public static void Main(string[] args)
{
ArraysPkgNamespaces arraysNs = new ArraysPkgNamespaces();
SBMLDocument doc = new SBMLDocument(arraysNs);
doc.setPackageRequired("arrays", true);
Model model = doc.createModel();
// create compartment
Compartment comp = model.createCompartment();
comp.setMetaId("dd");
comp.setId("s");
comp.setConstant(true);
// set dimensions
ArraysSBasePlugin compPlugin = (ArraysSBasePlugin)comp.getPlugin("arrays");
Dimension dim = compPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create species
Species species = model.createSpecies();
species.setId("A");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
ArraysSBasePlugin splugin = (ArraysSBasePlugin)species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
species = model.createSpecies();
species.setId("B");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
splugin = (ArraysSBasePlugin)species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
species = model.createSpecies();
species.setId("C");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
splugin = (ArraysSBasePlugin)species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create parameter
Parameter param = model.createParameter();
param.setId("n");
param.setValue(100);
param.setConstant(true);
// create reaction
Reaction reaction = model.createReaction();
reaction.setId("reaction1");
reaction.setReversible(false);
reaction.setFast(false);
ArraysSBasePlugin reactionPlugin = (ArraysSBasePlugin)reaction.getPlugin("arrays");
dim = reactionPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
SpeciesReference speciesRef = reaction.createReactant();
speciesRef.setSpecies("A");
speciesRef.setConstant(false);
ArraysSBasePlugin refPlugin = (ArraysSBasePlugin)speciesRef.getPlugin("arrays");
Index index = refPlugin.createIndex();
ASTNode ast = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ASTNode ci = new ASTNode(libsbml.AST_NAME);
ci.setName("A");
ast.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
ast.addChild(ci);
index.setMath(ast);
speciesRef = reaction.createProduct();
speciesRef.setSpecies("C");
speciesRef.setConstant(false);
refPlugin = (ArraysSBasePlugin)speciesRef.getPlugin("arrays");
index = refPlugin.createIndex();
ast = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("C");
ast.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
ast.addChild(ci);
index.setMath(ast);
libsbml.writeSBMLToFile(doc, "arrays1.xml");
}
public void test_RDFAnnotation_parseCVTerms()
{
XMLNode node = RDFAnnotationParser.parseCVTerms(m.getCompartment(0));
assertTrue(node.getNumChildren() == 1);
XMLNode rdf = node.getChild(0);
assertTrue(("RDF" == rdf.getName()));
assertTrue(("rdf" == rdf.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI()));
assertTrue(rdf.getNumChildren() == 1);
XMLNode desc = rdf.getChild(0);
assertTrue(("Description" == desc.getName()));
assertTrue(("rdf" == desc.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI()));
assertTrue(desc.getNumChildren() == 1);
XMLNode is1 = desc.getChild(0);
assertTrue(("is" == is1.getName()));
assertTrue(("bqbiol" == is1.getPrefix()));
assertTrue(is1.getNumChildren() == 1);
XMLNode Bag = is1.getChild(0);
assertTrue(("Bag" == Bag.getName()));
assertTrue(("rdf" == Bag.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI()));
assertTrue(Bag.getNumChildren() == 4);
XMLNode li = Bag.getChild(0);
assertTrue(("li" == li.getName()));
assertTrue(("rdf" == li.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI()));
assertTrue(li.getNumChildren() == 0);
XMLNode li1 = Bag.getChild(1);
assertTrue(("li" == li1.getName()));
assertTrue(("rdf" == li1.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI()));
assertTrue(li1.getNumChildren() == 0);
XMLNode li2 = Bag.getChild(2);
assertTrue(("li" == li2.getName()));
assertTrue(("rdf" == li2.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI()));
assertTrue(li2.getNumChildren() == 0);
XMLNode li3 = Bag.getChild(3);
assertTrue(("li" == li3.getName()));
assertTrue(("rdf" == li3.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI()));
assertTrue(li3.getNumChildren() == 0);
node = null;
XMLNode node1 = RDFAnnotationParser.parseCVTerms(null);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(null);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.parseCVTerms(m.getCompartment(2));
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(m.getCompartment(2));
assertTrue(node1 == null);
node1 = RDFAnnotationParser.parseCVTerms(m);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(m);
assertTrue(node1 == null);
Compartment c = new Compartment(3, 1);
c.setMetaId("_002");
node1 = RDFAnnotationParser.parseCVTerms(c);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(c);
assertTrue(node1 == null);
CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(23);
cv.addResource("http://myres");
c.addCVTerm(cv);
node1 = RDFAnnotationParser.createCVTerms(c);
assertTrue(node1 == null);
c = null;
Model m1 = new Model(3, 1);
m1.setMetaId("_002");
cv = new CVTerm(libsbml.MODEL_QUALIFIER);
cv.setModelQualifierType(23);
cv.addResource("http://myres");
m1.addCVTerm(cv);
node1 = RDFAnnotationParser.createCVTerms(m1);
assertTrue(node1 == null);
}
