protected override void Context() { base.Context(); _sbmlModel = new Model(3, 1); _sbmlInformation = new SBMLInformation(); //one compartment reaction _reaction = _sbmlModel.createReaction(); _reaction.setId("r1"); //reaction partner var s1 = _sbmlModel.createSpecies(); s1.setId("s1"); s1.setCompartment("default"); var s2 = _sbmlModel.createSpecies(); s2.setId("s2"); s2.setCompartment("default"); var m = new MoleculeInformation(s1); var m2 = new MoleculeInformation(s2); _sbmlInformation.MoleculeInformation.Add(m); _sbmlInformation.MoleculeInformation.Add(m2); //SRef var s1Ref = _reaction.createReactant(); s1Ref.setSpecies("s1"); s1Ref.setStoichiometry(1); var s2Ref = _reaction.createProduct(); s2Ref.setSpecies("s2"); s2Ref.setStoichiometry(2); _reaction.addProduct(s2Ref); //Modifier var mod = _reaction.createModifier(); mod.setId("mod"); mod.setName("mod"); mod.setSpecies("s1"); //Kinetic Law var kl = _reaction.createKineticLaw(); kl.setId("kl"); kl.setMath(libsbml.parseFormula("2*3")); }
public void test_Model_L1V1() { Model m = new Model(1,1); assertEquals( false, (m.hasRequiredElements()) ); m.createCompartment(); assertEquals( false, (m.hasRequiredElements()) ); m.createSpecies(); assertEquals( false, (m.hasRequiredElements()) ); m.createReaction(); assertEquals( true, m.hasRequiredElements() ); m = null; }
public void test_create_l1v1_units() { SBMLDocument d; Model m; Compartment c; KineticLaw kl; Parameter p; Reaction r; Species s; SpeciesReference sr; Unit u; UnitDefinition ud; d = new SBMLDocument(); m = new Model(2,4); d.setModel(m); ud = m.createUnitDefinition(); ud.setName( "substance"); u = m.createUnit(); u.setKind(libsbml.UNIT_KIND_MOLE); u.setScale(-3); ud = m.createUnitDefinition(); ud.setName( "mls"); u = m.createUnit(); u.setKind(libsbml.UNIT_KIND_MOLE); u.setScale(-3); u = m.createUnit(); u.setKind(libsbml.UNIT_KIND_LITER); u.setExponent(-1); u = m.createUnit(); u.setKind(libsbml.UNIT_KIND_SECOND); u.setExponent(-1); c = m.createCompartment(); c.setName( "cell"); s = m.createSpecies(); s.setName( "x0"); s.setCompartment( "cell"); s.setInitialAmount(1); s = m.createSpecies(); s.setName( "x1"); s.setCompartment( "cell"); s.setInitialAmount(1); s = m.createSpecies(); s.setName( "s1"); s.setCompartment( "cell"); s.setInitialAmount(1); s = m.createSpecies(); s.setName( "s2"); s.setCompartment( "cell"); s.setInitialAmount(1); p = m.createParameter(); p.setName( "vm"); p.setUnits( "mls"); p.setValue(2); p = m.createParameter(); p.setName( "km"); p.setValue(2); r = m.createReaction(); r.setName( "v1"); sr = m.createReactant(); sr.setSpecies( "x0"); sr = m.createProduct(); sr.setSpecies( "s1"); kl = m.createKineticLaw(); kl.setFormula( "(vm * s1)/(km + s1)"); r = m.createReaction(); r.setName( "v2"); sr = m.createReactant(); sr.setSpecies( "s1"); sr = m.createProduct(); sr.setSpecies( "s2"); kl = m.createKineticLaw(); kl.setFormula( "(vm * s2)/(km + s2)"); r = m.createReaction(); r.setName( "v3"); sr = m.createReactant(); sr.setSpecies( "s2"); sr = m.createProduct(); sr.setSpecies( "x1"); kl = m.createKineticLaw(); kl.setFormula( "(vm * s1)/(km + s1)"); d = null; }
public void test_Species_parent_create() { Model m = new Model(2,4); Species s = m.createSpecies(); ListOf lo = m.getListOfSpecies(); assertTrue( lo == s.getParentSBMLObject() ); assertTrue( lo == m.getSpecies(0).getParentSBMLObject() ); assertTrue( m == lo.getParentSBMLObject() ); }
public void test_Species_ancestor_create() { Model m = new Model(2,4); Species s = m.createSpecies(); ListOf lo = m.getListOfSpecies(); assertTrue( s.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( s.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ); assertTrue( s.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( s.getAncestorOfType(libsbml.SBML_EVENT) == null ); Species obj = m.getSpecies(0); assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ); assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( obj.getAncestorOfType(libsbml.SBML_EVENT) == null ); }
public void test_Model_createSpecies() { Model m = new Model(2,2); Species p = m.createSpecies(); assertTrue( m.getNumSpecies() == 1 ); assertTrue( (p).getLevel() == 2 ); assertTrue( (p).getVersion() == 2 ); m = null; }
public void test_SBML_C_parseL3Formula_modelPresent2() { Model model = new Model(3,1); Species p = model.createSpecies(); p.setId( "true");; ASTNode r = libsbml.parseL3FormulaWithModel("true", model); assertTrue( r.getType() == libsbml.AST_NAME ); assertTrue(( "true" == r.getName() )); assertTrue( r.getNumChildren() == 0 ); r = null; }
public void test_SBMLDocument_clone() { SBMLDocument o1 = new SBMLDocument(); o1.setLevelAndVersion(1,1,false); Model m = new Model(1,1); m.createCompartment(); m.createSpecies(); m.createReaction(); m.setId("foo"); o1.setModel(m); assertTrue( o1.getLevel() == 1 ); assertTrue( o1.getVersion() == 1 ); assertTrue( o1.getModel().getId() == "foo" ); assertTrue( o1.getModel().getLevel() == 1 ); assertTrue( o1.getModel().getVersion() == 1 ); assertTrue( o1.getModel().getSBMLDocument() == o1 ); SBMLDocument o2 = o1.clone(); assertTrue( o2.getLevel() == 1 ); assertTrue( o2.getVersion() == 1 ); assertTrue( o2.getModel().getId() == "foo" ); assertTrue( o2.getModel().getLevel() == 1 ); assertTrue( o2.getModel().getVersion() == 1 ); assertTrue( o2.getModel().getSBMLDocument() == o2 ); o2 = null; o1 = null; }