libSBML C++ API  libSBML 5.18.0 C++ API
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"
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");
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;
}
SpeciesReference
A reference to an SBML species in a reaction.
Definition: SpeciesReference.h:275
GROUP_KIND_CLASSIFICATION
@ GROUP_KIND_CLASSIFICATION
Definition: GroupsExtension.h:400
SBMLDocument::setModel
int setModel(const Model *m)
Sets the Model for this SBMLDocument to a copy of the given Model.
Definition: SBMLDocument.cpp:599
Compartment::setConstant
int setConstant(bool value)
Sets the value of the "constant" attribute of this Compartment object.
Definition: Compartment.cpp:681
SpeciesReferenceGlyph::setRole
void setRole(const std::string &role)
Sets the role based on a string.
Definition: SpeciesReferenceGlyph.cpp:338
Dimensions
Spatial dimensions of a 2D or 3D shape.
Definition: Dimensions.h:65
Reaction
An SBML reaction between species in an SBML model.
Definition: Reaction.h:218
CubicBezier::setBasePoint1
void setBasePoint1(const Point *p)
Initializes first base point with a copy of the given point.
Definition: CubicBezier.cpp:403
GraphicalObject::setId
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this GraphicalObject.
Definition: GraphicalObject.cpp:385
CubicBezier
A Cubic Bézier smooth curve.
Definition: CubicBezier.h:65
Point
Representation of a point.
Definition: Point.h:59
Curve
A curve connecting elements in a diagram.
Definition: Curve.h:211
Group::createMember
Member * createMember()
Creates a new Member object, adds it to this Group object and returns the Member object created.
Definition: Group.cpp:443
SimpleSpeciesReference::getId
virtual const std::string & getId() const
Returns the value of the "id" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:128
Group::setKind
int setKind(const GroupKind_t kind)
Sets the value of the "kind" attribute of this Group.
Definition: Group.cpp:229
Layout::createCompartmentGlyph
CompartmentGlyph * createCompartmentGlyph()
Creates a CompartmentGlyph object, adds it to the end of the compartment glyph objects list and retur...
Definition: Layout.cpp:1380
ReactionGlyph::createSpeciesReferenceGlyph
SpeciesReferenceGlyph * createSpeciesReferenceGlyph()
Creates a new SpeciesReferenceGlyph object, adds it to the end of the list of species reference objec...
Definition: ReactionGlyph.cpp:496
Curve::createLineSegment
LineSegment * createLineSegment()
Creates a new LineSegment and adds it to the end of the list.
Definition: Curve.cpp:359
SBMLTypes.h
Include all SBML types in a single header file.
Model::createReaction
Reaction * createReaction()
Creates a new Reaction inside this Model and returns it.
Definition: Model.cpp:1779
LayoutModelPlugin
Extension of Model.
Definition: LayoutModelPlugin.h:62
Reaction::getId
virtual const std::string & getId() const
Returns the value of the "id" attribute of this Reaction.
Definition: Reaction.cpp:375
Reaction::setReversible
int setReversible(bool value)
Sets the value of the "reversible" attribute of this Reaction.
Definition: Reaction.cpp:607
ReactionGlyph
A glyph for an SBML reaction.
Definition: ReactionGlyph.h:249
SPECIES_ROLE_SUBSTRATE
@ SPECIES_ROLE_SUBSTRATE
Definition: SpeciesReferenceRole.h:56
GroupsModelPlugin
Extension of Model.
Definition: GroupsModelPlugin.h:60
SpeciesGlyph::setSpeciesId
void setSpeciesId(const std::string &id)
Sets the id of the associated species object.
Definition: SpeciesGlyph.cpp:201
Member
The Member class defines what objects are parts of a Group.
Definition: Member.h:79
SBMLDocument::createModel
Model * createModel(const std::string sid="")
Creates a new Model inside this SBMLDocument, and returns a pointer to it.
Definition: SBMLDocument.cpp:643
LayoutModelPlugin::createLayout
Layout * createLayout()
Creates a new layout object and adds it to the list of layout objects and returns it.
Definition: LayoutModelPlugin.cpp:475
LineSegment::setEnd
void setEnd(const Point *end)
Initializes the end point with a copy of the given Point object.
Definition: LineSegment.cpp:369
SpeciesReferenceGlyph::getCurve
Curve * getCurve()
Returns the curve object for the species reference glyph.
Definition: SpeciesReferenceGlyph.cpp:365
Reaction::setFast
int setFast(bool value)
Sets the value of the "fast" attribute of this Reaction.
Definition: Reaction.cpp:620
Model::createSpecies
Species * createSpecies()
Creates a new Species inside this Model and returns it.
Definition: Model.cpp:1590
SpeciesReferenceGlyph::setSpeciesGlyphId
void setSpeciesGlyphId(const std::string &speciesGlyphId)
Sets the id of the associated species glyph.
Definition: SpeciesReferenceGlyph.cpp:284
SimpleSpeciesReference::setId
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:210
Group
Representation of a group of SBML components.
Definition: Group.h:171
GroupsExtensionTypes.h
Definition of GroupsExtensionTypes.
Compartment::setId
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Compartment object.
Definition: Compartment.cpp:474
Layout::createTextGlyph
TextGlyph * createTextGlyph()
Creates a TextGlyph object, adds it to the end of the text glyph objects list and returns a pointer t...
Definition: Layout.cpp:1443
Reaction::createReactant
SpeciesReference * createReactant()
Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it.
Definition: Reaction.cpp:955
SpeciesReferenceGlyph::setSpeciesReferenceId
void setSpeciesReferenceId(const std::string &id)
Sets the id of the associated species reference.
Definition: SpeciesReferenceGlyph.cpp:304
Species::setConstant
int setConstant(bool value)
Sets the "constant" attribute of this Species object.
Definition: Species.cpp:824
CubicBezier::setBasePoint2
void setBasePoint2(const Point *p)
Initializes second base point with a copy of the given point.
Definition: CubicBezier.cpp:452
Compartment
An SBML compartment, where species are located.
Definition: Compartment.h:484
SpeciesGlyph
A glyph for an SBML species.
Definition: SpeciesGlyph.h:59
Layout::createReactionGlyph
ReactionGlyph * createReactionGlyph()
Creates a ReactionGlyph object, adds it to the end of the reaction glyph objects list and returns a p...
Definition: Layout.cpp:1412
Group::setId
virtual int setId(const std::string &id)
Sets the value of the "id" attribute of this Group.
Definition: Group.cpp:208
SimpleSpeciesReference::setSpecies
int setSpecies(const std::string &sid)
Sets the "species" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:192
Layout
The layout of a diagram of an SBML model.
Definition: Layout.h:783
Model
An SBML model.
Definition: Model.h:479
Species::setId
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Species.
Definition: Species.cpp:586
LayoutPkgNamespaces
SBMLNamespaces extension for the package.
Layout::setId
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Layout.
Definition: Layout.cpp:449
TextGlyph::setGraphicalObjectId
int setGraphicalObjectId(const std::string &id)
Sets the id of the associated graphical object.
Definition: TextGlyph.cpp:241
GroupsModelPlugin::createGroup
Group * createGroup()
Creates a new Group object, adds it to this GroupsModelPlugin object and returns the Group object cre...
Definition: GroupsModelPlugin.cpp:227
GraphicalObject::getId
virtual const std::string & getId() const
Returns the value of the "id" attribute of this GraphicalObject.
Definition: GraphicalObject.cpp:367
LayoutExtensionTypes.h
Include all SBML types of layout extension in a single header file.
CompartmentGlyph
A glyph for an SBML compartment.
Definition: CompartmentGlyph.h:54
BoundingBox
A bounding box for an item in a diagram.
Definition: BoundingBox.h:58
LineSegment
Representation of a line.
Definition: LineSegment.h:63
Reaction::createProduct
SpeciesReference * createProduct()
Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it.
Definition: Reaction.cpp:983
ReactionGlyph::setReactionId
int setReactionId(const std::string &id)
Sets the id of the associated reaction.
Definition: ReactionGlyph.cpp:319
LineSegment::setStart
void setStart(const Point *start)
Initializes the start point with a copy of the given Point object.
Definition: LineSegment.cpp:322
SBMLDocument::setPackageRequired
int setPackageRequired(const std::string &package, bool flag)
Sets the required attribute value of the given package extension.
Definition: SBMLDocument.cpp:1439
Reaction::setId
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Reaction.
Definition: Reaction.cpp:516
TextGlyph::setOriginOfTextId
int setOriginOfTextId(const std::string &orig)
Sets the id of the origin of text.
Definition: TextGlyph.cpp:261
Layout::setDimensions
void setDimensions(const Dimensions *dimensions)
Sets the dimensions of the layout.
Definition: Layout.cpp:515
ReactionGlyph::getCurve
const Curve * getCurve() const
Returns the curve object for the reaction glyph.
Definition: ReactionGlyph.cpp:447
SpeciesReference::setConstant
int setConstant(bool flag)
Sets the "constant" attribute of this SpeciesReference to the given boolean flag.
Definition: SpeciesReference.cpp:395
SBMLNamespaces
Set of SBML Level + Version + namespace triples.
Definition: SBMLNamespaces.h:139
Curve::createCubicBezier
CubicBezier * createCubicBezier()
Creates a new CubicBezier and adds it to the end of the list.
Definition: Curve.cpp:374
CompartmentGlyph::setCompartmentId
int setCompartmentId(const std::string &id)
Sets the id of the associated compartment.
Definition: CompartmentGlyph.cpp:218
Layout::createSpeciesGlyph
SpeciesGlyph * createSpeciesGlyph()
Creates a SpeciesGlyph object, adds it to the end of the species glyph objects list and returns a poi...
Definition: Layout.cpp:1396
Species::setCompartment
int setCompartment(const std::string &sid)
Sets the "compartment" attribute of this Species object.
Definition: Species.cpp:665
Compartment::getId
virtual const std::string & getId() const
Returns the value of the "id" attribute of this Compartment.
Definition: Compartment.cpp:238
TextGlyph
A glyph for a text label.
Definition: TextGlyph.h:59
Model::setId
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Model.
Definition: Model.cpp:717
Model::createCompartment
Compartment * createCompartment()
Creates a new Compartment inside this Model and returns it.
Definition: Model.cpp:1563
SpeciesReferenceGlyph
A glyph for an SBML species reference.
Definition: SpeciesReferenceGlyph.h:65
Member::setIdRef
int setIdRef(const std::string &idRef)
Sets the value of the "idRef" attribute of this Member.
Definition: Member.cpp:234
GraphicalObject::setBoundingBox
void setBoundingBox(const BoundingBox *bb)
Sets the boundingbox for the GraphicalObject.
Definition: GraphicalObject.cpp:470
SPECIES_ROLE_PRODUCT
@ SPECIES_ROLE_PRODUCT
Definition: SpeciesReferenceRole.h:57
Species
An SBML species – a pool of entities.
Definition: Species.h:423
Species::getId
virtual const std::string & getId() const
Returns the value of the "id" attribute of this Species.
Definition: Species.cpp:273
LIBSBML_CPP_NAMESPACE_USE
#define LIBSBML_CPP_NAMESPACE_USE
Definition: libsbml-namespace.h:67
SBMLDocument
Overall SBML container object.
Definition: SBMLDocument.h:342
SBase::getPlugin
SBasePlugin * getPlugin(const std::string &package)
Returns a plug-in object (extension interface) for an SBML Level&#160;3 package extension with the given p...
Definition: SBase.cpp:3460
Species::setBoundaryCondition
int setBoundaryCondition(bool value)
Sets the "boundaryCondition" attribute of this Species object.
Definition: Species.cpp:791
Species::setHasOnlySubstanceUnits
int setHasOnlySubstanceUnits(bool value)
Sets the "hasOnlySubstanceUnits" attribute of this Species object.
Definition: Species.cpp:771
writeSBML
int writeSBML(const SBMLDocument_t *d, const char *filename)
Writes the given SBML document d to the file named by filename.