/**
 * @file    multi_example2.java
 * @brief   multi create example
 * @author  Sarah Keating
 * @author  Frank Bergmann
 *
 * <!--------------------------------------------------------------------------
 * 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
 * ------------------------------------------------------------------------ -->
 */

import org.sbml.libsbml.*;

public class multi_example2
{

    public static void main(String[] args)
    {
        System.loadLibrary("sbmlj");
        SBMLNamespaces sbmlns = new SBMLNamespaces(3,1,"multi",1);

        // create the document

        SBMLDocument document = new SBMLDocument(sbmlns);

        // set the required attribute to true
        SBMLDocumentPlugin  docPlug = 
                (SBMLDocumentPlugin)(document.getPlugin("multi"));
        docPlug.setRequired(true);


        // create the Model

        Model model=document.createModel();

        // create a  compartment

        Compartment  c = model.createCompartment();
        c.setId("membrane");
        c.setConstant(true);

        // set the multi attribute isType via the compartmentPlugin
        MultiCompartmentPlugin  compPlug = 
                (MultiCompartmentPlugin)(c.getPlugin("multi"));
        compPlug.setIsType(true);

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

        // create reaction
        Reaction r = model.createReaction();
        r.setId("r1");
        r.setFast(false);
        r.setReversible(false);

        // createReactant
        SpeciesReference sr = r.createReactant();
        sr.setId("sr1");
        sr.setSpecies("s1");
        sr.setConstant(false);

        KineticLaw kl = r.createKineticLaw();

        ASTNode  ci = new ASTNode(libsbml.AST_NAME);
        ci.setName("s1");
        MultiASTPlugin  astPlugin = (MultiASTPlugin)(ci.getPlugin("multi"));
        astPlugin.setSpeciesReference("r1");

        ASTNode  ci1 = new ASTNode(libsbml.AST_NAME);
        MultiASTPlugin  astPlugin1 = (MultiASTPlugin)(ci1.getPlugin("multi"));
        astPlugin1.setRepresentationType("sum");
        ci1.setName("s1");

        ASTNode math = new ASTNode(libsbml.AST_TIMES);
        math.addChild(ci);
        math.addChild(ci1);

        kl.setMath(math);

        libsbml.writeSBML(document,"multi_example2.xml");
    }

}