LibSBML convertFbcToCobra.java

/**
 * @file    convertFbcToCobra.java
 * @brief   Convert L3 with FBC to L2 with COBRA annotation
 * @author  Frank T. Bergmann
 *
 * 
 */

import org.sbml.libsbml.*;

public class convertFbcToCobra
{
  public static void main (String[] args)
  {
    if (args.length != 3)
    {
      println("Usage: java convertFbcToCobra input-filename output-filename");
      System.exit(2);
    }   

    SBMLReader reader     = new SBMLReader();
    SBMLWriter writer     = new SBMLWriter();

    SBMLDocument doc = reader.readSBML(args[0]);
    if (doc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
    {
      doc.printErrors();
    }
    else
    {
      /* create a new conversion properties structure */
      ConversionProperties props = new ConversionProperties();
                  
      /* add an option that we want to convert a model  with
         L3 FBC to L2 with COBRA annotation */
      props.addOption("convert fbc to cobra", true, "Convert FBC model to Cobra model");
          
          
      /* perform the conversion */
      if (doc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS)
      {
        println ("conversion failed ... ");
        System.exit(3); 
      }
      writer.writeSBML(doc, args[1]);
    }
  }


  static void println (String msg)
  {
    System.out.println(msg);
  }


  /**
   * Loads the SWIG-generated libSBML Java module when this class is
   * loaded, or reports a sensible diagnostic message about why it failed.
   */
  static
  {
    try
    {
      System.loadLibrary("sbmlj");
      // For extra safety, check that the jar file is in the classpath.
      Class.forName("org.sbml.libsbml.libsbml");
    }
    catch (UnsatisfiedLinkError e)
    {
      System.err.println("Error encountered while attempting to load libSBML:");
      System.err.println("Please check the value of your "
                         + (System.getProperty("os.name").startsWith("Mac OS")
                            ? "DYLD_LIBRARY_PATH" : "LD_LIBRARY_PATH") +
                         " environment variable and/or your" +
                         " 'java.library.path' system property (depending on" +
                         " which one you are using) to make sure it list the" +
                         " directories needed to find the " +
                         System.mapLibraryName("sbmlj") + " library file and" +
                         " libraries it depends upon (e.g., the XML parser).");
      System.exit(1);
    }
    catch (ClassNotFoundException e)
    {
      System.err.println("Error: unable to load the file 'libsbmlj.jar'." +
                         " It is likely that your -classpath command line " +
                         " setting or your CLASSPATH environment variable " +
                         " do not include the file 'libsbmlj.jar'.");
      e.printStackTrace();

      System.exit(1);
    }
    catch (SecurityException e)
    {
      System.err.println("Error encountered while attempting to load libSBML:");
      e.printStackTrace();
      System.err.println("Could not load the libSBML library files due to a"+
                         " security exception.\n");
      System.exit(1);
    }
  }
}

LibSBML, an application programming interface (API) library for SBML.

SBML Team http://www.sbml.org/ sbml-team@googlegroups.com