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/**
* @file convertCobraToFbc.java
* @brief Convert COBRA L2 to L3 with FBC
* @author Frank T. Bergmann
*
* <!--------------------------------------------------------------------------
* This sample program is distributed under a different license than the rest
* of libSBML. This program uses the open-source MIT license, as follows:
*
* Copyright (c) 2013-2016 by the California Institute of Technology
* (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
* and the University of Heidelberg (Germany), with support from the National
* Institutes of Health (USA) under grant R01GM070923. All rights reserved.
*
* Permission is hereby granted, free of charge, to any person obtaining a
* copy of this software and associated documentation files (the "Software"),
* to deal in the Software without restriction, including without limitation
* the rights to use, copy, modify, merge, publish, distribute, sublicense,
* and/or sell copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
* THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
* DEALINGS IN THE SOFTWARE.
*
* Neither the name of the California Institute of Technology (Caltech), nor
* of the European Bioinformatics Institute (EMBL-EBI), nor of the University
* of Heidelberg, nor the names of any contributors, may be used to endorse
* or promote products derived from this software without specific prior
* written permission.
* ------------------------------------------------------------------------ -->
*/
import org.sbml.libsbml.*;
public class convertCobraToFbc
{
public static void main (String[] args)
{
if (args.length != 3)
{
println("Usage: java convertCobraToFbc 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 an L2 model with
COBRA annotation to L3 with FBC */
props.addOption("convert cobra", true, "Convert 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);
}
}
}
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