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/**
* @file multi_example3.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_example3
{
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 the compartments
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 the speciesTypes
MultiModelPlugin modelPlug =
(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 =
(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");
// create a subListOfSpeciesFeatures
SubListOfSpeciesFeatures subloSF = spPlug.createSubListOfSpeciesFeatures();
subloSF.setRelation(libsbml.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");
subloSF.appendAndOwn(sf1);
sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a2");
sf1.setOccur(1);
sf1.setComponent("b2");
sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c2");
subloSF.appendAndOwn(sf1);
// create a second subListOfSpeciesfeatures
subloSF = spPlug.createSubListOfSpeciesFeatures();
subloSF.setRelation(libsbml.Relation_fromString("or"));
sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a3");
sf1.setOccur(1);
sf1.setComponent("b3");
sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c3");
subloSF.appendAndOwn(sf1);
sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a4");
sf1.setOccur(1);
sf1.setComponent("b4");
sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c4");
subloSF.appendAndOwn(sf1);
libsbml.writeSBML(document,"multi_example3.xml");
}
}
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