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/**
* \file layout_example1_L3.java
* \brief SBML Layout example
* \author Ralph Gauges
* \author Akiya Jouraku
* \author Frank Bergmann (adapted to use libsbml-5 package version)
*
/* 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_L3 {
/**
* @param args
*/
public static void main(String[] args) {
System.loadLibrary("sbmlj");
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "layout") 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,"layout",1,"LAYOUT");
//
SBMLNamespaces sbmlns = new SBMLNamespaces (3, 1, "layout", 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 layout package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("layout",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(LayoutExtension::XmlnsL3V1V1,"layout");
//
// (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,
// and package version
//
// LayoutPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument document = new SBMLDocument (sbmlns);
// set the "required" attribute of layout package to "true"
document.setPkgRequired ("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
//
// set the LayoutPkgNamespaces for Level 3 Version1 Layout Version 1
//
LayoutPkgNamespaces layoutns = new LayoutPkgNamespaces (3, 1, 1);
//
// Get a LayoutModelPlugin 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.
//
SBasePlugin basePlugin = (model.getPlugin ("layout"));
LayoutModelPlugin mplugin = (LayoutModelPlugin)basePlugin;
if (mplugin == null) {
System.err.println("[Fatal Error] Layout Extension Level "
+ layoutns.getLevel () + " Version "
+ layoutns.getVersion () + " package version "
+ layoutns.getPackageVersion () + " is not registered.");
System.exit(1);
}
//
// Creates a Layout object via LayoutModelPlugin object.
//
Layout layout = mplugin.createLayout ();
layout.setId ("Layout_1");
Dimensions dim = new Dimensions (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 = new BoundingBox (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 = new BoundingBox (layoutns, "bb2", 80, 26, 240, 24);
speciesGlyph1.setBoundingBox (bb);
TextGlyph textGlyph1 = layout.createTextGlyph ();
textGlyph1.setId ("TextGlyph_01");
bb = new 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 = new BoundingBox (layoutns, "bb3", 80, 170, 240, 24);
speciesGlyph2.setBoundingBox (bb);
TextGlyph textGlyph2 = layout.createTextGlyph ();
textGlyph2.setId ("TextGlyph_02");
bb = new 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 = new Point (layoutns, 165, 105);
ls.setStart (p);
p = new Point (layoutns, 165, 115);
ls.setEnd (p);
ReactionGlyph reactionGlyph2 = layout.createReactionGlyph ();
reactionGlyph2.setId ("ReactionGlyph_2");
reactionGlyph2.setReactionId (reaction2.getId ());
Curve reactionCurve2 = reactionGlyph2.getCurve ();
ls = reactionCurve2.createLineSegment ();
p = new Point (layoutns, 235, 105);
ls.setStart (p);
p = new 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 (libsbml.SPECIES_ROLE_SUBSTRATE);
Curve speciesReferenceCurve1 = speciesReferenceGlyph1.getCurve ();
CubicBezier cb = speciesReferenceCurve1.createCubicBezier ();
p = new Point (layoutns, 165, 105);
cb.setStart (p);
p = new Point (layoutns, 165, 90);
cb.setBasePoint1 (p);
p = new Point (layoutns, 165, 90);
cb.setBasePoint2 (p);
p = new 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 (libsbml.SPECIES_ROLE_PRODUCT);
Curve speciesReferenceCurve2 = speciesReferenceGlyph2.getCurve ();
cb = speciesReferenceCurve2.createCubicBezier ();
p = new Point (layoutns, 165, 115);
cb.setStart (p);
p = new Point (layoutns, 165, 130);
cb.setBasePoint1 (p);
p = new Point (layoutns, 165, 130);
cb.setBasePoint2 (p);
p = new 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 (libsbml.SPECIES_ROLE_SUBSTRATE);
Curve speciesReferenceCurve3 = speciesReferenceGlyph3.getCurve ();
cb = speciesReferenceCurve3.createCubicBezier ();
p = new Point (layoutns, 235, 115);
cb.setStart (p);
p = new Point (layoutns, 235, 130);
cb.setBasePoint1 (p);
p = new Point (layoutns, 235, 130);
cb.setBasePoint2 (p);
p = new 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 (libsbml.SPECIES_ROLE_PRODUCT);
Curve speciesReferenceCurve4 = speciesReferenceGlyph4.getCurve ();
cb = speciesReferenceCurve4.createCubicBezier ();
p = new Point (layoutns, 235, 105);
cb.setStart (p);
p = new Point (layoutns, 235, 90);
cb.setBasePoint1 (p);
p = new Point (layoutns, 235, 90);
cb.setBasePoint2 (p);
p = new Point (layoutns, 205, 60);
cb.setEnd (p);
libsbml.writeSBML (document, "layout_example1_L3-java.xml");
}
}
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libSBML 5.18.0 |
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