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/**
* \file layout_example1.java
* \brief SBML Layout example
* \author Ralph Gauges
*
/* 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 Gaugess
* 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
*
* Contributor(s):
*/
import org.sbml.libsbml.*;
public class layout_example1
{
/**
* Loads the SWIG generated libsbml Java module when this class is
* loaded.
*/
static
{
System.loadLibrary("sbmlj");
}
public static Point createPoint(double x, double y)
{
Point point = new Point();
point.setX(x);
point.setY(y);
return point;
}
public static Dimensions createDimensions(double width, double height)
{
Dimensions dim = new Dimensions();
dim.setWidth(width);
dim.setHeight(height);
return dim;
}
public static BoundingBox createBoundingBox(String id, double x, double y, double width, double height)
{
BoundingBox bounds = new BoundingBox();
bounds.setId(id);
bounds.setX(x);
bounds.setY(y);
bounds.setWidth(width);
bounds.setHeight(height);
return bounds;
}
public static void main (String args[])
{
// create the document
SBMLDocument document=new SBMLDocument(2,1);
// ensure the layout api is enabled
document.enablePackage(LayoutExtension.getXmlnsL2(),"layout", true);
// create the Model
Model model=document.createModel("TestModel");
// 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");
SpeciesReference reference1=reaction1.createReactant();
reference1.setSpecies(species1.getId());
reference1.setId("SpeciesReference_1");
reaction1.setReversible(false);
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
LayoutModelPlugin mplugin = (LayoutModelPlugin)(model.getPlugin("layout"));
Layout layout=mplugin.createLayout();
layout.setId("Layout_1");
layout.setDimensions(createDimensions(400,220));
// create the CompartmentGlyph
CompartmentGlyph compartmentGlyph=layout.createCompartmentGlyph();
compartmentGlyph.setId("CompartmentGlyph_1");
compartmentGlyph.setCompartmentId(compartment.getId());
compartmentGlyph.setBoundingBox(createBoundingBox("bb1", 5, 5, 390, 210));
// create the SpeciesGlyphs
SpeciesGlyph speciesGlyph1=layout.createSpeciesGlyph();
speciesGlyph1.setId("SpeciesGlyph_1");
speciesGlyph1.setSpeciesId(species1.getId());
speciesGlyph1.setBoundingBox(createBoundingBox("bb2", 80, 26, 240, 24));
TextGlyph textGlyph1=layout.createTextGlyph();
textGlyph1.setId("TextGlyph_01");
textGlyph1.setBoundingBox(createBoundingBox("bbA", 92, 26, 228, 24));
textGlyph1.setOriginOfTextId(speciesGlyph1.getId());
textGlyph1.setGraphicalObjectId(speciesGlyph1.getId());
SpeciesGlyph speciesGlyph2=layout.createSpeciesGlyph();
speciesGlyph2.setId("SpeciesGlyph_2");
speciesGlyph2.setSpeciesId(species2.getId());
speciesGlyph2.setBoundingBox(createBoundingBox("bb3", 80, 170, 240, 24));
TextGlyph textGlyph2=layout.createTextGlyph();
textGlyph2.setId("TextGlyph_02");
textGlyph2.setBoundingBox(createBoundingBox("bbB", 92, 170, 228, 24));
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();
ls.setStart(createPoint(165,105));
ls.setEnd(createPoint(165, 115));
ReactionGlyph reactionGlyph2=layout.createReactionGlyph();
reactionGlyph2.setId("ReactionGlyph_1");
reactionGlyph2.setReactionId(reaction2.getId());
Curve reactionCurve2=reactionGlyph2.getCurve();
ls=reactionCurve2.createLineSegment();
ls.setStart(createPoint(235, 105));
ls.setEnd(createPoint(235,115));
// add the SpeciesReferenceGlyphs
SpeciesReferenceGlyph speciesReferenceGlyph1=reactionGlyph1.createSpeciesReferenceGlyph();
speciesReferenceGlyph1.setId("SpeciesReferenceGlyph_1");
speciesReferenceGlyph1.setSpeciesGlyphId(speciesGlyph1.getId());
speciesReferenceGlyph1.setSpeciesReferenceId(reference1.getId());
speciesReferenceGlyph1.setRole(libsbmlConstants.SPECIES_ROLE_SUBSTRATE);
Curve speciesReferenceCurve1=speciesReferenceGlyph1.getCurve();
CubicBezier cb=speciesReferenceCurve1.createCubicBezier();
cb.setStart(createPoint(165.0,105.0));
cb.setBasePoint1(createPoint(165.0,90.0));
cb.setBasePoint2(createPoint(165.0,90.0));
cb.setEnd(createPoint(195.0,60.0));
SpeciesReferenceGlyph speciesReferenceGlyph2=reactionGlyph1.createSpeciesReferenceGlyph();
speciesReferenceGlyph2.setId("SpeciesReferenceGlyph_2");
speciesReferenceGlyph2.setSpeciesGlyphId(speciesGlyph2.getId());
speciesReferenceGlyph2.setSpeciesReferenceId(reference2.getId());
speciesReferenceGlyph2.setRole(libsbmlConstants.SPECIES_ROLE_PRODUCT);
Curve speciesReferenceCurve2=speciesReferenceGlyph2.getCurve();
cb=speciesReferenceCurve2.createCubicBezier();
cb.setStart(createPoint(165.0,115.0));
cb.setBasePoint1(createPoint(165.0,130.0));
cb.setBasePoint2(createPoint(165.0,130.0));
cb.setEnd(createPoint(195.0,160.0));
SpeciesReferenceGlyph speciesReferenceGlyph3=reactionGlyph2.createSpeciesReferenceGlyph();
speciesReferenceGlyph3.setId("SpeciesReferenceGlyph_3");
speciesReferenceGlyph3.setSpeciesGlyphId(speciesGlyph2.getId());
speciesReferenceGlyph3.setSpeciesReferenceId(reference3.getId());
speciesReferenceGlyph3.setRole(libsbmlConstants.SPECIES_ROLE_SUBSTRATE);
Curve speciesReferenceCurve3=speciesReferenceGlyph3.getCurve();
cb=speciesReferenceCurve3.createCubicBezier();
cb.setStart(createPoint(235.0,115.0));
cb.setBasePoint1(createPoint(235.0,130.0));
cb.setBasePoint2(createPoint(235.0,130.0));
cb.setEnd(createPoint(205.0,160.0));
SpeciesReferenceGlyph speciesReferenceGlyph4=reactionGlyph2.createSpeciesReferenceGlyph();
speciesReferenceGlyph4.setId("SpeciesReferenceGlyph_4");
speciesReferenceGlyph4.setSpeciesGlyphId(speciesGlyph1.getId());
speciesReferenceGlyph4.setSpeciesReferenceId(reference4.getId());
speciesReferenceGlyph4.setRole(libsbmlConstants.SPECIES_ROLE_PRODUCT);
Curve speciesReferenceCurve4=speciesReferenceGlyph4.getCurve();
cb=speciesReferenceCurve4.createCubicBezier();
cb.setStart(createPoint(235.0,105.0));
cb.setBasePoint1(createPoint(235.0,90.0));
cb.setBasePoint2(createPoint(235.0,90.0));
cb.setEnd(createPoint(205.0,60.0));
libsbml.writeSBML(document,"TestModel1-java.xml");
System.gc();
}
}
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