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//
// @file groups_example1.java
// @brief SBML Groups example
// @author Akiya Jouraku
// @author Frank Bergmann (java port)
//
// $Id: example1.java 11938 2010-09-20 02:04:23Z mhucka $
// $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/branches/libsbml-5/examples/groups/example1.java $
//
// This file is part of libSBML. Please visit http://sbml.org for more
// information about SBML, and the latest version of libSBML.
//
import org.sbml.libsbml.*;
public class groups_example1
{
public static void main(String[] args)
{
System.loadLibrary("sbmlj");
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "groups") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"groups",1,"GROUP");
//
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1,"groups",1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a groups package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("groups",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(GroupsExtension::XmlnsL3V1V1,"groups");
//
// (2) Creates a GroupsPkgNamespaces object (SBMLNamespace derived class for
// groups package. The class is basically used for createing an SBase derived
// objects defined in the groups package) with the given SBML level, version,
// and package version
//
// GroupsPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// create the Model
Model model=document.createModel();
// create the Compartment
Compartment compartment = model.createCompartment();
compartment.setId("cytosol");
compartment.setConstant(true);
compartment=model.createCompartment();
compartment.setId("mitochon");
compartment.setConstant(true);
// create the Species
Species species = model.createSpecies();
species.setId("ATPc");
species.setCompartment("cytosol");
species.setInitialConcentration(1);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
species = model.createSpecies();
species.setId("ATPm");
species.setCompartment("mitochon");
species.setInitialConcentration(2);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
// create the Groups
//
// Get a GroupsModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is SBasePlugin, and
// thus the value needs to be casted for the corresponding derived class.
//
GroupsModelPlugin mplugin = (GroupsModelPlugin)(model.getPlugin("groups"));
//
// Creates a Group object via GroupsModelPlugin object.
//
Group group = mplugin.createGroup();
group.setId("ATP");
group.setKind(libsbml.GROUP_KIND_CLASSIFICATION);
group.setSBOTerm("SBO:0000252");
Member member = group.createMember();
member.setIdRef("ATPc");
member = group.createMember();
member.setIdRef("ATPm");
libsbml.writeSBML(document,"groups_example1-java.xml");
}
}
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