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convertSBML.cpp

Example demonstrating how to convert SBML documents between SBML Levels.

/**
* @file convertSBML.cpp
* @brief Converts SBML documents between levels
* @author Michael Hucka
* @author Sarah Keating
* @author Ben Bornstein
*
* <!--------------------------------------------------------------------------
* 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) 2013-2014 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.
* ------------------------------------------------------------------------ -->
*/
#include <iostream>
#include <sbml/SBMLTypes.h>
using namespace std;
int
main (int argc, char *argv[])
{
const unsigned int latestLevel = SBMLDocument::getDefaultLevel();
const unsigned int latestVersion = SBMLDocument::getDefaultVersion();
if (argc != 3)
{
cout << "Usage: convertSBML input-filename output-filename" << endl
<< "This program will attempt to convert a model either to" << endl
<< "SBML Level " << latestLevel << " Version " << latestVersion
<< " (if the model is not already) or, if " << endl
<< "the model is already expressed in Level " << latestLevel
<< " Version " << latestVersion << ", this" << endl
<< "program will attempt to convert the model to Level 1 Version 2."
<< endl;
return 1;
}
const char* inputFile = argv[1];
const char* outputFile = argv[2];
SBMLDocument* document = readSBML(inputFile);
unsigned int errors = document->getNumErrors();
if (errors > 0)
{
cerr << "Encountered the following SBML errors:" << endl;
document->printErrors(cerr);
cerr << "Conversion skipped. Please correct the problems above first."
<< endl;
return errors;
}
/**
* If the given model is not already L2v4, assume that the user wants to
* convert it to the latest release of SBML (which is L2v4 currently).
* If the model is already L2v4, assume that the user wants to attempt to
* convert it down to Level 1 (specifically L1v2).
*/
unsigned int olevel = document->getLevel();
unsigned int oversion = document->getVersion();
bool success;
if (olevel < latestLevel || oversion < latestVersion)
{
cout << "Attempting to convert Level " << olevel << " Version " << oversion
<< " model to Level " << latestLevel
<< " Version " << latestVersion << "." << endl;
success = document->setLevelAndVersion(latestLevel, latestVersion);
}
else
{
cout << "Attempting to convert Level " << olevel << " Version " << oversion
<< " model to Level 1 Version 2." << endl;
success = document->setLevelAndVersion(1, 2);
}
errors = document->getNumErrors();
if (!success)
{
cerr << "Unable to perform conversion due to the following:" << endl;
document->printErrors(cerr);
cout << endl;
cout << "Conversion skipped. Either libSBML does not (yet)" << endl
<< "have the ability to convert this model or (automatic)" << endl
<< "conversion is not possible in this case." << endl;
delete document;
return errors;
}
else if (errors > 0)
{
cout << "Information may have been lost in conversion; but a valid model ";
cout << "was produced by the conversion.\nThe following information ";
cout << "was provided:\n";
document->printErrors(cout);
writeSBML(document, outputFile);
}
else
{
cout << "Conversion completed." << endl;
writeSBML(document, outputFile);
}
delete document;
return 0;
}