUUGUGAAACUGCAAAUGGCUCAUUAAAACAGUCACAAYGCAUUUGGCGAUCAAUUCUAAAUGGAUAUCUGUGGRAAUUCUAUAGUUAAUACAUGCACUAAAACUUAUCUUUGGGGAAAGGUUGUGGUCGUUAGUUACAGAACCAAUUCAAGCUAUGCUUGGACACUUGAAUGAUUCACAAUGACAAAUGAAUUACAUGGCAACAGCUGGUGAUAAUUCAUUCCAGUUUCUGACCUAUCAGCUUUCGACGGUAAGGUAUUGGCUUACCGUGGCAAUGACAGGUGACGGAGGAUUAGGGUUUGAUUCCGGAGAGGGAGCUUGAGAAAUGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGGCACAGGGAGGUAGUGACAAGAAAUAACAAUACAAGGCAUCCAUGUCUUGUACUUGGAAUGAAUGGAUUUUAAACCUUUCUAUAAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCGGUUAAAAAGCUCGUAGUUGGAUUUCUGCUGAGGAUGGCUGGUCCGCCCUCUGGGUGAGUAUUUGGCACAGCCUGAGCAUUUAUCUUGAAAGUACAACUGCACUUGACUGUGUGGUGUGUUAUUGAGAACAUUUACUUUGAGGAAAUCAGAGUGUUUCAAGCAGGUGUUUGGCCUUGAAUACAUUAGCAUGGAAUAAUAAUCAAGAUCGUGGUUCUUUUUUGUUGGUUUCUAGAAUUGAGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUCGUAUUUGAUUGUCAGAGGUGAAAUUCUUGGAUUUGUUAAAGACGGACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUUAAGGGAUCGAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACCAUGCCAACUAGAGAUUGGAGGUUGUUACUUGUAUGACUUUUUCAGCACCCUAUGCGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAAUGAGGAUUGACAGAUUGAUAGCUUUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGUUACAUGUAAUUUCGAUUAUGUGGGCAACUUCUUAGAGGGACKUUGUGUGUAUAAUGCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCUGCACGCGCGCUACACUGAUGUGUUCAACGAGUUUUCAACCUUGCCUGGAAAGGUUUGGUAAUUCUUGAACAGGCAUCGUGAUGGGGAUUGUUUAUUGCAAUUAUUAACCUUCAACGAGGAAUUCCUAGUAAGCUUGAGUCAUCAGCUUGUGCUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGARUGAUCCGGUGAAUAAUUUGGACUGUAGCAAUGUUCAGUUCUUGAACAAUGCAAUGGCAAAUUUAAUGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCUGUAGGUGAACCUGCAGAAGGAUCAAGC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq
new file mode 100644
index 0000000..1eb2af9
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.hermannii
+CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGGGGCAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGCAAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCAUUUAUAUGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGUGGCCCGUGCUGUGCGCGUAGUGCGUGCGGCGCUGGGGCGCGCUUUUGUGGAGGGCGGCGCGUCGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUACGAUGACCCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGCUACCAUUGUGUAGCUGCUUGUCCCUUCUUAGACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAGAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCUGGCCGCGGUGGAAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq
new file mode 100644
index 0000000..52c4664
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.invadans
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACAACUUUGUACUGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUCUACUCGACAGUACCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAUAAAUACCCAACUGCUUGUCGGACGGGUAGCAUUUAUUAGAUUGAAACCAAUUCACUUCGGUGAUUUUGUGUUGAAUCAUAAUAACUGUGCUGAUCGCUCUAAGCGAUAAGUCGAUUGAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGAUAUGGGCCUACCAUGGCGUUAACGGGUAACGGGGAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUUAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCUAAUUUAGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUUUGAGCGUCCGGUCGACGAAAUGUCAGUACUAUGGAUGUUUGGGCCAUAUUUUGUGAGGAUGCCUUUCUGCCAUUGAGUUGGUGGUUGGGUGGACUUGCAUCGUUUACUGUGAAAAAAUUAGAGUGUUUAAAGCAGGCGUUUGCUCAUUUGAAUACAUUAGCAUGGAAUAAUAAGAUACGACCUUGGUGGUCUAUUUUGUUGGUUUGCACGCCAGGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUCAUAUUUCAACGUCAGAGGUGAAAUUCUUGGAUCGUUGAAAGAUGAGCUUAGGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUCAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUGACCAUAAACUAUGCCGACUCGGGAUUGGCAGUCGUUUAAUUAGAAUGACCUUGUCAGCACCGUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCCGCGUGCUAAAUAGUCCUGCUUACCAAUUUGGUAGGUAAGGACUUCUUAGAGGGACUUUCAGUGACUAACUGAAGGAAGUUGGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGGUACGCUCAACGAGUAUAUAACCUUGAUCGAUAGGUCUGGGUAAUCUUUUGAAUACGUAUCGUGCUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAAGUCAUCAGCUUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGACUCGGUGAGAAAUUGGGACCGCUGUUUCGCUUGCUUCAUUGUGAGUGAAACGGUGGGAACUUUUUCUAACCUCGCCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq
new file mode 100644
index 0000000..9e4029d
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.kariana
+NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAAUCUUUUACUUUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAAUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAUCAAUACUCGACUCACGAAGAGUAGUAUUUAUUAGAUUGAAACCAACCGCUUCGGCGUGAUGUGGUGAUUCAUAAUAACUUUGCGAAUCGCAUGGUUUAACACCGGCGAUGGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGGAAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUAUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUGUGGUUGGAGAGCUCCUCCGUUCGCUUAGSUUCGUGCUGGAGCUUCUCCGUCCAUCCUUGGGUGGAUCCUGUGUGGCAUUCAGUUGUCGUGCAGGGGAUGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCUUGAAUAUAUUAGCAUGGAAUAAUGAGAUAGGACCUGGGUACUAUUUUGUUGGUUUGCGCACCGAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUUUGGAAGACGAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGUUGUUCGUUUUGACUCCGUCAGCACCUUAUGAGAAAUCACAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGUUGGGUGAAUGACUCGUUCAUUGACUACAGCUUCUUAGAGGGACGUUCAUCUCUUAAGAUGAAGGAGGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUGUUCCUUGGCCGAGAGGCCUGGGGAAUCUUGUUAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGACUGUUCUGCUUUAUUGUGGUCGGUUGCGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUCUCCGUAGGUGAACCUGCAGAAGGAUCAANNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq
new file mode 100644
index 0000000..e28f2e8
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.khaliulini
+UCCACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUCGAAGAUUAAGCCAUGCAAGUCUGUGAAUCUUUAUAGAGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCAUCGUGUGAACAUAACCAUGGUAAACUAUGGCUAAAUUGAUGGAUGAGGAUGUGACCUAUCAGCUUGACGGUACGGUAAGUGCGUACCGAGGCGAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAGCAUUUAUAUGUGGUAUGUUUAAAUAGCAUAUCGAAGUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAAUAGCGUCUGUGUUUAUUGCUGNGGUUAAAACGUGCGUAGUCUGGUUAAUGGCCUGAAGGUAACAUGCAUUUUCAUAGUGUAGGAUAUUUCAGGAACUUAUGCCUUGAGANAGGGAAGGGGUAAUGUUAUUUGGUAGCGAGAGGUGACAAUCGAUGACCUACCAAGGAGCGACAGAGGCGAAAGCGAUUACCAAUAACUGAUCUGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGAGGAUUAGAGACCCACGUAGUUCCUUGCAGUCAACGAUGCCAACGCUGUGGUGAUACUUGUCAUUGCAGAGGCGAAAGCUAGUGUAUGGGCUCCGGGGAUANUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCNGGUUAAUUUGACUCAACGCGGGAAAACUUACCCGGGCAGGCAAUUGUCGUGAGAAGCUAUUGUAGCUGAUGAUAUUGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGAGUGAUCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGAGUAUUUGGUUGAGAGACCAAAUAGACGGUGUCUGUAAAGACAAGGAAGCGACACCCAAUAACAGGUCUGUGAUGCCCGUAGAUGUCCGGGGCUCCACGCGCACUACAAUGGAUGGUAGUUUUUAUAAGCGGUAACCAUUCGUAGUUGGGAUUGACAUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACUAACGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGCGGGUGAAGAUGUGAGUGUAGACCAAUGGGAGGAUCAGUAUACUUGUGUGAGUUGAUUACGCUUGUGUAUUGUGACUGUUGUUAGCAUGAGCAUAAGAACCCGUGCAACUAGAUUGGAUGUAAGUCGUAACAAGGUAANCAUNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq
new file mode 100644
index 0000000..cd1bf7e
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.macrogynus
+UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUAAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGUUUAUACAAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAAUUUAUUUGAUAGUACCCUUUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCACAAAAGUCCUGACCUUUACGGAAGGGAUGCAGUUAUUAGAUACAAAACCAACCCGGGCAACCGGUUUUUUGGUGAUUCAUGAUAACUUUGCGGACCGCAUGGCCCUGCCGGCGGCGGGUCAUUCAAAUUUCUGCCCUAUCAACUGUCGAUGGUAGGAUAGAGGCCUACCAUGGUGAUAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACAAUAAAUAACGAUGCAGGACCUUUUGGUCUUUGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCAAGGGUUUUUUUCGUAGCUAGCCAUUGUUCCCUUUGCGGUCAAUGUGCAUUUGGCUACAGGCCCUUUUUUUCUGCUAGGAGAUGCGGCUCUUCUGCUUGUCAGCGGGGCUGCAGUUUUCCUAGCACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUUUUCUUUGCCUGAAUAUCUUAGCAUGGAAUAAUAGAAUAGGACUUUGGUUCUAUUUUGUUGGUUUCUAGGACUAGAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAGGAAAGACUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAAGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACGAUGCCGACCAGGGAUCGGGCGCUUGUAGUUUUUCCAAAAAGACACGCCCGGCACCUUUUGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUGGUAAGGAUUGACAGAUUGAAAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAUUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUUUCCUACUCGUUACUUGCUCAUGGGUUUUAUCUCAUGGCACGCAAGUUCUUAGCGGGACUGCUGGCGUUUAGCCAGAGGAAGUUCGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGCAGUCAGCAAGUUUUUUAACUGGCUGUAGUUCUUUCGGGAGCUAUGGUCGAUUUCCUUGCCCGAAAGGGUUGGGUAAUCUUUUGAAACUGCAUCGUGAUGGGGAUCGACCUUUGUAAUUAUCGGUCGUGAACGAGGAAUUCCUAGUAAGUGUGGGUCAUCAGCCCACGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGCUUAGUGAGAUUUUUGGAUUGUUGAGCGAUUGCAGCAAUGUGAACGCCCGACGAGAAAUUGAUCAAACUUGGUCAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq
new file mode 100644
index 0000000..8d7d7a0
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.majus
+NNNNNNNNNNNNNNNNNNNNNNNUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACCUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGACGCAUUUAUUAGAUAAAAGGUCGACACGGGCUCUGCCCGUUGCUGCGAUGAUUCAUGAUAACUUGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACUAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUACGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUCAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACUUUGGGUUGGGCCGGCCGGUCCGCCUCUGGUGUGCACCGGUCGUCUCGUCCCUUCUGCCGGCGAUGCGCUCCUGGCCUYAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUUAUAGGAUUUCGGUCCUAUUACGUUGGCCUUCGGGAUYGGAGUAAUGAUUAACAGGGACAGUYGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGGUAUCCCUCCGCGGCCAGCUUCUUAGAGGGACUACGGCCUUUUAGGCCGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUUAUAGCCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUGUUCGGAUCGCGGCGACGUGGGCGGUUCGCUGCCCGCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUGAGAGGAAGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq
new file mode 100644
index 0000000..8870493
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.michaelis
+NNNNNGGUUGAUUCUGCCUGACGUAGAACGCUAGUCUCACAGAUUCAGCCAUGCAAGUAGUAUGUAUGUAAUACACAAUGGCUCAGUAUCGAGUAUAGCUUUGCUCUCCAAGAUGUGAUACUUUCAGGAAACAGAAAAUAAAGCAUCUAUCUUCUAAAGUUUUUUAGAGGAGAGGAGAAGAAGCACUCACCUAUCAGUUAGUAGGUAUGGUAAGGGCAUACCUAGACGAAGACGGGUACGGGGAAGGCAACUUCGAUUCCGGAGAGGGCGCCUUUAGAGAUGGCGACCAGUUCUAAGGAGUGCAGCAGGCUCGAAACUUACCGAAUUAUAGAAUAGAGGUAGUGAUGGAAACGUUUAUAUAGAAAUACUGGUAAAGCAAGUAUUAUUAACUGAGGAAAGCUGGUGCCAGCAGCCGCGGUAAUACUUGCUCCAGGAGCUUAUUCGAUAUGUUGCGGUUAAAACGUCCGUAGUCGCGGCUGGGACUGACCUGUAAUCUAUUUGGUCAACAGAUAGAUAGGGGCAGUAGCAAGUUGGAAAAGAGCAAUUUGGUGUCAGCUAAUGGUAUGGGGAGGGGUAAAGUCUGAGGAUCCUGCAGGAGGAGCAAAGGCGUAAGCACUGACAAAGAUUGAUUCUGUUGAUCAAGGACAGAGGCUAGAGGAUCGAAUACGAUUAGAUACCGUAGUAGUUCUAGCAGUGACCGAUGAUGAUUUUGCCUUAUGCAAUAGAGAAAUCAAAAUAGAUCUCCGGGGAGUACAUGCGCACAGGAACUUAAGAAUUGACGGAAGCUAGCCACAAGGGUUGGAUUGUGCGGCUUAAUUUGACUCAAAGCGGAAAAGCUUACCAAGCUUAUUUAUUCAACGAGUAUUUAUCCGAGAGUAAAAUGGUGUGCAUGGCCGUUCCUAACACAUGGAGUGAUUUUGUGAUUAACCUUCCGUAAUCUGUGUAAAUCCUCAUAAUAGCUUGUUUGAAAAGAACAAUUCGAGCAAGAACAGGUCAGUGAUGUCCUUUGAUAGCUUGGGCUGCACGCGCAAUACAAUUUUUAUGUAGUAAGAUAUAGAUAGGGAUUGAGGGCUGAAAGCGCUCAUGAACACGGAAUAGCUAGUAACGUGAGUUCAAUAUACGGCGAUGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUGAUUUUUGAGUCAAUUAUAAUUGGCUACUUGAAUGAGUUAUUCUAAAACCGGUACAAGUCGUAACAAGGCUACGGUUGAAGAAUCAGCAGUAGGAUUAGCG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq
new file mode 100644
index 0000000..f9edb71
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.plicata
+CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUCGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGAUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGCAACGCGGGGUAACCCGUGGUACAAGUUAGAUAACAGGCCGACGCUUGACGAUUCAUAACUUUUUUUCUGAUCGCGCCUUGUGCGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGACGUGAAGGUAUUGUCUUCACGUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAAUAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGCUUGCGUAUGUCACCGAUGAUGCGGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGGGCGUCUGGCGGAGAGUAAAUCUUUGUCGGUCGCGCCUGCUUUUGUGGAGGGCGCGAGCGGGCGGCUUUACUGUCGCGCGUUCGCGGCGCCACCGUUUACUGUGAAUAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUUGUCCUUUUUGUUGGUUUGUGAGGCCGAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAGACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGACUGAAUUUGGCCCGCCCGGGACCCUCCGGGAAACCAAAGUGUUUGCUUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGGCGGGCUAUCGCUUGAUAGUACUGACCUUCCUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCCAACCCCCAAACCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUAUCCCUCUUGAACGAGGAAUACCUUGUAGGCGUGGGUCAUCAUCCCGCGCCGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGACUCGGGACCGCGCCGACUAGCGCGUCUAACGCGUUGGUUGUUGUGGAAACUUGUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq
new file mode 100644
index 0000000..88f7469
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.scoticae
+CACCAGGUUGAUUCUGCCUGACGUGUGUGCUAGUCUUGGGGACUUAGCCAUGCAAGCUAGCGAAGCGGAGCGGAGCGGCGGACGGCUCAGUAGGACGGCGAUAAUUCACCCGCGGCAGAAGAGGGAUAACCGCGGCAAGCUGCGGCUAAGACAAGGGAGGCUGUGUUGCGGGGAGGCGCACGCAGCGGACACGGCGGCGAAGAUGCCGACCUAUCAGCUAGUAGGUAGGGUAAGGGCCUACCUAGGCGACGACGGGUGACGGGGGGUGAGAGCCUGAUACCGGAGAGGGAGCCUGAGAAACAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUGCCCAAUCCCUACGGGGGGAGGCAGCUACAAGACGUGGGGAAGCCCCGGAAAGCACGGCAAAGGAGUGCGUAGCGACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGCACAUGUGUGUUGCUGCAGUUAAAACGUCCGUAGUCGGCCAUGAGGGGCAGUGAGGAAAGGGCUGUGCUCAAGGCGGUGUGCAGCGCGGGACCCGGGGCGAGAGGAACGGACGACGGGCGCGGGAUCUGGGGGCGAGAGGUGAAAAUCGGGGACCCUCUGGGGACGAGCGGAAGCGAAGGCGGCGCCCGAGGACGUGUCCGUUGAUCAAGGACGAAGGCCGGAGGAUCAAAGAUGAUUAGAGACCGUCGUAGUUCCGGCAGUAAACGAUGCCAACGGGGCGAAGCCAAGGGGCUGUGUCCGGGAGAAAUUGGAGUGUUUAGGCUCUGGGGAUAGUACGGUCGCAAGACAGAAACUUAAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAGCUUACCAGUGCCGCAUGCGCGGGAGAUUGGCGGCGGAGCGCCCCCGAGAUUGCGCAGGGAGUGGUGCAUGGCCGUUUGCAACACGUGGGGUGACCUGUCUGGUUGAUUCCGACAACGCGUGAGGCCUAGGGCGCAGGGCUGUGCGACGGGCCGCGGCAAGCGGCAGGAAGGGAGGCGAUAACAGGUCAGUGAUGCCCUCAGAUGCACUGGGCUGCACGCGCACUACAAUGGCGGGGCGAGACGGAGUGCCGAGAGGUGCGAAGGAGGCCUGGCUGCAGCGGGGAUGGGUGCCUGGAAGGGCGCCCUGAACGAGGAAUUCCUAGUAGCCGCGGGUCACCAAGCCGCGGCGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCACUACCUAAGAUGGAUGUGCAGGCGAGGUGGCUGGAGGGAAGGCAGCCGAGCCGGUGCAACUAGAUAAGGUAUAAGUCGUAACAAGGCUACGGUUGANNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq
new file mode 100644
index 0000000..54b1917
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.thaliana
+UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACGAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUAUGGAAGGGACGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGCCCGUUGCUCUGAUGAUUCAUGAUAACUCGACGGAUCGCAUGGCCUCUGUGCUGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUAACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACUGGGCUCUUUCGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGAUGGGUCGGCCGGUCCGCCUUUGGUGUGCAUUGGUCGGCUUGUCCCUUCGGUCGGCGAUACGCUCCUGGUCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGAUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUAUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAAUGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUCACACCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAGUGUUCGGAUCGCGGCGACGUGGGUGGUUCGCCGCCCGCGACGUCGCGAGAAGUCCACUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq
new file mode 100644
index 0000000..2598366
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq
@@ -0,0 +1,2 @@
+>d.16.e.A.verticilliflorum
+NNNNNNNNNGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUAAGAUGGUGAUACUGUGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUUUUUUCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAAUAAAUCUUGACUUUUGGAAGAGGAGCAUUUAUUAGAUAAGAGGUCAAUGCAAGCUUUGCUUGUUGCACUGAUGAUUCAUGAUAAUAGACGGAUCGCAUGGCCCCUGUGUCGGCGAUGCAUCAUUCAAGUUUCUGCCCUAUNAACUUUCGAUGGUAAGAUAUUGGCCUACUAUGGUGUUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUGCGGGGAGGUAGUGACAAAAAAUAACAAUACCGGGCUUUAACGAGUUUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAAUGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUUGGGUUGGGUUUGAUCGGUCUACCUUUGGGUGUGUACCGGUUACCUCGUCCCUCCUACCCAUGAUGCGCUUCUGGCCUUAAUUGGUCGGGUCGUGCCUUGGGUGCUGUUACUUUGAAGAAAUUAGUGUGCUCAAAGCAAGUUUGUGCUCUGGAUACAUUAGCAUGGGAUAACGUCAUAGGAUUUUGAUCCUAUUUGGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGUGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUACUUUUAGGACUCCGUUGGUACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCGUUAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGUGGAGGUACACCUUCAUGGGUAGCUUCUUAGAGGGACUAUGCCAACUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUUAUAGCCUUGACUAUUAGGUCUGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUUAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUUAUGGCGACGUNNNNGCUUUGCUGUCGGCGAUGUUGUGAGAAGUUCAUUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq
new file mode 100644
index 0000000..f2d9e72
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.bigemina
+UGAAUAGCAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUACAAGCUUUUUACGGUGAAACUGCGAAUGGCUCAUUACAACAGUUAUAGUUUCUUUGGAGUUCGUUUUCCAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACAAGUUCGAGGCCUUUUGGCGGCGUUUAUUAGUUCGUUAACCACUUUUUCUGGUGAUUCAUAAUAAACUUGCGAAUCGCUUUUGCGAUGUUCCAUUCAAGUUUCUGCCCCAUCAGCUUGACGGUAGGGUAUUGGCCUACCGAGGCAGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUUCGUCUUGUAAUUGGAAUGAUGGUGAUGUACAACCUCACCAGAGUACCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUAUUUCAGCCUCGCGUUUUUUCCCUUUUGUUGGGUCUUUUCGCUGGCUUUUUUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGACUUUUGUCUUGAAUACUUCAGCAUGGAAUAAUAGAGUAGGACCUUGGUUCUAUUUUGUUGGUUUUGAGCCUUGGUAAUGGUUAAUAGGAACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACCACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGGGAUUGGAGGUCGUCAUUUUCCGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAGAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGCUGCUUGGAUGUUGUCCUCGUUUGCUUCUUAGAGGGACUCCUGUGCUUCAAGCGUGGGGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUCCAUCGAGUUUGUCCUGUCCCGAAAGGGUUGGGUAAUCUUUAGUGUGCAUCGUGUCGGGGAUUGAUUUUUGCAAUUCUAAAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGGCUUUUCCGAUUCGUCGGUUUUGCCUAGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq
new file mode 100644
index 0000000..2c3855a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.bovis
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNUAGUCAUAUGCUUGUCUUAAAGACUAAGCCAUGCAUGUCUAAGUACCAGCUUGUUACGGUGAGACUGCGAAUGGCUCAUUACAACAGUUAUAGUUUCUUUGGAGUUCACUUUGCUAUGGAUAACCGCGCUAAUUGUGUGGCUAAUACACGUUUGAGGUUAUUACCGCGUUUACUGGUCUUGUGAUUUACAGUAACCUGCGACUCGCUUUUUGCGAUAUUCCAUUCAAGUUUCUGACCCAUCAGCUUGACGGUAGGGUAUUGGCCUCCCGAGGCAUCGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGCGAGACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUACCAAUACGGGGCUACUGCUCUGUAAUUGGCAUGGGGGCGACCUUCACCCUCGCCCGAGUACCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUACUUCACGUCCCCCGCUUGGUCCUUUCCUCGCCGGGACGCCUCGUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGUUUCGCCUGUAUAAUUGAGCAUGGAAUAACCUUGUAUGACCCUGUCGUACCGUUGGUUGACUUUGGGUAAUGGUUAAUAGGAACGGUUGGGGGCAUUCGUACUCGACUGUCAGAGGUGAAAUUCUUAGAUUUGUCGAUGACGCACGACUGCGAAAGCAUUUGCCAAGGACGCUUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCUUAAACUAUGCCGACUAGGGAUUGGUGGUCGUCGCCUCGACUCCGUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAGCGUAAGGAUUGACAGGUUGAUUGUCCUUUCUUGAUUCUCUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAUUUAGUCGCUCGGUCUCCGUCCGUGCGCACUUCAUAGAGGGACUCUGCGGCGUCAAGCUGCGGUGAGGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCUUGCCUCGUGUUUACCCUCGGCCGAUAGGCCUGGUAACCCCUAGUCUGCAUCGUGUUUGGGAUUGAUCUUUGCAAUUCUAGAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGAACCUGCUUGCGCGAUCCGUCGCCGCUCGCGGCCAGGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq
new file mode 100644
index 0000000..2699b8a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.canis
+NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACAAGCUUUUUACGGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGGUAUUCUUUUUCCAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACACGUUGGAGGCCUUUUGGCCGCGUUUAUUAGUUGUAAACCUCCGCUUGGUUUUCGGUGAUUCAUAAUAAACUUGCGAAUCGCUUUUAGCGAUGGACCAUUCAAGUUUCUGACCCAUCAGCUUGACGGUAGGGUAUUGGCCUACCGAGGCAGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUAAUGUCUUGUAAUUGGAAUGAUGGUGACUUAAACCCUCACCAGAGUAGCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUAUUUUUGCUUGGCGGUUUGUUGCCUUUGUGGCUUGAUUCCGCUUGGCUUUUGGCUUUUUGCCUUAUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGACUUUUGUCUUGAAUACUGUAGCAUGGAAUAAUAGAGUAGGACUUUGGUUCUAUUUUGUUGGUUUGGGAACCUUGGGUAAUGGUUANUAGGAACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGACGUUUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGUGAUUGGAGGUCGUCGUUUGUUUGACCCCUUCAGGAGCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAAACGGUAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGCGCUGGUUACUUGGUUUCCCGCUGCUUCUUAGAGGGACUUUGGGGCUUGAAGCUCCAAGGAAGAUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAUCGAGUGUUGCCCCUGGCCGAGAGGUCUGGGUAAUCUUUAGUAUGCAUCGUGACGGGGAUUGAUUUUUGUAAUUCUAAAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGGCUAUUCCGAUUCGUCGGUUUUGCCGUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq
new file mode 100644
index 0000000..dc4b931
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.coli
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUAACUACACAGUAAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUACAUUAAAUGGAUAACUGUAGAAAAACUAGAGCUAAUACAUGCCGAGGCCGUAAGGUCGUAUUUAUUAGAUAUUCCAAUUAAGGUGAAUCAUAAUAACUUCGCAAAUCGCGAUUUUGUCGCGAUAAAUCAUCCAAGUUUCUGCCCUAUCAUGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAUCUACGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUGGUGACAAGAUAUAACGACGCAAUUUAUUUUGUGAUUGUAGUGAGGGUAUUCCAAACCGAACCACUAGUACGAUUAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCAAGGCGUGUAUACUCUUUUUGAGUAUGCUACCUACUAGUCUCUGACUGUUACUGUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUUUGCAAGAAUACAUUAGCAUGGAAUAACGAAUGUGUCUAGAAUCUUGGUUAAUUCUAGAUUGCGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUGUUAAAGACUAACGUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGAUAGGGGAUCAAAGACAAUCAGAUACUGUCGUAGUCCUAUCUAUAAACUAUGCCGACUAGGGAUUGGAAUGGUUAUAACGCCGUUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGACUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAACCUGCUAACUAGUCUAAUCCAUUUUAUGGAAUAUGACUUCUUAGAGGGACUAUGUAUUUAAAUACAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAUAUGUCCUGGGCUGCACGCGUGCUACACUGAUGCAUACAACAAGUGCCUAGCCCGCCAGGGUAUGGCAAUCUCGAAUAUGCAUCGUGAUGGGGAUAGAUCUUUGCAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGUGCAAGUCAUCAUCUUGCAUUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUACCGGGUGAUCCGGUGAACCUUUUGGACCGCGAUGCGGAAAAAUAAGUAAACCAUAUCACCUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCANNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq
new file mode 100644
index 0000000..16f916b
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.emersonii
+UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUAAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGCUUUAUACAAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAAUUUAUUUGAUAGUACCCCAUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCACUCAAGUCCUGACCGCUUGUCGGAAGGGAUGCAGUUAUUAGAUACAAAACCAGCCCCGGGCAACCGGGUUUUCUGUUGGUGAUUCAUGCUAACUUUGCGGAUCGCAUAGCCUUUGUGCUGGCGACGGGUCAUUCAAAUUUCUGCCCUAUCAACUUUCGACGGUAGGAUAGAGGCCUACCGUGGUGAUAACGGGUAACGGGGAAUAAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACAAUAAAUAACGAUGCGGGGCCUUUUGGCCAUCGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCAGGGCUGUCUUUGUCACCUGGCCACUGAGCCUUURCGGCCAGUGUUGCUUUCGGGUGCGGGCCCUUUAUUUCUGCUGGGUGCUCCUUUGGGUUGGCUUUUGCUAGCUCGGGGGAUGUCUGCCCAGCACGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUUUUUUAAGCUUGAAUAUCUUAGCAUGGAAUAAUAGAAUAGGACUCUGGUUCUAUUUUGUUGGUUUCUGGGACUGGAGUAAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAGGAAAGACUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAAGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACGAUGCCGACCAGGGAUCGGGCGUCAUGUAGUUAUUCACAUAAAAGACGCGCCCGGCACCUUUUGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUGGUAAGGAUUGACAGAUUGAAAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAUUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUGAUCUGCUAAUUAGUUGGGCUUGCAUUUAUGCAAGUAAUCCAACUUCUUAGAGAGACUGCUGGCGUUUAGCCAGAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUAAGGUCAGCGAGUUUCAACUUGCUGGCUUAAGUUGAGUUUCGGCUCGGCUUAAGCUGGGAUUCCUUGGCCGUGAGGUCUGGGUAAUCUUUUGAAACCUUAUCGUGAUGGGGAUUGACCUUUGUAAUUAUCGGUCAUGAACGAGGAAUACCUAGUAAGUGUGGGUCAUCAACCCACGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGCUUAGUGAGAUUUUUGGAUUGCCGGGUGAUUGCAGCAAUGCGAACACUUGGCGAGAAAUUGCUCAAACUUGGUCAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq
new file mode 100644
index 0000000..3c16027
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.gelatinosum
+CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUACGACAAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAAAACGCGGGGUAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGCAAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGUGCGCGCCGGGCUGUGCGCGUAAUGCGUGUGGCGCGGGGCGUGCUUUUGUGGAGGGCGGCCGCUCGUGGCUUAACUGUUGCGGGUGUGCCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGUACCUAUUUUGUUGGUUUGUGAGGGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGUCCGGGACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGUUACCAUUGGUAGCUGUCGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAGAGCGUUUCCCAAUCCCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGACUUGGGACUGCUGCGAUCGGGGUUCAUUCUCUGGCCGCGGUGGGAACUUGUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq
new file mode 100644
index 0000000..76f7cfc
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.gibsoni
+NNNNNNNNNNNNNNNNNNNNNNNNNCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUUUUAUAUGGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAAAUUCGUUUCUACAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACAUGAUCGAGGUCCUUCUGGACUGCGUUUAUUAGACUCGAAACCUUCCCGCUUCGGCGGUUCCCGGUGAUUCAUAAUAAACAGCGAAUCGCAUGGCUUUUGCCGGCGAUAAUUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCAGCGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUACGGACACCGUGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUUAAGCUUUGUAAUUGGAAUGAUGGGAAUCCAAACCCCUUCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUCUGCCGCCGGGACUUCGUUCCCUUCGGGCUUCGUUUUCUCGGUGGCAUCCCUCUGGUUAAUUUGGGCCUCGGCCCUCUUUUUCCAGUUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUUUGCCUUGAAUACUUCAGCAUGGAAUAAUAAAGUAGGACUUUGGUUCUAUUUUGUUGGUUUCAGGACCAAAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGCUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACUAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAUUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAUAGUUAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGCAGCUGAGAAUAAACUUUGUUGUUUCAGCAUUGCUUCUUAGAGGGACUUUGCGGUCAUAAAUCGCAAGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAUCGAGUUUUAUCCUUGCCCGAAAGGGUUAGGUAAUCUUUAGUAUGCAUCGUGAUGGGGAUUGAUUAUUGCAAUUAUUAAUCAUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGACGUUUCUAAUUCGUUAGCAACGUCUAGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq
new file mode 100644
index 0000000..ee77a35
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.hamifera
+CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAACUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAAUUUCUUCGAUGGUAAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGGAACGCCGUGGUACAAAUUGGAUAUACAAACCAAUGUUUGGUGAUUCACAAUUUAUUUUCUGAUCGCACUUAUGUGCGACGCAUCGUUCAAAUUUCCGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCCAUCCGGACUCCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGCUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGCGGCGCGGGGCGUCCUCACGGACGGUUCUGCGGCGGCCGCCUUUGUGGAUGGGGGCUAGAGCGAUGUUUCAUUACAUUGCACUAGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAGUAAAUUAGCAUGGAGUAAUAGAAUAGGACCUGUGUUCUGUUUUGUUGGUUUGUGAGGCGCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGGGGCUGUUUUUGGCCCGCCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCGGUUACCGAUUUCUGGUAGCCAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGGGCGAAAGCUUUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGACAGACUGUGUUUCACGGACUGUCUGGCCCGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAAN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq
new file mode 100644
index 0000000..f71fd58
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.investiens
+NNNNNNNNNNNNNNNNNNNNNNNUAUAUGCUUGUCUAAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUCUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGCAACGCGGGGUAACCCGUGGUACAAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGAACGCAAGUUCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGGGCCCGGUGCUGUGCGCGUAAUGCGUGCGGCGCUUGGGCGCGCUUUUGUGGAGGGCGGCGCGUCGUGGCUUUGCUGUCGCGGUGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUGUCUAUUUUGUUGGUUUGUGAGGGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCAGGCAUUACGAUGACCUGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGUUACCAUUGGUAGCUGCUUGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUUUUAGGAUGCGCGAAAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGAUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCUGGCCGCGGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq
new file mode 100644
index 0000000..d4c4c9b
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.macrosporum
+CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUCUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGUUAUAGUUUCUUCGAUGUUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAUCACGCGGGGCAACCCGUGGUACGAAUCAGAUAUCAAACCAAUGUAUGGUGAUUCAUGAAUAUUUUUCGGAUCGCACUGUAUGGUGCGACACAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUAUCAUGGUUGUGACAGGUGACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAACUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGCAUAUGCGUCUUCUAAUUGGAAUGAGAACACGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUGUUGGCACGGGCCGGGCUGUGCGCGUCAUGCGUGCGGCCACGGGACGUGCUUUUGUGGAUGGCGGCCGCACGUGGCUUAAUUGUUGCGGGCGUGCCGGCGCCACCAUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACGUUAGCAUGGAAUAAUAGAAUAGGACUCGUUUCUAUUUUGUUGGUUUGUCAGUGGCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUCUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACUGCUGCGAAAGCGUUUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCGGGUACCCGUGUGGUAGCUGCUGCCCCUUCUUAGACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGGCCAACGGGUGAGGAUACGCGAGAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCUUUGGGACCGCCACGACCGGGGUUUACUCUCUGGCCGCAGUGGAAACUUAUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq
new file mode 100644
index 0000000..2225903
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.mandrillaris
+NNNNNNNNNNNNNNNNNNNNNNNUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACGGCGAGACUGCGGAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUUCCUUUAUUUUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCCCAAAGUCCCGACUGGGGGUCGCAAGGCUCUCUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCGAUGCAGGGUGGCUUGCUGCCCUGACCCAACGGUGAUUCAUAAUAACUCUAUCGAAUCGCACCAUGGUCCCCUCGUGGGAUCGGCGAUGCUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUCGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGUCUUGCAAAAAGACUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUCUCGGAGUGUUUGGCAGGGCUGGUCCGCCGAAAUAGGUGAGCACCGUCCUGCCCGCUCCUCUUGUCCGGGUUCUCAUCCCUGCUAUUCACUUAGUGGGGAACCAAAGGUUCUGUUCCCGCCCUCGGGUGGGGCAGGACUGGAGGCCCGGACCAUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGACAAGUCAAAACUGUCAUUGAAUAUAUUAGCAUGGGAUAAUGGAAUAAGCCUCUCUGCUUAUUUUGUUGGUUUCUAAGUAGGGAGAAAUGAUUGAUAGGGACAGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACCAGCGAUUGGGAGACGUUACACAUGCUGCCCAAAAGGCAGCAUGGAGGACUCCCCCAGCAGCUUGUGAGAAAUCAUAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGUCAUGCCAAUCCUGCUAUUCAAAACCAGGGGGUGAGCGCGGUGCGGUCGGCUCCAAUCUUCGGGUUGGGGUCGGUUCGUGCCCCUUGCCUUCUGGCGGUUGGAUUGGUAGAAGUACUUCUUAGAGGGACAAUCGGUGAUUAGCCGAGGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUUAAUUCAACGAGUGCCACACCUUGGCCGAAAGGUCUGGGUAAUCUUGUGAAAUUUAAUCGUGAUGGGGAUAGAUUAUUGUAAUUGUUAAUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUCUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUCUUCGGAGCUCGACCUCUCCGCGAUCCGGGCAACUGGGUCGUGAGGUUGGGCAAAGUCGAUUAAAUCUUACCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq
new file mode 100644
index 0000000..5e88cb9
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.mediterranea
+NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGCUUUAUACUGUGAACCUGCGGAUGGAUCAUUAUAUCAGUUAUAGUUUAUUUGAUAAUCUCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUAAACACCCAACCUCUGGACGGGUGGUAUUUAUUAGAUUGAAACCAAUAUGCUUCGGCAUUUUUGUGGUGAUUCAUAAUAACUUUGCGGAUCGCAUGGCCUUGAGCCGGCGACAGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUGACACGGCGUGGUCGUCUCAAUGAGUCUGUACCGUCGCAUGUGUCGCCAUCCUUGGUUAAAACUUGUCUGGCAUUAGGUUGUCGGGCUUGGGGAUAGCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCCGUUGAAUACAUUAGCAUGGAAUAAUAAGAUAAGACCCAGGUUCUAUUUUGUUGGUUUGCGUACCUAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUUGUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGACAAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUGGCGGUCGUUUUUCCGACUCCGUCAGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGGCGUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUUGGCGUAAUGAAUUUCAUUGCGUACAUCUUCUUAGAGGGACUUUGCGUGACUAACGCAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUAUAACCUUGACCGAGAGGCUGGGUAAUCUUUUAAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGUUCAUCAGACUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAAUUUCGGGACUGACUUUAGGUUGAUUUAUUUCGACUUAAGGUUGGGAACUUACUUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGUGAACCNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq
new file mode 100644
index 0000000..341c71c
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.microti.1
+NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUAUUUUACGCGUGGCGUUUAUUAGACUUUAACCAACCCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAAUUCGCUUCCGAGCGUUUUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUUCCCUUCGGGGUUCUAUUUUCCGGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGUACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq
new file mode 100644
index 0000000..e6f2747
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.microti.2
+NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCCUUUGGGAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGGCUUGGCAUCAUCUGGAUUUGGUGCCUUCGGGUACUGUUUCCAGGGUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAACCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAGCGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq
new file mode 100644
index 0000000..21c1754
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.microti.3
+NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUACGCGUGGCGUUUAUUAGACUUUAACCAGCCCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUUCGAGCGUUAUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUAUCCUUAAUUGGUUACUAUCUUCCAGUAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUAUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUAGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACUGAGAAACGUGGAUUCGUCCUUCGUUUUUCGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq
new file mode 100644
index 0000000..e92416b
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.microti.4
+NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGGCUUGGCAUCUUCUGGAUUUGGUGCCUUCGGGUACUAUUUUCCAGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUCGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq
new file mode 100644
index 0000000..ac524f3
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.microti.5
+NNNNNNNNNNNNNNNNNNNNNCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCUUCGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUGCCUUCGGGUACUAUUUUCCAGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUCGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq
new file mode 100644
index 0000000..f694c36
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.moritziana
+CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAAGACUAAGCCCUGCAAGUGCCUGUAUGAGUGUUUAUAUAACGAAACUGCGAAUGGCUCGGUAAAACAGUAAAAAUUUUUUCGGAGAAAAUACUACUCGGAUAACCGUAGUAAAGCUAGAGCUAAUACGUGCUACAAAAUGAGGCGAGCAAUCGUUCUCGUGGUACAAAAUAGAGAUACAACCCAGUUUUUACUGGUGAUUCAUACUUUUUUCUGAUCACACUUUUAUGUGUGUGACGCUCCGAUCAAAUUUCUGACCUAUCAACUAUGAUGGUAAGGUAGUGGCUUACCAUAGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGAACUUCGGGAGGUAGUGACAAGAAAUAGCAAUAGGGGGACCAAUGGUCUCUCUAAUUGGAAUGAAAACAAUGUAAACUCCUUAUUGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAACUUUGGCGAUGGUUGCUGAAACUCCGUAAGGAGAUUGAUGUAGCCUCGUCCUUGUGGAUUUUUGGGGGUGUGGUGGUACUUUAUUGUAUUGCUGCAUUUCCGCCACUGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAAGCGAUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUUCUGUUUUAUUGGUUUGUCUGUAUCAGGUAAUGAUUAACAGGGACGGUCGGGGGCAUUUGUAUUCCAGCGUUAGAGGUGAAAUUCUUGGAUCGUUGGAAGACAAACAGCUGCCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUGUAAACUAUGAGGCCUGGGGAUCGGGCGUGGCCUAUUGGUACGUUCGGCACCCUCCGGGAAACCAAAGCUUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGAAAAUGCUAUUAAACUGCGGUAGCAUCGAAAAUUUAAUCUUCUUAGACGGACUGUAGGCGUAUAGUCUAUGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAAUGGCUCAACGGGUGAGGUAGUGCGAAAGCAUGACCCAAUCUCUAAAUCCAUUCGUGCUGGGGAUAGAAGCUUGCAAUUAUCCUUCUUGAACGAGGAAUACCUUGUAAGCGCGAGUCAUCAUCUCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGAGCUGGGCGAAUUAGUGUUUAUUCACGAAUUUCCUGGUUUAAACUUGGUCAAACCUUACUACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq
new file mode 100644
index 0000000..e9dcbc1
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.ostreae
+NNNNNGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCCAAGUAUAAACACGUUUGUACUGUGAAACUGCAGAUGGCUCAUUAUAACAGUUAUAGUUUAUUUGACAUUGAACUGUUACACGGAUAACCGUAGUAACCUAGGGCUAAUACGUGACAAACCCUGCCUCGGCGGGAGUGCAUAUUAGCUGAAAACCAACUUUGGUUGAAUAAUAAUAUUUGUCGGAUCGCGUUGGCUUCGCCAGCGACAUGUCAUUCAAGUUUCUGACCUAUCAGCUUGACGGUAGGGUAUUGGCCUACCGUGGCUUUGACGGGUAACGGGGAAUGCGGGUUCGAUUCCGGAGAGGCAGCCUGAGAAACGGCUACCACAUCCACGGGAGGCAGCAGGUGCGCAAAUUACCCAAUUCUGACUCAGAGAGGUAGUGACAAGAAAUAACGAUAUGCGGCCAACUGGUUGCUUAUCCGGAAUGAGAACAAUGUAAAAACCUUAUCGAAUUCCAGCGGAGGGCAAGCCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCGCUAGCGUAUACUAAAGUUGUUGCUGUUAAAACGCUCGUAGUUGGAUAUCUGCCCCCGGGCCGGCCCGGUCGUCCGCGACCGCACACACGUGCAGAGCGGCCGCCCGGGGGCAUAAUUCAGGAACGCCGGUCUGGCCAUUUAAUUGGUCGGGCCGCUGGUCCUGAUCCUUUACUUUGAGAAAAUUAAAGUGCUCAAAGCAGGCUCGCGCCUGAAUGCAUUAGCAUGGAAUAAUAAGACACGACUUCGGCGCCGCCUCGGCGGUUGUUUUGUCGGUUUUGAGCUGGAGUAAUGAUUGAUAGAAACAAUUGGGGGUGCUAGUAUCGCCGGGCCAGAGGUAAAAUUCUUUAAUUCCGGUGAGACUAACUUAUGCGAAAGCAUUCACCAAGCGUGUUUUCUUUAAUCAAGAACUAAAGUUGGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCCAACCAUAAACGAUGUCAACUAAGCAUUGGGCUAUCAAACUUCCUCAGCACUUUUCGAGAAAUCAAAGUUUUCGGACUCAGGGGGAAGUAUGCUCGCAAGAGUGAAACUUAAAGGAAUUGACGGAAGGGCACCACAAGUUGUGGAGCCUGCGGCUUAAUUUGAUUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUAAAGUUCUUUCUUGAUUCUAUGCAUGGUGGUGCAUGGCCGUUCUUAGUCCCUAGGGUGACCCCUCUGGUUAAUUCCGAUAACGGACGAGACCCCACCCAUCUAACUAGCCGGCGCUAACCCGGCGCUCGGCGCCAGUUAGCGGGGUGCAGCAUUGCGCGCCCGGCUUCUUAGAGGGACUAUCUGUGUCUCCAGCAGAUGGAAGAUUGGGGCAAUAACAGGUCAGGAUGCCCUUAGAUGCUCUGGGCUGCACGCGCGCUACAAUGGUGCGUUCAACGAGUUUGACCCGGCUUGACAAGGCCGGGUAAUCUUCAACGCGCACCCAAGUUGGGAUAGAUGAUUGCAAUUGUUCAUCUUGAACAAGGAAUAUCUAGUAAACGCAAGUCAUCAACUUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUUCUACCGAUUGAAUAAUGAGGUGAAUUAGGUGGAUAAGAGCGCUCCGCGUUCUUAGAAGCUUCGUGAACCUUGUUAUUUAGAGGAAGGAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq
new file mode 100644
index 0000000..86d81a3
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.pacifica
+NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGCUUUAUACUGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAAUCUCUUACUACAUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUAAACACCCAACUGUUCGCGGACGGGUGGUAUUUAUUAGAUUGAAACCAAUAAGCUUCGGCUUUUUUGUGGUGAUUCAUAAUAACUUUGCGGAUCGCAUGGCCUCGAGCCGGCGACAGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUGAGUUCGUUUGGCCGGCCGUAAAGGUCUGUGCCGAAAUGUUAUUCGCCAUCCUUGGUGUAAUCUUGUCCGCCAUUAAGUUGUGUGGGCUUGAGGAUGCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCCGUUGAAUACAUUAGCAUGGAAUAAUAAGAUAGGACCCUGGUACUAUUUUGUUGGUUUGCGUACCUAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUUGUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGACAAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUGGCGGUCGUUUUUCUGACUCCGCCAGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUUGGCGCGAAUGAAUUUCAUUCCGUACAUCUUCUUAGAGGGACUUUGCGUGACUAACGCAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUAUAACCUUGCUCGAGAGGGCUGGGUAAUCUUUUAAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGUUCAUCAGACUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAAUUUCGGGACUGAUCGUUUGGUGGUUCAUUCUGCCUUACGAUCGGGAACUUACUUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq
new file mode 100644
index 0000000..8e89a0b
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.plumatellae
+CACCAGGUUGAUUCUGCCUGACGUAUGCGCUUGUCUUGAAGAUUUAGCCAUGCAAGCCAGUGACCGUAAGGAACGGCAGACAGCUCAGUAAUACAGUUAUAAUUUACUCGUAGGAUAUGGAUAACCAUGGAAAACUAUGGCUAAAACAUAGGGAAAAUACCGUCACAGGGAAUUUUGAGGUACUUGAUACGAUUAAGUUUCUGACCUAUUAGCUAGAUGGUAAGGUAAAGGCUUACCAUGGCUGUGAUGGGUAACGGGGGAUUAACGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCUAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUUCCUUAUCGGGAGAGGUAGUGAAGAGACGUGGAAUAUAAUUUAGCGAGGGCAUAUUAAAUGGCAGCCUGUAAACUGGAGGGCAAGCCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAACUAUUGUUGCUGUUAAAACGUCCGUAGUAGAUUAUGCUGUUACUAUGACAAAAAUGUAUAUCUCAAAUGAAAUAUAUAGCAUAGUACAAAGUAAAGAUAGGAACAGAUGAUGGCAGCAGUAUUUAAUAGUUAGAGGUGAAAAUCGAAGACCUAUUAAGGACUAUCAGAAGCGAAAGCGGCUGUCAAGGAUGUCUCCGUUUAUCAAGGACUCAAGCUGGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCCAGCUGUAAACCAUGCCAACUAGGUGAGGCCAUUAGGCUACGCCUUAGGAGAAAUCAAAGUUUUUGGGCUCAGGGGAUAGUACGAAAGCAAUUUUGAAACUUAAAGAGAUUGACGGAAGGAUACCACAAGGAUUGGAUUGUGCGGCUUAAUUUGACUCGACGCGGGACAACUUACCAGGGCCGAAUGUCUAUGAGAUUGGCGAUUUGAGAGAAUUCCCGAGAUUAGACAAAGGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACCUGUCAGGUUAAUUCCGAUAACGCGUGAGGCCCUAAAUGCAACAGUGUUGUAUGACGGACAGUGCAAACUGUAGGAAGGAGGGCGAUAACAGGUCAGUGAUGCCCCCAGAUGUUCUGGGCUGCACGCGCAAUACAAUAUAUGAAAUAGAAUAGAGUGUGAAAACACAUCAUUAAAUUCAUAUGUACCAGGGAUAAGCGCUUGUAAAUGCGUUUUGAACAUGGAAUUCCUAGUAAUCGCAGGUCAUUAUGCUGCGAUGAAUGUGUCCCUGUUCUUCGUACACACCGCCCGUCACUAUCUUAGAUGAAUGUAUAGGUGAAAUGGCUGGACGAAAGAAAGGCAGUUGAACCUGUGCAAUUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGGAGAACCUGUGGCAGGAUCAAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq
new file mode 100644
index 0000000..0f910b0
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq
@@ -0,0 +1,2 @@
+>d.16.e.B.rodhaini
+NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUUUUAUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCAUGUGCGUUUACGCAGCGUUUAUUAGACUAAACCAUCCCCUUUGGGUACCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUAACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUCAAAGCUUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUCGUCGUUUAUGCUCGCUUCCAAGCGUUUGUAAUUGACUUGGCAUCUUUGUGGAUUAGUGCGCAAGCAUUUUUCCACUAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAAUUGCCUUGAAUACUACAGCAUGGAAUAAUAAAGUAGGACUUUGGUUCUAUUUUGUUGGUUUUUGAGCCAUAGUAAUGGUUAAUAGGAGCAGUAGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAAAUGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUAUGGGACUACAUUUCAGUCUCAUUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUCCUUGGCCGGAAGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACUGAAGAACUUAGAUUCGUCUAAAGUUUUUUGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCNNNN
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq
new file mode 100644
index 0000000..7343a20
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq
@@ -0,0 +1,2 @@
+>d.16.e.G.vagum
+CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAACUCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAGGCAACUUUUGUCGUGGUAUAAAUUGGAGAUACAAACCAAUAUUUGGUGAUUCACGAUUUCUUUUCUGAUCGCACUAUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAACUUGGCGGGCGACGCAGGGCGUCUUUGCGGACGGUUCUGUAUCGGCCGCCUUUGUGGAGGGGGGCUUAGCGGUGCUUUAUUGCCUUGCUAAGUCGCUGCCACCGUUUACUGUGAAAAAAUUGGAGUGUUCAAAGCAGGCGUUUGCCUUGUACACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUUCUGUUUUGUUGGUUUGUGAGAAUUAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCUGCCGUCAGAGGUGAAAUUCUUAGAUUGGCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGGCGCUGCUUUAUGGCCCGCCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCGUUACCUCUUUCGGUAGCGAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUAGGCGAGAGCCUUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGUCGGACUGUGUUUUACAGACCAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGACCCUGCAGAAGGAUCAAGC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq
new file mode 100644
index 0000000..acaa018
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq
@@ -0,0 +1,2 @@
+>d.16.e.G.vavrai
+CACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUUAAAGAUUAAGCCAUGCAAGCCAGCGAAGGUAACGGAGCGGCGAACGGCUCAGUAGGACAGGGUUAUCUGACCACCGAACAGGAUAACCGCGGUAAUCUGUGGCUAAUACGUGUGUGGGUGAGACUCUGCCCUAUCAGCUUGGGGGUACGGUAAGUGCGUACCCUUGCGACGACGGGUAACGGGAAAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCACGUCCAAGGAUGGCAGCAGGCGCGGAAAUUACCCACUUGGAGGACCAGAGGUAGUGACGAGGCGUUUUUAAUGAGAAUAGUGUAAAAAGCUGUUCGAAAGCAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGUCUGCGUGUGUUGCUGCGGUUAAAGAGUGCGUAGUCGGGUUAUUUGCCAGCAAUAAAGGUGCAGUCUCUAACUGUAUAUUGUGCUGGUACUUUGAUCUAGGAACUGGAUAAAGGUUAUGGUAUUCGACAGCGAGGGGUGAAAAUUAAUGACCUGUUGAGGAGCGACUGAUGCGAAAGCGGUAAUCUAUGACGGGUUUGACGAUAAAGCGCGUAGGCAGGAGUAUCGAAGGCGAUUAGAGACCGUCGUAGUUCUUUGCAGUAAACGAUGCCAACAGGAAUGCAAGUGCUGUGUUCCUAGGGAAACUGAGUGUAUGGGCUCUGGGGAUAGUACAGGCGCAAGCUAGAAACUUGAGGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGACAACUUACCAGGGUAUGUGACAUUGAGCGAAGAGCAUGGAUGCGAUCUGUGUUCUGAUGAUGUUACGUGUGGUGCAUGGCCGUUCUUAACACGUGGGGUGACCUGUCUGGUUAAAUCCGAUAACGCGUGAGACCCUGGAUAAUGACGAUACUUGACAAGAGUAGGGAAGCUCGGGUCGAUAACAGGUCUGUGAUGCCCAUAGAUAUUUUGGGCGCCACGCGCACUACAUUGGGGAUGGUUACGUGAAACGGAACAUCCUUUCGGUUGGGAUUGACGUUUGUAAAUACGUCAUGAACUCGGAAUUCCUAGUAAUUUGUUGUCAUUAACGACAUAUGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGAAUGUGCGGAUGAAGUUGGUUAGGUCAAAAGAAUCCGUGCGAUUAGAUUGGAUACAAGUCGUAACAAGGUUACUGUAGGAGAACCUGCAGUAGGAUCAAUAA
diff --git a/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm
new file mode 100755
index 0000000..41ffe28
--- /dev/null
+++ b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm
@@ -0,0 +1,60 @@
+#!/usr/bin/perl
+package Scoregtwithunafold;
+use strict;
+use warnings;
+use File::Basename;
+
+sub test()
+{
+  my(%Config) = %{$_[1]};
+  my(%Sequences) = %{$_[2]};
+  my $logger = $_[3];
+
+  my $gtdir = $Config{"G_GTFOLD_DIR"};
+  my $unadir = $Config{"G_UNAFOLD_DIR"};
+  my $workdir = $Config{"G_WORK_DIR"};
+
+  my $key;
+  my $value;
+
+  while (($key, $value) = each(%Sequences)) {
+
+	  my $seqname=$key;
+	  my $path;
+	  my $suffix;
+
+	  my $seqfile = $value;
+	  my $gtout  = "$workdir$seqname-gt";
+	  my $unaout = "$workdir$seqname-una";
+	  my $gtoutfilename  = $workdir."$seqname-gt.ct";
+	  my $unaoutfilename = $workdir."$seqname-una.ct";
+
+	  my $gtcmd = "$gtdir/gtfold -m $seqfile --unafold -o $gtout > /dev/null";
+	  my $unacmd = "$unadir/hybrid-ss-min -s DAT $seqfile -o $unaout > /dev/null";
+	
+	  system("$gtcmd");
+	  system("$unacmd");
+	  my $gtfold_energy = `head -1 $gtoutfilename`;
+	  my $unafold_energy = `head -1 $unaoutfilename`;
+
+    if ($gtfold_energy =~ m/([0-9.-]+$)/) {
+      $gtfold_energy = $1;
+    }
+    if ($unafold_energy =~ m/dG = ([0-9.-]+)/) {
+      $unafold_energy = $1;
+    }
+
+    if ($gtfold_energy eq $unafold_energy) {
+      $logger->info("TEST PASSED: $seqname: Energy Value matched for MFE -> $gtfold_energy");
+    }
+    else {
+      $logger->error("TEST FAILED: $seqname: Energy Value Not Matched for MFE -> gtfold = $gtfold_energy, unafold = $unafold_energy");
+    }
+    #my $ctcmd1 = "/usr/local/bin/ct-energy $gtoutfilename";
+	  #my $ctcmd2 = "/usr/local/bin/ct-energy -s DAT $unaoutfilename";
+	  #system("$ctcmd1");
+	  #print "ct-energy = ";
+	  #system("$ctcmd2");
+  }
+}
+1;
diff --git a/gtfold-mfe/tests/scripts/start_test.pm b/gtfold-mfe/tests/scripts/start_test.pm
new file mode 100755
index 0000000..16e53c3
--- /dev/null
+++ b/gtfold-mfe/tests/scripts/start_test.pm
@@ -0,0 +1,94 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use Module::Load;
+
+use File::Basename;
+use File::Path;
+use Log::Log4perl qw(:easy);
+
+require 'test_utils.pl';
+
+my $configdir="../config";
+Log::Log4perl::init( "$configdir/root-logger.conf" );
+my $logger = Log::Log4perl->get_logger;
+
+$logger->info("Starting Tests...");
+
+# Read Parameter File
+my $paramfile = "$configdir/test-params.conf";
+
+# Create Work Directory
+my $workdir = "../work";
+$logger->info("Deleting directory $workdir");
+rmtree($workdir, 0, 1);
+$logger->info("Creating work directory $workdir");
+mkdir $workdir;
+
+my %Config;
+
+%Config = load_config_file($paramfile);
+
+###### Prepare a Hashmap of Sequences ######
+
+my %Sequences;
+my @seqdir_arr = @{$Config{"G_SEQUENCE_DIR"}};
+
+my $seq_include_regex = $Config{"G_INCLUDE_SEQUENCES"};
+my $seq_exclude_regex = $Config{"G_EXCLUDE_SEQUENCES"};
+
+foreach (@seqdir_arr) {
+
+  opendir(DIR, $_) || die $!;
+  while (my $seqfile = readdir(DIR)) {
+
+	  my $seqname;
+	  my $path;
+	  my $suffix;
+	  ($seqname,$path,$suffix) = fileparse($seqfile);
+
+	  if (-d $seqfile) {
+		  next;
+	  }
+
+    $seqfile = "$_$seqname";
+    my $seq_include = (not defined($seq_include_regex)) || ($seqname =~ /$seq_include_regex/);
+
+    my $seq_exclude = (not defined($seq_exclude_regex)) || ($seqname !~ /$seq_exclude_regex/);
+    if ( $seq_include && $seq_exclude ) {
+      $Sequences{$seqname} = $seqfile;
+      $logger->info("Selected Sequence ... $seqname");
+    }
+  }
+}
+
+my $test_include_regex = $Config{"G_INCLUDE_TESTS"};
+my $test_exclude_regex = $Config{"G_EXCLUDE_TESTS"};
+
+my $test_list_file = $Config{"G_TEST_LIST_FILE"};
+
+open(TESTLISTFILE, $test_list_file) || die("Could not open file: $test_list_file");
+
+  while (<TESTLISTFILE>) {
+
+      my $testname = $_;
+      chomp($testname);
+
+      $testname =~ s/^\s*//;     # Remove spaces at the start of the line
+      $testname =~ s/\s*$//;     # Remove spaces at the end of the line
+      if ( ($testname !~ /^#/) && ($testname ne "") ) {    # Ignore lines starting with # and blank lines
+
+      my $test_include = (not defined($test_include_regex)) || ($testname =~ /$seq_include_regex/);
+
+      my $test_exclude = (not defined($test_exclude_regex)) || ($testname !~ /$test_exclude_regex/);
+
+      if ( $test_include && $test_exclude ) {
+        my $module = $testname;
+        load($module);
+        $module->test(\%Config, \%Sequences, $logger);
+      }
+    
+    }
+
+  }
+
diff --git a/gtfold-mfe/tests/scripts/test_utils.pl b/gtfold-mfe/tests/scripts/test_utils.pl
new file mode 100755
index 0000000..2191bdf
--- /dev/null
+++ b/gtfold-mfe/tests/scripts/test_utils.pl
@@ -0,0 +1,84 @@
+#!/usr/bin/perl
+use strict;
+use File::Path;
+
+sub load_config_file()
+{
+  my $paramfile = $_[0];
+  my %Config;
+  my $Name;
+  my $Value;
+  my $line;
+  my $orig_value;
+  open(PARAMFILE, $paramfile) || die("Could not open file: $paramfile");
+
+  while (<PARAMFILE>) {
+
+    my $line = $_;
+    chomp($line);
+
+    $line =~ s/^\s*//;     # Remove spaces at the start of the line
+    $line =~ s/\s*$//;     # Remove spaces at the end of the line
+    if ( ($line !~ /^#/) && ($line ne "") ) {    # Ignore lines starting with # and blank lines
+      ($Name, $Value) = split (/=/, $line);    # Split each line into name value pairs
+
+      if ($Name =~ /G_INCLUDE_SEQUENCES|G_EXCLUDE_SEQUENCES|G_INCLUDE_TESTS|G_EXCLUDE_TESTS/) {
+        $orig_value= %Config->{$Name};
+        $Value =~ s/[.]/\\./g;
+        $Value =~ s/[*]/.\*/g;
+        if ($orig_value ne "") {
+          $Value = $orig_value."|".$Value;
+        }
+      }
+
+      if ($Name eq "G_SEQUENCE_DIR") {
+        my @seqdir_arr = %Config->{$Name};
+        push (@{%Config->{$Name}}, $Value);
+        next;
+      }
+
+      %Config->{$Name} = $Value;     # Create a hash of the name value pairs
+
+    }
+  }
+
+  $Value = %Config->{"G_INCLUDE_SEQUENCES"};
+
+#  printf($Value."\n");
+#  if ("rad" =~ /\G$Value/) {
+#    printf("matched1\n");
+#  }
+#  printf($Value."\n");
+#  if ("a.a.dvdsf" =~ /\G(rad|a\..*)/g) {
+#    printf("matched2\n");
+#  }
+#  printf($Value."\n");
+#  if ("daf" =~ /\G$Value/) {
+#    printf("matched3\n");
+#  }
+#  printf($Value."\n");
+#  if ("d.afdsf" =~ /\G$Value/) {
+#    printf("matched4\n");
+#  }
+#  printf($Value."\n");
+#  if ("acc1" =~ /\G$Value/) {
+#    printf("matched5\n");
+#  }
+#  printf($Value."\n");
+#  if ("acc11" =~ /\G$Value/) {
+#    printf("matched6\n");
+#  }
+#  printf($Value."\n");
+#  if ("a..afjlhfj" =~ /\G$Value/) {
+#    printf("matched7\n");
+#  }
+#  printf($Value."\n");
+#  if ("afdjs" =~ /\G$Value/) {
+#    printf("matched8\n");
+#  }
+
+#  printf ("@{%Config->{'G_SEQUENCE_DIR'}}\n");
+
+  return %Config;
+}
+1;

From f7923e671690bbe3cf7561a8304c18f1e7ba0d1d Mon Sep 17 00:00:00 2001
From: Manoj Soni <manoj6891@gmail.com>
Date: Sat, 1 Oct 2011 17:46:55 -0400
Subject: [PATCH 241/282] Partition Function calculation implementation
 completed

---
 gtfold-mfe/src/partition-func.c | 443 ++++++++++++++++++++++++++++++--
 1 file changed, 423 insertions(+), 20 deletions(-)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index 215b1ba..23ff1c9 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -1,4 +1,6 @@
 #include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include "partition-func.h"
 #include "energy.h"
 #include "algorithms-partition.h"
@@ -9,7 +11,7 @@
 #include "omp.h"
 #endif
 
-#define DEBUG_PF 1
+//#define DEBUG_PF 0
 
 #ifdef DEBUG_PF 
   #undef Ec
@@ -62,6 +64,58 @@ static void calc_s2(int i, int j);
 static void calc_s3(int i, int j);
 static double f(int j, int h, int l);
 
+static double get_u(int i, int j);
+static double get_ud(int i, int j);
+static double get_up(int i, int j);
+static double get_upm(int i, int j);
+static double get_u1(int i, int j);
+static double get_u1d(int i, int j);
+static double get_s1(int i, int j);
+static double get_s2(int i, int j);
+static double get_s3(int i, int j);
+
+
+static void set_u(int i, int j, double val);
+static void set_ud(int i, int j, double val);
+static void set_up(int i, int j, double val);
+static void set_upm(int i, int j, double val);
+static void set_u1(int i, int j, double val);
+static void set_u1d(int i, int j, double val);
+static void set_s1(int i, int j, double val);
+static void set_s2(int i, int j, double val);
+static void set_s3(int i, int j, double val);
+
+
+void errorAndExit(char* msg, int i, int j, double oldVal, double newVal){
+	printf(msg);
+	printf("i=%d,j=%d,oldVal=%0.1f,newVal=%0.1f\n",i,j,oldVal,newVal);
+	printf("\nprogram is exiting now due to above error\n");
+	exit(-1);
+}
+
+double get_u(int i, int j) {if(u[i][j]==-1) errorAndExit("get_u entry is -1.",i,j,-1,0); return u[i][j];}
+double get_ud(int i, int j) {if(ud[i][j]==-1) errorAndExit("get_ud entry is -1.\n",i,j,-1,0); return ud[i][j];}
+double get_up(int i, int j) {if(up[i][j]==-1) errorAndExit("get_up entry is -1.\n",i,j,-1,0); return up[i][j];}
+double get_upm(int i, int j) {if(upm[i][j]==-1) errorAndExit("get_upm entry is -1.\n",i,j,-1,0); return upm[i][j];}
+double get_u1(int i, int j) {if(u1[i][j]==-1) errorAndExit("get_u1 entry is -1.\n",i,j,-1,0); return u1[i][j];}
+double get_u1d(int i, int j) {if(u1d[i][j]==-1) errorAndExit("get_u1d entry is -1.\n",i,j,-1,0); return u1d[i][j];}
+double get_s1(int i, int j) {if(s1[i][j]==-1) errorAndExit("get_s1 entry is -1.\n",i,j,-1,0); return s1[i][j];}
+double get_s2(int i, int j) {if(s2[i][j]==-1) errorAndExit("get_s2 entry is -1.\n",i,j,-1,0); return s2[i][j];}
+double get_s3(int i, int j) {if(s3[i][j]==-1) errorAndExit("get_s3 entry is -1.\n",i,j,-1,0); return s3[i][j];}
+
+
+void set_u(int i, int j, double val) {if(u[i][j]!=-1 && u[i][j]!=val) errorAndExit("set_u entry is not -1.\n",i,j,u[i][j],val); u[i][j]=val;}
+void set_ud(int i, int j, double val) {if(ud[i][j]!=-1 && ud[i][j]!=val) errorAndExit("set_ud entry is not -1.\n",i,j,ud[i][j],val); ud[i][j]=val;}
+void set_up(int i, int j, double val) {if(up[i][j]!=-1 && up[i][j]!=val) errorAndExit("set_up entry is not -1.\n",i,j,up[i][j],val); up[i][j]=val;}
+void set_upm(int i, int j, double val) {if(upm[i][j]!=-1 && upm[i][j]!=val) errorAndExit("set_upm entry is not -1.\n",i,j,upm[i][j],val); upm[i][j]=val;}
+void set_u1(int i, int j, double val) {if(u1[i][j]!=-1 && u1[i][j]!=val) errorAndExit("set_u1 entry is not -1.\n",i,j,u1[i][j],val); u1[i][j]=val;}
+void set_u1d(int i, int j, double val) {if(u1d[i][j]!=-1 && u1d[i][j]!=val) errorAndExit("set_u1d entry is not -1.\n",i,j,u1d[i][j],val); u1d[i][j]=val;}
+void set_s1(int i, int j, double val) {if(s1[i][j]!=-1 && s1[i][j]!=val) errorAndExit("set_s1 entry is not -1.\n",i,j,s1[i][j],val); s1[i][j]=val;}
+void set_s2(int i, int j, double val) {if(s2[i][j]!=-1 && s2[i][j]!=val) errorAndExit("set_s2 entry is not -1.\n",i,j,s2[i][j],val); s2[i][j]=val;}
+void set_s3(int i, int j, double val) {if(s3[i][j]!=-1 && s3[i][j]!=val) errorAndExit("set_s3 entry is not -1.\n",i,j,s3[i][j],val); s3[i][j]=val;}
+
+
+
 double f(int j, int h, int l){
 	if(j - 1 == l)
 		return 1;
@@ -69,6 +123,37 @@ double f(int j, int h, int l){
 		return exp(-Ed3(h,l,l+1)/RT);
 }
 
+void printMatrix(double** u, int part_len){
+  int i,j; 
+  for (i = 0; i <= part_len+1; ++i)
+  {
+    for (j = 0; j <= part_len+1; ++j)
+      printf("%0.1f ",u[i][j]);
+    printf("\n");
+  }
+}
+
+void printAllMatrixes(){
+  printf("\n\nAfter calculation, u matrix:\n\n");
+  printMatrix(u,part_len);
+  printf("\n\nAfter calculation, ud matrix:\n\n");
+  printMatrix(ud,part_len);
+  printf("\n\nAfter calculation, up matrix:\n\n");
+  printMatrix(up,part_len);
+  printf("\n\nAfter calculation, upm matrix:\n\n");
+  printMatrix(upm,part_len);
+printf("\n\nAfter calculation, u1 matrix:\n\n");
+  printMatrix(u1,part_len);
+printf("\n\nAfter calculation, u1d matrix:\n\n");
+  printMatrix(u1d,part_len);
+printf("\n\nAfter calculation, s1 matrix:\n\n");
+  printMatrix(s1,part_len);
+printf("\n\nAfter calculation, s2 matrix:\n\n");
+  printMatrix(s2,part_len);
+printf("\n\nAfter calculation, s3 matrix:\n\n");
+  printMatrix(s3,part_len);
+
+}
 
 void calculate_partition(int len) 
 {
@@ -76,15 +161,21 @@ void calculate_partition(int len)
   part_len = len;
   create_partition_arrays();
   init_partition_arrays();
-  fill_partition_arrays();
 
-  for (i = 0; i <= part_len+1; ++i) 
+  /*printf("\nAfter initialization but before calculation, u matrix:\n\n");
+  for (i = 0; i <= part_len+1; ++i)
   {
     for (j = 0; j <= part_len+1; ++j)
       printf("%0.1f ",u[i][j]);
     printf("\n");
   }
 
+  printf("%4.4f\n",u[1][part_len]);*/
+
+  fill_partition_arrays();
+
+  //printAllMatrixes();
+
   printf("%4.4f\n",u[1][part_len]);
 }
 
@@ -112,9 +203,95 @@ void init_part_arrays_zeros(){
   }
 }
 
+void init_part_arrays_ones(){
+  int i,j,n;
+  n = part_len+1;
+  for(i=0; i<=n; ++i){
+    for(j=0; j<=n; ++j){
+      u[i][j]=1;
+      up[i][j]=1;
+      upm[i][j]=1;
+      ud[i][j]=1;
+      u1d[i][j]=1;
+
+      s1[i][j]=1;
+      s2[i][j]=1;
+      s3[i][j]=1;
+      u1[i][j]=1;
+    }
+  }
+}
+
+
+void init_part_arrays_negatives(){
+  int i,j,n;
+  n = part_len+1;
+  for(i=0; i<=n; ++i){
+    for(j=0; j<=n; ++j){
+      u[i][j]=-1;
+      up[i][j]=-1;
+      upm[i][j]=-1;
+      ud[i][j]=-1;
+      u1d[i][j]=-1;
+
+      s1[i][j]=-1;
+      s2[i][j]=-1;
+      s3[i][j]=-1;
+      u1[i][j]=-1;
+    }
+  }
+}
+
+void init_partition_arrays()
+{//ERROR_FOUND first nested for loop was wrongly written and iterated
+  //init_part_arrays_zeros();
+  //init_part_arrays_ones();
+  init_part_arrays_negatives();
+
+  int i, j;
+  int n = part_len;
+  for(i=1; i<=n; ++i){
+    for(j=i; j<=i+TURN && j<=n; ++j){ //if(j>n)continue;
+      u[i][j] = 1;
+      up[i][j] = 0;
+      ud[i][j] = 0;
+      u1[i][j] = 0;
+      u1d[i][j] =0 ;
+      s1[i][j] = 0;
+      s2[i][j] = 0;
+      s3[i][j] = 0;
+    }
+  }
+  for(i=1; (i+TURN)<=n; ++i){
+    //s1[i][i+TURN] = 0;
+    //s2[i][i+TURN] = 0;
+  }
+
+  for(i=1; (i+TURN+1)<=n; ++i){//ERROR no need to do this as it will already be calculated as zero only
+    //s1[i][i+TURN+1] = 0;
+    //s2[i][i+TURN+1] = 0;
+  }
+
+  /*for(i=1; i<=n-4; ++i){
+    s1[i][i+4] = 0;
+    s2[i][i+4] = 0;
+  }*/
+  for(i=1; i<=n; ++i){
+    u[i+1][i] = 1;
+    u1[i+1][i] = 0;
+    u1d[i+1][i] = 0;
+  }
+  for(i=1; i<=n-1; i++){
+    u1[i+2][i] = 0;
+  }
+  
+}
+
+/*
 void init_partition_arrays()
 {
-  init_part_arrays_zeros();
+  //init_part_arrays_zeros();
+  init_part_arrays_negatives();
 
   int i, j;							
   int n = part_len;
@@ -142,8 +319,8 @@ void init_partition_arrays()
   for(i=1; i<=n-1; i++){
     u1[i+2][i] = 0;
   }
-}
-
+}*/
+/*
 void fill_partition_arrays()
 {
   int b,i,j;
@@ -165,13 +342,46 @@ void fill_partition_arrays()
       calc_upm(i,j);
       calc_up(i,j);
       
+      calc_ud(i,j);
+      calc_u(i,j);
+    }
+  }
+}*/
+void fill_partition_arrays()
+{
+  int b,i,j;//printf("TURN=%d\n",TURN);
+  int n=part_len;
+  for(b=TURN+1; b<n; ++b){
+    for(i=1; i<=n-b; ++i){
+      j=i+b;
+
+      // Auxillary array//below condition is because they are already initialized for these i,j
+//	if((j-i)!=(TURN+1)){// && (j-i)!=(TURN) ){
+      calc_s1(i,j);
+      calc_s2(i,j);
+//	}
+      //calc_s3(i,j);
+
+      calc_upm(i,j);
+      calc_up(i,j);
+
+      calc_s3(i,j);//ERROR
+     // if (j < n) { // handled boundary condition
+        calc_u1d(i,j);
+        calc_u1(i,j);
+      //}
+
+      //calc_upm(i,j);
+      //calc_up(i,j);
+
       calc_ud(i,j);
       calc_u(i,j);
     }
   }
 }
 
-void calc_s1(int h, int j)
+
+/*void calc_s1(int h, int j)
 {
 		int l;						
 		for (l = h; l < j; ++l)
@@ -180,27 +390,59 @@ void calc_s1(int h, int j)
 						(exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+
 																				up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))));							
 		}
+}*/
+void calc_s1(int h, int j)//ERROR_FOUND s1[h][j]= instead of +=
+{//printf("Entering calc_s1: h=%d, j =%d\n",h,j);
+                int l;
+		double s1_val = 0.0;
+                for (l = h+1; l < j; ++l)//ERROR
+                {
+			double v1 = (get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)));
+			double v2 = (exp(-Ed3(h,l,l+1)/RT)*get_u(l+2,j));
+			double v3 = get_ud(l+1,j);
+			double v4 = (get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT)));
+			double val = v1*(v2+v3+v4);
+                        //double val = get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*(exp(-Ed3(h,l,l+1)/RT)*get_u(l+2,j)+(get_ud(l+1,j)+get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT))));
+			s1_val += val;
+                }
+		set_s1(h,j,s1_val);//s1[h][j] = s1_val;
+//printf("Exiting calc_s1: h=%d, j =%d, val=%.3f\n",h,j,s1[h][j]);
 }
 
+
 void calc_s2(int h, int j)
-{
-	int l;							
-	for (l = h; l < j; ++l)
-	{
-			s2[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
-										(exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1]+u1d[l+1][j-1]);							
+{//printf("Entering calc_s2: h=%d, j =%d\n",h,j);
+	int l;
+	double s2_val = 0.0;							
+	for (l = h+1; l < j; ++l)//ERROR
+	{//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)),(exp(-Ed3(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)));
+		double v1 = (get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)));
+		double v2 = (exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1));
+		double v3 = get_u1d(l+1,j-1);
+		double val = v1*(v2+v3);
+		//double val = get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)) * (exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1));							
+		s2_val += val;//Error: Eb is added
 	}
+	set_s2(h, j, s2_val);//s2[h][j] = s2_val;
+//printf("Exiting calc_s2: h=%d, j =%d, val=%.3f\n",h,j,s2[h][j]);
 }
 
 void calc_s3(int h, int j)
-{
-  int l;							
-  for (l = h; l < j; ++l)
+{//printf("Entering calc_s3: h=%d, j =%d\n",h,j);
+  int l;		
+	double s3_val = 0.0;					
+  for (l = h+1; l <= j && l+2<=part_len; ++l)//ERROR in for loop variable l
   {
-    s3[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
-      (f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + 
-       exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j] + u1d[l+1][j]);
+    	double v1 = (get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)));
+	double v2 = (f(j+1,h,l)*exp(-((j-l)*Eb)/RT));
+	double v3 = (exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j));
+	double v4 = get_u1d(l+1,j);
+	double val = v1*(v2+v3+v4);
+	//double val = get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*(f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j));
+  	s3_val += val;
   }
+ set_s3(h, j, s3_val);//s3[h][j] = s3_val;
+//printf("Exiting calc_s3: h=%d, j =%d, val=%.3f\n",h,j,s3[h][j]);
 }
 
 void create_partition_arrays()
@@ -231,7 +473,7 @@ void free_partition_arrays()
   freeTwoD(u1,len,len);
 }
 
-void calc_upm(int i, int j){
+/*void calc_upm(int i, int j){
 	double a = Ea, b=Eb, c=Ec;
 	double p_val = 0;
 	int l,h;
@@ -260,8 +502,48 @@ void calc_upm(int i, int j){
   else {
     upm[i][j] = 0;   
   }
+}*/
+
+void calc_upm(int i, int j){//printf("Entering calc_upm: i=%d, j =%d\n",i,j);
+        double a = Ea, b=Eb, c=Ec;
+        double p_val = 0;
+        int l,h;
+        double quadraticSum = 0;
+
+  if (canPair(RNA[i],RNA[j]))
+  {
+   for(l=i+2; l<j; ++l){
+	double v1 = (get_up(i+1,l) * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT));
+	double v2 = (exp((-1)*(Ed3(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1));
+	double v3 = get_u1d(l+1,j-1);
+	p_val = p_val + (v1*(v2+v3));
+        //p_val += (get_up(i+1,l) * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT) * (exp((-1)*(Ed3(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
+    }
+
+    for(l=i+3; l<j; ++l){
+	double v1 = (get_up(i+2,l)*exp((-1)*(a+2*c+b+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT));
+	double v2 = (exp((-1)*(Ed3(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1));
+	double v3 = get_u1d(l+1,j-1);
+	p_val = p_val + (v1*(v2+v3));
+        //p_val += (get_up(i+2,l)*exp((-1)*(a+2*c+b+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(Ed3(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
+    }
+
+    for(h=i+3; h<j-1; ++h){
+      quadraticSum += (get_s2(h,j) * exp((-1)*(a+2*c+(h-i-1)*b)/RT));
+    }
+    quadraticSum *= (exp((-1)*Ed3(i,j,i+1)/RT));
+
+    p_val += quadraticSum;
+    set_upm(i, j, p_val);//upm[i][j] = p_val;
+  }
+  else {
+    set_upm(i, j, 0.0);//upm[i][j] = 0;
+  }
+//printf("Exiting calc_upm: i=%d, j =%d, val=%.3f\n",i,j,upm[i][j]);
 }
 
+
+/*
 void calc_u1(int i, int j){
 	double b=Eb, c=Ec;
 	double p_val = u1d[i][j];
@@ -275,8 +557,25 @@ void calc_u1(int i, int j){
 	p_val += quadraticSum;
 	
 	u1[i][j] = p_val;
+}*/
+void calc_u1(int i, int j){//printf("Entering calc_u1: i=%d, j =%d\n",i,j);
+        double b=Eb, c=Ec;
+        double p_val = get_u1d(i,j);
+        int h;
+        double quadraticSum = 0;
+
+        for(h=i+1; h<j; ++h){
+                quadraticSum += (get_s3(h,j) * exp((-1)*(c+(h-i)*b)/RT));
+        }
+
+        p_val += quadraticSum;
+
+         set_u1(i, j, p_val);//u1[i][j] = p_val;
+//printf("Exiting calc_u1: i=%d, j =%d, val=%.3f\n",i,j,u1[i][j]);
 }
 
+
+/*
 void calc_u1d(int i, int j){
 	double b=Eb, c=Ec;
 	double p_val = 0;
@@ -287,8 +586,27 @@ void calc_u1d(int i, int j){
 	}
 
 	u1d[i][j] = p_val;
+}*/
+
+void calc_u1d(int i, int j){//printf("Entering calc_u1d: i=%d, j =%d\n",i,j);
+        double b=Eb, c=Ec;
+        double p_val = 0;
+        int l;
+
+        for(l=i+1; l<=j && l+2<=part_len; ++l){//ERROR in l,,,//up should be calculated before u1d
+                double v1 = (get_up(i,l)*exp((-1)*(c+auPenalty(i,l))/RT));
+		double v2 = (f(j+1,i,l)*exp((-1)*(j-l)*b/RT));
+		double v3 = (exp((-1)*(Ed3(i,l,l+1)+b)/RT)*get_u1(l+2,j));
+		double v4 = get_u1d(l+1,j);
+		p_val += (v1*(v2+v3+v4));
+		//p_val += (get_up(i,l)*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(Ed3(i,l,l+1)+b)/RT)*get_u1(l+2,j) + get_u1d(l+1,j)));
+        }
+
+         set_u1d(i, j, p_val);//u1d[i][j] = p_val;
+//printf("Exiting calc_u1d: i=%d, j =%d, val=%.3f\n",i,j,u1d[i][j]);
 }
 
+/*
 void calc_u(int i, int j)
 {
 	int uval = 1;
@@ -304,8 +622,26 @@ void calc_u(int i, int j)
 		uval += s1[ctr][j];
 	}
 	u[i][j] = uval;
+}*/
+void calc_u(int i, int j)
+{//printf("Entering calc_u: i=%d, j =%d\n",i,j);
+        int uval = 1 + get_up(i,j)*exp(-auPenalty(i,j)/RT);
+  int h;
+        int ctr;
+        uval +=  get_ud(i,j);
+
+  for (h = i+1; h < j; ++h) {
+                uval += (get_up(h,j) * exp( -(Ed5(h,j,h-1) + auPenalty(h,j)) / RT ));
+        }
+
+        for (ctr = i+1; ctr < j-1; ++ctr) {
+                uval += get_s1(ctr,j);
+        }
+        set_u(i, j, uval);//u[i][j] = uval;
+//printf("Exiting calc_u: i=%d, j =%d, val=%.3f\n",i,j,u[i][j]);
 }
 
+/*
 void calc_ud(int i, int j)
 {
 	int l;
@@ -326,8 +662,32 @@ void calc_ud(int i, int j)
 		udij += (val1 * (val2 + val3));
 	}
   ud[i][j]  = udij;
+}*/
+
+void calc_ud(int i, int j)
+{//printf("Entering calc_ud: i=%d, j =%d\n",i,j);
+        int l;
+  double udij = 0;
+
+        for (l = i+1; l < j; ++l)
+  {
+                double val1, val2, val3;
+                val1 = get_up(i,l);
+                val1 = val1 * exp(-auPenalty(i,l) / RT);
+
+                val2 = get_u(l+2,j);
+                val2 = val2 * exp(-Ed3(i,l,l+1)/RT);
+
+                val3 = get_ud(l+1,j);
+                val3 = val3 + get_up(l+1,j) * exp( -auPenalty(l+1,j) / RT );
+
+                udij += (val1 * (val2 + val3));
+        }
+  set_ud(i, j, udij);//ud[i][j]  = udij;
+//printf("Exiting calc_ud: i=%d, j =%d, val=%.3f\n",i,j,ud[i][j]);
 }
 
+/*
 void calc_up(int i, int j)
 {
   double up_val = 0.0;
@@ -356,4 +716,47 @@ void calc_up(int i, int j)
   else  {
     up[i][j] = 0;   
   }
+}*/
+
+void calc_up(int i, int j)
+{//printf("Entering calc_up: i=%d, j =%d\n",i,j);
+  double up_val = 0.0;
+  int p,q;
+
+  if (canPair(RNA[i],RNA[j]))// if(j-i>TURN)
+  {
+   /*for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
+      int minq = j-i+p-MAXLOOP-2;
+      if (minq < p+1+TURN) minq = p+1+TURN;
+      int maxq = (p==(i+1))?(j-2):(j-1);
+
+      for (q = minq; q <= maxq; q++) {
+       if (canPair(p,q)==0) continue;
+        up_val += (get_up(p,q) * exp(-eL(i,j,p,q)/RT));
+      }
+    }*/
+	int h,l;
+    for (h = i+1; h < j ; h++) {
+      for (l = h+1; l < j; l++) {
+        if (canPair(RNA[h],RNA[l])==0) continue;
+	if(h==(i+1) && l==(j-1)) continue;
+	//if((l-h)<=TURN) continue;
+        up_val += (get_up(h,l) * exp(-eL(i,j,h,l)/RT));
+      }
+    }
+
+	//ERROR below line should not be there
+    //up_val = up_val * exp(-Ed3(i,j,i+1)/RT);
+    up_val = up_val + exp(-eH(i,j)/RT );
+    up_val = up_val + (exp(-eS(i,j)/RT ) * get_up(i+1,j-1));
+    up_val = up_val + get_upm(i,j);
+
+    set_up(i, j, up_val);//up[i][j] = up_val;
+  }
+  else  {
+    set_up(i, j, 0.0);//up[i][j] = 0;
+  }
+//printf("Exiting calc_up: i=%d, j =%d, val=%.3f\n",i,j,up[i][j]);
 }
+
+

From c3fb23c438ba82453664c6d36fb05ef1c31dcce8 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@hpc18.cc.gt.atl.ga.us>
Date: Sat, 1 Oct 2011 18:46:32 -0400
Subject: [PATCH 242/282] added stochastic sampling

---
 gtfold-mfe/include/stochastic-sampling.h |  87 ++++
 gtfold-mfe/src/stochastic-sampling.cc    | 559 +++++++++++++++++++++++
 2 files changed, 646 insertions(+)
 create mode 100644 gtfold-mfe/include/stochastic-sampling.h
 create mode 100644 gtfold-mfe/src/stochastic-sampling.cc

diff --git a/gtfold-mfe/include/stochastic-sampling.h b/gtfold-mfe/include/stochastic-sampling.h
new file mode 100644
index 0000000..e318296
--- /dev/null
+++ b/gtfold-mfe/include/stochastic-sampling.h
@@ -0,0 +1,87 @@
+#ifndef __STOCHASTIC_SAMPLING__
+#define __STOCHASTIC_SAMPLING__
+
+#include <iostream>
+#include <stdlib.h>
+#include "partition-func.h"
+#include "energy.h"
+
+enum {U=0,UP,UD,U1,U1D};
+
+double randdouble();
+double U_0(int i, int j);
+double U_ij(int i, int j);
+double U_hj(int i, int h, int j);
+double U_il(int i, int j);
+double U_s1h(int i, int h, int j);
+double U_ihlj_case1(int i, int h, int l, int j);
+double U_ihlj_case2(int i, int h, int l, int j);  
+double U_ihlj_case3(int i, int h, int l, int j);
+double UD_il_case1(int i, int l, int j);
+double UD_il_case2(int i, int l, int j);
+double UD_il_case3(int i, int l, int j);
+double Q_ijH(int i, int j);
+double Q_ijS(int i, int j);
+double Q_ijM(int i, int j);
+double UPM_ip1l_case1(int i, int l, int j);
+double UPM_ip1l_case2(int i, int l, int j);
+double UPM_ip2l_case1(int i, int l , int j);
+double UPM_ip2l_case2(int i, int l , int j);
+double UPM_ijs2h(int i, int h , int j);
+double UPM_ijhl_case1(int i, int h, int l, int j);
+double UPM_ijhl_case2(int i, int h, int l, int j);
+double U1D_ij_il_case1(int i, int l, int j);
+double U1D_ij_il_case2(int i, int l, int j);
+double U1D_ij_il_case3(int i, int l, int j);
+double U1_ij(int i, int j);
+double U1_ij_s3h(int i, int h, int j);
+double U1_j_hl_case1(int h, int l, int j);
+double U1_j_hl_case2(int h, int l, int j);
+double U1_j_hl_case3(int h, int l, int j);
+
+struct base_pair 
+{
+  int i;
+  int j;
+  int t;
+
+  base_pair(int i_, int j_, int t_) : i(i_), j(j_), t(t_) {}
+  base_pair(const base_pair& bp) :i(bp.i), j(bp.j), t(bp.t) { }
+  base_pair& operator = (const base_pair& bp)  
+  {
+    if (this != &bp) 
+    {
+      i = bp.i;
+      j = bp.j;
+      t = bp.t;
+    }
+    return *this;
+  }
+
+  int type() const { return t ;} 
+  
+  bool isPaired() const 
+  {
+    return t == UP;
+  }
+
+  friend std::ostream& operator << (std::ostream& out, const base_pair& bp)
+  {
+    out << '(' << bp.i << '-' << bp.j << ')' << ' ' << bp.isPaired() << std::endl;
+    return out;
+  }
+};
+
+void set_single_stranded(int i, int j, int* structure);
+void set_base_pair(int i, int j, int* structure);
+
+void rnd_upm(int i, int j, int* structure);
+void rnd_u1d(int i, int j, int* structure);
+void  rnd_u1(int i, int j, int* structure);
+void  rnd_up(int i, int j, int* structure);
+void  rnd_ud(int i, int j, int* structure);
+void   rnd_u(int i, int j, int* structure);
+
+void rnd_structure(int* structure, int len);
+
+#endif
diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc
new file mode 100644
index 0000000..137cb09
--- /dev/null
+++ b/gtfold-mfe/src/stochastic-sampling.cc
@@ -0,0 +1,559 @@
+#include "stochastic-sampling.h"
+
+#include <assert.h>
+#include <stdio.h>
+#include <stack>
+
+std::stack<base_pair> g_stack;
+
+
+double randdouble()
+{
+  return rand()/(double(RAND_MAX)+1);
+}
+
+double U_0(int i, int j)
+{
+  return 1.0/u[i][j];
+}
+
+double U_ij(int i, int j)
+{
+  return up[i][j]*exp(-auPenalty(i,j)/RT)/u[i][j];
+}
+
+double U_hj(int i, int h, int j)
+{
+  return up[h][j]*exp(-(Ed5(h,j,h-1)+auPenalty(h,j))/RT)/u[i][j];
+}
+
+double U_il(int i, int j)
+{
+  return ud[i][j]/u[i][j];
+}
+
+double U_s1h(int i, int h, int j)
+{
+  return s1[h][j]/u[i][j];
+}
+
+double U_ihlj_case1(int i, int h, int l, int j)
+{
+  return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j];
+}
+
+double U_ihlj_case2(int i, int h, int l, int j)
+{
+  return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (ud[l+1][j]) /s1[h][j];
+}
+
+double U_ihlj_case3(int i, int h, int l, int j)
+{
+  return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))) /s1[h][j];
+}
+
+double UD_il_case1(int i, int l, int j)
+{
+  return (up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/u[i][j];  
+}
+
+double UD_il_case2(int i, int l, int j)
+{
+  return (up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/u[i][j];
+}
+
+double UD_il_case3(int i, int l, int j)
+{
+  return up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/u[i][j];
+}
+
+double Q_ijH(int i, int j)
+{
+  return exp(-eH(i,j)/RT)/up[i][j];
+}
+
+double Q_ijS(int i, int j)
+{
+  return exp(-eS(i,j)/RT)*up[i+1][j-1]/up[i][j];
+}
+
+double Q_ijM(int i, int j)
+{
+  return upm[i][j]/up[i][j];
+}
+
+double UPM_ip1l_case1(int i, int l, int j)
+{
+  return (up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * exp(-1*(Ed3(i+1,l,l+1)+Eb)/RT) * u1[l+2][j-1])/upm[i][j];
+}
+
+double UPM_ip1l_case2(int i, int l, int j)
+{
+  return (up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j];
+}
+
+double UPM_ip2l_case1(int i, int l , int j)
+{
+  return up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(Ed3(i+2,l,l+1)+Eb)/RT)*u1[l+2][j-1])/upm[i][j];
+}
+
+double UPM_ip2l_case2(int i, int l , int j)
+{
+  return (up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j];
+}
+
+
+double UPM_ijs2h(int i, int h , int j)
+{
+  return exp((-1)*Ed3(i,j,i+1)/RT)* (s2[h][j] * exp((-1)*(Ea+2*Ec+(h-i-1)*Eb)/RT))/upm[i][j];
+}
+
+
+double UPM_ijhl_case1(int i, int h, int l, int j)
+{
+  return up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j];
+}
+
+double UPM_ijhl_case2(int i, int h, int l, int j)
+{
+  return up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j];
+}
+
+// u1d : case 1
+double U1D_ij_il_case1(int i, int l, int j)
+{
+  return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1[i][j];
+}
+
+// u1d : case 2
+double U1D_ij_il_case2(int i, int l, int j)
+{
+  return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1[i][j];
+}
+
+// u1d : case 3
+double U1D_ij_il_case3(int i, int l, int j)
+{
+  return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1[i][j];
+}
+
+// u1
+double U1_ij(int i, int j)
+{
+  return u1d[i][j]/u1[i][j];
+}
+
+// u1 : sample h
+double U1_ij_s3h(int i, int h, int j)
+{
+  return (s3[h][j] * exp((-1)*(Ec+(h-i)*Eb)/RT))/u1[i][j];
+}
+
+// u1 : sample l
+double U1_j_hl_case1(int h, int l, int j)
+{
+  return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT))) /s3[h][j];
+}
+
+double U1_j_hl_case2(int h, int l, int j)
+{
+  return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j])) /s3[h][j];
+}
+
+double U1_j_hl_case3(int h, int l, int j)
+{
+  return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j])) /s3[h][j];
+}
+
+void rnd_u(int i, int j, int* structure)
+{
+  double rnd = randdouble();
+  double cum_prob = 0.0;
+
+  cum_prob += U_0(i,j);
+  if (rnd <= cum_prob)
+  {
+    set_single_stranded(i,j, structure);
+    return;
+  }
+  
+  cum_prob += U_ij(i, j);
+  if (rnd <= cum_prob)
+  {
+    base_pair bp(i,j,UP);
+    g_stack.push(bp);
+    return;
+  }
+
+  for (int h = i+1; h < j; ++h)
+  {
+    cum_prob += U_hj(i,h,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp(h,j,UP);
+      set_single_stranded(i,h-1,structure);
+      g_stack.push(bp);
+      return;
+    }
+  }
+  
+  cum_prob += U_il(i,j);
+  if (rnd <= cum_prob)
+  {
+    base_pair bp1(i,j,UD);
+    g_stack.push(bp1);
+    return;
+  }
+
+  int h1 = -1;
+  for (int h = i+1;  i < j-1; ++h)
+  {
+    cum_prob += U_s1h(i,h,j);
+    if (rnd <= cum_prob)
+    {
+      h1 = h;
+      break;
+    }
+  }
+  assert (h1 != -1) ;
+
+  rnd = randdouble();
+  cum_prob = 0;
+  for (int l = h1+1; l < j; ++l)
+  {
+    cum_prob += U_ihlj_case1(i,h1,l,j);
+    if (rnd <= cum_prob)
+    {
+      set_single_stranded(i,h1-1,structure);
+      base_pair bp1(h1,l,UP);
+      base_pair bp2(l+2,j,U);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return ;
+    }
+
+    cum_prob += U_ihlj_case2(i,h1,l,j);
+    if (rnd <= cum_prob)
+    {
+      set_single_stranded(i,h1-1,structure);
+      base_pair bp1(h1,l,UP);
+      base_pair bp2(l+1,j,UD);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return ;
+    }
+    
+    cum_prob += U_ihlj_case3(i,h1,l,j);
+    if (rnd <= cum_prob)
+    {
+      set_single_stranded(i,h1-1,structure);
+      base_pair bp1(h1,l,UP);
+      base_pair bp2(l+1,j,UP);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return ;
+    }
+  }
+  assert(0);
+}
+
+void rnd_ud(int i, int j, int* structure)
+{
+  double rnd = randdouble();
+  double cum_prob = 0.0;
+  
+  for (int l = i+1; l < j ; ++l)
+  {
+    cum_prob += UD_il_case1(i,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp1(i,l,UP);
+      base_pair bp2(l+2,j,U);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return;
+    }
+
+    cum_prob += UD_il_case2(i,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp1(i,l,UP);
+      base_pair bp2(l+1,j,UD);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return;
+    }
+
+    cum_prob += UD_il_case3(i,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp1(i,l,UP);
+      base_pair bp2(l+1,j,UP);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return;
+    }
+  }
+}
+
+void rnd_up(int i, int j, int* structure)
+{
+  double rnd = randdouble();
+
+//  printf("%d %d %d %d\n",i, structure[i], j, structure[j]);
+  
+//  if (structure[i] > 0){
+//    printf("ERROR\n");
+//  }
+//  if (structure[j] > 0) {
+//    printf("ERROR\n");
+//  }
+  
+  set_base_pair(i,j,structure);
+
+  rnd -= Q_ijH(i,j);
+  if (rnd <= 0)
+  {
+    set_single_stranded(i+1,j-1,structure);
+    return ;
+  }
+
+  rnd -= Q_ijS(i,j);
+  if (rnd  <= 0)
+  {
+    base_pair bp(i+1,j-1,UP);
+    g_stack.push(bp);
+    return ;
+  }
+
+  rnd -= Q_ijM(i,j);
+  if (rnd <= 0)
+  {
+    assert(0);
+    rnd_upm(i,j,structure);
+  }
+}
+
+void rnd_u1(int i, int j, int* structure)
+{
+  double rnd = randdouble();
+  double cum_prob = 0;
+  
+  cum_prob += U1_ij(i,j);
+  if (rnd <= cum_prob)
+  {
+    base_pair bp(i,j,U1D);
+    g_stack.push(bp);
+    return;
+  }
+
+  int h1 = -1;
+  for (int h = i+1; h < j-1; ++h) 
+  {
+    cum_prob += U1_ij_s3h(i,h,j);
+    if (rnd <= cum_prob)
+    {
+      h1 = h;
+      break;
+    }
+  }
+  
+  // sample l given h1 
+  rnd = randdouble();
+  cum_prob = 0;
+  for (int l = h1+1; l <= j ; ++l)
+  {
+    cum_prob += U1_j_hl_case1(h1,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp(h1,l,UP);
+      g_stack.push(bp);
+      return;
+    }
+
+    cum_prob += U1_j_hl_case2(h1,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp1(h1,l,UP);
+      base_pair bp2(l+2,j,U1);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return;
+    }
+    
+    cum_prob += U1_j_hl_case3(h1,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp1(h1,l,UP);
+      base_pair bp2(l+1,j,U1D);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return;
+    }
+  }
+}
+
+void rnd_u1d(int i, int j, int* structure)
+{
+  double rnd = randdouble();
+  double cum_prob = 0;
+  
+  for (int l = i+1; i <= j; ++j)
+  {
+    cum_prob += U1D_ij_il_case1(i,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp1(i,l,UP);
+      set_single_stranded(l+1,j,structure);
+      g_stack.push(bp1);
+      return;
+    }
+
+    cum_prob += U1D_ij_il_case2(i,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp1(i,l,UP);
+      base_pair bp2(l+2,j,U1);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return;
+    }
+    
+    cum_prob += U1D_ij_il_case3(i,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp1(i,l,UP);
+      base_pair bp2(l+1,j,U1D);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return;
+    }
+  }
+}
+
+void rnd_upm(int i, int j, int* structure)
+{
+  double rnd = randdouble();
+  double cum_prob = 0;
+
+  for (int l = i+2; l < j; ++l) 
+  {
+    cum_prob += UPM_ip1l_case1(i,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp1(i+1,l,UP);
+      base_pair bp2(l+2,j-1,U1);
+      g_stack.push(bp2);
+      g_stack.push(bp1);
+      return ;
+    }
+
+    cum_prob += UPM_ip1l_case2(i,l,j);
+    if (rnd <= cum_prob)
+    { 
+      base_pair bp1(i+1,l,UP);
+      base_pair bp2(l+1,j-1,U1D);
+      g_stack.push(bp2);
+      g_stack.push(bp1);
+    }
+  }
+
+  for (int l = i+3; l < j; ++l) 
+  {
+    cum_prob += UPM_ip2l_case1(i,l,j);
+    if (rnd <= cum_prob)
+    {
+      base_pair bp1(i+2,l,UP);
+      base_pair bp2(l+2,j-1,U1);
+      g_stack.push(bp2);
+      g_stack.push(bp1);
+      return ;
+    }
+
+    cum_prob += UPM_ip1l_case2(i,l,j);
+    if (rnd <= cum_prob)
+    { 
+      base_pair bp1(i+2,l,UP);
+      base_pair bp2(l+1,j-1,U1D);
+      g_stack.push(bp1);
+      g_stack.push(bp2);
+      return ;
+    }
+  }
+
+  int h1 = -1;
+  for (int h = i+3; h < j-1; ++j)
+  {
+    cum_prob += UPM_ijs2h(i,h,j);
+    if (rnd <= cum_prob)
+    {
+      h1 = h;
+      break;
+    }
+  }
+  
+  rnd = randdouble();
+  cum_prob = 0;
+  for (int l = h1+1; l < j; ++l)
+  {
+    cum_prob += UPM_ijhl_case1(i,h1,l,j);
+    if (rnd <= cum_prob)
+    {
+        base_pair bp1(h1,l,UP);
+        base_pair bp2(l+2,j-1,U1);
+        g_stack.push(bp1);
+        g_stack.push(bp2);
+        return;
+    }
+
+    cum_prob += UPM_ijhl_case2(i,h1,l,j);
+    if (rnd <= cum_prob)
+    {
+        base_pair bp1(h1,l,UP);
+        base_pair bp2(l+1,j-1,U1D);
+        g_stack.push(bp1);
+        g_stack.push(bp2);
+        return;
+    }
+  }
+}
+
+void rnd_structure(int* structure, int len)
+{
+  srand(rand());
+  base_pair first(1,len,U);
+  g_stack.push(first);
+
+  while (!g_stack.empty())
+  {
+    base_pair bp = g_stack.top();
+ //   std::cout << bp;
+    g_stack.pop();
+  
+    if (bp.type() == U)
+      rnd_u(bp.i,bp.j,structure);
+    else if (bp.type() == UD)
+      rnd_ud(bp.i,bp.j,structure);
+    else if (bp.type() == UP)
+      rnd_up(bp.i,bp.j,structure);
+    else if (bp.type() == U1)
+      rnd_u1(bp.i,bp.j,structure);
+    else if (bp.type() == U1D)
+      rnd_u1d(bp.i,bp.j,structure);
+    
+  }
+}
+
+void set_single_stranded(int i, int j, int* structure)
+{
+  for(;i<=j;++i) 
+    structure[i] = 0;
+}
+
+void set_base_pair(int i, int j, int* structure)
+{
+    assert(j-i > TURN);
+  //  printf("PAIRING %d %d\n",i,j);
+    structure[i] = j;
+    structure[j] = i;
+}

From 947fa1850cf9d0bdd9a314f19fb9b04bba7bf79f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@hpc18.cc.gt.atl.ga.us>
Date: Sat, 1 Oct 2011 18:47:06 -0400
Subject: [PATCH 243/282] added stochastic sampling files

---
 gtfold-mfe/src/Makefile.am | 4 ++--
 gtfold-mfe/src/Makefile.in | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am
index c595933..62cedca 100644
--- a/gtfold-mfe/src/Makefile.am
+++ b/gtfold-mfe/src/Makefile.am
@@ -16,10 +16,10 @@ gtfold_SOURCES = \
 	algorithms.c\
 	traceback.c\
 	subopt_traceback.cc\
-	algorithms-partition.c\
+	stochastic-sampling.cc\
+  algorithms-partition.c\
 	partition-dangle.c\
 	partition-func.c\
-	random-sample.cc\
 	shapereader.cc
 
 gtfold_LDFLAGS = 
diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in
index bad351a..d36b292 100644
--- a/gtfold-mfe/src/Makefile.in
+++ b/gtfold-mfe/src/Makefile.in
@@ -53,7 +53,7 @@ am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
 	energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \
 	subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \
 	partition-dangle.$(OBJEXT) partition-func.$(OBJEXT) \
-	random-sample.$(OBJEXT) shapereader.$(OBJEXT)
+	shapereader.$(OBJEXT) stochastic-sampling.$(OBJEXT)
 gtfold_OBJECTS = $(am_gtfold_OBJECTS)
 gtfold_DEPENDENCIES =
 gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
@@ -193,9 +193,9 @@ gtfold_SOURCES = \
 	traceback.c\
 	subopt_traceback.cc\
 	algorithms-partition.c\
+	stochastic-sampling.cc\
 	partition-dangle.c\
 	partition-func.c\
-	random-sample.cc\
 	shapereader.cc
 
 gtfold_LDFLAGS = 
@@ -283,6 +283,7 @@ distclean-compile:
 	-rm -f *.tab.c
 
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stochastic-sampling.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/constraints.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/energy.Po@am__quote@
@@ -292,7 +293,6 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-func.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/random-sample.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@

From 6bf57630f9f29236a1edf842cfdb1026843025e1 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@hpc18.cc.gt.atl.ga.us>
Date: Sat, 1 Oct 2011 18:48:31 -0400
Subject: [PATCH 244/282] changes related to stochastic sampling

---
 gtfold-mfe/include/options.h        |  2 ++
 gtfold-mfe/include/partition-func.h |  1 +
 gtfold-mfe/src/main.cc              | 34 +++++++++++++++++++++++++++++
 gtfold-mfe/src/options.cc           |  8 +++++++
 gtfold-mfe/src/partition-func.c     | 20 +++++------------
 5 files changed, 50 insertions(+), 15 deletions(-)

diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 5dbebf1..f0499a9 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -23,6 +23,7 @@ extern bool T_MISMATCH;
 extern bool UNAMODE;
 extern bool RNAMODE;
 extern bool CALC_PART_FUNC;
+extern bool RND_SAMPLE;
 
 extern string seqfile;
 extern string constraintsFile;
@@ -39,6 +40,7 @@ extern bool b_prefilter;
 extern int prefilter1;
 extern int prefilter2;
 extern int dangles;
+extern int num_rnd;
 
 extern bool LIMIT_DISTANCE;
 extern int contactDistance;
diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h
index 9761531..e87fc45 100644
--- a/gtfold-mfe/include/partition-func.h
+++ b/gtfold-mfe/include/partition-func.h
@@ -21,6 +21,7 @@ extern	double ** u1;
 
 extern int part_len;
 
+double f(int j, int h, int l);
 void calculate_partition(int len);
 void free_partition();
 
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 952aba1..77a23a5 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -43,6 +43,7 @@
 #include "traceback.h"
 #include "subopt_traceback.h"
 #include "shapereader.h"
+#include "stochastic-sampling.h"
 
 //#define DEBUG 1
 
@@ -291,6 +292,39 @@ int main(int argc, char** argv) {
     free_fold(seq.length());
     exit(0);
   }
+  if (RND_SAMPLE == true)
+  {
+    printf("\nComputing partition function...\n");
+    calculate_partition(seq.length());
+    
+    int* structure = new int[seq.length()+1];
+    srand(time(NULL));
+
+    if (num_rnd > 0 ) {
+      printf("\nSampling structures...\n");
+      for (int count = 1; count <= num_rnd; ++count) 
+      {
+        memset(structure, 0, (seq.length()+1)*sizeof(int));
+        rnd_structure(structure, seq.length());
+
+        std::string ensemble(seq.length()+1,'.');
+        for (int i = 1; i <= (int)seq.length(); ++ i) {
+       //     printf("%d %d\n",i,structure[i]);
+          if (structure[i] > 0 && ensemble[i] == '.')
+          {
+            ensemble[i] = '(';
+            ensemble[structure[i]] = ')';
+          }
+        }
+        std::cout << ensemble.substr(1) << std::endl;
+      }
+    }
+
+    free_partition();
+    free_fold(seq.length());
+    delete [] structure;
+    exit(0);
+  }
 
 	printf("\nComputing minimum free energy structure...\n");
 	fflush(stdout);
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 7b4a4ee..b600088 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -19,6 +19,7 @@ bool UNAMODE = false;
 bool RNAMODE = false;
 bool b_prefilter = false;
 bool CALC_PART_FUNC = false;
+bool RND_SAMPLE = false;
 
 string seqfile = "";
 string constraintsFile = "";
@@ -30,6 +31,7 @@ string outputDir = "";
 string shapeFile = "";
 string paramDir; // default value
 
+int num_rnd = 0;
 int dangles=-1;
 int prefilter1=2;
 int prefilter2=2;
@@ -184,6 +186,12 @@ void parse_options(int argc, char** argv) {
           help();
       } else if (strcmp(argv[i],"--partition") == 0) {
         CALC_PART_FUNC = true;
+      } else if (strcmp(argv[i],"--sample") == 0) {
+        RND_SAMPLE = true;
+        if(i < argc)
+          num_rnd = atoi(argv[++i]);
+        else
+          help();
       }
       else if (strcmp(argv[i], "--useSHAPE") == 0){
         if( i < argc){
diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index 215b1ba..b59bd2e 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -1,4 +1,5 @@
 #include <stdio.h>
+
 #include "partition-func.h"
 #include "energy.h"
 #include "algorithms-partition.h"
@@ -9,7 +10,7 @@
 #include "omp.h"
 #endif
 
-#define DEBUG_PF 1
+#define DEBUG_PF 0
 
 #ifdef DEBUG_PF 
   #undef Ec
@@ -60,7 +61,6 @@ static void calc_u1d(int i, int j);
 static void calc_s1(int i, int j);
 static void calc_s2(int i, int j);
 static void calc_s3(int i, int j);
-static double f(int j, int h, int l);
 
 double f(int j, int h, int l){
 	if(j - 1 == l)
@@ -72,20 +72,10 @@ double f(int j, int h, int l){
 
 void calculate_partition(int len) 
 {
-  int i, j;
   part_len = len;
   create_partition_arrays();
   init_partition_arrays();
   fill_partition_arrays();
-
-  for (i = 0; i <= part_len+1; ++i) 
-  {
-    for (j = 0; j <= part_len+1; ++j)
-      printf("%0.1f ",u[i][j]);
-    printf("\n");
-  }
-
-  printf("%4.4f\n",u[1][part_len]);
 }
 
 void free_partition()
@@ -176,7 +166,7 @@ void calc_s1(int h, int j)
 		int l;						
 		for (l = h; l < j; ++l)
 		{
-				s1[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
+				s1[h][j] += up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
 						(exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+
 																				up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))));							
 		}
@@ -187,7 +177,7 @@ void calc_s2(int h, int j)
 	int l;							
 	for (l = h; l < j; ++l)
 	{
-			s2[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
+			s2[h][j] += up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
 										(exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1]+u1d[l+1][j-1]);							
 	}
 }
@@ -197,7 +187,7 @@ void calc_s3(int h, int j)
   int l;							
   for (l = h; l < j; ++l)
   {
-    s3[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
+    s3[h][j] += up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
       (f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + 
        exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j] + u1d[l+1][j]);
   }

From 69d1e003e51a9df8e558f1dd9ab7d68b7caa51bb Mon Sep 17 00:00:00 2001
From: Manoj Soni <manoj6891@gmail.com>
Date: Sat, 1 Oct 2011 23:43:19 -0400
Subject: [PATCH 245/282] Partition Func overflow error due to int value
 resolved

---
 gtfold-mfe/src/partition-func.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index 23ff1c9..2086252 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -11,7 +11,7 @@
 #include "omp.h"
 #endif
 
-//#define DEBUG_PF 0
+//#define DEBUG_PF 1
 
 #ifdef DEBUG_PF 
   #undef Ec
@@ -174,7 +174,7 @@ void calculate_partition(int len)
 
   fill_partition_arrays();
 
-  //printAllMatrixes();
+  printAllMatrixes();
 
   printf("%4.4f\n",u[1][part_len]);
 }
@@ -348,7 +348,7 @@ void fill_partition_arrays()
   }
 }*/
 void fill_partition_arrays()
-{
+{//printf("RT=%d\n",RT);return;
   int b,i,j;//printf("TURN=%d\n",TURN);
   int n=part_len;
   for(b=TURN+1; b<n; ++b){
@@ -625,7 +625,7 @@ void calc_u(int i, int j)
 }*/
 void calc_u(int i, int j)
 {//printf("Entering calc_u: i=%d, j =%d\n",i,j);
-        int uval = 1 + get_up(i,j)*exp(-auPenalty(i,j)/RT);
+        double uval = 1 + get_up(i,j)*exp(-auPenalty(i,j)/RT);
   int h;
         int ctr;
         uval +=  get_ud(i,j);

From 91e43f34539d782146ca8f5b3308356e790ab5ed Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@hpc18.cc.gt.atl.ga.us>
Date: Sun, 2 Oct 2011 00:23:23 -0400
Subject: [PATCH 246/282] added checks

---
 gtfold-mfe/src/partition-func.c       |   2 +-
 gtfold-mfe/src/stochastic-sampling.cc | 143 +++++++++++++++-----------
 2 files changed, 83 insertions(+), 62 deletions(-)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index f21d4cb..9a2e691 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -173,7 +173,7 @@ void calculate_partition(int len)
 
   fill_partition_arrays();
 
-  printAllMatrixes();
+  //printAllMatrixes();
 
   printf("%4.4f\n",u[1][part_len]);
 }
diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc
index 137cb09..b89bad7 100644
--- a/gtfold-mfe/src/stochastic-sampling.cc
+++ b/gtfold-mfe/src/stochastic-sampling.cc
@@ -1,5 +1,6 @@
 #include "stochastic-sampling.h"
 
+#include "global.h"
 #include <assert.h>
 #include <stdio.h>
 #include <stack>
@@ -12,6 +13,11 @@ double randdouble()
   return rand()/(double(RAND_MAX)+1);
 }
 
+bool feasible(int i, int j)
+{
+  return j-i > TURN && canPair(RNA[i],RNA[j]);
+}
+
 double U_0(int i, int j)
 {
   return 1.0/u[i][j];
@@ -19,12 +25,12 @@ double U_0(int i, int j)
 
 double U_ij(int i, int j)
 {
-  return up[i][j]*exp(-auPenalty(i,j)/RT)/u[i][j];
+  return (feasible(i,j) == true)?up[i][j]*exp(-auPenalty(i,j)/RT)/u[i][j]:0;
 }
 
 double U_hj(int i, int h, int j)
 {
-  return up[h][j]*exp(-(Ed5(h,j,h-1)+auPenalty(h,j))/RT)/u[i][j];
+  return (feasible(h,j) == true)?up[h][j]*exp(-(Ed5(h,j,h-1)+auPenalty(h,j))/RT)/u[i][j]:0;
 }
 
 double U_il(int i, int j)
@@ -39,32 +45,32 @@ double U_s1h(int i, int h, int j)
 
 double U_ihlj_case1(int i, int h, int l, int j)
 {
-  return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j];
+  return feasible(h,l)?up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]:0;
 }
 
 double U_ihlj_case2(int i, int h, int l, int j)
 {
-  return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (ud[l+1][j]) /s1[h][j];
+  return feasible(h,l)?up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (ud[l+1][j]) /s1[h][j]:0;
 }
 
 double U_ihlj_case3(int i, int h, int l, int j)
 {
-  return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))) /s1[h][j];
+  return feasible(h,l)?up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))) /s1[h][j]:0;
 }
 
 double UD_il_case1(int i, int l, int j)
 {
-  return (up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/u[i][j];  
+  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/u[i][j]:0;  
 }
 
 double UD_il_case2(int i, int l, int j)
 {
-  return (up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/u[i][j];
+  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/u[i][j]:0;
 }
 
 double UD_il_case3(int i, int l, int j)
 {
-  return up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/u[i][j];
+  return feasible(i,l)?up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/u[i][j]:0;
 }
 
 double Q_ijH(int i, int j)
@@ -82,24 +88,29 @@ double Q_ijM(int i, int j)
   return upm[i][j]/up[i][j];
 }
 
+double Q_ijhlBI(int i, int j, int h, int l)
+{
+  return feasible(h,l)?exp(-1*eL(i,j,h,l)/RT)*up[h][l]/up[i][j]:0;
+}
+
 double UPM_ip1l_case1(int i, int l, int j)
 {
-  return (up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * exp(-1*(Ed3(i+1,l,l+1)+Eb)/RT) * u1[l+2][j-1])/upm[i][j];
+  return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * exp(-1*(Ed3(i+1,l,l+1)+Eb)/RT) * u1[l+2][j-1])/upm[i][j]:0;
 }
 
 double UPM_ip1l_case2(int i, int l, int j)
 {
-  return (up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j];
+  return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0;
 }
 
 double UPM_ip2l_case1(int i, int l , int j)
 {
-  return up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(Ed3(i+2,l,l+1)+Eb)/RT)*u1[l+2][j-1])/upm[i][j];
+  return feasible(i+2,l)?up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(Ed3(i+2,l,l+1)+Eb)/RT)*u1[l+2][j-1])/upm[i][j]:0;
 }
 
 double UPM_ip2l_case2(int i, int l , int j)
 {
-  return (up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j];
+  return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0;
 }
 
 
@@ -111,30 +122,30 @@ double UPM_ijs2h(int i, int h , int j)
 
 double UPM_ijhl_case1(int i, int h, int l, int j)
 {
-  return up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j];
+  return feasible(h,l)?up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]:0;
 }
 
 double UPM_ijhl_case2(int i, int h, int l, int j)
 {
-  return up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j];
+  return feasible(h,l)?up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]:0;
 }
 
 // u1d : case 1
 double U1D_ij_il_case1(int i, int l, int j)
 {
-  return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1[i][j];
+  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1[i][j]:0;
 }
 
 // u1d : case 2
 double U1D_ij_il_case2(int i, int l, int j)
 {
-  return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1[i][j];
+  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1[i][j]:0;
 }
 
 // u1d : case 3
 double U1D_ij_il_case3(int i, int l, int j)
 {
-  return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1[i][j];
+  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1[i][j]:0;
 }
 
 // u1
@@ -152,17 +163,17 @@ double U1_ij_s3h(int i, int h, int j)
 // u1 : sample l
 double U1_j_hl_case1(int h, int l, int j)
 {
-  return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT))) /s3[h][j];
+  return feasible(h,l)?(up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT))) /s3[h][j]:0;
 }
 
 double U1_j_hl_case2(int h, int l, int j)
 {
-  return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j])) /s3[h][j];
+  return feasible(h,l)?(up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j])) /s3[h][j]:0;
 }
 
 double U1_j_hl_case3(int h, int l, int j)
 {
-  return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j])) /s3[h][j];
+  return feasible(h,l)?(up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]:0;
 }
 
 void rnd_u(int i, int j, int* structure)
@@ -171,14 +182,14 @@ void rnd_u(int i, int j, int* structure)
   double cum_prob = 0.0;
 
   cum_prob += U_0(i,j);
-  if (rnd <= cum_prob)
+  if (rnd < cum_prob)
   {
     set_single_stranded(i,j, structure);
     return;
   }
   
   cum_prob += U_ij(i, j);
-  if (rnd <= cum_prob)
+  if (rnd < cum_prob)
   {
     base_pair bp(i,j,UP);
     g_stack.push(bp);
@@ -188,7 +199,7 @@ void rnd_u(int i, int j, int* structure)
   for (int h = i+1; h < j; ++h)
   {
     cum_prob += U_hj(i,h,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp(h,j,UP);
       set_single_stranded(i,h-1,structure);
@@ -198,7 +209,7 @@ void rnd_u(int i, int j, int* structure)
   }
   
   cum_prob += U_il(i,j);
-  if (rnd <= cum_prob)
+  if (rnd < cum_prob)
   {
     base_pair bp1(i,j,UD);
     g_stack.push(bp1);
@@ -206,10 +217,10 @@ void rnd_u(int i, int j, int* structure)
   }
 
   int h1 = -1;
-  for (int h = i+1;  i < j-1; ++h)
+  for (int h = i+1;  h < j-1; ++h)
   {
     cum_prob += U_s1h(i,h,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       h1 = h;
       break;
@@ -222,7 +233,7 @@ void rnd_u(int i, int j, int* structure)
   for (int l = h1+1; l < j; ++l)
   {
     cum_prob += U_ihlj_case1(i,h1,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       set_single_stranded(i,h1-1,structure);
       base_pair bp1(h1,l,UP);
@@ -233,7 +244,7 @@ void rnd_u(int i, int j, int* structure)
     }
 
     cum_prob += U_ihlj_case2(i,h1,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       set_single_stranded(i,h1-1,structure);
       base_pair bp1(h1,l,UP);
@@ -244,7 +255,7 @@ void rnd_u(int i, int j, int* structure)
     }
     
     cum_prob += U_ihlj_case3(i,h1,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       set_single_stranded(i,h1-1,structure);
       base_pair bp1(h1,l,UP);
@@ -265,7 +276,7 @@ void rnd_ud(int i, int j, int* structure)
   for (int l = i+1; l < j ; ++l)
   {
     cum_prob += UD_il_case1(i,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp1(i,l,UP);
       base_pair bp2(l+2,j,U);
@@ -275,7 +286,7 @@ void rnd_ud(int i, int j, int* structure)
     }
 
     cum_prob += UD_il_case2(i,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp1(i,l,UP);
       base_pair bp2(l+1,j,UD);
@@ -285,7 +296,7 @@ void rnd_ud(int i, int j, int* structure)
     }
 
     cum_prob += UD_il_case3(i,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp1(i,l,UP);
       base_pair bp2(l+1,j,UP);
@@ -300,26 +311,20 @@ void rnd_up(int i, int j, int* structure)
 {
   double rnd = randdouble();
 
-//  printf("%d %d %d %d\n",i, structure[i], j, structure[j]);
-  
-//  if (structure[i] > 0){
-//    printf("ERROR\n");
-//  }
-//  if (structure[j] > 0) {
-//    printf("ERROR\n");
-//  }
+  assert(structure[i] == 0);
+  assert(structure[j] == 0);
   
   set_base_pair(i,j,structure);
 
   rnd -= Q_ijH(i,j);
-  if (rnd <= 0)
+  if (rnd < 0)
   {
     set_single_stranded(i+1,j-1,structure);
     return ;
   }
 
   rnd -= Q_ijS(i,j);
-  if (rnd  <= 0)
+  if (rnd  < 0)
   {
     base_pair bp(i+1,j-1,UP);
     g_stack.push(bp);
@@ -327,11 +332,25 @@ void rnd_up(int i, int j, int* structure)
   }
 
   rnd -= Q_ijM(i,j);
-  if (rnd <= 0)
+  //printf ("%lf %d %d \n", Q_ijM(i,j),i,j);
+  if (rnd < 0)
   {
-    assert(0);
     rnd_upm(i,j,structure);
+    return;
   }
+
+  for (int h = i+1; h < j-1; ++h)
+    for (int l = h+1; l < j; ++l)
+    {
+      if (h == i+1 && l == j-1) continue;
+      rnd -= Q_ijhlBI(i,j,h,l);
+      if (rnd < 0)
+      {
+        base_pair bp(h,l,UP);
+        g_stack.push(bp);
+        return;
+      }
+    }
 }
 
 void rnd_u1(int i, int j, int* structure)
@@ -340,7 +359,7 @@ void rnd_u1(int i, int j, int* structure)
   double cum_prob = 0;
   
   cum_prob += U1_ij(i,j);
-  if (rnd <= cum_prob)
+  if (rnd < cum_prob)
   {
     base_pair bp(i,j,U1D);
     g_stack.push(bp);
@@ -351,7 +370,7 @@ void rnd_u1(int i, int j, int* structure)
   for (int h = i+1; h < j-1; ++h) 
   {
     cum_prob += U1_ij_s3h(i,h,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       h1 = h;
       break;
@@ -364,7 +383,7 @@ void rnd_u1(int i, int j, int* structure)
   for (int l = h1+1; l <= j ; ++l)
   {
     cum_prob += U1_j_hl_case1(h1,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp(h1,l,UP);
       g_stack.push(bp);
@@ -372,7 +391,7 @@ void rnd_u1(int i, int j, int* structure)
     }
 
     cum_prob += U1_j_hl_case2(h1,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+2,j,U1);
@@ -382,7 +401,7 @@ void rnd_u1(int i, int j, int* structure)
     }
     
     cum_prob += U1_j_hl_case3(h1,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,U1D);
@@ -401,7 +420,7 @@ void rnd_u1d(int i, int j, int* structure)
   for (int l = i+1; i <= j; ++j)
   {
     cum_prob += U1D_ij_il_case1(i,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp1(i,l,UP);
       set_single_stranded(l+1,j,structure);
@@ -410,7 +429,7 @@ void rnd_u1d(int i, int j, int* structure)
     }
 
     cum_prob += U1D_ij_il_case2(i,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp1(i,l,UP);
       base_pair bp2(l+2,j,U1);
@@ -420,7 +439,7 @@ void rnd_u1d(int i, int j, int* structure)
     }
     
     cum_prob += U1D_ij_il_case3(i,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp1(i,l,UP);
       base_pair bp2(l+1,j,U1D);
@@ -439,7 +458,7 @@ void rnd_upm(int i, int j, int* structure)
   for (int l = i+2; l < j; ++l) 
   {
     cum_prob += UPM_ip1l_case1(i,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp1(i+1,l,UP);
       base_pair bp2(l+2,j-1,U1);
@@ -449,7 +468,7 @@ void rnd_upm(int i, int j, int* structure)
     }
 
     cum_prob += UPM_ip1l_case2(i,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     { 
       base_pair bp1(i+1,l,UP);
       base_pair bp2(l+1,j-1,U1D);
@@ -461,7 +480,7 @@ void rnd_upm(int i, int j, int* structure)
   for (int l = i+3; l < j; ++l) 
   {
     cum_prob += UPM_ip2l_case1(i,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       base_pair bp1(i+2,l,UP);
       base_pair bp2(l+2,j-1,U1);
@@ -471,7 +490,7 @@ void rnd_upm(int i, int j, int* structure)
     }
 
     cum_prob += UPM_ip1l_case2(i,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     { 
       base_pair bp1(i+2,l,UP);
       base_pair bp2(l+1,j-1,U1D);
@@ -485,7 +504,7 @@ void rnd_upm(int i, int j, int* structure)
   for (int h = i+3; h < j-1; ++j)
   {
     cum_prob += UPM_ijs2h(i,h,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
       h1 = h;
       break;
@@ -497,7 +516,7 @@ void rnd_upm(int i, int j, int* structure)
   for (int l = h1+1; l < j; ++l)
   {
     cum_prob += UPM_ijhl_case1(i,h1,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
         base_pair bp1(h1,l,UP);
         base_pair bp2(l+2,j-1,U1);
@@ -507,7 +526,7 @@ void rnd_upm(int i, int j, int* structure)
     }
 
     cum_prob += UPM_ijhl_case2(i,h1,l,j);
-    if (rnd <= cum_prob)
+    if (rnd < cum_prob)
     {
         base_pair bp1(h1,l,UP);
         base_pair bp2(l+1,j-1,U1D);
@@ -552,8 +571,10 @@ void set_single_stranded(int i, int j, int* structure)
 
 void set_base_pair(int i, int j, int* structure)
 {
-    assert(j-i > TURN);
-  //  printf("PAIRING %d %d\n",i,j);
+    bool cond = j-i > TURN && canPair(RNA[i],RNA[j]);
+    if (cond == false) printf("UP(%d %d) = %lf \n",i,j,up[i][j]);
+    assert(cond);
+    //  printf("PAIRING %d %d\n",i,j);
     structure[i] = j;
     structure[j] = i;
 }

From 5e349a2dc0936d916faa4b079c2857133ddff2c8 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@hpc18.cc.gt.atl.ga.us>
Date: Sun, 2 Oct 2011 03:22:54 -0400
Subject: [PATCH 247/282] corrections in ML traceback

---
 gtfold-mfe/src/stochastic-sampling.cc | 42 +++++++++++++--------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc
index b89bad7..b91733d 100644
--- a/gtfold-mfe/src/stochastic-sampling.cc
+++ b/gtfold-mfe/src/stochastic-sampling.cc
@@ -60,17 +60,17 @@ double U_ihlj_case3(int i, int h, int l, int j)
 
 double UD_il_case1(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/u[i][j]:0;  
+  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/ud[i][j]:0;  
 }
 
 double UD_il_case2(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/u[i][j]:0;
+  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/ud[i][j]:0;
 }
 
 double UD_il_case3(int i, int l, int j)
 {
-  return feasible(i,l)?up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/u[i][j]:0;
+  return feasible(i,l)?up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/ud[i][j]:0;
 }
 
 double Q_ijH(int i, int j)
@@ -133,19 +133,19 @@ double UPM_ijhl_case2(int i, int h, int l, int j)
 // u1d : case 1
 double U1D_ij_il_case1(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1[i][j]:0;
+  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1d[i][j]:0;
 }
 
 // u1d : case 2
 double U1D_ij_il_case2(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1[i][j]:0;
+  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1d[i][j]:0;
 }
 
 // u1d : case 3
 double U1D_ij_il_case3(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1[i][j]:0;
+  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1d[i][j]:0;
 }
 
 // u1
@@ -184,7 +184,7 @@ void rnd_u(int i, int j, int* structure)
   cum_prob += U_0(i,j);
   if (rnd < cum_prob)
   {
-    set_single_stranded(i,j, structure);
+    //set_single_stranded(i,j, structure);
     return;
   }
   
@@ -202,7 +202,7 @@ void rnd_u(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       base_pair bp(h,j,UP);
-      set_single_stranded(i,h-1,structure);
+      //set_single_stranded(i,h-1,structure);
       g_stack.push(bp);
       return;
     }
@@ -235,7 +235,7 @@ void rnd_u(int i, int j, int* structure)
     cum_prob += U_ihlj_case1(i,h1,l,j);
     if (rnd < cum_prob)
     {
-      set_single_stranded(i,h1-1,structure);
+      //set_single_stranded(i,h1-1,structure);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+2,j,U);
       g_stack.push(bp1);
@@ -246,7 +246,7 @@ void rnd_u(int i, int j, int* structure)
     cum_prob += U_ihlj_case2(i,h1,l,j);
     if (rnd < cum_prob)
     {
-      set_single_stranded(i,h1-1,structure);
+      //set_single_stranded(i,h1-1,structure);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,UD);
       g_stack.push(bp1);
@@ -257,7 +257,7 @@ void rnd_u(int i, int j, int* structure)
     cum_prob += U_ihlj_case3(i,h1,l,j);
     if (rnd < cum_prob)
     {
-      set_single_stranded(i,h1-1,structure);
+      //set_single_stranded(i,h1-1,structure);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,UP);
       g_stack.push(bp1);
@@ -272,7 +272,6 @@ void rnd_ud(int i, int j, int* structure)
 {
   double rnd = randdouble();
   double cum_prob = 0.0;
-  
   for (int l = i+1; l < j ; ++l)
   {
     cum_prob += UD_il_case1(i,l,j);
@@ -305,12 +304,12 @@ void rnd_ud(int i, int j, int* structure)
       return;
     }
   }
+  assert(0);
 }
 
 void rnd_up(int i, int j, int* structure)
 {
   double rnd = randdouble();
-
   assert(structure[i] == 0);
   assert(structure[j] == 0);
   
@@ -319,7 +318,7 @@ void rnd_up(int i, int j, int* structure)
   rnd -= Q_ijH(i,j);
   if (rnd < 0)
   {
-    set_single_stranded(i+1,j-1,structure);
+    //set_single_stranded(i+1,j-1,structure);
     return ;
   }
 
@@ -332,7 +331,6 @@ void rnd_up(int i, int j, int* structure)
   }
 
   rnd -= Q_ijM(i,j);
-  //printf ("%lf %d %d \n", Q_ijM(i,j),i,j);
   if (rnd < 0)
   {
     rnd_upm(i,j,structure);
@@ -376,7 +374,8 @@ void rnd_u1(int i, int j, int* structure)
       break;
     }
   }
-  
+ 
+  assert(h1 != -1);
   // sample l given h1 
   rnd = randdouble();
   cum_prob = 0;
@@ -417,13 +416,13 @@ void rnd_u1d(int i, int j, int* structure)
   double rnd = randdouble();
   double cum_prob = 0;
   
-  for (int l = i+1; i <= j; ++j)
+  for (int l = i+1; l <= j; ++l)
   {
     cum_prob += U1D_ij_il_case1(i,l,j);
     if (rnd < cum_prob)
     {
       base_pair bp1(i,l,UP);
-      set_single_stranded(l+1,j,structure);
+      //set_single_stranded(l+1,j,structure);
       g_stack.push(bp1);
       return;
     }
@@ -474,6 +473,7 @@ void rnd_upm(int i, int j, int* structure)
       base_pair bp2(l+1,j-1,U1D);
       g_stack.push(bp2);
       g_stack.push(bp1);
+      return ;
     }
   }
 
@@ -489,7 +489,7 @@ void rnd_upm(int i, int j, int* structure)
       return ;
     }
 
-    cum_prob += UPM_ip1l_case2(i,l,j);
+    cum_prob += UPM_ip2l_case2(i,l,j);
     if (rnd < cum_prob)
     { 
       base_pair bp1(i+2,l,UP);
@@ -501,7 +501,7 @@ void rnd_upm(int i, int j, int* structure)
   }
 
   int h1 = -1;
-  for (int h = i+3; h < j-1; ++j)
+  for (int h = i+3; h < j-1; ++h)
   {
     cum_prob += UPM_ijs2h(i,h,j);
     if (rnd < cum_prob)
@@ -572,7 +572,7 @@ void set_single_stranded(int i, int j, int* structure)
 void set_base_pair(int i, int j, int* structure)
 {
     bool cond = j-i > TURN && canPair(RNA[i],RNA[j]);
-    if (cond == false) printf("UP(%d %d) = %lf \n",i,j,up[i][j]);
+    //if (cond == false) printf("UP(%d %d) = %lf \n",i,j,up[i][j]);
     assert(cond);
     //  printf("PAIRING %d %d\n",i,j);
     structure[i] = j;

From 8c2c06225b61987c8e4139fe8b336aa40d799b0a Mon Sep 17 00:00:00 2001
From: Manoj Soni <manoj6891@gmail.com>
Date: Mon, 3 Oct 2011 14:36:44 -0400
Subject: [PATCH 248/282] Wrapper function for Ed3 and Ed5 dangling functions
 added

---
 gtfold-mfe/include/partition-func.h   |  3 +-
 gtfold-mfe/src/partition-func.c       | 72 +++++++++++++++------------
 gtfold-mfe/src/stochastic-sampling.cc | 30 +++++------
 3 files changed, 57 insertions(+), 48 deletions(-)

diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h
index e87fc45..6532bea 100644
--- a/gtfold-mfe/include/partition-func.h
+++ b/gtfold-mfe/include/partition-func.h
@@ -20,7 +20,8 @@ extern	double ** s3;
 extern	double ** u1;
 
 extern int part_len;
-
+double ED3_new(int i, int j, int k);
+double ED5_new(int i, int j, int k);
 double f(int j, int h, int l);
 void calculate_partition(int len);
 void free_partition();
diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index 9a2e691..ad52a21 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -113,13 +113,21 @@ void set_s1(int i, int j, double val) {if(s1[i][j]!=-1 && s1[i][j]!=val) errorAn
 void set_s2(int i, int j, double val) {if(s2[i][j]!=-1 && s2[i][j]!=val) errorAndExit("set_s2 entry is not -1.\n",i,j,s2[i][j],val); s2[i][j]=val;}
 void set_s3(int i, int j, double val) {if(s3[i][j]!=-1 && s3[i][j]!=val) errorAndExit("set_s3 entry is not -1.\n",i,j,s3[i][j],val); s3[i][j]=val;}
 
+double ED3_new(int i, int j, int k){
+	//return Ed3(i,j,k);
+	return Ed5(j,i,k);
+}
 
+double ED5_new(int i, int j, int k){
+        //return Ed5(i,j,k);
+	return Ed3(j,i,k);
+}
 
 double f(int j, int h, int l){
 	if(j - 1 == l)
 		return 1;
 	else 
-		return exp(-Ed3(h,l,l+1)/RT);
+		return exp(-ED3_new(h,l,l+1)/RT);
 }
 
 void printMatrix(double** u, int part_len){
@@ -385,8 +393,8 @@ void fill_partition_arrays()
 		int l;						
 		for (l = h; l < j; ++l)
 		{
-				s1[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*
-						(exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+
+				s1[h][j] = up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))*
+						(exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+
 																				up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))));							
 		}
 }*/
@@ -396,12 +404,12 @@ void calc_s1(int h, int j)//ERROR_FOUND s1[h][j]= instead of +=
 		double s1_val = 0.0;
                 for (l = h+1; l < j; ++l)//ERROR
                 {
-			double v1 = (get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)));
-			double v2 = (exp(-Ed3(h,l,l+1)/RT)*get_u(l+2,j));
+			double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)));
+			double v2 = (exp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j));
 			double v3 = get_ud(l+1,j);
 			double v4 = (get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT)));
 			double val = v1*(v2+v3+v4);
-                        //double val = get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*(exp(-Ed3(h,l,l+1)/RT)*get_u(l+2,j)+(get_ud(l+1,j)+get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT))));
+                        //double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))*(exp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j)+(get_ud(l+1,j)+get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT))));
 			s1_val += val;
                 }
 		set_s1(h,j,s1_val);//s1[h][j] = s1_val;
@@ -414,12 +422,12 @@ void calc_s2(int h, int j)
 	int l;
 	double s2_val = 0.0;							
 	for (l = h+1; l < j; ++l)//ERROR
-	{//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)),(exp(-Ed3(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)));
-		double v1 = (get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)));
-		double v2 = (exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1));
+	{//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)),(exp(-ED3_new(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)));
+		double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)));
+		double v2 = (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1));
 		double v3 = get_u1d(l+1,j-1);
 		double val = v1*(v2+v3);
-		//double val = get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)) * (exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1));							
+		//double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)) * (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1));							
 		s2_val += val;//Error: Eb is added
 	}
 	set_s2(h, j, s2_val);//s2[h][j] = s2_val;
@@ -432,12 +440,12 @@ void calc_s3(int h, int j)
 	double s3_val = 0.0;					
   for (l = h+1; l <= j && l+2<=part_len; ++l)//ERROR in for loop variable l
   {
-    	double v1 = (get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)));
+    	double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)));
 	double v2 = (f(j+1,h,l)*exp(-((j-l)*Eb)/RT));
-	double v3 = (exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j));
+	double v3 = (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j));
 	double v4 = get_u1d(l+1,j);
 	double val = v1*(v2+v3+v4);
-	//double val = get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*(f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j));
+	//double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))*(f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j));
   	s3_val += val;
   }
  set_s3(h, j, s3_val);//s3[h][j] = s3_val;
@@ -482,18 +490,18 @@ void free_partition_arrays()
   {
    for(l=i+2; l<j; ++l){
       p_val += (up[i+1][l] * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT) * 
-          (exp((-1)*(Ed3(i+1,l,l+1)+b)/RT) * u1[l+2][j-1] + u1d[l+1][j-1]));
+          (exp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * u1[l+2][j-1] + u1d[l+1][j-1]));
     }
 
     for(l=i+3; l<j; ++l){
-      p_val += (up[i+2][l]*exp((-1)*(a+2*c+b+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * 
-          (exp((-1)*(Ed3(i+2,l,l+1)+b)/RT)*u1[l+2][j-1] + u1d[l+1][j-1]));
+      p_val += (up[i+2][l]*exp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT) * 
+          (exp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*u1[l+2][j-1] + u1d[l+1][j-1]));
     }
 
     for(h=i+3; h<j-1; ++h){
       quadraticSum += (s2[h][j] * exp((-1)*(a+2*c+(h-i-1)*b)/RT));	
     }
-    quadraticSum *= exp((-1)*Ed3(i,j,i+1)/RT);
+    quadraticSum *= exp((-1)*ED3_new(i,j,i+1)/RT);
 
     p_val += quadraticSum;
     upm[i][j] = p_val;
@@ -513,24 +521,24 @@ void calc_upm(int i, int j){//printf("Entering calc_upm: i=%d, j =%d\n",i,j);
   {
    for(l=i+2; l<j; ++l){
 	double v1 = (get_up(i+1,l) * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT));
-	double v2 = (exp((-1)*(Ed3(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1));
+	double v2 = (exp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1));
 	double v3 = get_u1d(l+1,j-1);
 	p_val = p_val + (v1*(v2+v3));
-        //p_val += (get_up(i+1,l) * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT) * (exp((-1)*(Ed3(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
+        //p_val += (get_up(i+1,l) * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT) * (exp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
     }
 
     for(l=i+3; l<j; ++l){
-	double v1 = (get_up(i+2,l)*exp((-1)*(a+2*c+b+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT));
-	double v2 = (exp((-1)*(Ed3(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1));
+	double v1 = (get_up(i+2,l)*exp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT));
+	double v2 = (exp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1));
 	double v3 = get_u1d(l+1,j-1);
 	p_val = p_val + (v1*(v2+v3));
-        //p_val += (get_up(i+2,l)*exp((-1)*(a+2*c+b+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(Ed3(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
+        //p_val += (get_up(i+2,l)*exp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
     }
 
     for(h=i+3; h<j-1; ++h){
       quadraticSum += (get_s2(h,j) * exp((-1)*(a+2*c+(h-i-1)*b)/RT));
     }
-    quadraticSum *= (exp((-1)*Ed3(i,j,i+1)/RT));
+    quadraticSum *= (exp((-1)*ED3_new(i,j,i+1)/RT));
 
     p_val += quadraticSum;
     set_upm(i, j, p_val);//upm[i][j] = p_val;
@@ -581,7 +589,7 @@ void calc_u1d(int i, int j){
 	int l;
 
 	for(l=i+1; l<=j; ++l){
-		p_val += (up[i][l]*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(Ed3(i,l,l+1)+b)/RT)*u1[l+2][j] + u1d[l+1][j]));
+		p_val += (up[i][l]*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(ED3_new(i,l,l+1)+b)/RT)*u1[l+2][j] + u1d[l+1][j]));
 	}
 
 	u1d[i][j] = p_val;
@@ -595,10 +603,10 @@ void calc_u1d(int i, int j){//printf("Entering calc_u1d: i=%d, j =%d\n",i,j);
         for(l=i+1; l<=j && l+2<=part_len; ++l){//ERROR in l,,,//up should be calculated before u1d
                 double v1 = (get_up(i,l)*exp((-1)*(c+auPenalty(i,l))/RT));
 		double v2 = (f(j+1,i,l)*exp((-1)*(j-l)*b/RT));
-		double v3 = (exp((-1)*(Ed3(i,l,l+1)+b)/RT)*get_u1(l+2,j));
+		double v3 = (exp((-1)*(ED3_new(i,l,l+1)+b)/RT)*get_u1(l+2,j));
 		double v4 = get_u1d(l+1,j);
 		p_val += (v1*(v2+v3+v4));
-		//p_val += (get_up(i,l)*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(Ed3(i,l,l+1)+b)/RT)*get_u1(l+2,j) + get_u1d(l+1,j)));
+		//p_val += (get_up(i,l)*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(ED3_new(i,l,l+1)+b)/RT)*get_u1(l+2,j) + get_u1d(l+1,j)));
         }
 
          set_u1d(i, j, p_val);//u1d[i][j] = p_val;
@@ -614,7 +622,7 @@ void calc_u(int i, int j)
 	uval +=  ud[i][j];
 	
   for (h = i+1; h < j; ++h) {
-		uval += up[h][j] * exp( -(Ed5(h,j,h-1) + auPenalty(h,j)) / RT );
+		uval += up[h][j] * exp( -(ED5_new(h,j,h-1) + auPenalty(h,j)) / RT );
 	}
 
 	for (ctr = i+1; ctr < j-1; ++ctr) {
@@ -630,7 +638,7 @@ void calc_u(int i, int j)
         uval +=  get_ud(i,j);
 
   for (h = i+1; h < j; ++h) {
-                uval += (get_up(h,j) * exp( -(Ed5(h,j,h-1) + auPenalty(h,j)) / RT ));
+                uval += (get_up(h,j) * exp( -(ED5_new(h,j,h-1) + auPenalty(h,j)) / RT ));
         }
 
         for (ctr = i+1; ctr < j-1; ++ctr) {
@@ -653,7 +661,7 @@ void calc_ud(int i, int j)
 		val1 = val1 * exp(-auPenalty(i,l) / RT);
 
 		val2 = u[l+2][j];
-		val2 = val2 * exp(-Ed3(i,l,l+1)/RT);
+		val2 = val2 * exp(-ED3_new(i,l,l+1)/RT);
 
 		val3 = ud[l+1][j];
 		val3 = val3 + up[l+1][j] * exp( -auPenalty(l+1,j) / RT );
@@ -675,7 +683,7 @@ void calc_ud(int i, int j)
                 val1 = val1 * exp(-auPenalty(i,l) / RT);
 
                 val2 = get_u(l+2,j);
-                val2 = val2 * exp(-Ed3(i,l,l+1)/RT);
+                val2 = val2 * exp(-ED3_new(i,l,l+1)/RT);
 
                 val3 = get_ud(l+1,j);
                 val3 = val3 + get_up(l+1,j) * exp( -auPenalty(l+1,j) / RT );
@@ -705,7 +713,7 @@ void calc_up(int i, int j)
       }
     }
 
-    up_val = up_val * exp(-Ed3(i,j,i+1)/RT);
+    up_val = up_val * exp(-ED3_new(i,j,i+1)/RT);
     up_val = up_val + exp(-eH(i,j)/RT );
     up_val = up_val + exp(-eS(i,j)/RT ) * up[i+1][j-1];
     up_val = up_val + upm[i][j];
@@ -745,7 +753,7 @@ void calc_up(int i, int j)
     }
 
 	//ERROR below line should not be there
-    //up_val = up_val * exp(-Ed3(i,j,i+1)/RT);
+    //up_val = up_val * exp(-ED3_new(i,j,i+1)/RT);
     up_val = up_val + exp(-eH(i,j)/RT );
     up_val = up_val + (exp(-eS(i,j)/RT ) * get_up(i+1,j-1));
     up_val = up_val + get_upm(i,j);
diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc
index b91733d..8ece94b 100644
--- a/gtfold-mfe/src/stochastic-sampling.cc
+++ b/gtfold-mfe/src/stochastic-sampling.cc
@@ -30,7 +30,7 @@ double U_ij(int i, int j)
 
 double U_hj(int i, int h, int j)
 {
-  return (feasible(h,j) == true)?up[h][j]*exp(-(Ed5(h,j,h-1)+auPenalty(h,j))/RT)/u[i][j]:0;
+  return (feasible(h,j) == true)?up[h][j]*exp(-(ED5_new(h,j,h-1)+auPenalty(h,j))/RT)/u[i][j]:0;
 }
 
 double U_il(int i, int j)
@@ -45,22 +45,22 @@ double U_s1h(int i, int h, int j)
 
 double U_ihlj_case1(int i, int h, int l, int j)
 {
-  return feasible(h,l)?up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]:0;
+  return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)* (exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]:0;
 }
 
 double U_ihlj_case2(int i, int h, int l, int j)
 {
-  return feasible(h,l)?up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (ud[l+1][j]) /s1[h][j]:0;
+  return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)* (ud[l+1][j]) /s1[h][j]:0;
 }
 
 double U_ihlj_case3(int i, int h, int l, int j)
 {
-  return feasible(h,l)?up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))) /s1[h][j]:0;
+  return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))) /s1[h][j]:0;
 }
 
 double UD_il_case1(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/ud[i][j]:0;  
+  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*ED3_new(i,l,l+1)/RT)*u[l+2][j])/ud[i][j]:0;  
 }
 
 double UD_il_case2(int i, int l, int j)
@@ -95,7 +95,7 @@ double Q_ijhlBI(int i, int j, int h, int l)
 
 double UPM_ip1l_case1(int i, int l, int j)
 {
-  return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * exp(-1*(Ed3(i+1,l,l+1)+Eb)/RT) * u1[l+2][j-1])/upm[i][j]:0;
+  return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * exp(-1*(ED3_new(i+1,l,l+1)+Eb)/RT) * u1[l+2][j-1])/upm[i][j]:0;
 }
 
 double UPM_ip1l_case2(int i, int l, int j)
@@ -105,29 +105,29 @@ double UPM_ip1l_case2(int i, int l, int j)
 
 double UPM_ip2l_case1(int i, int l , int j)
 {
-  return feasible(i+2,l)?up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(Ed3(i+2,l,l+1)+Eb)/RT)*u1[l+2][j-1])/upm[i][j]:0;
+  return feasible(i+2,l)?up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+Eb)/RT)*u1[l+2][j-1])/upm[i][j]:0;
 }
 
 double UPM_ip2l_case2(int i, int l , int j)
 {
-  return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0;
+  return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0;
 }
 
 
 double UPM_ijs2h(int i, int h , int j)
 {
-  return exp((-1)*Ed3(i,j,i+1)/RT)* (s2[h][j] * exp((-1)*(Ea+2*Ec+(h-i-1)*Eb)/RT))/upm[i][j];
+  return exp((-1)*ED3_new(i,j,i+1)/RT)* (s2[h][j] * exp((-1)*(Ea+2*Ec+(h-i-1)*Eb)/RT))/upm[i][j];
 }
 
 
 double UPM_ijhl_case1(int i, int h, int l, int j)
 {
-  return feasible(h,l)?up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]:0;
+  return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-ED3_new(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]:0;
 }
 
 double UPM_ijhl_case2(int i, int h, int l, int j)
 {
-  return feasible(h,l)?up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]:0;
+  return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]:0;
 }
 
 // u1d : case 1
@@ -139,7 +139,7 @@ double U1D_ij_il_case1(int i, int l, int j)
 // u1d : case 2
 double U1D_ij_il_case2(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1d[i][j]:0;
+  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(ED3_new(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1d[i][j]:0;
 }
 
 // u1d : case 3
@@ -163,17 +163,17 @@ double U1_ij_s3h(int i, int h, int j)
 // u1 : sample l
 double U1_j_hl_case1(int h, int l, int j)
 {
-  return feasible(h,l)?(up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT))) /s3[h][j]:0;
+  return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT))) /s3[h][j]:0;
 }
 
 double U1_j_hl_case2(int h, int l, int j)
 {
-  return feasible(h,l)?(up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j])) /s3[h][j]:0;
+  return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*u1[l+2][j])) /s3[h][j]:0;
 }
 
 double U1_j_hl_case3(int h, int l, int j)
 {
-  return feasible(h,l)?(up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]:0;
+  return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]:0;
 }
 
 void rnd_u(int i, int j, int* structure)

From e98206c36ac471a5b4ef26c6f464967d26c81930 Mon Sep 17 00:00:00 2001
From: Manoj Soni <manoj6891@gmail.com>
Date: Tue, 4 Oct 2011 23:12:34 -0400
Subject: [PATCH 249/282] u1d is now of length n+2 instead of length n+1 as
 suggested by shel

---
 gtfold-mfe/src/partition-func.c | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index ad52a21..51ceede 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -247,6 +247,11 @@ void init_part_arrays_negatives(){
       u1[i][j]=-1;
     }
   }
+  for(i=0; i<=n+1; ++i){
+   for(j=0; j<=n+1; ++j){
+    u1[i][j]=-1;
+   }
+  }
 }
 
 void init_partition_arrays()
@@ -288,7 +293,7 @@ void init_partition_arrays()
     u1[i+1][i] = 0;
     u1d[i+1][i] = 0;
   }
-  for(i=1; i<=n-1; i++){
+  for(i=1; i<=n; i++){//for(i=1; i<=n-1; i++){
     u1[i+2][i] = 0;
   }
   
@@ -463,7 +468,7 @@ void create_partition_arrays()
   s1 = mallocTwoD(len,len);
   s2 = mallocTwoD(len,len);
   s3 = mallocTwoD(len,len);
-  u1 = mallocTwoD(len,len);
+  u1 = mallocTwoD(len+1,len+1);//u1 = mallocTwoD(len,len);
 }
 
 void free_partition_arrays()
@@ -477,7 +482,7 @@ void free_partition_arrays()
   freeTwoD(s1,len,len);
   freeTwoD(s2,len,len);
   freeTwoD(s3,len,len);
-  freeTwoD(u1,len,len);
+  freeTwoD(u1,len+1,len+1);//freeTwoD(u1,len,len);
 }
 
 /*void calc_upm(int i, int j){
@@ -600,7 +605,7 @@ void calc_u1d(int i, int j){//printf("Entering calc_u1d: i=%d, j =%d\n",i,j);
         double p_val = 0;
         int l;
 
-        for(l=i+1; l<=j && l+2<=part_len; ++l){//ERROR in l,,,//up should be calculated before u1d
+        for(l=i+1; l<=j; ++l){//for(l=i+1; l<=j && l+2<=part_len; ++l){//ERROR in l,,,//up should be calculated before u1d
                 double v1 = (get_up(i,l)*exp((-1)*(c+auPenalty(i,l))/RT));
 		double v2 = (f(j+1,i,l)*exp((-1)*(j-l)*b/RT));
 		double v3 = (exp((-1)*(ED3_new(i,l,l+1)+b)/RT)*get_u1(l+2,j));

From 9d929f2854735c4bb54475666f9d6ceba5e6a149 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Wed, 5 Oct 2011 10:43:04 -0400
Subject: [PATCH 250/282] Fix suboptimal traceback code.

---
 gtfold-mfe/src/algorithms.c        | 506 ++++++++++++++---------------
 gtfold-mfe/src/subopt_traceback.cc | 360 ++++++++++----------
 gtfold-mfe/src/traceback.c         |   3 +-
 3 files changed, 436 insertions(+), 433 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index bdf40c4..ab53fa0 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -12,7 +12,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 GNU General Public License for more details.
 You should have received a copy of the GNU General Public License
 along with this program. If not, see <http://www.gnu.org/licenses/>.
-*/ 
+ */ 
 #include <stdio.h>
 #include <math.h>
 #include <time.h>
@@ -33,287 +33,287 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
 //#define DEBUG 1
 
 void initializeMatrix(int len) {
-	int i, j;
+  int i, j;
 
-	for (i = 1; i <= len; ++i) 
-		for (j = len; j >= i; --j) 
-			if (canPair(RNA[i],RNA[j]) && j-i > TURN) 
-				PP[i][j]  = 1;
+  for (i = 1; i <= len; ++i) 
+    for (j = len; j >= i; --j) 
+      if (canPair(RNA[i],RNA[j]) && j-i > TURN) 
+        PP[i][j]  = 1;
 }
 
 void prefilter(int len, int prefilter1, int prefilter2) {
-	char** in;
-	int i, j, k, count;
-
-	in = (char**)malloc(len*sizeof(char*));
-	for (i = 1; i <= len; ++i) in[i - 1] = (char*)malloc(len*sizeof(char));
-
-	for (i = 1; i <= len - prefilter2 + 1; ++i)
-		for (j = len; j >= prefilter2 && j >= i; --j) {
-			count = 0;
-			for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k)
-				if (PP[i + k][j - k] == 1) ++count;
-			if (count >= prefilter1)
-				for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k)
-					++in[i + k - 1][j - k - 1];
-		}
-
-	for (i = 1; i <= len; ++i) {
-		for (j = len; j >= i; --j)
-			if (!in[i - 1][j - 1]) PP[i][j] = 0;
-		free(in[i - 1]);
-	}
-
-	free(in);
+  char** in;
+  int i, j, k, count;
+
+  in = (char**)malloc(len*sizeof(char*));
+  for (i = 1; i <= len; ++i) in[i - 1] = (char*)malloc(len*sizeof(char));
+
+  for (i = 1; i <= len - prefilter2 + 1; ++i)
+    for (j = len; j >= prefilter2 && j >= i; --j) {
+      count = 0;
+      for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k)
+        if (PP[i + k][j - k] == 1) ++count;
+      if (count >= prefilter1)
+        for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k)
+          ++in[i + k - 1][j - k - 1];
+    }
+
+  for (i = 1; i <= len; ++i) {
+    for (j = len; j >= i; --j)
+      if (!in[i - 1][j - 1]) PP[i][j] = 0;
+    free(in[i - 1]);
+  }
+
+  free(in);
 }
 
 int calcVBI(int i, int j) {
-	int p=0, q=0;
-	int VBIij = INFINITY_;
-
-	for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
-		int minq = j-i+p-MAXLOOP-2;
-		if (minq < p+1+TURN) minq = p+1+TURN;
-		int maxq = (p==(i+1))?(j-2):(j-1);
-
-		for (q = minq; q <= maxq; q++) {
-			if (PP[p][q]==0) continue;
-			if (!canILoop(i,j,p,q)) continue;
-			VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
-		}
-	}
-
-	return VBIij;
+  int p=0, q=0;
+  int VBIij = INFINITY_;
+
+  for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
+    int minq = j-i+p-MAXLOOP-2;
+    if (minq < p+1+TURN) minq = p+1+TURN;
+    int maxq = (p==(i+1))?(j-2):(j-1);
+
+    for (q = minq; q <= maxq; q++) {
+      if (PP[p][q]==0) continue;
+      if (!canILoop(i,j,p,q)) continue;
+      VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij);
+    }
+  }
+
+  return VBIij;
 }
 
 int calcVBI1(int i, int j) {
-	int p=0, q=0;
-	int VBIij = INFINITY_;
-
-	for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
-		int minq = j-i+p-MAXLOOP-2;
-		if (minq < p+1+TURN) minq = p+1+TURN;
-		int maxq = (p==(i+1))?(j-2):(j-1);
-
-		for (q = minq; q <= maxq; q++) {
-			if (PP[p][q]==0) continue;
-			if (!canILoop(i,j,p,q)) continue;
-			VBIij = MIN(eL1(i, j, p, q) + V(p,q), VBIij);
-		}
-	}
-
-	return VBIij;
+  int p=0, q=0;
+  int VBIij = INFINITY_;
+
+  for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
+    int minq = j-i+p-MAXLOOP-2;
+    if (minq < p+1+TURN) minq = p+1+TURN;
+    int maxq = (p==(i+1))?(j-2):(j-1);
+
+    for (q = minq; q <= maxq; q++) {
+      if (PP[p][q]==0) continue;
+      if (!canILoop(i,j,p,q)) continue;
+      VBIij = MIN(eL1(i, j, p, q) + V(p,q), VBIij);
+    }
+  }
+
+  return VBIij;
 }
 
 int calcVBI2(int i, int j, int  len) {
-	int d, ii, jj; 
-	int energy = INFINITY_;
-
-	for (d = j-i-3; d >= TURN+1 && d >= j-i-2-MAXLOOP; --d) 
-		for (ii = i + 1; ii < j - d && ii <= len; ++ii)
-		{    
-			jj = d + ii;
-			if (PP[ii][jj]==1)
-				energy = MIN(energy, eL1(i, j, ii, jj) + V(ii, jj));
-		}    
-
-	return energy;
+  int d, ii, jj; 
+  int energy = INFINITY_;
+
+  for (d = j-i-3; d >= TURN+1 && d >= j-i-2-MAXLOOP; --d) 
+    for (ii = i + 1; ii < j - d && ii <= len; ++ii)
+    {    
+      jj = d + ii;
+      if (PP[ii][jj]==1)
+        energy = MIN(energy, eL1(i, j, ii, jj) + V(ii, jj));
+    }    
+
+  return energy;
 }
 
 int calculate(int len) { 
-								int b, i, j;
+  int b, i, j;
 #ifdef _OPENMP
-								if (g_nthreads > 0) omp_set_num_threads(g_nthreads);
+  if (g_nthreads > 0) omp_set_num_threads(g_nthreads);
 #endif
 
 #ifdef _OPENMP
 #pragma omp parallel
 #pragma omp master
-								fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
+  fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
 #endif
 
-								initializeMatrix(len);
-								if (g_unamode || g_prefilter_mode) {
-																prefilter(len,g_prefilter1,g_prefilter2);
-								}
-								
-								for (b = TURN+1; b <= len-1; b++) {
+  initializeMatrix(len);
+  if (g_unamode || g_prefilter_mode) {
+    prefilter(len,g_prefilter1,g_prefilter2);
+  }
+
+  for (b = TURN+1; b <= len-1; b++) {
 #ifdef _OPENMP
 #pragma omp parallel for private (i,j) schedule(guided)
 #endif
-																for (i = 1; i <= len - b; i++) {
-																								j = i + b;
-
-																								if (PP[i][j] == 1) {
-																																int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
-																																int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack
-
-																																// Internal Loop BEGIN
-																																if (g_unamode) 
-																																								VBI(i,j) = calcVBI1(i,j);
-																																else
-																																								VBI(i,j) = calcVBI(i,j);
-																																// Internal Loop END
-
-																																// Multi Loop BEGIN
-																																int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
-																																int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
-
-																																if (g_unamode || g_mismatch) { // unamode, terminal mismatch
-																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb);
-																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-1] + d5 + auPenalty(i,j) + Ea + Eb + Ec);
-																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-2] + d3 + auPenalty(i,j) + Ea + Eb + Ec);
-																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-2] + Estackm(i,j) + auPenalty(i,j) + Ea + Eb + 2*Ec);
-																																} else if (g_dangles == 2) { // -d2
-																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + d3 + d5 + auPenalty(i,j) + Ea + Eb);
-																																} else if (g_dangles == 0) { // -d0
-																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb);
-																																}	else { // default 
-																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb);
-																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-1] + d5 + auPenalty(i,j) + Ea + Eb + Ec);
-																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-2] + d3 + auPenalty(i,j) + Ea + Eb + Ec);
-																																								VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-2] + d3 + d5 + auPenalty(i,j) + Ea + Eb + 2*Ec);
-																																}
-																																VM(i,j) = canStack(i,j)?VM(i,j):INFINITY_;
-																																// Multi Loop END
-
-																																V(i,j) = MIN4(  eh,
-																																																es,
-																																																VBI(i,j),
-																																																VM(i,j));
-																								}
-																								else {
-																																V(i,j) = INFINITY_;
-																								}
-
-																								// Added auxillary storage WMPrime to speedup multiloop calculations
-																								int h;
-																								for (h = i+TURN+1 ; h <= j-TURN-2; h++) {
-																																WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); 
-																								}
-
-																								// WM begin
-																								int newWM = INFINITY_; 
-																								
-																								//ZS: This sum corresponds to when i,j are NOT paired with each other.
-																								//So we need to make sure only terms where i,j aren't pairing are considered. 
-																								newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM;
-
-																								if (g_unamode || g_mismatch) { // unamode
-																																newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
-																																newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
-																																newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
-																																if (i<j-TURN-2)
-																																								newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; 
-																								} else if (g_dangles == 2) {
-																																int energy = V(i,j) + auPenalty(i,j) + Eb;
-																																energy += (i==1)?Ed3(j,i,len):Ed3(j,i,i-1);
-																																/*if (j<len)*/ energy += Ed5(j,i,j+1);
-																																newWM = (canSS(i)&&canSS(j))?MIN(energy, newWM):newWM; //i,j dangle
-																								} else if (g_dangles == 0) {
-																																newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
-																								} else { // default
-																																newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
-																																newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
-																																newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
-																																newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; //i,j dangle
-																								}
-																								newWM = canSS(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; //i dangle
-																								newWM = canSS(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; //j dangle
-
-																								WMU(i,j) = WML(i,j) = newWM;
-																								// WM end
-																}
-								}
-						
-								for (j = TURN+2; j <= len; j++) {
-																int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
-																Wj = INFINITY_;
-																for (i = 1; i < j-TURN; i++) {
-																								Wij = Widjd = Wijd = Widj = INFINITY_;
-																								Wim1 = MIN(0, W[i-1]); 
-
-																								if (g_unamode || g_mismatch) { // unafold option
-																																Wij = V(i, j) + auPenalty(i, j) + Wim1;
-																																Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj;
-																																Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd;
-																																Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Estacke(j-1,i+1) + Wim1:Widjd;
-																																Wij = MIN4(Wij, Widjd, Wijd, Widj);
-																								} else if (g_dangles == 2) { // -d2 option
-																																int energy = V(i,j) +	 auPenalty(i,j) + Wim1;
-																																if (i>1) energy +=  Ed3(j,i,i-1);
-																																if (j<len) energy += Ed5(j,i,j+1);
-																																Widjd = (canSS(i)&&canSS(j))? energy:Widjd;
-																																Wij = MIN(Wij, Widjd);
-																								}	else if (g_dangles == 0) { // -d0 option
-																																Wij = V(i, j) + auPenalty(i, j) + Wim1;
-																								} else { // default
-																																Wij = V(i, j) + auPenalty(i, j) + Wim1;
-																																Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:INFINITY_;
-																																Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:INFINITY_;
-																																Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:INFINITY_;
-																																Wij = MIN4(Wij, Widjd, Wijd, Widj);
-																								}
-
-																								Wj = MIN(Wj,Wij); 
-																}
-																W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj;
-								}
+    for (i = 1; i <= len - b; i++) {
+      j = i + b;
+
+      if (PP[i][j] == 1) {
+        int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin
+        int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack
+
+        // Internal Loop BEGIN
+        if (g_unamode) 
+          VBI(i,j) = calcVBI1(i,j);
+        else
+          VBI(i,j) = calcVBI(i,j);
+        // Internal Loop END
+
+        // Multi Loop BEGIN
+        int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_;
+        int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_;
+
+        if (g_unamode || g_mismatch) { // unamode, terminal mismatch
+          VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb);
+          VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-1] + d5 + auPenalty(i,j) + Ea + Eb + Ec);
+          VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-2] + d3 + auPenalty(i,j) + Ea + Eb + Ec);
+          VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-2] + Estackm(i,j) + auPenalty(i,j) + Ea + Eb + 2*Ec);
+        } else if (g_dangles == 2) { // -d2
+          VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + d3 + d5 + auPenalty(i,j) + Ea + Eb);
+        } else if (g_dangles == 0) { // -d0
+          VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb);
+        }	else { // default 
+          VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb);
+          VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-1] + d5 + auPenalty(i,j) + Ea + Eb + Ec);
+          VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-2] + d3 + auPenalty(i,j) + Ea + Eb + Ec);
+          VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-2] + d3 + d5 + auPenalty(i,j) + Ea + Eb + 2*Ec);
+        }
+        VM(i,j) = canStack(i,j)?VM(i,j):INFINITY_;
+        // Multi Loop END
+
+        V(i,j) = MIN4(  eh,
+            es,
+            VBI(i,j),
+            VM(i,j));
+      }
+      else {
+        V(i,j) = INFINITY_;
+      }
+
+      // Added auxillary storage WMPrime to speedup multiloop calculations
+      int h;
+      for (h = i+TURN+1 ; h <= j-TURN-2; h++) {
+        WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); 
+      }
+
+      // WM begin
+      int newWM = INFINITY_; 
+
+      //ZS: This sum corresponds to when i,j are NOT paired with each other.
+      //So we need to make sure only terms where i,j aren't pairing are considered. 
+      newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM;
+
+      if (g_unamode || g_mismatch) { // unamode
+        newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
+        newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
+        newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
+        if (i<j-TURN-2)
+          newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; 
+      } else if (g_dangles == 2) {
+        int energy = V(i,j) + auPenalty(i,j) + Eb;
+        energy += (i==1)?Ed3(j,i,len):Ed3(j,i,i-1);
+        /*if (j<len)*/ energy += Ed5(j,i,j+1);
+        newWM = (canSS(i)&&canSS(j))?MIN(energy, newWM):newWM; //i,j dangle
+      } else if (g_dangles == 0) {
+        newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
+      } else { // default
+        newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); 
+        newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle
+        newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM;  //j dangle
+        newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; //i,j dangle
+      }
+      newWM = canSS(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; //i dangle
+      newWM = canSS(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; //j dangle
+
+      WMU(i,j) = WML(i,j) = newWM;
+      // WM end
+    }
+  }
+
+  for (j = 0; j <= len; j++) {
+    int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
+    Wj = INFINITY_;
+    for (i = 1; i < j-TURN; i++) {
+      Wij = Widjd = Wijd = Widj = INFINITY_;
+      Wim1 = MIN(0, W[i-1]); 
+
+      if (g_unamode || g_mismatch) { // unafold option
+        Wij = V(i, j) + auPenalty(i, j) + Wim1;
+        Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj;
+        Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd;
+        Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Estacke(j-1,i+1) + Wim1:Widjd;
+        Wij = MIN4(Wij, Widjd, Wijd, Widj);
+      } else if (g_dangles == 2) { // -d2 option
+        int energy = V(i,j) +	 auPenalty(i,j) + Wim1;
+        if (i>1) energy +=  Ed3(j,i,i-1);
+        if (j<len) energy += Ed5(j,i,j+1);
+        Widjd = (canSS(i)&&canSS(j))? energy:Widjd;
+        Wij = MIN(Wij, Widjd);
+      }	else if (g_dangles == 0) { // -d0 option
+        Wij = V(i, j) + auPenalty(i, j) + Wim1;
+      } else { // default
+        Wij = V(i, j) + auPenalty(i, j) + Wim1;
+        Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:INFINITY_;
+        Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:INFINITY_;
+        Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:INFINITY_;
+        Wij = MIN4(Wij, Widjd, Wijd, Widj);
+      }
+
+      Wj = MIN(Wj,Wij); 
+    }
+    W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj;
+  }
 
 #ifdef DEBUG
-								FILE* file = fopen("VBI.txt", "w");
-								int ii, jj;
-								for (ii = 1; ii <= len; ++ii) {    
-																for (jj = len; jj > ii; --jj) {
-																								fprintf(file, "%d %d %d\n",ii,jj,VBI(ii,jj));
-																}
-								}    
-								fclose(file);
-
-								file = fopen("Eh.txt", "w");
-								for (ii = 1; ii <= len; ++ii) {    
-																for (jj = len; jj > ii; --jj) {
-																				int eh = INFINITY_;
-																			 if (PP[ii][jj])	eh = eH(ii,jj);
-																				fprintf(file, "%d %d %d\n",ii,jj,eh>=INFINITY_?INFINITY_:eh);
-																}
-								}    
-								fclose(file);
-	
-								file = fopen("Es.txt", "w");
-								for (ii = 1; ii <= len; ++ii) {    
-																for (jj = len; jj > ii; --jj) {
-																				int es = INFINITY_;
-																				if (PP[ii][jj] && PP[ii+1][jj-1]) es = eS(ii,jj);
-																				fprintf(file, "%d %d %d\n",ii,jj,es>=INFINITY_?INFINITY_:es);
-																}
-								}    
-								fclose(file);
-															
-								file = fopen("BP.txt", "w");
-								for (ii = 1; ii <= len; ++ii) {    
-																for (jj = len; jj > ii; --jj) {
-																								fprintf(file, "%d %d %d\n",ii,jj,PP[ii][jj]);
-																}
-								}    
-								fclose(file);
-
-								file = fopen("VM.txt", "w");
-								for (ii = 1; ii <= len; ++ii) {    
-																for (jj = len; jj > ii; --jj) {
-																								fprintf(file, "%d %d %d\n",ii,jj,VM(ii,jj));
-																}
-								}    
-								fclose(file);
-
-								file = fopen("WM.txt", "w");
-								for (ii = 1; ii <= len; ++ii) {    
-																for (jj = len; jj > ii; --jj) {
-																								fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj));
-																}
-								}    
-								fclose(file);
+  FILE* file = fopen("VBI.txt", "w");
+  int ii, jj;
+  for (ii = 1; ii <= len; ++ii) {    
+    for (jj = len; jj > ii; --jj) {
+      fprintf(file, "%d %d %d\n",ii,jj,VBI(ii,jj));
+    }
+  }    
+  fclose(file);
+
+  file = fopen("Eh.txt", "w");
+  for (ii = 1; ii <= len; ++ii) {    
+    for (jj = len; jj > ii; --jj) {
+      int eh = INFINITY_;
+      if (PP[ii][jj])	eh = eH(ii,jj);
+      fprintf(file, "%d %d %d\n",ii,jj,eh>=INFINITY_?INFINITY_:eh);
+    }
+  }    
+  fclose(file);
+
+  file = fopen("Es.txt", "w");
+  for (ii = 1; ii <= len; ++ii) {    
+    for (jj = len; jj > ii; --jj) {
+      int es = INFINITY_;
+      if (PP[ii][jj] && PP[ii+1][jj-1]) es = eS(ii,jj);
+      fprintf(file, "%d %d %d\n",ii,jj,es>=INFINITY_?INFINITY_:es);
+    }
+  }    
+  fclose(file);
+
+  file = fopen("BP.txt", "w");
+  for (ii = 1; ii <= len; ++ii) {    
+    for (jj = len; jj > ii; --jj) {
+      fprintf(file, "%d %d %d\n",ii,jj,PP[ii][jj]);
+    }
+  }    
+  fclose(file);
+
+  file = fopen("VM.txt", "w");
+  for (ii = 1; ii <= len; ++ii) {    
+    for (jj = len; jj > ii; --jj) {
+      fprintf(file, "%d %d %d\n",ii,jj,VM(ii,jj));
+    }
+  }    
+  fclose(file);
+
+  file = fopen("WM.txt", "w");
+  for (ii = 1; ii <= len; ++ii) {    
+    for (jj = len; jj > ii; --jj) {
+      fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj));
+    }
+  }    
+  fclose(file);
 #endif
 
-								return W[len];
+  return W[len];
 }
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index 2d3d9ed..cbf7e7a 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -1,22 +1,22 @@
 /**
- GTfold: compute minimum free energy of RNA secondary structure
- Copyright (C) 2008  David A. Bader
- http://www.cc.gatech.edu/~bader
+GTfold: compute minimum free energy of RNA secondary structure
+Copyright (C) 2008  David A. Bader
+http://www.cc.gatech.edu/~bader
 
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
 
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- GNU General Public License for more details.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
 
- You should have received a copy of the GNU General Public License
- along with this program.  If not, see <http://www.gnu.org/licenses/>.
- 
- @author prashant {pgaurav@gatech.edu}
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+@author prashant {pgaurav@gatech.edu}
 
  */
 
@@ -39,194 +39,196 @@ static int length = -1;
 static int gflag = 0;
 
 void process(ss_map_t& subopt_data, int len) {
-								int count = 0 ;
-								ps_stack_t gstack;
-
-								// initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} 
-								ps_t first(0, len);
-								first.push(segment(1, len, lW, W[len]));	
-								gstack.push(first); // initialize the partial structure stacka
-
-								while (1) {
-																if (gstack.empty()) break; // exit
-																ps_t ps = gstack.top();
-																gstack.pop(); 
-
-																if (ps.empty()) {
-																								count++;
-																								subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
-																								continue;
-																}	
-																else {
-																								segment smt = ps.top();
-																								ps.pop();
-																								
-																								gflag = 0;
-																								if (smt.j_ - smt.i_ > TURN) {
-																																(*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack);
-																								}
-																								
-																								// discarded current segment, using remaining ones
-																								if (!gflag) {
-																																ps_t ps1(ps);
-																																gstack.push(ps1);
-																								}
-																}
-								}
-								
+        int count = 0;
+        ps_stack_t gstack;
+
+
+        // initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} 
+        ps_t first(0, len);
+        first.push(segment(1, len, lW, W[len]));	
+        gstack.push(first); // initialize the partial structure stacka
+
+        while (1) {
+                if (gstack.empty()) break; // exit
+                ps_t ps = gstack.top();
+                gstack.pop();
+
+                if (ps.empty()) {
+                        count++;
+                        subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
+                        continue;
+                }	
+                else {
+                       segment smt = ps.top();
+                        ps.pop();
+
+                        gflag = 0;
+                        if (smt.j_ - smt.i_ > TURN) {
+                                (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack);
+                        }
+
+                        // discarded current segment, using remaining ones
+                        if (!gflag) {
+                                ps_t ps1(ps);
+                                gstack.push(ps1);
+                        }
+                }
+        }
+
 #ifdef DEBUG 
-								printf("# SS = %d\n", count);
+        printf("# SS = %d\n", count);
 #endif
 }
 
 ss_map_t subopt_traceback(int len, int _delta) {
-								trace_func[0] = traceW;
-								trace_func[1] = traceV;
-								/* trace_func[2] = traceVBI;*/
-								trace_func[3] = traceVM;
-								trace_func[4] = traceWM;
-								trace_func[5] = traceWMPrime;
+        trace_func[0] = traceW;
+        trace_func[1] = traceV;
+        trace_func[2] = traceVBI;
+        trace_func[3] = traceVM;
+        trace_func[4] = traceWM;
+        trace_func[5] = traceWMPrime;
 
-								mfe = W[len];
-								delta = _delta;
-								length = len;
+        mfe = W[len];
+        delta = _delta;
+        length = len;
 
-								ss_map_t subopt_data;
-								process(subopt_data, len);
+        ss_map_t subopt_data;
+        process(subopt_data, len);
 
-								return subopt_data;
+        return subopt_data;
 }
 
 void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) {
-								// Hairpin Loop
-								if (eH(i,j) + ps.total()  <= mfe + delta) {
-																ps_t ps1(ps); 
-																ps1.accumulate(eH(i,j));
-																ps1.update(i, j, '(', ')');
-																push_to_gstack(gstack, ps1);
-								}
-
-								// Stack
-								if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) {
-																ps_t ps1(ps);
-																ps1.push(segment(i+1, j-1, lV, V(i+1, j-1)));
-																ps1.accumulate(eS(i,j));
-																ps1.update(i, j , '(', ')');
-																push_to_gstack(gstack, ps1);
-								}
-
-								// Internal Loop
-								if (VBI(i,j) + ps.total() <= mfe + delta) {
-																traceVBI(i,j,ps,gstack);
-								}
-
-								// Multiloop
-								if ( VM(i,j) + ps.total() <= mfe + delta) {
-																ps_t ps1(ps);
-																ps1.push(segment(i, j, lVM, VM(i,j)));
-																ps1.update(i, j, '(', ')');
-																push_to_gstack(gstack, ps1);
-								}
+        // Hairpin Loop
+        if (eH(i,j) + ps.total()  <= mfe + delta) {
+                ps_t ps1(ps); 
+                ps1.accumulate(eH(i,j));
+                ps1.update(i, j, '(', ')');
+                push_to_gstack(gstack, ps1);
+        }
+
+        // Stack
+        if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) {
+                ps_t ps1(ps);
+                ps1.push(segment(i+1, j-1, lV, V(i+1, j-1)));
+                ps1.accumulate(eS(i,j));
+                ps1.update(i, j , '(', ')');
+                push_to_gstack(gstack, ps1);
+        }
+
+        // Internal Loop
+        if (VBI(i,j) + ps.total() <= mfe + delta) {
+                traceVBI(i,j,ps,gstack);
+        }
+
+        // Multiloop
+        if ( VM(i,j) + ps.total() <= mfe + delta) {
+                ps_t ps1(ps);
+                ps1.push(segment(i, j, lVM, VM(i,j)));
+                ps1.update(i, j, '(', ')');
+                push_to_gstack(gstack, ps1);
+        }
 }
 
 void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) {
-								int p,q;
-
-								for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
-																int minq = j-i+p-MAXLOOP-2;
-																if (minq < p+1+TURN) minq = p+1+TURN;
-																int maxq = (p==(i+1))?(j-2):(j-1);
-																for (q = minq; q <= maxq; q++) {
-																								if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta) {
-																																ps_t ps1(ps);
-																																ps1.push(segment(p, q, lV, V(p, q)));
-																																ps1.update(i, j , '(', ')');
-																																ps1.accumulate(eL(i, j, p, q));
-																																push_to_gstack(gstack, ps1);
-																								}
-																}
-								}
+        int p,q;
+
+        for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
+                int minq = j-i+p-MAXLOOP-2;
+                if (minq < p+1+TURN) minq = p+1+TURN;
+                int maxq = (p==(i+1))?(j-2):(j-1);
+                for (q = minq; q <= maxq; q++) {
+                        if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta) {
+                                ps_t ps1(ps);
+                                ps1.push(segment(p, q, lV, V(p, q)));
+                                ps1.update(i, j , '(', ')');
+                                ps1.accumulate(eL(i, j, p, q));
+                                push_to_gstack(gstack, ps1);
+                        }
+                }
+        }
 }
 
-void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack) {
-								for (int i = 1; i < j-TURN; ++i) {
-																int wim1 =  MIN(0, W[i-1]);
-																int d3 = (i>1)?Ed3(j,i,i-1):0;
-																int d5 = (j<length)?Ed5(j,i,j+1):0;
-																
-																int Wij = V(i,j) + auPenalty(i, j) + d3 + d5 + wim1;
-																if (Wij + ps.total() <= mfe + delta ) {
-																								ps_t ps1(ps);
-																								ps1.push(segment(i, j, lV, V(i,j)));
-																								if (wim1 == W[i-1]) ps1.push(segment(1, i-1, lW, W[i-1]));
-																								ps1.accumulate(auPenalty(i, j) + d3 + d5);
-																								push_to_gstack(gstack, ps1);
-																}
-								}
-
-								if (W[j-1] + ps.total() <= mfe + delta) {
-																ps_t ps1(ps);
-																ps1.push(segment(1, j-1, lW, V(1,j-1)));
-																push_to_gstack(gstack, ps1);
-								}
+void traceW(int i, int j, ps_t& ps, ps_stack_t& gstack) {
+
+        for (int l = i; l < j-TURN; ++l) {
+                int wim1 =  MIN(0, W[l-1]);
+                int d3 = (l>i)?Ed3(j,l,l-1):0;
+                int d5 = (j<length)?Ed5(j,l,j+1):0;
+
+                int Wij = V(l,j) + auPenalty(l, j) + d3 + d5 + wim1;
+                if (Wij + ps.total() <= mfe + delta ) {
+                        ps_t ps1(ps);
+                        ps1.push(segment(l, j, lV, V(l,j)));
+                        if (wim1 == W[l-1]) ps1.push(segment(i, l-1, lW, W[l-1]));
+                        ps1.accumulate(auPenalty(l, j) + d3 + d5);
+                        push_to_gstack(gstack, ps1);
+                }
+        }
+
+        if (W[j-1] + ps.total() <= mfe + delta) {
+                ps_t ps1(ps);
+                ps1.push(segment(i, j-1, lW, W[j-1]));
+                push_to_gstack(gstack, ps1);
+        }
 }
-								
+
 void traceWM(int i, int j, ps_t& ps, ps_stack_t& gstack) {
-								int d3 = (i==1)?Ed3(j,i,length):Ed3(j,i,i-1);
-								int d5 = Ed5(j,i,j+1);
-								
-								if (V(i,j) + auPenalty(i, j) + Eb + d3 + d5 + ps.total() <= mfe + delta) {
-																ps_t ps_new(ps);
-																ps_new.accumulate(auPenalty(i, j) + Eb + d3 + d5);
-																ps_new.push(segment(i,j, lV, V(i,j)));
-																push_to_gstack(gstack, ps_new);
-								}
-								
-								if (WMPrime[i][j] + ps.total() <= mfe + delta) {
-																ps_t ps_new(ps);
-																ps_new.push(segment(i,j, lWMPrime, WMPrime[i][j]));
-																push_to_gstack(gstack, ps_new);
-								}
-								
-								if (WM(i+1,j) + Ec + ps.total() <= mfe + delta) {
-																ps_t ps_new(ps);
-																ps_new.accumulate(Ec);
-																ps_new.push(segment(i+1,j, lWM, WM(i+1,j)));
-																push_to_gstack(gstack, ps_new);
-								}
-								
-								if (WM(i,j-1) + Ec + ps.total() <= mfe + delta) {
-																ps_t ps_new(ps);
-																ps_new.accumulate(Ec);
-																ps_new.push(segment(i,j-1, lWM, WM(i,j-1)));
-																push_to_gstack(gstack, ps_new);
-								}
+        int d3 = (i==1)?Ed3(j,i,length):Ed3(j,i,i-1);
+        int d5 = Ed5(j,i,j+1);
+
+        if (V(i,j) + auPenalty(i, j) + Eb + d3 + d5 + ps.total() <= mfe + delta) {
+                ps_t ps_new(ps);
+                ps_new.accumulate(auPenalty(i, j) + Eb + d3 + d5);
+                ps_new.push(segment(i,j, lV, V(i,j)));
+                push_to_gstack(gstack, ps_new);
+        }
+
+        if (WMPrime[i][j] + ps.total() <= mfe + delta) {
+                ps_t ps_new(ps);
+                ps_new.push(segment(i,j, lWMPrime, WMPrime[i][j]));
+                push_to_gstack(gstack, ps_new);
+        }
+
+        if (WM(i+1,j) + Ec + ps.total() <= mfe + delta) {
+                ps_t ps_new(ps);
+                ps_new.accumulate(Ec);
+                ps_new.push(segment(i+1,j, lWM, WM(i+1,j)));
+                push_to_gstack(gstack, ps_new);
+        }
+
+        if (WM(i,j-1) + Ec + ps.total() <= mfe + delta) {
+                ps_t ps_new(ps);
+                ps_new.accumulate(Ec);
+                ps_new.push(segment(i,j-1, lWM, WM(i,j-1)));
+                push_to_gstack(gstack, ps_new);
+        }
 }
 
 void traceWMPrime(int i, int j, ps_t& ps, ps_stack_t& gstack) {
-								for (int h = i+TURN+1 ; h <= j-TURN-2; h++) {
-																if (WM(i,h-1) + WM(h,j) + ps.total() <= mfe + delta) {
-																								ps_t ps_new(ps);
-																								ps_new.push(segment(i,h-1, lWM, WM(i,h-1)));
-																								ps_new.push(segment(h,j, lWM, WM(h,j)));
-																								push_to_gstack(gstack, ps_new);
-																}
-								}
+        for (int h = i+TURN+1 ; h <= j-TURN-2; h++) {
+                if (WM(i,h-1) + WM(h,j) + ps.total() <= mfe + delta) {
+                        ps_t ps_new(ps);
+                        ps_new.push(segment(i,h-1, lWM, WM(i,h-1)));
+                        ps_new.push(segment(h,j, lWM, WM(h,j)));
+                        push_to_gstack(gstack, ps_new);
+                }
+        }
 }
 
 void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) {
-								int d3 = Ed3(i,j,j-1);
-								int d5 = Ed5(i,j,i+1);
-
-								if (WMPrime[i+1][j-1] + Ea + Eb + auPenalty(i, j) + d3 + d5 + ps.total() <= mfe + delta) {
-																ps_t ps_new(ps);
-																ps_new.accumulate(Ea + Eb + auPenalty(i, j) + d3 + d5); 
-																ps_new.push(segment(i+1,j-1, lWMPrime,WMPrime[i+1][j-1] ));
-																push_to_gstack(gstack, ps_new);
-								}
+        int d3 = Ed3(i,j,j-1);
+        int d5 = Ed5(i,j,i+1);
+
+        if (WMPrime[i+1][j-1] + Ea + Eb + auPenalty(i, j) + d3 + d5 + ps.total() <= mfe + delta) {
+                ps_t ps_new(ps);
+                ps_new.accumulate(Ea + Eb + auPenalty(i, j) + d3 + d5); 
+                ps_new.push(segment(i+1,j-1, lWMPrime,WMPrime[i+1][j-1] ));
+                push_to_gstack(gstack, ps_new);
+        }
 }
 
-void push_to_gstack(ps_stack_t& gstack , const ps_t& v) {
-								gflag = 1;
-								gstack.push(v);
+void push_to_gstack(ps_stack_t& gstack , ps_t& v) {
+        gflag = 1;
+        gstack.push(v);
 }
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 35c7c29..3e13199 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -56,7 +56,8 @@ void traceW(int j) {
 	int done = 0, i;
 	int wim1, flag = 1 ;
 	
-	assert(!(j == 0 || j == 1)); 
+  if (j == 0 || j == 1)
+    return;
 	
 	for (i = 1; i < j && !done; i++) {
 		if (j-i < TURN) continue;

From 4b1ad01498e30b62f115ef02f876375633f3fe74 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Thu, 6 Oct 2011 19:59:35 -0400
Subject: [PATCH 251/282] 1. Merge Pseudoknot Detection Tests. 2. Fix a
 segmentation fault issue that occurred due to change in subopt code fix.

---
 gtfold-mfe/src/algorithms.c                   |   2 +-
 gtfold-mfe/src/subopt_traceback.cc            |   2 +-
 gtfold-mfe/tests/config/test-list.conf        |   3 +-
 gtfold-mfe/tests/config/test-params.conf      |  13 ++-
 .../seq1.constraint                           |   4 +
 .../pseudoknot_detection_sequences/seq1.ct    |  20 ++++
 .../seq1.expectedresult                       |   1 +
 .../pseudoknot_detection_sequences/seq1.seq   |   1 +
 .../seq2.constraint                           |   2 +
 .../seq2.expectedresult                       |   1 +
 .../pseudoknot_detection_sequences/seq2.seq   |   1 +
 .../seq3.constraint                           |   3 +
 .../seq3.expectedresult                       |   1 +
 .../pseudoknot_detection_sequences/seq3.seq   |   1 +
 .../seq4.constraint                           |   4 +
 .../seq4.expectedresult                       |   1 +
 .../pseudoknot_detection_sequences/seq4.seq   |   1 +
 .../seq5.constraint                           |   1 +
 .../seq5.expectedresult                       |   1 +
 .../pseudoknot_detection_sequences/seq5.seq   |   1 +
 .../seq6.constraint                           |   5 +
 .../seq6.expectedresult                       |   1 +
 .../pseudoknot_detection_sequences/seq6.seq   |   1 +
 .../seq7.constraint                           |   4 +
 .../seq7.expectedresult                       |   1 +
 .../pseudoknot_detection_sequences/seq7.seq   |   1 +
 .../seq8.constraint                           |   4 +
 .../seq8.expectedresult                       |   1 +
 .../pseudoknot_detection_sequences/seq8.seq   |   1 +
 .../tests/scripts/PseudoKnotDetection.pm      |  49 +++++++++
 .../tests/scripts/Scoregtwithunafold.pm       |   2 +-
 gtfold-mfe/tests/scripts/start_test.pm        | 102 ++++++++++++------
 gtfold-mfe/tests/scripts/test_utils.pl        |   4 +-
 33 files changed, 197 insertions(+), 43 deletions(-)
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult
 create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq
 create mode 100755 gtfold-mfe/tests/scripts/PseudoKnotDetection.pm

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index ab53fa0..1f6da10 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -257,7 +257,7 @@ int calculate(int len) {
 
       Wj = MIN(Wj,Wij); 
     }
-    W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj;
+    W[j] = (j!=0 && canSS(j))?MIN(Wj, W[j-1]):Wj;
   }
 
 #ifdef DEBUG
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index cbf7e7a..b27b059 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -228,7 +228,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) {
         }
 }
 
-void push_to_gstack(ps_stack_t& gstack , ps_t& v) {
+void push_to_gstack(ps_stack_t& gstack, const ps_t& v) {
         gflag = 1;
         gstack.push(v);
 }
diff --git a/gtfold-mfe/tests/config/test-list.conf b/gtfold-mfe/tests/config/test-list.conf
index b339d8d..827ab10 100644
--- a/gtfold-mfe/tests/config/test-list.conf
+++ b/gtfold-mfe/tests/config/test-list.conf
@@ -1 +1,2 @@
-Scoregtwithunafold
+#Scoregtwithunafold
+PseudoKnotDetection
diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf
index 2922a50..d1fdec2 100644
--- a/gtfold-mfe/tests/config/test-params.conf
+++ b/gtfold-mfe/tests/config/test-params.conf
@@ -2,21 +2,26 @@
 G_GTFOLD_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/src/
 G_UNAFOLD_DIR=/home/users/rbanga/rna/unafold/install/bin/
 #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/
-G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/
-G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/23S_sequences/
+#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/
+G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/
+#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/23S_sequences/
 #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/Other_sequences/
 G_WORK_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/work/
 G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test-list.conf
 
-#Sequence Inclusion Filters
+# Sequence Inclusion Filters
 #G_INCLUDE_SEQUENCES=rad
 #G_INCLUDE_SEQUENCES=d.16.e.B.g*
 #G_INCLUDE_SEQUENCES=d.16.e.B.m*
 #G_INCLUDE_SEQUENCES=d.16.e.B.h*
-G_INCLUDE_SEQUENCES=d.16.e.G.va*
+#G_INCLUDE_SEQUENCES=d.16.e.G.va*
 #G_EXCLUDE_SEQUENCES=d.16.e.A.*
 #G_EXCLUDE_SEQUENCES=d.16.e.B.ma*
 #G_INCLUDE_SEQUENCES=acc1
 #G_INCLUDE_SEQUENCES=a.*j
 #G_INCLUDE_SEQUENCES=a..tb*
 
+# Local Sequence Directories
+
+# Directory containing sequences for testing pseudoknot detection logic
+L_PSEUDOKNOTDETECTION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/pseudoknot_detection_sequences/
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint
new file mode 100644
index 0000000..2a01386
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint
@@ -0,0 +1,4 @@
+F 1 19 2
+F 3 10 1
+F 4 8 1
+F 11 15 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct
new file mode 100644
index 0000000..da642b1
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct
@@ -0,0 +1,20 @@
+19	  dG = 10.1
+1	C	0	2	0	1
+2	C	1	3	0	2
+3	C	2	4	0	3
+4	C	3	5	0	4
+5	A	4	6	0	5
+6	A	5	7	0	6
+7	G	6	8	0	7
+8	A	7	9	0	8
+9	A	8	10	0	9
+10	G	9	11	0	10
+11	C	10	12	0	11
+12	A	11	13	0	12
+13	A	12	14	0	13
+14	A	13	15	0	14
+15	G	14	16	0	15
+16	A	15	17	0	16
+17	A	16	18	0	17
+18	G	17	19	0	18
+19	G	18	0	0	19
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult
new file mode 100644
index 0000000..573541a
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult
@@ -0,0 +1 @@
+0
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq
new file mode 100644
index 0000000..0964dc3
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq
@@ -0,0 +1 @@
+CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint
new file mode 100644
index 0000000..2a8e728
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint
@@ -0,0 +1,2 @@
+F 1 19 2
+F 15 21 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq
new file mode 100644
index 0000000..23023c5
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq
@@ -0,0 +1 @@
+CCAAAAAAAAAAAACAAGGAG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint
new file mode 100644
index 0000000..bcbe409
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint
@@ -0,0 +1,3 @@
+F 1 19 2
+F 3 10 2
+F 15 23 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq
new file mode 100644
index 0000000..6b590de
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq
@@ -0,0 +1 @@
+CCCCAAAAGGAAAACAAGGAAAG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint
new file mode 100644
index 0000000..cece32a
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint
@@ -0,0 +1,4 @@
+F 1 19 2
+F 3 18 1
+F 4 7 1
+F 11 15 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq
new file mode 100644
index 0000000..0964dc3
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq
@@ -0,0 +1 @@
+CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint
new file mode 100644
index 0000000..7029d7d
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint
@@ -0,0 +1 @@
+F 1 8 8
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq
new file mode 100644
index 0000000..0984ecd
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq
@@ -0,0 +1 @@
+CCCCCGGGGGGAAAGGG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint
new file mode 100644
index 0000000..adb4fdb
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint
@@ -0,0 +1,5 @@
+F 1 19 2
+F 3 10 1
+F 4 8 1
+F 11 15 1
+F 24 25 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq
new file mode 100644
index 0000000..9a1d7d8
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq
@@ -0,0 +1 @@
+CCCCAAGAAGCAAAGAAGGCCCACGAAAA
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint
new file mode 100644
index 0000000..2ce893a
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint
@@ -0,0 +1,4 @@
+F 0 19 2
+F 3 10 1
+F 4 8 1
+F 11 15 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq
new file mode 100644
index 0000000..0964dc3
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq
@@ -0,0 +1 @@
+CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint
new file mode 100644
index 0000000..65ea20f
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint
@@ -0,0 +1,4 @@
+F 1 19 2
+F 3 10 1
+F 4 8 1
+F 11 24 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq
new file mode 100644
index 0000000..0964dc3
--- /dev/null
+++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq
@@ -0,0 +1 @@
+CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/scripts/PseudoKnotDetection.pm b/gtfold-mfe/tests/scripts/PseudoKnotDetection.pm
new file mode 100755
index 0000000..1bdfc38
--- /dev/null
+++ b/gtfold-mfe/tests/scripts/PseudoKnotDetection.pm
@@ -0,0 +1,49 @@
+#!/usr/bin/perl
+package PseudoKnotDetection;
+use strict;
+use warnings;
+use File::Basename;
+
+sub test()
+{
+  my(%Config) = %{$_[1]};
+  my(%Sequences) = %{$_[2]};
+  my(%local_sequences) = %{$_[3]};
+  my $logger = $_[4];
+
+  my $gtdir = $Config{"G_GTFOLD_DIR"};
+  my $unadir = $Config{"G_UNAFOLD_DIR"};
+  my $workdir = $Config{"G_WORK_DIR"};
+
+  my $key;
+  my $value;
+
+  # For testing pseudoknot detection logic
+  # we may only test the sequences specified in local_sequences
+  while (($key, $value) = each(%local_sequences)) {
+
+	  my $seqname=$key;
+	  my $path;
+	  my $suffix;
+
+	  my $seqfile = $value;
+    my $dirname = dirname($seqfile);
+    my $constraint_file = "$dirname/$seqname.constraint";
+	  my $gtout  = "$workdir$seqname-gt";
+	  my $gtoutfilename  = $workdir."$seqname-gt.ct";
+
+	  my $gtcmd = "$gtdir/gtfold -c $constraint_file -m $seqfile -o $gtout > /dev/null 2>&1";
+	  my $x = system("$gtcmd") >> 8;
+
+    my $expected_result_file = "$dirname/$seqname.expectedresult";
+    my $expected_result = `head -n 1 $expected_result_file`;     
+
+    if ($expected_result =~ $x) {
+      $logger->error("TEST PASSED: $seqname: Return Value $x matched expected output $expected_result");
+    }
+    else {
+      $logger->error("TEST FAILED: $seqname: Return Value $x did not match expected output $expected_result");
+    }
+  }
+}
+1;
diff --git a/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm
index 41ffe28..7cdfb82 100755
--- a/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm
+++ b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm
@@ -8,7 +8,7 @@ sub test()
 {
   my(%Config) = %{$_[1]};
   my(%Sequences) = %{$_[2]};
-  my $logger = $_[3];
+  my $logger = $_[4];
 
   my $gtdir = $Config{"G_GTFOLD_DIR"};
   my $unadir = $Config{"G_UNAFOLD_DIR"};
diff --git a/gtfold-mfe/tests/scripts/start_test.pm b/gtfold-mfe/tests/scripts/start_test.pm
index 16e53c3..83fb8ee 100755
--- a/gtfold-mfe/tests/scripts/start_test.pm
+++ b/gtfold-mfe/tests/scripts/start_test.pm
@@ -10,9 +10,11 @@ use Log::Log4perl qw(:easy);
 require 'test_utils.pl';
 
 my $configdir="../config";
+
 Log::Log4perl::init( "$configdir/root-logger.conf" );
 my $logger = Log::Log4perl->get_logger;
 
+
 $logger->info("Starting Tests...");
 
 # Read Parameter File
@@ -37,30 +39,10 @@ my @seqdir_arr = @{$Config{"G_SEQUENCE_DIR"}};
 my $seq_include_regex = $Config{"G_INCLUDE_SEQUENCES"};
 my $seq_exclude_regex = $Config{"G_EXCLUDE_SEQUENCES"};
 
-foreach (@seqdir_arr) {
-
-  opendir(DIR, $_) || die $!;
-  while (my $seqfile = readdir(DIR)) {
-
-	  my $seqname;
-	  my $path;
-	  my $suffix;
-	  ($seqname,$path,$suffix) = fileparse($seqfile);
-
-	  if (-d $seqfile) {
-		  next;
-	  }
-
-    $seqfile = "$_$seqname";
-    my $seq_include = (not defined($seq_include_regex)) || ($seqname =~ /$seq_include_regex/);
-
-    my $seq_exclude = (not defined($seq_exclude_regex)) || ($seqname !~ /$seq_exclude_regex/);
-    if ( $seq_include && $seq_exclude ) {
-      $Sequences{$seqname} = $seqfile;
-      $logger->info("Selected Sequence ... $seqname");
-    }
-  }
-}
+%Sequences = find_sequences_from_dir(
+                seq_include_regex => $seq_include_regex,
+                seq_exclude_regex => $seq_exclude_regex,
+                seq_dirs => @seqdir_arr);
 
 my $test_include_regex = $Config{"G_INCLUDE_TESTS"};
 my $test_exclude_regex = $Config{"G_EXCLUDE_TESTS"};
@@ -78,17 +60,71 @@ open(TESTLISTFILE, $test_list_file) || die("Could not open file: $test_list_file
       $testname =~ s/\s*$//;     # Remove spaces at the end of the line
       if ( ($testname !~ /^#/) && ($testname ne "") ) {    # Ignore lines starting with # and blank lines
 
-      my $test_include = (not defined($test_include_regex)) || ($testname =~ /$seq_include_regex/);
+        my $test_include = (not defined($test_include_regex)) || ($testname =~ /$seq_include_regex/);
+        my $test_exclude = (not defined($test_exclude_regex)) || ($testname !~ /$test_exclude_regex/);
+
+        if ( $test_include && $test_exclude ) {
+          my $uppertestname = uc($testname);
+          my $local_sequence_dirname = "L_".$uppertestname."_SEQUENCE_DIR";
+          my $local_sequence_include_regex = $Config{"L_".$uppertestname."_SEQUENCE_INCLUDE"};
+          my $local_sequence_exclude_regex = $Config{"L_".$uppertestname."_SEQUENCE_EXCLUDE"};
+          my @local_sequence_dir;
+          my %local_sequences;
+
+          if (defined($Config{$local_sequence_dirname})) {
+            @local_sequence_dir = @{$Config{$local_sequence_dirname}};
+            %local_sequences = find_sequences_from_dir(
+                    seq_include_regex => $local_sequence_include_regex,
+                    seq_exclude_regex => $local_sequence_exclude_regex,
+                    seq_dirs => @local_sequence_dir);
+          }
+
+          my $module = $testname;
+          load($module);
+          $module->test(\%Config, \%Sequences, \%local_sequences, $logger);
+        }
+      }
+   }
 
-      my $test_exclude = (not defined($test_exclude_regex)) || ($testname !~ /$test_exclude_regex/);
 
-      if ( $test_include && $test_exclude ) {
-        my $module = $testname;
-        load($module);
-        $module->test(\%Config, \%Sequences, $logger);
-      }
-    
-    }
+sub find_sequences_from_dir
+{
 
+my %args = @_;
+
+my %seq_hash;
+my $include_regex = $args{seq_include_regex};
+my $exclude_regex = $args{seq_exclude_regex};
+my @seqdirs = $args{seq_dirs};
+
+if (scalar(@seqdirs) eq 0) {
+  return %seq_hash;
+}
+
+foreach (@seqdirs) {
+
+  opendir(DIR, $_) || die $!;
+  while (my $seqfile = readdir(DIR)) {
+
+	  my $seqname;
+	  my $path;
+	  my $suffix;
+	  ($seqname,$path,$suffix) = fileparse($seqfile, (".seq", ".constraint"));
+
+	  if ((-d $seqfile) || $suffix ne '.seq') {
+		  next;
+	  }
+
+    $seqfile = "$_$seqname$suffix";
+    my $seq_include = (not defined($include_regex)) || ($seqname =~ /$include_regex/);
+    my $seq_exclude = (not defined($exclude_regex)) || ($seqname !~ /$exclude_regex/);
+
+    if ( $seq_include && $seq_exclude ) {
+      $seq_hash{$seqname} = $seqfile;
+      $logger->info("Selected Sequence ... $seqname");
+    }
   }
 
+}
+  return %seq_hash;
+}
diff --git a/gtfold-mfe/tests/scripts/test_utils.pl b/gtfold-mfe/tests/scripts/test_utils.pl
index 2191bdf..2a62542 100755
--- a/gtfold-mfe/tests/scripts/test_utils.pl
+++ b/gtfold-mfe/tests/scripts/test_utils.pl
@@ -22,7 +22,7 @@ ()
     if ( ($line !~ /^#/) && ($line ne "") ) {    # Ignore lines starting with # and blank lines
       ($Name, $Value) = split (/=/, $line);    # Split each line into name value pairs
 
-      if ($Name =~ /G_INCLUDE_SEQUENCES|G_EXCLUDE_SEQUENCES|G_INCLUDE_TESTS|G_EXCLUDE_TESTS/) {
+      if ($Name =~ /.*_INCLUDE_SEQUENCES|.*_EXCLUDE_SEQUENCES|G_INCLUDE_TESTS|G_EXCLUDE_TESTS/) {
         $orig_value= %Config->{$Name};
         $Value =~ s/[.]/\\./g;
         $Value =~ s/[*]/.\*/g;
@@ -31,7 +31,7 @@ ()
         }
       }
 
-      if ($Name eq "G_SEQUENCE_DIR") {
+      if ($Name =~ /.*_SEQUENCE_DIR/) {
         my @seqdir_arr = %Config->{$Name};
         push (@{%Config->{$Name}}, $Value);
         next;

From 85b7ac7ba83b8e5e4abcbd73e87d884dcc042606 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Thu, 6 Oct 2011 20:53:18 -0400
Subject: [PATCH 252/282] Fix subopt error along with constraints error.

---
 gtfold-mfe/src/algorithms.c | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 1f6da10..0bbdceb 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -226,7 +226,8 @@ int calculate(int len) {
     }
   }
 
-  for (j = 0; j <= len; j++) {
+  W[0] = 0;
+  for (j = 1; j <= len; j++) {
     int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
     Wj = INFINITY_;
     for (i = 1; i < j-TURN; i++) {
@@ -257,7 +258,7 @@ int calculate(int len) {
 
       Wj = MIN(Wj,Wij); 
     }
-    W[j] = (j!=0 && canSS(j))?MIN(Wj, W[j-1]):Wj;
+    W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj;
   }
 
 #ifdef DEBUG

From 17c8e511357f8a870a7def09c3ef619a7af084fe Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 7 Oct 2011 14:24:07 -0400
Subject: [PATCH 253/282] Merge the set of sequences that can be used by tests.
 Filtered out the ones which contain ambiguous bases.

---
 gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq      | 2 ++
 .../tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq           | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq  | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq  | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq   | 2 ++
 .../tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq   | 2 ++
 .../tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq  | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq  | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq          | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq           | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq      | 2 ++
 .../tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq            | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq        | 2 ++
 .../tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq          | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq          | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq         | 2 ++
 .../tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq      | 2 ++
 .../tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq  | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq  | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq          | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq   | 2 ++
 .../tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq           | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq          | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq       | 2 ++
 .../tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq           | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq          | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq  | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq          | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq          | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq           | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq          | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq    | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq   | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq     | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq       | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq      | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq        | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq         | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq  | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq           | 2 ++
 gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq   | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq    | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq  | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq  | 2 ++
 .../tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq    | 2 ++
 .../tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq  | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq     | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq  | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq             | 2 ++
 .../tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq    | 2 ++
 .../tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq    | 2 ++
 .../tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq    | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq            | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq            | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq    | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq   | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq   | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq     | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq     | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq   | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq     | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq    | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq           | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq        | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq            | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq     | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq     | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq     | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq      | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq         | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq          | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq            | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq       | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq    | 2 ++
 gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq       | 2 ++
 308 files changed, 616 insertions(+)
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq
 create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq
 create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq

diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq
new file mode 100644
index 0000000..b8c95c6
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq
@@ -0,0 +1,2 @@
+>d.16.a.H.volcanii
+AUUCCGGUUGAUCCUGCCGGAGGUCAUUGCUAUUGGGGUCCGAUUUAGCCAUGCUAGUUGCACGAGUUCAUACUCGUGGCGAAAAGCUCAGUAACACGUGGCCAAACUACCCUACAGAGAACGAUAACCUCGGGAAACUGAGGCUAAUAGUUCAUACGGGAGUCAUGCUGGAAUGCCGACUCCCCGAAACGCUCAGGCGCUGUAGGAUGUGGCUGCGGCCGAUUAGGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAAGAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACGGGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCAAGUGCGAUAAGGGGACCCCAAGUGCGAGGGCAUAUAGUCCUCGCUUUUCUCGACCGUAAGGCGGUCGAGGAAUAAGAGCUGGGCAAGACCGGUGCCAGCCGCCGCGGUAAUACCGGCAGCUCAAGUGAUGACCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCACGAAGGUUCAUCGGGAAAUCCGCCAGCUCAACUGGCGGGCGUCCGGUGAAAACCACGUGGCUUGGGACCGGAAGGCUCGAGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGAUGGCGAAAGCACCUCGAGAAGACGGAUCCGACGGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCUCGCUAGGUGUGACACAGGCUACGAGCCUGUGUUGUGCCGUAGGGAAGCCGAGAAGCGAGCCGCCUGGGAAGUACGUCCGCAAGGAUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGAGCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCUCACCAGCUCCGACUACAGUGAUGACGAUCAGGUUGAUGACCUUAUCACGACGCUGUAGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCACUUCUAAUUGCCAGCAGCAGUUUCGACUGGCUGGGUACAUUAGAAGGACUGCCGCUGCUAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAGUAUGCCCCGAAUGAGCUGGGCUACACGCGGGCUACAAUGGUCGAGACAAUGGGUUGCUAUCUCGAAAGAGAACGCUAAUCUCCUAAACUCGAUCGUAGUUCGGAUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCAUUUCAAUAGAGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCAAAGCACCCGAGUGAGGUCCGGAUGAGGCCACCACACGGUGGUCGAAUCUGGGCUUCGCAAGGGGGCUUAAGUCGUAACAAGGUAGCCGUAGGGGAAUCUGCGGCUGGAUCACCUCCUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq
new file mode 100644
index 0000000..e3a500d
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq
@@ -0,0 +1,2 @@
+>d.16.a.Halobacterium.sp
+AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUUGUGCGGGUUUAGACCCGCAGCGGAAAGCUCAGUAACACGUGGCCAAGCUACCCUGUGGACGGGAAUACUCUCGGGAAACUGAGGCUAAUCCCCGAUAACGCUUUGCUCCUGGAAGGGGCAAAGCCGGAAACGCUCCGGCGCCACAGGAUGCGGCUGCGGUCGAUUAGGUAGACGGUGGGGUAACGGCCCACCGUGCCCAUAAUCGGUACGGGUUGUGAGAGCAAGAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACGGGGCGCAGCAGGCGCGAAACCUUUACACUGUACGAAAGUGCGAUAAGGGGACUCCGAGUGUGAAGGCAUAGAGCCUUCACUUUUGUACACCGUAAGGUGGUGCACGAAUAAGGACUGGGCAAGACCGGUGCCAGCCGCCGCGGUAAUACCGGCAGUCCGAGUGAUGGCCGAUCUUAUUGGGCCUAAAGCGUCCGUAGCUGGCUGAACAAGUCCGUUGGGAAAUCUGUCCGCUUAACGGGCAGGCGUCCAGCGGAAACUGUUCAGCUUGGGACCGGAAGACCUGAGGGGUACGUCUGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCGCCGGUGGCGAAAGCGCCUCAGGAGAACGGAUCCGACAGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGUCCGCUAGGUGUGGCGCAGGCUACGAGCCUGCGCUGUGCCGUAGGGAAGCCGAGAAGCGGACCGCCUGGGAAGUACGUCUGCAAGGAUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGAGCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCUCACCAGCCCCGACAGUAGUAAUGACGGUCAGGUUGAUGACCUUACCCGAGGCUACUGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCACUCCUAAUUGCCAGCAGUACCCUUUGGGUAGCUGGGUACAUUAGGUGGACUGCCGCUGCCAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAGUAUGCCCCGAAUGGGCUGGGCAACACGCGGGCUACAAUGGUCGAGACAAUGGGAAGCCACUCCGAGAGGAGGCGCUAAUCUCCUAAACUCGAUCGUAGUUCGGAUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGCAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCAAAUCACCCGAGUGGGGUUCGGAUGAGGCCGGCAUGCGCUGGUCAAAUCUGGGCUCCGCAAGGGGGAUUAAGUCGUAACAAGGUAGCCGUAGGGGAAUCUGCGGCUGGAUCACCUCCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq
new file mode 100644
index 0000000..c32cdc8
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq
@@ -0,0 +1,2 @@
+>d.16.a.P.abyssi
+CGUACUCCCUUAAUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGUGCCGACCCCGAAAGGGGGAGGUAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCUAGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq
new file mode 100644
index 0000000..14395d3
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq
@@ -0,0 +1,2 @@
+>d.16.a.P.horikoshii
+AUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGUGCCGACCCCGAAAGGGGGAGGUAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCUAGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq
new file mode 100644
index 0000000..0afb8fa
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq
@@ -0,0 +1,2 @@
+>d.16.a.S.solfataricus.2
+AAAUCCGGUUGAUCCUGCCGGACCCGACCGCUAUCGGGGUGGGGCUAAGCCAUGGGAGUCGUACGCUCCCGGGCAAGGGAGCGUGGCGGACGGCUGAGUAACACGUGGCUAACCUACCCUGAGGAGGGAGAUAACCCCGGGAAACUGGGGAUAAUCUCCCAUAGGCGAGGAGUCCUGGAACGGUUCCUCGCUGAAAGGCUCAUGGGCUAUUCCCCGCUCAUGAGCGCCUCAGGAUGGGGCUGCGGCCCAUCAGGUAGUUGGGGGGGUAAGGGCCCCCCAAGCCUAUAACGGGUAGGGGCCGUGAGAGCGGGAGCCCCCAGUUGGGCACUGAGACAAGGGCCCAGGCCCUACGGGGCGCACCAGGCGCGAAACGUCCCCAAUGCGCGGAAGCGUGAGGGCGCCACCCCGAGUGCUCCCGUAAGGGAGCUUUUCCCCGCUCUACAAAGGCGGGGGAAUAAGCGGGGGGCAAGUCUGGUGUCAGCCGCCGCGGUAAUACCAGCCCCGCGAGUGGUCGGGACUCUUACUGGGCCUAAAGCGCCCGUAGCCGGCCCGACAAGUCACUCCUUAAAGACCCCGGCUCAACCGGGGGAAUGGGGGUGAUACUGUCGGGCUAGGGGGCGGGAGAGGCCAGCGGUACUCCCGGAGUAGGGGCGAAAUCCUCAGAUCUCGGGAGGACCACCAGUGGCGAAAGCGGCUGGCUAGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGCAGCAAAAGGGAUUAGAUACCCCUGUAGUCCCGGCUGUAAACAAUGCAGGCUAGGUGUCACAUGGGCUUAGAGCCCAUGUGGUGCCGCAGGGAAGCCGUUAAGCCUGCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGAACCUGCGGCUCAAUUGGAGUCAACGCCUGGAAUCUUACUAGGGGAGACCGCAGGAUGACGGCCAGGCUAACGACCUUGCCUGACUCGCGGAGAGGAGGUGCAUGGCCGUCGCCAGCUCGUGUUGUGAAAUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCCACCACUAGUUGGUAUCCUGGUCUCCGGGCCGGGACCACACUAGUGGGACUGCCGGCGUAAGCCGGAGGAGGGAGGGGGCCACGGCAGGUCAGCAUGCCCCGAAACCCCUGGGCCGCACGCGGGUUACAAUGGCAGGGACAGCGGGAUUCCGACCCCGAAAGGGGAAGGUAAUCCCUUAAACCCUGCCGCAGUUGGGAUCGAGGGCUGAAACUCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCAGAUCAACAAUCUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCGCUCCACCCGAGUAGGAGAGGGGUGAGGCCCCUUGCCUUUGGGUGGGGGGUCGAGCUUCUCUCCUGCAAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq
new file mode 100644
index 0000000..8d706e8
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq
@@ -0,0 +1,2 @@
+>d.16.b.A.globiformis
+UUUCAACGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAUCCGGUGCUUGCACCGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGAGUAACCUGCCCUUGACUCUGGGAUAAGCCUGGGAAACUGGGUCUAAUACCGGAUAUGACUCCUCAUCGCAUGGUGGGGGGUGGAAAGCUUUUUGUGGUUUUGGAUGGACUCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGUGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGUAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUUUGUCGCGUCUGCCGUGAAAGUCCGGGGCUCAACUCCGGAUCUGCGGUGGGUACGGGCAGACUAGAGUGAUGUAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGAUGGCGAAGGCAGGUCUCUGGGCAUUAACUGACGCUGAGGAGCGAAAGCAUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGUUGGGCACUAGGUGUGGGGGACAUUCCACGUUUUCCGCGCCGUAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGCGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCAAGGCUUGACAUGGACCGGACCGCCGCAGAAAUGUGGUUUCUCCUUUUGGGGCCGGUUCACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUCCAUGUUGCCAGCGCGUAAUGGCGGGGACUCAUGGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAAUCAUCAUGCCCCUUAUGUCUUGGGCUUCACGCAUGCUACAAUGGCCGGUACAAAGGGUUGCGAUACUGUGAGGUGGAGCUAAUCCCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCAAGUCACGAAAGUUGGUAACACCCGAAGCCGGUGGCCUAACCCCUUGUGGGAGGGAGCCGUCGAAGGUGGGACUGGCGAUUGGGACUAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq
new file mode 100644
index 0000000..dca4e6e
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq
@@ -0,0 +1,2 @@
+>d.16.b.A.tumefaciens
+CUCAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAACGCCCCGCAAGGGGAGUGGCAGACGGGUGAGUAACGCGUGGGAAUCUACCGUGCCCUGCGGAAUAGCUCCGGGAAACUGGAAUUAAUACCGCAUACGCCCUACGGGGGAAAGAUUUAUCGGGGUAUGAUGAGCCCGCGUUGGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCCAUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGCAAGCCUGAUCCAGCCAUGCCGCGUGAGUGAUGAAGGCCUUAGGGUUGUAAAGCUCUUUCACCGGAGAAGAUAAUGACGGUAUCCGGAGAAGAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGCGCACGUAGGCGGAUAUUUAAGUCAGGGGUGAAAUCCCAGAGCUCAACUCUGGAACUGCCUUUGAUACUGGGUAUCUUGAGUAUGGAAGAGGUAAGUGGAAUUCCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGGAGGAACGCCAGUGGCGAAGGCGGCUUACUGGUCCAUUACUGACGCUGAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGUUAGCCGUCGGGCAGUAUACUGUUCGGUGGCGCAGCUAACGCAUUAAACAUUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGCAGAACCUUACCAGCUCUUGACAUUCGGGGUUUGGGCAGUGGAGACAUUGUCCUUCAGUUAGGCUGGCCCCAGAACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGCCCUUAGUUGCCAGCAUUUAGUUGGGCACUCUAAGGGGACUGCCGGUGAUAAGCCGAGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUACGGGCUGGGCUACACACGUGCUACAAUGGUGGUGACAGUGGGCAGCGAGACAGCGAUGUCGAGCUAAUCUCCAAAAGCCAUCUCAGUUCGGAUUGCACUCUGCAACUCGAGUGCAUGAAGUUGGAAUCGCUAGUAAUCGCAGAUCAGCAUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGUUUUACCCGAAGGUAGUGCGCUAACCGCAAGGAGGCAGCUAACCACGGUAGGGUCAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq
new file mode 100644
index 0000000..040091c
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq
@@ -0,0 +1,2 @@
+>d.16.b.Anabaena.sp
+GAAACGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGGUCUCUUCGGAGAUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUAGCUUCAGGUCGGGGACAACCACUGGAAACGGUGGCUAAUACCGGAUGUGCCGAAAGGUGAAAGAUUUAUUGCCUGAAGAUGAGCUCGCGUCUGAUUAGCUAGUUGGUGUGGUAAGAGCGCACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAGGGAGGAAGGCUCUUGGGUUGUAAACCUCUUUUCUCAGGGAAUAAAAAAAUGAAGGUACCUGAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCCGCAGGUGGCACUGUAAGUCUGCUGUUAAAGAGCAAGGCUCAACCUUGUAAAGGCAGUGGAAACUACAGAGCUAGAGUACGUUCGGGGCAGAGGGAAUUCCUGGUGUAGCGGUGAAAUGCGUAGAGAUCAGGAAGAACACCGGUGGCGAAAGCGCUCUGCUAGGCCGUAACUGACACUGAGGGACGAAAGCUAGGGGAGCGAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGCGUGGCUUGUAUCGACCCGAGCCGUGCCGGAGCCAACGCGUUAAGUAUCCCGCCUGGGGAGUACGCACGCAAGUGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAAGACUUGACAUGUCGCGAAUCUUCUUGAAAGGGAAGAGUGCCUUAGGGAGCGCGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUUUUAGUUGCCAGCAUUAAGUUGGGCACUCUAGAGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUACGUCUUGGGCUACACACGUACUACAAUGCUACGGACAGAGGGCAGCAAGCUAGCGAUAGCAAGCAAAUCCCGUAAACCGUAGCUCAGUUCAGAUCGCAGGCUGCAACUCGCCUGCGUGAAGGAGGAAUCGCUAGUAAUUGCAGGUCAGCAUACUGCAGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGCAACGCCCGAAGUCAUUACUCCAACUUUUAGGAGAGGAGGAUGCCUAAGGCAGUGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGUGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq
new file mode 100644
index 0000000..b4e37d1
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq
@@ -0,0 +1,2 @@
+>d.16.b.B.bronchiseptica2
+UGAACUGAAGAGUUUGAUCCUGGCUCAGAUUGAACGCUGGCGGGAUGCUUUACACAUGCAAGUCGGACGGCAGCACGGGCUUCGGCCUGGUGGCGAGUGGCGAACGGGUGAGUAAUGUAUCGGAACGUGCCCAGUAGCGGGGGAUAACUACGCGAAAGCGUGGCUAAUACCGCAUACGCCCUACGGGGGAAAGCGGGGGACCUUCGGGCCUCGCACUAUUGGAGCGGCCGAUAUCGGAUUAGCUAGUUGGUGGGGUAACGGCCUACCAAGGCGACGAUCCGUAGCUGGUUUGAGAGGACGACCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGGGGCAACCCUGAUCCAGCCAUCCCGCGUGUGCGAUGAAGGCCUUCGGGUUGUAAAGCACUUUUGGCAGGAAAGAAACGGCACGGGCUAAUAUCCUGUGCAACUGACGGUACCUGCAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGUGCGCAGGCGGUUCGGAAAGAAAGAUGUGAAAUCCCAGGGCUUAACCUUGGAACUGCAUUUUUAACUACCGGGCUAGAGUGUGUCAGAGGGAGGUGGAAUUCCGCGUGUAGCAGUGAAAUGCGUAGAUAUGCGGAGGAACACCGAUGGCGAAGGCAGCCUCCUGGGAUAACACUGACGCUCAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCCUAAACGAUGUCAACUAGCUGUUGGGGCCUUCGGGCCUUGGUAGCGCAGCUAACGCGUGAAGUUGACCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAUGAUGUGGAUUAAUUCGAUGCAACGCGAAAAACCUUACCUACCCUUGACAUGUCUGGAAUCCCGAAGAGAUUUGGGAGUGCUCGCAAGAGAACCGGAACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCAUUAGUUGCUACGAAAGGGCACUCUAAUGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUGGGUAGGGCUUCACACGUCAUACAAUGGUCGGGACAGAGGGUCGCCAACCCGCGAGGGGGAGCCAAUCCCAGAAACCCGAUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGUCGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUUUACCAGAAGUAGUUAGCCUAACCGCAAGGGGGGCGAUUACCACGGUAGGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq
new file mode 100644
index 0000000..818a7c0
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq
@@ -0,0 +1,2 @@
+>d.16.b.B.burgdorferi
+AUAACGAAGAGUUUGAUCCUGGCUUAGAACUAACGCUGGCAGUGCGUCUUAAGCAUGCAAGUCAAACGGGAUGUAGCAAUACAUUCAGUGGCGAACGGGUGAGUAACGCGUGGAUGAUCUACCUAUGAGAUGGGGAUAACUAUUAGAAAUAGUAGCUAAUACCGAAUAAGGUCAGUUAAUUUGUUAAUUGAUGAAAGGAAGCCUUUAAAGCUCUCGCUUGUAGAUGAGUCUGCGUCUUAUUAGCUAGUUGGUAGGGUAAAUGCCUACCAAGGCAAUGAUAAGUAACCGGCCUGAGAGGGUGAACGGUCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGCUAAGAAUCUUCCGCAAUGGGCGGAAGCCUGACGGAGCGACACUGCGUGAAUGAAGAAGGUCGAAAGAUUGUAAAAUUCUUUUAUAAAUGAGGAAUAAGCUUUGUAGGAAAUGACAAAGUGAUGACGUUAAUUUAUGAAUAAGCCCCGGCUAAUUACGUGCCAGCAGCCGCGGUAAUACGUAAGGGGCGAGCGUUGUUCGGGAUUAUUGGGCGUAAAGGGUGAGUAGGCGGAUAUAUAAGUCUAUGCAUAAAAUACCACAGCUCAACUGUGGACCUAUGUUGGAAACUAUAUGUCUAGAGUCUGAUAGAGGAAGUUAGAAUUUCUGGUGUAAGGGUGGAAUCUGUUGAUAUCAGAAAGAAUACCGGAGGCGAAGGCGAACUUCUGGGUCAAGACUGACGCUGAGUCACGAAAGCGUAGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCUACGCUGUAAACGAUGCACACUUGGUGUUAACUAAAAGUUAGUACCGAAGCUAACGUGUUAAGUGUGCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCAGGGCUUGACAUAUAUAGGAUAUAGUUAGAGAUAAUUAUUCCCCGUUUGGGGUCUAUAUACAGGUGCUGCAUGGUUGUCGUCAGCUCGUGCUGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUAUCUGUUACCAGCAUGUAAUGGUGGGGACUCAGAUAAGACUGCCGGUGAUAAGUCGGAGGAAGGUGAGGAUGACGUCAAAUCAUCAUGGCCCUUAUGUCCUGGGCUACACACGUGCUACAAUGGCCUGUACAAAGCGAAGCGAAACAGUGAUGUGAAGCAAAACGCAUAAAGCAGGUCUCAGUCCGGAUUGAAGUCUGAAACUCGACUUCAUGAAGUUGGAAUCGCUAGUAAUCGUAUAUCAGAAUGAUACGGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACACCACCCGAGUUGAGGAUACCCGAAGCUAUUAUUCUAACCCGUAAGGGAGGAAGGUAUUUAAGGUAUGUUUAGUGAGGGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAAGUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq
new file mode 100644
index 0000000..4c06124
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq
@@ -0,0 +1,2 @@
+>d.16.b.B.japonicum
+CCAACUUGAGAGUUUGAUCCUGGCUCAGAGCGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGGGCGUAGCAAUACGUCAGCGGCAGACGGGUGAGUAACGCGUGGGAACGUACCUUUUGGUUCGGAACAACACAGGGAAACUUGUGCUAAUACCGGAUAAGCCCUUACGGGGAAAGAUUUAUCGCCGAAAGAUCGGCCCGCGUCUGAUUAGCUAGUUGGUAGGGUAACGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGCAACCCUGAUCCAGCCAUGCCGCGUGAGUGAUGAAGGCCCUAGGGUUGUAAAGCUCUUUUGUGCGGGAAGAUAAUGACGGUACCGCAAGAAUAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGCUCGGAAUCACUGGGCGUAAAGGGUGCGUAGGCGGGUCUUUAAGUCAGGGGUGAAAUCCUGGAGCUCAACUCCAGAACUGCCUUUGAUACUGAAGAUCUUGAGUUCGGGAGAGGUGAGUGGAACUGCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGCAAGAACACCAGUGGCGAAGGCGGCUCACUGGCCCGAUACUGACGCUGAGGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGCCAGCCGUUAGUGGGUUUACUCACUAGUGGCGCAGCUAACGCUUUAAGCAUUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGCAGAACCUUACCAGCCCUUGACAUGUCCAGGACCGGUCGCAGAGAUGUGACCUUCUCUUCGGAGCCUGGAACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGUCCUUAGUUGCUACCAUUUAGUUGAGCACUCUAAGGAGACUGCCGGUGAUAAGCCGCGAGGAAGGUGGGGAUGGCGUCAAGUCCUCAUGGCCCUUACGGGCUGGGCUACACACGUGCUACAAUGGCGGUGACAAUGGGAUGCUAAGGGGCGACCCUUCGCAAAUCUCAAAAAGCCGUCUCAGUUCGGAUUGGGCUCUGCAACUCGAGCCCAUGAAGUUGGAAUCGCUAGUAAUCGUGGAUCAGCACGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGCUUUACCUGAAGACGGUGCGCUAACCAGCAAUGGAGGCAGCCGGCCACGGUAGGGUCAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq
new file mode 100644
index 0000000..9433d8f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq
@@ -0,0 +1,2 @@
+>d.16.b.B.subtilis
+UUUAUCGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGGACAGGUGGGAGCUUGCUCCCGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCUGUAAGACUGGGAUAACUCCGGGAAACCGGGGCUAAUACCGGAUGGUUGUUUGAACCGCAUGGUUCAAACAUAAAAGGUGGCUUCGGCUACCACUUACAGAUGGACCCGCGGCGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCAACGAUGCGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGACGAAAGUCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUUUUCGGAUCGUAAAGCUCUGUUGUUAGGGAAGAACAAGUACCGUUCGAAUAGGGCGGUACCUUGACGGUACCUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGGCUCGCAGGCGGUUUCUUAAGUCUGAUGUGAAAGCCCCCGGCUCAACCGGGGAGGGUCAUUGGAAACUGGGGAACUUGAGUGCAGAAGAGGAGAGUGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAACACCAGUGGCGAAGGCGACUCUCUGGUCUGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCCUCUGACAAUCCUAGAGAUAGGACGUCCCCUUCGGGGGCAGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGAUCUUAGUUGCCAGCAUUCAGUUGGGCACUCUAAGGUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGACAGAACAAAGGGCAGCGAAACCGCGAGGUUAAGCCAAUCCCACAAAUCUGUUCUCAGUUCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGCUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGUCGGUGAGGUAACCUUUUAGGAGCCAGCCGCCGAAGGUGGGACAGAUGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq
new file mode 100644
index 0000000..f65748e
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq
@@ -0,0 +1,2 @@
+>d.16.b.C.pneumoniae
+UUUUCUGAGAAUUUGAUCUUAGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAAUAAUGACUUCGGUUGUUAUUUAGUGGCGGAAGGGUUAGUAGUACAUAGAUAAUCUGCCCUCAACUUGGGGAUAACGGUUGGAAACGAUCGCUAAUACCGAAUGUAGUGUAAUUAGGCAUCUAAUAUAUAUUAAAGAAGGGGAUCUUCGGACCUUUCGGUUGAGGAAGAGUUUAUGCGAUAUCAGCUUGUUGGUGGGGUAAAAGCCCACCAAGGCGAUGACGUCUAGGCGGAUUGAGAGAUUGACCGCCAACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGAAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCCUUAGGGUUGUAAAGCACUUUCGCCUGGGAAUAAGAGAGAUUGGCUAAUAUCCAAUCGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGAAAGUUAGAUGUUAAAUUUUGGGGCUCAACCCCAAGUCAGCAUUUAAAACUAUCUUUCUAGAGGAUAGAUGGGGAAAAGGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUAUACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUGGUCUCAACCCCAUCCGUGUCGGAGCUAACGUGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGGACCUUACCUGGACUUGACAUGUAUUUGACAACUGUAGAAAUACAGCUUUCCGCAAGGACAGAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAGCACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGUCCAGGGCGACACACGUGCUACAAUGGUUAGUACAGAAGGUAGCAAGAUCGUGAGAUGGAGCAAAUCCUAAAAGCUAGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCCAUAACGCCGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUACCUUAAGUCGUUGACUCAACCUAUUUAUAGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUGGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq
new file mode 100644
index 0000000..4218316
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq
@@ -0,0 +1,2 @@
+>d.16.b.C.psittaci
+UUUUCUGAGAAUUUGAUCUUGGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAAUAAUGACUUCGGUUGUUAUUUAGUGGCGGAAGGGUUAGUAAUACAUAGAUAAUCUGUCCUCAACUUGGGAAUAACGGUUGGAAACGACCGCUAAUACCGAAUGUGGUAUGUUUAGGCAUCUAAAACAUAUUAAAGAAGGGGAUCUUCGGACCUUUCGGUUGAGGGAGAGUCUAUGGGAUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCUUUGACGUCUAGGCGGAUUGAGAGAUUGACCGCCAACACUGGGACUGAGACACUGCCCAGACUUCUACGGAAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGAAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCUCUAGGGUUGUAAAGCACUUUCGCUUGGGAAUAAGAGAGAUUGGCUAAUAUCCAAUCGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGAAAGUUAGAUGUUAAAUCUUGGGGCUCAACCCCAAGCCAGCAUCUAAUACUAUCUUUCUAGAGGGUAGAUGGAGAAAAGGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUACACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUAGUCUCAACCCUAUCCGUGUCGUAGCUAACGCGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGCUUGACAUGUAUUUGACCGCGGCAGAAAUGUCGUUUUCCGCAAGGACAGAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAACACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGCCCAGGGCUACACACGUGCUACAAUGGCCAGUACAGAAGGUAGCAAUAUCGUGAGAUGGAGCAAAUCCUCAAAGCUGGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCUAUAACGCCGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUGCCUUAAGUCGUUGACUCAACCUGCAAAGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUGGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq
new file mode 100644
index 0000000..5084a44
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq
@@ -0,0 +1,2 @@
+>d.16.b.C.testosteroni
+CGAACUAUAGAGUUUGAUCCUGGCUCAGAUUGAACGCUGGCGGCAUGCUUUACACAUGCAAGUCGAACGGUAACAGGUCUUCGGAUGCUGACGAGUGGCGAACGGGUGAGUAAUACAUCGGAACGUGCCUAGUAGUGGGGGAUAACUACUCGAAAGAGUAGCUAAUACCGCAUGAGAUCUACGGAUGAAAGCAGGGGACCUUCGGGCCUUGUGCUACUAGAGCGGCUGAUGGCAGAUUAGGUAGUUGGUGGGGUAAAGGCUUACCAAGCCUGCGAUCUGUAGCUGGUCUGAGAGGACGACCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUGCCGCGUGCAGGAUGAAGGCCCUCGGGUUGUAAACUGCUUUUGUACGGAACGAAAAGCCUGGGGCUAAUAUCCCCGGGUCAUGACGGUACCGUAAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGUGCGCAGGCGGUUUUGUAAGACAGUGGUGAAAUCCCCGGGCUCAACCUGGGAACUGCCAUUGUGACUGCAAGGCUAGAGUGCGGCAGAGGGGGAUGGAAUUCCGCGUGUAGCAGUGAAAUGCGUAGAUAUGCGGAGGAACACCGAUGGCGAAGGCAAUCCCCUGGGCCUGCACUGACGCUCAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCCUAAACGAUGUCAACUGGUUGUUGGGUCUUAACUGACUCAGUAACGAAGCUAACGCGUGAAGUUGACCGCCUGGGGAGUACGGCCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAUGAUGUGGUUUAAUUCGAUGCAACGCGAAAAACCUUACCCACCUUUGACAUGGCAGGAACUUACCAGAGAUGGUUUGGUGCUCGAAAGAGAACCUGCACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGCCAUUAGUUGCUACAUUCAGUUGAGCACUCUAAUGGGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUAGGUGGGGCUACACACGUCAUACAAUGGCUGGUACAAAGGGUUGCCAACCCGCGAGGGGGAGCUAAUCCCAUAAAGCCAGUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGUCACGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGCGGGUCUCGCCAGAAGUAGGUAGCCUAACCGUAAGGAGGGCGCUUACCACGGCGGGGUUCGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq
new file mode 100644
index 0000000..4ae3dc2
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq
@@ -0,0 +1,2 @@
+>d.16.b.C.trachomatis.L2
+UUUUCUGAGAAUUUGAUCUUGGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAGCAAUUGUUUCGGCAAUUGUUUAGUGGCGGAAGGGUUAGUAAUGCAUAGAUAAUUUGUCCUUAACUUGGGAAUAACGGUUGGAAACGGCCGCUAAUACCGAAUGUGGCGAUAUUUGGGCAUCCGAGUAACGUUAAAGAAGGGGAUCUUAGGACCUUUCGGUUAAGGGAGAGUCUAUGUGAUAUCAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCUAUGACGUCUAGGCGGAUUGAGAGAUUGGCCGCCAACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGGAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCUCUAGGGUUGUAAAGCACUUUCGCUUGGGAAUAAGAGAAGGCGGUUAAUACCCGCUGGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGUAAGUUAGUUGUCAAAGAUCGGGGCUCAACCCCGAGUCGGCAUCUAAUACUAUUUUUCUAGAGGGUAGAUGGAGAAAAGGGAAUUUCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUAUACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUGGUCUCAACCCCAUCCGUGUCGGAGCUAACGCGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGGACCUUACCUGGGUUUGACAUGUAUAUGACCGCGGCAGAAAUGUCGUUUUCCGCAAGGACAUAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAGCACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGCCCAGGGCGACACACGUGCUACAAUGGCCAGUACAGAAGGUAGCAAGAUCGUGAGAUGGAGCAAAUCCUCAAAGCUGGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCCAUAACGCCGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUACCUUAAGUCGUUGACUCAACCCGCAAGGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUAGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq
new file mode 100644
index 0000000..6f67dd9
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq
@@ -0,0 +1,2 @@
+>d.16.b.E.coli
+AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq
new file mode 100644
index 0000000..7592528
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq
@@ -0,0 +1,2 @@
+>d.16.b.Frankia.sp
+UUGAUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAGCGGGGAGCUUCGGCUCUCAGCGGCGAACGGGUGAGUAACACGUGGGCAACCUGCCCCGAGCUCUGGAAUAACCUCGGGAAACCGGGGCUAAUGCCGGAUAUGACAUUGCCGGGCAUCUGGUGGUGUGGAAAGAUUUAUCGGCUCGGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUGAUGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGCGGAAGCCUGACGCAGCGACGCCGCGUGGGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGACGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCACCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCCUGUUGCGUCGGCUGUGAAAACCCGGGGCUCAACUCCGGGCCUGCAGUCGAUACGGGCAGGCUAGAGUCCGGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGGUCUCUGGGCCGGAACUGACGCUAAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGUUGGGCGCUAGGUGUGGGGGACCUUCCACGGCCUCCGUGCCGCAGCUAACGCAUUAAGCGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCAGGGAAAUCUCGUAGAGAUACGGGGUCCGUAAGGGUCCUGCACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUCCUAUGUUGCCAGCGAGUCGUGUCGGGGACUCAUAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUACGUCCUGGGCUGCACACAUGCUACAAUGGCCGGUACAAAGGGCUGCGAUGCCGUGAGGUGGAGCGAAUCCCAAAAAGCCGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAAUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCUAACCCUUGUGGGGGGAGCCGUCGAAGGUGGGACCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq
new file mode 100644
index 0000000..dada154
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq
@@ -0,0 +1,2 @@
+>d.16.b.H.influenzae
+AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAACGGUAGCAGGAGAAAGCUUGCUUUCUUGCUGACGAGUGGCGGACGGGUGAGUAAUGCUUGGGAAUCUGGCUUAUGGAGGGGGAUAACGACGGGAAACUGUCGCUAAUACCGCGUAUUAUCGGAAGAUGAAAGUGCGGGACUGAGAGGCCGCAUGCCAUAGGAUGAGCCCAAGUGGGAUUAGGUAGUUGGUGGGGUAAAUGCCUACCAAGCCUGCGAUCUCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGGGGAACCCUGACGCAGCCAUGCCGCGUGAAUGAAGAAGGCCUUCGGGUUGUAAAGUUCUUUCGGUAUUGAGGAAGGUUGAUGUGUUAAUAGUACAUCAAAUUGACGUUAAAUACAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCGAGCGUUAAUCGGAAUAACUGGGCGUAAAGGGCACGCAGGCGGUUAUUUAAGUGAGGUGUGAAAGCCCUGGGCUUAACCUAGGAAUUGCAUUUCAGACUGGGUAACUAGAGUACUUUAGGGAGGGGUAGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAAUACCGAAGGCGAAGGCAGCCCCUUGGGAAUGUACUGACGCUCAUGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAAACGCUGUCGAUUUGGGGAUUGGGCUUAGAGCUUGGUGCCCGUAGCUAACGUGAUAAAUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUACUCUUGACAUCCUAAGAAGAGCUCAGAGAUGAGCUUGUGCCUUCGGGAACUUAGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGACUUGGUCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCGUAUACAGAGGGAAGCGAAGCUGCGAGGUGGAGCGAAUCUCAUAAAGUACGUCUAAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGAAUCAGAAUGUCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGUACCAGAAGUAGAUAGCUUAACCUUUUGGAGGGCGUUUACCACGGUAUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq
new file mode 100644
index 0000000..042147f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq
@@ -0,0 +1,2 @@
+>d.16.b.L.interrogans
+AACACGGAGAGUUUGAUCCUGGCUCAGAACUAACGCUGGCGGCGCGUCUUAAACAUGCAAGUCAAGCGGAGUAGCAAUACUCAGCGGCGAACGGGUGAGUAACACGUGGGUAAUCUUCCUCUGAGUCUGGGAUAACUUUCCGAAAGGGAAGCUAAUACUGGAUGGUCCCGAGAGAUCACAAGAUUUUUCGGGUAAAGAUUUAUUGCUCGGAGAUGAGCCCGCGUCCGAUUAGCUAGUUGGUGAGGUAAAGGCUCACCAAGGCGACGAUCGGUAGCCGGCCUGAGAGGGUGUUCGGCCACAAUGGAACUGAGACACGGUCCAUACUCCUACGGGAGGCAGCAGUUAAGAAUCUUGCUCAAUGGGGGGAACCUGAAGCAGCGACGCCGCGUGAACGAUGAAGGUCUUCGGAUUGUAAAGUUCAGUAAGCAGGGAAAAAUAAGCAGCAAUGUGAUGAUGGUACCUGCCUAAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAUGGUGCAAGCGUUGUUCGGAAUCAUUGGGCGUAAAGGGUGCGUAGGCGGACAUGUAAGUCAGGUGUGAAAACUGCGGGCUCAACUCGCAGCCUGCACUUGAAACUAUGUGUCUGGAGUUUGGGAGAGGCAAGUGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAGGAACACCAGUGGCGAAGGCGACUUGCUGGCCUAAAACUGACGCUGAGGCACGAAAGCGUGGGUAGUGAACGGGAUUAGAUACCCCGGUAAUCCACGCCCUAAACGUUGUCUACCAGUUGUUGGGGGUUUUAACCCUCAGUAACGAACCUAACGGAUUAAGUAGACCGCCUGGGGACUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGUCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAAAAACCUCACCUAGGCUUGACAUGGAGUGGAAUCAUGUAGAGAUACAUGAGCCUUCGGGCCGCUUCACAGGUGCUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCACCUUAUGUUGCCAUCAUUCAGUUGGGCACUCGUAAGGAACUGCCGGUGACAAACCGGAGGAAGGCGGGGAUGACGUCAAAUCCUCAUGGCCUUUAUGUCUAGGGCAACACACGUGCUACAAUGGCCGGUACAAAGGGUAGCCAACUCGCGAGGGGGAGCUAAUCUCAAAAAUCCGGUCCCAGUUCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGACCUUGUACACACCGCCCGUCACACCACCUGAGUGGGGAGCACCCGAAGUGGUCUUUGCCAACCGCAAGGAAGCAGACUACUAAGGUGAAACUCGUGAAGGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq
new file mode 100644
index 0000000..1c5e7c6
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq
@@ -0,0 +1,2 @@
+>d.16.b.M.gallisepticum
+UUUUCUGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGCAUGCCUAAUACAUGCAAGUCGAUCGGAUGUAGCAAUACAUUAGAGGCGAACGGGUGAGUAACACGUAUCCAAUCUGCCUUAUAGUGGGGGAUAACUAGUCGAAAGAUUAGCUAAUACCGCAUAACAAGUUAACUAUCGCAUGAGAAUAACUUUAAAGAAGCAACUGCUUCGCUAUAAGAUGAGGGUGCGGCAUAUCAGCUAGUUGGUGAGGGUAAUGGCCCACCAAGGCGAUGACGUGUAGUUAUGCUGAGAGGUAGAAUAACCACAAUGGGACUGAGACACGGCCCAUACUCCUACGGGAGGCAGCAGUAGGGAAUUUUUCACAAUGGACGAAAGUCUGAUGGAGCAAUGCCGCGUGAACGAUGAAGGUCUUUUUAGAUUGUAAAGUUCUUUUAUUUGGGAAGAACAGUUAGUAGAGUGGAAAGCUAUUAAUUUGACUGUACCAUUUGAAUAAGUAACGACUAACUAUGUGCCAGCAGUCGCGGUAAUACAUAGGUUGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAACAAGCGCAGGCGGAUUAGAAAGUCUGGUGUUAAAAGCAAUUGCUUAACGAUUGUAUGCAUUGGAAACUUCUAGUCUAGAGUUUGGUAGAGAGUCCUGGAACUCCAUGUGGAGCGGUGAAAUGCGUAGAUAUAUGGAAGAACACCAGAGGCGAAGGCGAGGACUUGGGCCAAUACUGACGCUUAGGCUUGAAAGUGUGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCACACUGUAAACGAUGGAUGUUAAGUGUCGGAGCGAAUACUUCGGUGCUGCAGUUAACACAUUAAACAUCCUGCCUGAGUAGUACAUUCGCAAGAAUGAAACUCAAACGGAAUUGACGGGGACCCGCACAAGUGGUGGAGCAUGUUGCUUAAUUCGACGGUACACGAAAAACCUUACCUAGACUUGACAUCUUGGGCGAAGCUAUAGAAAUAUAGUGGAGGUCAACCCAAUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUACUUUGUCUAACGAGACUGCCAACGUAAGUUGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGUCUAGGGCUGCAAACGUGCUACAAUGGCCAAUACAAACAGUUGCAAAUCCGUAAGGUGGAGCUAAUCUGUAAAGUUGGUCUCAGUUCGGAUUGAGGGCUGCAAUUCGCCCUCAUGAAGUCGGAAUCACUAGUAAUCGCGAAUCAGCCAUGUCGCGGUGAAUACGUUCUCGGGUCUUGUACACACCGCCCGUCAAACUAUGAGAGCUGGUAAUAUCUAAAACCGUGUUGCUAACCGCAAGGAAGCGCAUGUCUAGGGUAGGGCCGGUGAUUGGAGUUAAGUCGUAACAAGGUACCCCUACGAGAACGUGGGGGUGGAUUACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq
new file mode 100644
index 0000000..b13dc11
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq
@@ -0,0 +1,2 @@
+>d.16.b.M.genitalium
+CAAUUUUUUCUGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGCAUGCCUAAUACAUGCAAGUCGAUCGGAAGUAGCAAUACUUUAGAGGCGAACGGGUGAGUAACACGUAUCCAAUCUACCUUAUAAUGGGGGAUAACUAGUUGAAAAACUAGCUAAUACCGCAUAAGAACUUUAGUUCGCAUGAAUUAAAGUUGAAAGGACCUGCAAGGGUUCGUUAUUUGAUGAGGGUGCGCCAUAUCAGCUAGUUGGUAGGGUAAUGGCCUACCAAGGCAAUGACGUGUAGCUAUGCUGAGAAGUAGAAUAGCCACAAUGGGACUGAGACACGGCCCAUACUCCUACGGGAGGCAGCAGUAGGGAAUUUUUCACAAUGAGCGAAAGCUUGAUGGAGCAAUGCCGCGUGAACGAUGAAGGUCUUUUUGAUUGUAAAGUUCUUUUAUUUGGGAAGAAUGACUCUAGCAGGCAAUGGCUGGAGUUUGACUGUACCACUUUGAAUAAGUGACGACUAACUAUGUGCCAGCAGUCGCGGUAAUACAUAGGUCGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCAAGCGCAGGCGGAUUGAAAAGUCUGGUGUUAAAGGCAGCUGCUUAACAGUUGUAUGCAUUGGAAACUAUCAGUCUAGAGUGUGGUAGGGAGUUUUGGAAUUUCAUGUGGAGCGGUGAAAUGCGUAGAUAUAUGAAGGAACACCAGUGGCGAAGGCGAAAACUUAGGCCAUUACUGACGCUUAGGCUUGAAAGUGUGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCACACCGUAAACGAUAGAUACUAGCUGUCGGAGCGAUCCCUUCGGUAGUGAAGUUAACACAUUAAGUAUCUCGCCUGGGUAGUACAUUCGCAAGAAUGAAACUCAAACGGAAUUGACGGGGACCCGCACAAGUGGUGGAGCAUGUUGCUUAAUUCGACGGUACACGAAAAACCUUACCUAGACUUGACAUCCUUGGCAAAGUUAUGGAAACAUAAUGGAGGUUAACCGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUACAUUGUUUAACGAGACUGCUAAUGUAAAUUGGAGGAAGGAAGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGUCUAGGGCUGCAAACGUGCUACAAUGGCCAAUACAAACAGUAGCCAACUUGUAAAAGUGAGCAAAUCUGAAAAGUUGGUCUCAGUUCGGAUUGAGGGCUGCAAUUCGUCCUCAUGAAGCUGGAAUCACUAGUAAUCGCGAAUCAGCUAUGUCGCGGUGAAUACGUUCUCGGGUCUUGUACACACCGCCCGUCAAACUAUGAAAGCUGGUAAUAUUUAAAAACGUGUUGCUAACCUUUAUUGGAAGCGCAUGUCAAGGAUAGCACCGGUGAUUGGAGUUAAGUCGUAACAAGGUACCCCUACGAGAACGUGGGGGUGGAUCACCUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq
new file mode 100644
index 0000000..340893a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq
@@ -0,0 +1,2 @@
+>d.16.b.M.hyopneumoniae
+CGCAAUCAUGAGAGUUUGAUCCUGGCUCAGGAUAAACGCUAGCUGUGUGCUUAAUACAUGCAUGUUGAACGGAAUAUUUUAGUUCGCUAAAAUAUUUAGUAGCAAAUGGGUGAGUAACACGUACCUAACCUACCUUUUGGACUGGGAUAACCAUUGGAAACAGUGGCUAAUACCAGAUAUGAUAAAAAUUUGCAUGAAUUUUUAUUCAAAGGAGCCUUCAAGCUUCACCAAGAAAUGGGGGUGCGCAACAUUAGUUAGUUGGUAGGGUAAAAGCCUACCAAGACGAUGAUGUUUAGCGGGGCCAAGAGGUUGUACCGCCACACUGGGAUUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUAAGGAAUAUUCCACAAUAAGCGAAAGCUUGAUGGAGCGACACAGCGUGCAGGAUGAAGUCUUUCGGGAUGUAAACUGCUGUUGUAAGGGAAGAAAAAACUAGAUAGGAAAUGCUCUAGUCUUGACGGUACCUUAUUAGAAAGCGACGGCAAACUAUGUGCCAGCAGCCGCGGUAAUACAUAGGUCGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGUCCGUAGGUUUUUUGUUAAGUUUAAAGUUAAAUGCUAAAGCUCAACUUUAGUCCGCUUUAGAUACUGGCAAAAUAGAAUUAUGAAGAGGUUAGCGGAAUUCCUAGUGGAGUGGUGGAAUACGUAGAUAUUAGGAAGAACACCAAUAGGCGAAGGCAGCUAACUGGUCAUAUAUUGACACUAAGGGACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAUCAUUAGUUGGUGGCAAAAGUCACUAACACAGCUAACGCGUUAAAUGAUCCGCCUGAGUAGUAUGCUCGCAAGAGUGAAACUUAAAGGAAUUGACGGGAACCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUUGAAGAUACGCGUAGAACCUUACCCACUCUUGACAUUCUCGCAAAACUAUAGAGAUAUAGCCGAGGCUAACGAGAUCACAGAUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUAGGUUAAGUCCUGCAACGAGCGCAACCCUUUUCUUUAGUUGCUAACAUUUAGUUGAGAACCCUAAAGAUACUGCCGGCGCAAGCCGGAGGAAGGUGGGGACGACGUCAAAUCAUCAUGCCUCUUACGAGUGGGGCAACACACGUGCUACAAUGGCUACUACAAAGAGCAGCAAAACAGUGAUGUCAAGCUAAUCUCAAAAAAGUAGUCUCAGUUCGGAUUGAAGUCUGCAACUCGACUUCAUGAAGUCGGAAUCGCUAGUAAUCGCAGGUCAGCUAUACUGCGGUGAAUACGUUCUCGGGUUUUGUACACACCGCCCGUCACACCAUGGGAGUUGGUAAUGCCCAAAGUCGGUGAGUUAACUUCGGAGACCAUUGCCUAAGGCAGGACCGAUGACUGGGGUGAAGUCGUAACAAGGUAUCCCUACGAGAACGUGGGGAUGGAACACCUCCUUUCUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq
new file mode 100644
index 0000000..86728a4
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq
@@ -0,0 +1,2 @@
+>d.16.b.M.leprae
+UUGUUUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGAAAGGUCUCUAAAAAAUCUUUUUUAGAGAUACUCGAGUGGCGAACGGGUGAGUAACACGUGGGUAAUCUGCCCUGCACUUCAGGGAUAAGCUUGGGAAACUGGGUCUAAUACCGGAUAGGACUUCAAGGCGCAUGUCUUGUGGUGGAAAGCUUUUUGCGGUGCAGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUGACGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGUGUCCGGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCGACGCCGCGUGGGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCACCAUCGACGAAGGUCUGGGUUUUCUCGGAUUGACGGUAGGUGGAGAAGAAGCACCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCGAGCGUUGUCCGGAAUUACUGGGCGUAAAGAGCUCGUAGGUGGUUUGUCGCGUUGUUCGUGAAAUCUCACGGCUUAACUGUGAGCGUGCGGGCGAUACGGGCAGACUAGAGUACUGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGGAAUGCGCAGAUAUCAGGAGGAACACCAGUGGCGAAGGCGGGUCUCUGGGCAGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGUACUAGGUGUGGGUUUCCUUCCUUGGGAUCCGUGCCGUAGCUAACGCAUUAAGUACCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGUUUGACAUGCACAGGAUGCGUCUAGAGAUAGGCACUCCCUUGUGGCCUGUGUGCAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUCAUGUUGCCAGCACGUAAUGGUGGGGACUCGUGAGAGACUGCCGCGGUCAACUCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACACAUGCUACAAUGGCCGGUACAAAGGGCUGCGAUGCCGCAAGGUUAAGCGAAUCCUUUUAAAGCCGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGUCGGUAACACCCGAAGCCAGUGGCCUAACCCUCGGGAGGGAGCUGUCCAAGGUGGGAUCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq
new file mode 100644
index 0000000..539e3c1
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq
@@ -0,0 +1,2 @@
+>d.16.b.P.pacificensis
+AGAGUUUGAUCAUGGCUCAGAUUGAUCGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGGAACGAUGAUAGCUUGCUAUCAGGCGUCGAGCGGCGGACGGGUGAGUAAUACUUAGGAAUCUACCUAGUAGUGGGGGAUAGCUCGGGGAAACUCGAAUUAAUACCGCAUACGUCCUACGGGAGAAAGCAGGGGAUCAUUAGACCUUGCGCUAUUAGAUGAGCCUAAGUCGGAUUAGCUAGAUGGUGGGGUAAAGGCCUACCAUGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACCGGGACUGAGACACGGCCCGGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGGAACCUGAUCCAGCCAUGCCGCGUGUGUGAAGAAGGCCUUUUGGUUGUAAAGCACUUUAAGCAGUGAAGAAGACUCUUCGGUUAAUACCCGGGGACGAUGACAUUAGCUGCAGAAUAAGCACCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGAGCGUAGGUGGCUUGAUAAGUCAGAUGUGAAAUCCCCGGGCUUAACCUGGGAACUGCAUCUGAAACUGUUAGGCUAGAGUAGGUGAGAGGGAAGUAGAAUUUCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGAAGGAAUACCGAUGGCGAAGGCAGCUUCCUGGCAUCAUACUGACACUGAGGCUCGAAAGCGUGGGUAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCUACUAGUCGUUGGGUCCCUUGAGGACUUAGUGAUGCAGCUAACGCAAUAAGUAGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCCGGUCUUGACAUACACAGAAUCUUGUAGAGAUACGAGAGUGCCUUCGGGAAUUGUGAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCUUAGUUACCAGCGGGUUAAGCCGGGAACUCUAAGGAUACUGCCAGUGACAAACUGGAGGAAGGCGGGGACCACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGUAGGUACAGAGGGCAGCUACACAGCGAUGUGAUGCGAAUCUCAAAAAGCCUAUCGUAGUCCAGAUUGGAGUCUGCAACUCGACUCCAUGAAGUAGGAAUCGCUAGUAAUCGCGGAUCAGAAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGAUUGCACCAGAAGUGGUUAGCCUAACUUAGUGAGGGCGAUCACCACGGUGUGGUCGAUGACUGGGGUGAAGUCGUAACAAGGUAGCCCGUAGGGGAAACCUGCGGCGGUUGGAUCACCUCCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq
new file mode 100644
index 0000000..a0ca78a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq
@@ -0,0 +1,2 @@
+>d.16.b.P.vulgaris
+UAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAGCGGUAACAGGAGAAAGCUUGCUUUCUUGCUGACGAGCGGCGGACGGGUGAGUAAUGUAUGGGGAUCUGCCCGAUAGAGGGGGAUAACUACUGGAAACGGUGGCUAAUACCGCAUGACGUCUACGGACCAAAGCAGGGGCUCUUCGGACCUUGCGCUAUCGGAUGAACCCAUAUGGGAUUAGCUAGUAGGUGAGGUAAUGGCUCACCUAGGCAACGAUCUCUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUAGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGUGAUAAAGUUAAUACCUUUAUCAAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUCAAUUAAGUCAGAUGUGAAAGCCCCGAGCUUAACUUGGGAAUUGCAUCUGAAACUGGUUGGCUAGAGUCUUGUAGAGGGGGGUAGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACAAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAAACGAUGUCGAUUUAGAGGUUGUGGUCUUGAACUGUGGCUUCUGGAGCUAACGCGUUAAAUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUACUCUUGACAUCCAGCGAAUCCUUUAGAGAUAGAGGAGUGCCUUCGGGAACGCUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGCGUAAUGGCGGGAACUCAAAGGAGACUGCCGGUGAUAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCAGAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGAACUCAUAAAGUCUGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUAGAUCAGAAUGCUACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq
new file mode 100644
index 0000000..37dd472
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq
@@ -0,0 +1,2 @@
+>d.16.b.R.erythropolis
+UCAACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAGCGGUAAGGCCUUCGGGGUACACGAGCGGCGAACGGGUGAGUAACACGUGGGUGAUCUGCCCUGCACUUCGGGAUAAGCCUGGGAAACUGGGUCUAAUACCGGAUAUGACCUCCUAUCGCAUGGUGGGUGGUGGAAAGAUUUAUCGGUGCAGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGACGGGUAGCCGACCUGAGAGGGUGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGACGAAGCGCAAGUGACGGUACCUGCAGAAGAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGAGCAAGCGUUGUCCGGAAUUACUGGGCGUAAAGAGUUCGUAGGCGGUUUGUCGCGUCGUUUGUGAAAACCAGCAGCUCAACUGCUGGCUUGCAGGCGAUACGGGCAGACUUGAGUACUGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGGUCUCUGGGCAGUAACUGACGCUGAGGAACGAAAGCGUGGGUAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCGCUAGGUGUGGGUUCCUUCCACGGAAUCCGUGCCGUAGCUAACGCAUUAAGCGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGUUUGACAUAUACCGGAAAGCUGCAGAGAUGUGGCCCCCCUUGUGGUCGGUAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUAUCUUAUGUUGCCAGCACGUUAUGGUGGGGACUCGUAAGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACACAUGCUACAAUGGCCAGUACAGAGGGCUGCGAGACCGUGAGGUGGAGCGAAUCCCUUAAAGCUGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGUCGGUAACACCCGAAGCCGGUGGCUUAACCCCUUGUGGGAGGGAGCCGUCGAAGGUGGGAUCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq
new file mode 100644
index 0000000..4cea7ad
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq
@@ -0,0 +1,2 @@
+>d.16.b.R.felis.URRWXCal2
+GACAGAAUCAAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUAUCGGUAUGCUUAACACAUGCAAGUCGGACGGACUAAUUGGGGCUUGCUCCAAUUAGUUAGUGGCAGACGGGUGAGUAACACGUGGGAAUCUGCCCAUCAGUACGGAAUAACUUUUAGAAAUAAAAGCUAAUACCGUAUAUUCUCUACAGAGGAAAGAUUUAUCGCUGAUGGAUGAGCCCGCGUCAGAUUAGGUAGUUGGUGAGGUAACGGCUCACCAAGCCGACGAUCUGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUACCGAGUGAGUGAUGAAGGCCCUAGGGUUGUAAAGCUCUUUUAGCAAGGAAGAUAAUGACGUUACUUGCAGAAAAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGAGUGCGUAGGCGGUUUAGUAAGUUGGAAGUGAAAGCCCGGGGCUUAACCUCGGAAUUGCUUUCAAAACUACUAAUCUAGAGUGUAGUAGGGGAUGAUGGAAUUCCUAGUGUAGAGGUGAAAUUCUUAGAUAUUAGGAGGAACACCGGUGGCGAAGGCGGUCAUCUGGGCUACAACUGACGCUGAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAGAUAUCGGAAGAUUCUCUUUCGGUUUCGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCUCGCACAAGCGGUGGAGCAUGCGGUUUAAUUCGAUGUUACGCGAAAAACCUUACCAACCCUUGACAUGGUGGUCGCGGAUCGCAGAGAUGCUUUCCUUCAGCUCGGCUGGACCACACACAGGUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCAUUCUUAUUUGCCAGCGGGUAAUGCCGGGAACUAUAAGAAAACUGCCGGUGAUAAGCCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGGGUUGGGCUACACGCGUGCUACAAUGGUGUUUACAGAGGGAAGCAAGACGGCGACGUGGAGCAAAUCCCUAAAAGACAUCUCAGUUCGGAUUGUUCUCUGCAACUCGAGAGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCUCGGGCCUUGUACACACUGCCCGUCACGCCAUGGGAGUUGGUUUUACCUGAAGGUGGUGAGCUAACGCAAGAGGCAGCCAACCACGGUAAAAUUAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUUACCUCCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq
new file mode 100644
index 0000000..4768ec6
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq
@@ -0,0 +1,2 @@
+>d.16.b.R.prowazekii
+AUCAAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUAUCGGUAUGCUUAACACAUGCAAGUCGAACGGAUUAACUAGAGCUCGCUUUAGUUAAUUAGUGGCAGACGGGUGAGUAACACGUGGGAAUCUACCCAUCAGUACGGAAUAACUUUUAGAAAUAAAAGCUAAUACCGUAUAUUCUCUACGGAGGAAAGAUUUAUCGCUGAUGGAUGGGCCCGCGUCAGAUUAGGUAGUUGGUGAGGUAAUGGCUCACCAAGCCGACGAUCUGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUACCGAGUGAGUGAUGAAGGCCUUAGGGUUGUAAAGCUCUUUUAGCAAGGAAGAUAAUGACGUUACUUGCAGAAAAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGAGUGCGUAGGCGGUUUAGUAAGUUGGAAGUGAAAGCCCGGGGCUUAACCUCGGAAUUGCUUUCAAAACUACUAAUCUAGAGUGUAGUAGGGGAUGAUGGAAUUCCUAGUGUAGAGGUGAAAUUCUUAGAUAUUAGGAGGAACACCGGUGGCGAAGGCGGUCAUCUGGGCUACAACUGACGCUGAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAGAUAUCGGAGGAUUCUCUUUCGGUUUCGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCUCGCACAAGCGGUGGAGCAUGCGGUUUAAUUCGAUGUUACGCGAAAAACCUUACCAACCCUUGACAUGGUGGUUACGGAUUGCAGAGAUGCUUUCCUUCAGUUCGGCUGGGCCACACACAGGUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUUCUUAUUUGCCAGUGGGUAAUGCCGGGAACUAUAAGAAAACUGCCGGUGAUAAGCCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGGGUUGGGCUACACGCGUGCUACAAUGGUGUUUACAGAGGGAAGCAAUACGGUGACGUGGAGCAAAUCCCUAAAAGACAUCUCAGUUCGGAUUGUUCUCUGCAACUCGAGAGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCUCGGGCCUUGUACACACUGCCCGUCACGCCAUGGGAGUUGGUUUUACCUGAAGGUGGUGAGCUAACGCAAGAGGCAGCCAACCACGGUAAAAUUAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUUACCUCCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq
new file mode 100644
index 0000000..639b9c2
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.acidiscabies
+CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAUCACUCCUGCCUGCAUGGGCGGGGGUCGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGGAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCUGUGUUGCCAGCGUGCCCUUCGGGGUGACGGGGACUCACAGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAAGAGCUGCGAAACCGUGAGGUGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq
new file mode 100644
index 0000000..1181b57
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.aureus
+UUUUAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGAACGGACGAGAAGCUUGCUUCUCUGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGAUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUUGAACCGCAUGGUUCAAAAGUGAAAGACGGUCUUGCUGUCACUUAUAGAUGGAUCCGCGCUGCAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCAACGAUGCAUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGGCGAAAGCCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUCUUCGGAUCGUAAAACUCUGUUAUUAGGGAAGAACAUAUGUGUAAGUAACUGUGCACAUCUUGACGGUACCUAAUCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGCGCGUAGGCGGUUUUUUAAGUCUGAUGUGAAAGCCCACGGCUCAACCGUGGAGGGUCAUUGGAAACUGGAAAACUUGAGUGCAGAAGAGGAAAGUGGAAUUCCAUGUGUAGCGGUGAAAUGCGCAGAGAUAUGGAGGAACACCAGUGGCGAAGGCGACUUUCUGGUCUGUAACUGACGCUGAUGUGCGAAAGCGUGGGGAUCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGACCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAAAUCUUGACAUCCUUUGACAACUCUAGAGAUAGAGCCUUCCCCUUCGGGGGACAAAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAAGCUUAGUUGCCAUCAUUAAGUUGGGCACUCUAAGUUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACAUCAAAUCAUCAUGCCCCUUAUGAUUUGGGCUACACACGUGCUACAAUGGACAAUACAAAGGGCAGCGAAACCGCGAGGUCAAGCAAAUCCCAUAAAGUUGUUCUCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGCUGGAAUCGCUAGUAAUCGUAGAUCAGCAUGCUACGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGCCGGUGGAGUAACCUUUUAGGAGCCAGCCGUCGAAGGUGGGACAAAUGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq
new file mode 100644
index 0000000..2548398
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.bottropensis
+CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACAACACUCUCGGGCAUCCGAUGAGUGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUCGCCCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGGUGACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq
new file mode 100644
index 0000000..bc38f32
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.diastatochromogenes
+CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACAACCACUAGGGGCAUCUCUUGGUGGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAGUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq
new file mode 100644
index 0000000..8d346c2
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.eurythermus
+CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCUCCUUCGGGAGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGAGCCUCCAAGGCAUCUUGGAGGUUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUUAGAGAUAGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq
new file mode 100644
index 0000000..89dcb68
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.griseus
+CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCUUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAACACUCUGUCCCGCAUGGGACGGGGUUAAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCUAGCUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGUUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUAUACCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGUAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUGCGCGAGGCGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq
new file mode 100644
index 0000000..ea52e53
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.neyagawaensis
+CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGACGCGCUCGGGCAUCCGAUGUGCGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACGCCGGAAACACCCAGAGAUGGGUGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAGUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq
new file mode 100644
index 0000000..a046f62
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.nodosus
+UUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGAGCCGGGGAGGCAUCUCCCUGGUUGGAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGCCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCGCGUCGCGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUUAGAGAUAGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCCAAGGUGGGACUGGCGAUUGGGACGAAAUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq
new file mode 100644
index 0000000..f530e47
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.sampsonii
+CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCGCUUUCGGGCGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAUGACUGUCCAUCGCAUGGUGGAUGGUGUAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAGUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGUCUGGAGACAGGCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq
new file mode 100644
index 0000000..1155f53
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.scabiei
+CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGACACUCUCGGGCAUCCGAUGAGUGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCUAACCCGUAAGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq
new file mode 100644
index 0000000..8cd1523
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq
@@ -0,0 +1,2 @@
+>d.16.b.S.tendae
+CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACUGACCCUCGCAGGCAUCUGCGAGGUUCGAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGCAAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq
new file mode 100644
index 0000000..d849fb4
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq
@@ -0,0 +1,2 @@
+>d.16.b.Streptomyces.sp
+CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCUUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAAUACCUUCCCUCGCAUGGGGGUGGGUUCAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAGUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACAUCCAGAGAUGGGUGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCUUACGGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq
new file mode 100644
index 0000000..0e4a9bb
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq
@@ -0,0 +1,2 @@
+>d.16.b.Synechococcus.sp
+CAAAAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGGCUCUUCGGAGCUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUGCCUACAGGACGGGGACAACAGUUGGAAACGACUGCUAAUACCCGAUGUGCCGAGAGGUGAAACAUUUAUGGCCUGUAGAUGAGCUCGCGUCUGAUUAGCUAGUUGGUGGGGUAAGGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGCAAGCGACGGAGCAACGCCGCGUGGGGGAGGAAGGUUUUUGGACUGUAAACCCCUUUUCUCAGGGAAGAAGAAAGUGACGGUACCUGAGGAAUAAGCCUCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGGAGAGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGCCUGCAGGCGGUUAAUCAAGUCUGUUGUCAAAGCGUGGGGCUCAACCUCAUACAGGCAAUGGAAACUGAUUGACUAGAGUAUGGUAGGGGUAGCGGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAAGAACACCAGCGGCGAAAGCGCGCUACUGGGCCAUAACUGACGCUCAUGGACGAAAGCUAGGGGAGCGAAAGGGAUUAGAUACCCCUGUAGUCCUAGCCGUAAACGAUGAACACUAGGUGUUGCGUGAAUCGACCCGCGCAGUGCCGUAGCCAACGCGUUAAGUGUUCCGCCUGGGGAGUACGCACGCAAGUUGGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUCCCCCGAAUCUCUUGGAAACGAGAGAGUGCCUUCGGGAGCGGGGAGACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCACGUUUUUAGUUGCCAUCAUUCAGUUGGGCACUCUAGAGAAACUGCCGGUGACAAACCGGAGGAAGGUGUGGACGACGUCAAGUCAUCAUGCCCCUUACAUCCUGGGCUACACACGUACUACAAUGCUCCGGACAGCGAGACGCGAAGCCGCGAGGUGAAGCAAAUCUCCCAAACCGGGGCUCAGUUCAGAUUGCAGGCUGCAACUCGCCUGCAUGAAGGCGGAAUCGCUAGUAAUCGCAGGUCAGCAUACUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGUUGGCCAUGCCCGAAGUCGUUACCCUAACCGUUCGCGGAGGGGGGCGCCGAAGGUAGGGCUGAUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGUGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq
new file mode 100644
index 0000000..2d0e8e9
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq
@@ -0,0 +1,2 @@
+>d.16.b.T.maritima
+UAUAUGGAGGGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAACACAUGCAAGUCGAGCGGGGGAAACUCCCUUCGGGGAGGAGUACCCAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCCUCCGGAGGGGGAUAACCAGGGGAAACCCUGGCUAAUACCCCAUACGCUCCAUCAACGCAAGUUGGUGGAGGAAAGGGGCGUUUGCCCCGCCGGAGGAGGGGCCCGCGGCCCAUCAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGACGACGGGUAGCCGGCCUGAGAGGGUGGUCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGGACAAUGGGGGAAACCCUGAUCCAGCGACGCCGCGUGCGGGACGAAGCCCUUCGGGGUGUAAACCGCUGUGGCGGGGGAAGAAUAAGGUAGGGAGGAAAUGCCCUACCGAUGACGGUACCCCGCUAGAAAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCAAGCGUUACCCGGAUUUACUGGGCGUAAAGGGGGCGUAGGCGGCCUGGUGUGUCGGAUGUGAAAUCCCACGGCUCAACCGUGGGGCUGCAUCCGAAACUACCAGGCUUGGGGGCGGUAGAGGGAGACGGAACUGCCGGUGUAGGGGUGAAAUCCGUAGAUAUCGGCAGGAACGCCGGUGGGGAAGCCGGUCUCCUGGGCCGACCCCGACGCUGAGGCCCGAAAGCCAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACGAUGCCCACUAGGUGUGGGGGGGUAAUCCCUCCGUGCUGAAGCUAACGCGUUAAGUGGGCCGCCUGGGGAGUACGCCCGCAAGGGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCGUGUGGUUUAAUUGGAUGCUAAGCCAAGAACCUUACCAGGGCUUGACAUGCCGGUGGUACCUCCCCGAAAGGGGUAGGGACCCAGUCCUUCGGGACUGGGAGCCGGCACAGGUGGUGCACGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUGCCCCUAGUUGCCAGCGGUUCGGCCGGGCACUCUAGGGGGACUGCCGGCGACGAGCCGGAGGAAGGAGGGGAUGACGUCAGGUACUCGUGCCCCUUAUGCCCUGGGCGACACACGCGCUACAAUGGGCGGUACAAUGGGUUGCGACCCCGCGAGGGGGAGCCAAUCCCCAAAGCCGCCCUCAGUUCGGAUCGCAGGCUGCAACCCGCCUGCGUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCACCCGAGUCGGGGGCUCCCGAAGACACCUACCCCAACCCGAAAGGGAGGGGGGGUGUCGAGGGAGAACCUGGCGAGGGGGGCGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq
new file mode 100644
index 0000000..23d8958
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq
@@ -0,0 +1,2 @@
+>d.16.b.T.pallidum.A
+AUGAUGGAGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGUGCGUUUUAAGCAUGCAAGUCGAACGGCAAGGAAGCGAAUUUUCGUUUCUCUAGAGUGGCGGACUGGUGAGUAACGCGUGGGUAAUCUGCCUUUGAGAUGGGGAUAGCCUCUAGAAAUAGGGGGUAAUACCGAAUACGCUCUUUUGGACGUAGUCUUUGAGAGGAAAGGGGCUGCGGCCUCGCUCAGAGAUGAGCCUGCGACCCAUUAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGUCGAUGGGUAUCCGACCUGAGAGGGUGACCGGACACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGCUAAGAAUAUUCCGCAAUGGGCGAAAGCCUGACGGAGCGACACCGCGUGGAUGAGGAAGGUCGAAAGAUUGUAAAGUUCUUUUGCCGACGAAGAAUGAGGACGGGAGGGAAUGCCCGUUUGAUGACGGUAGUCGUGCGAAUAAGCCCCGGCUAAUUACGUGCCAGCAGCCGCGGUAACACGUAAGGGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGGCAUGCAGGCGGACUGGUAAGCCUGGUGUGAAAUCCCCGAGCUCAACUUGGGAACUGCACUGGGUACUGCUGGUCUAGAAUCACGGAGGGGAAACCGGAAUUCCAAGUGUAGGGGUGGAAUCUGUAGAUAUUUGGAAGAACACCGGUGGCGAAGGCGGGUUUCUGGCCGAUGAUUGACGCUGAGGUGCGAAGGUGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACACAGUAAACGAUGUACACUAGGUGUUGGGGCAUGAGUCUCGGCGCCGACGCGAACGCAUUAAGUGUACCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCCGGGUUUGACAUCAAGAGGAGCGCCGUAGAAAUGCGGUGGCGUAGCGAUACGCCUCUUGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUACUGCCAGUUGCCAGCAAGUGGUGUUGGGGACUCUGGCGGAACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUAUGUCCGGGGCUACACACGUGCUACAAUGGUUGCUACAGAGCGAUGCGAGGUUGUGAAGUGGAGCAAACCGCAAAAAGGCAAUCGUAGUCCGGAUUGAAGUCUGAAACUCGACUUCAUGAAGUUGGAAUCGCUAGUAAUCGCACAUCAGCAUGGUGCGGUGAAUGUGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUCCGAGUUGGAGAUACCCGAAGUCACUAGCCUAACCCGCAAGGGAGGGCGGUGCCGAAGGUAUGUUUGGUAAGGAGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq
new file mode 100644
index 0000000..575befd
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq
@@ -0,0 +1,2 @@
+>d.16.c.C.caldarium
+UAUAAUGGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGUAUGCCUAACACAUGCAAGUCGUACGAGAAUUUUAUUCUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCUCUAGGAGGGGGAUAACAGUUGGAAACGAUUGCUAAAACCCCAUAUGCCAUUAUUGGUGAAAAAGAUUUAUCUGCCUGGAGAUGAGCUCGCGGCUGAUUAGCUAGUUGGUAGGGUAAUGGCUUACCAAGGCAACGAUCAGUAGCUGGUCUUAGAGGAUGAUCAGCCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCACAAUGGGCGAAAGCCUGAUGGAGCAAUACCGUGUGAGGGAUGAAGGCCUGUGGGUUGUAAACCUCUUUUUUCAGGAAAGAAACUUUGACGGUACCUGAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCACUGGGCGUAAAGCGUCUGUAGGUGGUUUAUCAAGUCUGCUGUUAAAGCUUGAGGCUUAACCUCAAAAAAGCAGUGGAAACUGAUAGACUAGAGAAUGGUAGGGGCAGAGAGAAUUCUCAGUGUAGCGGUGAAAUGCGUAGAUAUUGAGAAGAAUACCGAUAGCGAAGGCGCUCUGCUGGGCCAUUACUGACACUCAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGAUGUUGUGUGAGUAAAAUUGUGCAGUAUCGAAGCUAACGCGUUAAGUAUCCCGCCUGGGAAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGACUUGACAUGUUACUAAUUUCCUUGAAAGAGGAAAGUGCCUUUGGGAAAGUAAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUACCAUCAUUAAGUUGGGGACUCUAAAGAGACUGCCGGUGAUAAACCGGAGGAAGGUAAGGAUGAGGUCAAGUCAUCAUGCCCCUUAUGUCCUGGGCUACACACGUGCUACAAUGGUUAGGACAAUAAGUCGCAAAUUCGUGAGAACUAGCUAAUCUUAUAAACCUAAUCUCAGUACGGAUUGUAGGCUGCAACUCGCCUACAUGAAGACGGAAUCGCUAGUAAUCGCUGGUCAGCUACACAGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGCUGGCCAUGUCCGAAAUCAUUACUCUAACCUUAAUGGAGGAGGAUGCUUAAGGCAGGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUUACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq
new file mode 100644
index 0000000..b5a551f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq
@@ -0,0 +1,2 @@
+>d.16.c.C.fragile
+UUGAAAUGGAGAGGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGAUAUGCUUAACACAUGCAAGUCGAACGAAUAUUAAGUUUUCUUAAAUUUGUAGAAAUUUAAUAUUAGUGGCGAACGGGUGAGUAACGCGUAAGAAUCUGCUUUUGGGUAAAGAAUAACAAUUGGAAACGAUUGCUAAUACUUUAUAGGCUGAGGAGUUAAAGGUUUUAUUUCCGCCCAGAAAUGAGCUUGCGUCUGAUUAGCUAGUUGGUAAGAUAAAAGCUUACCAAGGCAAUGAUCAGUAGUUGGUCUGAGAGGAUGAUCAACCACACUGGGACUGAGAUACGGCCCAGACCUUUACGGAGGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUAUCGCGUGAAGGAUGACGGCCUGUGGGUUGUAAACUUCUUUUCUUAAGAAAGAAUUCUGACGGUACUUAAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGAAAUUAUUGGGCGUAAAGAGUUUGUAGGUGGUUUUUUAAGUCUACUGUUAAAUAUCAGAGCUUAACUUUGAACAAGCAGUAUGAAACUAAUUAACUUGAGUUUGGUAGAGGCAGAGGGAACUCUCGAUGUAGUGGUGAAAUACGUAGAUAUCGGGGGGAACACCAGUAGCGAAAGCGCUCUGCUGGGCCAUAACUGACACUGAGAAACGAAAGCUAGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCUAGCUGUAAACGAUGGAUACUAAGUAUUGGGCUUUUUGAAGUUCAGUGUUGAAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGAAUUGACAUACUCGUUGGUUUUUUAGAAAUAAAAAACUGUUAAAGAGAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUGUUAUCUAGAGAGACUGCCGGUGAUAAACCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUAAGUCCUGGGCGACACACGUGCUACAAUGGUAUAGACAAAGGGAAGCAAAUCUGCGAAGAGUAGCAAAUCUCAAAAACUAUAUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGCUGGUCAGCCAUACAGCGGUGAAUAUGUUCUCGGGCCUUGUACACACCGCCCAUCACGCUCGAGAAAUUGGAAAUACCCAAAGUCAUCAUUCUAACCAUAUUUUUUGGAAGAUAAUGCCAAAGGUAGAGCUAGUGACUCAAGCGAAGUUGUAACAAGGUAACCGUACUGGAAGGUGCGGUUGGAUCACCUCCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq
new file mode 100644
index 0000000..665ca3f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq
@@ -0,0 +1,2 @@
+>d.16.c.C.reinhardtii
+AUCCAUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGAACGAGCAAAGCAAUUUGUGUAGUGGCGAACGGGUGCGUAACGCGUAAGAACCUACCUAUCGGAGGGGGAUAACAUUGGGAAACUGUUGCUAAUACCCCAUACAGCUGAGGAGUGAAAGGUGAAAAACCGCCGAUAGAGGGGCUUGCGUCUGAUUAGCUAGUUGGUGGGGGUAACGGCCUCCCAAGGCCACGAGCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUUCGCAAUGGGCGCAAGCGACGGAGCAAUGCCGCGUGCAGGAAGAAGGCCUGUGGGUCGUAAACUGCUUUUCUCAGAGAAGAAGUUCUGACGGUAUCUGAGGAAUAAGCACCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGGUGCAAGCGUUGUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUCGUAAAGUCUAAUGUCAAAUACCAGGGCUCAACCUUGGACCGGCAUUGGAGUACUCACGAGCUUGAGUACGGUAGGGGCAGAGGGAAUUCCAUGUGGAGCGGUGAAAUGCGUAGAGAUAUGGAGGAACACCAGUGGCGAAGGCGCUCUGCUGGGCCGAAACUGACACUGAGAGACGAAAGCUGGGGGAGCGAAUAGGAUUAGAUACCCUAGUAGUCCCAGCCGUAAACUAUGGAGACUAAGUGCUGCCGCAAGCAGUGCUGUAGCUAACGCGUUAAGUCUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGACCGCACAAGCGGUGGAUUAUGUGGAUUAAUUCGAUACAACGCGAAGAACCUUACCAGGGUUUGACAUGUCAAGAACCUCUCAGAAAUGGGAGGGUGCCCUAACGGACUUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCUGUGAAGUGUAUAGUUAAGUCUCAUAACGAGCGCAACCCUCGUCUUUAGUUGCCAUUUGGUUCUCUAAAGAGACUGCCAGUGUAAGCUGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACAUCCUGGGCUUCACACGUAAUACAAUGGUUGGGACAAUCAGAAGCGACUCGUGAGAGCUAGCGGCUCUGUUAAACCCAACCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUGAAGCCGGAAUCGCUAGUAAUCGCCAGUCAGCUAUAUGGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUUCUGCUCCAAGUCGUUACCCUAACCUUCGGGAGGGGGGCGCCUAAAGCAGGGCUAGUGACUAGGGUGAAGUCGUAACAAGGUAGGGCUACUGGAAGGUGGCCCUGGCUCACCUCCUUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq
new file mode 100644
index 0000000..c5ee178
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq
@@ -0,0 +1,2 @@
+>d.16.c.C.vulgaris
+UGCCUGCAGAGAGUUYGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGUACGCAUGCAAUUUGGCUUGCCAGAUUGCGAUGAGUGGCGGACGGGUGAGUAACACGUAAGAACCUACCUUUUGGAGAGGGAUAACCAUUGGAAACGAUGGCUAAUACCUCGUAUUGCUGAGAAGUGAAAGAUGAAAAUCGCCAAUAGAUGGGCUUGCGGCUGAUUAGCUUGUUGGUGAGGUAAUGGCUUACCAAGGCAAUGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGACAGCCUGACGGAGCAAUGCCGCGUGAAGGAUGAAGGCCUAUGGGUUGUAAACUUCUUUUCUCAGAGAAGAAGCAUUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUAAAAAGUCUCCUGUCAAAGAUCAGGGCUUAACCCUGGGCCGGCAGGAGAAACUCUUAGGCUAGAGUUUGGUAGGGGCAGAGGGAAUUCCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGGAGGAACACCAAAGGCGAAAGCACUCUGCUGGGCCAUAACUGACACUGAGAGACGAAAGCGAGGGGAGCAAAAGGGAUUAGAUACCCCUGUAGUCCUCGCCGUAAACGAUGGAUACUAGAUGUUGGGUAGGUUAAAUCACUCAGUAUCGUAGCUAACGCGUGAAGUAUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGACUUGACAUGCCACUUUUUCCCUGAAAGGGGAAGUUCCAGAGUGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCUUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUUUGAAUUGCCAGUAAUGGGAAAUUCAAAAGACUGCCGGUGACAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACGUCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGAGAUGCAAACCCGCGAGGGCUAGCCAACCUCAAAAACCCGGUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGCAGGUCAGCCAUACUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGCUGGCUAUGCCCAAAGUCGUUACCCCAACCUUUUAGGAGGGGGACGCCUAAGGCAGAGCUAGUGACUAGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGWGGYUGGAUCACCUCCUUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq
new file mode 100644
index 0000000..3b7fc1b
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq
@@ -0,0 +1,2 @@
+>d.16.c.Cryptomonas.sp
+AAAUCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGUACGAAAGUUUUUAACUUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCCUUAGGAGGAGGGGGAUAACAGCUGGAAACGGCUGCUAAUACUCCAUAUGCUGAAGAGUGAAAGGGAAACCACCUAAGGAAGAGCUCGCGUCUGAUUAGCUAGUUGGUAGGGUAAGGGCCUACCAAGGCGACGAUCAGUAGCUGGUUUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGCAAGCCUGACGGAGCAAUACCGCGUGAGGGAUGAAGGCCUGUGGGUUGUAAACCUCUUUUCUCAAGGAAGAAGUUCUGACGGUACUUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGAUGCAAGCGUUAUCCGGAAUUACUGGGCAUAAAGCGUCUGUAGGUUGUUUAGUAAGUCUGCUGUUAAAGACUAGGGCUUAACCCUAGAAAAGCAGUGGAAACUGCUAGACUUGAGUGUGGUAGAGGUAGAGGGAAUUCCUAGUGUAGCGGUGAAAUGCGUAGAUAUUAGGAAGAACACCAAUGGCGAAAGCACUUUACUGGGCCAUAACUGACACUGAGAGACGACAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGAUGUUGUACGUAUUAACCCGUACAGUAUCGUAGCUAAGGCGUUAAGUAUCCCGCCUGGGAAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUGUCACAAAUUUUCUUGAAAAAGAAAAGUGCCUUCGGGAAUGUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGUAACCCUUGUUUUUAGUUGCCAUCAUUAAGUUGGGCACUUUAAAAAGACUGCCGGUGAUAAACCGGAGGAAGGUGAGGACGACGUCAAGUCAGCAUGCCCCUUACACUCUGGGCUACACACGUACUACAAUGGUCGAGACAAAAAGUCGCAAACUUGUGAAAGUAAGCUAAUCUUAUAAACUCGAUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUAGUCAUACCCAAAGUCGUUACCUUAACCAUUCGGAGGGGGGCGCCUAAGGUAGGGUUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq
new file mode 100644
index 0000000..6c04b9e
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq
@@ -0,0 +1,2 @@
+>d.16.c.E.gracilis
+UGGAAAUGACGAGUUUGAUCCUUGCUCAGGGUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUUGAACGAAAUUACUAGCAAUAGUAAUUUAGUGGCGGACGGGUGAGUAAUAUGUAAGAAUCUGCGCUUGGGCGAGGAAUAACAGAUGGAAACGUUUGCUAAUGCCUCAUAAUUUACUAGAUCUAUGUGAGUAGCUAGUUAAAGAGAAUUUCGCCUAGGCAUGAGCUUGCAUCUGAUUAGCUUGUUGGUGAGGUAAAGGCUUACCAAGGCGACGAUCAGUAGCUGAUUUGAGAGGAUGAUCAGCCACACUGGGAUUGAGAACGGAACAGACUUCUACGGAAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGCAAGCCUGACGGAGCAAUACCGCGUGAAGGAAGACGGCCUUUGGGUUGAAAACCUCUUUUCUCAAAGAAGAAGAAAUGACGGUAUUUGAGGAAUAAGCAUCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGGAGAUGCGAGCGUUAUCCGGAAUUAUUGGGCGUAAAGAGUUUGUAGGCGGUCAAGUGUGUUUAAUGUUAAAAGUCAAAGCUUAACUUUGGAAGGGCAUUAAAAACUGCUAGACUUGAGUAUGGUAGGGGUGAAGGGAAUUUCCAGUGUAGCGGUGAAAUGCGUAGAGAUUGGAAAGAACACCAAUGGCGAAGGCACUUUUCUAGGCCAAUACUGACGCUGAGAAACGAAAGCUGAGGGAGCAAACAGGAUUAGAUACCCUGUAGUCUUGGCCGUAAACUAUGGAUACUAAGUGGUGCUGAAAGUGCACUGCUGUAGUUAACACGUUAAGUAUCCCGCCUGGGGAGUACGCUUGCACAAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACACGAAGAACCUUACCAGGAUUUGACAGGAUCUAGGAAGUUUGAAAGAACGCAGUACCUUCGGGUAUCUAGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUUUUUAAUUAACGCUUGUCAUUUAGAAAUACUGCUGGUUAUUACCGGAGGAAGGUGAGGACGACGUCAAGUCAUCAUGCCCCUUAUAUCCUGGGCUACACACGUGCUACAAUGGUUAAGACAAUAAGUUGCAAUUUUGUGAAAAUGAGCUAAUCUUAAAACUUAGCCUAAGUUCGGAUUGUAGGCUGAAACUCGCCUACAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGUCGGCUGUGCCCGAAGUUAUUAUCUUGCCUGAAAAGAGGGAAAUACCUAAGGCCUGGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGUGGCUGGAACAACUCC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq
new file mode 100644
index 0000000..13a55b3
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq
@@ -0,0 +1,2 @@
+>d.16.c.H.africana
+UCUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUUGAACGAGAAAUAGAACAACUAUUUCUAGUAGCGAACGGGUGCGUAAUUACAUAAGAACUUAUCCUUUUAAGAAGGAAAUAACAAAUAACAAAUGGAAACAUUUGCUAAUGUCCUAUAAGCUGAAAAGUAAAAGGAUUAAAUCCACUAAAGGUAAGGCUUAUGUCUAGUUAGUUGGUAAGGUAACAGCUUAACAAGACAAUGAUCAGUAAUUGGUCUGAGAGGAUGAUCAAUCACACUGGAACUGAGAUAAGGUCCAGACUCCUACGGGUGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCUGACGGGGCAAUGUUGCGUGAAGGCAGAAGGCCGAUAGGUUGUAAACUUCUUUUGUGAGAAAAUAAGGAAAAUGACAGUAUCUCAAGAAUAAGCAUCGGCUAACUUUGUGCCAGCAGCCGCGGUGAUACAGAGGAUGCGAGCAUUAUCCGGAAUUAUUGGGCGUAAAGUGUUUUAAGGUGGCUUUAUAAGUCUAUCGUUAAAUCUCAGAGCUUAACUCUGAUUAGGCGAUUGACUAUUAAGCUAGAGCUUUGAAUAAAGCAAGGGGAAUUUCUAAUGAAGCGGUUAAAUGCGUUGAGAUUGGAAAGAACACCAAGGGCGAAAGCACUCUGCUGGGCCAAAAUUGACACUGAUAAACGAAAGCUAGGGUAGCGAGAGGGAUUAGACACCCCAAUAGUCCUAGCUGUAAACAAUGGAUACUUAGCAUUACUAUAUGAAAAGAUAGCUAAGCUUAAAGCUAACGCAAUAAGUAUCCCGCCUGGGAAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGGCGGGGGUUCACGCAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUACCAGGGAUUGUAUGUCGUAAUCUUUCUGAAAAAGUAAGAUACGUAUUUAUUUAAUAAAUAAAUACGUAGACACAGGUGGUGCAUGGCUGUCGUCAGCCCGUGCUGUCAAGCGUAGGGUUAACUCCCAUAACGGGCGCAACUCCCAUGUUUAGUUACCAAUUUAUGGUACUCUAAACAAACAGCUAAUGAUAAAUACUAAAUUAGAGGAAGGUGGGGAAGACGUCAAGUCAUCAUGCCCUUUAUACUCUGGGCUACACGCGUGCUACAAUGGCUGGGACAAAAUGUUGCAAUUCUGUAAAGAUAUAGCAAAACAUAAAACCCAGUCUCAGUUCGGAUUCGGGCUGCAACUCGCCCGCAUGAAGUCGGAAUCGCUAGUAAUCGCUGGUCAGCAAUACAGCGGUGAAUAAGUCACCGGACCUUGUACACACCGCCCGUCACACUCAGGAAAUUGGUCAUGCCCUAACUCAUUUUAAUAUAAUGAUAAAGGUGAGGCUGGUAACUAGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq
new file mode 100644
index 0000000..7f1d3dd
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq
@@ -0,0 +1,2 @@
+>d.16.c.H.akashiwo
+UUUUAGGAUAUAAUUGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAGAGGUUUUUAAAGAUUUUUCUUAAAAAACUGAAAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUGCCUUUAGGAAAGGGACAACAUUUGGAAACGAAUGCUAAUACCUUAUAUGCCUAUUAUAACUUGUAUAAUUAAUAGGUGAAAAGUUUUCUGCCUAGAGAGGAGCUCGCGGCUGAUUAGCUAGUUGGUGGGGUAAUGGCCUACCAAGGCGACGAUCAGUAACUGAUUUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCUGCAAUGGGCGAAAGCCUGACAGAGCAAUACCGCGUGAGGGAUGACAGUCCUAUGGAUUGUAAACCUCUUUUUUCAGGGAGGAAGUUCUGACGUUACCUGAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGUGUUAUCCGGAAUCACUGGGCGUAAAGCGUCUGUAGGUGGUUUAAUGUGUCUGUUGUUAAAUCUUAAGGCUCAACCUUAAACCAGCAAUGGAAACUAUUAUGACUUGAGUGUGGUAGAGGUAGAGGGAAUUUCCAGUGGAGCGGUGAAAUGCGUAGAUAUUGGAAAGACCACCAAUGGCGAAGGCACUCUACUGGGCCAUUACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCUGUAAACGAUGGAUACUAGAUGUCGCAUGUAUCGACCCAUGCGGUAUUAUAGCUAACGCGUUAAGUAUCCCGCCUGGGAAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUAGUACGAAGUUUUUUGAAAAAAAAACCACCUUCGGGAACGUACAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGUAACCCUUGUUUUUAGUUGCCUUUCGAGGAUAUUUAGAAAGACUGCCGAUUAUAAAUCGGAGGAAGGUAAGGACGACGUCAAGUCAUCAUGCCCCUUACACUCUGGGCUACACACGUGCUACAUUGGGUAGAACAAUAAGUUGCUAAGUUGCGAAACCAAGCGAAUCUUCAAAUCUACUCUAAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUAAAGAUGGAAUCGCUAGUAAUCGCUGGUCAGCUACACAGCGGUGAAUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUCACACCCAAAGUCGUUAUUCUAACCGUUUGGAGGAAGGCGCCUAAGGUAGGAUUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUAUAAAGGUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq
new file mode 100644
index 0000000..516122e
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq
@@ -0,0 +1,2 @@
+>d.16.c.M.polymorpha
+UCUCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGUACGGGAAGGAUCCUAGUGGUGUUUCCAGUGGCGGACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGGACAACAGCUGGAAACGGUUGCUAAUACCCCAUAGGCUGAGGAGCAAAAGGAGGAAUCCGCCUAAGGAGGGGCUUGCGUCUGAUUAGCUAGUUGGUGAGGUAAUAGCUUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCUUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAACGUGACGGAGCAAUGCCGCGUGGAGGUAGAAGGCUCACGGGUCGUAAACUCCUUUUCUCAGAGAAGAUGCAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUUAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGAAAGAACACCAAUGGCGAAAGCACUCUUCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAAGCGCUGUGCUAUCGACCCGUGCAGUGCUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCCGUGAAUCUUUUUGAAAGAAAAGAGUGCCUUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCUUGUUUAGUUGCCAUCAUUAAGUUUGGAACCCUAAACAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACGCCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGGGUCGCGACCUCGCGAGAGAAAGCUAACCUCAAAAACCCGGCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUGGGAGCUGGCCAUGCCCGAAGUCGUUACUCUAACCGUAAGGAGGGGGGUGCCGAACAGGGGCUAGUGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq
new file mode 100644
index 0000000..09f3dac
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq
@@ -0,0 +1,2 @@
+>d.16.c.P.falciparum
+UUAUAUUGCGAGUUUGAUCCUAGCUCAGAAUUAACGCUAGAAAUAUACAUUACACAUGCAAAUUAAUGAUAAUAUCAUAGUGUAUAGGUGAGGAUAUAUAAAUUUUUAAUUUUAAAUAGAUUAUAAAUUUUAUUAAAUAAUAAUCUAUAAGCGCAAAAAUAUAUGUACUAUAUUAAAAAUUAAUAUUAUUUAAAAUAAAAUUUAUAUUUGAUUAACUAGUUGGUAAUUUAAAAGACUACCAAGGUUAUUAUCAAAAAUUGGUUUGAAAGAAUGUACAAUCACAUUAGGAUUGAAAUAAAGCCUAAAUUUUUAUAAAAAAUCAGCAGUGAGGAAUAUUUUACAAUAAGUGUAAGCUUGAUAAAGUAAUAUUUCUUUUAGGAAGACAGUAUUAUUAAAAUAUUGUAAACUUUUUAUUUUAUUUUUAAAUAUUGAUAAAAAUAAAAAAUAGUAUUUGCUAUUUCUGUGCCAGCAGCAGCGGUAAUACAGAAAAUGCAAGCGUUAUUCAUUUUAUUAGGCGUAAAGCGUUUUAAGGUUUUAUAUUAAUUUUAUGUUUAAAUAUUUAAAUUAAAUUUAAAAUAAAUUAAUAAAUAAUAAUAUAAUAGAGUAUUAUAAAAGUAUUAAGAAUUUUUUGAGAAGUAGUGAAAUACAAUGAUACAAAAAAGAAUAUCAAAGGCGGAAGCAUAAUACUAUAUAAUUACUGACACUUAAAAACGAAAGCUAAGGUAGCAAAUAGGAUUAGAUACCCUAGUAGUCUUAGCUGUAAACUAUGAAUAUUUUAUAUUUAUAUUUUAUAAAUAUAAUAACUAACGUGAUAAAUAUUCCGCCUGAGUAGUAUAUUCGCAAGAAUGAAAUUCAAAGGAAUUGACGGGAGCUUAUACAAGUGGUGGAACAUGUGGCUUAAUUCGAUGCAACACGAUAAACCUUACCAAAAUUUAACAAUAUUUUUAAUAUUAAGAAAUUAAUAUUUUAAUAAAAUAUAUAGGUAGUGCAUGGCUGUCGUCAGUUCGUGCUGUGAAGUGUUAAUUUUAGUAUUAUAACGAACGUAACCUUUUAUAAAAAAAAUUUUUAUAAUAAAUAAUAAUAAAGAUUACGUCAAGUCAUUAUGCUCCUUAUAUUUUGGGCUGCUCACGUGUUACAUAAAAUAUUACAAUAUUUUAUUAUAUGUUAAAUAUAAUAAUUAAAAUAUAUUUAUAGUUCAGAUUAUAAAUUGAAACUCAUUUAUAUAAAGAUGGAAUCACUAGUAAUCGCUAAUCAGAAUUAUAGCGGUGAAUAAGUUCUUAAGCUUUGUACACACCGCCCGUCACAUCUAAAAAGUAUCAUAUUAUAUAAAAAUUAUUGUUAAAUAAUAAUAUAUAAUUAUAUAAUUUAGAUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUAAUAAAAUAAAUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq
new file mode 100644
index 0000000..6a92f4d
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq
@@ -0,0 +1,2 @@
+>d.16.c.P.littoralis
+AAACUAUCGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUUACACAUGCAAGUCGUACGAAAGUGUUAAAACUUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUUUACCUUUAGGAGGGGAAUAACAGUUGGAAAUGACUGCUAAUGCCGCAUAUCGUAAUUAUGAGACAUAUCAUAACUAUGAAAGAAGAAAUUCGCCUAAAGAAAAGCUUGCGUCUGAUUAGCUAGUUGGUAAGGGUAAAGGCUACAAGGCGACGAUCAGUAGCUGGUUUGAGAGGACGACCAGUCACACUGGACUGAGACACGGUCCAGACUACUACGGGAGGCAGCAGUGGGGAAUUUUCUGCAAUGGGCGAAACUGAACAGAGCAAUACCGCGUGAGGGAAGAAAGCCCACAGGGUUGUAAACCUCUUUUGUCAAGGAAGAAGAUUCUGACGUUACUUGACGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGGACGGGGGAUGCAAGUGUUAUCCGGAAUUACUGGGCGUAAAGCGUUUGUAGGUGGUUUAGUAAGUCUAUUGUUAAAGCUUGAAGCUUAACUUCAAAAGUGUAAUAGAAACUACUAGACUUGAGGAUAGUAGGGGUAAAGGGAAUUUCCAGUGGAGCGGUGAAAUGCGUAGAGAUUGGAAGGACCACCGAUGGCGAAGGCACUUUACUGGGCUAUUUCUGACACUAAGAGACGAAAGCUAGGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCUGUAAACGAUGAAUACUAGAUGUUGCGUGUAUCGAUCCAUGCAGUAUCGUAGCUAACGCGUUAAGUAUUCCGCCUGGGAACUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGUGGCAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUUAUGUAAAUCUAUUUGAAAGAACAGAGUGCCCUCGGGAAUACAUAAACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUUCUAGUUGCUUUACAAAAGGAAUCUUGAAGACUGCCGGUUAUAAACCGGAGGAAGGUGAGGAUGACGUCAAGUCAUCAUGCCCCUUAUACCCUGGGCUACACACGUGCUACAUUGGAUAAGACAAAAAGUUGCGAAUUUGUGAAAAUAAGCUAAUCUUUAAACUUAUUCCUAAGUUCGGAUUGAAGGCUGCAACUCGCCUUCAUGAAGAUGGAAUCGCUAGUAAUCGCUGGUCAGCUAUACAGCGGUGAAUCCGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUUAUACCCGAAGUCGUUUUCUUAACCUUUUUGGAGAGAGGCGCCUAAGGUAAGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACGGGAACGUGCGGCUGGAUCACCUCCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq
new file mode 100644
index 0000000..42ff17e
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq
@@ -0,0 +1,2 @@
+>d.16.c.P.minor
+AUUUUUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCCUAACACAUGCAAGUCGAACUAGCUCUAGCGCAAGUUAGAGUGGGUGGCGGACGGGUGAGGAACACGUAAGAACCUACCCUUUGGAGGAGGAUAACUGUUGGAAACGGCAGCUAAUACUCCAUAUGCUGAGGAGUAAAAGGUCGAAAGGCCGCCAAGGGAUGGGCUUGCGUCUGAUUAGCUAGUUGGUGAGGUAAAUGCUUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAAGGAUGAAGGCCUGUGGGUUGUAAACUUCUUUUCUCAGAGACGAAUAAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUCCAAGUCUUUUGUCAAAUCCCAGAGCUUAACUUUGGAUCGGCACGAGAAACUCGAGAGCUUGAGUAUGGUAGGGGCAGAGGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAGAUCGGGAAGAACACCGAUGGCGAAAGCACUCUGCUGGGCCAUUACUGACACUGAGAGACGAAAGCUAAGGGAGCGAAUAGGAUUAGAUACCCUAGUAGUCUUAGCCGUAAACGAUGGAAACUAAGUGCUUGGGCCGCGAGUAAUCGCUGCUUGAGUCCUGUAGCUAACGCGUUAAGUUUCCCGCCUGGGAAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCCACUCUUUCGGGAGGUCAUGGUGAAAGCCAGUUUAGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUCUUGUUGCAACUUUGUUGUUAUCGAGAGAGACUGCCGGUGAUAAGUCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUACGCCCUGGGCAACACACGUGCUACAAUGGCCAGGACAAAGAGAUGCAACCUCGCAAGAGCAAGCCAACCUCAAAAACCUGGUCUCAGUUCGGAUUAGUCUCUGCAACCCGAGACUAUGAAGCCGGAAUCGCUAGUAAUCGCUGGUCAGCUAUACAGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGGAGCUGGCUAUGCCCAAAGUCGUUACCCCAACCGUUUGGAGGGGGAUGCCUAAGGCAGAGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq
new file mode 100644
index 0000000..69f34fd
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq
@@ -0,0 +1,2 @@
+>d.16.c.P.palmata
+ACACCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAAGGUUUUACCUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCCUUGGGAGGGGAAUAACAGUUGGAAACGAUUGCUAAUGCCCCAUAAGCUGAAAAGUAAAAUGAUUUUUCGCCCAGGGAUGAGCUCGCGCCUGAUUAGCUAGUUGGUAAGAUAAAAGCUUACCAAGGCAACGAUCAGUAGCUGGUUUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUUCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCUGACGGAGCAAUACCGCGUGAGGGAAGAAUGCCCGUGCGUUGUAAACCUCUUUUCUUAGGGAAGAAGCUCUGACGGUACCUAAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCACUGGGCGUAAAGUGUAGUAGGUGGCUUAUAAAGUCCGCUGUUAAAUCUUAGGGCUCAACCCUAAGCCAGCAGUAGAAACUUCUAGGCUAGAGUAUGGUAGGGGCAGAGGGAAUUCCCAGUGUAGCGGUGAAAUGCGUAGAUAUUGGGAAGAACACCAGAGGCGAAAGCGCUCUGCUAGGCCAUUACUGACACUCAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGAUGUUGCGCGUAUCGAUCCGUGCAGUAUCGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGAGCUUGACAUGUCACGAAUUUUUUCGAGAGAAAAAAGUGCCUUAGGGAACGUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUGCCAUCAUUUAGUUGGGCACUCUAGAGAGACUGCCGGUGACAAACCGGAGGAAGGUAAGGAUGACGUCAAGUCAGCAUGCCCCUUACGCUCUGGGCUACACACGUGCUACAAUGGUCGCGACAAAGAGUUGCCAGUCUGCAAAGACGCGCUAAUCUCAUAAACGUGGCCUCAGUUCGGAUUGUAGGCUGAAACUCGCCUACAUGAAGGUGGAAUCGCUAGUAAUCGCCGGUCAGCUACACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGAAGCUGGCCACGCCCAAAGUCGUUACCCUAACCUUUUGGAGGGGGGCGCCUAAGGCAGGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq
new file mode 100644
index 0000000..6ae32f5
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq
@@ -0,0 +1,2 @@
+>d.16.c.P.wickerhamii
+UGUGAAAACGAAGAGUUUGAUCCUGGCUCAGGAUAAACGCUGGCGGCAUGCUUAACACAUGCAAGUUGUACGAAGGUAUUUAUCUUUCGAGCUAAAUAUACUGAGUAGCGGACGGGUGAGUAACACGUAAGAAUCUACCUUUUGGAGAGGGAUAACUACUGGAAACGGUAGCUAAUACCUUAUAUUGCUGAGAAGUGAAAAAUGUAAAUUGCCAGAAGAUGAGCUUGCGCCUGAUUAGCUAGUUGGUGUGGUAACUGCAUACCAAGGCAAUGAUCAGUAGCUGUUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGAAGGAUGACGGCCUAUGGGUUGUAAACUUCUUUUCUCAGAAAAGAUUAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUUGUUUAAAAAGUAUUCUGUCAAAAAUUAGGGCUUAACCCUAUACAGGCAGAAUAAACUUUUAAGCUAGAGUUUGGUAGAGGCAGAGGGAAUUCCCGGUGGAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCAAAGGCGAAGGCACUCUGCUGGGCCAAUACUGACACUGAGAGACGAAAGCGAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUCGCUGUAAACGAUGGAUACUAGGUGUUGGGUGUAUCAAAAACAUUCAGUAUCGUAGCUAACGCAUUAAGUUUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGAACCCGCACAAUUGGUGGGGUACGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGAUUUGACAUGUCAUUUGUUUCUUCAACUUAAUACUUUAAUUUGUUUUAAGUAGAAACAUAAAAAAAUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCUUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUUUUGAAUUGCUUGGGGCAUUAUAUGCCUUUUUACAGAGGAAAUUCAAAAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUAUAUCCUGGGCGACACACGUGCUACAAUGGACGUAACAAAGAGAAGCUACUUCGCGAGAACAAGCUAAUCUCAAAAAUACGUUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCAAUAGUAAUCGCAGGUCAGCCACACUGCGGUGAAUACGUUUCCGGGUUUUGCACACACCGCCCGUCACACCACGGAAAUUGGCUACGCCCUAAAUCAUUACCCUAACCAUUCUGUGGAGGGGGAUGCCUAAGGCGGGGCUGGUAACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq
new file mode 100644
index 0000000..8de7320
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq
@@ -0,0 +1,2 @@
+>d.16.c.S.oleracea
+UCUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGGACGGGAAGUGGUGUUUCCAGUGGCGGACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGAACAACAGCUGGAAACGGCUGCUAAUACCCCGUAGGCUGAGAAGCAAAAGGAGGAAUCCGCCCGAGGAGGGGCUCGCGUCUGAUUAGCUAGUUGGUGAGGUAAUAGCUUACCAAGGCGAUGAUCAGUAGCUGGUCCGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGGAGGCAGAAGGCCCACGGGUCGUGAACUUCUUUUCCCGGAGAAGAAGCAAUGACGGUAUCCGGGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUUAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGAAAGAACACCAACGGCGAAAGCACUCUGCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCGAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGCGCUGUGCGUAUCGACCCGUGCAGUGUUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUACCAGGGCUUGACAUGCCGCGAAUCCUCUUGAAAGAGAGGGGUGCCUUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUGUUUAGUUGCCAACGUUGAGUUUGGAACCCUGAACAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAUCAUGCCCCUUAUGCCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGGGUCGCGAUCCCGCGAGGGUGAGCUAACCCCAAAAACCCGUCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUGGGAGCUGGCCAUGCCCGAAGUCGUUACCUUAACCGCAAGGAGGGGGAUGCCGAAGGCAGGGCUAGUGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq
new file mode 100644
index 0000000..b37e535
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq
@@ -0,0 +1,2 @@
+>d.16.c.T.gondii
+AAAUUAUUACGAGUUUGAUCCUGGCUCCGGAAGAACGCAAGAGAUGUGCUUAACACAUGCUAAUUGAAUGGUAUUAAUAUAUCAUAGUGUAAUAGUGAGUAAUGUAUGAGAAUUUAUUUUUAGAAUAUAAUAAAAAUUUAAUAAUUUAUAAUAAACGCAAUAGUGUUUUAAAAGAUAAUUAUUGUCUAAAAAAAAGCUCAUAUCUAAUUAGCUAGUUGGUGAAGUAAUAGUUUUACCAAGGCGAAGAUUAGUAGCUGCCUUGAGAGGGGAAACAGCCACAUAGAGAUUGAAAUACAGCUCUAACUCCUAAGGGGGGCAGCAGUGGGGAAUUUUCUGCCAAUAAGCGCAAGCUUGACAGAGCGUCAUCACAUGAAGGAGGAAGGCCUAUAAAGGUUGUAAACUUCUUUUGCUUAAAAAAAUAAUACUGACGUUUAAGUUUAAAAAGUAUCGGCUAACUCCGUGCCAGCAGCCGCGGUCAUACGGGGGAUACAAGCGUUUUCCAAAAUUACUGGGCGUAAAGUGUAUGUAGGUGGAUUGGUAUGUUCUUCCUUAAAUACUAUUUGAUAAAUUUAGAAAAAGGAAGAAAACUAUUAAUCUUGAGUUCGAUAAGGGUAAGAGGAAUUUUUUGAGGAGUAGUGAAAUGCGAAGAUACAAAAAAGAAGAUCAACAGCGAAAGCAUCUUACUGGGUCGAUACUGACACUGAGAUACGAAAGUUAAGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCUUAACUGUAAACAAUGGAUACUCGGUACUGGAGACAUUAAAUAUAUAAAUUCAGUACCCUAGCUAACGCGUUAAGUAUUCCGCCUGAGUAGUACGCUCGCAAGGGUGAAACUCAAAGGAAUUGACGGGGGCUCGUACAAGCGGUGGAGCACGUAAUUUAAUUCGAUGUAACGCGAUAAACCUUACCAGAACUAGACUAAAUUUAUUUUAAAUUAUUAAUAUUAAUUAAUAAAAAAUUUACAGGAGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCUACGAGCGCUACCCUUAUUUAAAGUUUUUUAUAUCUUUAAAAACAGACUAUAUAAAUUUUUGUACUAAAUUAGUAGGAAGGAGAGGAAAACGUCAAGUCUUUAUGCCCUUUAUGUUCUGGGCUACAUACGUGCUACAAUAGAUGGUACAAUAAUUUUUAAAAAUAAAUACAAUAUCAAUUUAUUUUUAAUUUAUUUGUGAAAAUAAAUGUAAUAAUUGAAAACCAUUUUUAGUUCGGAACAUAAACUGCAAUUUGUUUAUGUAAAGUUGGAAUCGCUAGUAAUCGCCGGUCAGCAUUACGGCGGUGAAUAAGUCUUCGAGCCUUGUACACACCGCCCGUCACGCCACGGAAAUUGAUUAUUUUUUAAAACUUUUGAUAAAAGGAUAAAUAAUAAUAAAUAACUGGGGUGAAGUCGUAACAAGGUAGCUGUACUGGAAGGUGCUGCUGGAUAAUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq
new file mode 100644
index 0000000..9bffa4d
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq
@@ -0,0 +1,2 @@
+>d.16.c.Z.mays
+CUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGAACGGGAAGUGGUGUUUCCAGUGGCGAACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGAACAACAACUGGAAACGGUUGCUAAUACCCCGUAGGCUGAGGAGCAAAAGGAGAAAUCCGCCCAAGGAGGGGCUCGCGUCUGAUUAGCUAGUUGGUGAGGCAAUAGCUUACCAAGGCGAUGAUCAGUAGCUGGUCCGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGGAGGUGGAAGGCCUACGGGUCGUCAACUUCUUUUCUCGGAGAAGAAACAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUCAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCAUUGAGAUCGGAAAGAACACCAACGGCGAAAGCACUCUGCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAGACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGUGCUGUGCGACUCGACCCGUGCAGUGCUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAGGCGAAGAACCUUACCAGGGCUUGACAUGCCGCGAAUCCUCUUGAAAGAGAGGGGUGCCCUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCUCGCAACGAGCGCAACCCUCGUGUUUAGUUGCCACUAUGAGUUUGGAACCCUGAACAGACCGCCGGUGUUAAGCCGGAGGAAGGAGAGGAUGAGGCCAAGUCAUCAUGCCCCUUAUGCCCUGGGCGACACACGUGCUACAAUGGGCGGGACAAAGGGUCGCGAUCUCGCGAGGGUGAGCUAACUCCAAAAACCCGUCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCAGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGCGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUAGGAGCUGGCCAGGUUUGAAGUCAUUACCCUUAACCGUAAGGAGGGGGAUGCCUAAGGCUAGGCUUGCGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq
new file mode 100644
index 0000000..32b6e40
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq
@@ -0,0 +1,2 @@
+>d.16.e.C.albicans
+UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUACCUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCCCGACUGUUUGGAAGGGAUGUAUUUAUUAGAUAAAAAAUCAAUGCCUUCGGGCUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAAAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGCUUGGCUGGCCGGUCCAUCUUUUUGAUGCGUACUGGACCCAGCCGAGCCUUUCCUUCUGGGUAGCCAUUUAUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCUUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUAUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGUAUCAGUAUUCAGUUGUCAGAGGUGAAAUUCUUGGAUUUACUGAAGACUAACUACUGCGAAAGCAUUUACCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGUUGUUGUUCUUUUAUUGACGCAAUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGCUGCUAGCAUUUGCUGGUAUAGUCACUUCUUAGAGGGACUAUCGACUUCAAGUCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUAUAAGCCUUGGCCGAGAGGUCUGGGAAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUGUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGGCCUCCGGAUUGGUUUAGGAAAGGGGGCAACCUCAUUCUGGAACCGAGAAGCUGGUCAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq
new file mode 100644
index 0000000..69158d5
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq
@@ -0,0 +1,2 @@
+>d.16.e.C.citrina
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCCCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGCGUCGAAGUGAGCUCGUUGCUUGUACUGAGAUGCCCUUCCAUCCUACUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGUUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGACCCGUUGCUUAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGUGGCCUUUAGGCUGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq
new file mode 100644
index 0000000..b680862
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq
@@ -0,0 +1,2 @@
+>d.16.e.C.crispus
+CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAACUACUACUUGGAUACCCGUAGUAAUUCUAGAGCUAAUACAAGCCUUAAAGCGACAUUUAUGUCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACAAUUUCUUUUCUGAUCGCACGUUAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGAGUGACGGAUCGUGGGUGCGAGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGAUACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAACGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGCAGUCCAGGGCGUCCUCGCGGACGGAUCUGGAGUUGGCCGCCUUUGUGGAUGGGGGCCUAGUGGAGCUUCACUGCUUCAUUGUGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUCCUGUUUUGUUGGUUUGUGAGGAUCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGGCGGAAGACAAACGGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGGAGGACUGUAUUUUGGCCUACCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCAGUACCGUUUUUUGGUACUGAGGCUUGCCUUCCUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAACUUUCCCUCUUGAACGAGGAACACCUUGUAAGCGUGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGAUGGAUGGAUUGUGUUUCACAAACUAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGACAGAAUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq
new file mode 100644
index 0000000..275fcb0
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq
@@ -0,0 +1,2 @@
+>d.16.e.C.lunata
+CACCAGGUUGAUUCUGCCUGACGUGGACACUUGCCUUGAAGAGUAAGCCAUGCAAGCUUGUGAAUAAAUCCUGAAACAGUGAACGGCUCAGUAGAACACAUUUCAUCUACCCAAGUUAAAAAUAACCAUGGGAAACUAUGGCUAAAUAUAAUUUGGAUGAGAGUGUGACCUAUCAGCUAGUAGGUACGGUAAGAGCGUACCUAGGCUAUGACGGGUAACGGGGAAUCAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUACCUAUGUAAUAUAAUUAUAUAGGGAUGAGGUAUGAUUUCAAAUCAUGCACGACAUACUGGAGGGCAAGGCUGGUGCCAGCAGCUGCGGUAAUUCCAGCUCCAGUAGUGUCUAUGUAAAUUGUUGCGGUUAAAACGUGCGUAGUCUGAUUUGCGAGAUCUAAAGUAAAGAUGCUUUUAUCUAAAAGUAGAAUAUUUUAGAGAUCAAAAAUCUUGAGACAGAGGAGAGGUAACGAAAUUCGAUGGCGAGAGGUGAAAAUUGAUGACCCAUCGAGGAGAAACAGAGGCGAAAGCGGUUACCAGAAGCUGUUCUGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGGCGAUUAGACACCGUCGUAGUUCCUUGCAGUAAACGAUGCCCACACUGAUGUGCUUAACGCAUGUCAGACGCAAAAGUUAAAGUGAGGCUCCGGGGAUAGUACGGUCGCAAGAUUGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCAGUACAGAUUACUAUCGUAUGAAGGAAUACCUGAUGAUGUAAUACGUGGUGCAUGGCCGUUCUUAACACGUGAAGUGAUUCCUCGUGUCAAAUCAGCUAACGCGUGAGAGGCGAGUCUUAUUUUAUAAAUAAGAGACGGCAUAGGCAACUAUGAGGAAGCAACGCCCAAUAACAGGUCCGUGAUGCCCGUAGAUGUUCUGGGCUCCACGCGCACUACAAUUAUAAAUACUAUUUUGUAAUUUAUAAUCAGUAGGGAUUGUUUGUUGUAAAACUUACAUGAACGUGGAAUUCCUAGUAUAUAGAUGUAAGCAACGUCUAUUGAAUAUUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGUUAUUAGGGGGAAGCUGAUAUAUUAUAUCAGAAGACUUCUGGUAACUAGAUUGGAUGUAAGUCGUAACAUGGUUGCAGUAGGUGAACCUGCCGCAGAUCAGUAG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq
new file mode 100644
index 0000000..0bf8af5
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq
@@ -0,0 +1,2 @@
+>d.16.e.C.neoformans
+UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGAAUUCAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUAUCUUGCUACAUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUGAAAAGCCCCGACUUCUGGAAGGGGUGUAUUUAUUAGAUAAAAAACCAAUGGGUUUCGGCCCUCUAUGGUGAAUCAUAAUAACUUCUCGAAUCGCAUGGCCUUGUGCCGGCGAUGCUUCAUUCAAAUAUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUAUCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGGCUCUUUUGGGCCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUCGAACUUCAGGUCUGGCGAGGCGGUCCUCCUCACGGAGUGCACUGUCUUGCUGGACCUUACCUCCUGGUGGUCCUGUAUGCUCUUUACUGGGUGUGCAGGGGAACCAGGAAUUUUACCUUGAAAAAAUUAGAGUGUUCAAAGCAGGCAAUCGCCCGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGGAUCGCCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUUGGUAUUCCGUUGCUAGAGGUGAAAUUCUUAGAUUGACGGAAGACCAACAACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAGGUUAGGGGAUCAAAAACGAUUAGAUACCGUUGUAGUCUUAACAGUAAACGAUGCCGACUAGGGAUCGGCCCACGUCAAUCUCUGACUGGGUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAACCUGCUAAAUAGUCAGGCCGGCUUUGGCUGGUCGUUUGACUUCUUAGAGGGACUGUCGGCGUCUAGUCGACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACUGAGCCAGCGAGUCUUACCGCCUUGGCCGAGAGGCCUGGGUAAUCUUGUGAAACUCAGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUACCUAGUAAGCGUGAGUCACCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGAUCUCCGGAUUGGCGUUGGGGAGCCGGCAACGGCACCCCUUGGCUGAGAAGCUGAUCAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAGUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq
new file mode 100644
index 0000000..6c217f5
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq
@@ -0,0 +1,2 @@
+>d.16.e.C.officinalis
+CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAAGACUAAGCCAUGCAAGUCUAAGUAUGAGGAAUAAUUAAGACGAAACUGCGAAUGGCUCGGUAAAACAGCAAUAAUUUCUUCGGUGAUUUUUACUACUCGGAUAAUCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAUGCUUGGGUUUACUCAGGCAGUGCCGUUUAGAUAACAACACCAACAUAUGGUGAUUCAUAAUCGUCUUUCGGAUCGCUGGCGAAAGCCGGCGACGCACCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAGUGUCUUACCAUGGUGGCAACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCAGACUCUGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGACCCAUAAAGUCUUCUAAUUGGAAUGAGAACAAGCUAAACAGCUUAUCGAGAAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGACUUUGGCAAUUCCGGAUGUGUGCGCGUCGUGCGCGCACUUUGCAGGGGUUGCUUUUGUGGGCAUGCGUGGGAUGAUGCGACUUUAUUGUCGAACGUCCCUACGCAACCACCUUUUACUGUGAGAAAAUUAGAGUGUUCAAAGCAGGCAAUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGGUCUUAUUUUGUUGGUUUGUUAGGGCUGAGUAAUGAUUAAGAGGGACAGUUGGGGGCAUUUGUAUUCAGGCGCUAGAGGUGAAAUUCUUAGAUUGCUGGAAGACAAACUGCUGCGAAAGCGUCUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGAGGAAUAUCGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGGGCUACUACCAUUUUGGUAGUACGUUUUCCCCUUCUUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGUGGAUCAGCGGGUCAGGUUGCACGAAAGUGUUUCCUAAUCUUUAAAUCCGCUCGUGAUGGGGAUUGACGGUUGCAAUUUUCCGUCAUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCUUUGGGAUUGCGAUGGAAAGAGCGUCUCGCUCGUUCUGUCGUGAGAACUCAGUCGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq
new file mode 100644
index 0000000..bb1658f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq
@@ -0,0 +1,2 @@
+>d.16.e.C.paradoxa
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUAUUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUACCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAACAAAUCCCGACUUCUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCAACACCGGGCAACCGGAUCCCUUGGUGAUUCAUAAUAACUUCUCGAAUCGCAUGGCUUUACGCCGGCGAUGCUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUAGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGCGCCUGAGAGAUGGCGACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCGCAACUCGCGGAGGUAGUGACAAUAAAUAACAAUACGGGGCUUUUCAAGUCUCGUAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCCAUUGGAGGGAAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUCGGAUUUCGGGGCGGGGCAGUCGGUCUGCCUAAUAGGUGUGUACUGGCUGUACCCGUCCUUCCUUCCGGGGAUGGGUGCUGCUCUUAACUGAGUGGCAUUCAGACACGGAUCUUUUACUUUGAGUAAAUUGGAGUGUUUAAAGCAGGCCUACGCUCUGAACAUUAUUAGCAUGGAAUAAUAAAAUAGGACCCUGGUUCUAUUUUGUUGGUUUCUAGGAUUGGGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUCAUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGAUGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACUUACGAUCAGCAGGUGUUAAUUUAACGACCCUGUUGGCAGUAUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUACUAAAUAGUUACACGAACUUCUAGUUCGUGGUCAACUUCUUAGAGGGACUAUUUGUGUCUAAUGAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACGAAUUCAACGAGUUUUUCCUUGACCGAUAGGUCUGGGUAAUCUUUGAAACUUCGUCGUGAUGGGGAUAGAUCAUUGCAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUCGGUCCGGUGAAAUCUUCGGAUCGUGGCCAUGUACCUGGUCUCCAGGAACAAGGUCGCGAGAAGUUGAUUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq
new file mode 100644
index 0000000..2b1cbde
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq
@@ -0,0 +1,2 @@
+>d.16.e.C.rubrum
+CACCCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAAUACGUGCCAUACGGCGAGGUUUUACCUCGUGGUACUAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACACUUAUUUUUCUGAUUGCACAUUUUUUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUUUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAAUGGGUUUUCUAAUUGGAAUGAGAACACGGUAAACAUCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGACGUUGGCGGGCGCCUCGAGUCGGCCUCACGGUCGAUCUUGUUGGCGGCCGCCUUUGUGGAGGGGGGCUUAGGUCGGUGCUUUAUUGUCACUCCUUUGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUCCUGUUUUGUUGGUUUGUGAGUAUCAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACCAUAAACUAUGAGGACUGGGGAUCGGGCGUGGCUAUUUGGUACGCUCGGCACCCUUCGGGAAACCAAAGUAUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCAGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACUUGGGCGUGCUAGCUAGGCGCUGUUACCAUUUCCGGUAGCGAGGCGGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAAAGCAUUUCCCAAUCUCUAAAUCCGCUCGUGAUGGGGAUAGAGGCUUGCAACUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGUCUGCAUGUCCUGUGUUUCACUUGUGUGCAGGUUGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq
new file mode 100644
index 0000000..658da2a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq
@@ -0,0 +1,2 @@
+>d.16.e.D.melanogaster
+AUUCUGGUUGAUCCUGCCAGUAGUUAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACACACGAAUUAAAAGUGAAACCGCAAAAGGCUCAUUAUAUCAGUUAUGGUUCCUUAGAUCGUUAACAGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCAAUUAAAACAUGAACCUUAUGGGACGUGUGCUUUUAUUAGGCUAAAACCAAGCGAUCGCAAGAUCGUUAUAUUGGUUGAACUCUAGAUAACAUGCAGAUCGUAUGGUCUUGUACCGACGACAGAUCUUUCAAAUGUCUGCCCUAUCAACUUUUGAUGGUAGUAUCUAGGACUACCAUGGUUGCAACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCACUCCCAGCUCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCAUAUCCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACAAGGACCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCGGUUAAAACGUUCGUAGUUGAACUUGUGCUUCAUACGGGUAGUACAACUUACAAUUGUGGUUAGUACUAUACCUUUAUGUAUGUAAGCGUAUUACCGGUGGAGUUCUUAUAUGUGAUUAAAUACUUGUAUUUUUUCAUAUGUUCCUCCUAUUUAAAAACCUGCAUUAGUGCUCUUAAACGAGUGUUAUUGUGGGCCGGUACUAUUACUUUGAACAAAUUAGAGUGCUUAAAGCAGGCUUCAAAUGCCUGAAUAUUCUGUGCAUGGGAUAAUGAAAUAAGACCUCUGUUCUGCUUUCAUUGGUUUUCAGAUCAAGAGGUAAUGAUUAAUAGAAGCAGUUUGGGGGCAUUAGUAUUACGACGCGAGAGGUGAAAUUCUUGGACCGUCGUAAGACUAACUUAAGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGAGGUUCGAAGGCGAUCAGAUACCGCCCUAGUUCUAACCAUAAACGAUGCCAGCUAGCAAUUGGGUGUAGCUACUUUUAUGGCUCUCUCAGUCGCUUCCGGGAAACCAAAGCUUUUUGGGCUCCGGGGGAAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCGAACAUAAGUGUGUAAGACAGAUUGAUAGCUCUUUCUCGAAUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCAAAUAUAUUAAAUAGAUAUCUUCAGGAUUAUGGUGCUGAAGCUUAUGUAGCCUUCAUUCAUGUUGGCAGUAAAAUGCUUAUUGUGUUUGAAUGUGUUUAUGUAAGUGGAGCCGUACCUGUUGGUUUGUCCCAUUAUAAGGACACUAGCUUCUUAAAUGGACAAAUUGCGUCUAGCAAUAAUGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACAAUGAAAGUAUCAACGUGUAUUUCCUAGACCGAGAGGUCCGGGUAAACCGCUGAACCACUUUCAUGCUUGGGAUUGUGAACUGAAACUGUUCACGAUGAACUUGGAAUUCCCAGUAAGUGUGAGUCAUUAACUCGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUUAUUUAGUGAGGUCUCCGGACGUGAUCACUGUGACGCCUUGCGUGUUACGGUUGUUUCGCAAAAGUUGACCGAACUUGAUUAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq
new file mode 100644
index 0000000..dcf55c6
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq
@@ -0,0 +1,2 @@
+>d.16.e.E.aediculatus
+AAUCUGGUUGAUCCUGCCAGUAGUCAUACGCUUGUCUCAAGGAUUAAGCCAUGCAUGUCUAAGUAUAAAGGAUUUAUAAUGAAACUGCAAAUGGCUCAUUCAAACAGUUAUAGUUUAUUUGAUAUUCAAGCUAAUAUUCUUAUUAGUUAAAUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUUACGGGGAACUUUACGGGACCCCAGCGUUUAUUAGAUUUAAACCAAUAUUCCGCAAGGUCUACUGAGAUGAUUCAUGAUAACUGAUCGAAUUGCUGGAACUCUAGCAAUAAAUCAUGUAGGUUUCUGCUUCCCAUCAGCUUGAUGGUAGUGUAUUGGACAACCAUGGCAUUCACGGGCUAUCGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAUAAACGGCUACCACUUCUACGGAAGGCAGCAGGCGCGAAAAUUAUCCAAUCCUGAUUCAGGGAGGUAGUGAAAGAAAUAAUGAACUAGGAUUUAUCCUGGGAUCACAAUGGGCUUGAUUUGCAAACACUUAGCGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGAGUAUAUAAACGUUCCUGCAGUUAUUCGAUGCUCGUAGUUGGAUUUCUGAGGUUGAGACGGGAGGGUGGCUAUGGCCAUCGCCCGACUCUUUCCUCAUCCACCUGUUUGCGAAGUCCGGGAUUGAUUUCUCGGCUUCGGGCGCAGUAUCUUACCAUUUCAAUAUUCGUAGUCUUCAUCGAUUAUGUUGUUUCUUUGAGCAAAUUAUAGUGUUUCAGGCAGGCGUGCGCCGGAAUACAUUAGCAUGGUAUAAACGAAUUGGACCGUGUGCCCGUAACUGGGCUUCUCCUUAUUGUUGGUUUGAAGGACACGGAGAUGGUUAAUAGGGACAGCGUUUAUUUCACAAGGAGGCAUUAGUAUUUAAUUUCCAGAGGUGAAAUUCUUUGAAAUAUUAAAGACUAACUUAUGCGAAAGCAUCGUUUGCCAAUGAUGUUUUCAUUAAUCAUUGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACGUUGCCGACUAGGGAUCGGAGGGCGUGCACAAUCCGCCUUCGGCACCUUACGAGAAAUCAAAGUCUUUUGGGUUCUGUGGGUAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAUCUUACCAGGUCCAGACAUAGCGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUAUUUUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUCGUCUGGUUAAUUCCGUUAAACGAACGAGACCUCAGCCUGCUAAAUAGUUGCUCGCCUUUUCUAUAAGACUUGACAACUUCUUAGAGGGACUUUGUGUGCAACCACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUACGUACAACGAGGUAUAUGUACUUGUACAUCAAUGCUGCUCCGAAAUAGACGAGCUUAAUCUUAUAAAUACGUAUCGUGCUGCGGAUAGAUCGUUGAAAUUAUGAAUCUUGAAGGUGGAAUUCCUAGUAAGCGCACGUCACUAACGUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCAAUUUCGAGUGAUCUGGUGAACCUCUUUGGACUGUCGAGCAAUCGCGAAAUUAGAGUGAACCUGACUACUUAGCAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAAUCUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq
new file mode 100644
index 0000000..2b84de0
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq
@@ -0,0 +1,2 @@
+>d.16.e.E.bieneusi
+CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGUCUCUGAGAUUAAGCCAUGCAUGUCAGUGAAGCCUUACGGUGGAACGGCGAACGGCUCAGUAAUGUUGCGGUAAUUUGGUCUCUGUGUGUAAACUAACCACGGUAACCUGUGGCUAAAAGCGGAGAAUAAGGCGCAACCCUAUCAGCUUGUUGGUAGUGUAAAGGACUACCAAGGCCAUGACGGGUAACGGGAAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUGUCCACUCCUUACGGGGGAGACAGUCAUGAGACGUGAGUAUAAGACCUGAGUGUAAAGACCUUAGGGUGAAGCAAUUGGAGGGCAAGCUUUGGUGCCAGCAGCCGCGGUAACUCCAACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAGGGUCCGUAGUCGUGAAUGCAAUUAAAUGUCGUUGUUCAAUAGCGAUGAGUUUGCUAAUGUUUGCGGAACGGAUAGGGAGUGUAGUAUAGACUGGCGAAGAAUGAAAUCUCAAGACCCAGUUUGGACUAACGGAGGCGAAGGCGACACUCUUAGACGUAUCUUAGGAUCAAGGACGAAGGCAGGAGUAUCGAAAGUGAUUAGACACCGCUGUAGUUCCUGCAGUAAACUAUGCCGACAGCCUGUGUGUGAGAAUACGUGGGCGGGAGAAAUCUUAGUGUUCGGGCUCUGGGGAUAGUACGCUCGCAAGGGUGAAACUUAAAGCGAAAUUGACGGAAGGACACUACCAGGAGUGGAUUGUGCUGCUUAAUUUAACUCAACGCGGGAAAACUUACCAGGGUCAAGUCAUUCGUUGAUSGAAUACGUGAGAAUGGCAGGAGUGGUGCAUGGCCGUUGGAAAUUGAUGGGGCGACCUUUAGCUUAAAUGCUUAAACCAGUGAGACCUCCUUGACAGGUGUUCUGUAACACAGGAGGGUGGAGGCUAUAACAGGUCCGUGAUGCCCUUAGAUAUCCUGGGCAGCAAGCGCAAUACAAUAUCUCUUCAGUAGACAAAGUGAUUUGAGAUGAGUAGGAUCUACGUUUGUAAAUACGUAGUGAAUAAGGAAUUCCUAGUAACGGUGCCUCAUCAAGGCAUGGUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUUUCAGAUGGUCAUAGGGAUGAAGAGCUUCGGCUCUGAAUAUCUAUGGCUAGAUAAAGUACAAGUCGUAACAAGGUUUCAGUUGGAGAACCAGCUGAAGGAUCAUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq
new file mode 100644
index 0000000..74a3bfa
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq
@@ -0,0 +1,2 @@
+>d.16.e.E.cuniculi
+CACCAGGUUGAUUCUGCCUGACGGAUGCUAUUCUCUGGGGCUAAGCCAUGCAUGCUUGUGAACUCUUUGUGGGGGAUUAGCGGACGGCUCAGUGAUAGCACGAUGAUUUGUUUGCGGGAUGAGCAGUAGCUGCGGGAAACUGCAGAUAGUGGUCUGCCCCUGUGGGGUUGGCAAGUAAGUUGUGGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGCAGACGGGAUACGGGGGAUCAGGGUUUGGUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUUGGGGAGGCGGUUAUGAGAAGUGAUGUGUGUGCGAGUGCAAAGGGGUCGCAUGUGAUUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCAAUAGUGUCUAUGGUGGAUGCUGCAGUUAAAAUGUCCGUAGUCUGUUGUGUAUGUCUUUGUGUGUGAUGUUUGUGGUUGUGUGUGGAUGUAGUGAUGUGUGUGGCAGAGGACGAGGGGCACUGGAUAGUUGGGCGAGAGGUGAAAUGCGAAGACCCUGACUGGACGAGCGGAAGCGAAGGCUGUGCUCUUGGACUAAUGUUGCGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACAGUGUGUGUUGUCCAUGAGAAAUCUUGAGUAUGCGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGCUCUGAAGGAUGCCUGUGAGUGCAUGGCAUGAGGCAUGCGGCGGUGGUGCAUGGCCGUUUUAAAUGGAUGGCGUGAGCUUUGUCUUAAGUUGCGUAAGAUGUGAGACCCUUUGACGGUGUUCUACGGAGCAAGGAGGGGAUGGAAAAGAACAGGUCCGUUAUGCCCUGAGAUGAGGCGGGCUGCACGCGCAUACGAUAGAUGGCGCUUCUGCCUGCUGUGAGGGAUGAAGCUGUGUAAGGGGCUUCUGAACGUGGAAUUCCUAGUAAUAGCGGCUGACGAAGCUGCUUUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGACGCACUGGACGAAGAUCGGAAGGUCUGAGUCCUGAGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq
new file mode 100644
index 0000000..f6afe21
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq
@@ -0,0 +1,2 @@
+>d.16.e.E.hellem
+CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAUUCUCUGGGGCUAAGCCAUGCAUGUUUAUGAAGCCUUUAUGGGGGAUUGACGGACGGCUCAGUGAUAGUACGAUGAUUUGAUUGGGUGCCUGGAUGUAACUGUGGGAAACUGCAGGUAAGUUCUGGGUGUGGUAGUUUUUAGCUACUGCGUACCGAGUAAGUUGUAGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGGAGACGGGAGACGGGGGAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUAUUGGGGAGGCGGUUAUGAGAAGUAAGAUGUUUAGCAAGUAUAAAUUUGUUGUGAUUUACUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCAGUAGUGUCUAUGGUGAAUGCUGCAGUUAAAAUGUCCGUAGUUGUUUGUAUGUCUUUUGUGUGAUGUUUAUAGUUUUUAGUGGAUGUAGUUUGGUUGUAGCAGAGGACGAGGGGCACUGGAUAGUUGGGCGAGGGGUGAAAUACGAAGACCCUGACUGGACGAAGAGAAGCGAAGGCUGUGUUCUUGGACUUUUGUGGUGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACUGUUUUAGUGUUGUCCGAGAGAAAUCUUAAGUAUGUGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGUUCUGAAGUGAGUGUGAGAGUGUUUUUACAUGAUGCUUACGGCGGUGGUGCAUGGCCGUUUUAAAUGGAUGGCGUGGGCUUUGGAUUAAGUUACGUAAGAUGUGAGACCCUUUUUGACUGUGCUCUAUGGGGCAAGGAAGGAAUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGAAGCGGGCGGCACGCGCACUACGAUAGAUGCCUAUGUGGGCUACUGUGAGGGAUGAAGCUGUGUAAUGGGCUUCUGAACGUGGAAUUCCUAGUAAGAAUGAUUGAACAAGUUAUUUUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGACGCAGUGGACGAAGAUUGAGAGGUCUGAGUCUUUCGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq
new file mode 100644
index 0000000..ad17f45
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq
@@ -0,0 +1,2 @@
+>d.16.e.E.histolytica
+UAUCUGGUUGAUCCUGCCAGUAUUAUAUGCUGAUGUUAAAGAUUAAGCCAUGCAUGUGUAAGUAUAAAGACCAAGUAGGAUGAAACUGCGGACGGCUCAUUAUAACAGUAAUAGUUUCUUUGGUUAGUAAAAUACAAGGAUAGCUUUGUGAAUGAUAAAGAUAAUACUUGAGACGAUCCAGUUUGUAUUAGUACAAAAUGGCCAAUUCAUUCAAUGAAUUGAGAAAUGACAUUCUAAGUGAGUUAGGAUGCCACGACAAUUGUAGAACACACAGUGUUUAACAAGUAACCAAUGAGAAUUUCUGAUCUAUCAAUCAGUUGGUAGUAUCGAGGACUACCAAGAUUAUAACGGAUAACGAGGAAUUGGGGUUCGACAUCGGAGAGGGAGCUUUACAGAUGGCUACCACUUCUAAGGAAGGCAGCAGGCSCGUAAAUUACCCACUUUCGAAUUGAAGAGGUAGUGACGACACAUAACUCUAGAGUUGAGUAAAAUCAAUUCUUGAAGGAAUGAGUAGGAGGUAAAUUCUCCUACGAAAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGUGUAUAUUAAAGUUGCUGUGAUUAAAACGCUCGUAGUUGAAUUAAAAUGUGGUUUUAUACAUUUUGAAGACUUUAUGUAAGUAAAGUUUCUAGAAAUGUUAAAUUAAAAUCAAAGAAGGAAACAAUUCAAGUAAUUGAGUUGUUAUUACUUUGAAUAAAAUAAGGUGUUUAAAGCAAAACAUUAUGUUAAUGAAUAUUCAAGCAUGGGACAAUGCUGAGGGGAUGUCAAUAAGACAUUUCGAGAGAAGGAUUAAAAGGAACAAUUGGGGUGAUUCAGAAAAUAACGGGAGAGGUGAAAAUCCAUGAUCGCUAUAAGAUGCACGAGAGCGAAAGCAUUUCACUCAACUGUGUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACUAUAAACGAUGUCAACCAAGGAUUGGAUGAAAUUCAGAUGUACAAAGAUAGAGAAGCAUUGUUUCUAGAUCUGAGUAUAUCAAUAUUACCUUGUUCAGAACUUAAAGAGAAAUCUUGAGUUUAUGGACUUCAGGGGGAGUAUGGUCACAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACACCAGGAGUGGAGCCUGCGCUUAAUUUGACUCAACACGGGAAAACUUACCAAGACCGAACAGUAGAAGGAAUGACAGAUUAAGAGUUCUUUCAUGAUUUAUUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCAGGUUAAUUCCGGUAACGAACGAGACUGAAACCUAUUAAUUAGUUUUCUGCCUAUAAGACAGAAAUGUUCGCAAGAACAGGUGCGUAAGUACCACUUCUUAAAGGGACACAUUUCAAUUGUCCUAUUUUAAUUGUAGUUAUCUAAUUUCGGUUAGACCUCUUUUAACGUGGGAAAAAGAAAAAGGAAGCAUUCAGCAAUAACAGGUCUGUGAUGCCCUUAGACAUCUUGGGCCGCACSCSCGCUACAAUGGAGUUACUAGAGAGUAUUUUAUCAUUUACACCUUAUUUAUUAGGCUUUGUCUAAUAAUUAAGGAUAGUAAGUGGUGUACCGAGAUUGAAAUAGUUAAGGAAAACUCAAAAGAACGUACAUGACAGGGAUAAAUGAUUGGAAUUAUUUGUUUUGAACGAGGAAUUCCUUGUAAUAUCGAGUCAUUAACUCGAGAUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUAAAGAGGUGAAAUUCUAGGAUUCUGUCUUAUAGAUAGAAAAAUGGAUUUAAAUCUCCUUAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq
new file mode 100644
index 0000000..ca7e6aa
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq
@@ -0,0 +1,2 @@
+>d.16.e.E.mobilis
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUGCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGAGGGCUCCAAUGUCCGCUGAUGCGUGUGCAGCGGAGCCCUCUCAUCCUUCUGUUAACGUUUCUUGGUAUUCAGUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUUCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUAUUGUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAGCCAAUCCCGAUUGGCCCCGACUUCUUAGAGGGACUUUGUGAUUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGCGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGGACAUCCUCGUGGUGUUUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq
new file mode 100644
index 0000000..69b8094
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq
@@ -0,0 +1,2 @@
+>d.16.e.E.schubergi
+CACCAGGUUGAUUCUGCCUGACGUAGACGCUAGUCUCUGAGAUUAAGCCAUGCAUGUCUAUGGAACAAGGACGAACAGCUCAGUAAAACUGCGAUGAUUCAGUCUGUCUGUCAAGAUAACCACGCGAAAGUGUGGCUAAGAGGGGACAGAACAAGACGCAGGACUAUCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACGGUGACGGUUGACGGGGAAUGAGGGUUCUAUACCGGAGAGGGAGCCUGAGAGAUAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUGUUUGGAGGAGGCAGUUAUGAGACGUGAGAAAGAGUGCUUGUAAAGAGAAGCAGGAGAAUUGGAGGGCAAGUUUGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGUAGUCGUGGAGACGGAAAGAGAGGCGGAGCCUCUUUGAGAUGCUCUGGAGAAGCCAACAGGGGGCACAGUAUACCAGGGCGAGAGAUGAAAUGCCAAGACCCCUGGUGGACUGAGCGAGGCGAAAGCGGUGCUCUUGUGGGUGUUCGGUGAUCAAGGACGAAGGCUGGAGGAUCGAAAGUGAUUAGAUACCGCUGUAGUUCCAGCAGUAAAAGAUGCCGACAUGCUCGGUGGCAACACGGGGCAGGGAGAAAUCUUAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGGGUGAAAAUUAAAGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGAAGCUUACCAGGGCCAAGUGCUGUGGAGAAAGGAGCAGUACAGAAGUGGUGCAUGGUCGUUGGAAAUUGAUGGGAUGACUUUGGCCUUAAAUGGCUGAAUGAGUGAGAUCUUUGGACAUGUUCCCACGGAACAGGAAGGGGAGGCUAUAACAGAUCAGAGAUGCCCUUAGAUGCCCUGGGCUGCACGCGCAAUACAAUAGCACGUAGACGUAGAGAACAACACGUGCUGAGGUGGACUGUGCUCUGCAAGGGGCACACGAAAGAGGAAUUCCUAGUAAGCGCCCAUCACCAGUGGGCGUUGAAUCAGUCCCUGUAGCUUGUACACACCGUCCGUCACUAUCUCAGAUGUUUUUCGGGAUGAAGAGUCCAGGCUCUGAAUAACGGAAAGUAGAUAAGAUGUAAGUCGUAGCAAGGUUGCGGUCGGUGAACCAUUAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq
new file mode 100644
index 0000000..a4c4989
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq
@@ -0,0 +1,2 @@
+>d.16.e.Encephalitozoon.sp
+CACCAGGUUGAUUCUGCCUGACGUGGAUGCUGUUCUCUGGGACUAAGCCAUGCAUGUUGAUGAACCUUGUGGGGGAUUGACGGACGGCUCAGUGAUAGUACGAUGAUUUGGUUGGCGGGAGAGCUGUAACUGCGGGAAACUGCAGGUAGGGGGCUAGGAGUGUUUUUGACACGAGCCAAGUAAGCUGUAGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGGAGACGGGAGACGGGGGAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUUGGGGAGGCGGUUAUGAGAAGUGAGUUUUUUUCGAGUGUAAAGGAGUCGAGAUUGAUUGGAGGGCAAGUCGCGUGCCAGCAGCCGCGGUAAUACCUGCUCCAAUAGUGUCUAUGGUGAAUGCUGCAGUUAAAAAGUCCGUAGUCUUUUGUAUGUCUUUGUUUGGGGGAUUAUGUCCUGAUGUGGAUGUAAGAGGUUUGGCAGAGGACGAGGGGCACCGGAUAGUUGGGCGAGGGGUGAAAUACGAAGACCCUGACUGGACGGACAGAAGCGAAGGCUGUGCUCUUGGACUUAUGUGACGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACUAUAUAGUGUUGUGCAUGAGAAAUCUUGAGUAUGUGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGUUCUGAAGCGGGCAGGAGAACGAGGACGGGAUGCGUGCGGCGGUGGUGCAUGGCCGUUUGAAAUGGAUGGCGUGAGCUUUGGAUUAAGUUGCGUAAGAUGUGAGACCCUUUGACAGUGCUCUUUGGGGCAAGGGAGGAAUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGAAGCGGGCGGCACGCGCACUACGAUAGAUGGCGAGGGAGCCUGCUGUGAGGGAUGAAGCUGUGUAAUGGGCUUCUGAACGUGGAAUUCCUAGUAAUAACGAUUGAACAAGUUGUUUUGAAUGGGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCCAAGAUGACGCAGUGGACGAAGAUUGGAAGGUCUGAGUCCUUCGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq
new file mode 100644
index 0000000..1b84530
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq
@@ -0,0 +1,2 @@
+>d.16.e.F.x.ananassa
+UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAAUCCCGACUUCUGAGAAGGGAUGCAUUUAUUAGAUAAAAGGUCAACGCGGGCUCUGCUCGCAUUGAUGAUUCAUGAUAACUCGACGGAUCGCACAGCCUUUGUGCUGGCGACGCAUCAUUCAAAUAUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGUUGGGUCGACCGGUCCGCCUUAUGGUGUGCACCGGUCGGCUCGUCCCUUCUACCGGCGAUACGCUCCUGGCCUUAACUGGCCGGGUCGUGCCUCCGGUGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGGUCCUAUUCUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUACUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUCGGGAGGUCUCCUCGGGCCAGCUUCUUAGAGGGACUAUGGCCGCUUAGCGAACCAAGUUUGAGGCAAUAACAGGUCUGUCAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUCUAUAGCCUUGGCCGACCACGGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUUGUUCGGAUCGCGGCGACGGGGGGCCGGUUCGCUGCCCGCGACGUCGCGAGAAGUUCCACUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq
new file mode 100644
index 0000000..4d70b84
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq
@@ -0,0 +1,2 @@
+>d.16.e.G.intestinalis
+CAUCCGGUCGAUCCUGCCGGAGCGCGACGCUCUCCCCAAGGACGAAGCCAUGCAUGCCCGCUCACCCGGGACGCGGCGGACGGCUCAGGACAACGGUUGCACCCCCCGCGGCGGUCCCUGCUAGCCGGACACCGCUGGCAACCCGGCGCCAAGACGUGCGCGCAAGGGCGGGCGCCCGCGGGCGAGCAGCGUGACGCAGCGACGGCCCGCCCGGGCUUCCGGGGCAUCACCCGGUCGGCGCGGUCGCGGCGCGCCGAGGGCCCGACGCCUGGCGGAGAAUCAGGGUUCGACUCCGGAGAGCGGGCCUGCGAGACGGCCCGCACAUCCAAGGACGGCAGCAGGCGCGGAACUUGCCCAAUGCGCGGCGCGCGAGGCAGCGACGGGGAGCGCGCGAGCGAGGCGGGCCCACAGCCCCCGCCGCGGAGCCGAGGGCAAGGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCGGCGAGCGUCGCGCGGCGCUGCUGCAGUUGAAACGCCCGUAGUUGGCCCCCCGCCGCCACGAGGAAACGGGAGCGCUCCAGGCAGGCCCGUUGGACCCGCCGCGUGGGACCGCGCAGCGGGCCGGCGCGCCGCGGCAGCCCCGAGGAGAGCGGGCGGGGGCACCGGUACCGGCCGGGGACGGGUGAAACAGGAUGAUCCCGCCGAGACCGCCGGCCGCGCAGGCGCCUGCCAAGACCGCCUCUGUCAAUCAAGGGCGAAGGCCGGGGGCUAGAAGGCGAUCAGACACCACCGUAUUCCCGGCCGUAAACGGUGCCGCCCCGCGGCCGGCGCGCGCGUCCCGCCGGCCGCCCAGGGAAACCGGGAGGCUCCGGGCUCUGGGGGGAGUAUGGCCGCAAGGCUGAAACUUGAAGGCAUUGACGGAGGGGUACCACCAGACGUGGAGUCUGCGGCUCAAUCUGACUCAACGCGCGCACCUCACCAGGCCCGGACGCGCGGAGGACCGACAGCCGGGCGCGCUUUCGCGAUCGCGCGGGCGGUGGUGCAUGGCCGCUCCCAGCCCGUGGCGCGAGCCGUCUGCUCCAUUGCGACAACGAGCGAGACCCCGGCCGCGGGCGCCGCGGGACGGCCCGCGCGAGCGGGAGGACGGCGGGGCGAUAGCAGGUCUGUGAUGCCCUCAGACGCCCUGGGCCGCACGCGCGCUACACUGGCGGGGCCAGCCGGCGCGCGCGAGGACGCGCGGAGCCCCCGCCGUGGCCGGGACCGCGGGCUGGAACGCCCCCGCGCACCAGGAAUGUCUUGUAGGCGCCCGCCCCCACCGCGCGCCGGACGCGUCCCUGCCCCUUGUACACACCGCCCGUCGCUCCUACCGACUGGGCGCGGCGGCGAGCGCCCCGGACGCGCGAAGGGCCGCGAGCCCCCGCGCCUGGAGGAAGGAGAAGUCGUAACAAGGUAUUCCGUAGGUGAACCUGCGGAUGGAUCCCUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq
new file mode 100644
index 0000000..6e4347c
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq
@@ -0,0 +1,2 @@
+>d.16.e.G.max
+UACUUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCAACACAGGCUCUGCCUGUUGCUUUGAUGAUUCAUGAUAACUCGUCGGAUCGCACGGCCUUUGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCAUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAUGGAUCCAUUGAAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGUUGGGUCGAUCGGUCCGCCUCCGGUGUGCACCGGUCGGCUCGUCCCUUCUGCCGGCGAUGCGCUCCUGUCCUUAACUGGCCGGGUCGUGCCUCCGGUGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACACCACAGGAUUCUGAUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUUUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAAAUAGCUAUGUGGAGGUAACCCUCCACGGCCAGCUUCUUAGAGGGACUAUGGCCGCUUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUCUAUAGCCUUGGCCGACAGGUCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUUGCGGCGACGUGAGCGGUUCGCUGCCCGCGACGUUGUGAGAAGUCCACUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq
new file mode 100644
index 0000000..2188860
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq
@@ -0,0 +1,2 @@
+>d.16.e.G.steinii
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCGAUGUCGUCUUGUUGAUUGUGCAGAGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCAGAGGCGCGCUUUAUCCGCCUUUGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGCUUAGCGGACACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACCGCGGAGUUCUCGUAAUUCUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq
new file mode 100644
index 0000000..78438aa
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq
@@ -0,0 +1,2 @@
+>d.16.e.Gracilariopsis.sp
+CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUAUAGGACUAAGCCAUGCAAGUGCAAGUAUGAGUGUAUUAUACAACGAAACUGCGAAUGGCUCUGUAAAACAGCUAUAAUUUCUUCGGUGCUAAAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCUACACAGCGACGCAAGUCGUGGUACAAAUUAGAUACACAAGCCAGCUUUUUUGGUGAUUCUAGAUUUUUUUUCUGAUCGCACAUUGUUGCGACGCACCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAAUGGCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAACUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGAUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAAUUUUGGCGUGUGAUUUGGGUCGUUCUCGCGGACGCGCUCAGGUUGUGCGCCUUUGUGGAGAGGGGGUGUGGUGGUGCUUGAGUGCGCUGCCAUGCUGCCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGAUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCCGGUUCUAUUUUGUUGGUUUGUUUGAAUCAGGUAAUGAUUAACAGGGACGGUUGGGGGCAUUCGUAUUCCGGCGCUAGAGGUGAAAUUCUUGGAUUGUCGGAAGACGAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGACAAGACUGAUUUAUGGCUUGUUCGGCAUCCUUCGAGAAAUCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCGUUACCAAUUGAGUUUGGUAGCGAGGCGGUGCCUUCCUAGACGGACUGUGGGCGUCUAGCCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAACGGCCCAACGAGUGGAGGAUGUGCGAGAGCAUUUCCGAAUCUCCAAAUCCGUUCGUGAUGGGGAUCGACGGUUGCAAUUUUCCGUCGUCAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUGGAUGCGCUGUUUUUAUGCAGACAUUUUGGCCUGAACCUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq
new file mode 100644
index 0000000..9c2f96f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq
@@ -0,0 +1,2 @@
+>d.16.e.H.anguillarum
+CACCAGGUUGAUUCUGCCUGACGUGGACGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAGGCGAAGCAUUUUGUGGAGCGGCGGAAGGCUCAGUAACGGGCGUCUAUUUGAUCUUCUGAGACGGACAACCUCUGUAACCGGAGGCCAAUACGUCAGAGGCACGGUUACCCUGUGUGGUGGUGUGCCGAAAGCAUUGCGCGGAAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUGUGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCGGUGAGGGCGGUAGUAAGGAGACGUGGAAACGAUGAGGAGGUAAAGAAUGCUCUGGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGGCUGCGUGACUGGCGUGAAAGGCCUUCUUUCAAGGGGGGCACAGCGCGGGGAAAGCAGAGGAUAAGGAGCGUUUUGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGGAACAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGUGCGUGCGCGCGACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGACCGCACGAGUGUUGUACACGAUAGGUCGAAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCUGUCCGGCAGACAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGCGUGGGCUGCACGCGCACUACAGUGGUCACAGAAAGAAUCGCGGAGAGACAAUGGUGAUCGAGAGGGAAUGAGCUUUGCAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCUGUAGCUGGAUCAGCG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq
new file mode 100644
index 0000000..4d623b3
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq
@@ -0,0 +1,2 @@
+>d.16.e.H.plana
+CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAAACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCCUAAGACGACGCAAGUCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACGAUUUCUUUUCUGAUUGCACUUUUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAGUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAAAUUUGGCGGGCGACUUAAGUCGUCUUUACCGACGAUCUUAGGUUGGCCGCCUUUGUGGAGGGGGGCCUAGUGGUGCUUAACCGCUUCGCUAGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUUCUAUUUUGUUGGUUUGUUAGGAUCGGGUAAUGAUUAAGAGGGAUGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGUUGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACAUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGCGGGGCUGUUUUUGGCCCGCCCGGCAUCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGGAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGUUAGCUAGGCGCCAUUACCCCUUUUGGUAGUGAGGCUAGCCUUCCUAAACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCCAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGAUAGUCGGUGUUUUCACAGAUCAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq
new file mode 100644
index 0000000..734e464
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq
@@ -0,0 +1,2 @@
+>d.16.e.H.rubra
+CAACCUGGUUGAUCCUGCCAGUGGUAUAGUCUUGUCUCAAGGACUAAGCCAUGCAAGUGCCAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGGGGGUAAUACUACCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCCGAAAGCGAGUCUCUCGCGGUACAAAUUGGAGACACAAGCCAAUAUUUUGGUGAUUCACAAUUUUUUUUCUGAUUGCACUUUUUAGUGCGACACCCCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAYUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUACUAAUUCAGUGAGGUAGUGACAAAGAGUAUCAAUAGGGGGGCCAUCGGCUCUUCUAGUUGGAAUGAGUACAGAGUAAACAAUUUAACGAGGACCAAUAGGAGGGCAAGCCAAGUGCCAGCAGCCGCGGUAAUACUUACUCCUAGGGUGUUUGUUCACAGUGCUGCAGUUAAAAAGUUCGUAGUCGGACCUAUGAGCUGGGCGGUGGUGUGGGCGCAAGCCUGUGGUGCCGCCCGGCUCUUUUGGGGAAAUGGCCGGAGUAGGGUUUUAAGCGGCUUUGCUCCGGGCGUCCCCCGUUUACUGUGAAAAAAUGAGAGUGUUCAAAGCAGGCGAUGAGCCGUGAAUACCAUAGCAUGGAAUAAUAGAAUAGGGCCGCUGAUGCCUAUUUUGUUGGUUUCGAGGUGUCGGGCAAUGAUUAAGAGGGACGGUUGGGGUCAUUUGUAUUAAGUCGUCAGAGGUGAAAUUCUUAGAUUGACGUAAGACAAACAGCUGCGAAAGCGUCUGACAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUAAGAACUGGGGAUCGGAAGAGUAUUUAAAUAGGGCUCAUCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAGUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGAGCGUGGUAGCUAGGGGACUUGUGCAUUUAUGCACGGGCUUUUUCUCCUUCCUACACGGACUGCUGGCGAAUAGUCAGCGGAAGCCUCAGGCAAUAACAGGUCUGUGAUGCCCUUUGAUGUUCUGGGCCGCACGCGCGCUGCACUGAGCGGACCAGCGGGCGAGGAUAGCCGAAAGGUUUUCCGGACCCUUAAAUUCGCUCGUGCUGGGGAUGGAGGCUUGCAAUUGUCCCUCUUGAACGAGGAAUACCUUGUAGGCGUGAGUCAUCAGCUCGCGCCGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGGGUGAGGAGGUGAGAAGUUGGGAGGUGUUGGUUCGGGCCCGCAAGGUGUCUGGGCUAGCGCUAAACUCGUUCAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq
new file mode 100644
index 0000000..c04feb9
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq
@@ -0,0 +1,2 @@
+>d.16.e.H.sapiens
+UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq
new file mode 100644
index 0000000..f212fda
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq
@@ -0,0 +1,2 @@
+>d.16.e.I.hoferi
+CAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACAACUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUAAUACCUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGAAAAAACCCGACUUCUGGAAGGGUUGUAUUUAUUAGAUACAGAACCACUGCAGGGCAACCUGGUUACUUGGUGAUUCAUAAUAACUUCGCGAAUCGAAUGGCUUGUGCCGUCGAUGAUUCAUUCAAAUCUCUGCCCUAUCAACUUUCGGUGGUAAGGUAUUGGCUUACCAUGGUUCCAACGGGUAACGGAGAAUUAGGGUUCGAUUCCCGAGAGGGAGCCUGAGAAACGGCUACCACUUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAAAAAUAACAAUACAGGAUCUUUAAAGGUCUUGUAAUUGGAAUGAGUACAAUUUAAACCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUUGGAAAUUGCUUACUGGUCGGCCGCAAGGUCUGUACUGGUACGGCAGUUUCUUCUUCUCGAAGGCAGUGGGUGCUCUUAAUUGAGUGUCUACUGAGUUCGGGACUUUUACUGUGAGAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCUUGAAUAUUGCAGCAUGGAAUAAUGGAAUAGGAUCCCGAUCUUAUUUUGUUGGUUUCUAAGAUCGAGAUAAUGAUUAAUAGGGACGGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGGAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCGUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUAGUGGACGUUUAAUAAUGACACCAUUAGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCCCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACCAGGUCCGGACAUAGGAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGCCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUACUAAAUAGUUACAUGAUUUUCGAAUCAUGGGCAACUUCUUAGGGGGACUAUUGGUGUAUAAUCAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGAGGUCAACGAGUAUCAUCCUUCACCGGAAGGUGCGGGUAAUCUUUUGAAACCUUAUCGUGAUGGGGAUAGAUCAUUGCAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGUUUAGUGAGGUCCUCGGACUGGUACAGCGCGUGGCAACACAUACUGCGCCGGGAAGUUGAACAAACUUGAUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCUAGU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq
new file mode 100644
index 0000000..aea2f0f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq
@@ -0,0 +1,2 @@
+>d.16.e.Ichthyosporidium.sp
+CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCUAAAGUUAAGCCAUGGAUGUCUAAGCAAAGCGUAAGUCGAGCGGCACAGGCUCAGUAACGGGCGAAUAUUUAAUCUCCUCGAGUGGAUAUCCUCUGUAACCGGAGGGCAAAACACAGGACGUGCAGUUGUAUAAGGAUUGUUCGUUUAACAUUAGUGGGGGAGAGUAAGACGCCAGUCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAUACGGAUACGGGGAAUUAUCGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCGGGUCCAAGGACAACAGCAGGCGCGAAAAUUACCGCAGCCUGCAUUCAGGUCGGUAGUAAGGAGACGUGUAAACGAUGUGCAGGUAAAGAAUGCACUGUAUACAGGAGGACAAGACUGGUGCCAGCACCCGCUGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGCGUUCGUAGUCGAACCGGGUUGAAUUGCGUGACAGUCAGACUCUCAAGGUGUGAUGAGCGCUGUGAUUCUGGGGAAUAAGGAGUGUUUAGGGGCCAGGGUAUUAAACGGCAAGCGGUGAAAUGUGUUGACCCGUUUAUGGAGCGACAGAGGCGAAAGGCUGGCCAGGGGCAAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACAAUGCCGAUGUUGUGGUGCCGUAACGGACGCAAAAGAGAAAUCUAGUAGGGCCCUGGGGAGAGUACACGCGCAACAGGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACACCUUACCGGGCCCACGGCCACACGAGUGUGACACACGAUAGCCGAGGAGUGGUGCAUGGCCCGUUAACGACAAGUGAGUGAUCUUUGGGUUAAGUCCGUAAAUUAGUGAGACCCCAGCAAAGGACAGGUGCGCAAAGCACAGGAAGGAUGGGUCAAGGACAGGUCAGUGAUGCCCUUAGAUGGUCCGGGCUGCACGCGCACUACAGUGGUCGCCGAAAUUUAGAUAUAGAGCUAAAGGCGAUCGAGAGGGAAUGAGCUUUGGAAGAGGCUCAGGAACGUGGAAUUGCUAGUAAUCGCGGACUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAUACGGUGCUCGGCGCGAGCAAGGUGAAAUCACUGAGCGAGCGCAAGGUACCGGAUCUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAUUAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq
new file mode 100644
index 0000000..0970601
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq
@@ -0,0 +1,2 @@
+>d.16.e.J.debaisieuxi
+CACCAGGUUGAUUCUGCCUGACGUAUGUGCUUGUCUUAAAGAUUUAGCCAUGCAAGUUAGUGAAACUUUUUAAGUGAAACGACAGACAGCUCAGUAAUACAGUAAUGAUUAACUUGCCUAAUAUAGGAUAACCUUGGUAACCUAAGGCUAACACUUUUUUCAAAUUAAAAUGUAGGUGAAACUAUUUUUAAUUUUUUUUUGGGGCAAUUAAGUUUCUGACCUAUCAGCUAGAUGUUAGGGUAAAGGCUUAACAUGGCUACAACGGGUAACGGAGAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAUUAGCUACCACGUCUAAGGAUGGCAGCAGGCGCGAAAAUUACCCAAUUCCUUAAUGGGAGAGGUAGUGAAAAGACAUGAUUUUCAUUUCGAUUGAGUCGGUACAUUAAAUAAGUACUGAAGCAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAAUAGUUGCUGCAGUUAAAAUGUCCGUAGUUGAUUUAAUUAAACUGUGAGUAAAUUAUAGAGCUCAAAACUAUAAGUAAGCAUGGUAUUAUAAGAUAAUAGGAACAGAUGAUGGCAAUAGUAUUCAAUAGUUAGAGGUGAAAAUUUAAGACCUAUUGAGGACUACCAGAAGCGAAAGCGAUUGUCAAGGAUGUCUCCAUUAAUAAGGGACUUAAGCUAGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCUAGCUGUAAACGAUGCCUACUAGGUGAUGUUUAAAUGGCUAUGCCUUAGGAGAAAUCAAAGUCUACGGGCUCUGGGGAUAGUAUACUGGCAACGGUGAAACUUAAAUGAAAUUGACGGAAGAAUACCACGAGGAGUGGAUUAUGCGGCUUAAUUUGACUCAACGCGGGACAACUUACCAGAGCCGAACCUGUAUGAGAAUUUAUAAUGUAAAUGAUAAUAGGGAAGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACUUGUCAGGUUAAUUCCGAUAACGCGUGAGGUUUAUUAAAUAAUUGUUUAUUUGACGGAUGAUAAGAAAUCAUAGGAAGUUAAGCUAUAACAGGUCGGUGAUGCCCCUAGAUGUUCUGGGCUGCACGCGUACUACAAUGAUAUAUUUAAUAUUAAUAUUGAGAAAUAUAACUCUAAUAUAUAUCGAAGCUGGGAUAAGCUAUUGUAAAUUAGUUUUGAACUUGGAAUUCCUAGUAAUCAUAAGUCAUUAUGUUAUGAUGAAUGCGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUAAGAUGGAUGUAUAGGUGAAAUGGCUAGACGUAAAUGGAAAGCAGUUAACCUGUGCAACUAAUAGGAUAUAAGUCGUAACAAGGCUGCUAUAGGUGAACCAGCAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq
new file mode 100644
index 0000000..b74a2ea
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq
@@ -0,0 +1,2 @@
+>d.16.e.L.acerinae
+CACCAGGUUGAUUCUGCCUGGUGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAAGCAAAGCUAGAAGUGGAGCGGCGCAAGGCUCAGUAACGGGCGGACAUUUGAUCUUCUCGUGUGGACAUCCUCUGUAAGCGGAGGGAAAAACACAGGACGCGCGGACGCAGCCCGUGGGUGUAACGGCGGUGGAGAAGAGUAAGACGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUGAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGCAGCCUGCCUCAGGGCGGUAGUAAGGAGACGUGAAUGCGAAGUGCUAGCAAAGAAAGCACUGACAACAGGAGGACAAGACUGGUGCCAGCACCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGGGUUCGUAGUCUGAGCGGAACGAGGGGUGUGACGGGUCCCAGCUCAAGGGGGACAUAGCACCGCGAUGCCGCGGAACAAGGAGCGUCUAGGGGCCAGGGUAUUAAGCGACGAGGGGUGAAAUCUGGUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGGCCAGGGGCGAGUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGUGCCGCAAGGCGACGCGGAAGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGUCCCGACGAUCGGAGGAGUGUGUUACACGAUAGGUCGGAGAGUGGUGCAUGGCCGUUAACGACGAGUGGGGUGACCUUUGGGUUAAGUCCGUGAAGUAGUGAGACCCCUGCCGCAAGGGACAGGUGCCGAACGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUCAGAUGGGCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAAGGAAGGAAAGAGAUAAAGGCGAUCGAGAGGGAACGAGCUUUGGAAGAGGCUCGGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAGGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq
new file mode 100644
index 0000000..1e52f3a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq
@@ -0,0 +1,2 @@
+>d.16.e.M.musculus
+UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCCUUCCCGGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUGAGCUCCCUCCCGGCUCCGGCCGGGGGUCGGGCGCCGGCGGCUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGUCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUGCGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq
new file mode 100644
index 0000000..93e0dc2
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq
@@ -0,0 +1,2 @@
+>d.16.e.M.racemosus
+UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAAUAAAUUUAUAUUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGAUCUACGUGACAUAUUCUUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAACCCAAACUUACGAAUGGGUGCACUUAUUAGAUAAAGCCAACGCUGGGUAAAACCAGUUUCCCUUGGUGAUUCAUAAUAAUUUAGCGGAUCGCAUGGCCUUGUGCUAGCGACAGUCCACUCGAUUUUCUGCCCUAUCAUGGUUGAGAUUGUAAGAUAGAGGCUUACAAUGCCUACAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUGCAGGGCCUUUAAGGUCUUGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAACGUCCGUAGUCAAAUUUUAGCCUUUAGAUGAGGUGGCCUGGUCUUCAUUGAUCAAGCUCGCUUUUAUCGAGGCUUUUUUUCUGGUUAUGCUAUGAAUAGCUUCGGUUGUUUAUAGUCUCUAGCCAGAUGAUUACCAUGAGCAAAUCAGAGUGUUUAAAGCAGGCUUUCAAGCUUGAAUGUGUUAGCAUGGAAUAAUGAAAUAUGACUUUAGUCCCUAUUUCGUUGGUUCAGGAACUUAAGUAAUGAUGAAUAGAAACGGUUGGGGACAUUUGUAUUUGGUCGCUAGAGGUGAAAUUCUUGGAUUGACCGAAGACAAACUACUGCGAAAGCAUUUGAUCCAGGACGUUUUCAUUGAUCAAGGUCUAAAGUUAAGGGAUCGAAGACGAUUAGAUACCGUCGUAGUCUUAACCACAAACUAUGCCGACUAGAGAUUGGGCUUGUUUAUUAUGACUAGCUCAGCAUCUUAGCGAAAGUAAAGUUUUUGGGUUCUGGGGGGAGUAUGGGACGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAAAGCUCUUUCUAGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAUUCUGCUAAAUAGGCAGGUCAACUUUUUAGUUGAUUAAUAGAUUUAUCUAUCUGGCUUCUUAGAGAGACUAUCGGCUUCAAGCCGAAGGAAGUUUUAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGAAAUCAGCGAGUUUAUAACCUUAGCCGGAAGGUUUGGGUAAACUUUUGAAAUUUCAUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGUUAUAGUGAGCAUAUGGGAUCAGUAGAAUUAGGUUGGCAACAACCUUUCUCUGCAGAGAACUAUGGCAAACUAGGCUAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq
new file mode 100644
index 0000000..100309a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq
@@ -0,0 +1,2 @@
+>d.16.e.Microsporidium.sp.DP119
+CACCAGGUUGAUUCUGCCUGGUGUAGAUGCUAGUUUCUAAGAUUUAGCCAUGCAUGUUUUGUGAAUUCUUACGAAGGAACGGCGAACGGCUCAGUAAUAUUGCGUUAAUCUGGUCUAAAUAUAAAAAUAACUACGGUAACCUGUAGCUAAUAAUUUAGAAUGAGACGCAAAUUUAUCAGUUUGUUGGUAGUGUAAUGGACUACCAAGACUAUGACGAAUAACGGGAAAUUAGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGUCCACUCUUUUAUGAGGAGACAGUUAUGAAACGUGAAUAUAAGUUUGAAUUUUAAAAUAAUUUAUUUUAUGCAAUUGGAGGGCAAGUUUUGGUGCCAGCAGCCGCGGUAAUACCAACUCCAAGAGUGUCUAUGAARGUUGCUGCAGUUAAAGCGUCCGUAGUUUUUUUAUUGCAAUUUAAAAACUAUGAUUAAAUUAGUUAAGUUUCCAAUACAUUGUGAAACGGAUAGGGAAAAUUGUAUAGCUAGGUGAAGAAUGAAAUCUCAAGACCCUAACUCGACAAACAGAGGCGAAGGCGAUUUUCUUAUACGUAUUCUUAAAUAAAGGACGAUAGUUAGAGGAUCGAAGGUGAUUAGAGACCGCUGUAGUUCUAACUGUAAACUUUGCCGACAUUUCAUAUUGUUUUGAUAAGAAAGGGAGAAAUCUUAGUUUUCGGGCUCUGGGGAUAGUACACUCGCAAGGGAGAAACUUAAAGCGAAAUUGACGGAAGAACACUACCAGGAGUGGAUUGUGCUGCUUAAUUUGACUCAACGCGGGAAAACUUACCAGAGUCAAAUAUAUUUAUGAUUUUUUUAAAUGAAAUAUAUAAAAGUGGUGCAUGGCCGUUGCAAAUUGAUGGGUUGACUUUUAACUUAAUUGUUGAAACCAGUGAGAUCAUUUAUGACUGGUAUUUUAAAUACAGGAAGGAAAUGGCAAUAACAGGUCCGCACGCCCUUAGACAUUCUGGGCUGCAAGCGCAAUACAAUAUCUUGUUAUUUAUAUUUAUUUAUACAAUUAUAUGUAGGAUUAAUUCUUGUAAAUGAAUUAUGAAUCAGGAAUUCCUAGUAAUAAUAUUUCAUUAAGAUAUUAUGAAUUUGUCCCUGUUCUUUGUACACACCGUCCGUCACUAUUUCAGAUGGUUAUAAAGAUGAAGAGCUAAGGUUCUGAAUAUUUAUAACUAGAUAAAGUACAAGUCGUAGCAAGGUUGCAGUCGGUGAACCAUCAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq
new file mode 100644
index 0000000..6ff328d
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq
@@ -0,0 +1,2 @@
+>d.16.e.O.colligata
+CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUGUCUGAGAUUAAGCCAUGCAUGUGAGUGAAUGUAGUAAGCAGGAACUGCGGACGGCUCAGUAAGACUACGAUGAAAUGAUCUGCGAAGAAGAAGUAACGGCGGGAAACUGAAGAAGAGAGUUUUUGAGAAUACUUGAAGGGAUGCGGAGAAGUGAUUUUUGAAGUGAUGUUGAGUAUUUGAGCGGAGUGUGUUGUAGACCUAUCAGCUGGUAGCUAGGGUAAUGGCCUAGGUAGGCGACGACGGGAGACGGGGGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUGUGGGGAGGCGGUUAUGAGACGUAUGAUAUUGUUAUGAAGCGGACGAUGAAAGAGUCAGUGGAUAUUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCGAUGGUGUCUAUGGUGAAUGCUGCGGUUAAAAAGUCUGUAGUCAAGUGAGGAUGUGUAUGAGUAUGAAGGUGAGUGAACUAGAGUUGAAUAAGCUUGUAUGUAUGAGGAGAGCAACGGAGGGGGUGCACUGGAUAGCUGGGCGAGAGGUGAAAUGUGAAGACCCUGGCUGGACGAACGGAGGCGAAGGCUGUGUGCCAUGACGAAUGUGAUGAUCAAGGACGAAGGCCAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUGGCAGUAAACGAUGCUGACGGGAUGACAUGUAUGUGUGUUAUGCAAGAGAAAUUGAGUAUGUGAGCUCUGGGGAUAGUAUGUUCGCAAGGGUGAAACUUAAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCAGGGCUGAAGAUGUGUGGAGAACUGAGAGGGGAGCACAUUGGCGGUGGUGCAUGGCCGUUUGAAACGGAUGGCGUGAGCUGAGGAUUAAUUUCCGGAAGGCGUGAGACCCACAAGACAGGUUGUUUGGAUGACAGGAGGGAGUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGUCCUGGGCGGCACGCGCACUACGAUACGUGUAUGAGAUGUGUGAGGGAUGAAUGUGUGGAAUGGCAUUCUGAACGUGGAAUUCCUAGUAAUGGUGGCUCAACAAGCCGACGUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUGAGAUGGCACAUGGGACGAACACCGAGGGGUGUGAGUCUUCUGUGGUAGAUGAGAUAUAAGUCGUAACAUGGCUGCGGUUGGAGAACCAGCUGCAGGAUCAUCA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq
new file mode 100644
index 0000000..7ec9865
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq
@@ -0,0 +1,2 @@
+>d.16.e.O.cuniculus
+UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGCGCUGACUCCCUUUGUGUGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCUCCCCGCCGGCCGGGGGGGUGGGGCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCAGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUCGCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGUGGAGGGUGCGUAGCGGGCGGUCCGCCGCGAGGCGAGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq
new file mode 100644
index 0000000..d6a7e62
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq
@@ -0,0 +1,2 @@
+>d.16.e.O.granulifera.1
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGUGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCUCGUUUGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUUGGUAUUCAUUUACUGGUUUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUCGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUCGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAACCAAUCUCCGAUUGGCUGCGACUUCUUAGAGGGACUUUGUGGGCCAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGCGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAACCUUUUGGACUGCGCGAGGCCCCGAGCCUUGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq
new file mode 100644
index 0000000..024562d
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq
@@ -0,0 +1,2 @@
+>d.16.e.O.granulifera.2
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAACUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUCUUACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGAUUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCACAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCUGAUGUCCGCAUGUUUGCGUGUGCAGAGCGCCCUCCCAUCCUUCUGUUAACGUUUCUUGGUAUUCAUUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUCGGGGGCAUUAGUACUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCAUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAACCAAUUCCGAUUGGCUCCGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACACAUACAACGAGUACAUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGUGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCAUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCUUACCGAUUUUGAGUGAUCCGGUGAACCUUUUGGACUGCGCGGAGUCUCGUGCUCUGUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq
new file mode 100644
index 0000000..f69e872
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq
@@ -0,0 +1,2 @@
+>d.16.e.O.longa
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUAAAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCUUUUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAAGGGGUGCCAAUGUCCGCUGUUGCGUGUUCAGCGGCGCCCCUUCAUCCUUCUGUUAACGUCUCGGGUAUUCAUUUACUCGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCUAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGUCCCGUUGCUAAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAACCUUUUGGACUGCGUGGUCCUCGUGGCCGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq
new file mode 100644
index 0000000..4acb186
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq
@@ -0,0 +1,2 @@
+>d.16.e.O.operophterae
+CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGCCUCCGAGGCUAAGCCAUGCAUGCCCGUGACGCAAGGAACGGCGAACGGCUCAGUAAUACUGCGAUGAUCUGCUCCGCGCGGACGAUAACUACGGGAAACUGUGGCUAAGAGCGCGGAUUGAGACGCAGCCCUAUCAGCAAGUUGGUAGUGUAACGGACUACCAAGGCGGCGACGGGUGACGGGAAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUCUCUUGCGAGGAGGCGGUUACGAGGCGUGACGGAAGGGCGCACUGUAAAGACGUGCGCGAACGCGAUUGGAGGGCAAGUUCGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAAAGUCCGUAGUCGGCACUGCGACGAAAGCGCGCUGCUCGAUGGCGCAGGCGUUGCAGGGGCUUGCGGAGCGGGCGGGGGGCACGGUAUAGGCAGGCGAGAGAUGAAAUGGCCAAGACCCUGCCUGGACCGACGGUGGCGAAGGCGGUGCCCUCGCACGCAUCUGUGGAUCAAGGACGAAGGCCGGAGGAUCGAAAGUGAUUAGAGACCGCUGUAGUUCCGGCAGUAAACGAUGCCGACACCGCGCGGCGGGGCUGCGCGGGGGGAGAAACCUUAGUGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGUGUGAAAAUUAAACGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGCACCUUACCAGGGCCACGCGCGCCUGAGACCGCAUGCGCGAGGCGCGCAGGAGUGGUGCAUGGUCGUUGCAAAUUGGUGGGGCGACUUUUGGCUUAAAUGCCGGAACGAGUGAGAUCUCCGAGACGGGUGCGCGCAGCACAGGAGGGUGGAGGCGAUAACAGAUCAGUGAUGCCCUUAGAUGCCCUGGGCUGCACGCGCAAUACAAUCCCCGCGCGCUGCACAGAACGGUCGCGGGGGUGUGGGACCGGCGCCUGUAAGGGCGCCGCGAACGAGGAAUUCCUAGUAACGGCGGCUCACCAAGCCGCGGUGAAUGUGUCCCUGUAGCUUGUACACACCGCCCGUCACUAUCUCAGAUGGCCGUGUCGGUGAAGGGAGCAAUCUCUGUGCCUCCGCGGCUAGAUAAGAUGUAAGUCGUAACAAGGUUGCGGUCGGUGAACCAGCAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq
new file mode 100644
index 0000000..aae8387
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq
@@ -0,0 +1,2 @@
+>d.16.e.O.quadricornutus
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGCUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGACGAUUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCUCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCGUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGAGUGCCAAUGUCGUCUUGUUGACUGUGCAGCGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGCUAUUUAUUUAGUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGUCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUACCUCCGUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUUGACUCGUUGCUAAGCGAGAUUAACUUCUUAGAGGGACUUUGUGACUARACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGAGGUCCUCGUGACUUUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq
new file mode 100644
index 0000000..e0d3525
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq
@@ -0,0 +1,2 @@
+>d.16.e.O.sativa
+UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGCAAGUAUGAACUAAUUCGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCCGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCCGCCCGCUGAUCCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCCUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCGCUUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCGCGGCCGGGCCGGUCCGCCUCACGGCAGGCACCGACCUGCUCGACCCUUCUGCCGGCGAUGCGCUCCUGGCCUUAACUGGCCGGGUUCGUGCCUCCGGCGCCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUAUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGGGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGCAGCUAGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGUAUCCAACGAGUAUAUAGCCUGGUCCGACAGGCCCGGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUCGCGGCGACGGGGGCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq
new file mode 100644
index 0000000..0d42d11
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.anophelis
+CACCAGGUUGAUUCUGCCUGACGUGGAUGCUCGCCUUAAAGACUAAGCCAUGCAAGUUUGCGAGCUGAGCAGCGAACGGCUCAGUAAAACAGGGCACUCUAACGCACGGAAGAGAUAACCACGGGAAACUGUGGCUGAGAAGUGCGAUGAGGCUCUGACCUAUUAGUUUGUCGGUACGGUAAGUGCGUACGGAGACGAUGAUGGGUAACGGGGGAUCAAGUCCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGCAACUUACCCAAUGAGGAUUGAGGUAGUGACGAGGCGUAGAUUGUGAGUUGAGAGUAAAGAACUUAACGAGAGCGACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGGGCGUAUGUGUGUGUUGCUGCGGUUAAAAAGCGCGUAGUUUGUGGUGUAGCGGGUCGUUGUGGGGCGAGAUCAAUGCGUUCUGUGUGACUUAUGCUCAUUGCUAGGGAGCGCGAGACGCCGGUGGUAUUCGGUAGCGAGGGGUGAAAACUGCAGACCUACCGAGGAGCGACAGAGGCGUAAGCGGCCGGCGAGUGCGGAUCCGACGAUCAAGCGCGUGGGCAGGAGUAUCGAAGACGAUUAGAGACCGUCGUAGUUCCUGCAGUAAACGAUGCCGACAUGGUUGAAUAGAAUUGACCAAAGGGAAACUGAGUGUACGGGCUCCGGGGAGAGUACGGGCGCAAGCCAGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGCGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGGCAACUUACCCGGGCCGCAGCCUCUUGAGAGGAAACCGAUGGGGCCUCGUGGUGCAUGGCCGUUCUCAACGCGAGGGGUGACCACUGAGUUAGUUCUGGCAAGCCGUGAGGCCCCUGUACUUUUGUAGACGGCGGACGGCAAGUCCGAGGAAGCGAGGGCGUAUAACAGGUCUGUGAUGCCCGCAGAUGUCCGGGGCUCCACGCGCACUACAAUAGCAAAUGGUAGACGAGAGUAAGUUUGUUGUGGUUGGGAUUGACGCUUGUAAAUGCGUCAUGAACGAGGAAUGCCUAGUAGUUGUCUGUCAGCAGCGGACAACGAAUAAGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGCGGUGCGGAUGAAGCUGCUACGUGGCAAGAAUCCGUGCUGCUAGAUUGGAUACAAGUCGUAACAUGGUUGCAGUAGGUGAACCUGCCGCAGAUCAAGCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq
new file mode 100644
index 0000000..bf550f0
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.anserina
+UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAUUACCUUACUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAUCCCGACUUCGGAAGGGAUGUGUUUAUUAGAUUAAAAACCAAUGCCCUCCGGGGCUCACUGGUGAUUCAUAAUAACCUCUCGAAUCGCACGGCCUUGCGCCGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGACGGCUGGGUCUUGGCCAGCCAUGGUGACAACGGGUAACGGGGAGUUAGGGCUCGACUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUACUGAUACAGGGCUCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGAGGUUAAAAAGCUCGUAGUUGAACCUUGGGCCCGGCCCUCCGGUCCCCCUCACCGGGUGCACUGGCUCGGCCGGGCCUUUCCUUCUGGAGAACCGCAUGCCCUUCACUGGGCGUGCCGGGGAACCAGGACUUUUACUCUGAACAAAUUAGAUCGCUUAAAGAAGGCCUAUGCUCGAAUAGUCUAGCAUGGAAUAAUGGAAUAGGACGUGUGGUUCUAUUUUGUUGGUUUCUAGGACCGCCGUAAUGAUUAAUAGGGACAGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUAAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAGGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGAUUAGGGAUCGGACGGUGUUAUUUUUUGACCCGUUCGGCACCUUGCGAUAAAUCAAAAUGUUUGGGCUCCUGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACGAUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUCGUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUGCUAAAUAGCCCGCAUCGCUUUGGCGGUGCGCCGGCUUCUUAGAGGGACUAUCGGCUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACAGAGCCAGCGAGUACUCCCUUGGCCGGAAGGCCCGGGUAAUCUUGUUAAACUCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUCAGUGAGGCUUCCGGACUGGCCCAGGGAGGUCGGCAACGCCAACCCAGGGCCGGAAAGCUAUCCAAACUCGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUCUCCGUUGGUGAACCAGCGGAGGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq
new file mode 100644
index 0000000..054fe8f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.carinii
+UACCUGGUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAGUUAUACAGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUAUCUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAUCCCGACUUUAUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCAAUGCCUUCGGGCUUUUUGGUGAUUCAUGAUAACUUCGCGGAUCGCAUGGCCUUGUGCUGGCGAUGAUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUUUCGACGGGUAACGGGGAAUAAGGGUUCUAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGGCUCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAGAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGAAUUUAGGGAUUGGUUGCCUGGUCCUCCGAAGUUGUGUGCACUGGCGCAACUGAUCCUUCCCUCCUGGAUUACCGGCUGCCCUUCGCUGGGUGUGCCGGAUAGCCAGGGCAUUUUACUUUGAGAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCUCGAAUACAUUAGCAUGGAAUAAUAAAAUAGGACAUGUGGUUCUAUUUUGUUGGUUUCUAGGACCAUUGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUCAAUUGUCAGAGGUGAAAUUCUUAGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGAGAUCGGGCGAUGUUUUUUUCUUGACUCGCUCGGCAUCUUAUGAGAAAUCAAAGUCUUCGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGAAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUGCUAAAUAGCCAGAUUAGCUUUUGCUGAUCGCGGGCUUCUUAGAGGGACUGUUGGCAUGAAGCCAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGACAGAGCCAGCAAGUUCAUUUUCCUUGGCCGAAAGGUCUGGGUAAUCUUGUGAAACUCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAAUGAGGUCUUCGGACUGGUGAUGGGUUAUUGGCAACGAUAAGCCUAUUACUGGAAAGUUGAUCAAAUUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq
new file mode 100644
index 0000000..3a8ce15
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.cristatellae
+CACCAGGUUGAUUCUGCCUGACGUAUGCGCUUGUCUUGAAGAUUUAGCCAUGCAAGCUAGCGAAGCCUUAUGGUGGAGCGGCGGACAGCUCAGUAAUACAGUUAUUAUUUACUCGUAGUAUGUAUACGGAUAACCAUGGUAAGCUAUGGCUAAUACGUGAACAGGUUAUUGCAUAGAUGAAACAGCGAUAACUGAGAGAGCAAUCGACUACGACUAAGUUUCUGGCCUAUCAGCUAGAUGGUAAGGUAAUGGCUUACCAUGGCUAUAACGGGUAACGGGAAAUCAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUUCCUUAGCGGGAGAGGUAGUGAAGAGACAUGAAGUUCUACUUAGAGACUGUACGGUAAAAUAGUACAGGAUCUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAAUAGUUGCUGCAGUUAAAACGUCCGUAGUUGAUCACAAGGUAUUCUUCUGCAUAGUAUUUGUGGAGUGUAUCUCGAUACUGUGAGAAAAAUAUGGUUCUCAAAGCGGAUUACGUGAGUAAUUUAGCAUGGGACAUGGUGAAUAUAGGAACAGAUGAUGGCAAUAGUAUUCAGCAGUUAGAGGUGAAAAUCGUUGACCUGCUGAGGACUCUCUGAAGCGAAAGCGAUUGUCAAGUAUGUCUCCGUUAAUAAAGGACUUAAGCUGGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCCAGCUGUAAACUAUGCCGACUAGGUGAGGCCGUCAGGCUGCGCCUUAGGAGAAAUCAAAGUUUUUGGGCUCUGGGGAUAGUAUGGAUGCAAAUCUGAAACUUAAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCAGGGCCGAAUGCAUAGGAGAUCGGCUGUCUGAGAGGGUACCCGAGAUUAUGCAGGAGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGGCCUGUCUGGUUAAUUCCGUAAACGCGUGAGGCCUGGGAAGCAAUUCAUUGCUUGACGGAUAGCGGCAAGCUAUAGGAAGACAGGCUAUAACAGGUCAGUGAUGCCCCUAGAUGUUCUGGGCUGCACGCGCAAUACAAUGGUAUAGUGAGACUAUGUACUGAAAAGUAUGCUUUAAGCUAUAUCGAAUCUGGGAUAAGCUCUUGUAAAUGAGUUUUGAACGAGGAAUUCCUAGUAAUCGCAGGUCAUAAUGCUGCGAUGAAUGCGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUUAGAUGGAUGUAUCGGUGAAAUGGCUGGACGAAAGAAAGGCAGUUGAACCUAUACAAUUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGGUGAACCUGUGGCAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq
new file mode 100644
index 0000000..66edb7f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.falciparum.A
+AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUAUAUAUAUAUUUUAUAUGUAGAAACUGCGAACGGCUCAUUAAAACAGUUAUAGUCUACUUGACAUUUUUAUUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCUUUAUUAUCCUUGAUUUUUAUCUUUGGAUAAGUAUUUGUUAGGCCUUAUAAGAAAAAAGUUAUUAACUUAAGGAAUUAUAACAAAGAAGUAACACGUAAUAAAUUUAUUUUAUUUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUGCAAGGCCAAUUUUUGGUUUUGUAAUUGGAAUGGUGGGAAUUUAAAACCUUCCCAGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAAUCGAUAUUUUAUUGUAACUAUUCUAGGGGAACUAUUUUAGCUUUUGGCUUUAAUACGCUUCCUCUAUUAUUAUGUUCUUUAAAUAACAAAGAUUCUUUUUAAAAUCCCCACUUUUGCUUUUGCUUUUUUGGGGAUUUUGUUACUUUGAGUAAAUUAGAGUGUUCAAAGCAAACAGUUAAAGCAUUUACUGUGUUUGAAUACUAUAGCAUGGAAUAACAAAAUUGAACAAGCUAAAAUUUUUUGUUCUUUUUUCUUAUUUUGGCUUAGUUACGAUUAAUAGGAGUAGCUUGGGGACAUUCGUAUUCAGAUGUCAGAGGUGAAAUUCUUAGAUUUUCUGGAGACGAACAACUGCGAAAGCAUUUGUCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUGCCGACUAGGUGUUGGAUGAAAGUGUUAAAAAUAAAAGUCAUCUUUCGAGGUGACUUUUAGAUUGCUUCCUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGCGAGUACACUAUAUUCUUAUUUGAAAUUGAACAUAGGUAACUAUACAUUUAUUCAGUAAUCAAAUUAGGAUAUUUUUAUUAAAAUAUCCUUUUCCCUGUUCUACUAAUAAAUUGUUUUUUACUCUAUUUCUCUCUUCUUUUAAGAAUGUACUUGCUUGAUUGAAAAGCUUCUUAGAGGAACAUUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUAUAUAACGAGUUUUUAAAAAUAUGCUUAUAUUUGUAUCUUUGAUGCUUAUAUUUUGCAUACUUUUCCUCCGCCGAAAGGCGUAGGUAAUCUUUAUCAAUAUAUAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUCAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUGAAUUGUUUGGACAAGAAAAAUUGAAUUAUAUUCUUUUUUUUCUGGAAAAACCGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq
new file mode 100644
index 0000000..b5b366a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.falciparum.S
+AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCACAGAUUAAGCCAUGCAAGUGAAAGUACAUAUGUAAGUAAUAUAUUGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGAUGUUUUUAAUAUAAGGAUAACUACGGAAAAUCUGUAGCUAAUACUUGUGAAAAUACCUUUUGAUAUAUACAUAUGUAUGUAUCAUUAAGGUAUGUAUUUGUUAGAUAUAAGAAUAAAAUAAAUAUAAUUGAAUUAUAACAAAGAAGAAACACAUAAAAUAUGUGUAUUAUCAAUCGAGUAUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGACCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAAAAGAGAGGUAGUGACAAGAAAUAACAAUACAAUAUCGAAAAAUGAUUUUGUAAUUGGAAUGAUAGGAAUUUACAAGGUUCCUAGAGAAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAAUUGUUGCAGUUAAAACGUUCGUAGUUGAAUAUUAAAGAAUCCGAUGUUUCAUUUAAACUGGUUUGGGAAAACCAAAUAUAUUAUAUAUUUUGCUUUGUUCAAAAUAAGGUUUUCUAAUAAAUUAUGUUUUUAUCAGAUAUGACAGAAUCUUUUUUAAAAUCUCUUCAAUAUGCUUUUAUUGCUUUUGAGAGGUUUUGUUACUUUGAGUAAAAUUAAGUGUUCAUAACAGACGGGUAGUCAUGAUUGAGUUCAUUGUGUUUGAAUACUACAGCAUGGAAUAACAAAUAUGAAUAAGCUAAUUAUUUUUUUUUUCAUUAUUUUUUUUGAUAUUCUUAUUAGCUUAGUUACGAUUAAUAGGAGUAGCUUUGGGGGCAUUCGUAUUCAGAUGUCAGAGGUGAAAUUCUAAGAUUUUCUGGAGACGGACUACUGCGAAAGCAUUUGCCUAAUCUAUUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUACCGACUAGGUGUUGGAUGAAUAUAAAAAAUAUAUAAAUAUGUAGCAUUUCUUAGGGAAUGUUGAUUUUAUAUUAGAAUUGCUUCCUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGUAAGUACACUAUAUUUUUAUUUGAAAUUGAAUAUAGGUUACUAUACGUUUAUUCAGUGUUCAAAUUAGGAUAUUUUUUUUAUUAAAAUAUUCUUUUCCCUGUUUUACUAAUAAUUUGUUUUUUUUUACUCUAUUUCUCUCUUCUUUUAAGAAUGUACUUGCUUGAUUAAAUAAAGCUUCUUAGAGGAACAGUGUGUAUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUAAACUAGGCUGCACGCGUGCUACAAUGAUAUAUAUAACAAGUUGUUAAAAAUGUACUUAUAAAUAAGUGUGUACAAUUUUUCCUGUACUGAAAAGUAUAGGUAAUCUUUAUCAGUAUAUAUCGUAAUUGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUUAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUAAAUUGUUUGGAUAUGAAUUAAAAUAAUGAAAUUUUAUAUUUCUGAUUUUUUCUAGAAGAACUGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq
new file mode 100644
index 0000000..74cb22c
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.hippoglossoideos
+CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUUUCAUAGGUUAAGCCAUGCAUGUGUAAGCGAAGCUUUUAGUGGAGCGGCGCAAGGCUCAGUAACGGGCGUCUGAUUUGAUCUCUCGGAGUGGACAACCUCUGUAACCGGAGGCCAAAACACGGGAGGGGCAUGCAGUGGAGAUGCCCCGAGAACAUUUAGUGAGAGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAGGACGGGUACGGGGAAUUAGAGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUGCAUUCAGGGCGGUAGUAAGGAAACGUGAAAACGAUGUGCAGGUAAAGAAUGCACUAGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGACUGCGUGACUGGCGUGAAAGACCCUUUUAUUCAUUCAAGGGGGGCGCAGCGCCGGAAAAGCAGGGAAUAAGGAGCGGCCGGGGCACAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGUGCAGGGGCGAUUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGAUGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCAGUUCUUAGACUGCGCCGCGGAAGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGACCGCACGAGUGUGGUACACGAUAGGUCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUUGUGAGACCCCUGCUGGCGAGCCAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCACACGAGUUUAUAGAUAGAAGAAAUGGUGAUCGAGAGGAAAUGAGCUUUGCAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGGUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq
new file mode 100644
index 0000000..0825b4a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.lepisma
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAGGUUAUACAAUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUAAAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAGGCUUUGCUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCGAUGUCCGCAUGUUGCGUGUGCAGAGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUUUCGAUUGGGAACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUGCAUACAACGAGUACUUCCCAGCUCCGAAAGGUAGCUGGUAAUCAGCAAUAUGCAUCGUGAUGGGGAUAGAUCCUUGGAAUUAUGGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAAUCAUUUGGACUGCGUGAGGUUUCGUACCUCGUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq
new file mode 100644
index 0000000..86c7a36
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.mirandellae
+CACCAGGUUGAUUCUGCCUGGCGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAAGCGAAGCAUUUUGUGGAGCGGCAUAAGGCUCAGUAACGGGCGUCUAUUUGAUCUCCUGAUGUGGACAACCUCUGUAACCGGAGGCCAAUACACAUGAGGCACUGUUUCCGUUUGGUGGGGUGUCAAUAGCUAUUUAAUUUUUAUAGCGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCGGUGAGGGCGGUAGUAAGGAGACGUGAAUACGAUGUGCAGGUAAAUAAUGCACUAGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGUGUUCGUAGUCGGGCUGCAUGACUGGCGUGAAAGACCUUCCUUUCAAGGGGGUACAGCGCGGGGAAAGCAGAGAAUAAGGAGCGUUUUGGGGUCAGGUUAUUAAGCGACGAGAGGUGAAAUUUAAUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGAGCGAGUUUUAUUCGCUUCGCGGAAGAGAAAUUUAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUCAACUCAACGUGGGACAGCUUACCAGGCCGGACGACCGCACGAGUGUAGUACACGAUAGGUUGAAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCUGUUACGAGUAAUGGUGACAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCACAGAAAGAGAUUAUUGAGAGAUAAUGGUGAUCGAGAGGGAAUGAGCUUUGUAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq
new file mode 100644
index 0000000..897f945
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.palmata
+UGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGGGGUAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGUUAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAGCGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGUGGCCCGUGCUGUGCGCGUAAUGCGUGCGGCGCUGGGGCGCGCUUUUGUGGAGGGCGGCGCGUUGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGCCGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGAUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCAGGCAUUACGAUGACCUGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGCUACCAUUGUGUAGCUGUUCGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAAAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCCGCGGUUGAGGCGUUUACGCCCUGGCCGCAGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGACAGAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq
new file mode 100644
index 0000000..a076ef4
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.pulvinata
+CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAUUUAUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGUUACACUACCGGAUAACCGUAGUAAAUCUAGAGCUAAUACGUGCCACUAAAACGGUGAAAACCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACAAUUUCUUUUCUGAUUGCAAUCAUGUUUUGCGACACAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUAUCAUGGUCGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAUCUUAUCGAGUAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAAUUUGGCGGGCGAUGUGGGGCGUCUUAACCGACGAUCUCAUGUCGGCUGCCUUUGUGGAGGGGGGCCUAGUGGUGCUUCACUGCAUUGUUAGGUUUCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUCCUGUUUUGUUGGUUUGUGAGGAUCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGGCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGUGAGACUGUUUUUGGCUCACCCGGCAUCCUUCGGGAAACCAAAGUAUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCUACUACCACUAUGGUAGUAAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGAUCAACGGGUGAGGAUGUGCGAGAGCAUUUCCCAAUCUCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCACGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGAUGAACUGUGCUACACAGAUUUUUUGGCCCGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq
new file mode 100644
index 0000000..76544cb
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.vivax.A
+AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUAUAUGCAUAUUUUAUAUGUAGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGACAUUUUUUCUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCCUUAGCACUCUUGAUUCAUUUCUUGAGUGUGUACUUGUUAAGCCUUUUAAGAAAAAAGUUAUUAACUUAAGGAAUUAUAACAAAGAAGCGACACGUAAUGGAUCCGUCCAUUUUUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUACAAGGCCAAUCUGGCUUUGUAAUUGGAAUGAUGGGAAUUUAAAACCUUCCCAAAACUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAAUCGAUAUUUUAAGCAACGCUUCUAGCUUAAUCCACAUAACUGAUACUUCGUAUCGACUUUGUGCGCAUUUUGCUAUUAUGUGUUCUUUUAAUUAAAAUGAUUCUUUUUAAGGACUUUCUUUGCUUCGGCUUGGAAGUCCUUGUUACUUUGAGUAAAUUAGAGUGUUCAAAGCAAACAGAUAUAGCAUUGCGCGUUUGAAUACUACAGCAUGGAAUAACAAAUUGAACAAGUCAGAAUUUUUGUUCUUUUUUCUUAUUUUGGCUUAGUUACGAUUAAUAGGAGUAGCUUGGGGGCAUUUGUAUUCAGAUGUCAGAGGUGAAAUUCUUAGAUUUUCUGGAGACAAACAACUGCGAAAGCAUUUGCCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUGCCGACUAGGCUUUGGAUGAAAGAUUUUAAAAUAAGAAUUUUCUCUUCGGAGUUUAUUCUUAGAUUGCUUCCUUCAGUGCCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGCAAAUACGACAUAUUCUUACGUGGGACUGAAUUCGGUUGAUUUGCUUACUUUGAAGAAAAUAUUGGGAUACGUAACAGUUUCCCUUUCCCUUUUCUACUUAGUUCGCUUUUCAUACUGUUUCUUUUUCGCGUAAGAAUGUAUUUGCUUGAUUGUAAAGCUUCUUAGAGGAACGAUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUGUAUAACGAGUUAUUAAAAUUACGAUUCAGCUUGCUGUUUCGUAUUUUUCCUCCACUGAAAAGUGUAGGUAAUCUUUAUCAGUACAUAUCGUGAUGGGGAUAGAUUGUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUCAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUGAAUUGUUUGGACAAGAAGAAGGGGGAUUAUAUCUCCUUUUUUCUGGAAAAACCGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq
new file mode 100644
index 0000000..13a90ad
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.vivax.S
+AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUACAUGCAUAUUUUUAUAUGCGGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGACAUUUUUUUCUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCUUUAAUGCUCUCGACGAAUGUCUUGGGCAUGUACUUGUUAAGCCUUUAUAAGAAAAAAGUUAAUAACUUAAGGAAUGAUAACAAAGAAGUGACACAUAGAAGGACCUGCGUCCAUUUAUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUUGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUACAAGACCAAAACUGGUUUUGUAAUUGGAAUGAUGGGAAUUUAAAUCCUUCCCAUAAUACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAACCAAUAUUUUAAUAACGCCGUUAGCUAGAUCCACAAGGGGUUGAGCCAAUCACGGUUUCGGCUUCUGUGCGCAUCCUACCUAUCAAGCGUUUUUUUAAUUAAAGUGUUUCUUUUUAAAAUCUUCUUUACCUUAACCAUAUGGAAGAUUUUGUUACUUUGAGUAAAUUAAAGUGUUCAUAGCAAACAGAUACAGCAUUGCGCGUUUUGAAUACUACAGCAUGGAAUAACAAAAUUGAACAAGUCAAAACUAUGUUUCUUUUUUUUUAUUUUUGGCUUAGUUACGAUUAAUAGGAGUAGUUUGGGGACAUUUGUAUUCAGAUGUCAGAGGUGAAAUUCUAAGAUUUUCUGGAGACAAACAACUGCGAAGGCAUUUGUCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUACCGACUAGGUUUUGGAUGAAAGUUAAACAAAUAAGGAUAGUCUCUUCGGGGAUAGUCCUUAGAUUUCUUCCUUCAGUACCCUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUGAGAGCUCUUUCUCGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGUAAGUACGACAUAUUUUUAUGUCGGAUUGGAUCUGGAUGAUUUGCUUAUAUUGAGGUGCAAUCUAAAUAGGGGAUUGCAAUUAUACUUCGUGUCGGUGUUUCUUAAUCGAAUAGCUGAUGCGUUUGGUAUAUUGCUUUCCUUUUUUUUAUUUCUGCGCUUCUUUACUUGGCUUAUCGUACCGUUUCCUUUUUGUGUAGAAAUGUAUUUGCAUUAUAUUAAAGCUUCUUAGAGGAACGAUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUGUACAACGAGUUAUUAAAAUUACGAUUCAGCUUGCUGUUACGUAUUUUUCCUCCACUGAAAAGUGUAGGUAAUCUUUAUCAGUACAUAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCACGAUUCAUUAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAAAGAUAUGAUGAAUUGUUUGGACAAGAAGAAAGGGGAUUAUAUCUUCUUUUUUCUGGAAAAACCGUAAAUCCUGUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq
new file mode 100644
index 0000000..64ca28d
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq
@@ -0,0 +1,2 @@
+>d.16.e.P.weissei
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGAGGGCGCCAAUGUCCGCUGAUUGCGUGUGCAGCGGUGCCCUCUCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUAGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGACCCGUUGCUAAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGUAAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACCGCGAAGUCCUCGUGGCUUUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq
new file mode 100644
index 0000000..7479150
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq
@@ -0,0 +1,2 @@
+>d.16.e.Ple.lanceolata
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGAUGAUUCAUAAUAACUGAUCGAAUCGCUUCGGCUUUGCCAGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGAGUGCCAAUGUCGUCUUGUUGACUGUGCAGCGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCAACCCGUUGCUAAGCGGGAAUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGAGGUCCUCGUGAUCUUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq
new file mode 100644
index 0000000..093c07a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq
@@ -0,0 +1,2 @@
+>d.16.e.R.carriebowensis
+CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUAAGUGAUUCUGAUGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAAUUUCUUCGAUGGUAACUUACUAUUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAAUGCGGGGUUUCGGCUCCGUGGUGCCAAUUAGAUAACAACACCAACAUUUGGUGAUUCAUAAUUUUCUUUCUGAUCGCUGCAUGCAUUGCGGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAGUGUCUUACCAUGGUGGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACUCCGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGACCCGAUGGGUGCCCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAAGUUGGUGGUCUUGCGGGUGCGCGCGUUGAGCGUACGCCUGUCGAGGCUGCUUUUGUGGAUUGCGCGCACGGGCGGCUUUAGUGUCGAACGUGUUGGGUUUCGCUGCUUUGGCGUUCACGCGGCAGAGCGGCGGAGGCGCAGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGGUUUUCCUAUUUUGUUGGUGUUGUGAGGGGCGAGUAAUGAUUAAGAGGGACAGUUGGGGGCACUUGUAUUCCGGCGCUAGAGGUGAAAUUCUUAGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGUGGAAUUGCGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUUUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGGGCUAUUACCGCUUUUUUUGGUAGUGAGAGCUUUUUUGACCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGAUCAGCGGGCGAGGAUGCGCGAAAGCGUUUCCUAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGGUUGCAAUUCUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAUUGUCGUGAGGGGAGCGUUUGCGCUCGUUUCGUGAAGAAAACUUGGUCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq
new file mode 100644
index 0000000..99deaaf
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq
@@ -0,0 +1,2 @@
+>d.16.e.R.leptophylla
+CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGAUAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAGACGACUCAAGUCGUGGUAUAAAUUGGAGAUACAAACCAAUAUUUGGUGAUUCACAAUUUCUUUUCUGAUUGCACUUUCGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUUUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAACUUGGCGGGCGACUUGCCUCGUCCUCGCGGAUGUUGGCAGGUCGGCCGCCUUUGUGGAGGGGGGCCUAGUGGUUCUUUACUGCAUCGCUAGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUUCUAUUUUGUUGGUUUGUUAGAAUCGGGUAAUGAUUAAGAGGGAUGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGUUGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACAUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGCGGGGCUGUCAUUUGGCCCGCCCGGCAUCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGGAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGUUAGCUAGGCGCCAUUACCGCUUUUGGUAGUGAGGCUAGCCUUCCUAAACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGCGAGGAUGUGCGAGAGCAUUUCCAAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCACGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAAAUGGACUGUGUUCUCACGGACCGUUUGGCCCAAACUUGGCCAAGCCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq
new file mode 100644
index 0000000..8a1603d
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq
@@ -0,0 +1,2 @@
+>d.16.e.R.norvegicus
+UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCCUUCCCGUGGGGGGGACGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCCCCUCCCGGCUCCGGCCGGGGGUCGGGCGCCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGUCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq
new file mode 100644
index 0000000..b728e04
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq
@@ -0,0 +1,2 @@
+>d.16.e.S.alba
+UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACGAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGUGCUGCUCUGAUGAUUCAUGAUAACUCGACGGAUCGCAUGGCCUUUGUGCUGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUAACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCAUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGAUGGGUCGCCCGGUCCGCGUUUGGUGAGCACCGGUCGGCUUGUCCCUUCUGUCGGCGAUACGCUCCUGGCCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGGACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUUUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAAGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUCACACCUUGGUCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAGUACUCGGAUCGCGGCGACGUGGGUGGUUCGCCGUCCGCGACGUCGCGAGAAGUUUUCUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq
new file mode 100644
index 0000000..7eb6818
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq
@@ -0,0 +1,2 @@
+>d.16.e.S.cerevisiae
+UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCGAUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGUGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq
new file mode 100644
index 0000000..3697105
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq
@@ -0,0 +1,2 @@
+>d.16.e.S.lemnae
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCCGACUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCAUUUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGAGGGGCGCCAAUGUCCGAUGUUUCGUGUGCAGCGGUGCCUCUCCAUCCUUCAGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCUGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGUUAAGCGGACUUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGCGGUCCUCGUGACUGUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq
new file mode 100644
index 0000000..2908cfd
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq
@@ -0,0 +1,2 @@
+>d.16.e.S.lophii
+CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGAUUUAGCCAUGCAUGUGUAAGCGAAGCGAUUAGUGAAGCGGCGGAAGGCUCAGUAACGGGCGAGUAUUUUAAUCUCUAGAACCGGACAACCUCAGGAAACAGAGGGGAAAACGGAGUAAGAGCAUGUGUUGUUAGCAUGUGAUGAGAACAACAGUGCAGGAGAGUAAGAAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUAUUUAGACGUAGACGGGUACGGGGGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCAAGAGGGCGGUAGUGAAGAGACGUGAAAACAAGUGUGUGUAAAAACCACAUGAGUAACUGUGGAGGGUCAAGGCUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCAGGAGUGUCUAUGAUGAUUGCUGCGAUUAAAAGGUCCGUAGUCGAAGAACAGUACUUGUUUGUAAUGUGGCUUAUCGAGAGCCGAAUAGAACGAGAAGAGUUCAGAGUAAGGAGYGAAGGAGGGCUAGAUUAUUGAGCAGCGAGAGGUGAAAUUUGAUGACCUGCUUUAGGAGUAACAGAGGCGAAAGCGCUAGUCAAGAACGAAUCCGAUGAUCAAGGACGUAGGCUGGAGGAUCGAAGACGAUUAGAGAGACCGUAGUAGUUCCAGCAGUAAACGAUGCCUACGCUGUUGUGGUUAUGAGCACGGCAGAAGAGAAAUCUAGUAGGGCUUUGGGGAGAGUACGCGCGCAAGCGAUAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAUACCCGAUGGCCGUGUGAGCGUAGUACGCGAUAGGUCAGAGAGUGGUGCAUGGCCGUUAACGACGAGUGGGGUGACCUUUGGGUUAAGUCCGCCGAAGUAGUGAGAUCCCUAGGAUACGAAAGUUAUCGACAGGUGUUAAAAACACAGGAAGGAAGGGGCAAGAACAGGGUCAGUGAUGCCCUUAGAUGGUAUGGGCUGCACGCGCACUACAGUGGUCACAGCAGAAACGGAUAGAAGUAAAUGUGAUCGAGAGGGAAUGAGCACUGUAAUGUGCACAGGAACGAGGAAUUGCUAGUAAUCGUUAUCUCAUUAAGAAGCGAUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAACCAGGUGCGAACAAGUGAAAGCGAGUGAGUGCAGGGUUCYAGAUCUGAUACAAGUCGUAACAAGGCAGCUGUAGGAGAACCAUUAGCAGGAAGCUUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq
new file mode 100644
index 0000000..022bce8
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq
@@ -0,0 +1,2 @@
+>d.16.e.S.mytilus
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCCAACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGAGGGGUGCCAAUGUCCGAUUGUUUCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGUUAAGCGGACUUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGUUCCGGUGAACCAUUUGGACCACGCGGUCUUCGUGACUGUGAGGAAAAUCUAGUAAACCAUAACACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq
new file mode 100644
index 0000000..3e571a9
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq
@@ -0,0 +1,2 @@
+>d.16.e.S.tuberosum
+UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACAAAUUCAGACUGUGAAACUGCGAAUGGCUCAUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGCCCGUUGCUGCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCAUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUAUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACUUUGGGAUGGCACGGCCGGUCCGCCCUAGGUGUGCACCGGUCGUCUUGUCCCUUCUGUCGGCGAUGCGCUCCUGGCCUUAAUGUGCCGGGUCGUGCCUCCGGCGCUGUUACUUGAAGAAAUUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUUAUAGGAUUCGGUCCUAUUUACGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACCGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGGUCGGCGGAUGUUGCUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGAAGGUAUCCCUUCGCGGCCAGCUUCUUAGAGGGACUACGGCCUUUUAGGCCGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGCUUAUAGCCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAAUGUUCGGAUCGCGGCGACGUGGGCGGUUCGCUGCCCGCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq
new file mode 100644
index 0000000..9a3b981
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq
@@ -0,0 +1,2 @@
+>d.16.e.T.cruzi
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUUUCAAGGACUUAGCCAUGCAUGCCUCAGAAUCACUGCAUUGCAGGAAUCUGCGCAUGGCUCAUUACAUCAGACGUAAUCUGCCGCAAAAAUCUUGCGGUCUCCGCAAAAUUGGAUAACUUGGCGAAACGCCAAGCUAAUACAUGAACCAACCGGAUGUUCUCUGUUCCGGCGGCAGGGCAACCUGCUGCCAUGGGACGUCCAGCGAAUGAAUGAAAGUAAAACCAAUGCCUUCACCGGGCAGUAACACUCAGAAGUGUUGAUUCAAUUCAUUCCGUGCGAAAGCCGGGUUUUUUAUCCGGCGUCUUUUGACGAACAACUGCCCUAUCAGCCAGCGAUGGCCGUGUAGUGGACUGCCAUGGCGUUGACGGGAGCGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACUUCUACGGAGGGCAGCAGGCGCGCAAAUUGCCCAAUGUCAAAAAAAAAAGAUGAGGCAGCGAAAAGAAAUAGAGCCGACAGUGCUUUUGCAUUGUCGUUUUCAAUGGGGGAUAUUUAAACCCAUCCAAAAUCGAGUAACAAUUGGAGGACAAGUCUGGUGCCAGCACCCGCGGUAAUUCCAGCUCCAAAAGCGUAUAUUAAUGCUGUUGCUGUUAAAGGGUUCGUAGUUGAAUUGAGGGCCUCUAAGGCGCAAUGGUUUAGUCCCAUCCACUUCGGAUUGGUGACCCAUGCCCUUGUGGUCCGUGAACAGACAUAUUCAGAAACAAAAAACACGGGAGUGGUACCUUUUCUGAUUAUCGCAUGUCAUGCAUGCCAGAGGGCGCCCGUGAUUUUUUACUGUGACUAAAAAAGUGUGACCAAAGCAGUCAUUCGACUUGAAUUAGAAAGCAUGGGAUAACAAAGGAGCAGCCUCUGGGCCACCGUUUCGGCUUUUGUUGGUUUUAAAAGUCCAUUGGAGAUUAUGGGGCAGUGUGACAAGCGGCUGGGUGGUUAUUCCACACACACGCACACUCCUUUUUUGGAUGUUGUGUCUCUGUGUGUGUGGCACUCGUCGCCUUUGUGGGAAAUCCGUGUGGCACUUGUUUGGUGUUGUUGGCAGACUUCGGUCUUGCCUUCACACACGUUUCACAUGUGUCAUGCCUUCCCUCAACUCACGGCAUCCAGGAAUGAAGGAGGGUAGUUCGGGGGAGAACGUACUGGUGCGUCAGAGGUGAAAUUCUUAGACCGCACCAAGACGAACUACAGCGAAGGCAUUCUUCAAGGAUACCUUCCUCAAUCAAGAACCAAAGUGUGGGGAUCGAAGAUGAUUAGAGACCAUUGUAGUCCACACUGCAAACGAUGACACCCAUGAAUUGGGGAGUUUUUGGUCGUAGGCGUGGUCGGGCUUGAUUAUAUUAUUUUUCAUCCCGUUCCUCGUCUCGCCAAUGAAUAUAUUAAAUUUACGUGCAUAUUCUUUUUGGUCUUCGUUUUUUUACGGCGAGGACCUUUAACGGGAAUAUCCUCAGCACGUUAUCUGACUUCUUCACGCGAAAGCUUUGAGGUUACAGUCUCAGGGGGGAGUACGUUCGCAAGAGUGAAACUUAAAGAAAUUGACGGAAUGGCACCACAAGACGUGGAGCGUGCGGUUUAAUUUGACUCAACACGGGGAACUUUACCAGAUCCGGACAGGGUGAGGAUUGACAGAUUGAGUGUUCUUUCUCGAUCCCCUGAAUGGUGGUGCAUGGCCGCUUUUGGUCGGUGGAGUGAUUUGUUUGGUUGAUUCCGUCAACGGACGAGAUCCAAGCUGCCCAGUAGGAUUCAGAAUUGCCCAUAGGAUAGCAAUCCCUUCCGCGGGUUUUACCCAAGGGGGGGCGGUAUUCGCUUGUAUCCUUCUCUGCGGGAUUCCUUGUUUUGCGCAAGGUGAGAUUUUGGGCAACAGCAGGUCUGUGAUGCUCCUCAAUGUUCUGGGCGACACGCGCACUACAAUGUCAGUGAGAACAAGAAAAACGACUCUUGUCGGACCUACUUGAUCAAAAGAGUGGGAAAACCCCGGAAUCACGUAGACCCACUUGGGACCGAGUAUUGCAAUUAUUGGUCGCGCAACGAGGAAUGUCUCGUAGGCGCAGCUCAUCAAACUGUGCCGAUUACGUCCCUGCCAUUUGUACACACCGCCCGUCGUUGUUUCCGAUGAUGGUGCAAUACAGGUGAUCGGACAGUCGAGUGCUUCACUUGACCGAAAGUUCACCGAUAUUUCUUCAAUAGAGGAAGCAAAAGUCGUAACAAGGUAGCUGUAGGUGAACCUGCAGAAGGAUCAAGCUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq
new file mode 100644
index 0000000..c3f9ae2
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq
@@ -0,0 +1,2 @@
+>d.16.e.T.gondii
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACGGCUAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGGUCUUUACUACAUGGAUAACCGUGGUAAUUCUAUGGCUAAUACAUGCGCACAUGCCUCUUCCCCUGGAAGGCAGUGUUUAUUAGAUACAGAACCAACCCACCUUCCGGUGGUCCUCAGGUGAUUCAUAGUAACCGAACGGAUCGCGUUGACUUCGGUCUGCGACGGAUCAUUCAAGUUUCUGACCUAUCAGCUUUCGACGGUACUGUAUUGGACUACCGUGGCAGUGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUUCAGGGAGGUAGUGACAAGAAAUAACAACACUGGAAAUUUCAUUUCUAGUGAUUGGAAUGAUAGGAAUCCAAACCCCUUUCAGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGCUGGAAGCAGCCAGUCCGCCCUCAGGGGUGUGCACUUGGUGAAUUCUAGCAUCCUUCUGGAUUUCUCCACACUUCAUUGUGUGGAGUUUUUUCCAGGACUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUGUCGCCUUGAAUACUGCAGCAUGGAAUAAUAAGAUAGGAUUUCGGCCCUAUUUUGUUGGUUUCUAGGACUGAAGUAAUGAUUAAUAGGGACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGCUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGAGAUAGGAAAACGUCAUGCUUGACUUCUCCUGCACCUUAUGAGAAACCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGGAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGGAUCAGGAACUUCGUGUUCUUGUAUCACUUCUUAGAGGGACUUUGCGUGUCUAACGCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCUGCACGCGCGCUACACUGAUGCAUCCAACGAGUUUAUAACCUUGGCCGAUAGGUCUAGGUAAUCUUGUGAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUCAACGAGGAAUGCCUAGUAGGCGCAAGUCAGCACGUUGCGCCGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGUUCCGGUGAAUUAUUCGGACCGUUUUGUGGCGCGUUCGUGCCCGAAAUGGGAAGUUUUGUGAACCUUAACACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq
new file mode 100644
index 0000000..22f2555
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq
@@ -0,0 +1,2 @@
+>d.16.e.T.hominis
+CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGCAAGCGAAGCCGGUGGUGGGGCGGCGCAAGGCUCAGUAACGGGCGACUGAUUUGAUCUCCCGGUGUGGACAACCUCUGUAAACGGAGGCCAAAACACAGGAGCGCCGUGUACAGAGACGGUGCGAGAACCGGAGGUGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGCAAAUUACCGAAGCCCGCGUUCGGGGCGGUAGUAAGGAGACGUGUAAGCGAUGUGCAGGUAAAAUAUGCACUGGUAACAGGAGGUAAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGGCUGCGUGACUGGGGUUUAAGGCCCGCUAUCGAGGCGGGCAGUGCGCCAGAAAAGCAGAGGAUGAGGAGCGGCCGGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAGCAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCGGUGAGCCGCCACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGGUCGCAUGAGUGUUGUACACGAUAGGCCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCCGGCGUGCCGGGACAGGUGCGCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAUGGCAGAGGUAGCCUGAAUGGCGAUCGAGAGGGAACGAGCUCUGGAAGGGGCUCGGGAACGAGGAAUUGCUAGUAAUCGUGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq
new file mode 100644
index 0000000..15995cb
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq
@@ -0,0 +1,2 @@
+>d.16.e.T.thermophila
+AACCUGGUUGAUCCUGCCAGUUACAUAUGCUUGUCUUAAAUAUUAACCCAUGCAUGUGCCAGUUCAGUAUUGAACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUUAAAGAUUACAUGGAUAACCGAGCUAAUUGUUGGGCUAAUACAUGCUUAAAAUUCCGUGUCCUGCGACCGGAACGUAUUUAUUAGAUAUUAGACCAAUCGCAGCAAUGUGAUUGAGAUGAAUCAAAGUAACUGAUCGGAUCGAGGUUUACCUCGAUAAAUCAUCUAAGUUUCUGCCCUAUCAGCUCUCGAUGGUAGUGUAUUGGACUACCAUGGCAGUCACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAACUACGGUUCGGCAGCAGGGAAGAAAAUUGGCCAAUCCUAAUUCAGGGAGCCAGUGACAAGAAAUAGCAAGCUGGGAAACUUACGUUUCUACGGCAUUGAAAUGAGAACAGUGUAAAUCUCUUAGCGAGGAACAAUUGGAGGGCAAGUCAUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUCUGUUCAGGUUCAUUUCGAUUCGUCGUGUGAAACUGGACAUACGUUUGCAAACUAAAAUCGGCCUUCACUGGUUCGACUUAGGGAGUAAACAUUUUACUGUGAAAAAAUUAGAGUGUUCCAGGCAGGUUUUAGCCCGAAUACAUUAGCAUGGAAUAAUGGAAUAGGACUAAGUCCAUUUUAUUGGUUCUUGGAUUUGGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUAGUCAGAGGUGAAAUUCUUGGAUUUAUUAAGGACUAACUAAUGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACUAUAAACUAUACCGACUCGGGAUCGGCUGGAAUAAAUGUCCAGUCGGCACCGUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGAAGUAUGGUACGCAAGUCUGAAACUUAAAGGAAUUGACGGAACAGCACACCAGAAGUGGAACCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACGAGCGCAAGACAGAGAAGGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGUCUGCUUGUAAAUAACAGGUUGUACUUCUUAGAGGGACUAUUGUGCAAUAAGCCAAUGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCCUAGACGUGCUCGGCCGCACGCGCGUUACAAUGACUGGCGCAAAAAGUAUUUCCUGUCCUGGGAAGGUACGGGUAAUCUUAUUAAUACCAGUCGUGUUAGGGAUAGUUCUUUGGAAUUGUGGAUCUUGAACGAGGAAUUUCUAGUAAGUGCAAGUCAUCAGCUUGCGUUGAUUAUGUCCCUGCCGUUUGUACACACCGCCCGUCGCUUGUAGUAACGAAUGGUCUGGUGAACCUUCUGGACUGCGACAGCAAUGUUGCGGAAAAAUAAGUAAACCCUACCAUUUGGAACAACAAGAAGUCGUAACAAGGUAUCUGUAGGUGAACCUGCAGAUGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq
new file mode 100644
index 0000000..627b884
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq
@@ -0,0 +1,2 @@
+>d.16.e.T.violacea.1
+CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGCUAACUUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAACACGCGGGGCAACCCGUGGUACCAAUUAGAUAUCAAGCCAACAUAUGGUGAUUCAUGAUUGUUUUUCUGAUCGCACGCGCAGUGCGACGCAUCGUUCAAGUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUCUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGCGGCCGGCGCUGUGCGCGUAAAUGCGUGCGGCGUUAAAGAAAAAAUUUAUUUUUUUUCGGGCGUGCUUUUGUGGAGGGCGACACGUGGUGGCUUGAUUGUUGCUGCGGGUCGGCGCCACUUUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGUCGUGAAUACGUUAGCAUGGGAAAAUGGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGAGCAUUACGAUGACUCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCUGUUACACAUGUUUGUGUAGCUCAGAAGCAAUAGAGGUUUUUUCUUUUCUUUUCUUUUCUUUCUUUUUUUCCUUUGAGCAAUUGAAGGGGGAGAGGUUUGAAAAAGGAAUGGAACGGAGACUCCUUACUCAUGUUGUUUUGUGCUCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUUUGGAUGCGCGAGAGCGUUUCCUAAUCCCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGAUUGCUGCGAUCGGAGUGUUUACGCUCUGGCCGCGGUGAAAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq
new file mode 100644
index 0000000..f847076
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq
@@ -0,0 +1,2 @@
+>d.16.e.U.gallina
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCUCGUUCGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUCUCGAUUGAAUCCGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGUGGGGUCUCGUGCCUCGUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq
new file mode 100644
index 0000000..8506647
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq
@@ -0,0 +1,2 @@
+>d.16.e.U.grandis
+AACCUGGUUGAUCCUGCCAGUAGUCAUACGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGAUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUCAAGGAAAGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUCGUGUCUAUUGUGAUGAUUCAUAAUAACUGAUCGAAUCGCAUAGUCUUUGGCUGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUGACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAGAAAUAACGGACUGAGCCUUUGGUUCAGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACCAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGGGGGUGACAAAGUCCGCUGAUGCGUGUGCUGCGUCGCCCCUUCAUCCUUCUGUUAACGUUUCUUGGUAUUCAGUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUUCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGGUCUCCUUUGUUGGUUUGAGGGACUCUAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGUGUGUAUUAUCCACCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUUAUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCAACGCAAUCUUAUUGCAUUUGACUUCUUAGAGGGACUUUGUGAUUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUGCAUACAGCGAGUACUUUCCAGCUCCGAGAGGCUGCUGGUAAUCAGCAAUAUGCAUCGUGCUUGGGAUUGAUCUUUGGAAUUAUAGAUCAUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUUCGGUGAACCUUUUGGACAGCGUUAGUUUCGGCUGAUGCUGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq
new file mode 100644
index 0000000..e4d1fb5
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq
@@ -0,0 +1,2 @@
+>d.16.e.U.maydis
+UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUACGCAAAUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGUUUCUUGCUACAUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCGUAAAAAGCCCCGACUUCUGGAAGGGGUGUAUUUAUUAGAUAAAAACCAUCCUCCUCGGAGUUUGGUGAUUCAUAAUAACUUCUCGAAUCGCACGGCCUUGUGCUGGCGAUGCUUCAUUCAAAUAUCUGCCCUAUCAACUGUCGAUGGUAGGAUAGAGGCCUACCAUGGUUGCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUGCAGGGCCCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACGAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAGUUUGGUCUCGGACGCUGGGUCUGCUUAAUUGCAUGUACUUGACGGUCCGAGACUUCCUUCUUGGUGAACGGCCGCCCUCGGGUGGUCCGGAACCAGGACUAUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCAUAGGCCCGAAUAUAUUAGCAUGGAAUAACAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGAACUGCCGUAAUGAUUAAAAGGGACAGCCGGGGGCAUUAGUAUUUGCACGCUAGAGGUGAAAUUCUUGGAUUGUGCAAAGACUUCCUACUGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAGGUUAGGGUAUCGAAAACGAUUAGAUACCGUUGUAGUCUUAACAGUAAACUAUGCCGACUCCGAAUCGGUCGAUGCUCAUUUCACUGGCUCGAUCGGCGCGGUACGAGAAAUCAAAGUUUUUGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACCGGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUGGCGCUUUCAUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUGACCUGCUAAAUAGACGGGUUGACAUUUUGUUGGCCCCUUAUGUCUUCUUAGAGGGACAAUCGACCGUCUAGGUGAUGGAGGCAAAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCCGGGCUGCACGCGCGCUACACUGACAGAGACAACGAGUGGAGCCCCUUGUCCGAAAUGACUGGGUAAACUUGUGAAACUUUGUCGUGCUGGGGAUGGAGCUUUGUAAUUUUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGGACUUGGGAGAGUACAUCGGGGAGCCAGCAAUGGCACCCUGACGGCUCAAACUCUUACAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUAUCUGUAGGUGAACCUGCAGAUGGAUCAUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq
new file mode 100644
index 0000000..7e0d307
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq
@@ -0,0 +1,2 @@
+>d.16.e.U.pisces
+AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAGGUUAUACAAUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAGGCUAUGCUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCAUGUUGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCUCGUUUUAUCAGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUCUCGAUUGGGAACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCCUUGGAAUUAUGGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGGGUGGCUUCGUGCCAACUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq
new file mode 100644
index 0000000..9cf06ee
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq
@@ -0,0 +1,2 @@
+>d.16.e.V.acridophagus
+CACCAGGUUGAUUCUGCCUGUUAUAUGUACUAGUGUCGAAGAUUUAGCCAUGCAUGCUUUACGAAUUCACAAGAAGAAGUGGCGGACAGCUCAGUAAUACAGUUAUAAUAUACUCUCUACUAAAGGAUAACCGCGGUAAGCUGCGGGUAAAACUUCAAGCUAUGUGUUUCAUGAAAGAAUUUAUAGUUCAGAGUGUUAGUUUCUGGCCUAUUAGUUAGUAGGUAAUGUAAGGGAUUACCUAGACUAUUAUGGGUAACGGGAGAUGAAUGUCUGAUACCGGAGAGGAAGCCUUAGAAACCGCUUUCACGUCCAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUCGUUUUUUAAGACGGAGGUAGUUAUGACACAUGUGAAUUAUUCACGAGGAAGAUCAAUAAAUCAGAUUUUUUUUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGUGCAUAUACAUGCUGUAGUUAGAAAGUUUGUAGCCGUAUAAGCUUGAAUCAGAGGAAAGGAGGACUCUUAAGGUAAACUUUAACUCUGGUCAAUGCUUAUAUUCGAAGCGGAUGGAGGCACUUGUAUUCAAUAGCGAGAGGUAAAAUUUGAUGACCUAUUGAGGACAAUCAGUAGCGAAAGCGAGUGUCUAGUACGCGUUUGAGGGUCAAGAACGUUAGCCGGAGGAUCGAAGAUGAUUAGAUACCGUUGUAGUUCCGGCCGUAAACCAUGCCUACUUGCCUUGUACAUAGUAUGAAGCAUAGAGAAAUUAAGAGUUUUUGGGCUCUAGGGAUAGUAAUCCGGCAACGGACAAACUUAAAGAAAUUGGCGGAAGGACACCACAAGGAGUGGAUUGUGCGGCUCAACUUGACUCAACACGGGAAAUCUUACCAGGGUCUGUAUAUGUGAGACUGUCCCAUUUAUGGUGGUACACGAUAAUAUACUGAGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACCUGUCAGGUUUAUUCCGGUAACGUGUGAGGUCACAGUAUUAAUAAGUAUUUUAAUAGACAGCUAAUGGUAAAUUAGAGGAAGUGUGACGAUAACAGGUCAGUGAUGCCCUUAGAUACCCUGGGCUGCACGCGCAAUACAUUGAGUAAGUCAUUUACAAUAGUAAUUUUGAAACUUACUCGCUACUGGGAUCAUCCUUUGUAAUUGGGAUGUGAACGUGGAAUUCCUAGUAAUCGUAGCUCACUAAGUUACGAUGAAUGUGUCCCUGUUCUUUGCACACACCGCCCGUCGCUAUCUAAGAUGGAUGUUGAUAUGAAAUUGCUGCUUGAAUGUGAGGUACUUGAGUAUUAACAACUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGAAGAAUCUGUGGCAAGAUCAUAC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq
new file mode 100644
index 0000000..b9bf68b
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq
@@ -0,0 +1,2 @@
+>d.16.e.V.corneae
+CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGUCUCUAAGAUUAAGCCAUGCAUGUUUCCUCAAUCAGGGACGAAUAGCUCAGUAAAACUGCGAUGAUUUAGUCUGGCUGUGUAGAUAACACGUGAAAAUGUAGCUAAGGGAAGGCAGAAUAAGACGCAGGACUAUCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACAGUGACGGUUGACGGGAAAUUAGGGUUUUGUACCGGAGAGGGAGCCUGAGAGAUUGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUCUUUGCAGGAGGCAGUUAUGAGACGUGAAGAUGAGUAUCUUGUAAAGAGGGAUAGGAGAAUUGGAGGGCAAGUUUGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGUAGUCAUAGAAGGGCAAAGAGAGAUGCGAGGUCUCACAGUGCGAUGAUGGAGGAGCCGAUGGGGAACAUAGUAUACCAGGGCGAGAGAUGAAAUGCCAAGACCCCUGGUGGACUGAGCGAGGCGAAGGCGAUGUUCUUGUAGGCAUUCGGUGAUCAAGGACGAAGGCUGGAGUAUCGAAAGUCAUUAGAUACCGCAGUAGUUCCAGCAGUAAAAGAUGCCGACAUGCUCAUUGGACACAGUGGGCAGGGAGAAAUCUUAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGGGUGAAAAUUAAAGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGAAACUUACCAGGGCCAAGUACUUGUGUAGAAACGAGCAAUACAGGAGUGGUGCAUGGUCGUUGGAAAUUGAUGGGAUGACUUUGACCUUAAAUGGUUGAAUGAGUGAGAUCUUUUGGACAUGUUCCGCACGGAACAGGAAGGAAAAGGCUAUAACAGAUCCGAGAUGCCCUCAGAUGCCCUGGGCUGCACGCGCAAUACAAUAGCAGGUAGAGAGAGAGACAGGAAGGUGCUCAGAUGGACUAUGUGCUGUAAGGCACAUACGAAAGAGGAAUUCCUAGUAAGUGUGUAUCAACAAUGGAUAUUGAAUAAGUCCCUGUAGCUUGUACACACCGCCCGUCACUAUCUCAGAUGUUUUUCAGGAUGAAGAGUCCAGGCUCUGAAUAAUGAAAAGUAGAUAAGAUGUAAGUCGUAACAAGGUUGCGGUUGGUGAACCAUUAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq
new file mode 100644
index 0000000..32ce19a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq
@@ -0,0 +1,2 @@
+>d.16.e.V.culicis
+CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGCAAGCGAAGCCGGUGGUGGAGCGGCGCAAGGCUCAGUAACGGGCGACUGAUUUGAUCUCCCGGUGUGGACAACCUCUAUAACCGGAGGCCAAAACACAGGAGGCGCGUGACACGGGCACGGGCGUGCAACCGGCAGGUGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGGAAAUUACCGAAGCCCGCGUUCGGGGCGGUAGUAAGGAGACGUGAAUACGAUGUGCAGGUAAAAUAUGCACUGGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGACGAUUGUUGCAGUUAAAGAGUUCGUAGUCGGGCUGCAUGACCGGCGCUGAAGGCUCCCUAUCGAGGGGGGCAGGGCGCCGGAAAAGCAGAGGAUGAGGAGCGGCCGGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAGCAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCGGUGCAGCCGCCACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGGGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGACAGCUUACCAGGCCCGACGGUCGCACGAGUGUGGUACACGAUAGGCCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCCGGCGCGCCGGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAUCAGUGCCCGAGCGGCAAUGGCGAUCGAGAGGGAACGAGCUCUGGAAGGGGCUCGGGAACGAGGAAUUGCUAGUAAUCGUGGGCUCAUUAAGACACGGUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGUAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq
new file mode 100644
index 0000000..ddad56b
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq
@@ -0,0 +1,2 @@
+>d.16.e.V.imperfecta
+CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUACUCUAAGAUUAACCCAUGCAUGUUAUUGAAUAUAAAGAAAAGACGAACAGCUCAGUAACUCUUAUUUGAUUUGAUGUAUUAGGACUCUAACUAUGUUAAAUUAUAGGUAACAAUAAUACAAUAAGAAUAAGAUCUAUCAGUUAGUUGUUAAGGUAAUGGCUUAACAAGACUAUGACGGAUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGAUUGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGAUAUUAUAUUGAGGCAGUUAUGAGUAGUAUUUUAUAAUUAUUGUAAUAUUGUAAGUACAUAUUACAAGAUAAAUCGGAGGGCAAAUCGAGUGCCAGCAGCCGCGGUAAUACUUGUUCCGAUAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCUGUAGUUUAUUUAUAAUAAGCAUUGUAAGGUAUACUGUAUGGUUAGGAGAGAGAUGAAAUGUGAUAACCCUAACUGGAUGAACAGAAGCGAAAGCUGUAUACUUAAAUGUAUUAUUAGAACAAGGACGUAAGCUAGAGGAUCGAAGAUGAUUAGAUACCAUUGUAGUUCUAGCAGUAAACUAUGUUGAAUCAUAGAUAUAUUUUGAUAUAUAUUUGUGUAGAGAAAUUAAGAUUAUAUUGACUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGUAAUUUACCAGGUAUAACAUGGUAUAAUAUUUUAUCAUGAUAGUGGUGCAUGGCCGUUUCCAAUGGAUGCUGUGAAGUAAUGAUUAAUUUCAACAAGAUGUGAGACCCUCAUUUAGACAGAUGUAGUGAUACAUAUGAAGGAGAGGAUUAAAACAGGUCCGUUAUGCCCUAAGAUAAUCUGGGUUGCACGCGCAAUACAAUAAUAUUUGAUAUUAUAAGGGAUAAUAUAAUGUAAGAUAUAUUUGAACAUGGAAUUGCUAGUAAAUUUUAUUUAAUAAGUAGAAUUGAAUGAGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGGUAUUAUCUAUGAACAAAUUUAUAAAGUGAAUAGAUAGUACUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAGCAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq
new file mode 100644
index 0000000..1ae37da
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq
@@ -0,0 +1,2 @@
+>d.16.e.V.necatrix
+CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUUCCCUAAGAUUAACCCAUGCAUGUUUUUGAUAUGGAAAAAUGGACUGCUCAGUAAUACUCACUUUAUUUAAUGUAUUAAAUUAGUAUAACUGCGUUAAAGUGUAGCAUAAGACAUAUACAGUAAGAGUGAGACCUAUCAGCUAGUUGUUAAGGUAAUGGCUUAACAAGGCAAUGACGGGUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGGAUUUUAUCUGAGGCAGUUAUGGGAAGUAAUAUUCUAUUGUUUCAUAUUGUAAAAGUAUAUGAGGUGAUUAAUUGGAGGGCAAAUCAAGUGCCAGCAGCCGCGGUAAUACUUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUUAUAUUUAAGAAGCAAUAUGAGGUGUACUGUAUAGUUGGGAGAGAGAUGAAAUGUGACGACCCUGACUGGACGAACAGAAGCGAAAGCUGUACACUUGUAUGUAUUUUUUGAACAAGGACGUAAGCUGGAGGAGCGAAGAUGAUUAGAUACCAUUGUAGUUCCAGCAGUAAACUAUGCCGACGAUGUGAUAUGAUAUUAAUUGUAUUAGAUGAUAGAAAUUUGAGUUUUUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCAGAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGUAACUUACCAAUAUUUUAUUCAGAGAAGAUUUUCGAUCUGAGAAUGAUAAUAGUGGUGCAUGGCCGUUUUCAAUGGAUGCUGUGAAGUUUUGAUUAAUUUCACCAAGACGUGAGACCCUUUUAUUAAUAGACAGACACAAUCAGUGUAGGAAGGAAAGGAUUAAAACAGGUCCGUUAUGCCCUCAGACAUUUUGGGCUGCACGCGCAAUACAAUAGAUAUAUAAUCUUUAUGGGAUAAUAUUUUGUAAGAGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAUUAAAUAAGUAGAAUUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGAUAUGUGUUGUGAAAUUAGUGAAAACUACUUGAACAAUAUGUAUUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq
new file mode 100644
index 0000000..ae6d794
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq
@@ -0,0 +1,2 @@
+>d.16.e.Vairimorpha.sp.C21
+CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUUCCCUAAGAUUAACCCAUGCAUGUUUUUGACAUUUGAAAAAUGGACUGCUCAGUAAUACUUACUUUAUUUAAUGUACAUUUGAAAAUAACUACGUUAAAGUGUAGAUAAGAUGUGUACAGUAAGAGUAAGACCUAUCAGCUAGUUGUUAAGGUAAUGGCUUAACAAGGCAGUGACGGGUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGGAUUUUUUCUGAGGCAGUUAUGGGAAGUAAUAUUAUAUUGUUUCAUAUUGUAAAAGUAUAUGAGGUGAUUAAUUGGAGGGCAAAUCAAGUGCCAGCAGCCGCGGUAAUACUUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUUAUGAUUAAGAAGCAAUAUGAGGUGUACUGUAUAGUUGGGAGAAAAAUGAAAUGUGACGACCCUGACUGGACGAACAGAAGCGAAAGCUGUACACUUGUAUGUAUUUUUUGAACAAGGACGUAAGCUGGAGGAGCGAAGAUGAUUAGAUACCAUUGUAGUUCCAGCAGUAAACUAUGCCAACGAUGUGAUAUGAUAUUAAUUGUAUUACAUGAUAGAAAUUUGAGUUUUUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGUAACUUACCAAUAUUUUAUUAUUCUGAGAUAAUUUUCCAAUUUGAGAAUGAUAAUAGUGGUGCAUGGCCGUUUUCAAUGGAUGCUGUGAAGUUUUGAUUAAUUUCAACAAGACGUGAGACCCUUUUUUAUAUAAGACAGACACAAUCAGUGUAGGAAGGAAAGGAUUAAAACAGGUCCGUUAUGCCCUCAGACAUUUUGGGCUGCACGCGCAAUACAAUAGAUAUAUAAUCUUUAUGGGAUAAUAUUUUGUAAGAGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAUUAAAUAAGUAGAAUUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGAUAUGUGUUAUGAAAAUAGUGAAAACUACUUGAACAAUAUGUAUUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq
new file mode 100644
index 0000000..780471c
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq
@@ -0,0 +1,2 @@
+>d.16.e.X.borealis
+UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCACGUGUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGAUCGCUCCAUCUGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGAGCGCUGACCCCCAGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGGGCCCCCGCGCCCCGGCCGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGUCCCCGUGACGGCGACGAUACAUUCGGAUGUCUGCCCUAUCAACUUUCGAUGGUACUUUCUGCGCCUACCAUGGUGACCACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACGCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACGAGGAUCUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAUCGAGCUGGCGGUCCGCCGCAAGGCGAGCUACCGCCUGUCCCAGCCCCUGCCUCUCGGCGCCUCCCCGAUGCUCUUGACUGAGUGUCCCGGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCCAAGCAGGCCGCGUCGCCUGGAUACUUCAGCUAGGAAUAAUGGAAUAGGACUCCGGUUCUAUUUUGUUGGUUUUCGGAACUGGGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGUGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGAACCAAAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUAGCGAUCCGGCGGCGUUAUUCCCAUGACCCGCCGAGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGAAAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCCUCCAUGCUAACUAGUUACGCGACCCCCGGCGGUCGGCGUCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACACGAGAUCGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGAACGGAUCAGCGUGUGUCUACCCUGCGCCGACAGGUGCGGGUAACCCGCUGAACCCCGUUCGUGAUAGGGAUCGGGGAUUGCAAUUAUUUCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUCGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGUCCUCGGAUCGGCCCCGCCGGGGUCGGCAACGGCCCUGGCGGAGCGCCGAGAAGACGAUCAAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq
new file mode 100644
index 0000000..ec9c5bb
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq
@@ -0,0 +1,2 @@
+>d.16.e.X.laevis
+UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCACGUGUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGAUCGCUCCAUCUGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGAGCGCUGACCCCCAGGGAUGCGUGCAUUUAUCAGACCAAAACCAAUCCGGGGCCCCCGCGCCCCGGCCGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGUCCCCGUGACGGCGACGAUACAUUCGGAUGUCUGCCCUAUCAACUUUCGAUGGUACUUUCUGCGCCUACCAUGGUGACCACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACGCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACGAGGAUCUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAUCGAGCUGGCGGUCCGCCGCGAGGCGAGCUACCGCCUGUCCCAGCCCCUGCCUCUCGGCGCCUCCCCGAUGCUCUUGACUGAGUGUCCCGGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCCAAGCAGGCCGCGUCGCCUGGAUACUUCAGCUAGGAAUAAUGGAAUAGGACUCCGGUUCUAUUUUGUUGGUUUUCGGAACUGGGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGUGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGAACCAAAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUAGCGAUCCGGCGGCGUUAUUCCCAUGACCCGCCGAGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGAAAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCCUCCAUGCUAACUAGUUACGCGACCCCCGGCGGUCGGCGUCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACACGAGAUCGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGAACGGAUCAGCGUGUGUCUACCCUGCGCCGACAGGUGCGGGUAACCCGCUGAACCCCGUUCGUGAUAGGGAUCGGGGAUUGCAAUUAUUUCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUCGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGUCCUCGGAUCGGCCCCGCCGGGGUCGGCCACGGCCCUGGCGGAGCGCCGAGAAGACGAUCAAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq
new file mode 100644
index 0000000..6dcff46
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq
@@ -0,0 +1,2 @@
+>d.16.e.Z.mays
+UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGCAAGUAUGAACUAAUUCGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCCGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCUGCCCGCCGAUCCGAUGAUUCAUGAUAACUUGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCGCGUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCCGGGCCGGGUGCCGCCGCCGUACGGGCAGAACCGACCGGCUCGACCCUUCUGCCGGCGAUGCGCUCCUGGCCUUAACUGGCCGGGUCGUGCCUCCGGGCCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGUGUUACUAAUAGGACCCCGCUGGCCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGUCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGUAGUUAGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCGCGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUCCAACGAGUAUAUAGCCUUGGCCGACAGGCCGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAGCUCGGCCGCACCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq
new file mode 100644
index 0000000..3994c56
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq
@@ -0,0 +1,2 @@
+>d.16.m.A.americana
+CAUAGGUUUGGUCCCAGCCUUCCUAUUGACUACUAAUAGACUUACACAUGCAAGCAUCCGCACCCCAGUGAAGACGCCCUUUAAAUCCACCUGAACCAAAAGGAGCUGGUAUCAAGCACACAUUUGUAGCUUAUGACGCCUUGCUCAGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAGCUAUGGACGAAAGUCUGACUAAGUCAUAUUGAUAAGGGUCGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCUAGUUAAUAGGAAUACGGCGUAAAGAGUGUUAAAGCAUCACACUAAAUAGAGUUAAAUUAUAACUAAGCUGUAAAAAGCCACAGCUGUAAUAAAAAUAGACAACGAAAGUGACUCUACAACCGCUGAUCACACUACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCAUAAACACAGGUAAUUGUAUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAAGGAACAAGAGUAAGCAUAAUAAUAGCACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGGGUUGGAAAGAAAUGGGCUACAUUUUCUAUUUCAAGAACACUCAACACGAAAGUUAUUAUGAAACUGAUGACUAAAGGAGGAUUUAGUAGUAAACUAAGAAUAGAGCGCUUAGUUGAAUUAGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAAACACGAUACACCUAAACUUAUUCACACGUAUUAACCGUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq
new file mode 100644
index 0000000..487d01e
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq
@@ -0,0 +1,2 @@
+>d.16.m.A.cahirinus
+AAUAGGUUUGGUCCUAGCCUUAUAAUUAGCUGAAAGUAAAAUUACACAUGCAAGACUCCCCACACCAGUGUCAAAUCCCUUAGAACUAGACAGCUAACCUAAGGAGAGGAUAUCAAGCACAUUAAUAUAGCUCAAGACAUCUCGCCAAGCCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCAAUGAACGAAAGUUUGACUUAGUUAUACUUCCAAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUUUUACGGCGUAAAAGGUGUUAUAUCUAAAACAAAUAGAAUUAAAACCUGACUUAUAUGUGAAAAUUCAUUGUCAGACAAAAACACAACCACGAAAGUGAUUCUAAUAAACCAAACACGAAAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUAAAUAAUUAAUAACAAAAUUAUUUGCCAGAGAACUACUAGCCAUAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAUACCCCGUUACACCUCACCACCCCUUGCUAAUCCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUCAAAAGGACACACAGUAAGCAAGAGCACAAACAUAAAAAAGUUAGGUCAAGGUGUAGCCCAUGAGGUGGGAAGUAAUGGGCUACAUUUUCUUAAAAAGAACACACGAAACCCUUUAUGAAAUUAAAGGAUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUGCGCACACACCGCCCGUCACCCUCCUCAAACUAAUCUUCAAGUAAAAUAAAUAAAAUUAAACUAACUAGAAUACGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq
new file mode 100644
index 0000000..eeb9896
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq
@@ -0,0 +1,2 @@
+>d.16.m.A.fulgens
+CAAAGGUUUGGUCCUAGCCUUCCCGUUAGUUCUUAAUAAAAUUACACAUGCAAGUAUCUACACCCCAGUGAAAAUGCCCUCCAAAUCACUAGUUGAUUAAAAGGAGCAGGUAUCAAGCACACUUUACAUAAGUAGCUCACAACACCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCUAUAAACGAAAGUUUGACUAAGUUAUAUUAAUAGAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUAACCCAAACUAACGGGCAUCCGGCGUAAAACGUGUUAAAGAAUCUACUCACAUUAAAGUUAAAACUUAAUCAGGCCGUAAAAAGCUACCGUUAACAUAAAAUACCUUACGAAAGUAACUUUAUUAAUUCUGAUUACACGACAGCUAAGGCCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAGUUUAGUAUAACAAAACUAUUCGCCAGAGAACUACUAGCAAUAGCCUAAAACUCAAAGGACUUGGCGGUGCUUUACACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUUACCACUUCUAGCUACUUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUCAAAAGGAAGCAAAGUAAGCAUAAUGAUUCCUGCAUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAAGUGGAAAGAAAUGGGCUACAUUUUCUAAACAAGAACACUAUACGAAAAUUUUUAUGAAAUUAAAACCUAAAGGUGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAGUUGAAUUGGGCUAUAAAGCACGCACACACCGCCCGUCACCCUCCUCAAACGUCAAGAUUUAAACCCAAUAUAUAAUCACAACAGACUAAACGCAAGAGGAGACAAGUCGUAACAAGGUAAGCGUACUGGAAGGUGUGCUUGGAUAAAC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq
new file mode 100644
index 0000000..2249b46
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq
@@ -0,0 +1,2 @@
+>d.16.m.B.brevicauda
+UAAAGGUUUGGUCCCAGCCUUCCUAUUAAUUGUUAGCAAAUUUACACAUGCAAGUAUCCGCGCCCCUGUGAGAAUACCCUUUAAAUCACCUAUGACUGAAAGGAGUAGGUAUCAAGCACACUUAUUUAUAAGUAGCUAAUCACACCUUGCUUAGCCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCCAUGAACGAAAGUUCGACUAAGUUAUGCUAAUAUUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGGUAGCGGCGUAAAGCGUGUUAAAGAACACUAAAUAAAAUAAAGAUAAAACUUGACUAGGCUGUAGAAAGCAACAGUCAAGACUAAAAUAAACUACGAAAGUGACUUUAUUACUUUUGAUCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUAGGUAAUUUAAUUAACAAAACUACUCGCCAGAGGACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCGCCCCUUGCUAAUACAGCUUAUAUACCGCCAUCUUCAGCAAACCCUUAAAAGGAAUAACAGUAAGCUUAAAUAUUUCACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGGCGGGAAGAAAUGGGCUACAUUUUCUAUAACUAGAAUAUUCACGAAAGUUUCUAUGAAACUAGAAACCAAAGGAGGAUUUAGUAGUAAGUUAAGAAUAGAGCGCUUAACUGAACCAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAUUUUAAGUCUACUGAUAUAUAAUCUCAGACUAACUAAUAUUAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACGAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq
new file mode 100644
index 0000000..f3a2a28
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq
@@ -0,0 +1,2 @@
+>d.16.m.B.taurus
+CAUAGGUUUGGUCCCAGCCUUCCUGUUAACUCUUAAUAAACUUACACAUGCAAGCAUCUACACCCCAGUGAGAAUGCCCUCUAGGUUAUUAAAACUAAGAGGAGCUGGCAUCAAGCACACACCCUGUAGCUCACGACGCCUUGCUUAACCACACCCCACGGGAAACAGCAGUGACAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGUUAUAUUAAUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAGCUAACAGGAGUACGGCGUAAAACGUGUUAAAGCACCAUACCAAAUAGGGUUAAAUUCUAACUAAGCUGUAAAAAGCCAUGAUUAAAAUAAAAAUAAAUGACGAAAGUGACCCUACAAUAGCCGACGCACUAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAGAUAAUUACAUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAAUUCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAAAAAAAGUAAGCGUAAUUAUGAUACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGAAAUGGGAAGAAAUGGGCUACAUUCUCUACACCAAGAGAAUCAAGCACGAAAGUUAUUAUGAAACCAAUAACCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAGAUUCAGUGCAUCUAACCCUAUUUAAACGCACUAGCUACAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq
new file mode 100644
index 0000000..ca47b03
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq
@@ -0,0 +1,2 @@
+>d.16.m.C.elegans
+UAAAGUUUUCUUUCAGGGAAUUAAAAUUUGAUCAUGGUUUAAGAUGAUUUAAAAUGGUAUUAUCUAAAUUUGAUUUACAGAGUAGGCAAUAAAAAUUUACCUCGGCAAUUUAUCGCUUGUAAAAUACUUGUUCCAGAAUAAUCGGCUAGACUUGUUAAAGCUUGUACUUUAAUUGAUGUUAAUUAUGAAAUUAUUAUAUUUUCUUUUAGAUCUAUGGUAGAAUUUGGAUUUAUAUUAGUGAAUUUUCAUAAUUUUAAGAUUUGUUGAACAAAGCAGAUUAGUACCUGGUUAGACAAAAAUUAAAAGAGCAGGAGUAAAGUUGUAUUUAAACUGAAAAGAUAUUGGCAGACAUUCUAAAUUAUCUUUGGAGGCUGAGUAGUAACUGAGAACCCUCAUUAACUACUUAAUUUUUUGACUCGUGUAUGAUCGUUUAUUUUAUUCUUAAGGAUUAUAAUAAAAAAUUUUUAAUUUAUUAAAAUAGAUAUAUACCCGGUUUAUGAUUUAAGAAACAUUUGGCCUACAAUAUUUUAUAUUAUGGAUUUUAGUUUUAGUUAACUAAAUGAAAUUGUAAAAGACAGUAAAAAAUUCUUAAUGUAUUUUUGAAGAUUAUCUAGAAGUGGUACAAAUCAUCCAUCAAUUGCCCAAAGGGGAGUAAGUUGUAGUAAAGUAGAUUUAGGGGAACCUGAAUCUAGUAAUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq
new file mode 100644
index 0000000..9bb815f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq
@@ -0,0 +1,2 @@
+>d.16.m.D.dugon
+UAAAGGUUUGGUCCUGGCCUUCUUAUUGGUUCUUAGCGAGCUUACACAUGCAAGUAUCCGCGCGCCAGUGAGAAUGCCCUUUAAAUCACUCCCGAUCAUAAAGGAGCAGGUAUCAAGCACACACUCAUGUAGCUCAUAACGCCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGAUAGAAAUUUAGCCAUAAACGAAAGUUUGACUAAGCUACGCUAUAUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAAUUAAUAAGUACCGGCGUAGAGCGUGUUUAGGAGAAGACCCAUAAAUAAAGUUAAAUCAGAUCCAAGCCGUAGAAAGCUAAAGAUCAGACAAAAAUAAUCCACGAAAGUGACUUUAUCAGCUCUGAACACACGAUAGCUAAGACACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCGAUAGCUUCCAACAAAGCUACCCGCCAGAGAACUACUAGCAAAAGCUUAAAACUCAAAGGACUUGACGGUGCUUCACAUCCCCCUAGAGGAGCCUGUCCCAUAAUCGAUAAACCCCGAUAAACCUCACCCCCACUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCCAACCCUUAAAAGGUGCAAAAGUAAGCUCAAUGAUAGCCAUAAAAAAGUUAGGUCAAGGUGUAGCCCAUGUGGAGGUCUAAGAUGGGCUACAUUUUCUCUUAGAGAACAAUCAACCAACGGACGUCACUAUGAAACAAGUGACCAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAACUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAUUCAUAACCAUUCCACCAUAUAUGAUCCUAAUAGCAUAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUACU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq
new file mode 100644
index 0000000..a39ca60
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq
@@ -0,0 +1,2 @@
+>d.16.m.D.geoffroii
+CAGAGGUUUGGUCCUGGCCUUACUGUUAAUUUUUAUUAGACCUACACAUGCAAGUUUCCGCAUCCCAGUGAGUAUGCCCUUUUAGCUUCACUGAAGUAUAAAGGAGCUGGUAUCAGGCACACUUAAUUAAGCAGCCCAUGACACCUUGUUUAACCACACCCCCACGGGUAACAGCAGUGACUAACAUUGAGCUAUAAACGAAAGUUUGACUAAAUCAUAAUAAAUAAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAACAGAAAAACGGCGUAAAGGGUGUUUAAGCAUAAACCUCAUAAAUAAAGUUAAAACUCAACUAUGCUGUAAUACGCCCUAGUUGGCAUUAAAAUAUACAACUUACGUGACUUUACUACUGCUGAAGACACUAAAGCUAAGGUACAAACUGGGAUUAGAGACCCCACUAUGCUUAGCCGUAAACCUAGGUAAUUAAAUAACAAAAUUACUCGCCAGAGAACUACUAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCCCUAGACCCUCCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCCCUUCUAGCUUAACAGUCUAUAUACCGCCAUCGUCAGCUCACCCCAAUAGGGCCCCAAAGUGAGCAAAAUCAUCUAAACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGCAAUGGGCUACAUUUUCUAUAUUAGAACAUAACGGAUUGUCUACUGAAAUAGAGGCAUGAAGGAGGAUUUAGUAGUAAAUUAAGAGUAGAGAGCUUAAUUGAAAUAGGCAAUAGGGUGCGUACACACCGCCCGUCACCCUCCUCGAUAAAGUAACCUUCAAUACCUAAUUAGAAUACGCUAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq
new file mode 100644
index 0000000..e7d211c
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq
@@ -0,0 +1,2 @@
+>d.16.m.D.novemcinctus
+CACAGGUCUGGUCCUAGCCUUACUAUUAAUUCAUAACAAAAUUACACAUGCAAGUAUCAGCACACCAGUGAGAAUGCCCUCUAACUCUUAUAGAUCAAAAGGAGCAAGCAUCAAGUACACACAGCCCUUACAGUAGCUCAUAACGCUUUGCUCAACCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCAAUAAGCGAAAGCUUGACUAAGUUAUGUUAUUAUAAGGGUUGGUAAAUUUCGUGCCAGCAACCGCGGUCAUACGAUUAACCCAAAUUAAUAGUUAUCGGCGUAAAGCGUGUUUAAGACACCUAGACAAUAGAGUUAAACCCUUACUACGCUGUAAAAAGCCUUAGUAGGACCAUAAACCCUUCAACGAAAGUGACUCUAAUUUAUCUGACUACACGAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACUAAAACAGUUCACAAACAAAACUGUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACAUCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAUACCUCACCACCCCUUGCUAAUACAGCCUAUAUACCGCCAUCUUCAGCAGACCCUAGUAAGGCACCACAGUGAGCACAAUAACAUACAUAAAGACGUUAGGUCAAGGUGUAGCUUAUGGGGUGGGAAGAAAUGGGCUACAUUUUCUAAUAAAGAGCAAAUACAAAAAACUUAAUGAAACAAUUUAAGACUAAGGUGGAUUUAGUAGUAAGCUAAAAAUAGAGAGUUUAGCUGAACCAGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCUUCAAUUAUAAGCGCCACAUAAACUAAAACACAUUAAUUCAGUAGCAACUAUAUAAGAAGAGACAAGUCGUAACAAGGUAAACAUACUGGAAAGUGUGUUUGGAUAAC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq
new file mode 100644
index 0000000..5620601
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq
@@ -0,0 +1,2 @@
+>d.16.m.D.virilis
+AUAAAGUUUUAUUUUGGCUUAAAAGUUUGUUAUUAAUUUGAUUUAUAUGUAAAUUUUUGUGUGAAUAUUUAAUAAUUUAAAAAAUUAUUAAAUUUAUUAUAAUCGCAGUAAUUAAUUUUAUUAGUUAAAGAAAUUUAGAAAUAGCAAUAUUAAAGAGUAUAGAUUAAAUUGGUGCCAGCAAUCGCGGUUACACCAAUUAUACAAAUGAAUUUUUUUAGUAAAAGUUAAAUUGGUUUAAUUUAAAUAUAAUUAAAUUUAUUAAGUGAAAUUUUAAAUUUAAAAUUUUUAUUAAGUGAAUAAUUGAAACUUGAAAAUUUUAAAUAAAAACUAGGAUUAGAUACCCUAUUAUUUAAAAUGUAAAUAUAAAUACUUAAGUAGUAAUAGUUAAGUUCUUGAAACUUAAAAAAUUUGGCGGUAUUUUAGUCUAUCCAGAGGAACCUGUUUUGUAAUCGAUAAUCCACGAUGGACCUUACUUAAGUUUGUAAUCAGUUUAUAUACCGUCGUUAUCAGAAUAUUUUAUAAGAAUAUUAAUAUUCAAUAAUUUUUAUUAAAAUUUAUAUCAGAUCAAGGUGUAGCUUAUAUUUAAGUAAUAAUGGGUUACAAUAAAUUUAUUUAAACGGAUAAAAUUAUGAAAAAAUUUUUGAAGGUGGAUUUGGUAGUAAAAUUAUAAAGAUUAAUAAUUUGAUUUUAGCUCUAAAAUAUGUACACAUCGCCCGUCGCUCUUAUUAUUAAGGUAAGAUAAGUCGUAACAUAGUAGAUGUACUGGAAAGUGUAUCUAGAAUGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq
new file mode 100644
index 0000000..52bb4a4
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq
@@ -0,0 +1,2 @@
+>d.16.m.E.rufescens
+CAAAGGUUUGGUCCUAGCCUUAUUAUUAGUUGUCAGUAAGAUUAUACAUGCAAGUAUCCGCCAACCAGUGAAAAUGCCCUCAUACUCGUCCACUACAAACGAUCCCAAAGGAGCCGAUAUCAAGCACACCCACGGUAGCUCAAGACAUCUUGCUCAGCCACACCCCCACGGGAUACAGCAGUAGUAAAAAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACUGAUUAGGGUUGGUCAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCAAAUUAAUGAUUAAACGGCGUAAAGUGUGGUUAAACACUUACCAAUGUAAAUAAAGUUAAACUAGCUCUCAGCUGUAAAAAGCUAAAGAUCUAUGGUAAAUAGACUAUUAAUGUAACUUUACUUAUAGUGAACCCACGAUAGCUAAGAUACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCGUAAACUUUGAUAAUUACUAACAAAAAUAUCCGCCAGAGAACUACAAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCCCUAGAGGAGCCUGUUGCAUAAUCGAUAAACCCCGAUAAACCCUACCAUCACUUGCUAAAUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAUAAGGAACAAUAGUAAGCUUAAACGCCCCCGCAAAAACGUUAGGUCAAGGUGUAACCUAUGUGAUGGAAAACAAUGGGCUACAUUUUCUACAUAAGAACACACGAACUCUUAUAUGAAAUUAUCAGAUAAAGGAGGAUUUAGAAGUAAGCCAGGAAUAGAGAGCCUGACUGAACUUGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUGUUUAAGACUAACAACCCUAUUACACUAAUACAAACAUAAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAGUAUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq
new file mode 100644
index 0000000..ec6581f
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq
@@ -0,0 +1,2 @@
+>d.16.m.G.gorilla
+AAUAGGUUUGGUCCUAGCCUUUCUAUUAACUCUUAGUAGGAUUACACAUGCAAGCAUCCCCGCCCCAGUGAGUCACCCUCUAAAUCACCACGAUCAAAAGGAACAAGCAUCAAGUACGCAGAAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCCAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGCCAAUAGAAAUCGGCGUAAAGAGUGUUUUAGAUCAAUCCCCCAAUAAAGCUAAAAUUCACCUGAGUUGUAAAAAACUCCAGCUGAUAUAAAAUAAACUACGAAAGUGGCUUUAAUAUAUCUGAACACACAAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACUUCAACAGUUAAAUUAACAAGACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCACAUCCUUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACGAAGGCCACAAAGUAAGCACAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACUUCAGAAAACUACGAUAACCCUUAUGAAACCUAAGGGUAGAAGGUGGAUUUAGCAGUAAACUAAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUCUAUAUAGAGGAGAUAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq
new file mode 100644
index 0000000..bb4f2d2
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq
@@ -0,0 +1,2 @@
+>d.16.m.H.amphibius
+UACAGGUUUGGUCCCAGCCUUUCUGUUAAUUUUUAAUAGAAUUACACAUGCAAGUAUCCACACCCCAGUGAGAAUGCCCUCUAAAUCACCCAGAUCAAAAGGAGCGGGUAUCAAGCACACCAUACACCGUAGCUCAAAACGCCCUGCUCAGCCACACCCCCACGGGAAACAGCAGUGACCAAAAUUAAGCCAUGAACGAAAGUUUGACUAAGCCAUAUUAACCAGAGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACUCAAACUAACAGAAAUACGGCGUAAAGCGUGUUAAAGAAUUAAAAGUACAAAUAAAGUUAAAUUCUAACUAAACUGUAAAAAGCCCUAACUAGAAUAAAAAUCUACUACAAAAGUGACUUUAACAAUACUGACCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAGAUAAUUCCAAAAACAAAACUAUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCAUACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUCCAGUCUAUAUACCGCCAUCUCCAGCAAACCCUAAAAAGGACUAAAAGUAAGCUCAACUAUUACACAUAAAGACGUUAGGUCAAGGUGUAACCUAUGGGCUGGGAAGAAAUGGGCUACAUUUUCUAGAACAAGAACACAACCCACCCGAACGAAAACUCCUAUGAAAGCUAGGAACUAAAGGAGGAUUUAGUAGUAAAUCAAGAGUAGAGUGCUUGAUUGAACAAGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAACACAAACCCAUAAACAUAAUAGCUAGACAAAACCAAAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACAAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq
new file mode 100644
index 0000000..5a42913
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq
@@ -0,0 +1,2 @@
+>d.16.m.H.auropunctatus
+CAAGGGUUUGGUCCUGGCCCUUCCAUUAGUUACUAAUAGGAUUACACAUGCAAGCCUCCGCAUCCCGGUGAAAAUGCCCUCUAAGUCAUAACUGACCUAAAGGAGCAGGUAUCAAGCACACAAAAUGUAGCUCAUAACGCCUUGCUCAGCCACACCCCCACGGGCUACAGCAGUGACAAAAAUUAAGCCAUGAAUGAAAGUUCGACUAAGCCAUAUUAAAUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUAACCCAGACUAAUAGACACACGGCGUAAAGCGUGUUCCAGAAACAACCUACCACUAAAGUUAAACCUUAACUAAGCCGUAAAAAGCCACAGUUAACAUGAAAAUACAACACGAAAGUAACUUUAAUACCCCAACUACACGACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAAUCUAGAUAGUUAACUUAACAAACCUAUCCGCCAGAGAACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACCUCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAAGGAAUAACAGUAAGCAAAAGUAUCUUAACAUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAGGUGGAAAGCAAUGGGCUACAUUUUCUACACAAGAACAUCUUACGAAAGUUUUUAUGAAAUCAAAAACUAAAGGAGGAUUUAGCAGUAAGCUGAGAAUAGAGCGCUCAGCUGAAUCGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUACACAAACCCAAACAUAACCUAUUAAAAUCACACUUAAUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUAAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq
new file mode 100644
index 0000000..d10d756
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq
@@ -0,0 +1,2 @@
+>d.16.m.H.lar.2
+AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCCCCUGGCAAGAUUACACAUGCAAGCAUCCCCGCCCCGGUGAAAUCGCCCUUCAAAUCACCCGUGAUCAAAAGGAGCAGGUAUCAAGCACGCAGUAAUGCAGCUCAAAACACCCUGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUGCCAACCCAGGGUUGGUCAACUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCCAGUUAAUAGAGCCCGGCGUAAAGAGUGUUUUAGAUUGCUCCCUAAUAAAGCUAAGCUCCAUCCAAGUCGUAAAAAACUCUGGCUGCUAUAAAAUAAACUACGAAAGUGGCUUUAACACCUCUGAAUACACAAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACUUCAACAGUCAAAUCAACAAGACUGCUCGCCAGAACACUACGAGCAACAGCUUAAAAAUCAAAGGACCUGGCGGUGCUUCACACCCCCCUAGAGGAGCCUGUCCUAUAAUCGAUAAACCCCGUUCAACCUCACCAUCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACAAAGGCUAUAAAGUAAGCACAAACACCCACAUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGAUGGGAAGAGAUGGGCUACAUUUUCUAUGCCAGAAAACCACGAUAACCCUCAUGAAACUUGAGCGGUCGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGUGCUUAGUUGAACAAGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGCAUAUUUCAAGGAACCCCUAACUAAAUACUCCACGCAUCUAUGUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAAC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq
new file mode 100644
index 0000000..88f8a65
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq
@@ -0,0 +1,2 @@
+>d.16.m.H.lar.geno
+AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCCCCUGGCAAGAUUACACAUGCAAGCAUCCCCGCCCCGGUGAAAUCGCCCUUCAAAUCACCCGUGAUCAAAAGGAGCAGGUAUCAAGCACGCAGUAAUGCAGCUCAAAACACCCUGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUGCCAACCCAGGGUUGGUCAACUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCCAGUUAAUAGAGCCCGGCGUAAAGAGUGUUUUAGAUUGCUCCCUAAUAAAGCUAAGCUCCAUCCAAGUCGUAAAAAACUCUGGCUGCUAUAAAAUAAACUACGAAAGUGGCUUUAACACCUCUGAAUACACAAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACUUCAACAGUCAAAUCAACAAGACUGCUCGCCAGAACACUACGAGCAACAGCUUAAAAAUCAAAGGACCUGGCGGUGCUUCACACCCCCCUAGAGGAGCCUGUCCUAUAAUCGAUAAACCCCGUUCAACCUCACCAUCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACAAAGGCUAUAAAGUAAGCACAAACACCCACAUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGAUGGGAAGAGAUGGGCUACAUUUUCUAUGCCAGAAAACCACGAUAACCCUCAUGAAACUUGAGCGGUCGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGUGCUUAGUUGAACAAGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGCAUAUUUCAAGGAACCCCUAACUAAAUACUCCACGCAUCUAUGUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAAC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq
new file mode 100644
index 0000000..6d7bbbc
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq
@@ -0,0 +1,2 @@
+>d.16.m.H.moschatus
+CAUAGGUUUGGUCCUGGCCCUACUGUUAAUUGUAAUUAGACCUACACAUGCAAGCUUCCACAAUCCGGUGAGAUAUGCCCUACAGAUUACUUACCAUAAUCGUUAAGGAGCGGGCAUCAGGCACACCACAGGUAGCCCAUCACGCCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGACUAAUAUUAAGCCAUAAACGAAAGUUUGACUAAAUCAUAAUUAAAUCAGGGUUGGUAAAUUUCGUGCCAGCCGCCGCGGUCAUACGAUUAACCCAAGUUAACAGAAAACCGGCGUAAAGCGUGUUUAAGCACAAACCUACAAAUAAAGCUAAGACGCAACUAAGCUGUAAUACGCUAUAGUCAACAUUAAAAUACACUACAAAAGUGGCUUUAAUACCGCUGAAGACACGACAGCUAAGACACAAACUGGGAUUAGAUACCCCACUAUGCUCAGCUUUAAACCAAGAUAAUUAAACAACAAAAUUAUUCGCCAGAGAACUACUAGCAAUCGCUUAAAACUCAAAGGACUUGGCGGUGUCCUAAACCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCACGAUACACCUCACCCCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCUGGCCCCAACACGGGUAAUAAAGCAGCAAGAUUACUCAACCGUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGCAAUGGGCUACAUUUUCUAAAUUAGAACAAACGAAUUAUCUUAUGAAACCUAAGACAUAUGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAACAGGCAAUAGGACGCGCACACACCGCCCGUCACCCUCCUCGAUAAAACUGGAUAAAUAACUAAUAACUCCGAGCACAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGAACAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq
new file mode 100644
index 0000000..790ca18
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq
@@ -0,0 +1,2 @@
+>d.16.m.H.sapiens.5
+AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGAACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAACCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACAGAAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUAAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq
new file mode 100644
index 0000000..7292f31
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq
@@ -0,0 +1,2 @@
+>d.16.m.H.sapiens.geno
+AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq
new file mode 100644
index 0000000..dfde3d8
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq
@@ -0,0 +1,2 @@
+>d.16.m.L.catta
+UAUAGGUUUGGUCCUGGCCUUACUAUUAGUUUACAGUAAGAUUACACAUGCAAGUAACCGCAUCCCAGUGAGAAUGCCCUCCAAAUCCCCUGAUUAAAAGGAGCAGGUAUCAAGCACACCAAUAGGUAGCUCACCACACCUUGCUAAACCACACCCCCACGGGAUACAGCAGUGAUUGAACUUAAGCAAUAAACGAAAGUUUGACUAAGCUAUACUGACACUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUAUUUCCCGGCGUAAAGUGUGUUUAAGAUUUAUAUAAAUAAAGUUAAUUUUUAUCCAAGCCGUAAAACGCCCCAGCUAAAACAAAACUAACCUACGAAAGUGACUUUAAUACUCUGAAGACACGACAACUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCGUAAACCUAAGUAAUUAACAAACAAAAUUACUCGCCAGAGCACUACAAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACUUCUUGCUAAUUCAACUUAUAUACCGCCAUCCCCAGCAAACCCUAUUAAGGCCCCAAAGUAAGCAAAAACACAUACAUAAAGACGUUAGGUCAAGGUGUAGUCAAUGAAGUGGAAAGAAAUGGGCUACAUUUUCUAAUAUUAGAACAACACCCCAACAGAAGCCUUUAUGAAACUAAAAGCCAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAUCACCAAUUAUUAAUUCACUAAUUCUACUAAACUCUAAACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAUUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq
new file mode 100644
index 0000000..5f34aee
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq
@@ -0,0 +1,2 @@
+>d.16.m.M.auratus
+AAAAGGUUUGGUCCUAGCCUUAUAGUUAGUUAGAGGUAGAGUUACACAUGCAAAUCUCUAUAAACCAGUGUCAAAUCCCUAGGUUUUACUUUAAACCCUAAGGAGAGGGUAUCAAGCACAUACACAUAUAUAGCUAAAGACACCUUGCCUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAAAUUAAGCCAUAAACGAAAGUUUGACUUAGUCAUACCUCAUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAACUAUUCUCCGGCGUAAAAUGUGUUUUUAUUACGAACAUAAUAGAAUUAAAACCCAACUAAUAUGUGAAAAUUCAUUGUUGGACUUAAAAUCAAUAACGAAAGUAAUUCUAAUUAUAUUAAUACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUAAGUGAUUAAAUAACAAAAUCACUUGCCUGAGAACUACUGGCCACAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUAUACCUUACCACCCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCUUAAAAAAGAACAAGAGUAAGCAAGAGAAUACCCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUGGGCUGGGAAGUAAUGGGCUACAUUUUCUUCUAAAGAACAGUUACGCUAUCCUCUAUGAAACUUAGAGGACAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUACGUACACACCGCCCGUCACCCUCCUCAAAUUAAGCUAACUGUUAACUAUACCUAAUAUUGACUCAUAAACUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq
new file mode 100644
index 0000000..1091d21
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq
@@ -0,0 +1,2 @@
+>d.16.m.M.musculus
+AAAGGUUUGGUCCUGGCCUUAUAAUUAAUUAGAGGUAAAAUUACACAUGCAAACCUCCAUAGACCGGUGUAAAAUCCCUUAAACAUUUACUUAAAAUUUAAGGAGAGGGUAUCAAGCACAUUAAAAUAGCUUAAGACACCUUGCCUUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAUAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACCUCUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUCUUCGGCGUAAAACGUGUCAACUAUAAAUAAAUAAAUAGAAUUAAAAUCCAACUUAUAUGUGAAAAUUCAUUGUUAGGACCUAAACUCAAUAACGAAAGUAAUUCUAGUCAUUUAUAAUACACGACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCAUAAACCUAAAUAAUUAAAUUUAACAAAACUAUUUGCCAGAGAACUACUAGCCAUAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGCUCUACCUCACCAUCUCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGUAUUAAAGUAAGCAAAAGAAUCAAACAUAAAAACGUUAGGUCAAGGUGUAGCCAAUGAAAUGGGAAGAAAUGGGCUACAUUUUCUUAUAAAAGAACAUUACUAUACCCUUUAUGAAACUAAAGGACUAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUUGAGCAAUGAAGUACGCACACACCGCCCGUCACCCUCCUCAAAUUAAAUUAAACUUAACAUAAUUAAUUUCUAGACAUCCGUUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq
new file mode 100644
index 0000000..276037b
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq
@@ -0,0 +1,2 @@
+>d.16.m.M.putorius
+CAAAGGUUUGGUCCUAGCCUUCCUAUUGAUUAUUAACAGAAUUACACAUGCAAGUCUCUACACCCCAGUGAGAAUGCCCUCCAAAUCUAUAUGUUGAUUAAAAGGAGCGGGUAUCAAGCACACUAAAUUAGUAGCUCAUAACGCCUUGCUCAACCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGCCAUGUUAACAAAGAGCUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAGCCCGAAUCAAUAGGCAAACGGCGUAAAACGUGUUAAGGAUUAUAUUAUAUUAAAGUUAAAAUUUGACAAGGCUGUAAAAAGCUACUGUUAAUAUAAGAUAAACCACGAAAGUGACUUUAUUACUUCCAUCAACACGAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACAUAAAUAAUUAUCACAACAAAAUUAUCUGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUCACCACUUCUAGCUUAAUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAGGGAAGAAAAGUAAGCACAAUAAUAUUACAUAAAAAAGUUAGGUCAAGGUGUAACCUAUGAAGUGGGAAGAAAUGGGCUACAUUUUCUAACCAAGAACACACUCACGAAAGUUUUUAUGAAAACUAAAAACUAAAGGUGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCCUCAAGCAACACACUCAAAUACUACAUAAUAAAAGUAAACCUAAAGCAAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGGUAAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq
new file mode 100644
index 0000000..c971496
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq
@@ -0,0 +1,2 @@
+>d.16.m.Manis.sp
+CAUAGGUUUGGUCCCAGCCUUUUUAUUAGUUUAUGAUAAAAUUACACAUGCAAGUAUCCGCCCUACGGUGAAAACGCCCUUUAGCCUUUACAAGUCAAAAGGAGCUGGUAUCAAGCACGCCAAUUUAAGGCAGCUAGUGACACCUUGCUUACGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAACCAUUAACGAAAGUUAGAUUUAGUUAUAUCAUUUAUGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCUAAUUAAUAAAAAACCGGCGUAAAAAGUGUCAAAGUGUAUUUAAAUCAAAUAAAAUUAAGCCCUAAUCAAGCUGUAAAAAGCCUCGAUUAUAGUAAAAAUAAACUAUGAAAAUAAUUUUAAUAAAACCCACACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCUUAAACCUAAAUAAUUAAUUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAAUAGCUUGAAACUCAAAGGACUUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUCCUAUAAACGAUAAACCCCGAUAAACCUCACCAAUCCUAGCUAAUGCAGCCUAUAUACCGCCAUCCUCAGCAAACCCUAAUAAAGGAACCAUAGUAAGCAAGAUCAUUGAAACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGAUUGGGAAGAGAUGGGCUACAUUUUCUAAAACAGAAUAAGACGAAUACCCUUAUGAAAAUAAGGGUUAAAGGAGGAUUUAGUAGUAAGACAAGAAUAGAGAGCUUGACUGAAUUAGGCCCUGAAGCACGCACACACCGCCCGUCACCCUCUUCAAAUUUCCAAAAAACAGUAAAUAUAUUAAUGAAUAACAAGAAUGAGAAGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAGGUGUGCUUGGAUAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq
new file mode 100644
index 0000000..4a5338a
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq
@@ -0,0 +1,2 @@
+>d.16.m.O.afer
+AUAAAGGUUUGGUCCUAGCCUUUCUAUUAGUUGACAGUAAAUUUAUACAUGCAAGUAUCUGCCUCCCAGUGAAAUAUGCCCUCUAAAUCCUUACCGGAUUAAAAGGAGCCGGUAUCAAGCUCACCUAGAGUAGCUCAUGACGCCUUGCUAAACCACGCCCCCACGGGAUACAGCAGUAAUAAAAAUUUAGCAAUGAACGAAAGUUUGACUAAGUUAUACUAUAACUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGUAAUACGGCGUAAAGCAUGAUUAGGGAAUAAUAUAAAUAAAGUUAAAUGUAAAUCAAAGCUGUAAAAAGCUCCUGAUUAACUUAAAAUAAAACACGAAAGUUACUUUACCACUCCUGAAUUCAUGAUAGCUAGGAUACAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCAUAAACUUAAAUAUUUCUCAACAAAAUUAUUCGCCAGAGAACUACAAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCAUCUAGAGGAGCCUGUUAUGUAAUCGAUAAACCCCGAUAUACCUCACCAUCACUUGCCAAUACAGCCUAUAUACCGCCAUCUUCAGCAAACCCUUACAAGGAAUAAUAGUAAGCCAAAUUAUUACCAUAAAAACGUUAGGUCAAGGUGUAGCCAAUGUGAUGGCAAUAAAUGGGCUACAUUUUCUAUUUUAAGAACAUAUCCCUACGAAAACCCAAAUGAAACCAAGGCUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAACUACUAGUAUUACUAAAAAUAUUUCACUACAUAAACGUACUAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq
new file mode 100644
index 0000000..fb058b0
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq
@@ -0,0 +1,2 @@
+>d.16.m.O.anatinus
+UAAAGGUUUGGUCCUAGCCUUACUGUUAGAUUUGAUUAGAUUUAUACAUGCAAGUAUCCGCAACCCAGUGAGAAUACCCUAAAAACUCUUAACAAGUUAGAAGGAGUAGAUAUCAGGCACACUAAAGUAGCCCACAACAUCUUGCCCUAGCCACACCCCCACGGGACACAGCAGUAAUAGAAAUUAGUCAAUAAACGCAAGUUUGAACAAGUCAUAAUCAAUAAGAGUCGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUGACUCAACCUAACAAAUAACGGUGUAAAACGUGUUUAAAAACUUAAACUAAUAAGAUUAAAGUAGAACUAAACUGUGAUAAGUCAUAGUUAAUACUAAAGCCAUCUACGAAAGUGAUCUUAGACUAAUUGAAUACACGAUAGCUAAGGUACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUCAAGUCGUUUAAUAACAAAACUACUCACCAGAGAACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCAUCUUUUGCCACUACUGUCUAUAUACCGCCAUCGUCAGCCAACCCUAAAAAGGAACAAAAGUAGGCGUAAUCAUUUUUCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUAAGAUGGAAGAAAUGGGCUACAUUUUCUACAUUAGAACAUACGAAAAACUCUAUGAAACUAGAGUAUUAAGGAGGAUUUAGUAGUAAGCCAAGAAUAGAGAGCUUGACUGAACUGGGCAAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAUCAAGCAACACAAACAUUCCUAAAAUCCCAACGCUUUUCAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACCGGAAGGUGUGCUUGGAAUAUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq
new file mode 100644
index 0000000..d11a7f6
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq
@@ -0,0 +1,2 @@
+>d.16.m.O.aries
+UAUAGGUUUGGUCCCAGCCUUCCUGUUAACUUUCAAUAGACUUAUACAUGCAAGCAUCCACGCCCCGGUGAGUAACGCCCUUCGAAUCACACAGGACUAAAAGGAGCAGGUAUCAAGCACACACUCUUGUAGCUCACAACGCCUUGCUUAACCACACCCCCACGGGAGACAGCAGUAACAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGUCAUAUUGACCAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCAAGCUAACAGGAGUACGGCGUAAAGCGUGUUAAAGCAUCAUACUAAAUAGAGUUAAAUUUUAAUUAAACUGUAAAAAGCCAUAAUUAUAACAAAAAUAAAUGACGAAAGUAACCCUACAAUAGCUGAUACACCAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAAAUAAUUAUAAAAACAAAAUUAUUCGCCAGAGUACUACCGCAACAGCCCGAAACUCAAAGGACUUGGCGGUGCUUUAUACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAAUCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAAGGGACAAAAGUAAGCUCAAUAAUAACACAUAAAGACGUUAGGUCAAGGUGUAACCUAUGGAGUGGGAAGAAAUGGGCUACAUUUUCUACCCAAGAAAAUUUAAUACGAAAGCCAUUAUGAAAUUAAUAGCCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUCAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAAAUAUGAUAUACUUAAACCUAUUUACAUAUAUCAACCACACGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq
new file mode 100644
index 0000000..018a895
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq
@@ -0,0 +1,2 @@
+>d.16.m.O.cuniculus
+UAAAGGUUUGGUCCUGGCCUUUUUAUUGUUUUGUAGCAACCUUACACAUGCAAGACUCCUCACGCCAGUGAGAAUGCCCUUAACAUCAAACUAGAUCAAGAGGAGCGGACAUUAAGCACACUAAUCAGUAGCUCAAGAUGCCUUGCUUAACCACACCCCCAAGGGAUACAGCAGUGAUAAAUAUUUAGCAAUGAACGUAAGUUUGACUAAGUUAUGCUACUUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAAAUAUCCGGCGUAAAGCGUGAUUAGAAUAAACAACAAAAUAAAAUCAAAUAACAACUAAGCUGUAGAAAGUAAUAGUUGCAAACAAAAAUAAACAACGAAAGUGAUUUUAUACUCUUCGAACUCACGAUAGCUAAGGCCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUUGAUAAUUUCAUAACAAAAUUAUUCGCCAGAGAACUACAAGCCAAAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCACCUAGAGGAGCCUGUUCCGUAAUCGAUAAACCCCGAUAAACCCUACCACUCUUUGCCAACUCAGCCUAUAUACCGCCAUCUUCAGCGAACCCUAAAAAGGAGCAAAAGUAAGCUCAAUUACCACCGUAAAAACGUUAGGUCAAGGUGUAGCCCAUAGAGUGGAGAGCAAUGGGCUACAUUUUCUACUUCAGAAUAUACGAAAGCCCUUAUGAAACUCUAAGGGCCAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGUGCUUAAUUGAACAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUGACAAAUAUUUACUUAUACCUAAUUACAUAAAUAGACAAGCAUAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACAUUU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq
new file mode 100644
index 0000000..bfc3821
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq
@@ -0,0 +1,2 @@
+>d.16.m.O.virginianus
+CAGAGGUUUGGUCCCAGCCUUCCUAUUAAUCCCUAGCAGACUUACACAUGCAAGUAUCCUCAUCCCAGUGAAAAUGCCCUCCAAGUCAAUAAAACUAAGAGGAGCUGGUAUCAAGCUCACACCCGUAGCUCAUGACGCCUUGCUCAGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAGCUAUAAACGAAAGUUUGACUAAGUCAUGCUAAUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAGUUAAUAGGCACACGGCGUAAAGCGUGUUUAAGCACUAUGCCAAAUAGAGUUAAACUCCAAUUAAGCUGUAAAAAGCCAUAAUCAAGACGAAAAUAAAUAACGAAAGUAACUUUACAACCGCUGAAACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAGUUAUAUAAACAAAACUAUUCGCCAGAGUACUACCGGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUUACCACCCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAACAAAAGUAAGCACAAUCAUUAUACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGGAGUGGAAAGAAAUGGGCUACAUUUUCUAAUCUAAGAAAACUCUUUACGAAAGUUACUAUGAAAUUAGUAACCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCUUCAAAUAGGCACAAUACACUUAAAUUUAAUUAUACGUAUUAAUCAUAUGAGAAGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq
new file mode 100644
index 0000000..d59ad6b
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq
@@ -0,0 +1,2 @@
+>d.16.m.P.cinereus
+UAAAGGUUUGAUCCUAGCCUUACUGUUAGUUUUAAUUAAACUUACACAUGCAAGUUUCCGCAACCCAGUGAGAAUGCCCCCAAAAUUUAUACACAAUUUAGCAGGAGCAGACAUCAGGUUCACUACAAAGUAGCCCAUAACGUCUUGUCCAACCACACCCCCACGGGAUACAGCAGUGAUUAACAUUAAGCUAUAAACGAAAGUUUGACUAAAUUAUAAUUAUCUAGGGCCGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUGACCCAAACUAACAGAUGUCGGCGUAAAGCGUGUACAAUCCAACAACCAAAAUAAGGCUAAAACUCAAUCAUGCUGUAAUACGCUAUAGCUAACAUUAAAAAAUGCAACCAAAGUGGCCUUAAUACUGACCAAAACACGACAGCUAAGACUCAAACUGGGAUUAGAUACCCCAUUAUGCUUUAGCGUAAACUUAGAUAGUUUAAUAACGAAACUAUUCGCCAGAGAACUACUAGCCAGCGCUUAAAACUCAAAGGACUUGACGGUGUCCUAAGCCCAUCUAGAGGAGCCUGUCCUAUAACCGAUGAACCCCGAUACACCCCACCUCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCCUACCCCAAUAGGGACCAAAAGUAAGCAAAAUCAUCAACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGAGGAAAGUGAUGGGCUACAUUUUCUAACAUAGAAAAUUACGGACUAUCUUAUGAAACCUAAGAUAUACGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAACAGGCAAUAGGACGCGUACACACCGCCCGUCACUCUCUUCAACAUAAACAAACCAAAUAACUAAUAAAAUAAAUAAAUAAAGAAGAGAAAAGUCGUAACAUGGUAAGUGUACCGGAAGGUGCACUUGGAUCAUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq
new file mode 100644
index 0000000..f347a38
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq
@@ -0,0 +1,2 @@
+>d.16.m.P.polycephalum
+GUUUUAAUAUAAUAAUGAGUUUGAUCCUGGCUCCGAGAGAAUGCUAGCAACUUACUUGAUACAUGCUAGUCGAACGCUUAUAUGAGCGUGGCGUACGAGCGACAAGGGCAAAGAUAGAAAAUACAUCAGUCAAGGGAAAUCCUAGAUUUAAAAGAUUAUAUCGCUGAAUGUAAGGUCUUUGUGAGAUUAGGUUGUUGGUAAGAUAAAAGCCUACCAAGCCGAUGAUCUCUAGCUGGUCUGAGAGGAUGUACAGCCGCGUCGGAAAUGCAAUAAGGUCCGGACUCCCUCGGGAGGCUGCAGUAGGGAAUCGUGAACAAUGUGCUAACGCUUGAUUCUAUAAUGUUGCGUGGGGGAUACAAAAAACAUUAUUUUAUACUUAUUGUUUUAUAAACAAAUUUAUAUAUAAAAUAGUGAUAAUUCUAGCAACGACUUAAGCGCAAUAAAAGUUUCCGUAAAAAGAGAUUUUUAUCUGUGUCUUCUGUAGCGUGCCUUUCUAGUAGACGGCAAGUUGUCUUAAACCCCUUUUUUUACGAUUAUAAUGACUGUAGUUAGUAUAUAUCUAUUUAUCAAGAUGAGGGUUGGUAAAUUACAUUUUGUUUGUUAGACUAAAAUACUCGAGCAAAAAUGCCUUAUGCUGCUUUGCUUAAAAAUAUCAAACCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAAACGGGGGGGGUUAGUGUUAUUCGUGAUGACUGGGCGUAAAGGGUACGUAGGCAGAUAAUUGAAAAUACAGUAAAAAACUGAGGUAAACCCUCUUCAUUCUGUAUUCACUCAUUAUCUUGAGUUCAGAAGGCGGUUUAUUGAAUUCUCGAAGGAAGGGUGAAAUCUGUUGAUAUCUGGAAGACAUUCGAUAGCGAAAGCAACAUCCGAUUCUGAUCUAACGCUCAGGUACUAAAGUAUGGGGAUCAAAUAGGAUUAGAGACCCUAGUAGUCCAUACCUUAAACAAUGAGUGUUCAACGUCUUUAAUAUAGUCAAUAUAUUUAGGGGGUUUAAAGCUAACGCGUGAAACACUCCGCCUGGGGAAUGUGGCCGCAAGGUCUAAACUCAAAGGAAUUGACGGUGACUUAUACAAGGGGUGGAGCAUGUGGUUUAAUUCGACAUACCGCGCAAAACCUUACCAAUUUUUGUAUCUGGUUUCUUUUCGUUAGCCAUUUAUUUGGUUAGCCUUCUUCUUUCUGUUGAAGGUCUACUACGAUAUCGAUUGAAGAUGUGGGUGUUUCUAUGCGUAAGCAUGAUCUAGCUAUUUUCAAUUAACGGUAACCAAUGACAAGAGCUGCAUGAUUGUCGUAAGUUCGUGCCGUGAGGUGUUGGGUUCAUUCCAUAAACGAACGCAACCCUUUUGAUUAGUUGCAUAAUGGAUGAAAGUUUAAACUGGAUAUCCAUGUUCACUAGUUCAACCAGCCCUUCUACCUUUAGGGAUUAAGGACAGGUCCACGUCAAAUCAUUAUGGCCUUAAUAGAUUGGGCUACACAUGUGCUACAUUGAUGAUCGACAACAAGAAGCAAUGGCGUGAGCCUGAGCAAAUCUUUAAAAGACAUUUCAGUCCGAAUUGUUCUUUGAAACUCAAGAGCAUGAAGCCGGAAUCUCUUGUAAUCGUGGAUCAUUACGCCACGGUGAAUUAGUACAAAAGUCACGUACAGACCGCCCGUCAUGCUAUGGAAACUAUUUGAAGUAGAAGUUACAAGGUUUCAAUUGUUUCGAUAGACCACCUUAUUGAAAGUUUUCAUAAGGCCUUGACAUUCUGUUGGCUUUGUACACGACUCUUUAUUUAGGGACUGGAGUAAAGUCGAAACAGGGUAGUGGUAGAAGAAUCUGCUGCUGGACCAUUAUUA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq
new file mode 100644
index 0000000..a016faf
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq
@@ -0,0 +1,2 @@
+>d.16.m.R.norvegicus
+AAAGGUUUGGUCCUGGCCUUAUAAUUAAUUGGAGGUAAGAUUACACAUGCAAACAUCCAUAAACCGGUGUAAAAUCCCUUAAAGAUUUGCCUAAAACUUAAGGAGAGGGCAUCAAGCACAUAAUAUAGCUCAAGACGCCUUGCCUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAUAUUAAGCAAUGAACGAAAGUUUGACUAAGCUAGUACCUCUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUUUUCGGCGUAAAACGUGCCAACUAUAAAUCUCAUAAUAGAAUUAAAAUCCAACUUAUAUGUGAAAAUUCAUUGUUAGGACCUAAGCCCAAUAACGAAAGUAAUUCUAAUCAUUUAUAUAAUGCACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUUAAUAAUUAAACCUACAAAAUUAUUUGCCAGAGAACUACUAGCUACAGCUUAAAACACAAAGGACUUGGCGGUACUUUAUAUCCGUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUCUACCUUACCCCUUCUCGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGCACUAAGUUAGCACAAGACAACAUAAAACGUUAGGUCAAGGUGUAGCCAAUGAAGCGGAAAGAAAUGGGCUACAUUUUCUUUUCCCAGAGAACAUUACGAAACCCUUAUGAAACUAAAGGACAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUACGCACACACCGCCCGUCACCCUCCUCAAAUUAGAUUGACAUUCACAUAUACAUAAUUUCACUAACAAAUUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq
new file mode 100644
index 0000000..1a6dfd1
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq
@@ -0,0 +1,2 @@
+>d.16.m.R.unicornis
+CAUAGGUUUGGUCCUAGCCUUUCUAUUAACUAUUAGUAAAAUUACACAUGCAAGUAUCCGCACUCCAGUGAGAAUGCCCUCUAAAUCACCCAUAACGAUUAAAAGGAGCAGGUAUCAAGUACACUAAUAACAGUAGCUAACAACACCUUGCUCAACCACACCCCCACGGGAGACAGCAGUGACAAAAAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACUAAGCAGAGCCGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUGACUCAAAUUAAUAGAACCUCGGCGUAAAGCGUGUCAAAGAUAUAACCCCUAAUAAAGUUAAAAACAUAGUUAAGCUGUAAAAAGCUAUAACCAAGAUAAAAUAAACCACGAAAGUGACUUUAAUAUAUCACCCACACUACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCCAAACUCAAAUAAUUCUUCCCAACAAAAUUAUUCGCCAGAGUACUACUAGCAACAGCCUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCCCUAGAGGAGCCUGUUCCAUAACCGAUAAACCCCGAUAAACCUUACCAGCCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCCAACCCUAAAAAGGAACCAAAGUAAGCACAAGUAUAAGACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGAUGGAGAGAAAUGGGCUACAUUUUCUACUUCAAGAACAACAACUACCCAAACGAAGGCUUUUAUGAAAUUAAAAGCUAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAACCAGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCCUUAAAUAUCAUAAACCACAACACAACAUAUUAACGUACGUUGAACAUAUAAAAGGAGACAAGUCGUAACAAGGUAAGUGUACUGGAAAGUGCGCUUGGAUAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq
new file mode 100644
index 0000000..ec9dd34
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq
@@ -0,0 +1,2 @@
+>d.16.m.S.aestuans
+UAUAGGUUUGGUCCUAGCCUUUUUAUUAAUUCUUAGUAGACUUACACAUGCAAGUAUCCCCGCCCCAGUGAGAAUGCCCUCUAUCUCCAUAAGGAUCUAAAGGUGCAGGUAUCAAGUACGCUCUCUCGAGCAGCUCAUGACACCUUGCUACACCACACCCCCACGGGACACAGCAGUGAUUAAAAUUGAGACAUAAACGAAAGUUUGACUGAGUUAUACUAAUAAUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCUAGUUAAUAAAACACGGCGUAAAGCGUGAUUAAGGAAUAACCCCAAAUAAGAUUAAGCUCUGACUAAGCUGUAAAAAGCCUUAGUUAAAAUAAAAAUUUAUAAACGAAAGUAAUCUUACAACCCCUGAAUUCACGAUAGCUAAGGCCCAAACCGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUACUCAAAUAACAAGAGUAUUCGCCAGAGAACUACUAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUAAACCUCACCACUCUUUGCAAUGUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAUAAGGUAUCGCAGUAAGCACAAGAAUUCUGCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUAGAGUGGGAAGAAAUGGGCUACAUUUUCUAAUUUCUUUAGAACAUUUCACGAUAGCUGUCAUGAAACAUGAUCAGCCCAAGGAGGAUUUAGUAGUAAGUUGGGAAUAGAGUGCCCAACUGAAUUGGGCAAUAAAGCACGCACACACCGCCCGUCACCCUCUUCAAGCAUCCAUGAUAACCCAUAUAAAUAAUACAAAAAUCUCCUAAUGCAAGAAGAGACAAGUCGUAACAAGGUAAACAUACUGGAAAGUGUGUUUGGAAUAUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq
new file mode 100644
index 0000000..e30ce56
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq
@@ -0,0 +1,2 @@
+>d.16.m.S.aquaticus
+UAAAAGGUUUGGUCCUGGCCUUUCUAUUAGCUGUCAGUAAAAUUACACAUGCAAGUAUCCGCGCCCCAGUGAAAAUGCCCUUGAAGUCAUCAUAGACAUAAAGGAGCCGGCAUCAAGUACACCAUAAUGGUAGCUAACGACGCCUUGCUUAGCCACGCCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCUAUGAACGAAAGUUUGACUAAGUUAUACUGAUAUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAAUAACCCAAGUUAAUAGAUACACGGCGUAAAGAGUGUUAAAGAACCUGGCAUUGUAAAUAAAGCUAAGACUUAACUAAGACGUAAAAAUCUCCAGUUAAAGUAAAAACAAACUACGAAAGUGGCUUUAUAUUAUUCUGAUCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUAAGACAAUCCAACUAACAAGAUUGUUCGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAGGGAGCCACAGUAAGCACAAGUAUAUACAUAAAAACGUUAGGUCAAGGUGUAGCUAAUGAGUUGGGAAGAAAUGGGCUACAUUUUCUAUAUCUAGAACACUUUAACGAAAGUCUUUAUGAAACGAAAGACUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGUGCUUAAUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUACUAAAGCCAGUCAAUAUACAUAAUAUAUAGGCAAUAAAUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUAAC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq
new file mode 100644
index 0000000..af65bac
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq
@@ -0,0 +1,2 @@
+>d.16.m.S.scrofa
+CACAGGUUUGGUCCUGGCCUUUCUAUUAAUUCUUAAUAAAAUUACACAUGCAAGUAUCCGCGCCCCGGUGAGAAUGCCCUCCAGAUCUUAAAGAUCAAAAGGAGCAGGUAUCAAGCACACCUAUAACGGUAGCUCAUAACGCCUUGCUCAACCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCCAUGAACGAAAGUUUGACUAAGUUAUAUUAAUUAGAGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGAUCCACGGCGUAAAGAGUGUUUAAGAAAAAAAAAUCACAAUAGAGUUAAAUUAUAACUAAGCUGUAAAAAGCCCUAGUUAAAAUAAAAUAACCCACGAAAGUGACUCUAAUAAUCCUGACACACGAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACCCAAAUAGUUACAUAACAAAACUAUUCGCCAGAGUACUACUCGCAACUGCCUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUUACCAACCCUUGCCAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAACAAUAGUAAGCACAAUCAUAGCACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGUUGGAAAGAAAUGGGCUACAUUUUCUACAUAAGAAUAUCCACCACACGAAAGUUUUUAUGAAACUAAAAACCAAAGGAGGAUUUAGCAGUAAAUCAAGAAUAGAGUGCUUGAUUGAAUAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGCAUGUAGUAAUAAAAAUAACCUAUAUUCAAUUACACAACCAUGCAAGAAGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUACC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq
new file mode 100644
index 0000000..5a2d1d3
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq
@@ -0,0 +1,2 @@
+>d.16.m.S.sinuspaulianus
+AAAAGAAAGAAUUUAAUUUUGGUUCCGAUUGAACGUUUUUCAGUAGUUUUAAGACAUGCAAAUCGUUAUUUCUGAAAGUAAAUUUUUAUUUAAAAUUAUAUAAAUAAUAACUAAAUAAAAAUGAUAAUAUGAAAUAAGGUGUAGAGGUGAGGAUAGUAAAUAAGAUACCCUGUAGUCUUCAUAGAUAGAAGAUAUUAUUCUAAGUAAAUUUUUUAAAUUUAUUACUAGUAUUUUUAAAUUAAUUUGCUUGCAUUAUAUAAAAUUAUAAUUGUUUUUCAUUAAUUGCAAAAAUUUAAAUAAAAAUGACUAAAGCAAAAAAAUUAUUUAAAUAACAAUAAUGUAAAAUAAAUGAAUAAAAUAAAAAAGCUAUUUUUAUUAAAAAAAGGAAAUUUUCUGCUAUAGGAUUCUAUUUAUUUUGAUUAGGUAGUUGGUAUGGGUAAAGGCCUACCAAGCCGACAAUCAAUAGCCAUGCUUGACAGAGCAGAUGGCCACAUUGGGAAUGAAAUCUCCCAAGUAGUUUUAUACUACCAGCAGUCAAGAAUAUUAGUCAAUGCUCGUAAGAGUGAACUAGCUAACUGAAAUCGCAAAUGUGUCAUUUGUGAUAAAGUAAGAGAAAAUUAUGAUAUUAUCUUACUACUAGUGCUGUCCAAAACUGGUGCCAGAAGACUCGGUAAGGCCAGAGGCGCAAACGUUAGUCGUCCUAAUCAGGCGUAAAGGGUUUGUAGGCUGCUUUGAAAGUCUUAUUAUUAUAAUAGCUAUUAAAUGAUAAGAUGAAUUGAAGCUAGAAUCUAAUAGAGGGUAAAACAAAUAAUAUUUAAAGUAAGGAUUAAAUCUCAAGAGUUUAGAUGGAAUACUAACGGUUAAAGCUUUUAUCUAUCUACAGAUUGACGCUGAGAAACGAAAGGGAGGUAAGGAAACAGGAUUAGAUACCCAACUACUGCUCCCUGUCAACGAUGAAUGGUGGUUGCUAGUUAUAACUACUUUAAGUAAAUAUUUUAUAUUAUAUAAGAUAAAAUAAGUAGUUAAAAUGACUGGUAGCGAUGCUAACGCGUUAACCAUUCCGCCUUGUGAGUACGACUGCAAAGUUGAAAACAAAAAAAUUAGUCGGUUUCGAAGCAAACGAAGUGAAGCAUGUUAUUUAAUACGAUAAUCCGCGUAAAAUCUUACCAGUUCUUGCAUACAAACUUUUUUUAUAAUAAUUUAAAUUAAAUUUUAAAUAGUUAUUUAAAAAGGAGUGUUUUUACUUUUUUAAAAAUACUUAGAUACAGGUGUUGCAUGGCUGUCGUCAGUCCGUGCUGUGAGAAGUUUGGUUAAAUCCGCUAACGGACAAAAUCCCUGUUGUUAAUUUAUACUUAACAAUUAAUGAUACUGAUAGAGCAUCAUUUGGGGCGAAGACAAGUCGUUAUGGCCCUCAUGAACUGGGCUAUAGACGUGCCACAAAGACUUUAACAAAGUGAAGCGAUACUGUUCCCUUAAUAUUUUUCUAAAGAAUUUUAUUAGAUUUAAUUAUAACAAUUAAAUUAUAGGGAAUUUAAGGAGGAGCUAAUCAUUAAAAAAAGUCAAACUAUUAAAUAUAGUCGGAUUGUCAUCUGAAACUCGGGGACAUGAAGAAGGAAUUUCGAGUAAUCGUUGAUCACUACGCAACGGUGAAGCUAGCAUUCGGAAUGAACUAACCGUCUGUCGCUGGGAAGGAGCUUAACUUGGUGGAAACUGGAAUGAAGUUUUAACUUUUACAAAAAUUAAAUUUUUAUUUAGUAUCUUUGAUAUUUUAUUUUUAAUUUAUUAGUUUUUUUUUCGUUAGAUUUUUUUUAAUUUAUUGCUUAAUUAAAAAGUAUUAUUUUUGUUUAAAGAAUAAAUACUUGUCUAACAAUGUUAAAUUUAAAACGAUUUUGUUAAGCAAAUUAGCUCUAGUUAAACCAAUUAAGUAACAUCUCAAAAGUCAUAGCAAGGUAGCCGUACUGGAAAGUGCUGCUGUAAAAUAAAACGA
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq
new file mode 100644
index 0000000..e00de33
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq
@@ -0,0 +1,2 @@
+>d.16.m.V.ursinus
+CAAAGGUUUGGUCCUAGCCUUACUGUUAAUUUUAAUUAAGCCUACACAUGCAAGUUUCCGCUGCCCAGUGAGAAUGCCCUCAAAAUUCUACAAUCGAAUCAACAGGAGCAGGUAUCAGGCACACCCAUCCCGGUAGCCCAUAACACCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGACUAACUUUAAGAUAUGAACGAAAGUUUGACUAAAUUAUAAUUAUACAGGGUUGGUAAAUUUCGUGCCAGCCGCCGCGGUCAUACGAUUAACCCAAAUUAACAGAACACCGGCGUAAAGCGUGUUUAAGCGCAAAUCUCAAAAUAAAGUUAAUACUUAACUAAACUGUAAUACGCCCUAGUUAACAUUAAAAUAAACAACUAAAGUGACUUUAAUUUCGCUGAAUACACGACAACUAAGACUCAAACUGGGAUUAGAUACCCCACUAUGCUUAGUCAUAAACCUAGGUAAUCCGAUAACAAAAUUAUUCGCCAGAGAACUACUAGCCACCGCUUAAAACUCAAAGGACUUGGCGGUGCUCUAAACCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCCCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCUCACCCCAAUAGGGAACAAAAGUGGGCAAAAUCAUUCACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGUAAUGGGCUACAUUUUCUAAAUUAGAAAACCAACGAACUAUCUCAUGAAACCCUGAGUCAUACGAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAAUAGGCAAUAGAGCGCGCACACACCGCCCGUCACCCUCCUCAACACAAACCGUCACAUUAACUAAUAAGUUAUCCAAAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAGGUGCACUUGGAGUAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq
new file mode 100644
index 0000000..dc25fe7
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq
@@ -0,0 +1,2 @@
+>d.16.m.X.laevis
+UAAAGGUUUGGUCCUAGCCUUAUUAUCAACUUUUUCUGAACUUACACAUGCAAGCAUCCGCACUCCCGUGAAAAUGCCCUUAAGCCUCUUAAACAGGGGAUAAGGAGCCGGUAUCAGGCACAACUAAUAGCCCAUGACACCUUGCUCUGCCACACCCACAAGGGAAUUCAGCAGUGAUAAACAUUGAACAUGAGCGACACAAAGCUCGAUUCAGUUACAGUAAAUAGAGUUGGUCAAUCUCGUGCCAGCCGCCGCGGUUAUACGAGAAACUCAAGUUGAUCAUUUUCGGCGUAAAGCGUGAUUAAAGUAACCCAAACUAGAGUCAAACUCCAACCAAGCUGUCGCCGCUUUCGUUGGUUUGAAGAACACUCACGAAAGUAACUCUACCCAUAUUACACUUGAACUCACGACCGCUAGGAAACAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCAUAAACUUUGACUACUUACGCAAAAAUCCGCCAGAACUACGAGCCUAAGCUUAAAACCCAAAGGACUUGGCGGUGCUCCAAACCCACCUAGAGGAGCCUGUUCUGUAAUCGAUACCCCUCGCUAAACCUCACCACUUCUUGCCAAACCCGCCUAUAUACCACCGUCGCCAGCCCACCUCGUGAGAGAUUCUUAGUAGGCUUAAUGAUUUUUCAUCAACACGUCAGGUCAAGGUGUAGCAUAUGAAGUGGGAAGAAAUGGGCUACAUUUUCUAUACCUUAGAAUAAACGCAAGAUCUCUAUGAAACCAGAUCGGAAGGCGGAUUUAGCAGUAAAGAGAAACAAGAGAGUUCUCUUUAAAACGGCCCUGGAGCGCGCACACACCGCCCGUCACCCUCUUCUACAAAAAUCAACCAAUUUUAUAAACACACAAUUAACACAAAGAAGAGGCAAGUCGUAACAUGGUAAGCACACCGGAAGGUGUGCUUGGAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq
new file mode 100644
index 0000000..47e7bd4
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq
@@ -0,0 +1,2 @@
+>d.16.m.Z.californianus
+CAAAGGUUUGGUCCUAGCCCUUCCGUUAGUUUUUAAUAAAAUUAUACAUGCAAGCUUCCACGCCCCAGUGAGAAUGCCCUUCAGAUCCCUACAGCCGAUCAAAAGGAGCGGGUAUCAAGCACACUCAACGAGUAGCUCACAACGCCUUGCUCAACCACACCCCCACGGGACACAGCAGUAAUAAAAAUUAAGCCAUGAACGAAAGUUCGACUAAGUUAUAUUAAUCAUAAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAACGGGCUCACGGCGUAAAGCGUGUAAAAGAUCUACCUACACUAAAGUUAAAAUUUAACCAAGCCGUAAAAAGCUGCCGUUAAUACAAAAUAUACUACGAAAGUGACUUUAAUAAUUCUGAUUACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAAUUCACUUAACAAAAUUAUCCGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCCCCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACCUCUUGCUAAUCCAGUCUAUAUACCGCCAUCCUCAGCAAACCCUUAAAAGGAAAGAAAGUAAGCAUAAUCAUCGCACGUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAGGUGGGAAGAAAUGGGCUACAUUUUCUAAACAAGAACACACCGUACGAAAGUUAUUAUGAAACUAAUAACUAAAGGUGGAUUUAGUAGUAAACUAAGAAUAGAGAGCUUAAUUGAACUGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAAUAACCUCAAAGCACAUACAUAAAUCAAUAUAAAACCAUAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq
new file mode 100644
index 0000000..10bd605
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq
@@ -0,0 +1,2 @@
+>d.16.m.Z.mays
+AAAAUCUGAGUUUGAUCCUGGCUCAGAAGGAACGCUAGCUAUAUGCUUAACACAUGCAAGUCGAACGUUGUUUUCGGGGAGCUGGGCAGAAGGAAAAGAGGCUCCUAGCUAAAGUUGUCUCGCCCUGCCUGCAGGGCGCGCGCAACGGCUUUGACCUAACGGCCUCCGUUUGCUGGAAUCGGAAUAGUUGAGAACAAAGUGGCGAACGGGUGCGUAACGCGUGGGAAUCUGCCGAACAGUUCGGGCCAAAUCCUGAAGAAAGCUCAAAAGCGCUGUUUGAUGAGCCUGCGUAGUAUUAGGUAGUUGGUCAGGUAAAGGCUGACCAAGCCAAUGAUGCUUAGCUGGUCUUUUCGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCGGACUCCCACGGGGGGCAGCAGUGGGGAAUCUUGGACAAUGGGCGAAAGCCCGAUCCAGCAAUAUCGCGUGAGUGAAGAAGGGCAAUGCCGCUUGUAAAGCUCUUUCGUCGAGUGCGCGAUCAUGACAGGACUCGAGGAAGAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGGGGGGGCAAGUGUUCUUCGGAAUGACUGGGCGUAAAGGGCACGUAGGCGGUGAAUCGGGUUGAAAGUGAAAGUCGCCAAAAAGUGGCGGAAUGCUCUCGAAACCAAUUCACUUGAGUGAGACAGAGGAGAGUGGAAUUUCGUGUGUAGGGGUGAAAUCCGUAGAUCUACGAAGGAACGCCAAAAGCGAAGGCAGCUCUCUGGGUCCCUACCGACGCUGGGGUGCGAAAGCAUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGAUGAGUGUUCGCCCUUGGUCUGUCUACGCUACGCUACGCGGAUCAGGGGCCCAGCUAACGCGUGAAACACUCCGCCUGGGGAGUACGGUCGCAAGACCGAAACUCAAAGGAAUUGACGGGGGCCUGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUACAACGCGCAAAACCUUACCAGCCCUUGACAUAUGAACAACAAAACCUGUCUUUAACGGGAUGGUACUUACUUUCAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUUGGUCAAGUCCUAUAACGAGCGAAACCCUCGUUUUGUGUUGCUGAGACAUGCGCCUAAGGAGAAAUAGCCGAGGAGCCGAGUGACGUGCCAGCGCUACUACUUGAUUGAGUGCCAGCACGUAGCUGUGCUUUCCGCAAGAAUUUCACCAUUGGGAGCCUCGAAGCACUUUCACGUGUGAACCGAAGUCGUCUUGCCGAACUCAAGACCCACGGAGACCUACCUAUAGUGACGUCAAAGUACCAGUGAGCAUGGAGGUUUGGUUAGGCUUGGUUACGACGACGUCGAGUUGGCGGCGGAGGAAGACUCGGCAUGAAGGCCAGCCGCCCGGUGGUGUGGUACGUAGUGGUAAUAGUACGCGCCCCGCUCCGAAACAAAGAAAAAGGUGCGUGCCGCACUCACGAGGGACUGCCAGUGAGAUACUGGAGGAAGGUGGGGAUGACGUCAAGUCCGCAUGGCCCUUAUGGGCUGGGCCACACACGUGCUACAAUGGCAAUGACAAUGGGAAGCAAGGCUGUAAGGCGGAGCGAAUCCGGAAAGAUUGCCUCAGUUCGGAUUGUUCUCUGCAACUCGGGAACAUGAAGUAGAAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUAUGUACCCGGGCCCUGUACACACCGCCCGUCACACCCUGGGAAUUGGUUUCGCCCGAAGCAUCGGACCAAUGAUCACCCAUGACUUCUGUGUACCACUAGUGCCACAAAGGCCUUUGGUGGUCUUAUUGGCGCAUACCACGGUGGGGUCUUCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGUGGCUGGAUUGAAUCCUUC
diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq
new file mode 100644
index 0000000..48e9291
--- /dev/null
+++ b/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq
@@ -0,0 +1,2 @@
+>d.16.y.C.paradoxa
+UACCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAAGAUCGCAAGAUCUUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUACCCUUAGGAGGGGGACAACAGUUGGAAACGACUGCUAAUACCCCAUAUGCCAUUCGUGGUGAAAAGAGUAAUCUGCCUGAGGAAGAGCUCGCGUCUGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAGGGAAGACGGCCUGUGGGUUGUAAACCUCUUUUCUUAGGGAAGAAUCAAUGACGGUACCUAAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCAUUGGGCGUAAAGAGUUCGUAGGUGGCUAAGCAAGUCUGUUGUUAAAGGCUGGGGCUUAACCCCAAAAAGGCAAUGGAAACUGUUUGGCUUGAGUACGGUAGGGGCAGAGGGAAUUCCUGGUGUAGCGGUGAAAUGCGUAGAUAUCAGGAAGAACACCGAUGGCGAAAGCACUCUGCUGGGCCGUUACUGACACUGAGGAACGAAAGCUAGGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGGUGUUGUGCGUAUCGACCCGUACAGUACCGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUGUCGCGAAUUUUCUUGAAAGAGAAAAGUGCCUUCGGGAACGCGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUUUUAGUUGCCAUCAUUCAGUUGGGCACUCUAAAGAGACUGCCGGUGACAAGCCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUAUACCCUGGGCUACACACGUACUACAAUGGUCGGGACAAUAGGUUGCCAACUUGCGAAAGUGAGCUAAUCCGUUAAACCCGGCCUCAGUUCAGAUUGCAGGCUGCAACUCGCCUGCAUGAAGGUGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGGAGUCGGCCAUGCCCGAAGUCGUUACCCUAACCAUUUCGGAGGGGGAUGCCUAAGGCAGGGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq
new file mode 100644
index 0000000..84b1c04
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq
@@ -0,0 +1,2 @@
+>d.5.a.D.mobilis
+ACGGUGCCCGACCCGGCCAUAGUGGCCGGGCAACACCCGGUCUCGUUUCGAACCCGGAAGUUAAGCCGGCCACGUCAGAACGGCCGUGAGGUCCGAGAGGCCUCGCAGCCGUUCUGAGCUGGGAUCGGGCACC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq
new file mode 100644
index 0000000..d202539
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq
@@ -0,0 +1,2 @@
+>d.5.a.H.marismortui
+UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCGGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAACCCGGUUCGCCGCCACC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq
new file mode 100644
index 0000000..1bfbb69
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq
@@ -0,0 +1,2 @@
+>d.5.a.H.mediterranei.1
+AUUAGGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCGCCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq
new file mode 100644
index 0000000..637ed19
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq
@@ -0,0 +1,2 @@
+>d.5.a.H.morrhuae.1
+UUAAGGCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUGGUUCGCCGCCUCCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq
new file mode 100644
index 0000000..1dd9dcf
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq
@@ -0,0 +1,2 @@
+>d.5.a.H.morrhuae.2
+UUAAGGCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUGGUUCGCCGCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq
new file mode 100644
index 0000000..dba1e06
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq
@@ -0,0 +1,2 @@
+>d.5.a.H.saccharovorum
+GGCAGCGGCCAUAGCGGUGGGGCGACACCCGUACCCAUUCCGAACACGGAAGUUAAGCCCACCAGCGUACCGGGAAGUACUGGAGUGAGCGAUCCUCUGGGAAGCGGGGUUCGCCGCCUGCCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq
new file mode 100644
index 0000000..13aca4b
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq
@@ -0,0 +1,2 @@
+>d.5.a.H.salinarum.1
+UUAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq
new file mode 100644
index 0000000..cd1707d
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq
@@ -0,0 +1,2 @@
+>d.5.a.H.salinarum.2
+UUAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq
new file mode 100644
index 0000000..149b7b4
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq
@@ -0,0 +1,2 @@
+>d.5.a.H.volcanii
+UUAAGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCACCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq
new file mode 100644
index 0000000..aa89660
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq
@@ -0,0 +1,2 @@
+>d.5.a.M.barkeri
+GGAGUUUGGCGCCAUAGCGGCAGUGUAACUCCUGUACCCAUCCCGAACACAGUAGAUAAGCCUGCCCGCGUUCCUUACUGUACUGAAGUGUGCGAGCCUUCGGGAACUCUGGAUCGCUGCCAUACUCACC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq
new file mode 100644
index 0000000..014e2e9
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq
@@ -0,0 +1,2 @@
+>d.5.a.M.fervidus
+GGGUACGGCGACCAUAGCGGGGGGGCCACACCUGAACCCGUUCCGAUCUCAGAAGUUAAGCCCCCCUGCGUUGGAGGUGGUACUGCAACGUUAGUUGCGGGAAGCCUCCAACGUCGCCGGCCCA
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq
new file mode 100644
index 0000000..0d9789e
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq
@@ -0,0 +1,2 @@
+>d.5.a.M.formicicum
+AGGUUGGCGGCCAUAGCGGAGGGGCCAUACCUGGUCUCGUUUCGAUCCCAGAAGUGAAGUCCUCCUGCGUUUUGUUGUUGUACUGUGGACGAGAGUCUAUGGGAAGCUCAUAACGCUGCCGGCCUC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq
new file mode 100644
index 0000000..173a5b8
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq
@@ -0,0 +1,2 @@
+>d.5.a.M.jannaschii.rrnA
+UGGUACGGCGGUCAUAGCGGGGGGGCCACACCCGAACCCAUCCCGAACUCGGAAGUUAAGCCCCCCAGCGAUGCCCCGAGUACUGCCAUCUGGCGGGAAAGGGGCGACGCCGCCGGCCAC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq
new file mode 100644
index 0000000..8df9051
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq
@@ -0,0 +1,2 @@
+>d.5.a.M.jannaschii.rrnB
+UGGUACGGCGGUCAUAGCGGGGGGGCCACACCCGAACCCAUCCCGAACUCGGAAGUUAAGCCCCCCAGCGAUGCCCCGAGUACUGCCAUCUGGCGGGAAAGGGGCGACACCGCCGGCCAC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq
new file mode 100644
index 0000000..ac65026
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq
@@ -0,0 +1,2 @@
+>d.5.a.M.thermautotrophicus.1
+GGGGCAUGGCGGUCAUGGCGCAGGGGUUAUACCUGAUCUCGUUUCGAUCUCAGUAGUUAAGUCCUGCUGCGUUGUGGGUGUGUACUGCGGUUUUUUGCUGUGGGAAGCCCACUUCACUGCCAGCCACU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq
new file mode 100644
index 0000000..2c27595
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq
@@ -0,0 +1,2 @@
+>d.5.a.M.thermolithotrophicus.2
+UGAUAUAACGGUCAUAGCGGAGGAGCCACAUCCGAUCCCGUCCCGAUCUCGGAAAUUAAGCCCUCCAGCGAUACCCUAAGUACUGCCAUUUGGUGGGAACAGGGUGACGCUGUUGAUCAC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq
new file mode 100644
index 0000000..bc9a31f
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq
@@ -0,0 +1,2 @@
+>d.5.a.M.tindarius.1
+GGAGUUUGGCGGCCAUAGCGGCGGGGCAAUUCCUGUACCCAUCCCGAACACAGAAGAUAAGCCCGCCUGCGUUCUAUACUGUACUAAAGUAUGAGAGUCUUUGGGAAAUAUGGAACGCUGCCAUCUCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq
new file mode 100644
index 0000000..2289727
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq
@@ -0,0 +1,2 @@
+>d.5.a.M.vacuolata
+GAUCUGGCAGCCAUAGCGGCAGGUGUAAUCCUGUACCCAUCCCGAACACAGUAGAUAAGCCUGCCCGCGUUCCUUGCCUGUACUGAAGUGUGCGAGCUUCGGGAACUCUGGAUCGUGCCAUAUCAGU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq
new file mode 100644
index 0000000..1e9fb96
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq
@@ -0,0 +1,2 @@
+>d.5.a.N.magadii
+UUAAGGCGGCCAUCGCGGCGGGGUUCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCUGCCUGCGUAUUGGUGAGUACUGGAGUGGGAGACCCUCUGGGAGAGCCGAUUCGCCGCCCCUACU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq
new file mode 100644
index 0000000..35940f9
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq
@@ -0,0 +1,2 @@
+>d.5.a.P.aerophilum
+GCCCCUAACCCGGCCAUAGGCGCCGGUGAUACGCCCGGUCUCAUCAGAACCCGGAAGCUAAGGCCGGCGCCGCGCUCGGGAGUACUGGGCUCCGCGAGGGCCCGGGAAACCGGCGUGCUGGGAGGGGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq
new file mode 100644
index 0000000..fe1e44d
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq
@@ -0,0 +1,2 @@
+>d.5.a.P.occultum
+UGGCCCGACCCGGCCAUAGCGGCCGGGCAACACCCGGACUCAUGUCGAACCCGGAAGUUAAGCCGGCCGCGUUGGGGGAUGCUGUGGGGUCCGCGAGGCCCCGCAGCGCCCCCAAGCCGGGAUCGGGCCG
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq
new file mode 100644
index 0000000..0db6b35
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq
@@ -0,0 +1,2 @@
+>d.5.a.P.woesei
+GGUACGGCGGUCAUAGCGGGGGGGCCACACCCGGUCUCAUUUCGAACCCGGAAGUUAAGCCCCCCAGCGAUCCCGGCUGUACUGCCCUCCGAGAGGGGGCGGGAACCGGGGACGCCGCCGGCCA
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq
new file mode 100644
index 0000000..5e79dbe
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq
@@ -0,0 +1,2 @@
+>d.5.a.S.solfataricus
+GCCCACCCGGUCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUAGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAUGGGUUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq
new file mode 100644
index 0000000..993246c
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq
@@ -0,0 +1,2 @@
+>d.5.a.Sulfolobus.sp.B12
+GCCCACCCGGCCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUGGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAUGGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq
new file mode 100644
index 0000000..a7dad6b
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq
@@ -0,0 +1,2 @@
+>d.5.a.T.acidophilum
+GGCAACGGUCAUAGCAGCAGGGAAACACCAGAUCCCAUUCCGAACUCGACGGUUAAGCCUGCUGCGUAUUGCGUUGUACUGUAUGCCGCGAGGGUACGGGAAGCGCAAUAUGCUGUUACCACU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq
new file mode 100644
index 0000000..91d9b16
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq
@@ -0,0 +1,2 @@
+>d.5.a.T.celer.1
+GGUACGGCGGUCAUAGCGGCGGGGUCACACCCGGUCUCGUUUCGACCCCGGAAGUUAAGCCCGCCAGCGAUCCCGGUUGUACUGCCCUCCGGGAGGGGGCGGGAAGCCGGGGACGCCGCCGGCCACU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq
new file mode 100644
index 0000000..758f2f3
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq
@@ -0,0 +1,2 @@
+>d.5.b.A.tumefaciens
+CGACCUGGUGGUCAUCGCGGGGCGGCUGCACCCGUUCCCUUUCCGAACACGGCCGUGAAACGCCCCAGCGCCAAUGGUACUUCGUCUCAAGACGCGGGAGAGUAGGUCGCUGCCAGGUCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq
new file mode 100644
index 0000000..42aafa3
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq
@@ -0,0 +1,2 @@
+>d.5.b.D.radiodurans.rrnB
+ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq
new file mode 100644
index 0000000..c43add3
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq
@@ -0,0 +1,2 @@
+>d.5.b.E.coli
+UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq
new file mode 100644
index 0000000..215d002
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq
@@ -0,0 +1,2 @@
+>d.5.b.G.stearothermophilus.2
+CCUAGUGGUGAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCCUCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGUCGCUGCUAGGC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq
new file mode 100644
index 0000000..c061b92
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq
@@ -0,0 +1,2 @@
+>d.5.b.G.stearothermophilus.3
+CCUAGUGACAAUAGCGAGAGAGGAAACACCCGUCUCCAUCCCGAACACGAAGGUUAAGCUCUCCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGUUGUCGCUAGGC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq
new file mode 100644
index 0000000..c3fb93d
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq
@@ -0,0 +1,2 @@
+>d.5.b.G.stearothermophilus.4
+CCUAGUGGUGAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCCUCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGCCGCUGCUAGGC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq
new file mode 100644
index 0000000..f3cf935
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq
@@ -0,0 +1,2 @@
+>d.5.b.M.genitalium
+UUUUGUUUGGUGCUAAUAUCGCUGUGGAAACACCUGGAACCAUCCCGAACCCAGCAGUUAAGCACAGUGGAGCUAAAUGUAGGUAGUAAUACUGAGAAUAGGUAAGCACCAAGCAAAA
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq
new file mode 100644
index 0000000..2eb8001
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq
@@ -0,0 +1,2 @@
+>d.5.e.A.aquaticus
+GUCAACGGCCAUACCACGUUGAAAGCACCGCUUCUCGUCCGAUCAGCAAAGUUAAGCAACGUUGGGUCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAACACCAGAUGCUGUUGACUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq
new file mode 100644
index 0000000..4691f30
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq
@@ -0,0 +1,2 @@
+>d.5.e.A.aurita.2
+GCCUACGACUAUACCACCAUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUUAAGUAUGGUAGGGCCGGGUCAGUACCUGGAUGGGUGACCGCCUGGGAACACCCGGUGUUGUAGGCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq
new file mode 100644
index 0000000..21ffcae
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq
@@ -0,0 +1,2 @@
+>d.5.e.A.domesticus
+GCCAACGUCCAUACCACGUUGAAAGCACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAGCGUCGGGCGCGGUUAGUACUUGGAUGGGUGACCGCCUGGGAACCCCGCGUGACGUUGGCAU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq
new file mode 100644
index 0000000..e343cc3
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq
@@ -0,0 +1,2 @@
+>d.5.e.A.equina
+GUCUACGGCCAUACCACCGGGAAAAUACCGGUUCUCGUCCGAUCACCGAAGUCAAGCCCGGUAGGGCCAGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCUGGUGCUGUAGACUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq
new file mode 100644
index 0000000..0b3da01
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq
@@ -0,0 +1,2 @@
+>d.5.e.A.immersus.1
+ACAUACGGCCAUAGAUUGAAGAAUAUACGGGAUCCCGUCCGCUCUCCCAUAGUCAAGCUUCUAAUCGCCAAGUUAGUACUGCGGUGGGUGACCACGCGGGAAUCCUUGGUGCUGUAUGU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq
new file mode 100644
index 0000000..336539c
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq
@@ -0,0 +1,2 @@
+>d.5.e.A.magnoliae
+GGCAACGACCAUACCACGUUGAAUACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCGUAGUUAGUACUUGGAUGGGUGACCGCUUGGGAACACUACGUGCCGUUGGCAU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq
new file mode 100644
index 0000000..8b924c3
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq
@@ -0,0 +1,2 @@
+>d.5.e.A.pernyi
+GACAACGUCCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGGGCGCGGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACCGCGUGACGUUGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq
new file mode 100644
index 0000000..bd70eab
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq
@@ -0,0 +1,2 @@
+>d.5.e.A.salina
+ACCAACGGCCAUACCACGUUGAAAGUACCCAGUCUCGUCAGAUCCUGGAAGUCACACAACGUCGGGCCCGGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACCGGGUGCUGUUGGCAU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq
new file mode 100644
index 0000000..311e3c2
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq
@@ -0,0 +1,2 @@
+>d.5.e.A.tabira
+GCUUACAGCCAUACUGUCCUGAGCACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGACAAGGCCUGGUUAGUACUUGGAUGGGAGACUGCCUGGGAAUACCAGGUGCUGUAAGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq
new file mode 100644
index 0000000..b3d1240
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq
@@ -0,0 +1,2 @@
+>d.5.e.B.napus
+GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq
new file mode 100644
index 0000000..c94dd69
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq
@@ -0,0 +1,2 @@
+>d.5.e.B.neritina
+GUUUACGGCCAUAUCACGUUGAAAACGCCAGUUCUCGUCCGAUCACUGAAGCUAAGCAACGUCGAGCCUGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCAGGUGCUGUAGACUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq
new file mode 100644
index 0000000..0f615ff
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq
@@ -0,0 +1,2 @@
+>d.5.e.B.taurus
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq
new file mode 100644
index 0000000..7d2da47
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq
@@ -0,0 +1,2 @@
+>d.5.e.B.vorax
+GUUAUCGGCCAUACUAAGCCAAAAGCACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGGCUUAAGGCAUGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGCCCAUGUGCUGAUAGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq
new file mode 100644
index 0000000..a05bd88
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq
@@ -0,0 +1,2 @@
+>d.5.e.B.vulgaris
+GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq
new file mode 100644
index 0000000..32ee26d
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq
@@ -0,0 +1,2 @@
+>d.5.e.C.carpio
+GCUUACGGCCAUACCACCCUGAGCACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAAGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq
new file mode 100644
index 0000000..91c3d86
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq
@@ -0,0 +1,2 @@
+>d.5.e.C.elegans.1
+GCUUACGACCAUAUCACGUUGAAUGCACGCCAUCCCGUCCGAUCUGGCAAGUUAAGCAACGUUGAGUCCAGUUAGUACUUGGAUCGGAGACGGCCUGGGAAUCCUGGAUGUUGUAAGCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq
new file mode 100644
index 0000000..4a4584e
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq
@@ -0,0 +1,2 @@
+>d.5.e.C.elegans.2
+GCUUACGACCAUAUCACGUUGAAUGCACGCCAUCCCGUCCGAUCUGGCAAGUUAAGCAACGUUGAGUCCAGUUAGUACUUGGAUCGGAGACGGCCUGGGAAUCCUGGAUGUUGUAAGCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq
new file mode 100644
index 0000000..4eef3e3
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq
@@ -0,0 +1,2 @@
+>d.5.e.C.quinquecirrha
+GCCUACGACCAUACCACCAUGAGUAUACCGGUUCUCGUCCGAUCACCGGAGUCAAGCAUGGUCGGGCCGGGUCAGUACCUGGAUGGGUGACCGCCUGGGAACACCUGGUGUUGUAGGCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq
new file mode 100644
index 0000000..0a9db8c
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq
@@ -0,0 +1,2 @@
+>d.5.e.C.revoluta
+GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGUUGGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUAAUAUUGCACCCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq
new file mode 100644
index 0000000..b9bba74
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq
@@ -0,0 +1,2 @@
+>d.5.e.C.vicina
+GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCAU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq
new file mode 100644
index 0000000..fe798c7
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq
@@ -0,0 +1,2 @@
+>d.5.e.D.mauritiana
+GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq
new file mode 100644
index 0000000..2a8d663
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq
@@ -0,0 +1,2 @@
+>d.5.e.D.melanogaster.1
+GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGCGGGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq
new file mode 100644
index 0000000..05ba8f8
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq
@@ -0,0 +1,2 @@
+>d.5.e.D.melanogaster.2
+GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGAGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCUCGUCCACAACUUUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq
new file mode 100644
index 0000000..e715502
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq
@@ -0,0 +1,2 @@
+>d.5.e.E.eurystomus
+GCUAUCGGCCAUACUAAGCCAAAUGCACCGGAUCCCUUCCGAACUCCGAAGUUAAGCGGUUUAAGGCCUGUUAAGUACUGAGGUGGGGGACCACUCGGGAACUUCAGGUGCUGAUAGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq
new file mode 100644
index 0000000..c73a6b7
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq
@@ -0,0 +1,2 @@
+>d.5.e.E.gracilis.1
+GAGUACGGCCAUACUACCGGGAAUACACCUGAACCCGUUCGAUUUCAGAAGUUAAGCCGGGUUAGGCCCAGUUAGUACUGAGUGGGCGACCACUUGGGAACACUGGGUGCUGUACGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq
new file mode 100644
index 0000000..895e4e4
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq
@@ -0,0 +1,2 @@
+>d.5.e.E.gracilis.2
+GGCGUACGGCCAUACUACCGGGAAUACACCUGAACCCGUUCGAUUUCAGAAGUUAAGCCUGGUCAGGCCCAGUUAGUACUGAGGUGGGCGACCACUUGGGAACACUGGGUGCUGUACGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq
new file mode 100644
index 0000000..33c38fc
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq
@@ -0,0 +1,2 @@
+>d.5.e.E.kokanica
+GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq
new file mode 100644
index 0000000..2b22082
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq
@@ -0,0 +1,2 @@
+>d.5.e.E.woodruffi
+GCUAUCGGCCAUACUAAGCCAAAUGCACCGGAUCCCAUCCGAACUCCGAAGUUAAGCGGUUUAAGGCCUGUUAAGUACUGAGGUGGGGGACCACUCGGGAACUUCAGGUGCUGAUAGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq
new file mode 100644
index 0000000..946b73c
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq
@@ -0,0 +1,2 @@
+>d.5.e.F.hygrometrica
+UGAUGCGGUCAUACCAAGGCUACUACACCAGAUCCCAUCAGAACUCUGAAGUUAAGCGCCUUUGGGCCGGAAUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCCGGUGCUGCAUCCAC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq
new file mode 100644
index 0000000..30eaebf
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq
@@ -0,0 +1,2 @@
+>d.5.e.F.neoformans.1
+AUCCACGGCCAUAGCCUUCAUAGAGCACCCUGCCCCGUCCGAUCCAGGAAGUUAAGCUGAACAGCGCUCGGUUAGUACCACGGUGGGGGACCACGUGGGAAUCCCGGGUGCCGUGGUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq
new file mode 100644
index 0000000..7b952b0
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq
@@ -0,0 +1,2 @@
+>d.5.e.G.arboreum
+GGGUGCGAUCAUACCAGCACUAAACCACCGGAUUCCAUCAGUGCUCCCCAGUUAAGCGUGCUUGGCCGAGAGUAGAACUAGGGUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq
new file mode 100644
index 0000000..cb7eb79
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq
@@ -0,0 +1,2 @@
+>d.5.e.G.biloba
+GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCACGCUUGGGCUGGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCCAGUGUUGCACCCUC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq
new file mode 100644
index 0000000..178c783
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq
@@ -0,0 +1,2 @@
+>d.5.e.G.gnemon
+GGGUGCGAUAAUACCACCGCUAACGUAUCGGAUCCGAUCAGAACUCCGUAAUUAAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCUCGGGAAGUCCUAGUGUUGCACCCAC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq
new file mode 100644
index 0000000..1d478a3
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq
@@ -0,0 +1,2 @@
+>d.5.e.G.riobambae
+GCCUACGGCCACACCACCCUGAACACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq
new file mode 100644
index 0000000..f67da34
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq
@@ -0,0 +1,2 @@
+>d.5.e.H.japonica
+GUCUACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGGGCCUGCCCAGUACUUGGAUGGGUGACCGCCUGGGAACAGCAGGUGUUGUAGACUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq
new file mode 100644
index 0000000..49bf2a1
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq
@@ -0,0 +1,2 @@
+>d.5.e.H.oculata
+GCCUGCGGCCAUACCACGUUGAAUGCACCGGUUCCCAUCUGAACACCGAAGUUAAGCAACGUCGGGCCAGCUUAGUACCUGGAUGGGUGACCGCCUGGGAAUCGCUGGUGCUGCAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq
new file mode 100644
index 0000000..55c19b9
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq
@@ -0,0 +1,2 @@
+>d.5.e.H.sanguinea
+GUCUACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGGGCCUGCCCAGUACUUGGAUGGGUGACCGCCUGGGAACAGCAGGUGUUGUAGACUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq
new file mode 100644
index 0000000..517c965
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq
@@ -0,0 +1,2 @@
+>d.5.e.H.sapiens.1
+AUCUAUGGCUGUACCGCUCUGAACGUGCACUAUCUCUUCUGAUCUCAAAAGCUAAGCAGGGUCAGGCCUGGUUAGUACUGGAAUGGGAGACCACAUGGGAAAACUGGGUGCUGUAGGCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq
new file mode 100644
index 0000000..1b449fa
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq
@@ -0,0 +1,2 @@
+>d.5.e.H.sapiens.2
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq
new file mode 100644
index 0000000..d82f578
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq
@@ -0,0 +1,2 @@
+>d.5.e.H.sapiens.3
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq
new file mode 100644
index 0000000..fdcdc80
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq
@@ -0,0 +1,2 @@
+>d.5.e.H.sapiens.4
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq
new file mode 100644
index 0000000..627f910
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq
@@ -0,0 +1,2 @@
+>d.5.e.H.sapiens.5
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq
new file mode 100644
index 0000000..01812e1
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq
@@ -0,0 +1,2 @@
+>d.5.e.H.sapiens.6
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq
new file mode 100644
index 0000000..a8577d9
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq
@@ -0,0 +1,2 @@
+>d.5.e.Hemicentrotus.sp
+GUUUACGACCAUACCAUGCUGAAUAUACCGGUUCUCGUCCGAUCACCGAAGUCAAGCAGCAUAGGGCCCGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGUUGUAGGCAU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq
new file mode 100644
index 0000000..fb02dc3
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq
@@ -0,0 +1,2 @@
+>d.5.e.I.iguana
+GCCUACGGCCAUACCACCCUGAACACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq
new file mode 100644
index 0000000..39aa1e2
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq
@@ -0,0 +1,2 @@
+>d.5.e.I.illecebrosus
+GCUUACGGCCAUAUCACGCUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGAGCCUAGUCAGUACUUGGAUGGGUGACCGCCUGGGAAUACUAGGUGCUGUAAGCAU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq
new file mode 100644
index 0000000..9a40744
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq
@@ -0,0 +1,2 @@
+>d.5.e.L.decidua
+GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCACGCUUGGGCUAGAGUAGUGCUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq
new file mode 100644
index 0000000..2d9f606
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq
@@ -0,0 +1,2 @@
+>d.5.e.L.edodes
+AUCCACGGCCAUAGGACUCUGAAAGAACCGCAUCCCGUCUGAUCUGCGCAGUUAACCAGAGUGCCGCCUAGUUAGUACCACGGUGGGGGACCACGCGGGAAUCCUAGGUGCUGUAGUUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq
new file mode 100644
index 0000000..73c1db0
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq
@@ -0,0 +1,2 @@
+>d.5.e.L.geniculatus
+GUCUACGACCAUAUCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGAGCGUGGUUAGUACGUGGAUGGGUGACCGCCUCGGAAUACCACGUGUUGUAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq
new file mode 100644
index 0000000..83e9877
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq
@@ -0,0 +1,2 @@
+>d.5.e.L.japonicum
+GCCUACGACCAUAUCACCCUGAAUACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGAGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGUUGUAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq
new file mode 100644
index 0000000..9d33a3c
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq
@@ -0,0 +1,2 @@
+>d.5.e.L.luteus
+AGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCUCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq
new file mode 100644
index 0000000..2e8a669
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq
@@ -0,0 +1,2 @@
+>d.5.e.L.usitatissimum
+GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGAAGUUAAACGUGCUUGGGCGAGAGUAGUACUAAGAUGGGUGACCUCUUGGGAAGUCCUCGUGUUGCACCCCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq
new file mode 100644
index 0000000..dfa7faa
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq
@@ -0,0 +1,2 @@
+>d.5.e.M.auratus
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq
new file mode 100644
index 0000000..046a55c
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq
@@ -0,0 +1,2 @@
+>d.5.e.M.fossilis
+GCUUACGGCCAUACCACCCUGAGCACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACUGCCUGGGAAUACCAGGUGUUGUAAGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq
new file mode 100644
index 0000000..1d4c204
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq
@@ -0,0 +1,2 @@
+>d.5.e.M.glyptostroboides
+GGGUGCGAUCAUACCAGCGUUAGUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGCCGGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCCGGUAUUGCACCCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq
new file mode 100644
index 0000000..fa29c33
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq
@@ -0,0 +1,2 @@
+>d.5.e.M.musculus
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq
new file mode 100644
index 0000000..3101592
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq
@@ -0,0 +1,2 @@
+>d.5.e.M.salmoides
+GCUUACGGCCACACCACCCUGAACACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGUCGUAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq
new file mode 100644
index 0000000..df2ff9f
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq
@@ -0,0 +1,2 @@
+>d.5.e.N.dofleini
+GUCUACGACCAUACCACAAUGAACACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAUUGUCGGGCCAGGAUAGUACCUGGAUGGGGGACCGCCUGGGAACGCCUGGUGUCGUAGACUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq
new file mode 100644
index 0000000..a966f10
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq
@@ -0,0 +1,2 @@
+>d.5.e.N.viridescens
+GCUUACGGCCAUACCACCCUGAAAGCACCUGAUCUCGUCUGAUCUCAGAAGUUAAGCAGGGUCGGGCCUGGUUAGUACCUGGAUGGGAGACCGCCUUGGAAUACCAGGUGCUGUAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq
new file mode 100644
index 0000000..0f05eee
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq
@@ -0,0 +1,2 @@
+>d.5.e.O.mykiss
+GCUUACGGCCAUACCAGCCUGAAUACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAAGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq
new file mode 100644
index 0000000..614084f
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq
@@ -0,0 +1,2 @@
+>d.5.e.O.sativa.1
+GGAUGCGAUCAUACCAGCACUAAAGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUUGUGUUGCAUCCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq
new file mode 100644
index 0000000..bb31e0b
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq
@@ -0,0 +1,2 @@
+>d.5.e.O.sativa.2
+GGAUGCGAUCAUACGAGGACGAAAGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUUGUGUUGCAUCCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq
new file mode 100644
index 0000000..9c4e025
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq
@@ -0,0 +1,2 @@
+>d.5.e.P.brevicirris
+GCCUACGGCCAUACUACGUUGAAAACACCGGUUCUCGUCUGAUCACCGAAGUUAAGCAACGUCGGGCCUGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCAGGUGCUGUAGGUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq
new file mode 100644
index 0000000..035e1ec
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq
@@ -0,0 +1,2 @@
+>d.5.e.P.coxalis
+GUCAACGGCCAUACCACGUUGAAAGCACCACUUCUCGUCCGAUCAGCGAAGUUAAGCAACGUUGGGUCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAACACCAGAUGCUGUUGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq
new file mode 100644
index 0000000..bb21939
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq
@@ -0,0 +1,2 @@
+>d.5.e.P.gouldii
+GCCUACGACCAUACCACGUUGAAAACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCCAGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCUGGUGUUGUAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq
new file mode 100644
index 0000000..cee3f47
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq
@@ -0,0 +1,2 @@
+>d.5.e.P.hybrida.1
+GGAUGCGAUCAUACCAGCACUAACGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUGGAAUGGGUGACCCUCCGGGAAGUCCUCGUGUUGCAUCCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq
new file mode 100644
index 0000000..4b4969f
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq
@@ -0,0 +1,2 @@
+>d.5.e.P.hybrida.2
+AGAUGCGAUCAUACCAGCACUAACGCACCGGAUCCCAUCAGAACUCCGAAGCUAAGCGUGCUUGGGCGAGAGUAGUACUGGAAUGGGUGACCCUCCGGGAAGUCCUCGUGUUGCAUCCCG
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq
new file mode 100644
index 0000000..0fe2e5f
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq
@@ -0,0 +1,2 @@
+>d.5.e.P.radiata
+GGGUGCGAUCAUACCAGCGUUAAUGCACCGAAUCCCAUCAGAACUCCGCAGUUUAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq
new file mode 100644
index 0000000..48aafa5
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq
@@ -0,0 +1,2 @@
+>d.5.e.P.reticulata
+GAUAGCGUCCAUACCACACUGAAAACACCGGUUCUCGUCCGAUCACCGCAGUUAAGCAGUGUCGGGCCCAGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACUGGGUGUCGCUACCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq
new file mode 100644
index 0000000..ac85b0c
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq
@@ -0,0 +1,2 @@
+>d.5.e.P.tetraurelia
+GUUGGUGGCCAUACUAAGCCUAAAGCACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGGCUUAAGGCGAGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGUCCUCGUGUUGACAACCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq
new file mode 100644
index 0000000..686043c
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq
@@ -0,0 +1,2 @@
+>d.5.e.P.waltl
+GCCUACGGCCAUACCACCCUGAAUGCGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAGGCAU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq
new file mode 100644
index 0000000..7356089
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq
@@ -0,0 +1,2 @@
+>d.5.e.Phytomonas.sp
+GGGUACGACCAUACUUGGCUGAAAGCACCACAUCCCGUCCGAUUUGUGAAGUUAAGCAGCCACAGGCUUAGUUAGUACUGAGGUCAGUGAUGACUCGGGAACCCUGAGUGCCGUACCCUCCACAACACUC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq
new file mode 100644
index 0000000..4611843
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq
@@ -0,0 +1,2 @@
+>d.5.e.Q.petraea
+GGGUGCGAUCAUACCAACACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGUUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq
new file mode 100644
index 0000000..b317aac
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq
@@ -0,0 +1,2 @@
+>d.5.e.R.norvegicus.1
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq
new file mode 100644
index 0000000..9bfefd4
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq
@@ -0,0 +1,2 @@
+>d.5.e.R.norvegicus.2
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq
new file mode 100644
index 0000000..97d8ffd
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq
@@ -0,0 +1,2 @@
+>d.5.e.R.norvegicus.3
+GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq
new file mode 100644
index 0000000..91ab62d
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq
@@ -0,0 +1,2 @@
+>d.5.e.S.aggregatum
+ACAGCCGUUCAUACCACACGGAGAAUACCGGAUCUCGUUCGAACUCCGCAGUCAAGCCGUGUCGGGCGUGCUCAGUACUACCAUAGGGGACUGGGUGGGAAGCGUGCGUGACGGCUGUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq
new file mode 100644
index 0000000..f821f70
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq
@@ -0,0 +1,2 @@
+>d.5.e.S.canicula
+GCCUACGGCCAUACUAGUCUGAAAACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGAUUCAGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCAGUAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq
new file mode 100644
index 0000000..99153a7
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq
@@ -0,0 +1,2 @@
+>d.5.e.S.cerevisiae
+GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUGUUAAGCUGGUAGAGCCUGACCGAGUAGUGUAUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq
new file mode 100644
index 0000000..7301bd3
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq
@@ -0,0 +1,2 @@
+>d.5.e.S.cynthia.XBM
+GCCAACGUCCAUACCAUGUUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUCAAGCAACAUCGGGCGUAGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACUACGUGAUGUUGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq
new file mode 100644
index 0000000..c309c20
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq
@@ -0,0 +1,2 @@
+>d.5.e.S.kowalevskii
+GCCUACGGCCAUACCACGUAGAAUGCACCGGUUCUCGUCCGAUCACCGAAGUUAAGCUGCGUCGGGCGUGGUUAGUACUUGCAUGGGAGACCGGCUGGGAAUACCACGUGCUGUAGGCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq
new file mode 100644
index 0000000..fbcd514
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq
@@ -0,0 +1,2 @@
+>d.5.e.S.officinalis
+GCUUACGGCCAUAUCACGCUGAAAACACCGGUUCUCGUCCGAACACCGAAGUUAAGCAACGUAGAGCCUGGUGAGUACUUGGAUGGGUGACCGCUUGGGAAUACCAGGUGCUGUAAGCAU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq
new file mode 100644
index 0000000..45e16c8
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq
@@ -0,0 +1,2 @@
+>d.5.e.S.pombe.1
+GUCUACGGCCAUACCUAGGCGAAAACACCAGUUCCCGUCCGAUCACUGCAGUUAAGCGUCUGAGGGCCUCGUUAGUACUAUGGUUGGAGACAACAUGGGAAUCCGGGGUGCUGUAGGCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq
new file mode 100644
index 0000000..dacd0d4
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq
@@ -0,0 +1,2 @@
+>d.5.e.T.aestivum
+GGAUGCGAUCAUACCAGCACUAAGGCAUCGGAUCCCGUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACAAGGAUGGGUGACCUCUUGGGAAGUCCUCGUGUUGCAUUCCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq
new file mode 100644
index 0000000..91d76b6
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq
@@ -0,0 +1,2 @@
+>d.5.e.T.borreli
+GGGUACGUCCAUACUUGGCUGAAAGCACCAUAUCCCGUCCGAUUUGUGAAGUUAAGCAGCCACAGGCUUAGUUAGUACUGAGGUCAGUGAUGACUUGGGAACCCUAAGUGUCGUACUCCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq
new file mode 100644
index 0000000..b4fe443
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq
@@ -0,0 +1,2 @@
+>d.5.e.T.cruzi
+GGGUACGACCAUACUUGGCCGAGUGCACCACAUCCCGUCCGAUUUGUGAAGUUAAGCGGCCACAGGCCUCGUUAGUACGGCGAUCAGUGAUGGCGCUGGAACCCGGGGUGCCGUACCCUU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq
new file mode 100644
index 0000000..0d095ee
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq
@@ -0,0 +1,2 @@
+>d.5.e.T.monococcum
+GGAUGCGAUCAUACCAGCACUAAAGCACCGGAUCCCAUCAGAACUCUGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUCGGAAGUCCUCGUGUUGCAUUCCC
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq
new file mode 100644
index 0000000..2846ec9
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq
@@ -0,0 +1,2 @@
+>d.5.e.T.thermophila.2
+GUUGUCGGCCAUACUAAGGUGAAAACACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGCCUUAAGGCUGGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGUCCCAGUGUCGAUAGCCU
diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq
new file mode 100644
index 0000000..5b30dba
--- /dev/null
+++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq
@@ -0,0 +1,2 @@
+>d.5.e.U.unicinctus
+GUCUACGGCCAUACCACGUUGAAAACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCCCGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCGGGUGCUGUAGACUU

From f5c75dd91e7ecc155417925e933b7063495da821 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 7 Oct 2011 15:26:41 -0400
Subject: [PATCH 254/282] Merge the README file.

---
 gtfold-mfe/tests/README | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 gtfold-mfe/tests/README

diff --git a/gtfold-mfe/tests/README b/gtfold-mfe/tests/README
new file mode 100644
index 0000000..7e55fcb
--- /dev/null
+++ b/gtfold-mfe/tests/README
@@ -0,0 +1,4 @@
+This directory contains the Test Framework for GTFold.
+The complete documentation can be accessed here:
+http://goo.gl/OliVA
+

From aac4e4ae96a2eccdaedbaa179c70aa8a55d72574 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 7 Oct 2011 16:13:20 -0400
Subject: [PATCH 255/282] Rename PseudoKnotDetection Tests to ExitCode Tests.

---
 .../default.expectedresult                    |  1 +
 .../data/exitcodes_sequences/seq1.constraint  |  4 +++
 .../tests/data/exitcodes_sequences/seq1.ct    | 20 +++++++++++++++
 .../exitcodes_sequences/seq1.expectedresult   |  1 +
 .../tests/data/exitcodes_sequences/seq1.seq   |  1 +
 .../data/exitcodes_sequences/seq2.constraint  |  2 ++
 .../exitcodes_sequences/seq2.expectedresult   |  1 +
 .../tests/data/exitcodes_sequences/seq2.seq   |  1 +
 .../data/exitcodes_sequences/seq3.constraint  |  3 +++
 .../exitcodes_sequences/seq3.expectedresult   |  1 +
 .../tests/data/exitcodes_sequences/seq3.seq   |  1 +
 .../data/exitcodes_sequences/seq4.constraint  |  4 +++
 .../exitcodes_sequences/seq4.expectedresult   |  1 +
 .../tests/data/exitcodes_sequences/seq4.seq   |  1 +
 .../data/exitcodes_sequences/seq5.constraint  |  1 +
 .../exitcodes_sequences/seq5.expectedresult   |  1 +
 .../tests/data/exitcodes_sequences/seq5.seq   |  1 +
 .../data/exitcodes_sequences/seq6.constraint  |  5 ++++
 .../exitcodes_sequences/seq6.expectedresult   |  1 +
 .../tests/data/exitcodes_sequences/seq6.seq   |  1 +
 .../data/exitcodes_sequences/seq7.constraint  |  4 +++
 .../exitcodes_sequences/seq7.expectedresult   |  1 +
 .../tests/data/exitcodes_sequences/seq7.seq   |  1 +
 .../data/exitcodes_sequences/seq8.constraint  |  4 +++
 .../exitcodes_sequences/seq8.expectedresult   |  1 +
 .../tests/data/exitcodes_sequences/seq8.seq   |  1 +
 .../{PseudoKnotDetection.pm => ExitCodes.pm}  | 25 ++++++++++++++-----
 27 files changed, 83 insertions(+), 6 deletions(-)
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult
 create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq
 rename gtfold-mfe/tests/scripts/{PseudoKnotDetection.pm => ExitCodes.pm} (61%)

diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult
new file mode 100644
index 0000000..573541a
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult
@@ -0,0 +1 @@
+0
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint
new file mode 100644
index 0000000..2a01386
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint
@@ -0,0 +1,4 @@
+F 1 19 2
+F 3 10 1
+F 4 8 1
+F 11 15 1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct
new file mode 100644
index 0000000..da642b1
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct
@@ -0,0 +1,20 @@
+19	  dG = 10.1
+1	C	0	2	0	1
+2	C	1	3	0	2
+3	C	2	4	0	3
+4	C	3	5	0	4
+5	A	4	6	0	5
+6	A	5	7	0	6
+7	G	6	8	0	7
+8	A	7	9	0	8
+9	A	8	10	0	9
+10	G	9	11	0	10
+11	C	10	12	0	11
+12	A	11	13	0	12
+13	A	12	14	0	13
+14	A	13	15	0	14
+15	G	14	16	0	15
+16	A	15	17	0	16
+17	A	16	18	0	17
+18	G	17	19	0	18
+19	G	18	0	0	19
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult
new file mode 100644
index 0000000..573541a
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult
@@ -0,0 +1 @@
+0
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq
new file mode 100644
index 0000000..0964dc3
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq
@@ -0,0 +1 @@
+CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint
new file mode 100644
index 0000000..2a8e728
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint
@@ -0,0 +1,2 @@
+F 1 19 2
+F 15 21 1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq
new file mode 100644
index 0000000..23023c5
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq
@@ -0,0 +1 @@
+CCAAAAAAAAAAAACAAGGAG
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint
new file mode 100644
index 0000000..bcbe409
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint
@@ -0,0 +1,3 @@
+F 1 19 2
+F 3 10 2
+F 15 23 1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq
new file mode 100644
index 0000000..6b590de
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq
@@ -0,0 +1 @@
+CCCCAAAAGGAAAACAAGGAAAG
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint
new file mode 100644
index 0000000..cece32a
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint
@@ -0,0 +1,4 @@
+F 1 19 2
+F 3 18 1
+F 4 7 1
+F 11 15 1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq
new file mode 100644
index 0000000..0964dc3
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq
@@ -0,0 +1 @@
+CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint
new file mode 100644
index 0000000..7029d7d
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint
@@ -0,0 +1 @@
+F 1 8 8
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq
new file mode 100644
index 0000000..0984ecd
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq
@@ -0,0 +1 @@
+CCCCCGGGGGGAAAGGG
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint
new file mode 100644
index 0000000..adb4fdb
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint
@@ -0,0 +1,5 @@
+F 1 19 2
+F 3 10 1
+F 4 8 1
+F 11 15 1
+F 24 25 1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq
new file mode 100644
index 0000000..9a1d7d8
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq
@@ -0,0 +1 @@
+CCCCAAGAAGCAAAGAAGGCCCACGAAAA
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint
new file mode 100644
index 0000000..2ce893a
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint
@@ -0,0 +1,4 @@
+F 0 19 2
+F 3 10 1
+F 4 8 1
+F 11 15 1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq
new file mode 100644
index 0000000..0964dc3
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq
@@ -0,0 +1 @@
+CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint
new file mode 100644
index 0000000..65ea20f
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint
@@ -0,0 +1,4 @@
+F 1 19 2
+F 3 10 1
+F 4 8 1
+F 11 24 1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult
new file mode 100644
index 0000000..d00491f
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult
@@ -0,0 +1 @@
+1
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq
new file mode 100644
index 0000000..0964dc3
--- /dev/null
+++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq
@@ -0,0 +1 @@
+CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/scripts/PseudoKnotDetection.pm b/gtfold-mfe/tests/scripts/ExitCodes.pm
similarity index 61%
rename from gtfold-mfe/tests/scripts/PseudoKnotDetection.pm
rename to gtfold-mfe/tests/scripts/ExitCodes.pm
index 1bdfc38..fbe7079 100755
--- a/gtfold-mfe/tests/scripts/PseudoKnotDetection.pm
+++ b/gtfold-mfe/tests/scripts/ExitCodes.pm
@@ -1,5 +1,5 @@
 #!/usr/bin/perl
-package PseudoKnotDetection;
+package ExitCodes;
 use strict;
 use warnings;
 use File::Basename;
@@ -17,10 +17,10 @@ sub test()
 
   my $key;
   my $value;
-
+  my %new_hash = (%local_sequences, %Sequences);
   # For testing pseudoknot detection logic
   # we may only test the sequences specified in local_sequences
-  while (($key, $value) = each(%local_sequences)) {
+  while (($key, $value) = each(%new_hash)) {
 
 	  my $seqname=$key;
 	  my $path;
@@ -32,14 +32,27 @@ sub test()
 	  my $gtout  = "$workdir$seqname-gt";
 	  my $gtoutfilename  = $workdir."$seqname-gt.ct";
 
-	  my $gtcmd = "$gtdir/gtfold -c $constraint_file -m $seqfile -o $gtout > /dev/null 2>&1";
+	  my $gtcmd;
+    if (-e $constraint_file) {
+      $gtcmd  = "$gtdir/gtfold -c $constraint_file -m $seqfile -o $gtout > /dev/null 2>&1";
+    }
+    else {
+      $gtcmd  = "$gtdir/gtfold -m $seqfile -o $gtout > /dev/null 2>&1";
+    }
+
 	  my $x = system("$gtcmd") >> 8;
 
     my $expected_result_file = "$dirname/$seqname.expectedresult";
-    my $expected_result = `head -n 1 $expected_result_file`;     
+    my $expected_result;
+    if (-e $expected_result_file) {
+      $expected_result = `head -n 1 $expected_result_file`;     
+    }
+    else {
+      $expected_result = 0;
+    }
 
     if ($expected_result =~ $x) {
-      $logger->error("TEST PASSED: $seqname: Return Value $x matched expected output $expected_result");
+      $logger->info("TEST PASSED: $seqname: Return Value $x matched expected output $expected_result");
     }
     else {
       $logger->error("TEST FAILED: $seqname: Return Value $x did not match expected output $expected_result");

From 8ed1a048238fd79197b4ee2d8112b42d24500e3c Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 7 Oct 2011 16:17:00 -0400
Subject: [PATCH 256/282] Remove pseudoknot detection sequences

---
 .../seq1.constraint                           |  4 ----
 .../pseudoknot_detection_sequences/seq1.ct    | 20 -------------------
 .../seq1.expectedresult                       |  1 -
 .../pseudoknot_detection_sequences/seq1.seq   |  1 -
 .../seq2.constraint                           |  2 --
 .../seq2.expectedresult                       |  1 -
 .../pseudoknot_detection_sequences/seq2.seq   |  1 -
 .../seq3.constraint                           |  3 ---
 .../seq3.expectedresult                       |  1 -
 .../pseudoknot_detection_sequences/seq3.seq   |  1 -
 .../seq4.constraint                           |  4 ----
 .../seq4.expectedresult                       |  1 -
 .../pseudoknot_detection_sequences/seq4.seq   |  1 -
 .../seq5.constraint                           |  1 -
 .../seq5.expectedresult                       |  1 -
 .../pseudoknot_detection_sequences/seq5.seq   |  1 -
 .../seq6.constraint                           |  5 -----
 .../seq6.expectedresult                       |  1 -
 .../pseudoknot_detection_sequences/seq6.seq   |  1 -
 .../seq7.constraint                           |  4 ----
 .../seq7.expectedresult                       |  1 -
 .../pseudoknot_detection_sequences/seq7.seq   |  1 -
 .../seq8.constraint                           |  4 ----
 .../seq8.expectedresult                       |  1 -
 .../pseudoknot_detection_sequences/seq8.seq   |  1 -
 25 files changed, 63 deletions(-)
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult
 delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq

diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint
deleted file mode 100644
index 2a01386..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint
+++ /dev/null
@@ -1,4 +0,0 @@
-F 1 19 2
-F 3 10 1
-F 4 8 1
-F 11 15 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct
deleted file mode 100644
index da642b1..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct
+++ /dev/null
@@ -1,20 +0,0 @@
-19	  dG = 10.1
-1	C	0	2	0	1
-2	C	1	3	0	2
-3	C	2	4	0	3
-4	C	3	5	0	4
-5	A	4	6	0	5
-6	A	5	7	0	6
-7	G	6	8	0	7
-8	A	7	9	0	8
-9	A	8	10	0	9
-10	G	9	11	0	10
-11	C	10	12	0	11
-12	A	11	13	0	12
-13	A	12	14	0	13
-14	A	13	15	0	14
-15	G	14	16	0	15
-16	A	15	17	0	16
-17	A	16	18	0	17
-18	G	17	19	0	18
-19	G	18	0	0	19
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult
deleted file mode 100644
index 573541a..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult
+++ /dev/null
@@ -1 +0,0 @@
-0
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq
deleted file mode 100644
index 0964dc3..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq
+++ /dev/null
@@ -1 +0,0 @@
-CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint
deleted file mode 100644
index 2a8e728..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint
+++ /dev/null
@@ -1,2 +0,0 @@
-F 1 19 2
-F 15 21 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult
deleted file mode 100644
index d00491f..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult
+++ /dev/null
@@ -1 +0,0 @@
-1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq
deleted file mode 100644
index 23023c5..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq
+++ /dev/null
@@ -1 +0,0 @@
-CCAAAAAAAAAAAACAAGGAG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint
deleted file mode 100644
index bcbe409..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint
+++ /dev/null
@@ -1,3 +0,0 @@
-F 1 19 2
-F 3 10 2
-F 15 23 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult
deleted file mode 100644
index d00491f..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult
+++ /dev/null
@@ -1 +0,0 @@
-1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq
deleted file mode 100644
index 6b590de..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq
+++ /dev/null
@@ -1 +0,0 @@
-CCCCAAAAGGAAAACAAGGAAAG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint
deleted file mode 100644
index cece32a..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint
+++ /dev/null
@@ -1,4 +0,0 @@
-F 1 19 2
-F 3 18 1
-F 4 7 1
-F 11 15 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult
deleted file mode 100644
index d00491f..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult
+++ /dev/null
@@ -1 +0,0 @@
-1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq
deleted file mode 100644
index 0964dc3..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq
+++ /dev/null
@@ -1 +0,0 @@
-CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint
deleted file mode 100644
index 7029d7d..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint
+++ /dev/null
@@ -1 +0,0 @@
-F 1 8 8
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult
deleted file mode 100644
index d00491f..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult
+++ /dev/null
@@ -1 +0,0 @@
-1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq
deleted file mode 100644
index 0984ecd..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq
+++ /dev/null
@@ -1 +0,0 @@
-CCCCCGGGGGGAAAGGG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint
deleted file mode 100644
index adb4fdb..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint
+++ /dev/null
@@ -1,5 +0,0 @@
-F 1 19 2
-F 3 10 1
-F 4 8 1
-F 11 15 1
-F 24 25 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult
deleted file mode 100644
index d00491f..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult
+++ /dev/null
@@ -1 +0,0 @@
-1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq
deleted file mode 100644
index 9a1d7d8..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq
+++ /dev/null
@@ -1 +0,0 @@
-CCCCAAGAAGCAAAGAAGGCCCACGAAAA
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint
deleted file mode 100644
index 2ce893a..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint
+++ /dev/null
@@ -1,4 +0,0 @@
-F 0 19 2
-F 3 10 1
-F 4 8 1
-F 11 15 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult
deleted file mode 100644
index d00491f..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult
+++ /dev/null
@@ -1 +0,0 @@
-1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq
deleted file mode 100644
index 0964dc3..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq
+++ /dev/null
@@ -1 +0,0 @@
-CCCCAAGAAGCAAAGAAGG
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint
deleted file mode 100644
index 65ea20f..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint
+++ /dev/null
@@ -1,4 +0,0 @@
-F 1 19 2
-F 3 10 1
-F 4 8 1
-F 11 24 1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult
deleted file mode 100644
index d00491f..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult
+++ /dev/null
@@ -1 +0,0 @@
-1
diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq
deleted file mode 100644
index 0964dc3..0000000
--- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq
+++ /dev/null
@@ -1 +0,0 @@
-CCCCAAGAAGCAAAGAAGG

From 7b4289c25806a2dd07d68c9f543a78c3af6b7554 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Thu, 13 Oct 2011 22:17:44 -0400
Subject: [PATCH 257/282] Test to Compare CT structure returned by GTFold and
 UNAFold.

---
 gtfold-mfe/tests/config/test-params.conf      |   8 +-
 .../tests/scripts/CompareGTCTwithUNACT.pm     |  64 ++++
 gtfold-mfe/tests/scripts/compare_ct.pl        | 339 ++++++++++++++++++
 3 files changed, 407 insertions(+), 4 deletions(-)
 create mode 100755 gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm
 create mode 100755 gtfold-mfe/tests/scripts/compare_ct.pl

diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf
index d1fdec2..5b649f8 100644
--- a/gtfold-mfe/tests/config/test-params.conf
+++ b/gtfold-mfe/tests/config/test-params.conf
@@ -1,9 +1,9 @@
 # Important directory variables
 G_GTFOLD_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/src/
 G_UNAFOLD_DIR=/home/users/rbanga/rna/unafold/install/bin/
-#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/
+G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/
 #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/
-G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/
+#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/
 #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/23S_sequences/
 #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/Other_sequences/
 G_WORK_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/work/
@@ -14,7 +14,7 @@ G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test-
 #G_INCLUDE_SEQUENCES=d.16.e.B.g*
 #G_INCLUDE_SEQUENCES=d.16.e.B.m*
 #G_INCLUDE_SEQUENCES=d.16.e.B.h*
-#G_INCLUDE_SEQUENCES=d.16.e.G.va*
+#G_INCLUDE_SEQUENCES=d.16.e.E.bieneusi
 #G_EXCLUDE_SEQUENCES=d.16.e.A.*
 #G_EXCLUDE_SEQUENCES=d.16.e.B.ma*
 #G_INCLUDE_SEQUENCES=acc1
@@ -24,4 +24,4 @@ G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test-
 # Local Sequence Directories
 
 # Directory containing sequences for testing pseudoknot detection logic
-L_PSEUDOKNOTDETECTION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/pseudoknot_detection_sequences/
+#L_EXITCODES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/exitcodes_sequences/
diff --git a/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm b/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm
new file mode 100755
index 0000000..ddabcdc
--- /dev/null
+++ b/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm
@@ -0,0 +1,64 @@
+#!/usr/bin/perl
+package CompareGTCTwithUNACT;
+use strict;
+use warnings;
+use Error;
+use File::Basename;
+use Exception::Class;
+
+require "compare_ct.pl"; 
+
+sub test()
+{
+  my(%Config) = %{$_[1]};
+  my(%Sequences) = %{$_[2]};
+  my $logger = $_[4];
+
+  my $epsilon = 0.001;
+  my $gtdir = $Config{"G_GTFOLD_DIR"};
+  my $unadir = $Config{"G_UNAFOLD_DIR"};
+  my $workdir = $Config{"G_WORK_DIR"};
+
+  my $key;
+  my $value;
+
+  while (($key, $value) = each(%Sequences)) {
+
+	  my $seqname=$key;
+	  my $path;
+	  my $suffix;
+
+	  my $seqfile = $value;
+	  my $gtout  = "$workdir$seqname-gt";
+	  my $unaout = "$workdir$seqname-una";
+	  my $gtoutfilename  = $workdir."$seqname-gt.ct";
+	  my $unaoutfilename = $workdir."$seqname-una.ct";
+
+	  my $gtcmd = "$gtdir/gtfold -m $seqfile --unafold -o $gtout > /dev/null";
+	  my $unacmd = "$unadir/hybrid-ss-min -s DAT $seqfile -o $unaout > /dev/null";
+	
+	  system("$gtcmd");
+	  system("$unacmd");
+
+    my @result;
+    eval {
+      @result = compare_ct_structures($gtoutfilename, $unaoutfilename);
+    };
+    my $exception;
+    if ($exception = Exception::Class->caught('CompareCTException')) {
+      $logger->error("Test Failed: $seqname: $exception\n");
+      next;
+    }
+
+    my $diff1 = abs(1 - $result[0]);
+    my $diff2 = abs(1 - $result[1]);
+    if ($diff1 < $epsilon || $diff2 < $epsilon) {
+      $logger->info("TEST PASSED: $seqname: Specificity = $result[0], Selectivity = $result[1]");
+    }
+    else {
+      $logger->info("TEST FAILED: $seqname: Specificity = $result[0], Selectivity = $result[1]\n".
+                    "More Information: $result[2] $result[3]");
+    }
+  }
+}
+1;
diff --git a/gtfold-mfe/tests/scripts/compare_ct.pl b/gtfold-mfe/tests/scripts/compare_ct.pl
new file mode 100755
index 0000000..7196ffe
--- /dev/null
+++ b/gtfold-mfe/tests/scripts/compare_ct.pl
@@ -0,0 +1,339 @@
+#!/usr/bin/perl 
+
+use paul_specials;
+use Error;
+use Exception::Class('CompareCTException');
+
+sub compare_ct_structures()
+{
+my $ref_filename=$_[0];
+my $filename=$_[1];
+
+open(REF, "< $ref_filename");
+open(RNA, "< $filename");
+
+#printf "opened files $ref_filename and $filename\n\n\n";
+
+@ref_struct = read_struct_ct(*REF);
+@struct = read_struct_ct(*RNA);
+
+my $rlen = length($ref_struct[0]);
+my $slen = length($struct[0]);
+my $ref_seq = $ref_struct[0];
+my $seq = $struct[0];
+
+$ref_struct[0]=$rlen;
+$struct[0]=$slen;
+
+my $ref_dotb = table_to_bracket(\@ref_struct);
+my $dotb = table_to_bracket(\@struct);
+
+$dotb =~ s/\(/\{/g;
+$dotb =~ s/\)/\}/g;
+
+    $_ = $ref_seq;
+    my $ref_nogaps = tr/\-//;
+    $_ = $seq;
+    my $nogaps = tr/\-//;
+
+
+    if (($rlen-$ref_nogaps) != ($slen-$nogaps)){
+	      CompareCTException->throw(error => "seq lengths aren't equal (reference = $rlen, prediction = $slen)!
+$rlen-$ref_nogaps ne $slen-$nogaps
+ref_nogaps = $ref_nogaps
+nogaps     = $nogaps
+
+>ref
+$ref_seq
+$ref_dotb
+>str
+$seq\n\n\n");
+    }
+
+#print ">ref1
+#$ref_seq
+#$ref_dotb
+#>str1
+#$seq
+#$dotb\n\n\n";
+
+#If different lengths, gap or delete as appropriate:
+while ($rlen != $slen){
+    
+    for (my $i = 0; $i < length($ref_seq); $i++){
+	if ( substr($ref_seq,$i,1) =~ '\-'){  
+	    
+	    if (substr($ref_dotb,$i,1)  =~ '\.' ){
+		substr($ref_seq,$i,1) = "";
+		substr($ref_dotb,$i,1) = "";
+		$i--;
+	    }
+	    elsif ((substr($seq,$i,1) ne substr($ref_seq,$i,1)) && (substr($ref_dotb,$i,1)  ne '\.') ) {
+		substr($seq,$i,0) = ".";
+		substr($dotb,$i,0) = ".";
+		
+		substr($ref_seq,$i,1) = ".";
+		
+		
+	    }
+		}
+    }
+    
+    
+    for (my $i = 0; $i < length($seq); $i++){
+	
+	if ( substr($seq,$i,1) =~ '\-'){  
+	    
+	    if (substr($dotb,$i,1)  =~ '\.' ){
+		substr($seq,$i,1) = "";
+		substr($dotb,$i,1) = "";
+		$i--;
+	    }
+	    elsif (substr($seq,$i,1) ne substr($ref_seq,$i,1) && (substr($dotb,$i,1)  ne '\.')) {
+		substr($ref_seq,$i,0) = ".";
+		substr($ref_dotb,$i,0) = ".";
+		substr($seq,$i,1) = ".";
+		
+	    }
+	}
+	
+    }
+#print ">ref
+#$ref_seq
+#$ref_dotb
+#>str
+#$seq
+#$dotb\n\n";
+    @ref_struct = make_pair_table($ref_dotb); 
+    @struct = make_pair_table($dotb);
+    
+    #Update lengths after gapping
+    $rlen = length($ref_seq);
+    $slen = length($seq);
+    
+}
+
+
+
+#print ">ref
+#$ref_seq
+#$ref_dotb
+#>str
+#$seq\n";
+
+
+
+my $rcount = 0;
+my $scount = 0; 
+my $true_pos = 0; 
+my $true_neg = 0; 
+my $false_neg = 0; 
+my $false_pos = 0;
+my $conflict = 0;
+my $contradict = 0;
+my $temp = 0;
+
+for (my $i=1; $i<=$rlen; $i++){
+    
+    #printf "%6d %6d\n", $ref_struct[$i], $struct[$i];
+
+    if ($ref_struct[$i]>0 && $ref_struct[$i]>$i){
+	$rcount++;
+	#print "$rcount: $i-$ref_struct[$i]\n";
+    }
+    
+    if ($struct[$i]>0 && $struct[$i]>$i){
+	$scount++;
+    }
+
+    if (($ref_struct[$i]==$struct[$i]) && $ref_struct[$i]>0 && $ref_struct[$i]>$i){
+	#printf "%6d %6d\n", $ref_struct[$i], $struct[$i];
+	$true_pos++;
+	$temp = $struct[$i];
+	substr($dotb,$i-1,1) = '(';
+	substr($dotb,$temp-1,1) = ')';
+    }
+    elsif (($ref_struct[$i]!=$struct[$i]) && $struct[$i]>0 && $struct[$i]>$i){
+      
+      #print "struct: $i . $struct[$i]\n";
+      
+      $prime5 = $i;
+      $prime3 = $struct[$i];
+      
+      if ($ref_struct[$prime3]>0 || $ref_struct[$prime5]>0){
+	#print "   ref: $ref_struct[$prime3] . $ref_struct[$ref_struct[$prime3]] : $ref_struct[$prime5] . $ref_struct[$ref_struct[$prime5]]\n";
+	$contradict++;
+	
+	substr($dotb,$prime5-1,1) = '<';
+	substr($dotb,$prime3-1,1) = '>';
+	
+
+      }
+      else {
+	#check nested!
+	$j=$prime5;
+	$b=1;
+	while ($b && $j<$prime3 ) {
+	  
+	  if ( ($ref_struct[$j]>0 && $ref_struct[$j]<$prime5) || $ref_struct[$j]>$prime3 ) {
+	    $b=0;
+	    $conflict++;
+	    #print "conflict $ref_struct[$j] . $j\n";
+	    
+	    substr($dotb,$prime5-1,1) = '[';
+	    substr($dotb,$prime3-1,1) = ']';
+	    
+	  }
+	  $j++;
+	}
+
+      }
+      
+      
+    }
+    
+    for (my $j=$i+4; $j<=$rlen; $j++){
+	
+	my $x = substr($ref_seq,$i-1,1);
+	my $y = substr($ref_seq,$j-1,1);
+	
+	if (ispair($x,$y) ){
+	    $true_neg++;
+	    #print "$x $i $y $j\n";
+	}
+	
+    }
+    
+
+}
+
+
+#$false_pos = $scount - $true_pos;
+$false_pos = $conflict + $contradict;
+$false_neg = $rcount - $true_pos;
+
+$true_neg=$true_neg-$true_pos-$false_pos;
+
+my $sensitivity = 0;
+my $selectivity =0;
+if ($rcount>0){
+    $sensitivity = $true_pos/($false_neg + $true_pos); #$rcount;
+}
+if ($scount>0){
+    $selectivity = $true_pos/($false_pos + $true_pos); #$scount;
+}
+
+my $approx_corr = ($sensitivity + $selectivity)/2;
+my $N = $true_pos + $false_pos + $false_neg + $true_neg;
+
+my $corr_coeff  = 0;
+if ($true_pos>0){ 
+$corr_coeff  = ($N*$sensitivity*$selectivity - $true_pos)/sqrt(($N*$sensitivity - $true_pos)*($N*$selectivity - $true_pos));
+}
+
+
+my $MCC  = 0;
+my $MCCquotient = (($true_pos+$false_pos)*($true_pos+$false_neg)*($true_neg+$false_pos)*($true_neg+$false_neg));
+
+if ($MCCquotient>0){
+$MCC = ($true_pos*$true_neg - $false_pos*$false_neg)/sqrt( $MCCquotient  );
+}
+
+$old_false_pos = $scount - $true_pos;
+$compatable = $old_false_pos - $false_pos;
+
+#print ">ref
+#$ref_seq
+#$ref_dotb
+#>str
+#$seq\n";
+#print "$dotb\n";
+
+my $comparison_result = "
+seq length =         %6d
+num of bps in ref =  %6d 
+num of bps in sub =  %6d
+Basepair distance =  %6d
+true positives =     %6d
+true negatives =     %6d
+false positive =     %6d 
+\t contradict = $contradict
+\t conflict   = $conflict 
+\t compatable = $compatable
+false negative =     %6d
+sensitivity =        %1.3f
+selectivity =        %1.3f
+Approximate correlation = %1.3f
+Correlation Coefficient = %1.3f 
+Matthews Corr. Coeff.   = %1.3f 
+
+\n\n", $rlen, $rcount, $scount, $false_pos+$false_neg+$compatable, $true_pos, $true_neg, $false_pos, $false_neg, $sensitivity, $selectivity, $approx_corr, $corr_coeff, $MCC;
+
+my $latex_comparison_result = "LaTeX:
+Subj. File & BPs in Ref. & BPs in Subj. & TPs (sens.)& FPs (select.) & Matthews Corr. Coeff. (approx. corr.) & \\\\
+$filename & %d & %d & %d (%2.1f) & %d (%2.1f) & %1.3f (%2.1f) \\\\ \n\n", 
+$rcount, $scount, $true_pos,  $sensitivity*100, $false_pos, $selectivity*100, $MCC, $approx_corr*100;
+
+#printf "%1.4f\t%1.4f\n",
+#$sensitivity, $selectivity;
+
+  return ($sensitivity, $selectivity, $comparison_result, $latex_comparison_result);
+}
+
+sub read_struct_ct{
+
+$fileptr = $_[0];
+my $seq = "";
+
+my $i=-1;
+while ( <$fileptr> ){
+
+    @F = split;
+
+    #if ((/ = /) && ($#F!=5)) {
+    #    next;
+    #}
+    
+    if ($i>=0){
+    
+    $seq .= $F[1];
+    $table[$i] = $F[4];
+}
+    $i++;
+
+    #if ($F[4]==0) {$s .= "."; next}
+    #$s .= "(" if ($F[0]<$F[4]);
+    #$s .= ")" if ($F[0]>$F[4]);
+}
+
+
+  $seq  =~ tr/a-z/A-Z/;
+#print "2: $seq\n\n";
+
+return ($seq, @table);
+
+}
+
+sub ispair{
+    my ($x, $y) = @_;
+    
+    if ( ($x eq 'A' && $y eq 'U')||($x eq 'U' && $y eq 'A') ) {
+	
+	return 1;
+    }
+    elsif ( ($x eq 'G' && $y eq 'C')||($x eq 'C' && $y eq 'G') ) {
+	
+	return 1;
+    }
+    elsif ( ($x eq 'G' && $y eq 'U')||($x eq 'U' && $y eq 'G') ) {
+	
+	return 1;
+    }
+    
+    else {
+	return 0;
+    }
+}
+
+# End of file
+1;

From 82ca1b236138b1bbb3260a192cb4da0ae13d3832 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Thu, 13 Oct 2011 22:56:43 -0400
Subject: [PATCH 258/282] Added meaningful names to some sequence files.

---
 .../{seq5.constraint => base_pair_distance1.constraint}           | 0
 .../{seq2.expectedresult => base_pair_distance1.expectedresult}   | 0
 .../exitcodes_sequences/{seq5.seq => base_pair_distance1.seq}     | 0
 .../{seq6.constraint => base_pair_distance2.constraint}           | 0
 .../{seq3.expectedresult => base_pair_distance2.expectedresult}   | 0
 .../exitcodes_sequences/{seq6.seq => base_pair_distance2.seq}     | 0
 .../{seq4.constraint => duplicate_base1.constraint}               | 0
 .../{seq4.expectedresult => duplicate_base1.expectedresult}       | 0
 .../data/exitcodes_sequences/{seq1.seq => duplicate_base1.seq}    | 0
 .../{seq7.constraint => invalid_base_number1.constraint}          | 0
 .../{seq5.expectedresult => invalid_base_number1.expectedresult}  | 0
 .../exitcodes_sequences/{seq4.seq => invalid_base_number1.seq}    | 0
 .../{seq8.constraint => invalid_base_number2.constraint}          | 0
 .../{seq6.expectedresult => invalid_base_number2.expectedresult}  | 0
 .../exitcodes_sequences/{seq7.seq => invalid_base_number2.seq}    | 0
 .../{seq1.constraint => normal_struct1.constraint}                | 0
 .../{seq1.expectedresult => normal_struct1.expectedresult}        | 0
 .../data/exitcodes_sequences/{seq8.seq => normal_struct1.seq}     | 0
 .../{seq2.constraint => pseudoknot1.constraint}                   | 0
 .../{seq7.expectedresult => pseudoknot1.expectedresult}           | 0
 .../tests/data/exitcodes_sequences/{seq2.seq => pseudoknot1.seq}  | 0
 .../{seq3.constraint => pseudoknot2.constraint}                   | 0
 .../{seq8.expectedresult => pseudoknot2.expectedresult}           | 0
 .../tests/data/exitcodes_sequences/{seq3.seq => pseudoknot2.seq}  | 0
 24 files changed, 0 insertions(+), 0 deletions(-)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq5.constraint => base_pair_distance1.constraint} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq2.expectedresult => base_pair_distance1.expectedresult} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq5.seq => base_pair_distance1.seq} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq6.constraint => base_pair_distance2.constraint} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq3.expectedresult => base_pair_distance2.expectedresult} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq6.seq => base_pair_distance2.seq} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq4.constraint => duplicate_base1.constraint} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq4.expectedresult => duplicate_base1.expectedresult} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq1.seq => duplicate_base1.seq} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq7.constraint => invalid_base_number1.constraint} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq5.expectedresult => invalid_base_number1.expectedresult} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq4.seq => invalid_base_number1.seq} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq8.constraint => invalid_base_number2.constraint} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq6.expectedresult => invalid_base_number2.expectedresult} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq7.seq => invalid_base_number2.seq} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq1.constraint => normal_struct1.constraint} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq1.expectedresult => normal_struct1.expectedresult} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq8.seq => normal_struct1.seq} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq2.constraint => pseudoknot1.constraint} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq7.expectedresult => pseudoknot1.expectedresult} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq2.seq => pseudoknot1.seq} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq3.constraint => pseudoknot2.constraint} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq8.expectedresult => pseudoknot2.expectedresult} (100%)
 rename gtfold-mfe/tests/data/exitcodes_sequences/{seq3.seq => pseudoknot2.seq} (100%)

diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.constraint
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint
rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.constraint
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.expectedresult
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult
rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.expectedresult
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.seq
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq
rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.seq
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.constraint
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint
rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.constraint
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.expectedresult
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult
rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.expectedresult
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.seq
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq
rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.seq
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.constraint
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint
rename to gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.constraint
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.expectedresult
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult
rename to gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.expectedresult
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.seq
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq
rename to gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.seq
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.constraint
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint
rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.constraint
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.expectedresult
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult
rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.expectedresult
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.seq
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq
rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.seq
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.constraint
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint
rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.constraint
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.expectedresult
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult
rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.expectedresult
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.seq
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq
rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.seq
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.constraint
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint
rename to gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.constraint
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.expectedresult
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult
rename to gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.expectedresult
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.seq
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq
rename to gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.seq
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.constraint
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint
rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.constraint
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.expectedresult
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult
rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.expectedresult
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.seq
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq
rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.seq
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.constraint
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint
rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.constraint
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.expectedresult
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult
rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.expectedresult
diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.seq
similarity index 100%
rename from gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq
rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.seq

From 0926b47ff7c9b954f8a1aad5deab7f030477ed6f Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Thu, 13 Oct 2011 22:59:11 -0400
Subject: [PATCH 259/282] Cleanup - Delete a file.

---
 .../tests/data/exitcodes_sequences/seq1.ct    | 20 -------------------
 1 file changed, 20 deletions(-)
 delete mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct

diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct
deleted file mode 100644
index da642b1..0000000
--- a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct
+++ /dev/null
@@ -1,20 +0,0 @@
-19	  dG = 10.1
-1	C	0	2	0	1
-2	C	1	3	0	2
-3	C	2	4	0	3
-4	C	3	5	0	4
-5	A	4	6	0	5
-6	A	5	7	0	6
-7	G	6	8	0	7
-8	A	7	9	0	8
-9	A	8	10	0	9
-10	G	9	11	0	10
-11	C	10	12	0	11
-12	A	11	13	0	12
-13	A	12	14	0	13
-14	A	13	15	0	14
-15	G	14	16	0	15
-16	A	15	17	0	16
-17	A	16	18	0	17
-18	G	17	19	0	18
-19	G	18	0	0	19

From 594093c6caf8b373ea49db9388649232bae75675 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 14 Oct 2011 01:34:07 -0400
Subject: [PATCH 260/282] Merge Suboptimal Structure matching test.

---
 gtfold-mfe/tests/config/test-list.conf        |  4 +-
 gtfold-mfe/tests/config/test-params.conf      |  4 +-
 .../tests/data/subopt_sequences/combseq.seq   |  1 +
 .../tests/data/subopt_sequences/combseq3.seq  |  1 +
 .../tests/data/subopt_sequences/combseq4.seq  |  1 +
 .../tests/data/subopt_sequences/cs1.seq       |  1 +
 .../tests/scripts/SuboptMatchStructures.pm    | 70 +++++++++++++++++++
 7 files changed, 80 insertions(+), 2 deletions(-)
 create mode 100644 gtfold-mfe/tests/data/subopt_sequences/combseq.seq
 create mode 100644 gtfold-mfe/tests/data/subopt_sequences/combseq3.seq
 create mode 100644 gtfold-mfe/tests/data/subopt_sequences/combseq4.seq
 create mode 100644 gtfold-mfe/tests/data/subopt_sequences/cs1.seq
 create mode 100755 gtfold-mfe/tests/scripts/SuboptMatchStructures.pm

diff --git a/gtfold-mfe/tests/config/test-list.conf b/gtfold-mfe/tests/config/test-list.conf
index 827ab10..fbc5593 100644
--- a/gtfold-mfe/tests/config/test-list.conf
+++ b/gtfold-mfe/tests/config/test-list.conf
@@ -1,2 +1,4 @@
 #Scoregtwithunafold
-PseudoKnotDetection
+#ExitCodes
+#CompareGTCTwithUNACT
+SuboptMatchStructures
diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf
index 5b649f8..98f99cc 100644
--- a/gtfold-mfe/tests/config/test-params.conf
+++ b/gtfold-mfe/tests/config/test-params.conf
@@ -1,6 +1,7 @@
 # Important directory variables
 G_GTFOLD_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/src/
 G_UNAFOLD_DIR=/home/users/rbanga/rna/unafold/install/bin/
+G_RNAFOLD_DIR=/usr/local/bin/
 G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/
 #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/
 #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/
@@ -24,4 +25,5 @@ G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test-
 # Local Sequence Directories
 
 # Directory containing sequences for testing pseudoknot detection logic
-#L_EXITCODES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/exitcodes_sequences/
+L_EXITCODES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/exitcodes_sequences/
+L_SUBOPTMATCHSTRUCTURES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/subopt_sequences/
diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq.seq
new file mode 100644
index 0000000..ac737d0
--- /dev/null
+++ b/gtfold-mfe/tests/data/subopt_sequences/combseq.seq
@@ -0,0 +1 @@
+CCCAAAAGGGAAAACCCAAAAGGG
diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq
new file mode 100644
index 0000000..2b55c97
--- /dev/null
+++ b/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq
@@ -0,0 +1 @@
+CCCCAAAAGGGGAAAACCCCAAAAGGGGAAAACCCCAAAAGGGG
diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq
new file mode 100644
index 0000000..c2722ec
--- /dev/null
+++ b/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq
@@ -0,0 +1 @@
+CCCCAAAACCCCAAAAGGGGAAAAGGGG
diff --git a/gtfold-mfe/tests/data/subopt_sequences/cs1.seq b/gtfold-mfe/tests/data/subopt_sequences/cs1.seq
new file mode 100644
index 0000000..5e4009c
--- /dev/null
+++ b/gtfold-mfe/tests/data/subopt_sequences/cs1.seq
@@ -0,0 +1 @@
+CAAAAGAAAACAAAAG
diff --git a/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm
new file mode 100755
index 0000000..1697a46
--- /dev/null
+++ b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm
@@ -0,0 +1,70 @@
+#!/usr/bin/perl
+package SuboptNumStructures;
+use strict;
+use warnings;
+use File::Basename;
+
+sub test()
+{
+  my(%Config) = %{$_[1]};
+  my(%Sequences) = %{$_[2]};
+  my(%local_sequences) = %{$_[3]};
+  my $logger = $_[4];
+
+  my $gtdir = $Config{"G_GTFOLD_DIR"};
+  my $rnadir = $Config{"G_RNAFOLD_DIR"};
+  my $workdir = $Config{"G_WORK_DIR"};
+
+  my $key;
+  my $value;
+  my %new_hash = (%local_sequences);
+  # For testing pseudoknot detection logic
+  # we may only test the sequences specified in local_sequences
+  while (($key, $value) = each(%new_hash)) {
+
+	  my $seqname=$key;
+	  my $path;
+	  my $suffix;
+
+	  my $seqfile = $value;
+    my $dirname = dirname($seqfile);
+	  my $gtout  = "$workdir$seqname-gt";
+    my $rnaout = "$workdir$seqname-rna";
+	  my $gtoutfilename  = $workdir."$seqname-gt.ct";
+
+    my $energy;
+    for ($energy = 1; $energy <=10; ++$energy) {
+
+      my $gtfile = $gtout.$energy;
+      my $rnafile = $rnaout.$energy."_ss.txt";
+  	  my $gtcmd;
+      my $rnacmd;
+      $gtcmd  = "$gtdir/gtfold --subopt $energy $seqfile -o $gtfile > /dev/null 2>&1";
+      $rnacmd  = "$rnadir/RNAsubopt -s DAT -e $energy < $seqfile > $rnafile";
+
+	    system("$gtcmd");
+	    system("$rnacmd");
+
+      my $gtsubopt_file = $gtfile."_ss.txt";
+      my $rnasubopt_file = $rnafile;
+
+      my $gtsorted = $gtsubopt_file."_sorted";
+      my $rnasubopt_sorted = $rnafile."_sorted";
+      `cat $gtsubopt_file | sed '/[A-Z]/d' | sort -o $gtsorted`;
+      `cat $rnasubopt_file | sed '/[A-Z]/d' | sort -o $rnasubopt_sorted`;
+      #`sort $gtsubopt_file -o $gtsorted`;
+      #`sort $rnasubopt_file -o $rnasubopt_sorted`;
+
+      my $diff_str = `diff $gtsorted $rnasubopt_sorted`;
+      #print $diff_str;
+
+      if ($diff_str eq "") {
+        $logger->info("TEST PASSED: $seqname: energy delta = $energy: Suboptimal Structures matched");
+      }
+      else {
+        $logger->error("TEST FAILED: $seqname: energy delta = $energy: Suboptimal Structures not matched\n $diff_str");
+      }
+    }
+  }
+}
+1;

From d966815f1590f2bda3891a251ec493fdac15ef8d Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 14 Oct 2011 01:39:41 -0400
Subject: [PATCH 261/282] Output formatting for saving suboptimal structures to
 a file changed to match rna subopt.

---
 gtfold-mfe/src/main.cc | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 952aba1..89ba476 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -44,7 +44,7 @@
 #include "subopt_traceback.h"
 #include "shapereader.h"
 
-//#define DEBUG 1
+#define DEBUG 1
 
 using namespace std;
 
@@ -227,11 +227,11 @@ void save_subopt_file(string outputFile, ss_map_t& ss_data,
 	outfile.open(outputFile.c_str());
 	char buff[1024];
 
-	sprintf(buff,"%s\t%0.2f", seq.c_str(), energy/100.0);
+	sprintf(buff,"%s %6.2f", seq.c_str(), energy/100.0);
 	outfile << buff << std::endl;
 	for (ss_map_t::iterator it = ss_data.begin(); it!= ss_data.end(); ++it) 
 	{
-		sprintf(buff,"%s %0.2f", (it->first).c_str(), it->second/100.0);
+		sprintf(buff,"%s %6.2f", (it->first).c_str(), it->second/100.0);
 		//outfile << it->first << '\t' << it->second/100.0 << std::endl;
 		outfile << buff << std::endl;
 	}

From d069c655169184e8d32f4908f9c6bcd0be701584 Mon Sep 17 00:00:00 2001
From: Manoj Soni <manoj6891@gmail.com>
Date: Fri, 14 Oct 2011 14:21:22 -0400
Subject: [PATCH 262/282] Few Bug removed from partition function and options
 for getting structure count by partition function added

---
 gtfold-mfe/include/energy.h         |   3 +-
 gtfold-mfe/include/options.h        |   1 +
 gtfold-mfe/include/partition-func.h |   9 +-
 gtfold-mfe/src/energy.c             |   1 +
 gtfold-mfe/src/main.cc              |  66 ++++----
 gtfold-mfe/src/options.cc           |   7 +-
 gtfold-mfe/src/partition-func.c     | 239 +++++++++++++++++-----------
 7 files changed, 203 insertions(+), 123 deletions(-)

diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h
index f742042..b4beeb3 100644
--- a/gtfold-mfe/include/energy.h
+++ b/gtfold-mfe/include/energy.h
@@ -19,7 +19,8 @@ extern int **PP;
 #define WMU(i,j) WM[i][j]
 #define WML(i,j) WM[j][i]
 #define VBI(i,j) VBI[indx[j]+i]
-#define RT ((0.00198721 * 310.15) * 100.00)
+//#define RT ((0.00198721 * 310.15) * 100.00)
+extern const float RT;
 
 #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0)
 
diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index f0499a9..7965698 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -24,6 +24,7 @@ extern bool UNAMODE;
 extern bool RNAMODE;
 extern bool CALC_PART_FUNC;
 extern bool RND_SAMPLE;
+extern bool PF_COUNT_MODE;
 
 extern string seqfile;
 extern string constraintsFile;
diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h
index 6532bea..b2e8c80 100644
--- a/gtfold-mfe/include/partition-func.h
+++ b/gtfold-mfe/include/partition-func.h
@@ -22,8 +22,15 @@ extern	double ** u1;
 extern int part_len;
 double ED3_new(int i, int j, int k);
 double ED5_new(int i, int j, int k);
+double EA_new();
+double EB_new();
+double EC_new();
+double eS_new(int i, int j);
+double eL_new(int i, int j, int p, int q);
+double eH_new(int i, int j);
+double auPenalty_new(int i, int j);
 double f(int j, int h, int l);
-void calculate_partition(int len);
+void calculate_partition(int len, int pf_count_mode);
 void free_partition();
 
 #ifdef __cplusplus
diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index bc71d37..314d35a 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -18,6 +18,7 @@ int *indx;
 int **PP; 
 
 int alloc_flag = 0;
+const float RT = ((0.00198721 * 310.15)*10000); //* 100.00);
 
 void create_tables(int len) {	
 	V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 77a23a5..07f6b19 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -287,43 +287,47 @@ int main(int argc, char** argv) {
   if (CALC_PART_FUNC == true)
   {
     printf("\nComputing partition function...\n");
-    calculate_partition(seq.length());
+    int pf_count_mode = 0;
+    if(PF_COUNT_MODE) pf_count_mode=1;
+    calculate_partition(seq.length(),pf_count_mode);
     free_partition();
     free_fold(seq.length());
     exit(0);
   }
   if (RND_SAMPLE == true)
   {
-    printf("\nComputing partition function...\n");
-    calculate_partition(seq.length());
-    
-    int* structure = new int[seq.length()+1];
-    srand(time(NULL));
-
-    if (num_rnd > 0 ) {
-      printf("\nSampling structures...\n");
-      for (int count = 1; count <= num_rnd; ++count) 
-      {
-        memset(structure, 0, (seq.length()+1)*sizeof(int));
-        rnd_structure(structure, seq.length());
-
-        std::string ensemble(seq.length()+1,'.');
-        for (int i = 1; i <= (int)seq.length(); ++ i) {
-       //     printf("%d %d\n",i,structure[i]);
-          if (structure[i] > 0 && ensemble[i] == '.')
-          {
-            ensemble[i] = '(';
-            ensemble[structure[i]] = ')';
-          }
-        }
-        std::cout << ensemble.substr(1) << std::endl;
-      }
-    }
-
-    free_partition();
-    free_fold(seq.length());
-    delete [] structure;
-    exit(0);
+	  printf("\nComputing partition function...\n");
+	  int pf_count_mode = 1;
+	  //if(PF_COUNT_MODE) pf_count_mode=1;
+	  calculate_partition(seq.length(),pf_count_mode);
+
+	  int* structure = new int[seq.length()+1];
+	  srand(time(NULL));
+
+	  if (num_rnd > 0 ) {
+		  printf("\nSampling structures...\n");
+		  for (int count = 1; count <= num_rnd; ++count) 
+		  {
+			  memset(structure, 0, (seq.length()+1)*sizeof(int));
+			  rnd_structure(structure, seq.length());
+
+			  std::string ensemble(seq.length()+1,'.');
+			  for (int i = 1; i <= (int)seq.length(); ++ i) {
+				  //     printf("%d %d\n",i,structure[i]);
+				  if (structure[i] > 0 && ensemble[i] == '.')
+				  {
+					  ensemble[i] = '(';
+					  ensemble[structure[i]] = ')';
+				  }
+			  }
+			  std::cout << ensemble.substr(1) << std::endl;
+		  }
+	  }
+
+	  free_partition();
+	  free_fold(seq.length());
+	  delete [] structure;
+	  exit(0);
   }
 
 	printf("\nComputing minimum free energy structure...\n");
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index b600088..8a9082f 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -20,6 +20,7 @@ bool RNAMODE = false;
 bool b_prefilter = false;
 bool CALC_PART_FUNC = false;
 bool RND_SAMPLE = false;
+bool PF_COUNT_MODE = false;
 
 string seqfile = "";
 string constraintsFile = "";
@@ -74,6 +75,7 @@ void help() {
     printf("\nBETA OPTIONS\n");
     printf("   --bpp                Calculate base pair probabilities.\n");
     printf("   --partition          Calculate the partition function.\n");
+    printf("   --pf_count          Calculate the structure count using partition function and zero energy value.\n");
     printf("   --subopt NUM         Calculate suboptimal structures within NUM kcal/mol\n");
     printf("                        of the MFE. (Uses -d 2 treatment of dangling energies.)\n");
     printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE.\n");      
@@ -186,7 +188,10 @@ void parse_options(int argc, char** argv) {
           help();
       } else if (strcmp(argv[i],"--partition") == 0) {
         CALC_PART_FUNC = true;
-      } else if (strcmp(argv[i],"--sample") == 0) {
+      } else if (strcmp(argv[i],"--pf_count") == 0) {
+        CALC_PART_FUNC = true;
+	PF_COUNT_MODE = true;
+      }  else if (strcmp(argv[i],"--sample") == 0) {
         RND_SAMPLE = true;
         if(i < argc)
           num_rnd = atoi(argv[++i]);
diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index 51ceede..fcd1b1d 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -6,34 +6,7 @@
 #include "algorithms-partition.h"
 #include "global.h"
 #include "utils.h"
-
-#ifdef _OPENMP 
-#include "omp.h"
-#endif
-
-//#define DEBUG_PF 1
-
-#ifdef DEBUG_PF 
-  #undef Ec
-  #undef Eb
-  #undef Ea
-  #define Ec 0
-  #define Eb 0
-  #define Ea 0
-  #define eS StackE
-  #define eH HairE
-  #define eL ILoopE
-  #define Ed3 D3
-  #define Ed5 D5
-  #define auPenalty Etp
-#endif
-
-int StackE(int i, int j) { return 0; }
-int HairE(int i, int j) { return 0; }
-int ILoopE(int i, int j, int ip, int jp) { return 0; }
-int D3(int i, int j, int k) { return 0; } 
-int D5(int i, int j, int k) { return 0; }
-int Etp(int i, int j) { return 0; }
+//#include "options.h"
 
 double ** u;
 double ** up;
@@ -47,6 +20,7 @@ double ** s3;
 double ** u1;
 
 int part_len;
+int PF_COUNT_MODE_;
 
 static void create_partition_arrays();
 static void init_partition_arrays();
@@ -113,21 +87,71 @@ void set_s1(int i, int j, double val) {if(s1[i][j]!=-1 && s1[i][j]!=val) errorAn
 void set_s2(int i, int j, double val) {if(s2[i][j]!=-1 && s2[i][j]!=val) errorAndExit("set_s2 entry is not -1.\n",i,j,s2[i][j],val); s2[i][j]=val;}
 void set_s3(int i, int j, double val) {if(s3[i][j]!=-1 && s3[i][j]!=val) errorAndExit("set_s3 entry is not -1.\n",i,j,s3[i][j],val); s3[i][j]=val;}
 
+double myExp(double arg){
+	double posArgMultRT = (-1)*arg*RT;
+	if(posArgMultRT>=INFINITY_){
+		//printf("WARN: posArgMultRT is greater than or equal to INFINITY_, hence returning zero\n");
+		return 0;
+	}
+	return exp(arg);
+}
+
+double eS_new(int i, int j){
+	if(PF_COUNT_MODE_) return 0;
+        return eS(i,j);
+}
+
+double eH_new(int i, int j){
+        if(PF_COUNT_MODE_) return 0;
+        return eH(i,j);
+}
+
+double eL_new(int i, int j, int p, int q){
+        if(PF_COUNT_MODE_) return 0;
+        return eL(i,j,p,q);
+}
+
 double ED3_new(int i, int j, int k){
+        if(PF_COUNT_MODE_) return 0;
 	//return Ed3(i,j,k);
 	return Ed5(j,i,k);
+	//return Ed5(i,j,k);
+	//return Ed3(j,i,k);
 }
 
 double ED5_new(int i, int j, int k){
+        if(PF_COUNT_MODE_) return 0;
         //return Ed5(i,j,k);
 	return Ed3(j,i,k);
+	//return Ed3(i,j,k);
+	//return Ed5(j,i,k);
+}
+
+double EA_new(){
+        if(PF_COUNT_MODE_) return 0;
+	return Ea;
+}
+
+double EB_new(){
+        if(PF_COUNT_MODE_) return 0;
+        return Eb;
+}
+
+double EC_new(){
+        if(PF_COUNT_MODE_) return 0;
+        return Ec;
+}
+
+double auPenalty_new(int i, int j){
+        if(PF_COUNT_MODE_) return 0;
+	return auPenalty(i,j);
 }
 
 double f(int j, int h, int l){
 	if(j - 1 == l)
 		return 1;
 	else 
-		return exp(-ED3_new(h,l,l+1)/RT);
+		return myExp(-ED3_new(h,l,l+1)/RT);
 }
 
 void printMatrix(double** u, int part_len){
@@ -162,8 +186,9 @@ printf("\n\nAfter calculation, s3 matrix:\n\n");
 
 }
 
-void calculate_partition(int len) 
-{
+void calculate_partition(int len, int pf_count_mode) 
+{printf("RT=%f\n",RT);//RT=RT/100;
+  PF_COUNT_MODE_ = pf_count_mode;
   int i, j;
   part_len = len;
   create_partition_arrays();
@@ -398,9 +423,9 @@ void fill_partition_arrays()
 		int l;						
 		for (l = h; l < j; ++l)
 		{
-				s1[h][j] = up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))*
-						(exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+
-																				up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))));							
+				s1[h][j] = up[h][l]*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))*
+						(myExp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+
+																				up[l+1][j]*myExp(-(auPenalty_new(l+1,j)/RT))));							
 		}
 }*/
 void calc_s1(int h, int j)//ERROR_FOUND s1[h][j]= instead of +=
@@ -409,12 +434,12 @@ void calc_s1(int h, int j)//ERROR_FOUND s1[h][j]= instead of +=
 		double s1_val = 0.0;
                 for (l = h+1; l < j; ++l)//ERROR
                 {
-			double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)));
-			double v2 = (exp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j));
+			double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)));
+			double v2 = (myExp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j));
 			double v3 = get_ud(l+1,j);
-			double v4 = (get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT)));
+			double v4 = (get_up(l+1,j)*myExp(-(auPenalty_new(l+1,j)/RT)));
 			double val = v1*(v2+v3+v4);
-                        //double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))*(exp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j)+(get_ud(l+1,j)+get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT))));
+                        //double val = get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))*(myExp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j)+(get_ud(l+1,j)+get_up(l+1,j)*myExp(-(auPenalty_new(l+1,j)/RT))));
 			s1_val += val;
                 }
 		set_s1(h,j,s1_val);//s1[h][j] = s1_val;
@@ -427,12 +452,12 @@ void calc_s2(int h, int j)
 	int l;
 	double s2_val = 0.0;							
 	for (l = h+1; l < j; ++l)//ERROR
-	{//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)),(exp(-ED3_new(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)));
-		double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)));
-		double v2 = (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1));
+	{//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)),(myExp(-ED3_new(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)));
+		double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)));
+		double v2 = (myExp(-(ED3_new(h,l,l+1)+EB_new())/RT)*get_u1(l+2,j-1));
 		double v3 = get_u1d(l+1,j-1);
 		double val = v1*(v2+v3);
-		//double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)) * (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1));							
+		//double val = get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)) * (myExp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1));							
 		s2_val += val;//Error: Eb is added
 	}
 	set_s2(h, j, s2_val);//s2[h][j] = s2_val;
@@ -445,12 +470,12 @@ void calc_s3(int h, int j)
 	double s3_val = 0.0;					
   for (l = h+1; l <= j && l+2<=part_len; ++l)//ERROR in for loop variable l
   {
-    	double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)));
-	double v2 = (f(j+1,h,l)*exp(-((j-l)*Eb)/RT));
-	double v3 = (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j));
+    	double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)));
+	double v2 = (f(j+1,h,l)*myExp(-((j-l)*EB_new())/RT));
+	double v3 = (myExp(-(ED3_new(h,l,l+1)+EB_new())/RT)*get_u1(l+2,j));
 	double v4 = get_u1d(l+1,j);
 	double val = v1*(v2+v3+v4);
-	//double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))*(f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j));
+	//double val = get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))*(f(j+1,h,l)*myExp(-((j-l)*Eb)/RT) + myExp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j));
   	s3_val += val;
   }
  set_s3(h, j, s3_val);//s3[h][j] = s3_val;
@@ -494,19 +519,19 @@ void free_partition_arrays()
   if (canPair(RNA[i],RNA[j]) && j-i > TURN)
   {
    for(l=i+2; l<j; ++l){
-      p_val += (up[i+1][l] * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT) * 
-          (exp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * u1[l+2][j-1] + u1d[l+1][j-1]));
+      p_val += (up[i+1][l] * myExp((-1)*(a+2*c+auPenalty_new(i+1,l))/RT) * 
+          (myExp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * u1[l+2][j-1] + u1d[l+1][j-1]));
     }
 
     for(l=i+3; l<j; ++l){
-      p_val += (up[i+2][l]*exp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT) * 
-          (exp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*u1[l+2][j-1] + u1d[l+1][j-1]));
+      p_val += (up[i+2][l]*myExp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * 
+          (myExp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*u1[l+2][j-1] + u1d[l+1][j-1]));
     }
 
     for(h=i+3; h<j-1; ++h){
-      quadraticSum += (s2[h][j] * exp((-1)*(a+2*c+(h-i-1)*b)/RT));	
+      quadraticSum += (s2[h][j] * myExp((-1)*(a+2*c+(h-i-1)*b)/RT));	
     }
-    quadraticSum *= exp((-1)*ED3_new(i,j,i+1)/RT);
+    quadraticSum *= myExp((-1)*ED3_new(i,j,i+1)/RT);
 
     p_val += quadraticSum;
     upm[i][j] = p_val;
@@ -517,7 +542,9 @@ void free_partition_arrays()
 }*/
 
 void calc_upm(int i, int j){//printf("Entering calc_upm: i=%d, j =%d\n",i,j);
-        double a = Ea, b=Eb, c=Ec;
+        double a = EA_new();
+	double b = EB_new();
+	double c = EC_new();
         double p_val = 0;
         int l,h;
         double quadraticSum = 0;
@@ -525,25 +552,25 @@ void calc_upm(int i, int j){//printf("Entering calc_upm: i=%d, j =%d\n",i,j);
   if (canPair(RNA[i],RNA[j]))
   {
    for(l=i+2; l<j; ++l){
-	double v1 = (get_up(i+1,l) * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT));
-	double v2 = (exp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1));
+	double v1 = (get_up(i+1,l) * myExp((-1)*(a+2*c+auPenalty_new(i+1,l))/RT));
+	double v2 = (myExp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1));
 	double v3 = get_u1d(l+1,j-1);
 	p_val = p_val + (v1*(v2+v3));
-        //p_val += (get_up(i+1,l) * exp((-1)*(a+2*c+auPenalty(i+1,l))/RT) * (exp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
+        //p_val += (get_up(i+1,l) * myExp((-1)*(a+2*c+auPenalty_new(i+1,l))/RT) * (myExp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
     }
 
     for(l=i+3; l<j; ++l){
-	double v1 = (get_up(i+2,l)*exp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT));
-	double v2 = (exp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1));
+	double v1 = (get_up(i+2,l)*myExp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT));
+	double v2 = (myExp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1));
 	double v3 = get_u1d(l+1,j-1);
 	p_val = p_val + (v1*(v2+v3));
-        //p_val += (get_up(i+2,l)*exp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
+        //p_val += (get_up(i+2,l)*myExp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * (myExp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
     }
 
     for(h=i+3; h<j-1; ++h){
-      quadraticSum += (get_s2(h,j) * exp((-1)*(a+2*c+(h-i-1)*b)/RT));
+      quadraticSum += (get_s2(h,j) * myExp((-1)*(a+2*c+(h-i-1)*b)/RT));
     }
-    quadraticSum *= (exp((-1)*ED3_new(i,j,i+1)/RT));
+    quadraticSum *= (myExp((-1)*ED3_new(i,j,i+1)/RT));
 
     p_val += quadraticSum;
     set_upm(i, j, p_val);//upm[i][j] = p_val;
@@ -551,7 +578,7 @@ void calc_upm(int i, int j){//printf("Entering calc_upm: i=%d, j =%d\n",i,j);
   else {
     set_upm(i, j, 0.0);//upm[i][j] = 0;
   }
-//printf("Exiting calc_upm: i=%d, j =%d, val=%.3f\n",i,j,upm[i][j]);
+//printf("Exiting calc_upm: i=%d, j =%d, val=%.3f\n",i,j,upm[i][j]/up[i][j]);
 }
 
 
@@ -563,7 +590,7 @@ void calc_u1(int i, int j){
 	double quadraticSum = 0;
 	
 	for(h=i+1; h<=j; ++h){
-		quadraticSum += (s3[h][j] * exp((-1)*(c+(h-i)*b)/RT));
+		quadraticSum += (s3[h][j] * myExp((-1)*(c+(h-i)*b)/RT));
 	}
 	
 	p_val += quadraticSum;
@@ -571,13 +598,14 @@ void calc_u1(int i, int j){
 	u1[i][j] = p_val;
 }*/
 void calc_u1(int i, int j){//printf("Entering calc_u1: i=%d, j =%d\n",i,j);
-        double b=Eb, c=Ec;
+        double b = EB_new();
+	double c = EC_new();
         double p_val = get_u1d(i,j);
         int h;
         double quadraticSum = 0;
 
         for(h=i+1; h<j; ++h){
-                quadraticSum += (get_s3(h,j) * exp((-1)*(c+(h-i)*b)/RT));
+                quadraticSum += (get_s3(h,j) * myExp((-1)*(c+(h-i)*b)/RT));
         }
 
         p_val += quadraticSum;
@@ -594,24 +622,25 @@ void calc_u1d(int i, int j){
 	int l;
 
 	for(l=i+1; l<=j; ++l){
-		p_val += (up[i][l]*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(ED3_new(i,l,l+1)+b)/RT)*u1[l+2][j] + u1d[l+1][j]));
+		p_val += (up[i][l]*myExp((-1)*(c+auPenalty_new(i,l))/RT) * (f(j+1,i,l)*myExp((-1)*(j-l)*b/RT) + myExp((-1)*(ED3_new(i,l,l+1)+b)/RT)*u1[l+2][j] + u1d[l+1][j]));
 	}
 
 	u1d[i][j] = p_val;
 }*/
 
 void calc_u1d(int i, int j){//printf("Entering calc_u1d: i=%d, j =%d\n",i,j);
-        double b=Eb, c=Ec;
+        double b = EB_new();
+	double c = EC_new();
         double p_val = 0;
         int l;
 
         for(l=i+1; l<=j; ++l){//for(l=i+1; l<=j && l+2<=part_len; ++l){//ERROR in l,,,//up should be calculated before u1d
-                double v1 = (get_up(i,l)*exp((-1)*(c+auPenalty(i,l))/RT));
-		double v2 = (f(j+1,i,l)*exp((-1)*(j-l)*b/RT));
-		double v3 = (exp((-1)*(ED3_new(i,l,l+1)+b)/RT)*get_u1(l+2,j));
+                double v1 = (get_up(i,l)*myExp((-1)*(c+auPenalty_new(i,l))/RT));
+		double v2 = (f(j+1,i,l)*myExp((-1)*(j-l)*b/RT));
+		double v3 = (myExp((-1)*(ED3_new(i,l,l+1)+b)/RT)*get_u1(l+2,j));
 		double v4 = get_u1d(l+1,j);
 		p_val += (v1*(v2+v3+v4));
-		//p_val += (get_up(i,l)*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(ED3_new(i,l,l+1)+b)/RT)*get_u1(l+2,j) + get_u1d(l+1,j)));
+		//p_val += (get_up(i,l)*myExp((-1)*(c+auPenalty_new(i,l))/RT) * (f(j+1,i,l)*myExp((-1)*(j-l)*b/RT) + myExp((-1)*(ED3_new(i,l,l+1)+b)/RT)*get_u1(l+2,j) + get_u1d(l+1,j)));
         }
 
          set_u1d(i, j, p_val);//u1d[i][j] = p_val;
@@ -627,7 +656,7 @@ void calc_u(int i, int j)
 	uval +=  ud[i][j];
 	
   for (h = i+1; h < j; ++h) {
-		uval += up[h][j] * exp( -(ED5_new(h,j,h-1) + auPenalty(h,j)) / RT );
+		uval += up[h][j] * myExp( -(ED5_new(h,j,h-1) + auPenalty_new(h,j)) / RT );
 	}
 
 	for (ctr = i+1; ctr < j-1; ++ctr) {
@@ -637,13 +666,13 @@ void calc_u(int i, int j)
 }*/
 void calc_u(int i, int j)
 {//printf("Entering calc_u: i=%d, j =%d\n",i,j);
-        double uval = 1 + get_up(i,j)*exp(-auPenalty(i,j)/RT);
+        double uval = 1 + get_up(i,j)*myExp(-auPenalty_new(i,j)/RT);
   int h;
         int ctr;
         uval +=  get_ud(i,j);
 
   for (h = i+1; h < j; ++h) {
-                uval += (get_up(h,j) * exp( -(ED5_new(h,j,h-1) + auPenalty(h,j)) / RT ));
+                uval += (get_up(h,j) * myExp( -(ED5_new(h,j,h-1) + auPenalty_new(h,j)) / RT ));
         }
 
         for (ctr = i+1; ctr < j-1; ++ctr) {
@@ -663,13 +692,13 @@ void calc_ud(int i, int j)
   {
 		double val1, val2, val3;
 		val1 = up[i][l];
-		val1 = val1 * exp(-auPenalty(i,l) / RT);
+		val1 = val1 * myExp(-auPenalty_new(i,l) / RT);
 
 		val2 = u[l+2][j];
-		val2 = val2 * exp(-ED3_new(i,l,l+1)/RT);
+		val2 = val2 * myExp(-ED3_new(i,l,l+1)/RT);
 
 		val3 = ud[l+1][j];
-		val3 = val3 + up[l+1][j] * exp( -auPenalty(l+1,j) / RT );
+		val3 = val3 + up[l+1][j] * myExp( -auPenalty_new(l+1,j) / RT );
 
 		udij += (val1 * (val2 + val3));
 	}
@@ -685,13 +714,13 @@ void calc_ud(int i, int j)
   {
                 double val1, val2, val3;
                 val1 = get_up(i,l);
-                val1 = val1 * exp(-auPenalty(i,l) / RT);
+                val1 = val1 * myExp(-auPenalty_new(i,l) / RT);
 
                 val2 = get_u(l+2,j);
-                val2 = val2 * exp(-ED3_new(i,l,l+1)/RT);
+                val2 = val2 * myExp(-ED3_new(i,l,l+1)/RT);
 
                 val3 = get_ud(l+1,j);
-                val3 = val3 + get_up(l+1,j) * exp( -auPenalty(l+1,j) / RT );
+                val3 = val3 + get_up(l+1,j) * myExp( -auPenalty_new(l+1,j) / RT );
 
                 udij += (val1 * (val2 + val3));
         }
@@ -714,13 +743,13 @@ void calc_up(int i, int j)
 
       for (q = minq; q <= maxq; q++) {
         if (canPair(p,q)==0) continue;
-        up_val += (up[p][q] * exp(-eL(i,j,p,q)/RT));
+        up_val += (up[p][q] * myExp(-eL_new(i,j,p,q)/RT));
       }
     }
 
-    up_val = up_val * exp(-ED3_new(i,j,i+1)/RT);
-    up_val = up_val + exp(-eH(i,j)/RT );
-    up_val = up_val + exp(-eS(i,j)/RT ) * up[i+1][j-1];
+    up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT);
+    up_val = up_val + myExp(-eH_new(i,j)/RT );
+    up_val = up_val + myExp(-eS_new(i,j)/RT ) * up[i+1][j-1];
     up_val = up_val + upm[i][j];
 
     up[i][j] = up_val;
@@ -730,6 +759,37 @@ void calc_up(int i, int j)
   }
 }*/
 
+void printUPprobabilities(int i, int j){
+	int h,l;
+	double maxIntLoopProb = 0.0;
+        int h_max=-1, l_max=-1;
+	double sum=0.0;
+    for (h = i+1; h < j ; h++) {
+      for (l = h+1; l < j; l++) {
+        if (canPair(RNA[h],RNA[l])==0) continue;
+        if(h==(i+1) && l==(j-1)) continue;
+        //if((l-h)<=TURN) continue;
+         double intLoopProb = (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT))/up[i][j];
+	sum+=intLoopProb;
+	 if(intLoopProb > maxIntLoopProb){ maxIntLoopProb = intLoopProb; h_max=h; l_max=l;}
+      }
+    }
+
+        //ERROR below line should not be there
+    //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT);
+    double hpProb = myExp(-((double)eH_new(i,j))/RT )/up[i][j];
+    double stackProb = (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1))/up[i][j];
+    double upmProb = get_upm(i,j)/up[i][j];
+
+    if(maxIntLoopProb>=hpProb && maxIntLoopProb>=stackProb && maxIntLoopProb >=upmProb) printf("INT ");
+    else if(hpProb>=maxIntLoopProb && hpProb>=stackProb && hpProb>=upmProb) printf("HPL ");
+    else if(stackProb>=hpProb && stackProb>=maxIntLoopProb && stackProb>=upmProb) printf("STK ");
+    else if(upmProb>=hpProb && upmProb>=stackProb && upmProb>=maxIntLoopProb) printf("UPM ");
+
+printf("printing probabilities: i=%d, j =%d, upmProb=%.6f, stackProb=%.6f, hpProb=%.6f, maxIntLoopProb=%.6f,  sumIntLoopProbs=%.6f, h_max=%d, l_max=%d\n",i,j, upmProb, stackProb, hpProb, maxIntLoopProb,sum,h_max,l_max);
+
+}
+
 void calc_up(int i, int j)
 {//printf("Entering calc_up: i=%d, j =%d\n",i,j);
   double up_val = 0.0;
@@ -744,7 +804,7 @@ void calc_up(int i, int j)
 
       for (q = minq; q <= maxq; q++) {
        if (canPair(p,q)==0) continue;
-        up_val += (get_up(p,q) * exp(-eL(i,j,p,q)/RT));
+        up_val += (get_up(p,q) * myExp(-eL_new(i,j,p,q)/RT));
       }
     }*/
 	int h,l;
@@ -753,17 +813,18 @@ void calc_up(int i, int j)
         if (canPair(RNA[h],RNA[l])==0) continue;
 	if(h==(i+1) && l==(j-1)) continue;
 	//if((l-h)<=TURN) continue;
-        up_val += (get_up(h,l) * exp(-eL(i,j,h,l)/RT));
+        up_val += (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT));
       }
     }
 
 	//ERROR below line should not be there
-    //up_val = up_val * exp(-ED3_new(i,j,i+1)/RT);
-    up_val = up_val + exp(-eH(i,j)/RT );
-    up_val = up_val + (exp(-eS(i,j)/RT ) * get_up(i+1,j-1));
+    //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT);
+    up_val = up_val + myExp(-((double)eH_new(i,j))/RT );
+    up_val = up_val + (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1));
     up_val = up_val + get_upm(i,j);
 
     set_up(i, j, up_val);//up[i][j] = up_val;
+    //printUPprobabilities(i,j);
   }
   else  {
     set_up(i, j, 0.0);//up[i][j] = 0;

From f587da4138bfa2dd6fde09bd51cbb79875c13437 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 14 Oct 2011 19:45:55 -0400
Subject: [PATCH 263/282] Constraint Verification Tests - The tests generate
 random constraints and verifies that they are not violated in the generated
 structure.

---
 gtfold-mfe/src/algorithms.c                   |   2 +-
 gtfold-mfe/tests/config/test-list.conf        |   3 +-
 gtfold-mfe/tests/config/test-params.conf      |   7 +
 .../data/constraints_sequences/combseq3.seq   |   1 +
 .../tests/scripts/ConstraintsVerification.pm  | 162 ++++++++++++++++++
 5 files changed, 173 insertions(+), 2 deletions(-)
 create mode 100644 gtfold-mfe/tests/data/constraints_sequences/combseq3.seq
 create mode 100755 gtfold-mfe/tests/scripts/ConstraintsVerification.pm

diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 0bbdceb..7d81bfe 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -229,7 +229,7 @@ int calculate(int len) {
   W[0] = 0;
   for (j = 1; j <= len; j++) {
     int i, Wj, Widjd, Wijd, Widj, Wij, Wim1;
-    Wj = INFINITY_;
+    Wj = 0;
     for (i = 1; i < j-TURN; i++) {
       Wij = Widjd = Wijd = Widj = INFINITY_;
       Wim1 = MIN(0, W[i-1]); 
diff --git a/gtfold-mfe/tests/config/test-list.conf b/gtfold-mfe/tests/config/test-list.conf
index fbc5593..bff0017 100644
--- a/gtfold-mfe/tests/config/test-list.conf
+++ b/gtfold-mfe/tests/config/test-list.conf
@@ -1,4 +1,5 @@
 #Scoregtwithunafold
 #ExitCodes
 #CompareGTCTwithUNACT
-SuboptMatchStructures
+#SuboptMatchStructures
+ConstraintsVerification
diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf
index 98f99cc..81ad292 100644
--- a/gtfold-mfe/tests/config/test-params.conf
+++ b/gtfold-mfe/tests/config/test-params.conf
@@ -26,4 +26,11 @@ G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test-
 
 # Directory containing sequences for testing pseudoknot detection logic
 L_EXITCODES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/exitcodes_sequences/
+L_SUBOPTMATCHSTRUCTURES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/
 L_SUBOPTMATCHSTRUCTURES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/subopt_sequences/
+L_SUBOPTMATCHSTRUCTURES_MIN_ENERGY=0
+L_SUBOPTMATCHSTRUCTURES_MAX_ENERGY=1
+L_SUBOPTMATCHSTRUCTURES_ENERGY_STRIDE=1
+L_SUBOPTMATCHSTRUCTURES_INCLUDE_SEQUENCES=d.5.a.H.*
+L_CONSTRAINTSVERIFICATION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/constraints_sequences/
+L_CONSTRAINTSVERIFICATION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/constraints_sequences/
diff --git a/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq b/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq
new file mode 100644
index 0000000..2b55c97
--- /dev/null
+++ b/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq
@@ -0,0 +1 @@
+CCCCAAAAGGGGAAAACCCCAAAAGGGGAAAACCCCAAAAGGGG
diff --git a/gtfold-mfe/tests/scripts/ConstraintsVerification.pm b/gtfold-mfe/tests/scripts/ConstraintsVerification.pm
new file mode 100755
index 0000000..22617bb
--- /dev/null
+++ b/gtfold-mfe/tests/scripts/ConstraintsVerification.pm
@@ -0,0 +1,162 @@
+#!/usr/bin/perl
+package ConstraintsVerification;
+use strict;
+use warnings;
+use File::Basename;
+
+require 'test_utils.pl';
+
+sub test()
+{
+  my(%Config) = %{$_[1]};
+  my(%Sequences) = %{$_[2]};
+  my(%local_sequences) = %{$_[3]};
+  my $logger = $_[4];
+
+  my $gtdir = $Config{"G_GTFOLD_DIR"};
+  my $unadir = $Config{"G_UNAFOLD_DIR"};
+  my $workdir = $Config{"G_WORK_DIR"};
+
+  my $key;
+  my $value;
+  my %new_hash = (%local_sequences, %Sequences);
+
+  while (($key, $value) = each(%new_hash)) {
+
+	  my $seqname=$key;
+	  my $path;
+	  my $suffix;
+
+	  my $seqfile = $value;
+    my $dirname = dirname($seqfile);
+    my $constraint_file = "$workdir/$seqname.constraint";
+	  my $gtout  = "$workdir$seqname-gt";
+	  my $gtoutfilename  = $workdir."$seqname-gt.ct";
+
+	  my $gtcmd;
+    $gtcmd  = "$gtdir/gtfold $seqfile -o $gtout > /dev/null 2>&1";
+	  system("$gtcmd");
+    my $len = get_seq_len_from_ctfile($gtoutfilename);
+    my $CONSFILE;
+    open($CONSFILE, '>', $constraint_file) or die "Couldn't open $_";
+    generate_constraints(1, $len, $CONSFILE);
+    close $CONSFILE;
+
+    my $gtout_constraints = $gtout."_constraints";
+    my $gtout_constraints_filename = "$gtout_constraints.ct";
+    $gtcmd  = "$gtdir/gtfold -c $constraint_file $seqfile -o $gtout_constraints > /dev/null 2>&1";
+	  my $exitcode = system("$gtcmd") >> 8;
+
+    if ($exitcode != 0) {
+      $logger->error("TEST FAILED: $seqname : Assertion Failed, Exit Code incorrect: $exitcode. Constraint File: $constraint_file");
+      next;
+    }
+
+    my @violated_constraints = verify_constraints($gtout_constraints_filename, $constraint_file);
+    if (@violated_constraints) {
+      my @vc = join(',', @violated_constraints);
+      print scalar(@violated_constraints);
+      $logger->error("TEST FAILED: $seqname : Constraints Violated: Input Constraint File $constraint_file. Violated Constraints:\n @vc");
+    }
+    else {
+      $logger->info("TEST PASSED: $seqname : Input Constraint File $constraint_file");
+    }
+  }
+}
+
+sub generate_constraints
+{
+  my $i = shift;
+  my $j = shift;
+  my $CONSFILE = shift;
+
+  return if ($j-$i< 4); 
+  
+  my $r = rand();
+  print $CONSFILE "F $i $j 1\n" if $r <0.4;
+  print $CONSFILE "P $i $j 1\n" if $r >0.4 && $r<0.8;
+  print $CONSFILE "P $i 0 1\n" if $r >0.8;
+
+  my $range = $j-$i;
+  my $ii = int(rand($range)) + $i;
+  $range = $j-$ii;
+  my $jj = int(rand($range)) + $ii;
+
+  generate_constraints($i+1,$ii-1, $CONSFILE);
+  generate_constraints($jj+1,$j-1, $CONSFILE);
+}
+
+sub get_seq_len_from_ctfile
+{
+  my $filename = shift;
+  open(IN, "<$filename");
+  my $header  = <IN>; # ignore first line
+  close IN;
+  my ($len, $dG) = split(' ', $header);
+  return $len;
+}
+
+sub verify_constraints {
+
+  my $ctfilename = shift;
+  my $cffilename = shift;
+
+  open CT, $ctfilename;
+  open CF, $cffilename;
+
+  my %ct_hash = ();
+  my @rna;
+  my $count=1;
+
+  my $header  = <CT>; # ignore first line
+  while (<CT>)
+  {
+    my @ff = split(' ', $_);
+    $ct_hash{$ff[0]} = $ff[4];
+    $rna[$count] = $ff[1];
+    ++$count;
+  }
+
+  my @violated_constraints = ();
+  while(<CF>) 
+  {
+    chomp;
+    my @ff = split(' ', $_);
+    if ($ff[0] eq 'P' && $ff[2] == 0) { # case SS
+      if ($ct_hash{$ff[1]} != 0) {
+        print $_."\n";
+        push(@violated_constraints, $_);
+      }
+    }
+    elsif ($ff[0] eq 'P' && $ct_hash{$ff[1]} == $ff[2] && $ct_hash{$ff[2]} == $ff[1]) { # case P
+        print $_."\n";
+        print "$ct_hash{$ff[1]} $ct_hash{$ff[2]}\n";
+      push(@violated_constraints, $_);
+    }
+    elsif ($ff[0] eq 'F' && $ff[2] == 0)	{
+      my $b = canPair($rna[$ff[1]], $rna[$ff[2]]); 	
+      if ($b == 1) {
+        print $_."\n";
+        push(@violated_constraints, $_);
+      }
+    }
+  }
+
+  close CT;
+  close CF;
+
+  return @violated_constraints;
+}
+
+sub canPair {
+	 my ( $i, $j) = @_;
+	# (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). 
+	 return 1 if ($i eq 'A' && $j eq 'U') ;
+	 return 1 if ($i eq 'U' && $j eq 'A') ;
+	 return 1 if ($i eq 'C' && $j eq 'G') ;
+	 return 1 if ($i eq 'G' && $j eq 'C') ;
+	 return 1 if ($i eq 'G' && $j eq 'U') ;
+	 return 1 if ($i eq 'U' && $j eq 'G') ;
+	 return 0;
+}
+1;

From c9ea34380121988d1084b54f089a97fa7cf47d18 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@hpc18.cc.gt.atl.ga.us>
Date: Sun, 16 Oct 2011 10:48:53 -0400
Subject: [PATCH 264/282] adding changes to sampling

---
 gtfold-mfe/include/stochastic-sampling.h |   6 +-
 gtfold-mfe/src/main.cc                   |   8 +-
 gtfold-mfe/src/stochastic-sampling.cc    | 131 ++++++++++++++++-------
 3 files changed, 99 insertions(+), 46 deletions(-)

diff --git a/gtfold-mfe/include/stochastic-sampling.h b/gtfold-mfe/include/stochastic-sampling.h
index e318296..68fea91 100644
--- a/gtfold-mfe/include/stochastic-sampling.h
+++ b/gtfold-mfe/include/stochastic-sampling.h
@@ -67,7 +67,7 @@ struct base_pair
 
   friend std::ostream& operator << (std::ostream& out, const base_pair& bp)
   {
-    out << '(' << bp.i << '-' << bp.j << ')' << ' ' << bp.isPaired() << std::endl;
+    out << '(' << bp.i << '-' << bp.j << ')' << ' ' << bp.t << std::endl;
     return out;
   }
 };
@@ -76,12 +76,12 @@ void set_single_stranded(int i, int j, int* structure);
 void set_base_pair(int i, int j, int* structure);
 
 void rnd_upm(int i, int j, int* structure);
-void rnd_u1d(int i, int j, int* structure);
+void rnd_u1d(int i, int j, int* structure) ;
 void  rnd_u1(int i, int j, int* structure);
 void  rnd_up(int i, int j, int* structure);
 void  rnd_ud(int i, int j, int* structure);
 void   rnd_u(int i, int j, int* structure);
 
-void rnd_structure(int* structure, int len);
+double rnd_structure(int* structure, int len);
 
 #endif
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 07f6b19..1d5e1e3 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -297,8 +297,8 @@ int main(int argc, char** argv) {
   if (RND_SAMPLE == true)
   {
 	  printf("\nComputing partition function...\n");
-	  int pf_count_mode = 1;
-	  //if(PF_COUNT_MODE) pf_count_mode=1;
+	  int pf_count_mode = 0;
+	  if(PF_COUNT_MODE) pf_count_mode=1;
 	  calculate_partition(seq.length(),pf_count_mode);
 
 	  int* structure = new int[seq.length()+1];
@@ -309,7 +309,7 @@ int main(int argc, char** argv) {
 		  for (int count = 1; count <= num_rnd; ++count) 
 		  {
 			  memset(structure, 0, (seq.length()+1)*sizeof(int));
-			  rnd_structure(structure, seq.length());
+			  double energy = rnd_structure(structure, seq.length());
 
 			  std::string ensemble(seq.length()+1,'.');
 			  for (int i = 1; i <= (int)seq.length(); ++ i) {
@@ -320,7 +320,7 @@ int main(int argc, char** argv) {
 					  ensemble[structure[i]] = ')';
 				  }
 			  }
-			  std::cout << ensemble.substr(1) << std::endl;
+			  std::cout << ensemble.substr(1) << ' ' << energy << std::endl;
 		  }
 	  }
 
diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc
index 8ece94b..a311e10 100644
--- a/gtfold-mfe/src/stochastic-sampling.cc
+++ b/gtfold-mfe/src/stochastic-sampling.cc
@@ -6,7 +6,7 @@
 #include <stack>
 
 std::stack<base_pair> g_stack;
-
+int energy = 0;
 
 double randdouble()
 {
@@ -25,12 +25,12 @@ double U_0(int i, int j)
 
 double U_ij(int i, int j)
 {
-  return (feasible(i,j) == true)?up[i][j]*exp(-auPenalty(i,j)/RT)/u[i][j]:0;
+  return (feasible(i,j) == true)?up[i][j]*exp(-auPenalty_new(i,j)/RT)/u[i][j]:0;
 }
 
 double U_hj(int i, int h, int j)
 {
-  return (feasible(h,j) == true)?up[h][j]*exp(-(ED5_new(h,j,h-1)+auPenalty(h,j))/RT)/u[i][j]:0;
+  return (feasible(h,j) == true)?up[h][j]*exp(-(ED5_new(h,j,h-1)+auPenalty_new(h,j))/RT)/u[i][j]:0;
 }
 
 double U_il(int i, int j)
@@ -45,42 +45,42 @@ double U_s1h(int i, int h, int j)
 
 double U_ihlj_case1(int i, int h, int l, int j)
 {
-  return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)* (exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]:0;
+  return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]:0;
 }
 
 double U_ihlj_case2(int i, int h, int l, int j)
 {
-  return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)* (ud[l+1][j]) /s1[h][j]:0;
+  return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (ud[l+1][j]) /s1[h][j]:0;
 }
 
 double U_ihlj_case3(int i, int h, int l, int j)
 {
-  return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))) /s1[h][j]:0;
+  return (feasible(h,l)&&feasible(l+1,j))?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty_new(l+1,j)/RT))) /s1[h][j]:0;
 }
 
 double UD_il_case1(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*ED3_new(i,l,l+1)/RT)*u[l+2][j])/ud[i][j]:0;  
+  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*exp(-1*ED3_new(i,l,l+1)/RT)*u[l+2][j])/ud[i][j]:0;  
 }
 
 double UD_il_case2(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/ud[i][j]:0;
+  return feasible(i,l)?(up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*ud[l+1][j])/ud[i][j]:0;
 }
 
 double UD_il_case3(int i, int l, int j)
 {
-  return feasible(i,l)?up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/ud[i][j]:0;
+  return (feasible(i,l)&&feasible(l+1,j))?up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty_new(l+1,j))/ud[i][j]:0;
 }
 
 double Q_ijH(int i, int j)
 {
-  return exp(-eH(i,j)/RT)/up[i][j];
+  return exp(-eH_new(i,j)/RT)/up[i][j];
 }
 
 double Q_ijS(int i, int j)
 {
-  return exp(-eS(i,j)/RT)*up[i+1][j-1]/up[i][j];
+  return exp(-eS_new(i,j)/RT)*up[i+1][j-1]/up[i][j];
 }
 
 double Q_ijM(int i, int j)
@@ -88,64 +88,77 @@ double Q_ijM(int i, int j)
   return upm[i][j]/up[i][j];
 }
 
+/*
+double Q_ijBI(int i, int j)
+{
+  double sum = 0;
+  for (int h = i+1; h < j-1; ++h)
+    for (int l = h+1; l < j; ++l)
+    {
+      if (h == i+1 && l == j-1) continue;
+      sum += feasible(h,l)?(exp(-1*eL_new(i,j,h,l)/RT)*up[h][l]):0; 
+    }
+  return sum/up[i][j];
+}*/
+
 double Q_ijhlBI(int i, int j, int h, int l)
 {
-  return feasible(h,l)?exp(-1*eL(i,j,h,l)/RT)*up[h][l]/up[i][j]:0;
+  return feasible(h,l)?exp(-1*eL_new(i,j,h,l)/RT)*up[h][l]/up[i][j]:0;
 }
 
 double UPM_ip1l_case1(int i, int l, int j)
 {
-  return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * exp(-1*(ED3_new(i+1,l,l+1)+Eb)/RT) * u1[l+2][j-1])/upm[i][j]:0;
+  return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(EA_new()+2*EC_new()+auPenalty_new(i+1,l))/RT) * exp(-1*(ED3_new(i+1,l,l+1)+EB_new())/RT) * u1[l+2][j-1])/upm[i][j]:0;
 }
 
 double UPM_ip1l_case2(int i, int l, int j)
 {
-  return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0;
+  return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(EA_new()+2*EC_new()+auPenalty_new(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0;
 }
 
 double UPM_ip2l_case1(int i, int l , int j)
 {
-  return feasible(i+2,l)?up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+Eb)/RT)*u1[l+2][j-1])/upm[i][j]:0;
+  return feasible(i+2,l)?up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+EB_new())/RT)*u1[l+2][j-1])/upm[i][j]:0;
 }
 
 double UPM_ip2l_case2(int i, int l , int j)
 {
-  return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0;
+  return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0;
 }
 
 
 double UPM_ijs2h(int i, int h , int j)
 {
-  return exp((-1)*ED3_new(i,j,i+1)/RT)* (s2[h][j] * exp((-1)*(Ea+2*Ec+(h-i-1)*Eb)/RT))/upm[i][j];
+  return exp((-1)*ED3_new(i,j,i+1)/RT)* (s2[h][j] * exp((-1)*(EA_new()+2*EC_new()+(h-i-1)*EB_new())/RT))/upm[i][j];
 }
 
 
 double UPM_ijhl_case1(int i, int h, int l, int j)
 {
-  return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-ED3_new(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]:0;
+  return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (exp(-ED3_new(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]:0;
 }
 
 double UPM_ijhl_case2(int i, int h, int l, int j)
 {
-  return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]:0;
+  return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]:0;
 }
 
 // u1d : case 1
 double U1D_ij_il_case1(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1d[i][j]:0;
+  return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*EB_new()/RT)))/u1d[i][j]:0;
 }
 
 // u1d : case 2
 double U1D_ij_il_case2(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(ED3_new(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1d[i][j]:0;
+  return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT)*(exp((-1)*(ED3_new(i,l,l+1)+EB_new())/RT)*u1[l+2][j]))/u1d[i][j]:0;
 }
 
 // u1d : case 3
 double U1D_ij_il_case3(int i, int l, int j)
 {
-  return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1d[i][j]:0;
+  return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT) * u1d[l+1][j])/u1d[i][j]:0;
 }
 
 // u1
@@ -157,40 +170,43 @@ double U1_ij(int i, int j)
 // u1 : sample h
 double U1_ij_s3h(int i, int h, int j)
 {
-  return (s3[h][j] * exp((-1)*(Ec+(h-i)*Eb)/RT))/u1[i][j];
+  return (s3[h][j] * exp((-1)*(EC_new()+(h-i)*EB_new())/RT))/u1[i][j];
 }
 
 // u1 : sample l
 double U1_j_hl_case1(int h, int l, int j)
 {
-  return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT))) /s3[h][j]:0;
+  return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*EB_new())/RT))) /s3[h][j]:0;
 }
 
 double U1_j_hl_case2(int h, int l, int j)
 {
-  return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*u1[l+2][j])) /s3[h][j]:0;
+  return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (exp(-(ED3_new(h,l,l+1)+EB_new())/RT)*u1[l+2][j])) /s3[h][j]:0;
 }
 
 double U1_j_hl_case3(int h, int l, int j)
 {
-  return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]:0;
+  return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]:0;
 }
 
 void rnd_u(int i, int j, int* structure)
 {
   double rnd = randdouble();
   double cum_prob = 0.0;
+ 
 
   cum_prob += U_0(i,j);
   if (rnd < cum_prob)
   {
     //set_single_stranded(i,j, structure);
+    //energy += 0;
     return;
   }
   
   cum_prob += U_ij(i, j);
   if (rnd < cum_prob)
   {
+    energy += auPenalty_new(i,j);
     base_pair bp(i,j,UP);
     g_stack.push(bp);
     return;
@@ -201,6 +217,7 @@ void rnd_u(int i, int j, int* structure)
     cum_prob += U_hj(i,h,j);
     if (rnd < cum_prob)
     {
+      energy += ED5_new(h,j,h-1)+auPenalty_new(h,j);
       base_pair bp(h,j,UP);
       //set_single_stranded(i,h-1,structure);
       g_stack.push(bp);
@@ -226,6 +243,7 @@ void rnd_u(int i, int j, int* structure)
       break;
     }
   }
+
   assert (h1 != -1) ;
 
   rnd = randdouble();
@@ -236,6 +254,7 @@ void rnd_u(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       //set_single_stranded(i,h1-1,structure);
+      energy += (ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1));
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+2,j,U);
       g_stack.push(bp1);
@@ -246,6 +265,7 @@ void rnd_u(int i, int j, int* structure)
     cum_prob += U_ihlj_case2(i,h1,l,j);
     if (rnd < cum_prob)
     {
+      energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l));
       //set_single_stranded(i,h1-1,structure);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,UD);
@@ -257,6 +277,7 @@ void rnd_u(int i, int j, int* structure)
     cum_prob += U_ihlj_case3(i,h1,l,j);
     if (rnd < cum_prob)
     {
+      energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + auPenalty_new(l+1,j));
       //set_single_stranded(i,h1-1,structure);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,UP);
@@ -264,6 +285,7 @@ void rnd_u(int i, int j, int* structure)
       g_stack.push(bp2);
       return ;
     }
+    
   }
   assert(0);
 }
@@ -277,6 +299,7 @@ void rnd_ud(int i, int j, int* structure)
     cum_prob += UD_il_case1(i,l,j);
     if (rnd < cum_prob)
     {
+      energy += (auPenalty_new(i,l) + ED3_new(i,l,l+1));
       base_pair bp1(i,l,UP);
       base_pair bp2(l+2,j,U);
       g_stack.push(bp1);
@@ -287,6 +310,7 @@ void rnd_ud(int i, int j, int* structure)
     cum_prob += UD_il_case2(i,l,j);
     if (rnd < cum_prob)
     {
+      energy += auPenalty_new(i,l);
       base_pair bp1(i,l,UP);
       base_pair bp2(l+1,j,UD);
       g_stack.push(bp1);
@@ -297,6 +321,7 @@ void rnd_ud(int i, int j, int* structure)
     cum_prob += UD_il_case3(i,l,j);
     if (rnd < cum_prob)
     {
+      energy += (auPenalty_new(i,l) + auPenalty_new(l+1,j));
       base_pair bp1(i,l,UP);
       base_pair bp2(l+1,j,UP);
       g_stack.push(bp1);
@@ -310,28 +335,32 @@ void rnd_ud(int i, int j, int* structure)
 void rnd_up(int i, int j, int* structure)
 {
   double rnd = randdouble();
+  double cum_prob = 0;
+  //printf("%d %d %1.6lf %1.6lf %1.6lf %1.6lf\n",i,j,rnd,Q_ijH(i,j),Q_ijS(i,j), Q_ijM(i,j));
   assert(structure[i] == 0);
   assert(structure[j] == 0);
   
   set_base_pair(i,j,structure);
 
-  rnd -= Q_ijH(i,j);
-  if (rnd < 0)
+  cum_prob += Q_ijH(i,j);
+  if (rnd < cum_prob)
   {
+    energy += eH_new(i,j);
     //set_single_stranded(i+1,j-1,structure);
     return ;
   }
 
-  rnd -= Q_ijS(i,j);
-  if (rnd  < 0)
+  cum_prob += Q_ijS(i,j);
+  if (rnd < cum_prob)
   {
+    energy += eS_new(i,j);
     base_pair bp(i+1,j-1,UP);
     g_stack.push(bp);
     return ;
   }
 
-  rnd -= Q_ijM(i,j);
-  if (rnd < 0)
+  cum_prob += Q_ijM(i,j);
+  if (rnd < cum_prob)
   {
     rnd_upm(i,j,structure);
     return;
@@ -341,14 +370,17 @@ void rnd_up(int i, int j, int* structure)
     for (int l = h+1; l < j; ++l)
     {
       if (h == i+1 && l == j-1) continue;
-      rnd -= Q_ijhlBI(i,j,h,l);
-      if (rnd < 0)
+      cum_prob += Q_ijhlBI(i,j,h,l);
+      if (rnd < cum_prob)
       {
+        energy += eL_new(i,j,h,l);
         base_pair bp(h,l,UP);
         g_stack.push(bp);
         return;
       }
     }
+
+  assert(0);
 }
 
 void rnd_u1(int i, int j, int* structure)
@@ -370,6 +402,7 @@ void rnd_u1(int i, int j, int* structure)
     cum_prob += U1_ij_s3h(i,h,j);
     if (rnd < cum_prob)
     {
+      energy += (EC_new()+(h-i)*EB_new());
       h1 = h;
       break;
     }
@@ -384,6 +417,8 @@ void rnd_u1(int i, int j, int* structure)
     cum_prob += U1_j_hl_case1(h1,l,j);
     if (rnd < cum_prob)
     {
+      int tt =  (j == l)?0:ED3_new(h1,l,l+1);
+      energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new());
       base_pair bp(h1,l,UP);
       g_stack.push(bp);
       return;
@@ -392,6 +427,7 @@ void rnd_u1(int i, int j, int* structure)
     cum_prob += U1_j_hl_case2(h1,l,j);
     if (rnd < cum_prob)
     {
+      energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new());
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+2,j,U1);
       g_stack.push(bp1);
@@ -402,6 +438,7 @@ void rnd_u1(int i, int j, int* structure)
     cum_prob += U1_j_hl_case3(h1,l,j);
     if (rnd < cum_prob)
     {
+      energy += ED5_new(h1,l,h1-1)+auPenalty_new(h1,l);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,U1D);
       g_stack.push(bp1);
@@ -409,6 +446,8 @@ void rnd_u1(int i, int j, int* structure)
       return;
     }
   }
+
+  assert(0);
 }
 
 void rnd_u1d(int i, int j, int* structure)
@@ -421,6 +460,8 @@ void rnd_u1d(int i, int j, int* structure)
     cum_prob += U1D_ij_il_case1(i,l,j);
     if (rnd < cum_prob)
     {
+      int tt = (j==l)?(0):(ED5_new(i,l,l+1));
+      energy += ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new());
       base_pair bp1(i,l,UP);
       //set_single_stranded(l+1,j,structure);
       g_stack.push(bp1);
@@ -430,6 +471,7 @@ void rnd_u1d(int i, int j, int* structure)
     cum_prob += U1D_ij_il_case2(i,l,j);
     if (rnd < cum_prob)
     {
+      energy += (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new());
       base_pair bp1(i,l,UP);
       base_pair bp2(l+2,j,U1);
       g_stack.push(bp1);
@@ -440,6 +482,7 @@ void rnd_u1d(int i, int j, int* structure)
     cum_prob += U1D_ij_il_case3(i,l,j);
     if (rnd < cum_prob)
     {
+      energy += (EC_new()+auPenalty_new(i,l));
       base_pair bp1(i,l,UP);
       base_pair bp2(l+1,j,U1D);
       g_stack.push(bp1);
@@ -447,6 +490,8 @@ void rnd_u1d(int i, int j, int* structure)
       return;
     }
   }
+
+  assert(0);
 }
 
 void rnd_upm(int i, int j, int* structure)
@@ -459,6 +504,7 @@ void rnd_upm(int i, int j, int* structure)
     cum_prob += UPM_ip1l_case1(i,l,j);
     if (rnd < cum_prob)
     {
+      energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new()) ;
       base_pair bp1(i+1,l,UP);
       base_pair bp2(l+2,j-1,U1);
       g_stack.push(bp2);
@@ -469,6 +515,7 @@ void rnd_upm(int i, int j, int* structure)
     cum_prob += UPM_ip1l_case2(i,l,j);
     if (rnd < cum_prob)
     { 
+      energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l));
       base_pair bp1(i+1,l,UP);
       base_pair bp2(l+1,j-1,U1D);
       g_stack.push(bp2);
@@ -482,6 +529,7 @@ void rnd_upm(int i, int j, int* structure)
     cum_prob += UPM_ip2l_case1(i,l,j);
     if (rnd < cum_prob)
     {
+      energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new());
       base_pair bp1(i+2,l,UP);
       base_pair bp2(l+2,j-1,U1);
       g_stack.push(bp2);
@@ -492,6 +540,7 @@ void rnd_upm(int i, int j, int* structure)
     cum_prob += UPM_ip2l_case2(i,l,j);
     if (rnd < cum_prob)
     { 
+      energy += EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l);
       base_pair bp1(i+2,l,UP);
       base_pair bp2(l+1,j-1,U1D);
       g_stack.push(bp1);
@@ -499,17 +548,18 @@ void rnd_upm(int i, int j, int* structure)
       return ;
     }
   }
-
   int h1 = -1;
   for (int h = i+3; h < j-1; ++h)
   {
     cum_prob += UPM_ijs2h(i,h,j);
-    if (rnd < cum_prob)
+    if (rnd < cum_prob )
     {
+      energy += (ED3_new(i,j,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new());
       h1 = h;
       break;
     }
   }
+  assert(h1!=-1);
   
   rnd = randdouble();
   cum_prob = 0;
@@ -518,6 +568,7 @@ void rnd_upm(int i, int j, int* structure)
     cum_prob += UPM_ijhl_case1(i,h1,l,j);
     if (rnd < cum_prob)
     {
+        energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1));
         base_pair bp1(h1,l,UP);
         base_pair bp2(l+2,j-1,U1);
         g_stack.push(bp1);
@@ -528,6 +579,7 @@ void rnd_upm(int i, int j, int* structure)
     cum_prob += UPM_ijhl_case2(i,h1,l,j);
     if (rnd < cum_prob)
     {
+        energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l));
         base_pair bp1(h1,l,UP);
         base_pair bp2(l+1,j-1,U1D);
         g_stack.push(bp1);
@@ -535,13 +587,15 @@ void rnd_upm(int i, int j, int* structure)
         return;
     }
   }
+  assert(0);
 }
 
-void rnd_structure(int* structure, int len)
+double rnd_structure(int* structure, int len)
 {
   srand(rand());
   base_pair first(1,len,U);
   g_stack.push(first);
+  energy = 0;
 
   while (!g_stack.empty())
   {
@@ -561,6 +615,7 @@ void rnd_structure(int* structure, int len)
       rnd_u1d(bp.i,bp.j,structure);
     
   }
+  return (double)energy/100.0;
 }
 
 void set_single_stranded(int i, int j, int* structure)
@@ -572,9 +627,7 @@ void set_single_stranded(int i, int j, int* structure)
 void set_base_pair(int i, int j, int* structure)
 {
     bool cond = j-i > TURN && canPair(RNA[i],RNA[j]);
-    //if (cond == false) printf("UP(%d %d) = %lf \n",i,j,up[i][j]);
     assert(cond);
-    //  printf("PAIRING %d %d\n",i,j);
     structure[i] = j;
     structure[j] = i;
 }

From c008412a78ff920cd5c33f23097edea4931918b5 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@hpc18.cc.gt.atl.ga.us>
Date: Wed, 19 Oct 2011 23:41:30 -0400
Subject: [PATCH 265/282] fixes to sampling algorithm

---
 gtfold-mfe/src/main.cc                | 33 ++++++++++++-
 gtfold-mfe/src/stochastic-sampling.cc | 71 ++++++++++++++++++++++++---
 2 files changed, 95 insertions(+), 9 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 1d5e1e3..0ecb57e 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -303,6 +303,7 @@ int main(int argc, char** argv) {
 
 	  int* structure = new int[seq.length()+1];
 	  srand(time(NULL));
+    std::map<std::string,std::pair<int,double> >  uniq_structs;
 
 	  if (num_rnd > 0 ) {
 		  printf("\nSampling structures...\n");
@@ -320,9 +321,39 @@ int main(int argc, char** argv) {
 					  ensemble[structure[i]] = ')';
 				  }
 			  }
-			  std::cout << ensemble.substr(1) << ' ' << energy << std::endl;
+        std::map<std::string,std::pair<int,double> >::iterator iter ;
+        if ((iter =uniq_structs.find(ensemble.substr(1))) != uniq_structs.end())
+        {
+          std::pair<int,double>& pp = iter->second;
+          pp.first++;
+        }
+        else {
+          uniq_structs.insert(make_pair(ensemble.substr(1),std::pair<int,double>(1,energy))); 
+        }
+			  //std::cout << ensemble.substr(1) << ' ' << energy << std::endl;
 		  }
 	  }
+    
+    int pcount = 0;
+    int maxCount = 0; std::string bestStruct;
+    double bestE = INFINITY;
+
+    std::map<std::string,std::pair<int,double> >::iterator iter ;
+    for (iter = uniq_structs.begin(); iter != uniq_structs.end();  ++iter)
+    {
+      const std::string& ss = iter->first;
+      const std::pair<int,double>& pp = iter->second;
+    //  printf("%s\tp=%lf, e=%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second);
+      pcount += pp.first;
+      if (pp.first > maxCount)
+      {
+        maxCount = pp.first;
+        bestStruct  = ss;
+        bestE = pp.second;
+      }
+    }
+    assert(num_rnd == pcount);
+    printf("Most favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd);
 
 	  free_partition();
 	  free_fold(seq.length());
diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc
index a311e10..a9b962f 100644
--- a/gtfold-mfe/src/stochastic-sampling.cc
+++ b/gtfold-mfe/src/stochastic-sampling.cc
@@ -5,8 +5,11 @@
 #include <stdio.h>
 #include <stack>
 
+int ss_verbose = 0; 
+
 std::stack<base_pair> g_stack;
-int energy = 0;
+
+double energy = 0;
 
 double randdouble()
 {
@@ -118,18 +121,18 @@ double UPM_ip1l_case2(int i, int l, int j)
 
 double UPM_ip2l_case1(int i, int l , int j)
 {
-  return feasible(i+2,l)?up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+EB_new())/RT)*u1[l+2][j-1])/upm[i][j]:0;
+  return feasible(i+2,l)?up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+EB_new())/RT)*u1[l+2][j-1])/upm[i][j]:0;
 }
 
 double UPM_ip2l_case2(int i, int l , int j)
 {
-  return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0;
+  return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0;
 }
 
 
 double UPM_ijs2h(int i, int h , int j)
 {
-  return exp((-1)*ED3_new(i,j,i+1)/RT)* (s2[h][j] * exp((-1)*(EA_new()+2*EC_new()+(h-i-1)*EB_new())/RT))/upm[i][j];
+  return exp((-1)*ED3_new(j,i,i+1)/RT)* (s2[h][j] * exp((-1)*(EA_new()+2*EC_new()+(h-i-1)*EB_new())/RT))/upm[i][j];
 }
 
 
@@ -207,6 +210,8 @@ void rnd_u(int i, int j, int* structure)
   if (rnd < cum_prob)
   {
     energy += auPenalty_new(i,j);
+    if (ss_verbose == 1) 
+      printf("(%d %d) %lf\n",i,j,auPenalty_new(i,j)/100.0);
     base_pair bp(i,j,UP);
     g_stack.push(bp);
     return;
@@ -218,6 +223,8 @@ void rnd_u(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += ED5_new(h,j,h-1)+auPenalty_new(h,j);
+      if (ss_verbose == 1) 
+        printf("(%d %d) %lf\n",i,j,(ED5_new(h,j,h-1)+auPenalty_new(h,j)) /100.0);
       base_pair bp(h,j,UP);
       //set_single_stranded(i,h-1,structure);
       g_stack.push(bp);
@@ -255,6 +262,8 @@ void rnd_u(int i, int j, int* structure)
     {
       //set_single_stranded(i,h1-1,structure);
       energy += (ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1));
+      if (ss_verbose == 1) 
+        printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)) /100.0);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+2,j,U);
       g_stack.push(bp1);
@@ -266,6 +275,8 @@ void rnd_u(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l));
+      if (ss_verbose == 1) 
+        printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0);
       //set_single_stranded(i,h1-1,structure);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,UD);
@@ -278,6 +289,8 @@ void rnd_u(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + auPenalty_new(l+1,j));
+      if (ss_verbose == 1) 
+        printf("(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + auPenalty_new(l+1,j))/100.0);
       //set_single_stranded(i,h1-1,structure);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,UP);
@@ -300,6 +313,8 @@ void rnd_ud(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += (auPenalty_new(i,l) + ED3_new(i,l,l+1));
+      if (ss_verbose == 1) 
+        printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l) + ED3_new(i,l,l+1))/100.0);
       base_pair bp1(i,l,UP);
       base_pair bp2(l+2,j,U);
       g_stack.push(bp1);
@@ -311,6 +326,8 @@ void rnd_ud(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += auPenalty_new(i,l);
+      if (ss_verbose == 1) 
+        printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l))/100.0);
       base_pair bp1(i,l,UP);
       base_pair bp2(l+1,j,UD);
       g_stack.push(bp1);
@@ -322,6 +339,8 @@ void rnd_ud(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += (auPenalty_new(i,l) + auPenalty_new(l+1,j));
+      if (ss_verbose == 1) 
+        printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l) + auPenalty_new(l+1,j))/100.0);
       base_pair bp1(i,l,UP);
       base_pair bp2(l+1,j,UP);
       g_stack.push(bp1);
@@ -336,7 +355,6 @@ void rnd_up(int i, int j, int* structure)
 {
   double rnd = randdouble();
   double cum_prob = 0;
-  //printf("%d %d %1.6lf %1.6lf %1.6lf %1.6lf\n",i,j,rnd,Q_ijH(i,j),Q_ijS(i,j), Q_ijM(i,j));
   assert(structure[i] == 0);
   assert(structure[j] == 0);
   
@@ -346,6 +364,8 @@ void rnd_up(int i, int j, int* structure)
   if (rnd < cum_prob)
   {
     energy += eH_new(i,j);
+    if (ss_verbose == 1) 
+      printf("Hairpin(%d %d) %lf\n",i,j, (eH_new(i,j))/100.0);
     //set_single_stranded(i+1,j-1,structure);
     return ;
   }
@@ -354,6 +374,8 @@ void rnd_up(int i, int j, int* structure)
   if (rnd < cum_prob)
   {
     energy += eS_new(i,j);
+    if (ss_verbose == 1) 
+      printf("Stack(%d %d) %lf\n",i,j, (eS_new(i,j))/100.0);
     base_pair bp(i+1,j-1,UP);
     g_stack.push(bp);
     return ;
@@ -374,6 +396,8 @@ void rnd_up(int i, int j, int* structure)
       if (rnd < cum_prob)
       {
         energy += eL_new(i,j,h,l);
+        if (ss_verbose == 1) 
+          printf("IntLoop(%d %d) %lf\n",i,j, (eL_new(i,j,h,l))/100.0);
         base_pair bp(h,l,UP);
         g_stack.push(bp);
         return;
@@ -403,6 +427,8 @@ void rnd_u1(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += (EC_new()+(h-i)*EB_new());
+      if (ss_verbose == 1) 
+        printf("U1_ij_s3h(%d %d) %lf\n",i,j, (EC_new()+(h-i)*EB_new())/100.0);
       h1 = h;
       break;
     }
@@ -419,6 +445,8 @@ void rnd_u1(int i, int j, int* structure)
     {
       int tt =  (j == l)?0:ED3_new(h1,l,l+1);
       energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new());
+      if (ss_verbose == 1) 
+        printf("U1_j_hl_case1(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new())/100.0);
       base_pair bp(h1,l,UP);
       g_stack.push(bp);
       return;
@@ -428,6 +456,8 @@ void rnd_u1(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new());
+      if (ss_verbose == 1) 
+        printf("U1_j_hl_case2(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new())/100.0);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+2,j,U1);
       g_stack.push(bp1);
@@ -439,6 +469,8 @@ void rnd_u1(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += ED5_new(h1,l,h1-1)+auPenalty_new(h1,l);
+      if (ss_verbose == 1) 
+        printf("U1_j_hl_case3(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,U1D);
       g_stack.push(bp1);
@@ -462,6 +494,8 @@ void rnd_u1d(int i, int j, int* structure)
     {
       int tt = (j==l)?(0):(ED5_new(i,l,l+1));
       energy += ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new());
+      if (ss_verbose == 1) 
+        printf("U1D_ij_il_case1(%d %d) %lf\n",i,j, ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new())/100.0);
       base_pair bp1(i,l,UP);
       //set_single_stranded(l+1,j,structure);
       g_stack.push(bp1);
@@ -472,6 +506,8 @@ void rnd_u1d(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new());
+      if (ss_verbose == 1) 
+        printf("U1D_ij_il_case2(%d %d) %lf\n",i,j, (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new())/100.0);
       base_pair bp1(i,l,UP);
       base_pair bp2(l+2,j,U1);
       g_stack.push(bp1);
@@ -483,6 +519,8 @@ void rnd_u1d(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += (EC_new()+auPenalty_new(i,l));
+      if (ss_verbose == 1) 
+        printf("U1D_ij_il_case3(%d %d) %lf\n",i,j, (EC_new()+auPenalty_new(i,l))/100.0);
       base_pair bp1(i,l,UP);
       base_pair bp2(l+1,j,U1D);
       g_stack.push(bp1);
@@ -498,6 +536,8 @@ void rnd_upm(int i, int j, int* structure)
 {
   double rnd = randdouble();
   double cum_prob = 0;
+  if (ss_verbose == 1)
+    printf("Multiloop(%d %d)\n",i,j);
 
   for (int l = i+2; l < j; ++l) 
   {
@@ -505,6 +545,8 @@ void rnd_upm(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new()) ;
+      if (ss_verbose == 1) 
+        printf("(%d %d) %s %lf\n",i,j, "UPM_ip1l_case1",(EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new())/100.0);
       base_pair bp1(i+1,l,UP);
       base_pair bp2(l+2,j-1,U1);
       g_stack.push(bp2);
@@ -516,6 +558,8 @@ void rnd_upm(int i, int j, int* structure)
     if (rnd < cum_prob)
     { 
       energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l));
+      if (ss_verbose == 1) 
+        printf("(%d %d)  %s %lf\n",i,j,"UPM_ip1l_case2", (EA_new()+2*EC_new()+auPenalty_new(i+1,l))/100.0);
       base_pair bp1(i+1,l,UP);
       base_pair bp2(l+1,j-1,U1D);
       g_stack.push(bp2);
@@ -529,7 +573,9 @@ void rnd_upm(int i, int j, int* structure)
     cum_prob += UPM_ip2l_case1(i,l,j);
     if (rnd < cum_prob)
     {
-      energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new());
+      energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new());
+      if (ss_verbose == 1) 
+        printf("%s(%d %d) %lf\n", "UPM_ip2l_case1", i,j,(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new())/100.0);
       base_pair bp1(i+2,l,UP);
       base_pair bp2(l+2,j-1,U1);
       g_stack.push(bp2);
@@ -540,7 +586,9 @@ void rnd_upm(int i, int j, int* structure)
     cum_prob += UPM_ip2l_case2(i,l,j);
     if (rnd < cum_prob)
     { 
-      energy += EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l);
+      energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l));
+      if (ss_verbose == 1) 
+       printf("%s(%d %d) %lf\n", "UPM_ip2l_case2",i,j,(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/100.0);
       base_pair bp1(i+2,l,UP);
       base_pair bp2(l+1,j-1,U1D);
       g_stack.push(bp1);
@@ -554,7 +602,9 @@ void rnd_upm(int i, int j, int* structure)
     cum_prob += UPM_ijs2h(i,h,j);
     if (rnd < cum_prob )
     {
-      energy += (ED3_new(i,j,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new());
+      energy += (ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new());
+      if (ss_verbose == 1) 
+       printf("%s(%d %d) %lf\n", "UPM_ijs2h",i,j,(ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new())/100.0);
       h1 = h;
       break;
     }
@@ -569,6 +619,8 @@ void rnd_upm(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
         energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1));
+        if (ss_verbose == 1) 
+          printf("%s(%d %d) %lf\n","UPM_ijhl_case1",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1))/100.0);
         base_pair bp1(h1,l,UP);
         base_pair bp2(l+2,j-1,U1);
         g_stack.push(bp1);
@@ -580,6 +632,8 @@ void rnd_upm(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
         energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l));
+        if (ss_verbose == 1) 
+          printf("%s(%d %d)  %lf\n", "UPM_ijhl_case2",i,j,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0);
         base_pair bp1(h1,l,UP);
         base_pair bp2(l+1,j-1,U1D);
         g_stack.push(bp1);
@@ -592,6 +646,7 @@ void rnd_upm(int i, int j, int* structure)
 
 double rnd_structure(int* structure, int len)
 {
+  //printf("%lf %lf %lf\n", EA_new(), EB_new(), EC_new());
   srand(rand());
   base_pair first(1,len,U);
   g_stack.push(first);

From a1f5d30a839aea6c5a0baa2c791092e88b074ad5 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@hpc18.cc.gt.atl.ga.us>
Date: Wed, 19 Oct 2011 23:58:41 -0400
Subject: [PATCH 266/282] adding fix of Eb and Ec

---
 gtfold-mfe/src/partition-func.c | 163 ++++++++++++++------------------
 1 file changed, 73 insertions(+), 90 deletions(-)

diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index fcd1b1d..da7649a 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -6,6 +6,7 @@
 #include "algorithms-partition.h"
 #include "global.h"
 #include "utils.h"
+#include <assert.h>
 //#include "options.h"
 
 double ** u;
@@ -60,9 +61,9 @@ static void set_s3(int i, int j, double val);
 
 
 void errorAndExit(char* msg, int i, int j, double oldVal, double newVal){
-	printf(msg);
+	printf("%s", msg);
 	printf("i=%d,j=%d,oldVal=%0.1f,newVal=%0.1f\n",i,j,oldVal,newVal);
-	printf("\nprogram is exiting now due to above error\n");
+	printf("%s","\nprogram is exiting now due to above error\n");
 	exit(-1);
 }
 
@@ -112,19 +113,21 @@ double eL_new(int i, int j, int p, int q){
 }
 
 double ED3_new(int i, int j, int k){
-        if(PF_COUNT_MODE_) return 0;
-	//return Ed3(i,j,k);
-	return Ed5(j,i,k);
-	//return Ed5(i,j,k);
-	//return Ed3(j,i,k);
+  if(PF_COUNT_MODE_) return 0;
+  //if (j-i > TURN && canPair(RNA[i],RNA[j])) {
+  //  assert(Ed5(j,i,k)<0.1);
+  //}
+  return Ed5(j,i,k);
 }
 
 double ED5_new(int i, int j, int k){
-        if(PF_COUNT_MODE_) return 0;
-        //return Ed5(i,j,k);
+  if(PF_COUNT_MODE_) return 0;
+  if (k<1) return 0; 
+  
+  //if (j-i > TURN && canPair(RNA[i],RNA[j])) {
+  //  assert(Ed3(j,i,k)<0.1);
+  //}
 	return Ed3(j,i,k);
-	//return Ed3(i,j,k);
-	//return Ed5(j,i,k);
 }
 
 double EA_new(){
@@ -134,12 +137,12 @@ double EA_new(){
 
 double EB_new(){
         if(PF_COUNT_MODE_) return 0;
-        return Eb;
+        return Ec;
 }
 
 double EC_new(){
         if(PF_COUNT_MODE_) return 0;
-        return Ec;
+        return Eb;
 }
 
 double auPenalty_new(int i, int j){
@@ -189,7 +192,7 @@ printf("\n\nAfter calculation, s3 matrix:\n\n");
 void calculate_partition(int len, int pf_count_mode) 
 {printf("RT=%f\n",RT);//RT=RT/100;
   PF_COUNT_MODE_ = pf_count_mode;
-  int i, j;
+  //int i, j;
   part_len = len;
   create_partition_arrays();
   init_partition_arrays();
@@ -448,38 +451,34 @@ void calc_s1(int h, int j)//ERROR_FOUND s1[h][j]= instead of +=
 
 
 void calc_s2(int h, int j)
-{//printf("Entering calc_s2: h=%d, j =%d\n",h,j);
+{
 	int l;
 	double s2_val = 0.0;							
 	for (l = h+1; l < j; ++l)//ERROR
-	{//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)),(myExp(-ED3_new(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)));
+	{
 		double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)));
 		double v2 = (myExp(-(ED3_new(h,l,l+1)+EB_new())/RT)*get_u1(l+2,j-1));
 		double v3 = get_u1d(l+1,j-1);
 		double val = v1*(v2+v3);
-		//double val = get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)) * (myExp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1));							
-		s2_val += val;//Error: Eb is added
+    s2_val += val;//Error: Eb is added
 	}
-	set_s2(h, j, s2_val);//s2[h][j] = s2_val;
-//printf("Exiting calc_s2: h=%d, j =%d, val=%.3f\n",h,j,s2[h][j]);
+	set_s2(h, j, s2_val);
 }
 
 void calc_s3(int h, int j)
-{//printf("Entering calc_s3: h=%d, j =%d\n",h,j);
+{
   int l;		
 	double s3_val = 0.0;					
   for (l = h+1; l <= j && l+2<=part_len; ++l)//ERROR in for loop variable l
   {
-    	double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)));
-	double v2 = (f(j+1,h,l)*myExp(-((j-l)*EB_new())/RT));
-	double v3 = (myExp(-(ED3_new(h,l,l+1)+EB_new())/RT)*get_u1(l+2,j));
-	double v4 = get_u1d(l+1,j);
-	double val = v1*(v2+v3+v4);
-	//double val = get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))*(f(j+1,h,l)*myExp(-((j-l)*Eb)/RT) + myExp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j));
-  	s3_val += val;
+    double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)));
+    double v2 = (f(j+1,h,l)*myExp(-((j-l)*EB_new())/RT));
+    double v3 = (myExp(-(ED3_new(h,l,l+1)+EB_new())/RT)*get_u1(l+2,j));
+    double v4 = get_u1d(l+1,j);
+    double val = v1*(v2+v3+v4);
+    s3_val += val;
   }
  set_s3(h, j, s3_val);//s3[h][j] = s3_val;
-//printf("Exiting calc_s3: h=%d, j =%d, val=%.3f\n",h,j,s3[h][j]);
 }
 
 void create_partition_arrays()
@@ -542,35 +541,33 @@ void free_partition_arrays()
 }*/
 
 void calc_upm(int i, int j){//printf("Entering calc_upm: i=%d, j =%d\n",i,j);
-        double a = EA_new();
-	double b = EB_new();
-	double c = EC_new();
-        double p_val = 0;
-        int l,h;
-        double quadraticSum = 0;
+  double a = EA_new();
+  double b = EB_new();
+  double c = EC_new();
+  double p_val = 0;
+  int l,h;
+  double quadraticSum = 0;
 
   if (canPair(RNA[i],RNA[j]))
   {
-   for(l=i+2; l<j; ++l){
-	double v1 = (get_up(i+1,l) * myExp((-1)*(a+2*c+auPenalty_new(i+1,l))/RT));
-	double v2 = (myExp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1));
-	double v3 = get_u1d(l+1,j-1);
-	p_val = p_val + (v1*(v2+v3));
-        //p_val += (get_up(i+1,l) * myExp((-1)*(a+2*c+auPenalty_new(i+1,l))/RT) * (myExp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
+    for(l=i+2; l<j; ++l){
+      double v1 = (get_up(i+1,l) * myExp((-1)*(a+2*c+auPenalty_new(i+1,l))/RT));
+      double v2 = (myExp((-1)*(ED3_new(i+1,l,l+1)+b)/RT) * get_u1(l+2,j-1));
+      double v3 = get_u1d(l+1,j-1);
+      p_val = p_val + (v1*(v2+v3));
     }
 
     for(l=i+3; l<j; ++l){
-	double v1 = (get_up(i+2,l)*myExp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT));
-	double v2 = (myExp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1));
-	double v3 = get_u1d(l+1,j-1);
-	p_val = p_val + (v1*(v2+v3));
-        //p_val += (get_up(i+2,l)*myExp((-1)*(a+2*c+b+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * (myExp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1) + get_u1d(l+1,j-1)));
+      double v1 = (get_up(i+2,l)*myExp((-1)*(a+2*c+b+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/RT));
+      double v2 = (myExp((-1)*(ED3_new(i+2,l,l+1)+b)/RT)*get_u1(l+2,j-1));
+      double v3 = get_u1d(l+1,j-1);
+      p_val = p_val + (v1*(v2+v3));
     }
 
     for(h=i+3; h<j-1; ++h){
       quadraticSum += (get_s2(h,j) * myExp((-1)*(a+2*c+(h-i-1)*b)/RT));
     }
-    quadraticSum *= (myExp((-1)*ED3_new(i,j,i+1)/RT));
+    quadraticSum *= (myExp((-1)*ED3_new(j,i,i+1)/RT));
 
     p_val += quadraticSum;
     set_upm(i, j, p_val);//upm[i][j] = p_val;
@@ -578,7 +575,7 @@ void calc_upm(int i, int j){//printf("Entering calc_upm: i=%d, j =%d\n",i,j);
   else {
     set_upm(i, j, 0.0);//upm[i][j] = 0;
   }
-//printf("Exiting calc_upm: i=%d, j =%d, val=%.3f\n",i,j,upm[i][j]/up[i][j]);
+  //printf("Exiting calc_upm: i=%d, j =%d, val=%.3f\n",i,j,upm[i][j]/up[i][j]);
 }
 
 
@@ -760,76 +757,62 @@ void calc_up(int i, int j)
 }*/
 
 void printUPprobabilities(int i, int j){
-	int h,l;
-	double maxIntLoopProb = 0.0;
-        int h_max=-1, l_max=-1;
-	double sum=0.0;
-    for (h = i+1; h < j ; h++) {
-      for (l = h+1; l < j; l++) {
-        if (canPair(RNA[h],RNA[l])==0) continue;
-        if(h==(i+1) && l==(j-1)) continue;
-        //if((l-h)<=TURN) continue;
-         double intLoopProb = (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT))/up[i][j];
-	sum+=intLoopProb;
-	 if(intLoopProb > maxIntLoopProb){ maxIntLoopProb = intLoopProb; h_max=h; l_max=l;}
-      }
+  int h,l;
+  double maxIntLoopProb = 0.0;
+  int h_max=-1, l_max=-1;
+  double sum=0.0;
+  for (h = i+1; h < j ; h++) {
+    for (l = h+1; l < j; l++) {
+      if (canPair(RNA[h],RNA[l])==0) continue;
+      if(h==(i+1) && l==(j-1)) continue;
+      //if((l-h)<=TURN) continue;
+      double intLoopProb = (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT))/up[i][j];
+      sum+=intLoopProb;
+      if(intLoopProb > maxIntLoopProb){ maxIntLoopProb = intLoopProb; h_max=h; l_max=l;}
     }
+  }
 
-        //ERROR below line should not be there
-    //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT);
-    double hpProb = myExp(-((double)eH_new(i,j))/RT )/up[i][j];
-    double stackProb = (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1))/up[i][j];
-    double upmProb = get_upm(i,j)/up[i][j];
+  //ERROR below line should not be there
+  //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT);
+  double hpProb = myExp(-((double)eH_new(i,j))/RT )/up[i][j];
+  double stackProb = (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1))/up[i][j];
+  double upmProb = get_upm(i,j)/up[i][j];
 
-    if(maxIntLoopProb>=hpProb && maxIntLoopProb>=stackProb && maxIntLoopProb >=upmProb) printf("INT ");
-    else if(hpProb>=maxIntLoopProb && hpProb>=stackProb && hpProb>=upmProb) printf("HPL ");
-    else if(stackProb>=hpProb && stackProb>=maxIntLoopProb && stackProb>=upmProb) printf("STK ");
-    else if(upmProb>=hpProb && upmProb>=stackProb && upmProb>=maxIntLoopProb) printf("UPM ");
+  if(maxIntLoopProb>=hpProb && maxIntLoopProb>=stackProb && maxIntLoopProb >=upmProb) printf("INT ");
+  else if(hpProb>=maxIntLoopProb && hpProb>=stackProb && hpProb>=upmProb) printf("HPL ");
+  else if(stackProb>=hpProb && stackProb>=maxIntLoopProb && stackProb>=upmProb) printf("STK ");
+  else if(upmProb>=hpProb && upmProb>=stackProb && upmProb>=maxIntLoopProb) printf("UPM ");
 
-printf("printing probabilities: i=%d, j =%d, upmProb=%.6f, stackProb=%.6f, hpProb=%.6f, maxIntLoopProb=%.6f,  sumIntLoopProbs=%.6f, h_max=%d, l_max=%d\n",i,j, upmProb, stackProb, hpProb, maxIntLoopProb,sum,h_max,l_max);
+  printf("printing probabilities: i=%d, j =%d, upmProb=%.6f, stackProb=%.6f, hpProb=%.6f, maxIntLoopProb=%.6f,  sumIntLoopProbs=%.6f, h_max=%d, l_max=%d\n",i,j, upmProb, stackProb, hpProb, maxIntLoopProb,sum,h_max,l_max);
 
 }
 
 void calc_up(int i, int j)
 {//printf("Entering calc_up: i=%d, j =%d\n",i,j);
   double up_val = 0.0;
-  int p,q;
+  //int p,q;
 
   if (canPair(RNA[i],RNA[j]))// if(j-i>TURN)
   {
-   /*for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) {
-      int minq = j-i+p-MAXLOOP-2;
-      if (minq < p+1+TURN) minq = p+1+TURN;
-      int maxq = (p==(i+1))?(j-2):(j-1);
-
-      for (q = minq; q <= maxq; q++) {
-       if (canPair(p,q)==0) continue;
-        up_val += (get_up(p,q) * myExp(-eL_new(i,j,p,q)/RT));
-      }
-    }*/
-	int h,l;
+    int h,l;
     for (h = i+1; h < j ; h++) {
       for (l = h+1; l < j; l++) {
         if (canPair(RNA[h],RNA[l])==0) continue;
-	if(h==(i+1) && l==(j-1)) continue;
-	//if((l-h)<=TURN) continue;
+        if(h==(i+1) && l==(j-1)) continue;
         up_val += (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT));
       }
     }
 
-	//ERROR below line should not be there
+    //ERROR below line should not be there
     //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT);
     up_val = up_val + myExp(-((double)eH_new(i,j))/RT );
     up_val = up_val + (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1));
     up_val = up_val + get_upm(i,j);
 
     set_up(i, j, up_val);//up[i][j] = up_val;
-    //printUPprobabilities(i,j);
+
   }
   else  {
     set_up(i, j, 0.0);//up[i][j] = 0;
   }
-//printf("Exiting calc_up: i=%d, j =%d, val=%.3f\n",i,j,up[i][j]);
 }
-
-

From ea006938011a19b85853794ea86debc90c2f3ec2 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav@hpc18.cc.gt.atl.ga.us>
Date: Fri, 21 Oct 2011 18:16:40 -0400
Subject: [PATCH 267/282] fix RT scaling factor

---
 gtfold-mfe/src/energy.c | 2 +-
 gtfold-mfe/src/main.cc  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 314d35a..7ac6fbe 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -18,7 +18,7 @@ int *indx;
 int **PP; 
 
 int alloc_flag = 0;
-const float RT = ((0.00198721 * 310.15)*10000); //* 100.00);
+const float RT = ((0.00198721 * 310.15)*100); //* 100.00);
 
 void create_tables(int len) {	
 	V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 0ecb57e..30e1eab 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -343,7 +343,7 @@ int main(int argc, char** argv) {
     {
       const std::string& ss = iter->first;
       const std::pair<int,double>& pp = iter->second;
-    //  printf("%s\tp=%lf, e=%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second);
+      //  printf("%s\tp=%lf, e=%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second);
       pcount += pp.first;
       if (pp.first > maxCount)
       {

From 2d8a3299320cda0a0108e3062261c74c76dba350 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 21 Oct 2011 18:25:17 -0400
Subject: [PATCH 268/282] print sampling probablities

---
 gtfold-mfe/src/main.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 30e1eab..99a8f91 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -343,7 +343,7 @@ int main(int argc, char** argv) {
     {
       const std::string& ss = iter->first;
       const std::pair<int,double>& pp = iter->second;
-      //  printf("%s\tp=%lf, e=%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second);
+      printf("%s\t%lf\t%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second);
       pcount += pp.first;
       if (pp.first > maxCount)
       {
@@ -353,7 +353,7 @@ int main(int argc, char** argv) {
       }
     }
     assert(num_rnd == pcount);
-    printf("Most favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd);
+    printf("\nMost favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd);
 
 	  free_partition();
 	  free_fold(seq.length());

From c8b8ccd2386987d5884f39b18c7fa8fcd327c71f Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 26 Oct 2011 10:46:06 -0400
Subject: [PATCH 269/282] added boltzmann prob calculation

---
 gtfold-mfe/src/energy.c         |  1 +
 gtfold-mfe/src/main.cc          | 26 ++++++++++++++++++++++++--
 gtfold-mfe/src/partition-func.c |  4 +++-
 3 files changed, 28 insertions(+), 3 deletions(-)

diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c
index 7ac6fbe..a4259bd 100644
--- a/gtfold-mfe/src/energy.c
+++ b/gtfold-mfe/src/energy.c
@@ -19,6 +19,7 @@ int **PP;
 
 int alloc_flag = 0;
 const float RT = ((0.00198721 * 310.15)*100); //* 100.00);
+const float RT_ = (0.00198721 * 310.15);
 
 void create_tables(int len) {	
 	V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int));
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 99a8f91..014ce16 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -299,11 +299,12 @@ int main(int argc, char** argv) {
 	  printf("\nComputing partition function...\n");
 	  int pf_count_mode = 0;
 	  if(PF_COUNT_MODE) pf_count_mode=1;
-	  calculate_partition(seq.length(),pf_count_mode);
+	  double U = calculate_partition(seq.length(),pf_count_mode);
 
 	  int* structure = new int[seq.length()+1];
 	  srand(time(NULL));
     std::map<std::string,std::pair<int,double> >  uniq_structs;
+    std::map<double,int>  energy_freq;;
 
 	  if (num_rnd > 0 ) {
 		  printf("\nSampling structures...\n");
@@ -330,6 +331,15 @@ int main(int argc, char** argv) {
         else {
           uniq_structs.insert(make_pair(ensemble.substr(1),std::pair<int,double>(1,energy))); 
         }
+
+        std::map<double,int >::iterator iter1 ;
+        if ((iter1 = energy_freq.find(energy)) != energy_freq.end()) {
+          int& freq = iter1->second;
+          ++freq;
+        }
+        else {
+          energy_freq.insert(make_pair(energy,1)); 
+        }
 			  //std::cout << ensemble.substr(1) << ' ' << energy << std::endl;
 		  }
 	  }
@@ -343,7 +353,11 @@ int main(int argc, char** argv) {
     {
       const std::string& ss = iter->first;
       const std::pair<int,double>& pp = iter->second;
-      printf("%s\t%lf\t%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second);
+      const double& estimated_p =  (double)pp.first/(double)num_rnd;
+      const double& energy = pp.second;
+      double actual_p = pow(2.718281,-1.0*energy/RT_)/U;
+
+      printf("%s\t%lf\t%lf\t%lf\n",ss.c_str(),energy,actual_p,estimated_p);
       pcount += pp.first;
       if (pp.first > maxCount)
       {
@@ -355,6 +369,14 @@ int main(int argc, char** argv) {
     assert(num_rnd == pcount);
     printf("\nMost favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd);
 
+    std::map<double,int >::iterator iter1 ;
+    int eCount = 0;
+    for (iter1 = energy_freq.begin(); iter1 != energy_freq.end(); ++iter1) {
+       eCount += iter1->second;
+      //printf("%4.6f\t%0.6f\t%d\n",iter1->first,(double)iter1->second/(double)num_rnd,iter1->second);
+    }
+    assert(num_rnd == eCount);
+
 	  free_partition();
 	  free_fold(seq.length());
 	  delete [] structure;
diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c
index da7649a..4547364 100644
--- a/gtfold-mfe/src/partition-func.c
+++ b/gtfold-mfe/src/partition-func.c
@@ -189,7 +189,7 @@ printf("\n\nAfter calculation, s3 matrix:\n\n");
 
 }
 
-void calculate_partition(int len, int pf_count_mode) 
+double calculate_partition(int len, int pf_count_mode) 
 {printf("RT=%f\n",RT);//RT=RT/100;
   PF_COUNT_MODE_ = pf_count_mode;
   //int i, j;
@@ -212,6 +212,8 @@ void calculate_partition(int len, int pf_count_mode)
   //printAllMatrixes();
 
   printf("%4.4f\n",u[1][part_len]);
+
+  return u[1][part_len];
 }
 
 void free_partition()

From ded86f0ebc7a8952d22bee98f523462e2e595ed3 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Wed, 26 Oct 2011 11:03:11 -0400
Subject: [PATCH 270/282] changed part func to return U

---
 gtfold-mfe/include/energy.h         | 1 +
 gtfold-mfe/include/partition-func.h | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h
index b4beeb3..30d3fd3 100644
--- a/gtfold-mfe/include/energy.h
+++ b/gtfold-mfe/include/energy.h
@@ -21,6 +21,7 @@ extern int **PP;
 #define VBI(i,j) VBI[indx[j]+i]
 //#define RT ((0.00198721 * 310.15) * 100.00)
 extern const float RT;
+extern const float RT_;
 
 #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0)
 
diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h
index b2e8c80..e9bdffa 100644
--- a/gtfold-mfe/include/partition-func.h
+++ b/gtfold-mfe/include/partition-func.h
@@ -30,7 +30,7 @@ double eL_new(int i, int j, int p, int q);
 double eH_new(int i, int j);
 double auPenalty_new(int i, int j);
 double f(int j, int h, int l);
-void calculate_partition(int len, int pf_count_mode);
+double  calculate_partition(int len, int pf_count_mode);
 void free_partition();
 
 #ifdef __cplusplus

From 3f7c982e637742f713fef4d8146edb70c31a459e Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Tue, 1 Nov 2011 23:23:36 -0400
Subject: [PATCH 271/282] fixed energy traceback

---
 gtfold-mfe/src/main.cc                | 106 +++++++++++---------------
 gtfold-mfe/src/stochastic-sampling.cc |  42 +++++-----
 2 files changed, 64 insertions(+), 84 deletions(-)

diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 014ce16..f5dbc21 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -304,24 +304,24 @@ int main(int argc, char** argv) {
 	  int* structure = new int[seq.length()+1];
 	  srand(time(NULL));
     std::map<std::string,std::pair<int,double> >  uniq_structs;
-    std::map<double,int>  energy_freq;;
-
-	  if (num_rnd > 0 ) {
-		  printf("\nSampling structures...\n");
-		  for (int count = 1; count <= num_rnd; ++count) 
-		  {
-			  memset(structure, 0, (seq.length()+1)*sizeof(int));
-			  double energy = rnd_structure(structure, seq.length());
-
-			  std::string ensemble(seq.length()+1,'.');
-			  for (int i = 1; i <= (int)seq.length(); ++ i) {
-				  //     printf("%d %d\n",i,structure[i]);
-				  if (structure[i] > 0 && ensemble[i] == '.')
-				  {
-					  ensemble[i] = '(';
-					  ensemble[structure[i]] = ')';
-				  }
-			  }
+	  
+    if (num_rnd > 0 ) {
+      printf("\nSampling structures...\n");
+
+      for (int count = 1; count <= num_rnd; ++count) 
+      {
+        memset(structure, 0, (seq.length()+1)*sizeof(int));
+        double energy = rnd_structure(structure, seq.length());
+
+        std::string ensemble(seq.length()+1,'.');
+        for (int i = 1; i <= (int)seq.length(); ++ i) {
+          //     printf("%d %d\n",i,structure[i]);
+          if (structure[i] > 0 && ensemble[i] == '.')
+          {
+            ensemble[i] = '(';
+            ensemble[structure[i]] = ')';
+          }
+        }
         std::map<std::string,std::pair<int,double> >::iterator iter ;
         if ((iter =uniq_structs.find(ensemble.substr(1))) != uniq_structs.end())
         {
@@ -331,53 +331,35 @@ int main(int argc, char** argv) {
         else {
           uniq_structs.insert(make_pair(ensemble.substr(1),std::pair<int,double>(1,energy))); 
         }
+         // std::cout << ensemble.substr(1) << ' ' << energy << std::endl;
+      }
 
-        std::map<double,int >::iterator iter1 ;
-        if ((iter1 = energy_freq.find(energy)) != energy_freq.end()) {
-          int& freq = iter1->second;
-          ++freq;
-        }
-        else {
-          energy_freq.insert(make_pair(energy,1)); 
-        }
-			  //std::cout << ensemble.substr(1) << ' ' << energy << std::endl;
-		  }
-	  }
-    
-    int pcount = 0;
-    int maxCount = 0; std::string bestStruct;
-    double bestE = INFINITY;
-
-    std::map<std::string,std::pair<int,double> >::iterator iter ;
-    for (iter = uniq_structs.begin(); iter != uniq_structs.end();  ++iter)
-    {
-      const std::string& ss = iter->first;
-      const std::pair<int,double>& pp = iter->second;
-      const double& estimated_p =  (double)pp.first/(double)num_rnd;
-      const double& energy = pp.second;
-      double actual_p = pow(2.718281,-1.0*energy/RT_)/U;
-
-      printf("%s\t%lf\t%lf\t%lf\n",ss.c_str(),energy,actual_p,estimated_p);
-      pcount += pp.first;
-      if (pp.first > maxCount)
+      int pcount = 0;
+      int maxCount = 0; std::string bestStruct;
+      double bestE = INFINITY;
+
+      std::map<std::string,std::pair<int,double> >::iterator iter ;
+      for (iter = uniq_structs.begin(); iter != uniq_structs.end();  ++iter)
       {
-        maxCount = pp.first;
-        bestStruct  = ss;
-        bestE = pp.second;
+        const std::string& ss = iter->first;
+        const std::pair<int,double>& pp = iter->second;
+        const double& estimated_p =  (double)pp.first/(double)num_rnd;
+        const double& energy = pp.second;
+        double actual_p = pow(2.718281,-1.0*energy/RT_)/U;
+
+        printf("%s\t%lf\t%lf\t%lf\n",ss.c_str(),energy,actual_p,estimated_p);
+        pcount += pp.first;
+        if (pp.first > maxCount)
+        {
+          maxCount = pp.first;
+          bestStruct  = ss;
+          bestE = pp.second;
+        }
       }
-    }
-    assert(num_rnd == pcount);
-    printf("\nMost favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd);
-
-    std::map<double,int >::iterator iter1 ;
-    int eCount = 0;
-    for (iter1 = energy_freq.begin(); iter1 != energy_freq.end(); ++iter1) {
-       eCount += iter1->second;
-      //printf("%4.6f\t%0.6f\t%d\n",iter1->first,(double)iter1->second/(double)num_rnd,iter1->second);
-    }
-    assert(num_rnd == eCount);
-
-	  free_partition();
+      assert(num_rnd == pcount);
+      printf("\nMost favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd);
+    } 
+    free_partition();
 	  free_fold(seq.length());
 	  delete [] structure;
 	  exit(0);
diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc
index a9b962f..bdc9ee9 100644
--- a/gtfold-mfe/src/stochastic-sampling.cc
+++ b/gtfold-mfe/src/stochastic-sampling.cc
@@ -201,8 +201,6 @@ void rnd_u(int i, int j, int* structure)
   cum_prob += U_0(i,j);
   if (rnd < cum_prob)
   {
-    //set_single_stranded(i,j, structure);
-    //energy += 0;
     return;
   }
   
@@ -260,7 +258,6 @@ void rnd_u(int i, int j, int* structure)
     cum_prob += U_ihlj_case1(i,h1,l,j);
     if (rnd < cum_prob)
     {
-      //set_single_stranded(i,h1-1,structure);
       energy += (ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1));
       if (ss_verbose == 1) 
         printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)) /100.0);
@@ -277,7 +274,7 @@ void rnd_u(int i, int j, int* structure)
       energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l));
       if (ss_verbose == 1) 
         printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0);
-      //set_single_stranded(i,h1-1,structure);
+      
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,UD);
       g_stack.push(bp1);
@@ -428,7 +425,7 @@ void rnd_u1(int i, int j, int* structure)
     {
       energy += (EC_new()+(h-i)*EB_new());
       if (ss_verbose == 1) 
-        printf("U1_ij_s3h(%d %d) %lf\n",i,j, (EC_new()+(h-i)*EB_new())/100.0);
+        printf("U1_ij_s3h(%d) %lf\n",h, (EC_new()+(h-i)*EB_new())/100.0);
       h1 = h;
       break;
     }
@@ -446,7 +443,7 @@ void rnd_u1(int i, int j, int* structure)
       int tt =  (j == l)?0:ED3_new(h1,l,l+1);
       energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new());
       if (ss_verbose == 1) 
-        printf("U1_j_hl_case1(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new())/100.0);
+        printf("U1_j_hl_case1(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new())/100.0);
       base_pair bp(h1,l,UP);
       g_stack.push(bp);
       return;
@@ -457,7 +454,7 @@ void rnd_u1(int i, int j, int* structure)
     {
       energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new());
       if (ss_verbose == 1) 
-        printf("U1_j_hl_case2(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new())/100.0);
+        printf("U1_j_hl_case2(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new())/100.0);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+2,j,U1);
       g_stack.push(bp1);
@@ -470,7 +467,7 @@ void rnd_u1(int i, int j, int* structure)
     {
       energy += ED5_new(h1,l,h1-1)+auPenalty_new(h1,l);
       if (ss_verbose == 1) 
-        printf("U1_j_hl_case3(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0);
+        printf("U1_j_hl_case3(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0);
       base_pair bp1(h1,l,UP);
       base_pair bp2(l+1,j,U1D);
       g_stack.push(bp1);
@@ -492,12 +489,12 @@ void rnd_u1d(int i, int j, int* structure)
     cum_prob += U1D_ij_il_case1(i,l,j);
     if (rnd < cum_prob)
     {
-      int tt = (j==l)?(0):(ED5_new(i,l,l+1));
+      int tt = (j==l)?(0):(ED3_new(i,l,l+1));
       energy += ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new());
-      if (ss_verbose == 1) 
-        printf("U1D_ij_il_case1(%d %d) %lf\n",i,j, ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new())/100.0);
+      if (ss_verbose == 1) {
+        printf("U1D_ij_il_case1(%d %d %d) %lf\n",i,l,j, ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new())/100.0);
+      }
       base_pair bp1(i,l,UP);
-      //set_single_stranded(l+1,j,structure);
       g_stack.push(bp1);
       return;
     }
@@ -507,7 +504,7 @@ void rnd_u1d(int i, int j, int* structure)
     {
       energy += (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new());
       if (ss_verbose == 1) 
-        printf("U1D_ij_il_case2(%d %d) %lf\n",i,j, (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new())/100.0);
+        printf("U1D_ij_il_case2(%d %d) %lf\n",i,l, (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new())/100.0);
       base_pair bp1(i,l,UP);
       base_pair bp2(l+2,j,U1);
       g_stack.push(bp1);
@@ -520,7 +517,7 @@ void rnd_u1d(int i, int j, int* structure)
     {
       energy += (EC_new()+auPenalty_new(i,l));
       if (ss_verbose == 1) 
-        printf("U1D_ij_il_case3(%d %d) %lf\n",i,j, (EC_new()+auPenalty_new(i,l))/100.0);
+        printf("U1D_ij_il_case3(%d %d) %lf\n",i,l, (EC_new()+auPenalty_new(i,l))/100.0);
       base_pair bp1(i,l,UP);
       base_pair bp2(l+1,j,U1D);
       g_stack.push(bp1);
@@ -528,7 +525,6 @@ void rnd_u1d(int i, int j, int* structure)
       return;
     }
   }
-
   assert(0);
 }
 
@@ -537,7 +533,7 @@ void rnd_upm(int i, int j, int* structure)
   double rnd = randdouble();
   double cum_prob = 0;
   if (ss_verbose == 1)
-    printf("Multiloop(%d %d)\n",i,j);
+    printf("Multiloop (%d %d)\n",i,j);
 
   for (int l = i+2; l < j; ++l) 
   {
@@ -545,8 +541,9 @@ void rnd_upm(int i, int j, int* structure)
     if (rnd < cum_prob)
     {
       energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new()) ;
-      if (ss_verbose == 1) 
+      if (ss_verbose == 1) {
         printf("(%d %d) %s %lf\n",i,j, "UPM_ip1l_case1",(EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new())/100.0);
+      }
       base_pair bp1(i+1,l,UP);
       base_pair bp2(l+2,j-1,U1);
       g_stack.push(bp2);
@@ -603,9 +600,10 @@ void rnd_upm(int i, int j, int* structure)
     if (rnd < cum_prob )
     {
       energy += (ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new());
-      if (ss_verbose == 1) 
-       printf("%s(%d %d) %lf\n", "UPM_ijs2h",i,j,(ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new())/100.0);
       h1 = h;
+      if (ss_verbose == 1) {
+       printf("%s(%d) %lf\n", "UPM_ijs2h",h1,(ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new())/100.0);
+      }
       break;
     }
   }
@@ -620,7 +618,7 @@ void rnd_upm(int i, int j, int* structure)
     {
         energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1));
         if (ss_verbose == 1) 
-          printf("%s(%d %d) %lf\n","UPM_ijhl_case1",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1))/100.0);
+          printf("%s(%d %d) %lf\n","UPM_ijhl_case1",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1))/100.0);
         base_pair bp1(h1,l,UP);
         base_pair bp2(l+2,j-1,U1);
         g_stack.push(bp1);
@@ -633,7 +631,7 @@ void rnd_upm(int i, int j, int* structure)
     {
         energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l));
         if (ss_verbose == 1) 
-          printf("%s(%d %d)  %lf\n", "UPM_ijhl_case2",i,j,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0);
+          printf("%s(%d %d)  %lf\n", "UPM_ijhl_case2",h1,l,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0);
         base_pair bp1(h1,l,UP);
         base_pair bp2(l+1,j-1,U1D);
         g_stack.push(bp1);
@@ -650,7 +648,7 @@ double rnd_structure(int* structure, int len)
   srand(rand());
   base_pair first(1,len,U);
   g_stack.push(first);
-  energy = 0;
+  energy = 0.0;
 
   while (!g_stack.empty())
   {

From 29cc8073c91c784f23532a932b63d37fe0e08644 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@ubuntu.(none)>
Date: Fri, 4 Nov 2011 11:52:41 -0700
Subject: [PATCH 272/282] Implementation of Unique Multiloop Decomposition

---
 gtfold-mfe/include/subopt_traceback.h |  11 +-
 gtfold-mfe/src/main.cc                |   2 +-
 gtfold-mfe/src/subopt_traceback.cc    | 262 +++++++++++++++++++++++++-
 3 files changed, 267 insertions(+), 8 deletions(-)

diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h
index fd819b6..2ab2241 100644
--- a/gtfold-mfe/include/subopt_traceback.h
+++ b/gtfold-mfe/include/subopt_traceback.h
@@ -30,7 +30,9 @@
 #include <map>
 #include <vector>
 
-enum label {lW=0, lV, lVBI, lVM, lWM, lWMPrime};
+#define UNIQUE_MULTILOOP_DECOMPOSITION
+
+enum label {lW=0, lV, lVBI, lVM, lWM, lWMPrime, lM, lM1};
 extern const char* lstr[]; 
 
 struct segment 
@@ -177,7 +179,7 @@ struct pstruct
 		return st_v.empty();
 	}
 
-	void print()
+	void print() const
 	{
 		SEGSTACK st = st_segment;
 		std::cout <<'[' << ' ' ;
@@ -225,4 +227,9 @@ void traceWM(int i, int j, ps_t &  ps, ps_stack_t & gs);
 void traceWMPrime(int i, int j, ps_t &  ps, ps_stack_t & gs);
 //void traceWM(ps_t& ps, ps_map_t& filter);
 
+#ifdef UNIQUE_MULTILOOP_DECOMPOSITION
+void traceM(int i, int j, ps_t & ps, ps_stack_t & gs);
+void traceM1(int i, int j, ps_t & ps, ps_stack_t & gs);
+#endif
+
 #endif
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 89ba476..67e8a1b 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -225,7 +225,7 @@ void save_subopt_file(string outputFile, ss_map_t& ss_data,
 {
 	ofstream outfile;
 	outfile.open(outputFile.c_str());
-	char buff[1024];
+	char buff[4096];
 
 	sprintf(buff,"%s %6.2f", seq.c_str(), energy/100.0);
 	outfile << buff << std::endl;
diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index b27b059..150d6bc 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -28,18 +28,102 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "global.h"
 #include "subopt_traceback.h"
 
+#include <iostream>
+#include <iterator>
+#include <cstdlib>
+
 //#define DEBUG 1
 
-const char* lstr[] = {"W", "V", "VBI", "VM", "WM", "WMPrime"};
+using std::pair;
+using std::cout;
+using std::endl;
+
+const char* lstr[] = {"W", "V", "VBI", "VM", "WM", "WMPrime", "fm", "fm1"};
 
-void (*trace_func[6]) (int i, int j, ps_t& ps, ps_stack_t& gs);
+void (*trace_func[8]) (int i, int j, ps_t& ps, ps_stack_t& gs);
 static int delta = 0;
 static int mfe = INFINITY_;
 static int length = -1;
 static int gflag = 0;
 
+#ifdef UNIQUE_MULTILOOP_DECOMPOSITION
+
+static int FM1[1500][1500] = {{0}};
+static int FM[1500][1500] = {{0}};
+
+static inline int Ed5_new(int i, int j, int k) {
+  return (k!=0) ? Ed3(j, i, k) : Ed3(j,i,length);
+}
+
+static inline int Ed3_new(int i, int j, int k) {
+  return (k!=length+1)?Ed5(j, i, k) : Ed5(j, i, 1);
+}
+
+void calculate_fm1() {
+
+  //printf("length %d\n", length);
+  //printf("Ea: %d , Eb: %d , Ec: %d\n", Ea, Eb, Ec);
+
+  for (int i = 1; i <= length; ++i) {
+    for (int j = i+1; j <= length; ++j) {
+      //printf("\nFinding FM1[%d][%d]\n", i, j);
+      int min = INFINITY_;
+      for (int l = i+TURN+1; l <= j; ++l) {
+        int d5 = Ed5_new(i,l,i-1);
+        int d3 = Ed3_new(i,l,l+1);
+
+        int fm1 = V(i,l) + auPenalty(i,l) + d5 + d3 + Ec*(j-l) + Eb;
+
+        //printf("l: %d\n", l);
+        //printf("V(%d, %d): %d, auPenalty: %d, Ed3(%d, %d, %d): %d, Ed5(%d, %d, %d): %d\n",
+        //        i, l, V(i,l),
+        //        auPenalty(i,l),
+        //        i, l, i-1, d5,
+        //        i, l, l+1, d3
+        //      );
+        //printf("min: %d, fm1: %d, final_min: %d\n", min, fm1, MIN(min,fm1));
+        min = MIN(min, fm1);
+      }
+      FM1[i][j] = min;
+      //printf("Value: %d ", FM1[i][j]);
+    }
+    //printf("\n");
+  }
+
+}
+
+void calculate_fm() {
+
+  for (int i = 1; i <= length; ++i) {
+    for (int j = i+1; j <= length;++j) {
+      int min1 = INFINITY_;
+      for (int k = i+TURN+1; k <= j-TURN-1; ++k) {
+        int x = FM[i][k-1] + FM1[k][j];
+        min1 = MIN(min1, x);
+      }
+      int min2 = INFINITY_;
+      for (int k = i; k <= j-TURN-1; ++k) {
+        int x = FM1[k][j] + Ec*(k-i);
+        min2 = MIN(min2, x);
+      }
+      FM[i][j] = MIN(min1, min2);
+      //printf("%d %d %d ", i, j, FM[i][j]);
+    }
+    //printf("\n");
+  }
+}
+
+#endif
+
 void process(ss_map_t& subopt_data, int len) {
         int count = 0;
+        length = len;
+
+#ifdef UNIQUE_MULTILOOP_DECOMPOSITION
+        calculate_fm1();
+        calculate_fm();
+#endif
+
         ps_stack_t gstack;
 
 
@@ -55,7 +139,13 @@ void process(ss_map_t& subopt_data, int len) {
 
                 if (ps.empty()) {
                         count++;
-                        subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
+                        //pair<ss_map_t::iterator, bool> ins_result;
+                        // ins_result = subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
+                        //if (ins_result.second == false) {
+                          //printf("Duplicate Structure!!!");
+                         // exit(1);
+                        //}
+                        cout << ps.str << endl;
                         continue;
                 }	
                 else {
@@ -76,7 +166,7 @@ void process(ss_map_t& subopt_data, int len) {
         }
 
 #ifdef DEBUG 
-        printf("# SS = %d\n", count);
+        //printf("# SS = %d\n", count);
 #endif
 }
 
@@ -87,6 +177,10 @@ ss_map_t subopt_traceback(int len, int _delta) {
         trace_func[3] = traceVM;
         trace_func[4] = traceWM;
         trace_func[5] = traceWMPrime;
+#ifdef UNIQUE_MULTILOOP_DECOMPOSITION
+        trace_func[6] = traceM;
+        trace_func[7] = traceM1;
+#endif
 
         mfe = W[len];
         delta = _delta;
@@ -99,8 +193,11 @@ ss_map_t subopt_traceback(int len, int _delta) {
 }
 
 void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) {
+
+        //printf("V %d %d\n", i, j);
         // Hairpin Loop
         if (eH(i,j) + ps.total()  <= mfe + delta) {
+                //printf("hairpin\n");
                 ps_t ps1(ps); 
                 ps1.accumulate(eH(i,j));
                 ps1.update(i, j, '(', ')');
@@ -109,6 +206,7 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) {
 
         // Stack
         if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) {
+                //printf("stack %d %d %d %d\n", i, j, eS(i,j), V(i+1,j-1));
                 ps_t ps1(ps);
                 ps1.push(segment(i+1, j-1, lV, V(i+1, j-1)));
                 ps1.accumulate(eS(i,j));
@@ -118,16 +216,56 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) {
 
         // Internal Loop
         if (VBI(i,j) + ps.total() <= mfe + delta) {
+                //printf("internal loop\n");
                 traceVBI(i,j,ps,gstack);
         }
 
+#ifdef UNIQUE_MULTILOOP_DECOMPOSITION
+        int k;
+
+        for (k = i+2; k <= j-TURN-1; ++k) {
+
+          int kenergy1 = FM[i+1][k] + FM1[k+1][j-1];
+          int d5 = Ed5(i, j, i+1);
+          int d3 = Ed3(i, j, j-1);
+          int aup = auPenalty(i,j);
+          int kenergy2 = d5 + d3 + aup + Ea + Eb;
+          int kenergy_total = kenergy1 + kenergy2;
+          if (i == 4 && j == 41) {
+            //printf("ps: ");
+            ps.print();
+            //printf("\n");
+          }
+          //printf("FM[%d][%d]: %d FM1[%d][%d]: %d\n", i+1, k, FM[i+1][k], k+1, j-1, FM1[k+1][j-1]);
+          //printf("Ed3(%d, %d, %d): %d Ed5(%d, %d, %d): %d Ea: %d\n",
+          //   i,j,i+1, Ed5_new(i,j,i+1), i, j, j-1, Ed3_new(i,j,j-1), Ea);
+          //printf("Ed5(%d, %d, %d): %d Ed3(%d, %d, %d): %d Ea: %d %d %d\n",
+          //   i,j,i+1, Ed5(i,j,i+1), i, j, i+1, Ed3(i,j,j-1), Ea, auPenalty(i,j), Eb);
+          //printf("kenergy_total: %d ps.total(): %d mfe+delta: %d  i: %d j: %d k: %d\n", kenergy_total,
+          //  ps.total(), mfe+delta, i, j, k);
+          if (kenergy_total + ps.total() <= mfe + delta) {
+            //printf("multiloop\n");
+            ps_t ps1(ps);
+            ps1.push(segment(i+1,k, lM, FM[i+1][k]));
+            ps1.push(segment(k+1,j-1, lM1, FM1[k+1][j-1]));
+            ps1.accumulate(kenergy2);
+            ps1.update(i,j,'(',')');
+            //printf("auPenalty: %d\n", auPenalty(i,j));
+            push_to_gstack(gstack, ps1);
+          }
+        }
+#else
+
         // Multiloop
-        if ( VM(i,j) + ps.total() <= mfe + delta) {
+        if (VM(i,j) + ps.total() <= mfe + delta) {
                 ps_t ps1(ps);
                 ps1.push(segment(i, j, lVM, VM(i,j)));
                 ps1.update(i, j, '(', ')');
                 push_to_gstack(gstack, ps1);
         }
+
+#endif
+
 }
 
 void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) {
@@ -151,6 +289,7 @@ void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) {
 
 void traceW(int i, int j, ps_t& ps, ps_stack_t& gstack) {
 
+        //printf("W %d %d\n", i, j);
         for (int l = i; l < j-TURN; ++l) {
                 int wim1 =  MIN(0, W[l-1]);
                 int d3 = (l>i)?Ed3(j,l,l-1):0;
@@ -173,10 +312,118 @@ void traceW(int i, int j, ps_t& ps, ps_stack_t& gstack) {
         }
 }
 
+#ifdef UNIQUE_MULTILOOP_DECOMPOSITION
+void traceM1(int i, int j, ps_t& ps, ps_stack_t& gstack) {
+
+  //printf("M1 %d %d\n", i, j);
+  //if (i == 14)
+    //printf("%d %d\n", FM1[i][j-1], FM1[i][j-1] + Ec + ps.total());
+
+  if (FM1[i][j-1] + Ec + ps.total() <= mfe + delta) {
+    //printf("here1\n");
+    ps_t ps1(ps);
+    ps1.push(segment(i, j-1, lM1, FM1[i][j-1]));
+    ps1.accumulate(Ec);
+    push_to_gstack(gstack, ps1);
+  }
+
+  //printf("V(i,j):%d  Ed5_new: %d Ed3_new: %d\n", V(i,j), Ed5_new(i,j,i-1), Ed3_new(i,j,j+1));
+  int d5;
+  int d3;
+  int aup;
+  //d5 = (i != 1) ? Ed5(i,j,i-1) : Ed5(i,j,length);
+  //d3 = (j != length) ? Ed3(i,j,j+1) : Ed3(i,j,1);
+  d5 = Ed5_new(i, j, i-1);
+  d3 = Ed3_new(i, j, j+1);
+  aup = auPenalty(i,j);
+
+  if (V(i,j) + d5 + d3 + aup + Eb + ps.total() <= mfe + delta) {
+    //printf("here2\n");
+    ps_t ps1(ps);
+    ps1.push(segment(i, j, lV, V(i,j)));
+    ps1.accumulate(d5 + d3 + aup + Eb);
+    ps1.update(i,j,'(',')');
+    //printf("auPenalty: %d\n", auPenalty(i,j));
+    push_to_gstack(gstack, ps1);
+  }
+}
+
+void traceM(int i, int j, ps_t& ps, ps_stack_t& gstack) {
+
+  //printf("M %d %d\n", i, j);
+  int d5, d3;
+  int aup;
+
+  if (FM[i][j-1] + Ec + ps.total() <= mfe + delta) {
+    //printf("here11\n");
+    ps_t ps1(ps);
+    ps1.push(segment(i, j-1, lM, FM[i][j-1]));
+    ps1.accumulate(Ec);
+    push_to_gstack(gstack, ps1);
+  }
+
+  //printf("V(i,j):%d  Ed5_new: %d Ed3_new: %d\n", V(i,j), Ed5_new(i,j,i-1), Ed3_new(i,j,j+1));
+  //d5 = (i != 1) ? Ed3(i,j,i-1) : Ed3(i,j,length);
+  //d3 = (j != length) ? Ed5(i,j,j+1) : Ed5(i,j,1);
+  d5 = Ed5_new(i, j, i-1);
+  d3 = Ed3_new(i, j, j+1);
+  aup = auPenalty(i,j);
+  if (V(i,j) + d5 + d3 + Eb + aup + ps.total() <= mfe + delta) {
+    //printf("here12\n");
+    ps_t ps1(ps);
+    ps1.push(segment(i, j, lV, V(i,j)));
+    ps1.accumulate(d5 + d3 + Eb + aup);
+    ps1.update(i,j,'(',')');
+    push_to_gstack(gstack, ps1);
+  }
+
+
+  for (int k = i+TURN+1; k <= j-TURN-1; ++k) {
+
+    d5 = Ed5_new(k+1, j, k);
+    d3 = Ed3_new(k+1, j, j+1);
+    aup = auPenalty(k+1, j);
+
+    if (FM[i][k] + V(k+1,j) + d5 + d3
+         + Eb + aup + ps.total() <= mfe + delta) {
+      //printf("here3\n");
+      ps_t ps1(ps);
+      ps1.push(segment(i, k, lM, FM[i][k]));
+      ps1.push(segment(k+1, j, lV, V(k+1,j)));
+      ps1.accumulate(d5 + d3 + Eb + aup);
+      //printf("auPenalty: %d\n", auPenalty(i,k));
+      ps1.update(k+1,j,'(',')');
+      push_to_gstack(gstack, ps1);
+    }
+  }
+
+  for (int k = i; k <= j-TURN-1; ++k) {
+
+    d5 = Ed5_new(k+1, j, k);
+    d3 = Ed3_new(k+1, j, j+1);
+    aup = auPenalty(k+1, j);
+
+    if (V(k+1,j) + d5 + d3
+         + Eb + Ec*(k-i+1) + aup + ps.total() <= mfe+delta) {
+      //printf("here4\n");
+      ps_t ps1(ps);
+      ps1.push(segment(k+1, j, lV, V(k+1,j)));
+      ps1.accumulate(d5 + d3 + Eb + Ec*(k-i+1) + aup);
+      ps1.update(k+1, j, '(', ')');
+      //printf("auPenalty: %d\n", auPenalty(k+1,j));
+      push_to_gstack(gstack, ps1);
+    }
+  }
+}
+
+#endif
+
 void traceWM(int i, int j, ps_t& ps, ps_stack_t& gstack) {
         int d3 = (i==1)?Ed3(j,i,length):Ed3(j,i,i-1);
         int d5 = Ed5(j,i,j+1);
 
+        //printf("WM %d %d\n", i, j);
+        //printf("normal auPenalty: %d\n", auPenalty(i,j));
         if (V(i,j) + auPenalty(i, j) + Eb + d3 + d5 + ps.total() <= mfe + delta) {
                 ps_t ps_new(ps);
                 ps_new.accumulate(auPenalty(i, j) + Eb + d3 + d5);
@@ -217,6 +464,8 @@ void traceWMPrime(int i, int j, ps_t& ps, ps_stack_t& gstack) {
 }
 
 void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) {
+
+        //printf("VM %d %d\n", i, j);
         int d3 = Ed3(i,j,j-1);
         int d5 = Ed5(i,j,i+1);
 
@@ -231,4 +480,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) {
 void push_to_gstack(ps_stack_t& gstack, const ps_t& v) {
         gflag = 1;
         gstack.push(v);
+        //printf("Pushing to gstack: \n");
+//        v.print();
+        //printf("\n");
 }

From 90b4481f7a3a74329483a468836af8cdac898481 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@ubuntu.(none)>
Date: Fri, 11 Nov 2011 08:47:51 -0800
Subject: [PATCH 273/282] Added a Sample Test Module

---
 gtfold-mfe/tests/scripts/SampleTest.pm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100755 gtfold-mfe/tests/scripts/SampleTest.pm

diff --git a/gtfold-mfe/tests/scripts/SampleTest.pm b/gtfold-mfe/tests/scripts/SampleTest.pm
new file mode 100755
index 0000000..9686997
--- /dev/null
+++ b/gtfold-mfe/tests/scripts/SampleTest.pm
@@ -0,0 +1,26 @@
+#!/usr/bin/perl
+package SampleTest;
+use strict;
+use warnings;
+
+sub test()
+{
+  my(%Config) = %{$_[1]};
+  my(%Sequences) = %{$_[2]};
+  my(%local_sequences) = %{$_[3]};
+  my $logger = $_[4];
+
+  my $gtdir = $Config{"G_GTFOLD_DIR"};
+  my $unadir = $Config{"G_UNAFOLD_DIR"};
+  my $workdir = $Config{"G_WORK_DIR"};
+
+  my $key;
+  my $value;
+  my %new_hash = (%local_sequences, %Sequences);
+
+  while (($key, $value) = each(%new_hash)) {
+
+	  my $seqname=$key;
+  }
+}
+1;

From cdd5c97417e064260bd818a17ce1ff9cab35e260 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@ubuntu.(none)>
Date: Fri, 11 Nov 2011 10:33:56 -0800
Subject: [PATCH 274/282] Pretty Output for Suboptimal Structures Match Test.
 Output sent to a separate file.

---
 .../tests/scripts/SuboptMatchStructures.pm    | 80 ++++++++++++++++---
 1 file changed, 68 insertions(+), 12 deletions(-)

diff --git a/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm
index 1697a46..fa9d7ed 100755
--- a/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm
+++ b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm
@@ -1,5 +1,5 @@
 #!/usr/bin/perl
-package SuboptNumStructures;
+package SuboptMatchStructures;
 use strict;
 use warnings;
 use File::Basename;
@@ -14,12 +14,24 @@ sub test()
   my $gtdir = $Config{"G_GTFOLD_DIR"};
   my $rnadir = $Config{"G_RNAFOLD_DIR"};
   my $workdir = $Config{"G_WORK_DIR"};
+  my $min_energy = $Config{"L_SUBOPTMATCHSTRUCTURES_MIN_ENERGY"};
+  my $max_energy = $Config{"L_SUBOPTMATCHSTRUCTURES_MAX_ENERGY"};
+  my $energy_stride = $Config{"L_SUBOPTMATCHSTRUCTURES_ENERGY_STRIDE"};
+
+  if (not(defined($min_energy))) {
+    $min_energy = 0;
+  }
+  if (not(defined($max_energy))) {
+    $max_energy = 3;
+  }
+  if (not(defined($energy_stride))) {
+    $energy_stride = 1;
+  }
 
   my $key;
   my $value;
   my %new_hash = (%local_sequences);
-  # For testing pseudoknot detection logic
-  # we may only test the sequences specified in local_sequences
+
   while (($key, $value) = each(%new_hash)) {
 
 	  my $seqname=$key;
@@ -32,8 +44,11 @@ sub test()
     my $rnaout = "$workdir$seqname-rna";
 	  my $gtoutfilename  = $workdir."$seqname-gt.ct";
 
+    my %gtstruct_hash;
+    my %rnastruct_hash;
+
     my $energy;
-    for ($energy = 1; $energy <=10; ++$energy) {
+    for ($energy=$min_energy; $energy<=$max_energy; $energy=$energy+$energy_stride) {
 
       my $gtfile = $gtout.$energy;
       my $rnafile = $rnaout.$energy."_ss.txt";
@@ -50,19 +65,60 @@ sub test()
 
       my $gtsorted = $gtsubopt_file."_sorted";
       my $rnasubopt_sorted = $rnafile."_sorted";
-      `cat $gtsubopt_file | sed '/[A-Z]/d' | sort -o $gtsorted`;
-      `cat $rnasubopt_file | sed '/[A-Z]/d' | sort -o $rnasubopt_sorted`;
-      #`sort $gtsubopt_file -o $gtsorted`;
-      #`sort $rnasubopt_file -o $rnasubopt_sorted`;
+      my $gtstructs = `cat $gtsubopt_file | sed '/[A-Z]/d' | sed '/^\$/d'`;
+      my $rnastructs = `cat $rnasubopt_file | sed '/[A-Z]/d' | sed '/^\$/d'`;
+
+      %gtstruct_hash = split('[ \n]',$gtstructs);
+      %rnastruct_hash = split('[ \n]',$rnastructs);
+
+      my $diff_file_name = "$workdir$seqname\_$energy.diff"; 
+
+      open (DIFF_FILE, ">> $diff_file_name");
+
+      my $diff = 0;
+      foreach my $key ( keys %gtstruct_hash )
+      {
+        my $change = $gtstruct_hash{$key} 
+        unless ( (exists $rnastruct_hash{$key}) && $gtstruct_hash{$key} eq $rnastruct_hash{$key} );
+        # gotta check for existence to quiet warnings.
+        if(defined($change) && $change ne "") {
+          print DIFF_FILE $key. "\nGTFOLD Energy: ". $gtstruct_hash{$key};
+          if (exists $rnastruct_hash{$key}) {
+            print DIFF_FILE "\nRNASubopt Energy: ". $rnastruct_hash{$key};
+          }
+          else {
+            print DIFF_FILE "\nRNASubopt Energy: No corresponding structure";
+          }
+          print DIFF_FILE "\n";
+          $diff = 1;
+        }
+      }
+
+      foreach my $key ( keys %rnastruct_hash )
+      {
+        my $change = $rnastruct_hash{$key} 
+        unless ( (exists $gtstruct_hash{$key}) && $gtstruct_hash{$key} eq $rnastruct_hash{$key} );
+        # gotta check for existence to quiet warnings.
+        if(defined($change) && $change ne "") {
+          print DIFF_FILE $key. "\nRNASubopt Energy: ". $rnastruct_hash{$key};
+          if (exists $gtstruct_hash{$key}) {
+            print DIFF_FILE "\nGTFOLD Energy: ". $gtstruct_hash{$key};
+          }
+          else {
+            print DIFF_FILE "\nGTFOLD Energy: No corresponding structure";
+          }
+          print DIFF_FILE "\n";
+          $diff = 1;
+        }
+      }
 
-      my $diff_str = `diff $gtsorted $rnasubopt_sorted`;
-      #print $diff_str;
+      close DIFF_FILE;
 
-      if ($diff_str eq "") {
+      if ($diff == 0) {
         $logger->info("TEST PASSED: $seqname: energy delta = $energy: Suboptimal Structures matched");
       }
       else {
-        $logger->error("TEST FAILED: $seqname: energy delta = $energy: Suboptimal Structures not matched\n $diff_str");
+        $logger->error("TEST FAILED: $seqname: energy delta = $energy: Suboptimal Structures not matched. Difference Written to file $diff_file_name");
       }
     }
   }

From 45111dc19f1b21cb9ec0a3bda5e5b14c267ac1a9 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 18 Nov 2011 11:57:02 -0500
Subject: [PATCH 275/282] adding stochastic smaplign changes

---
 gtfold-mfe/include/stochastic-sampling.h |  1 +
 gtfold-mfe/src/main.cc                   | 69 +++-------------------
 gtfold-mfe/src/stochastic-sampling.cc    | 73 ++++++++++++++++++++++++
 3 files changed, 81 insertions(+), 62 deletions(-)

diff --git a/gtfold-mfe/include/stochastic-sampling.h b/gtfold-mfe/include/stochastic-sampling.h
index 68fea91..38f037f 100644
--- a/gtfold-mfe/include/stochastic-sampling.h
+++ b/gtfold-mfe/include/stochastic-sampling.h
@@ -83,5 +83,6 @@ void  rnd_ud(int i, int j, int* structure);
 void   rnd_u(int i, int j, int* structure);
 
 double rnd_structure(int* structure, int len);
+void batch_sample(int num_rnd, int length, double U);
 
 #endif
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index f5dbc21..d183fea 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -19,6 +19,7 @@
  */
 
 #include <iostream>
+#include <limits>
 #include <iomanip>
 #include <fstream>
 #include <string>
@@ -278,9 +279,9 @@ int main(int argc, char** argv) {
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
 	if (SUBOPT_ENABLED) 
-									readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, 1, T_MISMATCH);
+    readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, 1, T_MISMATCH);
 	else
-									readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
+    readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
 
 	printRunConfiguration(seq);
 
@@ -294,74 +295,18 @@ int main(int argc, char** argv) {
     free_fold(seq.length());
     exit(0);
   }
+  
   if (RND_SAMPLE == true)
   {
-	  printf("\nComputing partition function...\n");
+    printf("\nComputing partition function...\n");
 	  int pf_count_mode = 0;
 	  if(PF_COUNT_MODE) pf_count_mode=1;
 	  double U = calculate_partition(seq.length(),pf_count_mode);
+ 
+    batch_sample(num_rnd, seq.length(), U); 
 
-	  int* structure = new int[seq.length()+1];
-	  srand(time(NULL));
-    std::map<std::string,std::pair<int,double> >  uniq_structs;
-	  
-    if (num_rnd > 0 ) {
-      printf("\nSampling structures...\n");
-
-      for (int count = 1; count <= num_rnd; ++count) 
-      {
-        memset(structure, 0, (seq.length()+1)*sizeof(int));
-        double energy = rnd_structure(structure, seq.length());
-
-        std::string ensemble(seq.length()+1,'.');
-        for (int i = 1; i <= (int)seq.length(); ++ i) {
-          //     printf("%d %d\n",i,structure[i]);
-          if (structure[i] > 0 && ensemble[i] == '.')
-          {
-            ensemble[i] = '(';
-            ensemble[structure[i]] = ')';
-          }
-        }
-        std::map<std::string,std::pair<int,double> >::iterator iter ;
-        if ((iter =uniq_structs.find(ensemble.substr(1))) != uniq_structs.end())
-        {
-          std::pair<int,double>& pp = iter->second;
-          pp.first++;
-        }
-        else {
-          uniq_structs.insert(make_pair(ensemble.substr(1),std::pair<int,double>(1,energy))); 
-        }
-         // std::cout << ensemble.substr(1) << ' ' << energy << std::endl;
-      }
-
-      int pcount = 0;
-      int maxCount = 0; std::string bestStruct;
-      double bestE = INFINITY;
-
-      std::map<std::string,std::pair<int,double> >::iterator iter ;
-      for (iter = uniq_structs.begin(); iter != uniq_structs.end();  ++iter)
-      {
-        const std::string& ss = iter->first;
-        const std::pair<int,double>& pp = iter->second;
-        const double& estimated_p =  (double)pp.first/(double)num_rnd;
-        const double& energy = pp.second;
-        double actual_p = pow(2.718281,-1.0*energy/RT_)/U;
-
-        printf("%s\t%lf\t%lf\t%lf\n",ss.c_str(),energy,actual_p,estimated_p);
-        pcount += pp.first;
-        if (pp.first > maxCount)
-        {
-          maxCount = pp.first;
-          bestStruct  = ss;
-          bestE = pp.second;
-        }
-      }
-      assert(num_rnd == pcount);
-      printf("\nMost favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd);
-    } 
     free_partition();
 	  free_fold(seq.length());
-	  delete [] structure;
 	  exit(0);
   }
 
diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc
index bdc9ee9..53b2f3b 100644
--- a/gtfold-mfe/src/stochastic-sampling.cc
+++ b/gtfold-mfe/src/stochastic-sampling.cc
@@ -3,7 +3,10 @@
 #include "global.h"
 #include <assert.h>
 #include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include <stack>
+#include <map>
 
 int ss_verbose = 0; 
 
@@ -671,6 +674,76 @@ double rnd_structure(int* structure, int len)
   return (double)energy/100.0;
 }
 
+void batch_sample(int num_rnd, int length, double U)
+{
+	  int* structure = new int[length+1];
+	  srand(time(NULL));
+    std::map<std::string,std::pair<int,double> >  uniq_structs;
+	  
+    if (num_rnd > 0 ) {
+      printf("\nSampling structures...\n");
+      int count,nsamples =0;
+      for (count = 1; count <= num_rnd; ++count) 
+      {
+        memset(structure, 0, (length+1)*sizeof(int));
+        double energy = rnd_structure(structure, length);
+
+        std::string ensemble(length+1,'.');
+        for (int i = 1; i <= (int)length; ++ i) {
+          if (structure[i] > 0 && ensemble[i] == '.')
+          {
+            ensemble[i] = '(';
+            ensemble[structure[i]] = ')';
+          }
+        }
+        //double myEnegry = -88.4;
+        //++nsamples;
+        //if (fabs(energy-myEnegry)>0.0001) continue; //TODO: debug
+        //++count;
+
+        std::map<std::string,std::pair<int,double> >::iterator iter ;
+        if ((iter =uniq_structs.find(ensemble.substr(1))) != uniq_structs.end())
+        {
+          std::pair<int,double>& pp = iter->second;
+          pp.first++;
+        }
+        else {
+          uniq_structs.insert(make_pair(ensemble.substr(1),std::pair<int,double>(1,energy))); 
+        }
+        
+        // std::cout << ensemble.substr(1) << ' ' << energy << std::endl;
+      }
+      std::cout << nsamples << std::endl;
+      int pcount = 0;
+      int maxCount = 0; std::string bestStruct;
+      double bestE = INFINITY;
+
+      std::map<std::string,std::pair<int,double> >::iterator iter ;
+      for (iter = uniq_structs.begin(); iter != uniq_structs.end();  ++iter)
+      {
+        const std::string& ss = iter->first;
+        const std::pair<int,double>& pp = iter->second;
+        const double& estimated_p =  (double)pp.first/(double)num_rnd;
+        const double& energy = pp.second;
+        double actual_p = pow(2.718281,-1.0*energy/RT_)/U;
+
+        printf("%s %lf %lf %lf %d\n",ss.c_str(),energy,actual_p,estimated_p,pp.first);
+        pcount += pp.first;
+        if (pp.first > maxCount)
+        {
+          maxCount = pp.first;
+          bestStruct  = ss;
+          bestE = pp.second;
+        }
+      }
+      assert(num_rnd == pcount);
+      printf("\nMax frequency structure : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd);
+      
+    }
+
+	  delete [] structure;
+}
+
 void set_single_stranded(int i, int j, int* structure)
 {
   for(;i<=j;++i) 

From 99e46c42c525ca86193c43e51c26885aee11d613 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@ubuntu.(none)>
Date: Fri, 18 Nov 2011 10:50:58 -0800
Subject: [PATCH 276/282] Adding Paul Specials

---
 gtfold-mfe/tests/scripts/paul_specials.pm | 163 ++++++++++++++++++++++
 1 file changed, 163 insertions(+)
 create mode 100755 gtfold-mfe/tests/scripts/paul_specials.pm

diff --git a/gtfold-mfe/tests/scripts/paul_specials.pm b/gtfold-mfe/tests/scripts/paul_specials.pm
new file mode 100755
index 0000000..304260d
--- /dev/null
+++ b/gtfold-mfe/tests/scripts/paul_specials.pm
@@ -0,0 +1,163 @@
+package paul_specials;
+
+use strict;
+use warnings;
+
+require      Exporter;
+our @ISA       = qw(Exporter);
+our @EXPORT    = qw( table_to_bracket table_to_bracket5 make_pair_table);
+
+#input is base-pair table, output is dot-bracket notation. NOte: $table[0]=seq_length. 
+#ADD PKNOTS SUPPORT!
+sub table_to_bracket {
+    
+    my $ref = shift;
+    my $dotb = ".";
+    my $temp = 0;
+
+    my @tbl = @$ref; #
+    my $len = $tbl[0];
+
+    for (my $j = 0; $j < $len; $j++ ) {
+	substr($dotb, $j, 1) = ".";
+    }
+    #print "\n$dotb\n\n";
+    
+    for (my $j = 1; $j < $len+1; $j++ ) {
+	
+	if ($tbl[$j]>$j) {
+	    substr($dotb, $j-1, 1) = "\(";
+	    $temp = $tbl[$j] - 1;
+	    substr($dotb, $temp, 1) = "\)";
+	}
+
+    }
+    
+    return $dotb;
+}
+
+sub table_to_bracket5 {
+    
+    my $ref = shift;
+    my $dotb = ".";
+    my $temp = 0;
+
+    my @tbl = @$ref; 
+    my $len = $tbl[0]+1;
+
+    #print "table_to_bracket: len = $len\n";
+    
+    for (my $j = 0; $j < $len; $j++ ) {
+	substr($dotb, $j, 1) = ".";
+    }
+    
+    for (my $j = 0; $j < $len; $j++ ) {
+	
+	if ($tbl[$j+1]>$j+1) {
+	    substr($dotb, $j, 1) = "\(";
+	    $temp = $tbl[$j+1] - 2;
+	    substr($dotb, $temp, 1) = "\)";
+	}
+	#elsif ($tbl[$j+1]== 0) {
+	#    substr($dotb, $j, 1) = "\.";
+	#}
+    }
+    
+    return $dotb;
+}
+
+
+
+sub make_pair_table {
+    my $str = shift;
+    my $i;
+    my @bps = ();
+    my @bps_square = ();
+    my @bps_curly = ();
+    my @bps_angle = ();
+    my @pair_table;
+    my $prime5;
+    my $prime3;
+    my $count = 0;
+    
+    my $len = length($str);
+    
+    #print "make_pair_table: len = $len\n";
+
+    $pair_table[0] = $len;
+
+    for (my $j = 0; $j < $len; $j++ ) {
+	$pair_table[$j+1] = 0;
+	if ( substr($str,$j,1) =~ '\(' ){
+	    push(@bps, $j);
+	    ++$count;
+	}	
+	elsif ( substr($str,$j,1) =~ '\)' ){
+	    $prime5 = pop(@bps);
+	    $prime3 = $j;
+	    $pair_table[$prime3+1] = $prime5+1;
+	    $pair_table[$prime5+1] = $prime3+1;
+	    --$count;
+	    #print "base-pair: $pair_table[$i][$prime3] . $pair_table[$i][$prime5]\n"
+	}
+	elsif ( substr($str,$j,1) =~ '\[' ){
+	    push(@bps_square, $j);
+	    ++$count;
+	}	
+	elsif ( substr($str,$j,1) =~ '\]' ){
+	    $prime5 = pop(@bps_square);
+	    $prime3 = $j;
+	    $pair_table[$prime3+1] = $prime5+1;
+	    $pair_table[$prime5+1] = $prime3+1;
+	    --$count;
+	}
+	elsif ( substr($str,$j,1) =~ '\{' ){
+	    push(@bps_curly, $j);
+	    ++$count;
+	}	
+	elsif ( substr($str,$j,1) =~ '\}' ){
+	    $prime5 = pop(@bps_curly);
+	    $prime3 = $j;
+	    $pair_table[$prime3+1] = $prime5+1;
+	    $pair_table[$prime5+1] = $prime3+1;
+	    --$count;
+	}
+	elsif ( substr($str,$j,1) =~ '\<' ){
+	    push(@bps_angle, $j);
+	    ++$count;
+	}	
+	elsif ( substr($str,$j,1) =~ '\>' ){
+	    $prime5 = pop(@bps_angle);
+	    $prime3 = $j;
+	    $pair_table[$prime3+1] = $prime5+1;
+	    $pair_table[$prime5+1] = $prime3+1;
+	    --$count;
+	}
+    }
+    
+#({[<.>]})
+    
+#print "pair table:\n";
+#for ($i = 1; $i < $len+1; $i++ ) {
+#    print "$pair_table[$i] ";
+#}
+    
+#print "\n";
+#
+#print "pair_table = $#pair_table\n";    
+
+if ($count){
+    print "Unbalanced brackets in:
+$str\n";
+    die;
+}    
+
+
+    return @pair_table;
+    
+}
+
+
+
+
+1;

From 7fa3ab83096aedd2aaf92c7f65decf3d76cf6a30 Mon Sep 17 00:00:00 2001
From: Rohit Banga <iamrohitbanga@gmail.com>
Date: Fri, 18 Nov 2011 14:36:10 -0500
Subject: [PATCH 277/282] Duplicate Structures should be reported if partial
 structure encountered again in suboptimal traceback.

---
 gtfold-mfe/src/subopt_traceback.cc | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc
index 150d6bc..d67a852 100644
--- a/gtfold-mfe/src/subopt_traceback.cc
+++ b/gtfold-mfe/src/subopt_traceback.cc
@@ -139,13 +139,13 @@ void process(ss_map_t& subopt_data, int len) {
 
                 if (ps.empty()) {
                         count++;
-                        //pair<ss_map_t::iterator, bool> ins_result;
-                        // ins_result = subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
-                        //if (ins_result.second == false) {
-                          //printf("Duplicate Structure!!!");
-                         // exit(1);
-                        //}
-                        cout << ps.str << endl;
+                        pair<ss_map_t::iterator, bool> ins_result;
+                        ins_result = subopt_data.insert(std::make_pair<std::string,int>(ps.str,ps.ae_));
+                        if (ins_result.second == false) {
+                          printf("Duplicate Structure!!!");
+                          exit(1);
+                        }
+                        //cout << ps.str << endl;
                         continue;
                 }	
                 else {

From fb6500bef4d684ce051bb0cf8575449405b4de97 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 15 Dec 2011 22:08:31 -0500
Subject: [PATCH 278/282] code cleanup

---
 gtfold-mfe/include/boltzmann_main.h   |   6 +
 gtfold-mfe/include/constraints.h      |   7 +-
 gtfold-mfe/include/main.h             |  17 +-
 gtfold-mfe/include/mfe_main.h         |   8 +
 gtfold-mfe/include/options.h          |  13 +-
 gtfold-mfe/include/subopt_main.h      |   6 +
 gtfold-mfe/include/utils.h            |   7 +-
 gtfold-mfe/src/Makefile.am            |   7 +-
 gtfold-mfe/src/Makefile.in            |  36 ++-
 gtfold-mfe/src/algorithms.c           |   2 +-
 gtfold-mfe/src/boltzmann_main.cc      | 197 +++++++++++
 gtfold-mfe/src/constraints.cc         |  15 +-
 gtfold-mfe/src/global.cc              | 227 +++++++++++++
 gtfold-mfe/src/main.cc                | 274 ++--------------
 gtfold-mfe/src/mfe_main.cc            | 448 ++++++++++++++++++++++++++
 gtfold-mfe/src/options.cc             |   8 +-
 gtfold-mfe/src/shapereader.cc         |   6 +
 gtfold-mfe/src/stochastic-sampling.cc |   4 +-
 gtfold-mfe/src/subopt_main.cc         | 158 +++++++++
 gtfold-mfe/src/traceback.c            |   8 +-
 gtfold-mfe/src/utils.cc               |  17 +-
 21 files changed, 1180 insertions(+), 291 deletions(-)
 create mode 100644 gtfold-mfe/include/boltzmann_main.h
 create mode 100644 gtfold-mfe/include/mfe_main.h
 create mode 100644 gtfold-mfe/include/subopt_main.h
 create mode 100644 gtfold-mfe/src/boltzmann_main.cc
 create mode 100644 gtfold-mfe/src/global.cc
 create mode 100644 gtfold-mfe/src/mfe_main.cc
 create mode 100644 gtfold-mfe/src/subopt_main.cc

diff --git a/gtfold-mfe/include/boltzmann_main.h b/gtfold-mfe/include/boltzmann_main.h
new file mode 100644
index 0000000..50841d4
--- /dev/null
+++ b/gtfold-mfe/include/boltzmann_main.h
@@ -0,0 +1,6 @@
+#ifndef _BPP_MAIN_H_
+#define _BPP_MAIN_H_
+
+int boltzmann_main(int argc, char** argv);
+
+#endif
diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h
index 9805dbd..f21e115 100644
--- a/gtfold-mfe/include/constraints.h
+++ b/gtfold-mfe/include/constraints.h
@@ -13,11 +13,11 @@ extern int nFBP;
 
 #define BP(i,j) BP[ind[j]+i]
 
+
 int init_constraints(const char* constr_file, int length) ;
 void free_constraints(int length) ;
 void print_constraints(int length) ;
 
-
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -34,6 +34,11 @@ int forcePair(int i, int j);
 
 int withinCD(int i, int j);
 int verify_structure();
+
+void enable_constraints(int b);
+void enable_limit_distance(int b);
+void set_contact_distance(int dist);
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/gtfold-mfe/include/main.h b/gtfold-mfe/include/main.h
index 7faf980..8fe342e 100644
--- a/gtfold-mfe/include/main.h
+++ b/gtfold-mfe/include/main.h
@@ -27,20 +27,13 @@
 
 using namespace std;
 
-void init_fold(string seq);
-void free_fold(int len);
+//void init_fold(string seq);
+//void free_fold(int len);
 
-bool encodeSequence(string seq);
+//bool encodeSequence(string seq);
 void limit_contact_distance(int lCD, int length);
 
-bool is_valid_base(char c)
-{	
-	return ( (c-'A' == 0) || (c-'a' == 0) || 
-			 (c-'C' == 0) || (c-'c' == 0) ||
-			 (c-'G' == 0) || (c-'g' == 0) ||
-			 (c-'U' == 0) || (c-'u' == 0));
-}
-
+/*
 void trim_spaces(std::string& str)
 {
 	// Trim Both leading and trailing spaces
@@ -73,5 +66,5 @@ void tokenize(const std::string& str, std::vector<std::string>& tokens, const st
 		pos = str.find_first_of(delimiters, lastPos);
 	}
 }
-	
+	*/
 #endif
diff --git a/gtfold-mfe/include/mfe_main.h b/gtfold-mfe/include/mfe_main.h
new file mode 100644
index 0000000..683be07
--- /dev/null
+++ b/gtfold-mfe/include/mfe_main.h
@@ -0,0 +1,8 @@
+#ifndef _MFE_MAIN_H_
+#define _MFE_MAIN_H_
+
+int mfe_main(int argc, char** argv);
+void init_fold(const char* seq);
+void free_fold(int len);
+
+#endif
diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h
index 7965698..a1ecd7a 100644
--- a/gtfold-mfe/include/options.h
+++ b/gtfold-mfe/include/options.h
@@ -8,10 +8,11 @@
 
 using namespace std;
 
-extern bool ILSA;
-extern bool NOISOLATE;
+//extern bool ILSA;
+//extern bool NOISOLATE;
 //extern bool USERDATA;
 //extern bool PARAMS;
+/*
 extern bool LIMIT_DISTANCE;
 extern bool BPP_ENABLED;
 extern bool SUBOPT_ENABLED;
@@ -45,11 +46,11 @@ extern int num_rnd;
 
 extern bool LIMIT_DISTANCE;
 extern int contactDistance;
+*/
 
-
-void help();
-void parse_options(int argc, char** argv);
-void printRunConfiguration(string seq);
+//void help();
+//void parse_options(int argc, char** argv);
+//void printRunConfiguration(string seq);
 
 
 #endif
diff --git a/gtfold-mfe/include/subopt_main.h b/gtfold-mfe/include/subopt_main.h
new file mode 100644
index 0000000..1f26e43
--- /dev/null
+++ b/gtfold-mfe/include/subopt_main.h
@@ -0,0 +1,6 @@
+#ifndef _SUBOPT_MAIN_H_
+#define _SUBOPT_MAIN_H_
+
+int subopt_main(int argc, char** argv);
+
+#endif
diff --git a/gtfold-mfe/include/utils.h b/gtfold-mfe/include/utils.h
index 8b33655..a8e5c28 100644
--- a/gtfold-mfe/include/utils.h
+++ b/gtfold-mfe/include/utils.h
@@ -3,7 +3,6 @@
 
 #include "constants.h"
 
-
 #define MIN(X,Y) ((X) < (Y) ? (X) : (Y))
 #define MAX(X,Y) ((X) > (Y) ? (X) : (Y))
 #define MIN4(W,X,Y,Z) MIN(MIN(W,X),MIN(Y,Z))
@@ -12,5 +11,11 @@
 char baseToDigit(const char* base) ;
 unsigned char encode(char base);
 int isWatsonCrickBase(char base);
+double get_seconds();
+
+#ifdef __cplusplus
+extern "C"
+#endif
+int is_valid_base(char c);
 
 #endif
diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am
index 62cedca..8a1ba22 100644
--- a/gtfold-mfe/src/Makefile.am
+++ b/gtfold-mfe/src/Makefile.am
@@ -7,17 +7,20 @@ bin_PROGRAMS = gtfold
 
 gtfold_SOURCES = \
 	main.cc\
-	loader.cc\
+	mfe_main.cc\
+  loader.cc\
 	utils.cc\
 	options.cc\
 	constraints.cc\
-	global.c\
+	global.cc\
 	energy.c\
 	algorithms.c\
 	traceback.c\
+	subopt_main.cc\
 	subopt_traceback.cc\
 	stochastic-sampling.cc\
   algorithms-partition.c\
+  boltzmann_main.cc\
 	partition-dangle.c\
 	partition-func.c\
 	shapereader.cc
diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in
index d36b292..86a7787 100644
--- a/gtfold-mfe/src/Makefile.in
+++ b/gtfold-mfe/src/Makefile.in
@@ -31,7 +31,7 @@ PRE_INSTALL = :
 POST_INSTALL = :
 NORMAL_UNINSTALL = :
 PRE_UNINSTALL = :
-POST_UNINSTALL = :
+POST_UNINSTALL = : 
 build_triplet = @build@
 host_triplet = @host@
 target_triplet = @target@
@@ -48,12 +48,13 @@ CONFIG_CLEAN_FILES =
 CONFIG_CLEAN_VPATH_FILES =
 am__installdirs = "$(DESTDIR)$(bindir)"
 PROGRAMS = $(bin_PROGRAMS)
-am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \
-	options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \
-	energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \
-	subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \
-	partition-dangle.$(OBJEXT) partition-func.$(OBJEXT) \
-	shapereader.$(OBJEXT) stochastic-sampling.$(OBJEXT)
+am_gtfold_OBJECTS = main.$(OBJEXT) mfe_main.$(OBJEXT) loader.$(OBJEXT) \
+	utils.$(OBJEXT) options.$(OBJEXT) constraints.$(OBJEXT) \
+	global.$(OBJEXT) energy.$(OBJEXT) algorithms.$(OBJEXT) \
+	traceback.$(OBJEXT) subopt_main.$(OBJEXT) \
+	subopt_traceback.$(OBJEXT) stochastic-sampling.$(OBJEXT) \
+	algorithms-partition.$(OBJEXT) boltzmann_main.$(OBJEXT) partition-dangle.$(OBJEXT) \
+	partition-func.$(OBJEXT) shapereader.$(OBJEXT)
 gtfold_OBJECTS = $(am_gtfold_OBJECTS)
 gtfold_DEPENDENCIES =
 gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \
@@ -183,18 +184,21 @@ AM_CFLAGS = $(OPENMP_CFLAGS) -DDATADIR='$(datadir)/@PACKAGE@'
 AM_CXXFLAGS = -DDATADIR='$(datadir)/@PACKAGE@'
 gtfold_SOURCES = \
 	main.cc\
-	loader.cc\
+	mfe_main.cc\
+  loader.cc\
 	utils.cc\
 	options.cc\
 	constraints.cc\
-	global.c\
+	global.cc\
 	energy.c\
 	algorithms.c\
 	traceback.c\
+	subopt_main.cc\
 	subopt_traceback.cc\
-	algorithms-partition.c\
 	stochastic-sampling.cc\
-	partition-dangle.c\
+  algorithms-partition.c\
+  boltzmann_main.cc\
+  partition-dangle.c\
 	partition-func.c\
 	shapereader.cc
 
@@ -255,8 +259,11 @@ install-binPROGRAMS: $(bin_PROGRAMS)
 	while read type dir files; do \
 	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
 	    test -z "$$files" || { \
-	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+	      echo "$(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
 	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+        ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtmfe || exit $$?;\
+        ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtsubopt || exit $$?;\
+        ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtboltzmann || exit $$?;\
 	    } \
 	; done
 
@@ -283,17 +290,20 @@ distclean-compile:
 	-rm -f *.tab.c
 
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stochastic-sampling.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/boltzmann_main.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/constraints.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/energy.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/global.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/loader.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mfe_main.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-func.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stochastic-sampling.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_main.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@
diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c
index 7d81bfe..07f987f 100644
--- a/gtfold-mfe/src/algorithms.c
+++ b/gtfold-mfe/src/algorithms.c
@@ -129,7 +129,7 @@ int calculate(int len) {
 #ifdef _OPENMP
 #pragma omp parallel
 #pragma omp master
-  fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
+  if (g_verbose) fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads());
 #endif
 
   initializeMatrix(len);
diff --git a/gtfold-mfe/src/boltzmann_main.cc b/gtfold-mfe/src/boltzmann_main.cc
new file mode 100644
index 0000000..f590dc6
--- /dev/null
+++ b/gtfold-mfe/src/boltzmann_main.cc
@@ -0,0 +1,197 @@
+#include <iostream>
+#include <cstdio>
+#include <cstdlib>
+#include <string>
+#include <cstring>
+
+#include "global.h"
+#include "loader.h"
+#include "algorithms-partition.h"
+#include "boltzmann_main.h"
+#include "partition-func.h"
+#include "mfe_main.h"
+#include "stochastic-sampling.h"
+#include "algorithms.h"
+#include "traceback.h"
+
+using namespace std;
+
+static bool CALC_PART_FUNC = false;
+static bool PF_COUNT_MODE = false;
+static bool BPP_ENABLED = false;
+static bool PARAM_DIR = false;
+static bool RND_SAMPLE = false;
+
+static string seqfile = "";
+static string outputPrefix = "";
+static string outputDir = "";
+static string outputFile = "";
+static string paramDir; // default value
+static string bppOutFile = "";
+static int num_rnd = 0;
+
+static void help() {
+    printf("Usage: gtboltzmann [OPTION]... FILE\n\n");
+
+    printf("   FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n");
+
+    printf("OPTIONS\n");
+ 
+    printf("   --partition          Calculate the partition function.\n");
+    printf("   --sample   INT       Sample number of structures equal to INT\n");
+    printf("   --pf_count           Calculate the structure count using partition function and zero energy value.\n");
+    printf("   --bpp                Calculate base pair probabilities.\n");
+    printf("\n");
+    printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
+    printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
+    printf("   -h, --help           Output help (this message) and exit.\n");
+    printf("   -w, --workdir DIR    Path of directory where output files will be written.\n");
+    exit(-1);
+}
+
+static void parse_options(int argc, char** argv) {
+  int i;
+
+  for(i=1; i<argc; i++) {
+    if(argv[i][0] == '-') {
+      if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
+        help(); 
+      } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+        if(i < argc) {
+          paramDir = argv[++i];
+          PARAM_DIR = true;
+        }
+        else {
+          help();
+        }
+      } 
+      else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
+        if(i < argc)
+          outputPrefix = argv[++i];
+        else
+          help();
+      } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
+        if(i < argc)
+          outputDir = argv[++i];
+        else
+          help();
+      } else if(strcmp(argv[i], "--bpp") == 0) {
+        BPP_ENABLED = true;
+      }
+      else if (strcmp(argv[i],"--partition") == 0) {
+        CALC_PART_FUNC = true;
+      } else if (strcmp(argv[i],"--pf_count") == 0) {
+        CALC_PART_FUNC = true;
+        PF_COUNT_MODE = true;
+      }  else if (strcmp(argv[i],"--sample") == 0) {
+        RND_SAMPLE = true;
+        if(i < argc)
+          num_rnd = atoi(argv[++i]);
+        else
+          help();
+      }
+
+    } else {
+      seqfile = argv[i];
+    }
+  }
+
+  if(seqfile.empty()) {
+    printf("Missing input file.\n");
+    help();
+  }
+
+// If no output file specified, create one
+  if(outputPrefix.empty()) {
+    // base it off the input file
+    outputPrefix += seqfile;
+
+    size_t pos;
+    // extract file name from the path
+    if ((pos=outputPrefix.find_last_of('/')) > 0) {
+      outputPrefix = outputPrefix.substr(pos+1);
+    }
+
+    // and if an extension exists, remove it ...
+    if(outputPrefix.find(".") != string::npos)
+      outputPrefix.erase(outputPrefix.rfind("."));
+  }
+
+  // If output dir specified
+  if (!outputDir.empty()) {
+    outputFile += outputDir;
+    outputFile += "/";
+    bppOutFile += outputDir;
+    bppOutFile += "/";
+  }
+  // ... and append the .ct
+  outputFile += outputPrefix;
+  outputFile += ".ct";
+
+  bppOutFile += outputPrefix;	
+  bppOutFile += "_bpp.txt";	
+}
+
+
+int boltzmann_main(int argc, char** argv) {
+  std::string seq;
+
+  parse_options(argc, argv);
+
+  if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) {
+    printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
+    exit(-1);
+  }
+
+	init_fold(seq.c_str());
+
+  readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, 0, 0, 0);
+
+	calculate(seq.length()) ; 
+	trace(seq.length());
+  
+  if (CALC_PART_FUNC == true)
+  {
+    printf("\nComputing partition function...\n");
+    int pf_count_mode = 0;
+    if(PF_COUNT_MODE) pf_count_mode=1;
+
+    calculate_partition(seq.length(),pf_count_mode);
+    free_partition();
+  } else if (RND_SAMPLE == true) {
+    printf("\nComputing partition function...\n");
+	  int pf_count_mode = 0;
+	  if(PF_COUNT_MODE) pf_count_mode=1;
+	  double U = calculate_partition(seq.length(),pf_count_mode);
+ 
+    batch_sample(num_rnd, seq.length(), U); 
+
+    free_partition();
+  }
+  else if(BPP_ENABLED){
+    printf("\n");
+    printf("Calculating partition function\n");
+    double ** Q,  **QM, **QB, **P;
+    Q = mallocTwoD(seq.length() + 1, seq.length() + 1);
+    QM = mallocTwoD(seq.length() + 1, seq.length() + 1);
+    QB = mallocTwoD(seq.length() + 1, seq.length() + 1);
+    P = mallocTwoD(seq.length() + 1, seq.length() + 1);
+
+
+    fill_partition_fn_arrays(seq.length(), Q, QB, QM);
+    fillBasePairProbabilities(seq.length(), Q, QB, QM, P);
+    printBasePairProbabilities(seq.length(), structure, P, bppOutFile.c_str());
+    printf("Saved BPP output in %s\n",bppOutFile.c_str());
+
+    freeTwoD(Q, seq.length() + 1, seq.length() + 1);
+    freeTwoD(QM, seq.length() + 1, seq.length() + 1);
+    freeTwoD(QB, seq.length() + 1, seq.length() + 1);
+    freeTwoD(P, seq.length() + 1, seq.length() + 1);
+  } else {
+    printf("No valid option specified !\n\n");
+    help();
+  }
+
+	free_fold(seq.length());
+  return EXIT_SUCCESS;
+}
diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
index ce96636..b1f2a1b 100644
--- a/gtfold-mfe/src/constraints.cc
+++ b/gtfold-mfe/src/constraints.cc
@@ -41,12 +41,18 @@ int** FBP;
 int nPBP;
 int nFBP;
 
+static bool CONS_ENABLED = false;
+static bool LIMIT_DISTANCE = false;
+static int contactDistance = -1;
+
+void enable_constraints(int b) {CONS_ENABLED = b;}
+void enable_limit_distance(int b) {LIMIT_DISTANCE = b;}
+void set_contact_distance(int dist) {contactDistance = dist;}
+
 static int load_constraints(const char* constr_file, int seq_length, int verbose=0) {
 	
-
 	fprintf(stdout, "- Running with constraints\n");
 
-
 	std::ifstream cfcons;
 	cfcons.open(constr_file, std::ios::in);
     if (cfcons == 0) {
@@ -164,8 +170,9 @@ static int load_constraints(const char* constr_file, int seq_length, int verbose
 }
 
 int init_constraints(const char* constr_file,int length) {
-	load_constraints(constr_file, length);
-
+  enable_constraints(true);
+  load_constraints(constr_file, length);
+  
 
 	int i,j,it,k;
 	ind = (int*) malloc((length+1) * sizeof(int));
diff --git a/gtfold-mfe/src/global.cc b/gtfold-mfe/src/global.cc
new file mode 100644
index 0000000..eb91d90
--- /dev/null
+++ b/gtfold-mfe/src/global.cc
@@ -0,0 +1,227 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <fstream>
+
+#include "utils.h"
+#include "global.h"
+#include "constraints.h"
+
+unsigned char *RNA; 
+int *structure; 
+unsigned int chPairKey;
+
+int g_nthreads;
+int g_dangles;
+int g_unamode;
+int g_mismatch;
+int g_verbose;
+int g_prefilter_mode;
+int g_prefilter1;
+int g_prefilter2;
+
+void init_global_params(int len) {
+	RNA = (unsigned char *) malloc((len+1)* sizeof(unsigned char));
+	if (RNA == NULL) {
+		perror("Cannot allocate variable 'RNA'");
+		exit(-1);
+	}
+	structure = (int *) malloc((len+1) * sizeof(int));
+	if (structure == NULL) {
+		perror("Cannot allocate variable 'structure'");
+		exit(-1);
+	}
+
+	init_checkPair();
+}
+
+void free_global_params() {
+	free(structure);
+	free(RNA);
+}
+
+void print_sequence(int len) {
+	int i;
+	for (i = 1; i <= len; i++) {
+		if (RNA[i] == BASE_A)
+			printf("A");
+		else if (RNA[i] == BASE_C)
+			printf("C");
+		else if (RNA[i] == BASE_G)
+			printf("G");
+		else if (RNA[i] == BASE_U)
+			printf("U");
+		else
+			printf("N");
+	}
+	printf("\n");
+}
+
+void print_structure(int len) {
+	int i = 1;
+	for (i = 1; i <= len; i++) 
+	{
+		if (structure[i] > 0 && structure[i] > i)
+			printf("(");
+		else if (structure[i] > 0 && structure[i] < i)
+			printf(")");
+		else
+			printf(".");
+	}
+	printf("\n");
+}
+
+int read_sequence_file(const char* filename, std::string& seq) {
+	seq = "";
+
+	ifstream fs;
+	fs.open(filename, ios::in);
+	if (!fs.good()) return FAILURE;
+
+	string line;
+	while(fs.good()) {
+		getline(fs, line);
+		// exclude lines starting with FASTA comment characters
+		if(line[0] != ';' && line[0] != '>' && line.length() > 0)
+			seq += line;
+	}
+
+	fs.close();
+
+    size_t loc;
+    while((loc = seq.find(" ")) != string::npos)
+        seq.erase(loc, 1);
+
+	return SUCCESS;
+}
+
+bool encodeSequence(string seq) {
+	unsigned int unspecifiedBaseCount=0;
+	unsigned int unspecifiedBases[seq.length()];
+
+	for(unsigned int i=1; i<=seq.length(); i++) {
+		RNA[i] = encode(seq[i-1]);
+
+		// die on non-IUPAC codes
+		if (RNA[i]=='X') {
+			fprintf(stderr, "ERROR: Non-IUPAC nucleotide code at position: %d (%c)\n", i, seq[i-1]);
+			fprintf(stderr, "See http://www.bioinformatics.org/sms/iupac.html for valid codes.\n");
+			return false;
+		}
+
+		// add non-canonical IUPAC codes to the warning list
+		if(!isWatsonCrickBase(seq[i-1]))
+			unspecifiedBases[unspecifiedBaseCount++]=i;
+	}
+
+	// just print a warning for non-canonical IUPAC codes
+	if(unspecifiedBaseCount > 0) {
+		printf("\nIncompletely-specified IUPAC codes have been detected at position%s: ", unspecifiedBaseCount == 1 ? "" : "s");
+
+		// put [0] first for nice comma separation
+		printf("%d (%c)", unspecifiedBases[0], seq.at(unspecifiedBases[0]-1));
+		for(unsigned int i=1; i<unspecifiedBaseCount; i++)
+			printf(", %d (%c)", unspecifiedBases[i], seq[unspecifiedBases[i]-1]);
+
+		printf("\nPlease replace with fully-specified IUPAC codes (A,C,G,U,T) and retry.\n");
+		return false;
+	}
+
+	return true;
+}
+
+
+void print_header() {
+	printf("GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n");
+	printf("(c) 2007-2011  D.A. Bader, C.E. Heitsch, S.C. Harvey\n");
+	printf("Georgia Institute of Technology\n\n");
+}
+
+
+void save_ct_file(string outputFile, string seq, int energy) {
+
+	ofstream outfile;
+	outfile.open(outputFile.c_str());
+
+	outfile << seq.length() << "\t  dG = " << energy/100.0 << endl;
+	//outfile << seq.length() << "\tdG = " << energy/100.0 << "\t" << seqfile << endl;
+
+	unsigned int i = 1;
+	for(i=1; i <= seq.length(); i++)
+		outfile << i << "\t" << seq[i-1] << "\t" << i-1 << "\t" << (i+1)%(seq.length()+1) << "\t" << structure[i] << "\t" << i << endl;
+
+	outfile.close();
+}
+
+void init_checkPair() {
+	int i, j;
+	chPairKey = 0;
+	for (i = 0; i < 4; i++)
+		for (j = 0; j < 4; j++)
+			chPairKey += checkPair(i, j) << ((i << 2) + j);
+}
+
+int update_checkPair(int i, int j) {
+	int r = 0;
+	if (!((i >= 0 && i <=3 )&&(j >=0 && j <=3)))
+		return r;
+	if (!(chPairKey & (1 << ((i << 2) + j)))) {
+		chPairKey += 1 << ((i << 2) + j);	
+		r = 1;
+	}
+	return r;
+}
+
+int canPair(int a, int b) {
+	return (chPairKey & (1 << (((a)<<2) + (b))));
+}
+
+/*
+void help() {
+    printf("Usage: gtfold [OPTION]... FILE\n\n");
+
+    printf("   FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n");
+
+    printf("OPTIONS\n");
+    printf("   -c, --constraints FILE\n");
+    printf("                        Load constraints from FILE.  See Constraint syntax below.\n");
+    printf("   -d, --dangle INT     Restricts treatment of dangling energies (INT=0,2),\n"); 
+    printf("                        see below for details.\n");
+    printf("   -h, --help           Output help (this message) and exit.\n");
+    printf("   -l, --limitCD INT    Set a maximum base pair contact distance to INT. If no\n");
+    printf("                        limit is given, base pairs can be over any distance.\n");
+    printf("   -m  --mismatch       Enable terminal mismatch calculations\n");
+//    printf("   -n, --noisolate      Prevent isolated base pairs from forming.\n");
+    printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
+    printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
+    printf("   -t, --threads INT    Limit number of threads used to INT.\n");
+    printf("   -v, --verbose        Run in verbose mode (includes loop-by-loop energy decomposition\n");
+    printf("                        and confirmation of constraints satisfied).\n");
+    printf("   -w, --workdir DIR    Path of directory where output files will be written.\n");
+    printf("   --prefilter INT      Prohibits any basepair which does not have appropriate\n");
+    printf("                        neighboring nucleotides such that it could be part of\n");
+    printf("                        a helix of length INT.\n");
+    printf("   --rnafold            Run as RNAfold default mode (ViennaPackage version 1.8.5).\n");
+    printf("   --unafold            Run as UNAfold default mode (version 3.8), subject to traceback\n");
+    printf("                        implementation.\n");
+
+    printf("\nBETA OPTIONS\n");
+    printf("   --bpp                Calculate base pair probabilities.\n");
+    printf("   --partition          Calculate the partition function.\n");
+    printf("   --pf_count          Calculate the structure count using partition function and zero energy value.\n");
+    printf("   --subopt NUM         Calculate suboptimal structures within NUM kcal/mol\n");
+    printf("                        of the MFE. (Uses -d 2 treatment of dangling energies.)\n");
+    printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE.\n");      
+
+    printf("\nConstraint syntax:\n");
+    printf("\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n");
+    printf("\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n");
+    printf("\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
+
+    printf("\nDangle:\n");
+    printf("\tINT=0 ignores dangling energies (mostly for debugging).\n");
+    printf("\tINT=2 dangling energies are added for nucleotides on either\n");
+    printf("\tside of each branch in multi-loops and external loops.\n");
+    printf("\tAll other values for INT are ignored.\n");
+    exit(-1);
+}
+*/
diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc
index 13942f4..1689af9 100644
--- a/gtfold-mfe/src/main.cc
+++ b/gtfold-mfe/src/main.cc
@@ -24,258 +24,43 @@
 #include <fstream>
 #include <string>
 #include <math.h>
-#include <time.h>
-#include <sys/time.h>
 #include <sstream>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
 #include "main.h"
+#include "mfe_main.h"
+#include "boltzmann_main.h"
+#include "subopt_main.h"
 #include "utils.h"
-#include "loader.h"
-#include "options.h"
 #include "global.h"
-#include "energy.h"
-#include "algorithms.h"
-#include "algorithms-partition.h"
-#include "partition-func.h"
-#include "constraints.h"
-#include "traceback.h"
-#include "subopt_traceback.h"
-#include "shapereader.h"
-#include "stochastic-sampling.h"
 
-#define DEBUG 1
-
-using namespace std;
-
-double get_seconds() {
-	struct timeval tv;
-	gettimeofday(&tv, NULL);
-	return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0;
-}
-
-void init_fold(string seq) {
-	int len = seq.length();
-
-	init_global_params(len);
-
-	if (!encodeSequence(seq)) {
-		free_fold(seq.length());
-		exit(0);
-	}
-	
-	create_tables(len);
-	
-	if (CONS_ENABLED) {
-		init_constraints(constraintsFile.c_str(), len);
-	}
-
-	if (SHAPE_ENABLED) {
-		readSHAPEarray(shapeFile.c_str(),len);
-	}
-
-	if (UNAMODE) {
-									if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n");
-									if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n");
-									if (dangles == 0 || dangles == 2) 
-																	printf("Ignoring -d option, using --unafold\n");
-									if (b_prefilter == 1) 
-																	printf("Ignoring --prefilter option, using --unafold\n");
-									T_MISMATCH = false;
-									PARAM_DIR = false;
-									dangles = -1;
-									b_prefilter = false;
-	}
-	
-	if (RNAMODE) {
-									if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n");
-									if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n");
-									if (dangles == 0 || dangles == 2) 
-																	printf("Ignoring -d option, using --rnafold\n");
-									if (b_prefilter == 1) 
-																	printf("Ignoring --prefilter option, using --rnafold\n");
-									T_MISMATCH = false;
-									PARAM_DIR = false;
-									dangles = -1;
-									b_prefilter = false;
-	}
-
-	if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) {
-									if (T_MISMATCH) printf("Ignoring -m option, using -d option\n");
-									T_MISMATCH = false;
-	} else {
-									if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n");	
-									dangles = -1;
-	}
-
-	g_nthreads = nThreads;
-	g_unamode  = UNAMODE;
-	g_mismatch = T_MISMATCH;
-	g_verbose  = VERBOSE;
-	g_prefilter_mode  = b_prefilter;
-	g_prefilter1  = prefilter1;
-	g_prefilter2  = prefilter2;
-	g_dangles = dangles;
-
-	#ifdef DEBUG
-	printf("g_nthreads = %d\n", g_nthreads);
-	printf("g_unamode = %d\n", g_unamode);
-	printf("g_mismatch = %d\n", g_mismatch);
-	printf("g_prefilter_mode = %d\n", g_prefilter_mode);
-	printf("g_dangles = %d\n", g_dangles);
-
-#endif
-
-}
-
-void free_fold(int len) {
-	if (CONS_ENABLED) 
-		free_constraints(len);
-	if (SHAPE_ENABLED){
-		free_shapeArray(len);
-	}
-
-	free_tables(len);
-	free_global_params();
-}
-
-/**
- * Read the sequence out of the given filename and store it in seq
- *
- * @param filename A c string with the file to open
- * @param seq A C++ string object (passed by reference) to save to
- * @return SUCCESS or FAILURE
- */
-int read_sequence_file(const char* filename, std::string& seq) {
-	seq = "";
-
-	ifstream fs;
-	fs.open(filename, ios::in);
-	if (!fs.good()) return FAILURE;
-
-	string line;
-	while(fs.good()) {
-		getline(fs, line);
-		// exclude lines starting with FASTA comment characters
-		if(line[0] != ';' && line[0] != '>' && line.length() > 0)
-			seq += line;
-	}
-
-	fs.close();
-
-    size_t loc;
-    while((loc = seq.find(" ")) != string::npos)
-        seq.erase(loc, 1);
-
-	return SUCCESS;
-}
-
-/**
- * Encode the given string of letters into an RNA sequence.
- *
- * This handles IUPAC codes and places the results into the array RNA.
- *
- * @param seq The string to encode
- * @return A boolean representing success or failure of the encoding.  Failure
- *         can occur when seeing unknown IUPAC codes.
- */
-bool encodeSequence(string seq) {
-	unsigned int unspecifiedBaseCount=0;
-	unsigned int unspecifiedBases[seq.length()];
-
-	for(unsigned int i=1; i<=seq.length(); i++) {
-		RNA[i] = encode(seq[i-1]);
-
-		// die on non-IUPAC codes
-		if (RNA[i]=='X') {
-			fprintf(stderr, "ERROR: Non-IUPAC nucleotide code at position: %d (%c)\n", i, seq[i-1]);
-			fprintf(stderr, "See http://www.bioinformatics.org/sms/iupac.html for valid codes.\n");
-			return false;
-		}
-
-		// add non-canonical IUPAC codes to the warning list
-		if(!isWatsonCrickBase(seq[i-1]))
-			unspecifiedBases[unspecifiedBaseCount++]=i;
-	}
-
-	// just print a warning for non-canonical IUPAC codes
-	if(unspecifiedBaseCount > 0) {
-		printf("\nIncompletely-specified IUPAC codes have been detected at position%s: ", unspecifiedBaseCount == 1 ? "" : "s");
-
-		// put [0] first for nice comma separation
-		printf("%d (%c)", unspecifiedBases[0], seq.at(unspecifiedBases[0]-1));
-		for(unsigned int i=1; i<unspecifiedBaseCount; i++)
-			printf(", %d (%c)", unspecifiedBases[i], seq[unspecifiedBases[i]-1]);
-
-		printf("\nPlease replace with fully-specified IUPAC codes (A,C,G,U,T) and retry.\n");
-		return false;
-	}
-
-	return true;
-}
-
-void print_header() {
-	printf("GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n");
-	printf("(c) 2007-2011  D.A. Bader, C.E. Heitsch, S.C. Harvey\n");
-	printf("Georgia Institute of Technology\n\n");
-}
-
-void save_subopt_file(string outputFile, ss_map_t& ss_data, 
-		const string& seq, int energy)
-{
-	ofstream outfile;
-	outfile.open(outputFile.c_str());
-	char buff[4096];
-
-	sprintf(buff,"%s %6.2f", seq.c_str(), energy/100.0);
-	outfile << buff << std::endl;
-	for (ss_map_t::iterator it = ss_data.begin(); it!= ss_data.end(); ++it) 
-	{
-		sprintf(buff,"%s %6.2f", (it->first).c_str(), it->second/100.0);
-		//outfile << it->first << '\t' << it->second/100.0 << std::endl;
-		outfile << buff << std::endl;
-	}
-
-	outfile.close();
-}
-
-/**
- * Save the output to a ct file
- *
- * @param outputFile The file to save to
- * @param energy The MFE energy (multiplied by 100)
- */
-void save_ct_file(string outputFile, string seq, int energy) {
-
-	ofstream outfile;
-	outfile.open(outputFile.c_str());
-
-	outfile << seq.length() << "\t  dG = " << energy/100.0 << endl;
-	//outfile << seq.length() << "\tdG = " << energy/100.0 << "\t" << seqfile << endl;
-
-	unsigned int i = 1;
-	for(i=1; i <= seq.length(); i++)
-		outfile << i << "\t" << seq[i-1] << "\t" << i-1 << "\t" << (i+1)%(seq.length()+1) << "\t" << structure[i] << "\t" << i << endl;
-
-	outfile.close();
-}
 
 int main(int argc, char** argv) {
-	std::string seq;
-	int energy;
-	double t1;
-	
-	print_header();
+  print_header();
+  
+  std::string cmd = argv[0];
+
+  if (cmd.find("gtmfe") != std::string::npos) {
+    mfe_main(argc, argv);
+  } else if (cmd.find("gtsubopt") != std::string::npos){
+    subopt_main(argc,argv);
+  } else if (cmd.find("gtboltzmann") != std::string::npos) {
+    boltzmann_main(argc,argv);
+  }
 
-	parse_options(argc, argv);
+	return EXIT_SUCCESS;
+}
 
+	/*
 	if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) {
 		printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
 		exit(-1);
-	}
-	init_fold(seq);
+	}*/
+
+  /*
+	//init_fold(seq);
 	
 	// Read in thermodynamic parameters. Always use Turner99 data (for now)
 	if (SUBOPT_ENABLED) 
@@ -292,7 +77,7 @@ int main(int argc, char** argv) {
     if(PF_COUNT_MODE) pf_count_mode=1;
     calculate_partition(seq.length(),pf_count_mode);
     free_partition();
-    free_fold(seq.length());
+    //free_fold(seq.length());
     exit(0);
   }
   
@@ -306,7 +91,7 @@ int main(int argc, char** argv) {
     batch_sample(num_rnd, seq.length(), U); 
 
     free_partition();
-	  free_fold(seq.length());
+	  //free_fold(seq.length());
 	  exit(0);
   }
 
@@ -335,7 +120,7 @@ int main(int argc, char** argv) {
 		
 		printf("Subopt structures saved in %s\n", suboptFile.c_str());
 		save_subopt_file(suboptFile, subopt_data, seq, energy);	
-		free_fold(seq.length());
+		//free_fold(seq.length());
 		exit(0);
 	}
 	
@@ -368,7 +153,8 @@ int main(int argc, char** argv) {
 			fprintf(stderr, "Constraint file: %s\n", constraintsFile.c_str());
 		}
 	}
-
+  */
+/*
 	if(BPP_ENABLED){
 		printf("\n");
 		printf("Calculating partition function\n");
@@ -389,14 +175,14 @@ int main(int argc, char** argv) {
 		freeTwoD(QB, seq.length() + 1, seq.length() + 1);
 		freeTwoD(P, seq.length() + 1, seq.length() + 1);
 	}
-
+*/
 	// release the malloc'd arrays
-	free_fold(seq.length());
+	//free_fold(seq.length());
 /*
 	dangle_struct partition;
 	partition = malloc_partition_arrays_d(seq.length());
 	fill_partition_arrays_d(partition);
 	printf("Done with the partition functioni.\n");
 */
-	return EXIT_SUCCESS;
-}
+	//return EXIT_SUCCESS;
+//}
diff --git a/gtfold-mfe/src/mfe_main.cc b/gtfold-mfe/src/mfe_main.cc
new file mode 100644
index 0000000..0525ea2
--- /dev/null
+++ b/gtfold-mfe/src/mfe_main.cc
@@ -0,0 +1,448 @@
+/*
+ GTfold: compute minimum free energy of RNA secondary structure
+ Copyright (C) 2007-2011  David A. Bader, Christine E. Heitsch, 
+ and Steve C. Harvey
+ http://www.cc.gatech.edu/~bader
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <string>
+#include <math.h>
+#include <sstream>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <cassert>
+
+#include "main.h"
+#include "mfe_main.h"
+#include "utils.h"
+#include "loader.h"
+//#include "options.h"
+#include "global.h"
+#include "energy.h"
+#include "algorithms.h"
+#include "constraints.h"
+#include "traceback.h"
+#include "shapereader.h"
+
+using namespace std;
+
+static bool PARAM_DIR = false;
+//static bool LIMIT_DISTANCE;
+static bool CONS_ENABLED = false;
+static bool VERBOSE = false;
+static bool SHAPE_ENABLED = false;
+static bool T_MISMATCH = false;
+static bool UNAMODE = false;
+static bool RNAMODE = false;
+static bool b_prefilter = false;
+
+static string seqfile = "";
+static string constraintsFile = "";
+static string outputPrefix = "";
+static string outputFile = "";
+static string outputDir = "";
+static string shapeFile = "";
+static string paramDir; // default value
+
+static int dangles=-1;
+static int prefilter1=2;
+static int prefilter2=2;
+
+static int nThreads = -1;
+static int contactDistance = -1;
+
+static void help();
+void printRunConfiguration(string seq);
+void parse_mfe_options(int argc, char** argv);
+
+void init_fold(const char* seq) {
+  assert(seq != NULL);
+  int len = strlen(seq);
+
+  init_global_params(len);
+
+  if (!encodeSequence(seq)) {
+    free_fold(len);
+    exit(0);
+  }
+
+  create_tables(len);
+
+  if (CONS_ENABLED) {
+    init_constraints(constraintsFile.c_str(), len);
+  }
+
+  if (SHAPE_ENABLED) {
+    readSHAPEarray(shapeFile.c_str(),len);
+  }
+
+  if (UNAMODE) {
+    if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n");
+    if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n");
+    if (dangles == 0 || dangles == 2) 
+      printf("Ignoring -d option, using --unafold\n");
+    if (b_prefilter == 1) 
+      printf("Ignoring --prefilter option, using --unafold\n");
+    T_MISMATCH = false;
+    PARAM_DIR = false;
+    dangles = -1;
+    b_prefilter = false;
+  }
+
+  if (RNAMODE) {
+    if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n");
+    if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n");
+    if (dangles == 0 || dangles == 2) 
+      printf("Ignoring -d option, using --rnafold\n");
+    if (b_prefilter == 1) 
+      printf("Ignoring --prefilter option, using --rnafold\n");
+    T_MISMATCH = false;
+    PARAM_DIR = false;
+    dangles = -1;
+    b_prefilter = false;
+  }
+
+  if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) {
+    if (T_MISMATCH) printf("Ignoring -m option, using -d option\n");
+    T_MISMATCH = false;
+  } else {
+    if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n");	
+    dangles = -1;
+  }
+
+  g_nthreads = nThreads;
+  g_unamode  = UNAMODE;
+  g_mismatch = T_MISMATCH;
+  g_verbose  = VERBOSE;
+  g_prefilter_mode  = b_prefilter;
+  g_prefilter1  = prefilter1;
+  g_prefilter2  = prefilter2;
+  g_dangles = dangles;
+
+#ifdef DEBUG
+  printf("g_nthreads = %d\n", g_nthreads);
+  printf("g_unamode = %d\n", g_unamode);
+  printf("g_mismatch = %d\n", g_mismatch);
+  printf("g_prefilter_mode = %d\n", g_prefilter_mode);
+  printf("g_dangles = %d\n", g_dangles);
+
+#endif
+
+}
+
+void free_fold(int len) {
+	if (CONS_ENABLED) 
+		free_constraints(len);
+	if (SHAPE_ENABLED){
+		free_shapeArray(len);
+	}
+
+	free_tables(len);
+	free_global_params();
+}
+
+
+int mfe_main(int argc, char** argv) {
+	std::string seq;
+	int energy;
+	
+	parse_mfe_options(argc, argv);
+
+	if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) {
+		printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
+		exit(-1);
+	}
+
+	init_fold(seq.c_str());
+	
+	// Read in thermodynamic parameters. Always use Turner99 data (for now)
+  readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH);
+	printRunConfiguration(seq);
+
+	printf("\nComputing minimum free energy structure...\n");
+	fflush(stdout);
+
+	double t1 = get_seconds();
+	energy = calculate(seq.length()) ; 
+	t1 = get_seconds() - t1;
+	
+	printf("Done.\n\n");
+	printf("Results:\n");
+	if (energy >= MAXENG)	
+		printf("- Minimum Free Energy: %12.4f kcal/mol\n", 0.00);
+	else
+		printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00);
+	printf("- MFE runtime: %9.6f seconds\n", t1);
+
+	t1 = get_seconds();
+	trace(seq.length());
+	t1 = get_seconds() - t1;
+	
+	printf("\n");
+	print_sequence(seq.length());
+	print_structure(seq.length());
+
+	if (CONS_ENABLED)
+		print_constraints(seq.length());
+
+	if (SHAPE_ENABLED && VERBOSE)
+		print_shapeArray(seq.length());
+
+	save_ct_file(outputFile, seq, energy);
+	printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str());
+
+	if(CONS_ENABLED && VERBOSE){
+		printf("Verifying that structure fulfills constraint criteria... ");
+		if(verify_structure()){
+			printf("OK\n");
+		}
+		else{
+			printf("ERROR: NOT OK!!\n");
+			fprintf(stderr, "ERROR: Structure does not fulfill constraint criteria.\n");
+			fprintf(stderr, "Structure file: %s\n", outputFile.c_str());
+			fprintf(stderr, "Constraint file: %s\n", constraintsFile.c_str());
+		}
+	}
+
+	free_fold(seq.length());
+	
+  return EXIT_SUCCESS;
+}
+
+
+void parse_mfe_options(int argc, char** argv) {
+  int i;
+
+  for(i=1; i<argc; i++) {
+    if(argv[i][0] == '-') {
+      if(strcmp(argv[i], "--help") == 0 || strcmp(argv[i], "-h") == 0) {
+        help();
+      } else if(strcmp(argv[i], "--constraints") == 0 || strcmp(argv[i], "-c") == 0) {
+        if(i < argc) {
+          constraintsFile = argv[++i];
+          CONS_ENABLED = true;
+        }
+        else
+          help();
+      } else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) {
+        if(i < argc){
+          contactDistance = atoi(argv[++i]);
+          stringstream ss;
+          ss << contactDistance;
+          if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i])) {
+            //LIMIT_DISTANCE = true;
+            enable_limit_distance(true);  
+            set_contact_distance(contactDistance);
+          }
+          else
+            help();
+        }
+        else
+          help();
+      }else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) {
+        if(i < argc)
+          outputPrefix = argv[++i];
+        else
+          help();
+      } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) {
+        if(i < argc)
+          outputDir = argv[++i];
+        else
+          help();
+      } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) {
+        if(i < argc) {
+          paramDir = argv[++i];
+          PARAM_DIR = true;
+        }
+        else
+          help();
+      } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) {
+        std::string cmd = argv[i];
+        if(i < argc) {
+          dangles = atoi(argv[++i]);
+          if (!(dangles == 0 || dangles == 2)) {
+            dangles = -1;
+            printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str());
+          } 
+        } else
+          help();
+      } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) {
+        T_MISMATCH = true;
+      } else if (strcmp(argv[i], "--unafold") == 0) {
+        UNAMODE = true;
+      } else if (strcmp(argv[i], "--rnafold") == 0) {
+        RNAMODE = true;
+      } else if (strcmp(argv[i], "--prefilter") == 0) {
+        if(i < argc) {
+          prefilter1 = atoi(argv[++i]);
+          if (prefilter1 <= 0 ) {
+            printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n");
+            help();
+          }
+          b_prefilter = true;
+          prefilter2 = prefilter1;
+        } else 
+          help();
+      }
+      else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) {
+        if(i < argc)
+          nThreads = atoi(argv[++i]);
+        else
+          help();	
+      } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) {
+        VERBOSE = true;
+      }
+      else if (strcmp(argv[i], "--useSHAPE") == 0){
+        if( i < argc){
+          shapeFile = argv[++i];
+          SHAPE_ENABLED = true;
+        }
+        else
+          help();
+      }				
+    } else {
+      seqfile = argv[i];
+    }
+  }
+
+  // Must have an input file specified
+  if(seqfile.empty()) {
+    help();
+    printf("Missing input file.\n");
+  }
+
+  // If no output file specified, create one
+  if(outputPrefix.empty()) {
+    // base it off the input file
+    outputPrefix += seqfile;
+
+    size_t pos;
+    // extract file name from the path
+    if ((pos=outputPrefix.find_last_of('/')) > 0) {
+      outputPrefix = outputPrefix.substr(pos+1);
+    }
+
+    // and if an extension exists, remove it ...
+    if(outputPrefix.find(".") != string::npos)
+      outputPrefix.erase(outputPrefix.rfind("."));
+  }
+
+  // If output dir specified
+  if (!outputDir.empty()) {
+    outputFile += outputDir;
+    outputFile += "/";
+  }
+  // ... and append the .ct
+  outputFile += outputPrefix;
+  outputFile += ".ct";
+
+}
+
+
+void printRunConfiguration(string seq) {
+	bool standardRun = true;
+
+	printf("Run Configuration:\n");
+	if (RNAMODE == true) {
+		printf("+ running in rnafold mode\n");
+		standardRun = false;
+	} 
+	if (UNAMODE == true) {
+		printf("+ running in unafold mode\n");
+		standardRun = false;
+	}
+	if (dangles == 0 || dangles == 2) {
+		printf("+ running in dangle %d mode\n", dangles);
+		standardRun = false;
+	} 
+	if (T_MISMATCH == true) {
+		printf("+ enabled terminal mismatch calculations\n");
+		standardRun = false;
+	}
+	if (b_prefilter == true) {
+		printf("+ running with prefilter value = %d\n",prefilter1);
+		standardRun = false;
+	}
+
+	if(!constraintsFile.empty()) {
+		printf("- using constraint file: %s\n", constraintsFile.c_str());
+		standardRun = false;
+	}
+
+	if(!shapeFile.empty()){
+		printf("- using SHAPE data file: %s\n", shapeFile.c_str());
+	}
+	if (contactDistance != -1) {
+		printf("- maximum contact distance: %d\n", contactDistance);
+		standardRun = false;
+	}
+
+	if(standardRun)
+		printf("- standard\n");
+
+	printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str());
+	printf("- input file: %s\n", seqfile.c_str());
+	printf("- sequence length: %d\n", (int)seq.length());
+	printf("- output file: %s\n", outputFile.c_str());
+}
+
+static void help() {
+    printf("Usage: gtmfe [OPTION]... FILE\n\n");
+
+    printf("   FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n");
+
+    printf("OPTIONS\n");
+    printf("   -c, --constraints FILE\n");
+    printf("                        Load constraints from FILE.  See Constraint syntax below.\n");
+    printf("   -d, --dangle INT     Restricts treatment of dangling energies (INT=0,2),\n"); 
+    printf("                        see below for details.\n");
+    printf("   -h, --help           Output help (this message) and exit.\n");
+    printf("   -l, --limitCD INT    Set a maximum base pair contact distance to INT. If no\n");
+    printf("                        limit is given, base pairs can be over any distance.\n");
+    printf("   -m  --mismatch       Enable terminal mismatch calculations\n");
+//    printf("   -n, --noisolate      Prevent isolated base pairs from forming.\n");
+    printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
+    printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
+    printf("   -t, --threads INT    Limit number of threads used to INT.\n");
+    printf("   -v, --verbose        Run in verbose mode (includes loop-by-loop energy decomposition\n");
+    printf("                        and confirmation of constraints satisfied).\n");
+    printf("   -w, --workdir DIR    Path of directory where output files will be written.\n");
+    printf("   --prefilter INT      Prohibits any basepair which does not have appropriate\n");
+    printf("                        neighboring nucleotides such that it could be part of\n");
+    printf("                        a helix of length INT.\n");
+    printf("   --rnafold            Run as RNAfold default mode (ViennaPackage version 1.8.5).\n");
+    printf("   --unafold            Run as UNAfold default mode (version 3.8), subject to traceback\n");
+    printf("                        implementation.\n");
+
+    printf("   -s, --useSHAPE FILE  Use SHAPE constraints from FILE.\n");      
+
+    printf("\nConstraint syntax:\n");
+    printf("\tF i j k  # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n");
+    printf("\tP i j k  # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n");
+    printf("\tP i 0 k  # make bases from i to i+k-1 single stranded bases.\n");
+
+    printf("\nDangle:\n");
+    printf("\tINT=0 ignores dangling energies (mostly for debugging).\n");
+    printf("\tINT=2 dangling energies are added for nucleotides on either\n");
+    printf("\tside of each branch in multi-loops and external loops.\n");
+    printf("\tAll other values for INT are ignored.\n");
+    exit(-1);
+}
+
diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc
index 8a9082f..30889de 100644
--- a/gtfold-mfe/src/options.cc
+++ b/gtfold-mfe/src/options.cc
@@ -44,6 +44,8 @@ int contactDistance = -1;
 /**
  * Print the help message and quit.
  */
+
+/*
 void help() {
     printf("Usage: gtfold [OPTION]... FILE\n\n");
 
@@ -92,10 +94,12 @@ void help() {
     printf("\tAll other values for INT are ignored.\n");
     exit(-1);
 }
+*/
 
 /**
  * Parse the options from argc and argv and save them into global state.
  */
+/*
 void parse_options(int argc, char** argv) {
   int i;
 
@@ -252,12 +256,13 @@ void parse_options(int argc, char** argv) {
   bppOutFile += outputPrefix;	
   bppOutFile += "_bpp.txt";	
 }
-
+*/
 /**
  * Prints the run configuration for this run.
  *
  * The lines that start with a '-' are normal options, the '+' are beta options.
  */
+/*
 void printRunConfiguration(string seq) {
 	bool standardRun = true;
 
@@ -320,3 +325,4 @@ void printRunConfiguration(string seq) {
 	printf("- sequence length: %d\n", (int)seq.length());
 	printf("- output file: %s\n", outputFile.c_str());
 }
+*/
diff --git a/gtfold-mfe/src/shapereader.cc b/gtfold-mfe/src/shapereader.cc
index fcbcbc5..006f8a1 100644
--- a/gtfold-mfe/src/shapereader.cc
+++ b/gtfold-mfe/src/shapereader.cc
@@ -14,6 +14,12 @@ using namespace std;
 double* SHAPEarray;
 int* SHAPEenergies;
 
+static bool SHAPE_ENABLED = false;
+
+void enable_shape(bool b) {
+  SHAPE_ENABLED = b;
+}
+
 void free_shapeArray(int len){
 	free(SHAPEarray);
 }
diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc
index 53b2f3b..b831ff8 100644
--- a/gtfold-mfe/src/stochastic-sampling.cc
+++ b/gtfold-mfe/src/stochastic-sampling.cc
@@ -682,7 +682,7 @@ void batch_sample(int num_rnd, int length, double U)
 	  
     if (num_rnd > 0 ) {
       printf("\nSampling structures...\n");
-      int count,nsamples =0;
+      int count; //nsamples =0;
       for (count = 1; count <= num_rnd; ++count) 
       {
         memset(structure, 0, (length+1)*sizeof(int));
@@ -713,7 +713,7 @@ void batch_sample(int num_rnd, int length, double U)
         
         // std::cout << ensemble.substr(1) << ' ' << energy << std::endl;
       }
-      std::cout << nsamples << std::endl;
+      //std::cout << nsamples << std::endl;
       int pcount = 0;
       int maxCount = 0; std::string bestStruct;
       double bestE = INFINITY;
diff --git a/gtfold-mfe/src/subopt_main.cc b/gtfold-mfe/src/subopt_main.cc
new file mode 100644
index 0000000..2aff56b
--- /dev/null
+++ b/gtfold-mfe/src/subopt_main.cc
@@ -0,0 +1,158 @@
+#include <string>
+#include <cstring>
+#include <cstdio>
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <map>
+
+#include "loader.h"
+#include "algorithms.h"
+#include "subopt_traceback.h"
+#include "global.h"
+#include "utils.h"
+#include "mfe_main.h"
+
+
+using namespace std;
+
+static string seqfile = "";
+static string suboptFile = "";
+static double suboptDelta = 0;
+static string outputPrefix = "";
+static string outputFile = "";
+static string outputDir = "";
+static string paramDir = "";
+static bool PARAM_DIR = false;
+static void help();
+
+void save_subopt_file(string outputFile, ss_map_t& ss_data, 
+		const string& seq, int energy)
+{
+	ofstream outfile;
+	outfile.open(outputFile.c_str());
+	char buff[4096];
+
+	sprintf(buff,"%s %6.2f", seq.c_str(), energy/100.0);
+	outfile << buff << std::endl;
+	for (ss_map_t::iterator it = ss_data.begin(); it!= ss_data.end(); ++it) 
+	{
+		sprintf(buff,"%s %6.2f", (it->first).c_str(), it->second/100.0);
+		//outfile << it->first << '\t' << it->second/100.0 << std::endl;
+		outfile << buff << std::endl;
+	}
+
+	outfile.close();
+}
+
+void parse_options(int argc, char** argv) {
+  int i;
+
+  for(i=1; i<argc; i++) {
+    if(argv[i][0] == '-') {
+      if(strcmp(argv[i], "--help") == 0 || 
+          strcmp(argv[i], "-h") == 0) {
+        help(); 
+      } else if (strcmp(argv[i], "--paramdir") == 0 || 
+          strcmp(argv[i], "-p") == 0) {
+        if(i < argc) {
+          paramDir = argv[++i];
+          PARAM_DIR = true;
+        }
+        else {
+          help();
+        }
+      }
+      else if(strcmp(argv[i], "--subopt") == 0) {
+        g_dangles = 2;
+        if(i < argc)
+          suboptDelta = atof(argv[++i]);
+        else
+          help();
+      } 
+    } else {
+      seqfile = argv[i];
+    }
+  }
+
+// If no output file specified, create one
+  if(outputPrefix.empty()) {
+    // base it off the input file
+    outputPrefix += seqfile;
+
+    size_t pos;
+    // extract file name from the path
+    if ((pos=outputPrefix.find_last_of('/')) > 0) {
+      outputPrefix = outputPrefix.substr(pos+1);
+    }
+
+    // and if an extension exists, remove it ...
+    if(outputPrefix.find(".") != string::npos)
+      outputPrefix.erase(outputPrefix.rfind("."));
+  }
+
+  // If output dir specified
+  if (!outputDir.empty()) {
+    outputFile += outputDir;
+    outputFile += "/";
+    suboptFile += outputDir;
+    suboptFile += "/";
+  }
+  // ... and append the .ct
+  outputFile += outputPrefix;
+  outputFile += ".ct";
+  suboptFile += outputPrefix;	
+  suboptFile += "_ss.txt";	
+
+
+}
+
+static void help() {
+    printf("Usage: gtsubopt [OPTION]... FILE\n\n");
+
+    printf("   FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n");
+
+    printf("OPTIONS\n");
+    printf("   --subopt NUM         Calculate suboptimal structures within NUM kcal/mol\n");
+    printf("                        of the MFE. (Uses -d 2 treatment of dangling energies.)\n");
+    printf("\n"); 
+    printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
+    printf("   -p  --paramdir DIR   Path to directory from which parameters are to be read\n");
+    printf("   -h, --help           Output help (this message) and exit.\n");
+    printf("   -w, --workdir DIR    Path of directory where output files will be written.\n");
+    exit(-1);
+}
+
+void subopt_main(int argc, char** argv) {
+
+  string seq = "";
+  parse_options(argc, argv);
+
+  if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) {
+    printf("Failed to open sequence file: %s.\n\n", seqfile.c_str());
+    exit(-1);
+  }
+  init_fold(seq.c_str());
+  
+  readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, 0, 1, 0);
+
+	int energy = calculate(seq.length()) ; 
+  
+  double t1 = get_seconds();
+  ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta);
+  t1 = get_seconds() - t1;
+  
+  printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str());
+	printf("- input file: %s\n", seqfile.c_str());
+	printf("- sequence length: %d\n", (int)seq.length());
+  printf("\n");
+  printf("Subopt traceback running time: %9.6f seconds\n", t1);
+
+  printf("Subopt structures saved in %s\n", suboptFile.c_str());
+  save_subopt_file(suboptFile, subopt_data, seq, energy);	
+
+  printf("+ calculating suboptimal structures within %f kcal/mol of MFE\n", suboptDelta);
+  printf("+ suboptimal structures file: %s\n", suboptFile.c_str());
+
+	free_fold(seq.length());
+}
diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c
index 3e13199..6d461a8 100644
--- a/gtfold-mfe/src/traceback.c
+++ b/gtfold-mfe/src/traceback.c
@@ -47,9 +47,11 @@ void trace(int len) {
 	printf("\n");
 	
 	traceW(len);
-	printf("- sum of energy of Loops:   	  %12.2f kcal/mol\n", total_en/100.0);
-	printf("- sum of energy of External Loop: %12.2f kcal/mol\n", total_ex/100.0);
-	return;
+  if (g_verbose == 1) {
+    printf("- sum of energy of Loops:   	  %12.2f kcal/mol\n", total_en/100.0);
+    printf("- sum of energy of External Loop: %12.2f kcal/mol\n", total_ex/100.0);
+  }
+  return;
 }
 
 void traceW(int j) {
diff --git a/gtfold-mfe/src/utils.cc b/gtfold-mfe/src/utils.cc
index 8c6ffbe..8c218c9 100644
--- a/gtfold-mfe/src/utils.cc
+++ b/gtfold-mfe/src/utils.cc
@@ -1,6 +1,21 @@
 #include "utils.h"
-#include <string.h>
+#include <cstring>
 #include <string>
+#include <time.h>
+#include <sys/time.h>
+
+double get_seconds() {
+	struct timeval tv;
+	gettimeofday(&tv, NULL);
+	return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0;
+}
+
+int is_valid_base(char c) {	
+	return ( (c-'A' == 0) || (c-'a' == 0) || 
+			 (c-'C' == 0) || (c-'c' == 0) ||
+			 (c-'G' == 0) || (c-'g' == 0) ||
+			 (c-'U' == 0) || (c-'u' == 0));
+}
 
 char baseToDigit(const char* base) {
 	if (!strcmp(base, "A")) {

From 70d4e4dfce452f6d2efc575bf68bc286e140f04e Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 15 Dec 2011 22:09:55 -0500
Subject: [PATCH 279/282] adding changes in global vars

---
 gtfold-mfe/include/global.h | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h
index c452b2a..23ec167 100644
--- a/gtfold-mfe/include/global.h
+++ b/gtfold-mfe/include/global.h
@@ -3,6 +3,11 @@
 
 #include "constants.h"
 
+#ifdef __cplusplus
+#include <string>
+using namespace std;
+#endif
+
 extern unsigned char *RNA; 
 extern int *structure; 
 extern int* constraints;
@@ -18,10 +23,10 @@ extern int g_prefilter2;
 
 extern unsigned int chPairKey;
 
-// The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). 
+// The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) 
+//  and (U,G). 
 #define checkPair(i, j) (((((i)-(j)) % 2) == 1 || (((i)-(j)) % 2)== -1) && (!( ((i)==BASE_A && (j)==BASE_C) || ((i)==BASE_C && (j)==BASE_A) )))
 
-
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -30,10 +35,17 @@ void init_global_params(int len);
 void free_global_params();
 void print_sequence(int len); 
 void print_structure(int len); 
+void print_header() ;
 #ifdef __cplusplus
 }
 #endif
 
+#ifdef __cplusplus
+int read_sequence_file(const char* filename, std::string& seq);
+bool encodeSequence(string seq);
+void save_ct_file(string outputFile, string seq, int energy) ;
+#endif
+
 void init_checkPair(); 
 int  update_checkPair(int i, int j);
 

From 6d5a9f9e6599f8c70bcb23ae8c8b77bfac186f3d Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 15 Dec 2011 22:22:31 -0500
Subject: [PATCH 280/282] removing file

---
 gtfold-mfe/src/global.c | 92 -----------------------------------------
 1 file changed, 92 deletions(-)
 delete mode 100644 gtfold-mfe/src/global.c

diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c
deleted file mode 100644
index 1c2d45b..0000000
--- a/gtfold-mfe/src/global.c
+++ /dev/null
@@ -1,92 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-
-#include "global.h"
-#include "constraints.h"
-
-unsigned char *RNA; 
-int *structure; 
-unsigned int chPairKey;
-
-int g_nthreads;
-int g_dangles;
-int g_unamode;
-int g_mismatch;
-int g_verbose;
-int g_prefilter_mode;
-int g_prefilter1;
-int g_prefilter2;
-
-void init_global_params(int len) {
-	RNA = (unsigned char *) malloc((len+1)* sizeof(unsigned char));
-	if (RNA == NULL) {
-		perror("Cannot allocate variable 'RNA'");
-		exit(-1);
-	}
-	structure = (int *) malloc((len+1) * sizeof(int));
-	if (structure == NULL) {
-		perror("Cannot allocate variable 'structure'");
-		exit(-1);
-	}
-
-	init_checkPair();
-}
-
-void free_global_params() {
-	free(structure);
-	free(RNA);
-}
-
-void print_sequence(int len) {
-	int i;
-	for (i = 1; i <= len; i++) {
-		if (RNA[i] == BASE_A)
-			printf("A");
-		else if (RNA[i] == BASE_C)
-			printf("C");
-		else if (RNA[i] == BASE_G)
-			printf("G");
-		else if (RNA[i] == BASE_U)
-			printf("U");
-		else
-			printf("N");
-	}
-	printf("\n");
-}
-
-void print_structure(int len) {
-	int i = 1;
-	for (i = 1; i <= len; i++) 
-	{
-		if (structure[i] > 0 && structure[i] > i)
-			printf("(");
-		else if (structure[i] > 0 && structure[i] < i)
-			printf(")");
-		else
-			printf(".");
-	}
-	printf("\n");
-}
-
-void init_checkPair() {
-	int i, j;
-	chPairKey = 0;
-	for (i = 0; i < 4; i++)
-		for (j = 0; j < 4; j++)
-			chPairKey += checkPair(i, j) << ((i << 2) + j);
-}
-
-int update_checkPair(int i, int j) {
-	int r = 0;
-	if (!((i >= 0 && i <=3 )&&(j >=0 && j <=3)))
-		return r;
-	if (!(chPairKey & (1 << ((i << 2) + j)))) {
-		chPairKey += 1 << ((i << 2) + j);	
-		r = 1;
-	}
-	return r;
-}
-
-inline int canPair(int a, int b) {
-	return (chPairKey & (1 << (((a)<<2) + (b))));
-}

From e492adcde5dc4a2a272b9ce4f62182c70bfbc473 Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Thu, 15 Dec 2011 23:13:46 -0500
Subject: [PATCH 281/282] + adding new options + script to add symlink

---
 gtfold-mfe/createsymlinks.sh     |  8 ++++++
 gtfold-mfe/src/boltzmann_main.cc | 48 +++++++++++++++++++++++++-------
 gtfold-mfe/src/createsymlinks.sh |  8 ++++++
 gtfold-mfe/src/subopt_main.cc    |  5 ++++
 4 files changed, 59 insertions(+), 10 deletions(-)
 create mode 100644 gtfold-mfe/createsymlinks.sh
 create mode 100644 gtfold-mfe/src/createsymlinks.sh

diff --git a/gtfold-mfe/createsymlinks.sh b/gtfold-mfe/createsymlinks.sh
new file mode 100644
index 0000000..99db1bd
--- /dev/null
+++ b/gtfold-mfe/createsymlinks.sh
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+BINDIR=/home/users/pgaurav/git-hub/gtfold_final/bin
+echo 'creating symlinks under' $BINDIR
+ln -sf gtfold $BINDIR/gtmfe
+ln -sf gtfold $BINDIR/gtsubopt
+ln -sf gtfold $BINDIR/gtboltzmann
+
diff --git a/gtfold-mfe/src/boltzmann_main.cc b/gtfold-mfe/src/boltzmann_main.cc
index f590dc6..b423c0e 100644
--- a/gtfold-mfe/src/boltzmann_main.cc
+++ b/gtfold-mfe/src/boltzmann_main.cc
@@ -21,6 +21,8 @@ static bool PF_COUNT_MODE = false;
 static bool BPP_ENABLED = false;
 static bool PARAM_DIR = false;
 static bool RND_SAMPLE = false;
+static bool CALC_PF_DO = false;
+static bool CALC_PF_DS = false;
 
 static string seqfile = "";
 static string outputPrefix = "";
@@ -37,9 +39,13 @@ static void help() {
 
     printf("OPTIONS\n");
  
-    printf("   --partition          Calculate the partition function.\n");
+    printf("   --partition          Calculate the partition function (default is using sfold reccurences).\n");
+    printf("   --partition -dS      Calculate the partition function using sfold reccurences.\n");
+    printf("   --partition -d0      Calculate the partition function using -d0 reccurences.\n");
+    printf("   --partition -d2      Calculate the partition function using -d2 reccurences (Under implementation).\n");
+
     printf("   --sample   INT       Sample number of structures equal to INT\n");
-    printf("   --pf_count           Calculate the structure count using partition function and zero energy value.\n");
+    printf("   --pfcount           Calculate the structure count using partition function and zero energy value.\n");
     printf("   --bpp                Calculate base pair probabilities.\n");
     printf("\n");
     printf("   -o, --output NAME    Write output files with prefix given in NAME\n");
@@ -80,7 +86,14 @@ static void parse_options(int argc, char** argv) {
       }
       else if (strcmp(argv[i],"--partition") == 0) {
         CALC_PART_FUNC = true;
-      } else if (strcmp(argv[i],"--pf_count") == 0) {
+      } else if (strcmp(argv[i],"-dS") == 0) {
+        CALC_PF_DS = true;  
+      } else if (strcmp(argv[i],"-d0") == 0) {
+        CALC_PF_DO = true;  
+      } else if (strcmp(argv[i],"-d2") == 0) {
+        help();
+      }
+      else if (strcmp(argv[i],"--pfcount") == 0) {
         CALC_PART_FUNC = true;
         PF_COUNT_MODE = true;
       }  else if (strcmp(argv[i],"--sample") == 0) {
@@ -147,11 +160,27 @@ int boltzmann_main(int argc, char** argv) {
 
   readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, 0, 0, 0);
 
-	calculate(seq.length()) ; 
-	trace(seq.length());
-  
-  if (CALC_PART_FUNC == true)
-  {
+  if (CALC_PART_FUNC == true && CALC_PF_DS == true) {
+    printf("\nComputing partition function in -dS mode ...\n");
+    calculate_partition(seq.length(),0);
+    free_partition();
+  } 
+  else if (CALC_PART_FUNC == true && CALC_PF_DO == true) {
+    printf("\nCalculating partition function in -d0 mode ...\n");
+    double ** Q,  **QM, **QB, **P;
+    Q = mallocTwoD(seq.length() + 1, seq.length() + 1);
+    QM = mallocTwoD(seq.length() + 1, seq.length() + 1);
+    QB = mallocTwoD(seq.length() + 1, seq.length() + 1);
+    P = mallocTwoD(seq.length() + 1, seq.length() + 1);
+
+
+    fill_partition_fn_arrays(seq.length(), Q, QB, QM);
+    freeTwoD(Q, seq.length() + 1, seq.length() + 1);
+    freeTwoD(QM, seq.length() + 1, seq.length() + 1);
+    freeTwoD(QB, seq.length() + 1, seq.length() + 1);
+    freeTwoD(P, seq.length() + 1, seq.length() + 1);
+  }
+  else if (CALC_PART_FUNC == true) {
     printf("\nComputing partition function...\n");
     int pf_count_mode = 0;
     if(PF_COUNT_MODE) pf_count_mode=1;
@@ -167,8 +196,7 @@ int boltzmann_main(int argc, char** argv) {
     batch_sample(num_rnd, seq.length(), U); 
 
     free_partition();
-  }
-  else if(BPP_ENABLED){
+  } else if(BPP_ENABLED) {
     printf("\n");
     printf("Calculating partition function\n");
     double ** Q,  **QM, **QB, **P;
diff --git a/gtfold-mfe/src/createsymlinks.sh b/gtfold-mfe/src/createsymlinks.sh
new file mode 100644
index 0000000..e0ac203
--- /dev/null
+++ b/gtfold-mfe/src/createsymlinks.sh
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+BINDIR='.'
+echo 'creating symlinks under' $BINDIR
+ln -sf gtfold $BINDIR/gtmfe
+ln -sf gtfold $BINDIR/gtsubopt
+ln -sf gtfold $BINDIR/gtboltzmann
+
diff --git a/gtfold-mfe/src/subopt_main.cc b/gtfold-mfe/src/subopt_main.cc
index 2aff56b..96b2ac5 100644
--- a/gtfold-mfe/src/subopt_main.cc
+++ b/gtfold-mfe/src/subopt_main.cc
@@ -75,6 +75,11 @@ void parse_options(int argc, char** argv) {
     }
   }
 
+  if(seqfile.empty()) {
+    printf("Missing input file.\n");
+    help();
+  }
+
 // If no output file specified, create one
   if(outputPrefix.empty()) {
     // base it off the input file

From 1957922ab4c69fab0907d85c6ad085f931b0687d Mon Sep 17 00:00:00 2001
From: Prashant Gaurav <pgaurav3@gatech.edu>
Date: Fri, 16 Dec 2011 11:14:48 -0500
Subject: [PATCH 282/282] added creation of symlinks

---
 gtfold-mfe/createsymlinks.sh | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/gtfold-mfe/createsymlinks.sh b/gtfold-mfe/createsymlinks.sh
index 99db1bd..1427a56 100644
--- a/gtfold-mfe/createsymlinks.sh
+++ b/gtfold-mfe/createsymlinks.sh
@@ -1,8 +1,14 @@
 #!/bin/sh
+if [ $# != 1 ]
+then
+echo "Usage: sh createsymlinks.sh <INSTALLDIR>"
+exit -1
+fi
 
-BINDIR=/home/users/pgaurav/git-hub/gtfold_final/bin
+BINDIR=$1 
 echo 'creating symlinks under' $BINDIR
-ln -sf gtfold $BINDIR/gtmfe
-ln -sf gtfold $BINDIR/gtsubopt
-ln -sf gtfold $BINDIR/gtboltzmann
+cd $BINDIR
+ln -sf gtfold gtmfe
+ln -sf gtfold gtsubopt
+ln -sf gtfold gtboltzmann