private SBMLDocument createSBMLDocument() {
SBMLDocument doc = new SBMLDocument();
Model m = doc.createModel();
m.setId("model");
Compartment c = m.createCompartment();
c.setId("comp1");
c.setSize(1.0);
return doc;
}
public static void main(String[] args) {
if (args.length != 1) {
println("Usage: java printAnnotation filename");
System.exit(1);
}
String filename = args[0];
SBMLDocument document;
SBMLReader reader = new SBMLReader();
document = reader.readSBML(filename);
long errors = document.getNumErrors();
println("\nfilename: " + filename + "\n");
if (errors > 0) {
document.printErrors();
System.exit((int) errors);
}
/* Model */
Model m = document.getModel();
printAnnotation(m);
for (int i = 0; i < m.getNumReactions(); i++) {
Reaction re = m.getReaction(i);
printAnnotation(re);
/* SpeciesReference (Reactant) */
for (int j = 0; j < re.getNumReactants(); j++) {
SpeciesReference rt = re.getReactant(j);
if (rt.isSetAnnotation()) print(" ");
printAnnotation(rt, (rt.isSetSpecies() ? rt.getSpecies() : ""));
}
/* SpeciesReference (Product) */
for (int j = 0; j < re.getNumProducts(); j++) {
SpeciesReference rt = re.getProduct(j);
if (rt.isSetAnnotation()) print(" ");
printAnnotation(rt, (rt.isSetSpecies() ? rt.getSpecies() : ""));
}
/* ModifierSpeciesReference (Modifier) */
for (int j = 0; j < re.getNumModifiers(); j++) {
ModifierSpeciesReference md = re.getModifier(j);
if (md.isSetAnnotation()) print(" ");
printAnnotation(md, (md.isSetSpecies() ? md.getSpecies() : ""));
}
/* KineticLaw */
if (re.isSetKineticLaw()) {
KineticLaw kl = re.getKineticLaw();
if (kl.isSetAnnotation()) print(" ");
printAnnotation(kl);
/* Parameter */
for (int j = 0; j < kl.getNumParameters(); j++) {
Parameter pa = kl.getParameter(j);
if (pa.isSetAnnotation()) print(" ");
printAnnotation(pa);
}
}
}
/* Species */
for (int i = 0; i < m.getNumSpecies(); i++) {
Species sp = m.getSpecies(i);
printAnnotation(sp);
}
/* Compartment */
for (int i = 0; i < m.getNumCompartments(); i++) {
Compartment sp = m.getCompartment(i);
printAnnotation(sp);
}
/* FunctionDefinition */
for (int i = 0; i < m.getNumFunctionDefinitions(); i++) {
FunctionDefinition sp = m.getFunctionDefinition(i);
printAnnotation(sp);
}
/* UnitDefinition */
for (int i = 0; i < m.getNumUnitDefinitions(); i++) {
UnitDefinition sp = m.getUnitDefinition(i);
printAnnotation(sp);
}
/* Parameter */
for (int i = 0; i < m.getNumParameters(); i++) {
Parameter sp = m.getParameter(i);
printAnnotation(sp);
}
/* Rule */
for (int i = 0; i < m.getNumRules(); i++) {
Rule sp = m.getRule(i);
printAnnotation(sp);
}
/* InitialAssignment */
for (int i = 0; i < m.getNumInitialAssignments(); i++) {
InitialAssignment sp = m.getInitialAssignment(i);
printAnnotation(sp);
}
/* Event */
for (int i = 0; i < m.getNumEvents(); i++) {
Event sp = m.getEvent(i);
printAnnotation(sp);
/* Trigger */
if (sp.isSetTrigger()) {
Trigger tg = sp.getTrigger();
if (tg.isSetAnnotation()) print(" ");
printAnnotation(tg);
}
/* Delay */
if (sp.isSetDelay()) {
Delay dl = sp.getDelay();
if (dl.isSetAnnotation()) print(" ");
printAnnotation(dl);
}
/* EventAssignment */
for (int j = 0; j < sp.getNumEventAssignments(); j++) {
EventAssignment ea = sp.getEventAssignment(j);
if (ea.isSetAnnotation()) print(" ");
printAnnotation(ea);
}
}
/* SpeciesType */
for (int i = 0; i < m.getNumSpeciesTypes(); i++) {
SpeciesType sp = m.getSpeciesType(i);
printAnnotation(sp);
}
/* Constraint */
for (int i = 0; i < m.getNumConstraints(); i++) {
Constraint sp = m.getConstraint(i);
printAnnotation(sp);
}
System.exit((int) errors);
}
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();
}