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();
}
public static void main(String[] args) {
System.loadLibrary("sbmlj");
if (args.length != 2) {
System.out.println(" usage: addingEvidenceCodes_2 <input-filename> <output-filename>");
System.out.println(" Adds controlled vocabulary term to a species");
System.out.println();
System.exit(2);
}
SBMLDocument d = libsbml.readSBML(args[0]);
long errors = d.getNumErrors();
if (errors > 0) {
System.out.println("Read Error(s):");
d.printErrors();
System.out.println("Correct the above and re-run.");
} else {
long n = d.getModel().getNumSpecies();
if (n <= 0) {
System.out.println("Model has no species.\n Cannot add CV terms\n");
} else {
Species s = d.getModel().getSpecies(0);
/*
* check that the species has a metaid no CVTerms will be added
* if there is no metaid to reference
*/
if (!s.isSetMetaId()) s.setMetaId("metaid_0000052");
CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_OCCURS_IN);
cv1.addResource("urn:miriam:obo.go:GO%3A0005764");
s.addCVTerm(cv1);
// now create the additional annotation
// <rdf:Statement>
// <rdf:subject rdf:resource="#metaid_0000052"/>
// <rdf:predicate
// rdf:resource="http://biomodels.net/biology-qualifiers/occursIn"/>
// <rdf:object rdf:resource="urn:miriam:obo.go:GO%3A0005764"/>
// <bqbiol:isDescribedBy>
// <rdf:Bag>
// <rdf:li rdf:resource="urn:miriam:obo.eco:ECO%3A0000004"/>
// <rdf:li rdf:resource="urn:miriam:pubmed:7017716"/>
// </rdf:Bag>
// </bqbiol:isDescribedBy>
// </rdf:Statement>
/* attributes */
XMLAttributes blank_att = new XMLAttributes();
XMLAttributes resource_att = new XMLAttributes();
/* create the outer statement node */
XMLTriple statement_triple =
new XMLTriple("Statement", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
XMLToken statement_token = new XMLToken(statement_triple, blank_att);
XMLNode statement = new XMLNode(statement_token);
/* create the subject node */
XMLTriple subject_triple =
new XMLTriple("subject", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "#" + s.getMetaId());
XMLToken subject_token = new XMLToken(subject_triple, resource_att);
XMLNode subject = new XMLNode(subject_token);
/* create the predicate node */
XMLTriple predicate_triple =
new XMLTriple("predicate", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "http://biomodels.net/biology-qualifiers/occursIn");
XMLToken predicate_token = new XMLToken(predicate_triple, resource_att);
XMLNode predicate = new XMLNode(predicate_token);
/* create the object node */
XMLTriple object_triple =
new XMLTriple("object", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.go:GO%3A0005764");
XMLToken object_token = new XMLToken(object_triple, resource_att);
XMLNode object_ = new XMLNode(object_token);
/* create the bqbiol node */
XMLTriple bqbiol_triple =
new XMLTriple("isDescribedBy", "http://biomodels.net/biology-qualifiers/", "bqbiol");
XMLToken bqbiol_token = new XMLToken(bqbiol_triple, blank_att);
XMLNode bqbiol = new XMLNode(bqbiol_token);
/* create the bag node */
XMLTriple bag_triple =
new XMLTriple("Bag", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
XMLToken bag_token = new XMLToken(bag_triple, blank_att);
XMLNode bag = new XMLNode(bag_token);
/* create each li node and add to the bag */
XMLTriple li_triple =
new XMLTriple("li", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.eco:ECO%3A0000004");
XMLToken li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
XMLNode li = new XMLNode(li_token);
bag.addChild(li);
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:pubmed:7017716");
li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
li = new XMLNode(li_token);
bag.addChild(li);
/* add the bag to bqbiol */
bqbiol.addChild(bag);
/* add subject, predicate, object and bqbiol to statement */
statement.addChild(subject);
statement.addChild(predicate);
statement.addChild(object_);
statement.addChild(bqbiol);
/*
* create a top-level RDF element this will ensure correct
* merging
*/
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
xmlns.add("http://purl.org/dc/elements/1.1/", "dc");
xmlns.add("http://purl.org/dc/terms/", "dcterms");
xmlns.add("http://www.w3.org/2001/vcard-rdf/3.0#", "vCard");
xmlns.add("http://biomodels.net/biology-qualifiers/", "bqbiol");
xmlns.add("http://biomodels.net/model-qualifiers/", "bqmodel");
XMLTriple RDF_triple =
new XMLTriple("RDF", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
XMLToken RDF_token = new XMLToken(RDF_triple, blank_att, xmlns);
XMLNode annotation = new XMLNode(RDF_token);
/* add the staement node to the RDF node */
annotation.addChild(statement);
s.appendAnnotation(annotation);
libsbml.writeSBML(d, args[1]);
}
}
System.exit((int) errors);
}
