public void test_internal_consistency_check_99916_rule() { SBMLDocument d = new SBMLDocument(2,4); long errors; Species s = new Species(2,4); d.setLevelAndVersion(1,2,false); Model m = d.createModel(); Compartment c = m.createCompartment(); c.setId("c"); s.setId("s"); s.setCompartment("c"); s.setConstant(true); m.addSpecies(s); Rule r = m.createAssignmentRule(); r.setVariable("s"); r.setFormula("2"); errors = d.checkInternalConsistency(); assertTrue( errors == 2 ); d = null; }
public void test_internal_consistency_check_99919() { SBMLDocument d = new SBMLDocument(2,4); long errors; Species s = new Species(2,4); d.setLevelAndVersion(1,2,false); Model m = d.createModel(); Compartment c = m.createCompartment(); c.setId("c"); s.setId("s"); s.setCompartment("c"); s.setHasOnlySubstanceUnits(true); m.addSpecies(s); errors = d.checkInternalConsistency(); assertTrue( errors == 0 ); d = null; }
public void test_SBMLConvert_convertToL1_Species_Concentration() { SBMLDocument d = new SBMLDocument(2,1); Model m = d.createModel(); string sid = "C"; Compartment c = new Compartment(2,1); Species s = new Species(2,1); c.setId(sid); c.setSize(1.2); m.addCompartment(c); s.setId( "s" ); s.setCompartment(sid); s.setInitialConcentration(2.34); m.addSpecies(s); assertTrue( d.setLevelAndVersion(1,2,true) == true ); Species s1 = m.getSpecies(0); assertTrue( s1 != null ); assertTrue(( "C" == s1.getCompartment() )); assertTrue( m.getCompartment( "C").getSize() == 1.2 ); assertTrue( s1.getInitialConcentration() == 2.34 ); assertTrue( s1.isSetInitialConcentration() == true ); d = null; }
public void test_internal_consistency_check_99916_reaction() { SBMLDocument d = new SBMLDocument(2,4); long errors; Species s = new Species(2,4); d.setLevelAndVersion(1,2,false); Model m = d.createModel(); Compartment c = m.createCompartment(); c.setId("c"); Reaction r = m.createReaction(); r.setId("r"); SpeciesReference sr = r.createReactant(); s.setId("s"); s.setCompartment("c"); s.setConstant(true); sr.setSpecies("s"); m.addSpecies(s); errors = d.checkInternalConsistency(); assertTrue( errors == 0 ); d = null; }
public void test_Species_L1() { Species s = new Species(1,2); assertEquals( false, (s.hasRequiredAttributes()) ); s.setId("s"); assertEquals( false, (s.hasRequiredAttributes()) ); s.setCompartment("c"); assertEquals( false, (s.hasRequiredAttributes()) ); s.setInitialAmount(2); assertEquals( true, s.hasRequiredAttributes() ); s = null; }
public void test_Species_copyConstructor() { Species o1 = new Species(2,4); o1.setId("c"); o1.setSpeciesType("c1"); assertTrue( o1.getId() == "c" ); assertEquals(o1.getSpeciesType(), "c1"); Species o2 = new Species(o1); assertTrue( o2.getId() == "c" ); assertEquals(o2.getSpeciesType(), "c1"); assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() ); o2 = null; o1 = null; }
public void test_Model_getSpecies() { Species s1 = new Species(2,4); Species s2 = new Species(2,4); s1.setId( "Glucose" ); s2.setId( "Glucose_6_P" ); s1.setCompartment( "c"); s2.setCompartment( "c"); M.addSpecies(s1); M.addSpecies(s2); assertTrue( M.getNumSpecies() == 2 ); s1 = M.getSpecies(0); s2 = M.getSpecies(1); assertTrue(( "Glucose" == s1.getId() )); assertTrue(( "Glucose_6_P" == s2.getId() )); }
public void test_Model_addSpecies5() { Model m = new Model(2,2); Species s = new Species(2,2); s.setId( "s"); s.setCompartment( "c"); Species s1 = new Species(2,2); s1.setId( "s"); s1.setCompartment( "c"); int i = m.addSpecies(s); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( m.getNumSpecies() == 1 ); i = m.addSpecies(s1); assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID ); assertTrue( m.getNumSpecies() == 1 ); s = null; s1 = null; m = null; }
public void test_Model_addSpecies() { Species s = new Species(2,4); s.setId( "s"); s.setCompartment( "c"); M.addSpecies(s); assertTrue( M.getNumSpecies() == 1 ); }
public void test_Model_getNumSpeciesWithBoundaryCondition() { Species s1 = new Species(2,4); Species s2 = new Species(2,4); Species s3 = new Species(2,4); s1.setId( "s1"); s2.setId( "s2"); s3.setId( "s3"); s1.setCompartment( "c1"); s2.setCompartment( "c2"); s3.setCompartment( "c3"); s1.setBoundaryCondition(true); s2.setBoundaryCondition(false); s3.setBoundaryCondition(true); assertTrue( M.getNumSpecies() == 0 ); assertTrue( M.getNumSpeciesWithBoundaryCondition() == 0 ); M.addSpecies(s1); assertTrue( M.getNumSpecies() == 1 ); assertTrue( M.getNumSpeciesWithBoundaryCondition() == 1 ); M.addSpecies(s2); assertTrue( M.getNumSpecies() == 2 ); assertTrue( M.getNumSpeciesWithBoundaryCondition() == 1 ); M.addSpecies(s3); assertTrue( M.getNumSpecies() == 3 ); assertTrue( M.getNumSpeciesWithBoundaryCondition() == 2 ); }
public void test_Species_setId4() { Species c = new Species(2,2); int i = c.setId( "cell"); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertEquals( true, c.isSetId() ); assertTrue(( "cell" == c.getId() )); i = c.setId(""); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertEquals( false, c.isSetId() ); c = null; }
public void test_Species_setId2() { Species c = new Species(2,2); int i = c.setId( "1cell"); assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE ); assertEquals( false, c.isSetId() ); c = null; }
public void test_Species_parent_add() { Species ia = new Species(2,4); ia.setId("s"); ia.setCompartment("c"); Model m = new Model(2,4); m.addSpecies(ia); ia = null; ListOf lo = m.getListOfSpecies(); assertTrue( lo == m.getSpecies(0).getParentSBMLObject() ); assertTrue( m == lo.getParentSBMLObject() ); }
public void test_Model_addSpecies2() { Model m = new Model(2,2); Species s = new Species(2,1); s.setId( "s"); s.setCompartment( "c"); int i = m.addSpecies(s); assertTrue( i == libsbml.LIBSBML_VERSION_MISMATCH ); assertTrue( m.getNumSpecies() == 0 ); s = null; m = null; }
public void test_Model_getSpeciesById() { Species s1 = new Species(2,4); Species s2 = new Species(2,4); s1.setId( "Glucose" ); s2.setId( "Glucose_6_P" ); s1.setCompartment( "c"); s2.setCompartment( "c"); M.addSpecies(s1); M.addSpecies(s2); assertTrue( M.getNumSpecies() == 2 ); assertTrue( M.getSpecies( "Glucose" ) != s1 ); assertTrue( M.getSpecies( "Glucose_6_P") != s2 ); assertTrue( M.getSpecies( "Glucose2" ) == null ); }
public void test_Model_addSpecies3() { Model m = new Model(2,2); Species s = new Species(1,2); s.setId( "s"); s.setCompartment( "c"); s.setInitialAmount(2); int i = m.addSpecies(s); assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH ); assertTrue( m.getNumSpecies() == 0 ); s = null; m = null; }
public void test_ListOf_copyConstructor() { ListOf o1 = new ListOf(); Species s = new Species(2,1); s.setId("species_1"); o1.append(s); s = null; ListOf o2 = new ListOf(o1); assertTrue( o2.size() == 1 ); assertTrue( ((Species) o2.get(0)).getId() == "species_1" ); assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() ); o2 = null; o1 = null; }
public void test_L3_Species_hasRequiredAttributes() { Species s = new Species(3,1); assertEquals( false, s.hasRequiredAttributes() ); s.setId( "id"); assertEquals( false, s.hasRequiredAttributes() ); s.setCompartment( "cell"); assertEquals( false, s.hasRequiredAttributes() ); s.setHasOnlySubstanceUnits(false); assertEquals( false, s.hasRequiredAttributes() ); s.setBoundaryCondition(false); assertEquals( false, s.hasRequiredAttributes() ); s.setConstant(false); assertEquals( true, s.hasRequiredAttributes() ); s = null; }
public void test_Species_ancestor_add() { Species ia = new Species(2,4); Model m = new Model(2,4); ia.setId("s"); ia.setCompartment("c"); m.addSpecies(ia); ia = null; ListOf lo = m.getListOfSpecies(); 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 ); }