/**
 * @file    example3.cpp
 * @brief   multi create example
 * @author  Sarah Keating
 *
 * <!--------------------------------------------------------------------------
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 *
 * Copyright (C) 2009-2013 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *
 * Copyright (C) 2006-2008 by the California Institute of Technology,
 *     Pasadena, CA, USA 
 *
 * Copyright (C) 2002-2005 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. Japan Science and Technology Agency, Japan
 *
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation.  A copy of the license agreement is provided
 * in the file named "LICENSE.txt" included with this software distribution
 * and also available online as http://sbml.org/software/libsbml/license.html
 * ------------------------------------------------------------------------ -->
 */

#include <sbml/SBMLTypes.h>
#include <sbml/packages/multi/common/MultiExtensionTypes.h>


using namespace std;
LIBSBML_CPP_NAMESPACE_USE

int
main (int argc, char* argv[])
{
  SBMLNamespaces sbmlns(3,1,"multi",1);

  // create the document

  SBMLDocument *document = new SBMLDocument(&sbmlns);

  // set the required attribute to true
  MultiSBMLDocumentPlugin * docPlug = 
    static_cast<MultiSBMLDocumentPlugin*>(document->getPlugin("multi"));
  docPlug->setRequired(true);


  // create the Model

  Model* model=document->createModel();

  // create the compartments

  Compartment * c = model->createCompartment();
  c->setId("membrane");
  c->setConstant(true);

  // set the multi attribute isType via the compartmentPlugin
  MultiCompartmentPlugin * compPlug = 
    static_cast<MultiCompartmentPlugin*>(c->getPlugin("multi"));
  compPlug->setIsType(true);

  // create the speciesTypes

  MultiModelPlugin * modelPlug = 
    static_cast<MultiModelPlugin*>(model->getPlugin("multi"));

  MultiSpeciesType * st = modelPlug->createMultiSpeciesType();
  st->setId("stX");
  st->setCompartment("membrane");

  // create species
  Species *s = model->createSpecies();
  s->setId("s1");
  s->setCompartment("membrane");
  s->setBoundaryCondition(false);
  s->setHasOnlySubstanceUnits(false);
  s->setConstant(false);

  // set the multi attribute speciesType via the compartmentPlugin
  MultiSpeciesPlugin * spPlug = 
    static_cast<MultiSpeciesPlugin*>(s->getPlugin("multi"));
  spPlug->setSpeciesType("stX");

  // create species feature
  SpeciesFeature *sf = spPlug->createSpeciesFeature();
  sf->setSpeciesFeatureType("a");
  sf->setOccur(1);
  sf->setComponent("b");

  SpeciesFeatureValue *sfv = sf->createSpeciesFeatureValue();
  sfv->setValue("c");

  // set the relation attribute on the listOfSpeciesfeatures element
  ListOfSpeciesFeatures * loSF = spPlug->getListOfSpeciesFeatures();
  loSF->setRelation(Relation_fromString("or"));

  // create a subListOfSpeciesFeatures
  loSF = spPlug->createSubListOfSpeciesFeatures();
  loSF->setRelation(Relation_fromString("and"));

  // add speciesFeatures to the subList
  SpeciesFeature *sf1 = new SpeciesFeature(3, 1, 1);
  sf1->setSpeciesFeatureType("a1");
  sf1->setOccur(1);
  sf1->setComponent("b1");

  SpeciesFeatureValue *sfv1 = sf1->createSpeciesFeatureValue();
  sfv1->setValue("c1");

  loSF->appendAndOwn(sf1);

  sf1 = new SpeciesFeature(3, 1, 1);
  sf1->setSpeciesFeatureType("a2");
  sf1->setOccur(1);
  sf1->setComponent("b2");

  sfv1 = sf1->createSpeciesFeatureValue();
  sfv1->setValue("c2");

  loSF->appendAndOwn(sf1);

  // create a second subListOfSpeciesfeatures
  loSF = spPlug->createSubListOfSpeciesFeatures();
  loSF->setRelation(Relation_fromString("or"));

  sf1 = new SpeciesFeature(3, 1, 1);
  sf1->setSpeciesFeatureType("a3");
  sf1->setOccur(1);
  sf1->setComponent("b3");

  sfv1 = sf1->createSpeciesFeatureValue();
  sfv1->setValue("c3");

  loSF->appendAndOwn(sf1);

  sf1 = new SpeciesFeature(3, 1, 1);
  sf1->setSpeciesFeatureType("a4");
  sf1->setOccur(1);
  sf1->setComponent("b4");

  sfv1 = sf1->createSpeciesFeatureValue();
  sfv1->setValue("c4");

  loSF->appendAndOwn(sf1);

  writeSBML(document,"multi_example3.xml");
 
  delete document;

  return 0;
}
