Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
269 changes: 269 additions & 0 deletions doc/cmaple/alignment_8h_source.html

Large diffs are not rendered by default.

94 changes: 94 additions & 0 deletions doc/cmaple/annotated.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,94 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=11"/>
<meta name="generator" content="Doxygen 1.9.8"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>CMAPLE: Class List</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr id="projectrow">
<td id="projectalign">
<div id="projectname">CMAPLE<span id="projectnumber">&#160;2.0.0</span>
</div>
<div id="projectbrief">C++ MAximum Parsimonious Likelihood Estimation</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.9.8 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
var searchBox = new SearchBox("searchBox", "search/",'.html');
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */
</script>
<div id="main-nav"></div>
</div><!-- top -->
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<div id="MSearchResults">
<div class="SRPage">
<div id="SRIndex">
<div id="SRResults"></div>
<div class="SRStatus" id="Loading">Loading...</div>
<div class="SRStatus" id="Searching">Searching...</div>
<div class="SRStatus" id="NoMatches">No Matches</div>
</div>
</div>
</div>
</div>

<div class="header">
<div class="headertitle"><div class="title">Class List</div></div>
</div><!--header-->
<div class="contents">
<div class="textblock">Here are the classes, structs, unions and interfaces with brief descriptions:</div><div class="directory">
<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span>]</div><table class="directory">
<tr id="row_0_" class="even"><td class="entry"><span style="width:0px;display:inline-block;">&#160;</span><span id="arr_0_" class="arrow" onclick="toggleFolder('0_')">&#9660;</span><span class="icona"><span class="icon">N</span></span><b>cmaple</b></td><td class="desc"></td></tr>
<tr id="row_0_0_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classcmaple_1_1_alignment.html" target="_self">Alignment</a></td><td class="desc"></td></tr>
<tr id="row_0_1_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_0_1_" class="arrow" onclick="toggleFolder('0_1_')">&#9660;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classcmaple_1_1_model.html" target="_self">Model</a></td><td class="desc"></td></tr>
<tr id="row_0_1_0_" class="odd"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structcmaple_1_1_model_1_1_model_params.html" target="_self">ModelParams</a></td><td class="desc"></td></tr>
<tr id="row_0_2_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classcmaple_1_1_model_base.html" target="_self">ModelBase</a></td><td class="desc"></td></tr>
<tr id="row_0_3_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classcmaple_1_1_params_builder.html" target="_self">ParamsBuilder</a></td><td class="desc"></td></tr>
<tr id="row_0_4_" class="even"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classcmaple_1_1_seq_region.html" target="_self">SeqRegion</a></td><td class="desc"></td></tr>
<tr id="row_0_5_" class="odd"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classcmaple_1_1_tree.html" target="_self">Tree</a></td><td class="desc"></td></tr>
</table>
</div><!-- directory -->
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by&#160;<a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.8
</small></address>
</body>
</html>
Binary file added doc/cmaple/bc_s.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added doc/cmaple/bc_sd.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
103 changes: 103 additions & 0 deletions doc/cmaple/classcmaple_1_1_alignment-members.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,103 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=11"/>
<meta name="generator" content="Doxygen 1.9.8"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>CMAPLE: Member List</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr id="projectrow">
<td id="projectalign">
<div id="projectname">CMAPLE<span id="projectnumber">&#160;2.0.0</span>
</div>
<div id="projectbrief">C++ MAximum Parsimonious Likelihood Estimation</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.9.8 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
var searchBox = new SearchBox("searchBox", "search/",'.html');
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */
</script>
<div id="main-nav"></div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<div id="MSearchResults">
<div class="SRPage">
<div id="SRIndex">
<div id="SRResults"></div>
<div class="SRStatus" id="Loading">Loading...</div>
<div class="SRStatus" id="Searching">Searching...</div>
<div class="SRStatus" id="NoMatches">No Matches</div>
</div>
</div>
</div>
</div>

<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><b>cmaple</b></li><li class="navelem"><a class="el" href="classcmaple_1_1_alignment.html">Alignment</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="headertitle"><div class="title">cmaple::Alignment Member List</div></div>
</div><!--header-->
<div class="contents">

<p>This is the complete list of members for <a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a>, including all inherited members.</p>
<table class="directory">
<tr class="even"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#a5a429c944ebac9aef2a2e20094a5dc2b">Alignment</a>()</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#a88ba338239e3863ced3d5dc3e63a350f">Alignment</a>(std::istream &amp;aln_stream, const std::string &amp;ref_seq=&quot;&quot;, const InputType format=IN_AUTO, const cmaple::SeqRegion::SeqType seqtype=cmaple::SeqRegion::SEQ_AUTO)</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#a128c4d12df8c70419d75edb9fd7b8d58">Alignment</a>(const std::string &amp;aln_filename, const std::string &amp;ref_seq=&quot;&quot;, const InputType format=IN_AUTO, const cmaple::SeqRegion::SeqType seqtype=cmaple::SeqRegion::SEQ_AUTO)</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#aee3f54a67adb568735bbc1db96944e3ba5b481bc6c5d186f4e2912ab9636411f5">IN_AUTO</a> enum value</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#aee3f54a67adb568735bbc1db96944e3ba4e2c0251b5ac83d386bc3ba19cf528e4">IN_FASTA</a> enum value</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#aee3f54a67adb568735bbc1db96944e3baa1d0d04b8d6e30dc1340d981bf223e80">IN_MAPLE</a> enum value</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#aee3f54a67adb568735bbc1db96944e3ba70a7e3edeb35284e39c8f9fe7214fde1">IN_PHYLIP</a> enum value</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#aee3f54a67adb568735bbc1db96944e3ba2fed9cbb7e537d6a2976264543c712cc">IN_UNKNOWN</a> enum value</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#aee3f54a67adb568735bbc1db96944e3b">InputType</a> enum name</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#a1d0cc7a3b1321c2f22351e8801a8890a">read</a>(std::istream &amp;aln_stream, const std::string &amp;ref_seq=&quot;&quot;, const InputType format=IN_AUTO, const cmaple::SeqRegion::SeqType seqtype=cmaple::SeqRegion::SEQ_AUTO)</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#a669f8cd477943459407b7ed32c934816">read</a>(const std::string &amp;aln_filename, const std::string &amp;ref_seq=&quot;&quot;, const InputType format=IN_AUTO, const cmaple::SeqRegion::SeqType seqtype=cmaple::SeqRegion::SEQ_AUTO)</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#a7cc0a73cc105173130dac55d78786f43">write</a>(std::ostream &amp;aln_stream, const InputType &amp;format=IN_MAPLE)</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#a793e2c9b076c92298d812e35aa073952">write</a>(const std::string &amp;aln_filename, const InputType &amp;format=IN_MAPLE, const bool overwrite=false)</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html#a36d8b2bbaf72d21162d6e273bb3674e1">~Alignment</a>()</td><td class="entry"><a class="el" href="classcmaple_1_1_alignment.html">cmaple::Alignment</a></td><td class="entry"></td></tr>
</table></div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by&#160;<a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.8
</small></address>
</body>
</html>
Loading