/**
 * @file    unsetAnnotation.cpp
 * @brief   unset annotation for each element
 * @author  Akiya Jouraku
 *
 * $Id: unsetAnnotation.cpp 10121 2009-08-28 11:47:20Z sarahkeating $
 * $HeadURL: http://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/examples/c++/unsetAnnotation.cpp $
 *
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 */


#include <iostream>

#include <sbml/SBMLTypes.h>
#include "util.h"


using namespace std;
LIBSBML_CPP_NAMESPACE_USE

int
main (int argc, char* argv[])
{
  if (argc != 3)
  {
    cout << endl << "Usage: unsetAnnotation <input-filename> <output-filename>" << endl << endl;
    return 1;
  }

  unsigned int i,j;
  const char* filename   = argv[1];
  SBMLDocument* document;
  SBMLReader reader;

  document = reader.readSBML(filename);

  unsigned int errors = document->getNumErrors();

  if(errors > 0)
  {
    document->printErrors(cerr);
    delete document;

    return errors;
  }

  Model* m = document->getModel();
  m->unsetAnnotation();

  for(i=0; i < m->getNumReactions(); i++)
  {
    Reaction* re = m->getReaction(i);
    re->unsetAnnotation();

    for(j=0; j < re->getNumReactants(); j++)
    {
      SpeciesReference* rt = re->getReactant(j);
      rt->unsetAnnotation();
    }

    for(j=0; j < re->getNumProducts(); j++)
    {
      SpeciesReference* rt = re->getProduct(j);
      rt->unsetAnnotation();
    }

    for(j=0; j < re->getNumModifiers(); j++)
    {
      ModifierSpeciesReference* md = re->getModifier(j);
      md->unsetAnnotation();
    }

    if(re->isSetKineticLaw())
    {
      KineticLaw* kl = re->getKineticLaw();
      kl->unsetAnnotation();

      for(j=0; j < kl->getNumParameters(); j++)
      {
        Parameter* pa = kl->getParameter(j);
        pa->unsetAnnotation();
      }
    }

  }

  for(i=0; i < m->getNumSpecies(); i++)
  {
    Species* sp = m->getSpecies(i);
    sp->unsetAnnotation();
  }

  for(i=0; i < m->getNumCompartments(); i++)
  {
    Compartment* sp = m->getCompartment(i);
    sp->unsetAnnotation();
  }

  for(i=0; i < m->getNumFunctionDefinitions(); i++)
  {
    FunctionDefinition* sp = m->getFunctionDefinition(i);
    sp->unsetAnnotation();
  }

  for(i=0; i < m->getNumUnitDefinitions(); i++)
  {
    UnitDefinition* sp = m->getUnitDefinition(i);
    sp->unsetAnnotation();
  }

  for(i=0; i < m->getNumParameters(); i++)
  {
    Parameter* sp = m->getParameter(i);
    sp->unsetAnnotation();
  }

  for(i=0; i < m->getNumRules(); i++)
  {
    Rule* sp = m->getRule(i);
    sp->unsetAnnotation();
  }

  for(i=0; i < m->getNumInitialAssignments(); i++)
  {
    InitialAssignment* sp = m->getInitialAssignment(i);
    sp->unsetAnnotation();
  }

  for(i=0; i < m->getNumEvents(); i++)
  {
    Event* sp = m->getEvent(i);
    sp->unsetAnnotation();

    for(j=0; j < sp->getNumEventAssignments(); j++)
    {
      EventAssignment* ea = sp->getEventAssignment(j);
      ea->unsetAnnotation();
    }
  }

  for(i=0; i < m->getNumSpeciesTypes(); i++)
  {
    SpeciesType* sp = m->getSpeciesType(i);
    sp->unsetAnnotation();
  }

  for(i=0; i < m->getNumConstraints(); i++)
  {
    Constraint* sp = m->getConstraint(i);
    sp->unsetAnnotation();
  }

  writeSBML(document, argv[2]);

  delete document;
  return errors;
}


