/**
 * @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) 2013-2017 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;

}
