groups_example2.cpp

Simple example of writing a model that uses the SBML Level 3 Groups package and also the SBML Level 3 Layout package.

/**
 * @file    example2.cpp
 * @brief   SBML Groups/Layout example
 * @author  Ralph Gauges
 * @author  Akiya Jouraku (Modified for layout and groups extensions in libSBML 5)
 *
 */
/* 
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 *  
 * Copyright 2004 European Media Laboratories Research gGmbH
 */


#include "sbml/SBMLTypes.h"
#include "sbml/packages/layout/common/LayoutExtensionTypes.h"
#include "sbml/packages/groups/common/GroupsExtensionTypes.h"

LIBSBML_CPP_NAMESPACE_USE

int main(int argc,char** argv){

//
// set the SBMLNamespaces with Layout Level 3 Version 1 Package Version1
// and Groups Level 3 Version 1 Package Version 1
//
SBMLNamespaces sbmlns(3,1);
sbmlns.addPkgNamespace("layout",1);
sbmlns.addPkgNamespace("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 the given SBML level, version,
//     and one of pakage names, packge version, and then adds a namespace
//     of another package to the object. 
//
//         SBMLNamespaces sbmlns(3,1,"layout",1);
//         sbmlns.addPkgNamespace("groups",1);
//
//        OR
//
//         SBMLNamespaces sbmlns(3,1,"groups",1);
//         sbmlns.addPkgNamespace("layout",1);
//
// (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 and then adds a namespace of another package to the object.
//
//        GroupsPkgNamespaces sbmlns(3,1,1);
//        sbmlns.addPkgNamespace("layout",1);
//
// (3) Creates a LayoutPkgNamespaces object (SBMLNamespace derived class for
//     layout package. The class is basically used for createing an SBase derived
//     objects defined in the layout package) with the given SBML level, version, 
//     and package version and then adds a namespace of another package to the object.
//
//        LayoutPkgNamespaces sbmlns(3,1,1);
//        sbmlns.addPkgNamespace("groups",1);
//     


// create the document

SBMLDocument *document=new SBMLDocument(&sbmlns);
document->setPackageRequired("groups", false);
document->setPackageRequired("layout", false);

// create the Model

Model* model=document->createModel();
model->setId("TestModel");
document->setModel(model);


// create the Compartment

Compartment* compartment=model->createCompartment();
compartment->setId("Compartment_1");
compartment->setConstant(true);

// create the Species

Species* species1=model->createSpecies();
species1->setId("Species_1");
species1->setCompartment(compartment->getId());
species1->setHasOnlySubstanceUnits(false);
species1->setBoundaryCondition(false);
species1->setConstant(false);

Species* species2=model->createSpecies();
species2->setId("Species_2");
species2->setCompartment(compartment->getId());
species2->setHasOnlySubstanceUnits(false);
species2->setBoundaryCondition(false);
species2->setConstant(false);

// create the Reactions

Reaction* reaction1=model->createReaction();
reaction1->setId("Reaction_1");
reaction1->setReversible(false);
reaction1->setFast(false);

SpeciesReference* reference1=reaction1->createReactant();
reference1->setSpecies(species1->getId());
reference1->setId("SpeciesReference_1");
reference1->setConstant(false);


SpeciesReference* reference2=reaction1->createProduct();
reference2->setSpecies(species2->getId());
reference2->setId("SpeciesReference_2");
reference2->setConstant(false);

Reaction* reaction2=model->createReaction();
reaction2->setId("Reaction_2");
reaction2->setReversible(false);
reaction2->setFast(false);


SpeciesReference* reference3=reaction2->createReactant();
reference3->setSpecies(species2->getId());
reference3->setId("SpeciesReference_3");
reference3->setConstant(false);

SpeciesReference* reference4=reaction2->createProduct();
reference4->setSpecies(species1->getId());
reference4->setId("SpeciesReference_4");
reference4->setConstant(false);


// create the Layout

LayoutPkgNamespaces layoutns(3,1,1);

//
// 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.
//
LayoutModelPlugin* mpluginLayout = static_cast<LayoutModelPlugin*>(model->getPlugin("layout"));
Layout* layout=mpluginLayout->createLayout();

layout->setId("Layout_1");
Dimensions dim(&layoutns, 400.0,220.0);
layout->setDimensions(&dim);


// create the CompartmentGlyph

CompartmentGlyph* compartmentGlyph=layout->createCompartmentGlyph();
compartmentGlyph->setId("CompartmentGlyph_1");
compartmentGlyph->setCompartmentId(compartment->getId());
BoundingBox bb(&layoutns, "bb1",5,5,390,210);
compartmentGlyph->setBoundingBox(&bb);


// create the SpeciesGlyphs

SpeciesGlyph* speciesGlyph1=layout->createSpeciesGlyph();
speciesGlyph1->setId("SpeciesGlyph_1");
speciesGlyph1->setSpeciesId(species1->getId());
bb=BoundingBox(&layoutns, "bb2",80,26,240,24);
speciesGlyph1->setBoundingBox(&bb);

TextGlyph* textGlyph1=layout->createTextGlyph();
textGlyph1->setId("TextGlyph_01");
bb=BoundingBox(&layoutns, "bbA",92,26,228,24);
textGlyph1->setBoundingBox(&bb);
textGlyph1->setOriginOfTextId(speciesGlyph1->getId());
textGlyph1->setGraphicalObjectId(speciesGlyph1->getId());

SpeciesGlyph* speciesGlyph2=layout->createSpeciesGlyph();
speciesGlyph2->setId("SpeciesGlyph_2");
speciesGlyph2->setSpeciesId(species2->getId());
bb=BoundingBox(&layoutns, "bb3",80,170,240,24);
speciesGlyph2->setBoundingBox(&bb);

TextGlyph* textGlyph2=layout->createTextGlyph();
textGlyph2->setId("TextGlyph_02");
bb=BoundingBox(&layoutns, "bbB",92,170,228,24);
textGlyph2->setBoundingBox(&bb);
textGlyph2->setOriginOfTextId(speciesGlyph2->getId());
textGlyph2->setGraphicalObjectId(speciesGlyph2->getId());

// create the ReactionGlyphs

ReactionGlyph* reactionGlyph1=layout->createReactionGlyph();
reactionGlyph1->setId("ReactionGlyph_1");
reactionGlyph1->setReactionId(reaction1->getId());

Curve* reactionCurve1=reactionGlyph1->getCurve();
LineSegment* ls=reactionCurve1->createLineSegment();
Point p(&layoutns,165,105);
ls->setStart(&p);
p=Point(&layoutns,165,115);
ls->setEnd(&p);

ReactionGlyph* reactionGlyph2=layout->createReactionGlyph();
reactionGlyph2->setId("ReactionGlyph_1");
reactionGlyph2->setReactionId(reaction2->getId());

Curve* reactionCurve2=reactionGlyph2->getCurve();
ls=reactionCurve2->createLineSegment();
p=Point(&layoutns,235,105);
ls->setStart(&p);
p=Point(&layoutns,235,115);
ls->setEnd(&p);

// add the SpeciesReferenceGlyphs

SpeciesReferenceGlyph* speciesReferenceGlyph1=reactionGlyph1->createSpeciesReferenceGlyph();
speciesReferenceGlyph1->setId("SpeciesReferenceGlyph_1");
speciesReferenceGlyph1->setSpeciesGlyphId(speciesGlyph1->getId());
speciesReferenceGlyph1->setSpeciesReferenceId(reference1->getId());
speciesReferenceGlyph1->setRole(SPECIES_ROLE_SUBSTRATE);

Curve* speciesReferenceCurve1=speciesReferenceGlyph1->getCurve();
CubicBezier* cb=speciesReferenceCurve1->createCubicBezier();
p=Point(&layoutns,165,105);
cb->setStart(&p);
p=Point(&layoutns,165,90);
cb->setBasePoint1(&p);
p=Point(&layoutns,165,90);
cb->setBasePoint2(&p);
p=Point(&layoutns,195,60);
cb->setEnd(&p);

SpeciesReferenceGlyph* speciesReferenceGlyph2=reactionGlyph1->createSpeciesReferenceGlyph();
speciesReferenceGlyph2->setId("SpeciesReferenceGlyph_2");
speciesReferenceGlyph2->setSpeciesGlyphId(speciesGlyph2->getId());
speciesReferenceGlyph2->setSpeciesReferenceId(reference2->getId());
speciesReferenceGlyph2->setRole(SPECIES_ROLE_PRODUCT);

Curve* speciesReferenceCurve2=speciesReferenceGlyph2->getCurve();
cb=speciesReferenceCurve2->createCubicBezier();
p=Point(&layoutns,165,115);
cb->setStart(&p);
p=Point(&layoutns,165,130);
cb->setBasePoint1(&p);
p=Point(&layoutns,165,130);
cb->setBasePoint2(&p);
p=Point(&layoutns,195,160);
cb->setEnd(&p);


SpeciesReferenceGlyph* speciesReferenceGlyph3=reactionGlyph2->createSpeciesReferenceGlyph();
speciesReferenceGlyph3->setId("SpeciesReferenceGlyph_3");
speciesReferenceGlyph3->setSpeciesGlyphId(speciesGlyph2->getId());
speciesReferenceGlyph3->setSpeciesReferenceId(reference3->getId());
speciesReferenceGlyph3->setRole(SPECIES_ROLE_SUBSTRATE);

Curve* speciesReferenceCurve3=speciesReferenceGlyph3->getCurve();
cb=speciesReferenceCurve3->createCubicBezier();
p=Point(&layoutns,235,115);
cb->setStart(&p);
p=Point(&layoutns,235,130);
cb->setBasePoint1(&p);
p=Point(&layoutns,235,130);
cb->setBasePoint2(&p);
p=Point(&layoutns,205,160);
cb->setEnd(&p);

SpeciesReferenceGlyph* speciesReferenceGlyph4=reactionGlyph2->createSpeciesReferenceGlyph();
speciesReferenceGlyph4->setId("SpeciesReferenceGlyph_4");
speciesReferenceGlyph4->setSpeciesGlyphId(speciesGlyph1->getId());
speciesReferenceGlyph4->setSpeciesReferenceId(reference4->getId());
speciesReferenceGlyph4->setRole(SPECIES_ROLE_PRODUCT);

Curve* speciesReferenceCurve4=speciesReferenceGlyph4->getCurve();
cb=speciesReferenceCurve4->createCubicBezier();
p=Point(&layoutns,235,105);
cb->setStart(&p);
p=Point(&layoutns,235,90);
cb->setBasePoint1(&p);
p=Point(&layoutns,235,90);
cb->setBasePoint2(&p);
p=Point(&layoutns,205,60);
cb->setEnd(&p);

//
// Create Group
//

//
// 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* mpluginGroups = static_cast<GroupsModelPlugin*>(model->getPlugin("groups"));

//
// Creates a Group object via GroupsModelPlugin object.
//
Group* group = mpluginGroups->createGroup();

group->setId("role_substrate");
group->setKind(GROUP_KIND_CLASSIFICATION);

Member* member = group->createMember();
member->setIdRef("SpeciesReferenceGlyph_1");

member = group->createMember();
member->setIdRef("SpeciesReferenceGlyph_3");

group = mpluginGroups->createGroup();
group->setId("role_product");

member = group->createMember();
member->setIdRef("SpeciesReferenceGlyph_2");

member = group->createMember();
member->setIdRef("SpeciesReferenceGlyph_4");


writeSBML(document,"groups_example2.xml");
delete document;

}