libSBML C++ API  5.18.0
example1.cpp

An example layout.

/**
* @file example1.cpp
* @brief SBML Layout example
* @author Ralph Gauges
* @author Akiya Jouraku (Modified this file for layout package of SBML Level 3
* in libSBML 5)
*
* Copyright 2004 European Media Laboratories Research gGmbH
*
* 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; either version 2.1 of the License, or
* any later version.
*
* This library is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
* MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
* documentation provided hereunder is on an "as is" basis, and the
* European Media Laboratories Research gGmbH have no obligations to
* provide maintenance, support, updates, enhancements or modifications.
* In no event shall the European Media Laboratories Research gGmbH be
* liable to any party for direct, indirect, special, incidental or
* consequential damages, including lost profits, arising out of the use of
* this software and its documentation, even if the European Media
* Laboratories Research gGmbH have been advised of the possibility of such
* damage. See the GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this library; if not, write to the Free Software Foundation,
* Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
* The original code contained here was initially developed by:
*
* Ralph Gauges
* Bioinformatics Group
* European Media Laboratories Research gGmbH
* Schloss-Wolfsbrunnenweg 31c
* 69118 Heidelberg
* Germany
*
* http://www.eml-research.de/english/Research/BCB/
* mailto:ralph.gauges@eml-r.villa-bosch.de
*/
#include "sbml/Model.h"
#include "sbml/Species.h"
#include "sbml/Reaction.h"
#if (!defined LIBSBML_HAS_PACKAGE_LAYOUT)
#error "This example requires libSBML to be built with the layout extension."
#endif
int main(int argc, char** argv)
{
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name.
//
SBMLNamespaces sbmlns(2, 4);
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with the following other style.
//
// (2) Creates a LayoutPkgNamespaces object (SBMLNamespace derived class
// for layout package. The class is basically used for createing an
// SBase derived objects belonging to the layout package) with the
// given SBML level, version. (Package version is not required by
// Layout extension of SBML Level 2)
//
// LayoutPkgNamespaces sbmlns(2, 4);
//
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
// create the Model
Model* model = document->createModel();
model->setId("TestModel");
document->setModel(model);
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("Compartment_1");
// create the Species
Species* species1 = model->createSpecies();
species1->setId("Species_1");
species1->setCompartment(compartment->getId());
Species* species2 = model->createSpecies();
species2->setId("Species_2");
species2->setCompartment(compartment->getId());
// create the Reactions
Reaction* reaction1 = model->createReaction();
reaction1->setId("Reaction_1");
reaction1->setReversible(false);
SpeciesReference* reference1 = reaction1->createReactant();
reference1->setSpecies(species1->getId());
reference1->setId("SpeciesReference_1");
SpeciesReference* reference2 = reaction1->createProduct();
reference2->setSpecies(species2->getId());
reference2->setId("SpeciesReference_2");
Reaction* reaction2 = model->createReaction();
reaction2->setId("Reaction_2");
reaction2->setReversible(false);
SpeciesReference* reference3 = reaction2->createReactant();
reference3->setSpecies(species2->getId());
reference3->setId("SpeciesReference_3");
SpeciesReference* reference4 = reaction2->createProduct();
reference4->setSpecies(species1->getId());
reference4->setId("SpeciesReference_4");
// create the Layout
LayoutPkgNamespaces layoutns(2, 4);
= static_cast<LayoutModelPlugin*>(model->getPlugin("layout"));
Layout* layout = mplugin->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);
writeSBML(document,"layout_example1_L2.xml");
delete document;
}