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/**
* @file flattenModel.cpp
* @brief SBML hierarchical composition flattening example
* @author Sarah Keating
*
* <!--------------------------------------------------------------------------
* 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) 2013-2018 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 <sstream>
#include <sbml/SBMLTypes.h>
#include <sbml/extension/SBMLExtensionRegister.h>
#include <sbml/conversion/SBMLConverterRegistry.h>
#ifdef LIBSBML_HAS_PACKAGE_COMP
#include <sbml/packages/comp/common/CompExtensionTypes.h>
#endif
LIBSBML_CPP_NAMESPACE_USE
using namespace std;
const string usage = "Usage: flattenModel [-p] inputFile outputFile\n"
" -p : list unused ports";
int main(int argc,char** argv)
{
bool leavePorts = false;
if (argc < 3)
{
cout << usage << endl;
return 1;
}
else if (argc == 3)
{
if ( string("-p") == string(argv[1]) )
{
cout << usage << endl;
return 1;
}
}
int argIndex = 1;
if ( string("-p") == string(argv[1]) )
{
leavePorts = true;
++argIndex;
}
if (SBMLExtensionRegistry::isPackageEnabled("comp") == false)
{
cerr << "The version of libsbml being used does not have the comp"
<< " package code enabled" << endl;
return 1;
}
const char* inputFile = argv[argIndex];
const char* outputFile = argv[argIndex+1];
SBMLDocument* document = readSBML(inputFile);
if (document->getNumErrors() > 0)
{
cerr << "Encountered the following SBML errors:" << endl;
document->printErrors(cerr);
return 1;
}
ConversionProperties* props = new ConversionProperties();
props->addOption("flatten comp");
props->addOption("leavePorts", leavePorts);
SBMLConverter* converter =
SBMLConverterRegistry::getInstance().getConverterFor(*props);
converter->setDocument(document);
int result = converter->convert();
if (result != LIBSBML_OPERATION_SUCCESS)
{
cerr << "Conversion failed\n";
document->printErrors();
}
writeSBML(document, outputFile);
delete converter;
delete document;
}
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