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#!/usr/bin/perl
# -*-Perl-*-
#
# @file example1.pl
# @brief SBML Groups example
# @author Akiya Jouraku
# @author Frank Bergmann (perl port)
#
# $Id: example1.pl 11938 2010-09-20 02:04:23Z mhucka $
# $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/branches/libsbml-5/examples/groups/example1.pl $
#
# This file is part of libSBML. Please visit http://sbml.org for more
# information about SBML, and the latest version of libSBML.
#
use blib '../../src/bindings/perl';
use LibSBML;
use strict;
#
# 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");
#
my $sbmlns = new LibSBML::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
my $document = new LibSBML::SBMLDocument($sbmlns);
# create the Model
my $model=$document->createModel();
# create the Compartment
my $compartment = $model->createCompartment();
$compartment->setId("cytosol");
$compartment->setConstant(1);
my $compartment=$model->createCompartment();
$compartment->setId("mitochon");
$compartment->setConstant(1);
# create the Species
my $species = $model->createSpecies();
$species->setId("ATPc");
$species->setCompartment("cytosol");
$species->setInitialConcentration(1);
$species->setHasOnlySubstanceUnits(0);
$species->setBoundaryCondition(0);
$species->setConstant(0);
$species = $model->createSpecies();
$species->setId("ATPm");
$species->setCompartment("mitochon");
$species->setInitialConcentration(2);
$species->setHasOnlySubstanceUnits(0);
$species->setBoundaryCondition(0);
$species->setConstant(0);
# 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.
#
my $mplugin = $model->getPlugin("groups");
#
# Creates a Group object via GroupsModelPlugin object.
#
my $group = $mplugin->createGroup();
$group->setId("ATP");
$group->setKind("classification");
$group->setSBOTerm("SBO:0000252");
my $member = $group->createMember();
$member->setIdRef("ATPc");
$member = $group->createMember();
$member->setIdRef("ATPm");
LibSBML::writeSBML($document,"groups_example1-perl.xml");
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