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_SpeciesReference_Modifier_parent_create_model() { Model m = new Model(2,4); Reaction r = m.createReaction(); ModifierSpeciesReference sr = m.createModifier(); ListOf lo = r.getListOfModifiers(); assertTrue( lo == sr.getParentSBMLObject() ); assertTrue( lo == r.getModifier(0).getParentSBMLObject() ); assertTrue( r == lo.getParentSBMLObject() ); }
public void test_Reaction_parent_create() { Model m = new Model(2,4); Reaction r = m.createReaction(); ListOf lo = m.getListOfReactions(); assertTrue( lo == m.getReaction(0).getParentSBMLObject() ); assertTrue( lo == r.getParentSBMLObject() ); assertTrue( m == lo.getParentSBMLObject() ); }
public void test_KineticLaw_parent_create_model() { Model m = new Model(2,4); Reaction r = m.createReaction(); KineticLaw kl = r.createKineticLaw(); assertTrue( r == kl.getParentSBMLObject() ); assertTrue( r == r.getKineticLaw().getParentSBMLObject() ); r = null; }
public void test_KineticLaw_Parameter_parent_create_model() { Model m = new Model(2,4); Reaction r = m.createReaction(); KineticLaw kl = m.createKineticLaw(); Parameter p = m.createKineticLawParameter(); assertTrue( kl.getNumParameters() == 1 ); ListOfParameters lop = kl.getListOfParameters(); assertTrue( r == kl.getParentSBMLObject() ); assertTrue( kl == lop.getParentSBMLObject() ); assertTrue( lop == p.getParentSBMLObject() ); assertTrue( lop == kl.getParameter(0).getParentSBMLObject() ); kl = null; }
public void test_SpeciesReference_Reactant_ancestor_create_model() { Model m = new Model(2,4); Reaction r = m.createReaction(); SpeciesReference sr = m.createReactant(); ListOf lo = r.getListOfReactants(); assertTrue( sr.getAncestorOfType(libsbml.SBML_REACTION) == r ); assertTrue( sr.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ); assertTrue( sr.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( sr.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( sr.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null ); SpeciesReference obj = r.getReactant(0); assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r ); assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ); assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null ); }
public void test_SBML_C_parseL3Formula_modelPresent4() { Model model = new Model(3,1); Reaction p = model.createReaction(); p.setId( "pi");; ASTNode r = libsbml.parseL3FormulaWithModel("pi", model); assertTrue( r.getType() == libsbml.AST_NAME ); assertTrue(( "pi" == r.getName() )); assertTrue( r.getNumChildren() == 0 ); r = 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_KineticLaw_ancestor_create_model() { Model m = new Model(2,4); Reaction r = m.createReaction(); KineticLaw kl = r.createKineticLaw(); assertTrue( kl.getAncestorOfType(libsbml.SBML_REACTION) == r ); assertTrue( kl.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( kl.getAncestorOfType(libsbml.SBML_DELAY) == null ); assertTrue( kl.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); KineticLaw obj = r.getKineticLaw(); assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r ); assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( obj.getAncestorOfType(libsbml.SBML_DELAY) == null ); r = null; }
public void test_Model_createReaction() { Model m = new Model(2,2); Reaction p = m.createReaction(); assertTrue( m.getNumReactions() == 1 ); assertTrue( (p).getLevel() == 2 ); assertTrue( (p).getVersion() == 2 ); m = null; }
public void test_Model_createReactant() { Model m = new Model(2,2); Reaction p = m.createReaction(); SpeciesReference sr = m.createReactant(); assertTrue( p.getNumReactants() == 1 ); assertTrue( (sr).getLevel() == 2 ); assertTrue( (sr).getVersion() == 2 ); m = null; }
public void test_Model_createKineticLawParameters() { Model m = new Model(2,2); Reaction r = m.createReaction(); KineticLaw kl = m.createKineticLaw(); Parameter p = m.createKineticLawParameter(); assertTrue( r.isSetKineticLaw() == true ); assertTrue( kl.getNumParameters() == 1 ); assertTrue( (p).getLevel() == 2 ); assertTrue( (p).getVersion() == 2 ); m = null; }
public void test_Model_createKineticLaw() { Model m = new Model(2,2); Reaction p = m.createReaction(); KineticLaw kl = m.createKineticLaw(); assertTrue( p.isSetKineticLaw() == true ); assertTrue( (kl).getLevel() == 2 ); assertTrue( (kl).getVersion() == 2 ); m = null; }
public void test_SBML_C_parseL3Formula_modelPresent6() { Model model = new Model(3,1); Reaction p = model.createReaction(); SpeciesReference sr = p.createProduct(); sr.setId( "AVOGADRO");; ASTNode r = libsbml.parseL3FormulaWithModel("avogadro", model); assertTrue( r.getType() == libsbml.AST_NAME_AVOGADRO ); assertTrue(( "avogadro" == r.getName() )); assertTrue( r.getNumChildren() == 0 ); r = null; }
public void test_SpeciesReference_Reactant_parent_create_model() { Model m = new Model(2,4); Reaction r = m.createReaction(); SpeciesReference sr = m.createReactant(); ListOf lo = r.getListOfReactants(); assertTrue( lo == r.getReactant(0).getParentSBMLObject() ); assertTrue( lo == sr.getParentSBMLObject() ); assertTrue( r == lo.getParentSBMLObject() ); }
public void test_KineticLaw_Parameter_ancestor_create_model() { Model m = new Model(2,4); Reaction r = m.createReaction(); KineticLaw kl = m.createKineticLaw(); Parameter p = m.createKineticLawParameter(); assertTrue( kl.getNumParameters() == 1 ); ListOfParameters lop = kl.getListOfParameters(); assertTrue( p.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl ); assertTrue( p.getAncestorOfType(libsbml.SBML_LIST_OF) == lop ); assertTrue( p.getAncestorOfType(libsbml.SBML_REACTION) == r ); assertTrue( p.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( p.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( p.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null ); Parameter obj = kl.getParameter(0); assertTrue( obj.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl ); assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lop ); assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r ); assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null ); kl = null; }
public void test_Reaction_ancestor_create() { Model m = new Model(2,4); Reaction r = m.createReaction(); ListOf lo = m.getListOfReactions(); assertTrue( r.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( r.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ); assertTrue( r.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( r.getAncestorOfType(libsbml.SBML_EVENT) == null ); Reaction obj = m.getReaction(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_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_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; }