public void test_ListOf_append() { Model m = new Model(2,4); m.createCompartment(); ListOf loc = m.getListOfCompartments(); assertTrue( loc.size() == 1 ); SBase c = new Compartment(2,4); int i = loc.append(c); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( loc.size() == 2 ); SBase sp = new Species(2,4); i = loc.append(sp); assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT ); assertTrue( loc.size() == 2 ); m = null; sp = null; }
public void test_Model_L1V2() { Model m = new Model(1,2); assertEquals( false, (m.hasRequiredElements()) ); m.createCompartment(); assertEquals( true, m.hasRequiredElements() ); m = 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_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_Compartment_parent_create() { Model m = new Model(2,4); Compartment c = m.createCompartment(); ListOf lo = m.getListOfCompartments(); assertTrue( lo == m.getCompartment(0).getParentSBMLObject() ); assertTrue( lo == c.getParentSBMLObject() ); assertTrue( m == lo.getParentSBMLObject() ); }
public void test_Compartment_ancestor_create() { Model m = new Model(2,4); Compartment c = m.createCompartment(); ListOf lo = m.getListOfCompartments(); assertTrue( c.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( c.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ); assertTrue( c.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( c.getAncestorOfType(libsbml.SBML_EVENT) == null ); Compartment obj = m.getCompartment(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_createCompartment() { Model m = new Model(2,2); Compartment p = m.createCompartment(); assertTrue( m.getNumCompartments() == 1 ); assertTrue( (p).getLevel() == 2 ); assertTrue( (p).getVersion() == 2 ); m = null; }
public void test_internal_consistency_check_99904_model() { SBMLDocument d = new SBMLDocument(2,4); long errors; d.setLevelAndVersion(1,2,false); Model m = new Model(2,4); Compartment c = m.createCompartment(); c.setId("cc"); m.setMetaId("mmm"); d.setModel(m); errors = d.checkInternalConsistency(); assertTrue( errors == 1 ); assertTrue( d.getError(0).getErrorId() == 20201 ); d = null; }
public void test_SBML_C_parseL3Formula_modelPresent3() { Model model = new Model(3,1); Compartment p = model.createCompartment(); p.setId( "NaN");; ASTNode r = libsbml.parseL3FormulaWithModel("NaN", model); assertTrue( r.getType() == libsbml.AST_NAME ); assertTrue(( "NaN" == r.getName() )); assertTrue( r.getNumChildren() == 0 ); r = null; }
public void test_SBMLDocument_setModel2() { SBMLDocument d = new SBMLDocument(2,2); Model m1 = new Model(1,2); m1.createCompartment(); int i = d.setModel(m1); assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH ); assertTrue( d.getModel() == null ); d = 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; }