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DISCLAIMER: WORK IN PROGRESS

The system was successfully built and tested on MacOSX Snow Leopard.

TODO

  • streamline the automatic building process for all supported systems
  • package the resulting files as a standalone library

Where to find LibSBGN C++?

LibSBGN C++ can be found in the SVN repository.

To download the latest version on your machine:

svn co https://libsbgn.svn.sourceforge.net/svnroot/libsbgn libsbgn

What's in the LibSBGN C++ folder?

SBGN C++ binder

sbgn.cxx and sbgn.hxx [FOR REFERENCE ONLY, MAY NOT BE UP-TO-DATE]

This library can read and write SBGN-ML files, and validate their syntax against the schema.

Example of code using the binder

sbgn2txt.cxx

  • in = some *.sbgn files
  • out = a text description (or validation errors, if any)

Tools required to generate the binder

makefile [included], and a local installation of the XSD converter [NOT INCLUDED]

  • "make libsbgn" generates sbgn.cxx and sbgn.hxx from the current XSD
  • "make test" compiles and runs sbgn2txt on all *.sbgn files in the test-files folder

How to (re)build the binder?

sbgn.hxx and sbgn.cxx are generated automatically from SBGN.xsd.

To stay up-to-date with the latest specifications, these files should be rebuilt whenever the XSD is modified.

==Download the XSD => C++ conversion tool==

  • Download the correct version of the conversion tool for your platform
  • Uncompress the downloaded file in the current directory.

We'll call the resulting directory XSD2CPP in the following instructions.

Test the conversion tool

Make sure the conversion tool works properly on your system:

cd XSD2CPP/examples/cxx/tree/hello make

If not, consult the tool's documentation to fix the problem (cf. XSD2CPP/documentation)

Build LibSBGN C++

  • Modify the first line of the makefile to link to the correct root directory:

root := ./XSD2CPP/examples

  • To update the binder against the latest version of the XSD, and run tests against all the test files:

make

How to reuse the binder?

In order to reuse sbgn.hxx and sbgn.cxx in your own project, you need to be able to link to a copy of libxsd (cf. XSD2CPP/libxsd)

For building and linking options (dependencies, system specific settings, etc.), have a look at XSD2CPP/examples/build

Refer to sbgn2txt.cxx for examples of how to invoke the library in your own code, e.g.:

Read an SBGN-ML file

try {  xml_schema::properties props; // to store information on the XSD for validation purposes  props.schema_location ("http://sbgn.org/libsbgn/pd/0.1", "../resources/SBGN.xsd");    auto_ptrlibsbgn::pd_0_1::sbgn mysbgnobject ( libsbgn::pd_0_1::sbgn_ (sbgnmlfile, 0, props) );  // [..] do something with mysbgnobject } // validation errors result in an exception being thrown catch (const xml_schema::exception& e) {  cerr << "SBGN-ML parsing error: " << e << endl; }

==Traverse the SBGN-ML structure== // For each map for (libsbgn::pd_0_1::sbgn::map_const_iterator m (mysbgnobject->map ().begin ()); m != s->map ().end (); ++m) {  cout << "Map" << endl;

// For each high level glyph for (libsbgn::pd_0_1::map::glyph_const_iterator g (m->glyph ().begin ()); g != m->glyph ().end (); ++g)  {   cout << "\tGlyph " << g.id() << " (" << g.class_() << ")" << endl; // process glyph internal attributes and elements: label, subglyphs, etc. }

// For each arc for (libsbgn::pd_0_1::map::arc_const_iterator a (m->arc ().begin ()); a != m->arc ().end (); ++a)  {    cout << "\tArc from " << a->source() << " to " << a->target() << " (" << a->class_() << ")" << endl;    // process arc internal attributes and elements: geometric path, stoichiometry, etc.  } }