public void setUp() { string filename = "../../annotation/test/test-data/annotationL3.xml"; d = libsbml.readSBML(filename); m = d.getModel(); c = m.getCompartment(0); }
public void test_SBMLConvertStrict_convertNonStrictSBO() { SBMLDocument d = new SBMLDocument(2,4); Model m = d.createModel(); Compartment c = m.createCompartment(); c.setId( "c"); c.setConstant(false); (c).setSBOTerm(64); assertTrue( d.setLevelAndVersion(2,3,true) == false ); assertTrue( d.getLevel() == 2 ); assertTrue( d.getVersion() == 4 ); assertTrue( d.setLevelAndVersion(2,2,true) == false ); assertTrue( d.getLevel() == 2 ); assertTrue( d.getVersion() == 4 ); assertTrue( d.setLevelAndVersion(2,1,true) == true ); assertTrue( d.getLevel() == 2 ); assertTrue( d.getVersion() == 1 ); Compartment c1 = d.getModel().getCompartment(0); assertTrue( (c1).getSBOTerm() == -1 ); assertTrue( d.setLevelAndVersion(1,2,true) == true ); assertTrue( d.getLevel() == 1 ); assertTrue( d.getVersion() == 2 ); Compartment c2 = d.getModel().getCompartment(0); assertTrue( (c2).getSBOTerm() == -1 ); d = null; }
public void test_SBMLConvertStrict_convertL1ParamRule() { SBMLDocument d = new SBMLDocument(1,2); Model m = d.createModel(); Compartment c = m.createCompartment(); c.setId( "c"); Parameter p = m.createParameter(); p.setId( "p"); Parameter p1 = m.createParameter(); p1.setId( "p1"); ASTNode math = libsbml.parseFormula("p"); Rule ar = m.createAssignmentRule(); ar.setVariable( "p1"); ar.setMath(math); ar.setUnits( "mole"); assertTrue( d.setLevelAndVersion(2,1,true) == true ); assertTrue( d.getLevel() == 2 ); assertTrue( d.getVersion() == 1 ); Rule r1 = d.getModel().getRule(0); assertTrue( r1.getUnits() == "" ); d = null; }
public void test_ReadSBML_notes() { Reaction r; KineticLaw kl; string s = wrapSBML_L2v3("<listOfReactions>" + "<reaction name='J1'>" + " <kineticLaw formula='k1*X0'>" + " <notes>This is a test note.</notes>" + " <listOfParameters>" + " <parameter name='k1' value='0'/>" + " </listOfParameters>" + " </kineticLaw>" + "</reaction>" + "</listOfReactions>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); r = M.getReaction(0); kl = r.getKineticLaw(); assertTrue( kl.getNotes() != null ); string notes = kl.getNotes().getChild(0).getCharacters(); assertTrue( ( "This is a test note." != notes ) == false ); }
public void test_Model_ancestor_create() { SBMLDocument d = new SBMLDocument(); Model m = d.createModel(); assertTrue( m.getAncestorOfType(libsbml.SBML_DOCUMENT) == d ); Model obj = d.getModel(); assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == d ); d = null; }
public void test_ReadSBML_line_col_numbers() { //setXMLParser(); SBase sb; string s = "<?xml version='1.0' encoding='UTF-8'?>\n" + "<sbml xmlns='http://www.sbml.org/sbml/level2' level='2' version='1'>\n" + " <model id='testModel' name='testModel'>\n" + " <listOfReactions> <reaction/> </listOfReactions>\n" + " </model>\n" + "</sbml>\n"; D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M != null ); sb = M; sb = M.getListOfReactions(); sb = M.getReaction(0); }
public void test_SBMLConvert_convertToL3_stoichiometryMath() { SBMLDocument d = new SBMLDocument(2,1); Model m = d.createModel(); Compartment c = m.createCompartment(); c.setId( "c" ); Species s = m.createSpecies(); s.setId( "s"); s.setCompartment( "c"); Reaction r = m.createReaction(); SpeciesReference sr = r.createReactant(); sr.setSpecies( "s"); StoichiometryMath sm = sr.createStoichiometryMath(); ASTNode ast = libsbml.parseFormula("c*2"); sm.setMath(ast); assertTrue( m.getNumRules() == 0 ); assertTrue( sr.isSetId() == false ); assertTrue( d.setLevelAndVersion(3,1,false) == true ); m = d.getModel(); r = m.getReaction(0); sr = r.getReactant(0); assertTrue( m.getNumRules() == 1 ); assertTrue( sr.isSetId() == true ); Rule rule = m.getRule(0); assertTrue( sr.getId() == rule.getVariable() ); d = null; }
public void test_SBMLConvert_convertToL2v4_DuplicateAnnotations_model() { SBMLDocument d = new SBMLDocument(2,1); Model m = d.createModel(); string annotation = "<rdf/>\n<rdf/>"; int i = (m).setAnnotation(annotation); assertTrue( d.getLevel() == 2 ); assertTrue( d.getVersion() == 1 ); assertTrue( (m).getAnnotation().getNumChildren() == 2 ); assertTrue( d.setLevelAndVersion(2,4,true) == true ); assertTrue( d.getLevel() == 2 ); assertTrue( d.getVersion() == 4 ); m = d.getModel(); assertTrue( (m).getAnnotation().getNumChildren() == 1 ); d = null; }
public void test_SBMLDocument_setModel3() { SBMLDocument d = new SBMLDocument(2,2); Model m1 = new Model(2,2); int i = d.setModel(m1); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( d.getModel() != null ); d = null; }
public void test_SBMLDocument_setModel() { SBMLDocument d = new SBMLDocument(2,4); Model m1 = new Model(2,4); Model m2 = new Model(2,4); Model mout; assertTrue( d.getModel() == null ); int i = d.setModel(m1); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); mout = d.getModel(); assertTrue( mout != null ); assertTrue( mout != m1 ); i = d.setModel(d.getModel()); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); mout = d.getModel(); assertTrue( mout != null ); assertTrue( mout != m1 ); i = d.setModel(m2); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); mout = d.getModel(); assertTrue( mout != null ); assertTrue( mout != m2 ); d = null; }
public void test_Model_parent_add() { SBMLDocument d = new SBMLDocument(2,4); Model m = new Model(2,4); d.setModel(m); assertTrue( d == d.getModel().getParentSBMLObject() ); d = null; }
public void test_ReadSBML_Model() { string s = wrapXML("<sbml level='1' version='1'>" + " <model name='testModel'></model>" + "</sbml>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue(( "testModel" == M.getId() )); }
public void test_ReadSBML_Model_L2() { string s = wrapXML("<sbml level='2' version='1'>" + " <model id='testModel'> </model>" + "</sbml>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertEquals( true, M.isSetId() ); assertEquals( false, M.isSetName() ); assertTrue(( "testModel" == M.getId() )); }
public void test_ReadSBML_metaid_Unit() { SBase sb; UnitDefinition ud; string s = wrapSBML_L2v1("<listOfUnitDefinitions>" + " <unitDefinition metaid='ud'>" + " <listOfUnits metaid='lou'>" + " <unit metaid='u'/>" + " </listOfUnits>" + " </unitDefinition>" + "</listOfUnitDefinitions>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M != null ); ud = M.getUnitDefinition(0); sb = ud; assertEquals( true, sb.isSetMetaId() ); assertTrue(( "ud" == sb.getMetaId() )); sb = ud.getListOfUnits(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lou" == sb.getMetaId() )); sb = ud.getUnit(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "u" == sb.getMetaId() )); }
public void test_ReadSBML_metaid_Reaction() { SBase sb; Reaction r; string s = wrapSBML_L2v1("<listOfReactions>" + " <reaction metaid='r'>" + " <listOfReactants metaid='lor'>" + " <speciesReference metaid='sr1'/>" + " </listOfReactants>" + " <listOfProducts metaid='lop'>" + " <speciesReference metaid='sr2'/>" + " </listOfProducts>" + " <listOfModifiers metaid='lom'>" + " <modifierSpeciesReference metaid='msr'/>" + " </listOfModifiers>" + " <kineticLaw metaid='kl'/>" + " </reaction>" + "</listOfReactions>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M != null ); r = M.getReaction(0); sb = r; assertEquals( true, sb.isSetMetaId() ); assertTrue(( "r" == sb.getMetaId() )); sb = r.getListOfReactants(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lor" == sb.getMetaId() )); sb = r.getReactant(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "sr1" == sb.getMetaId() )); sb = r.getListOfProducts(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lop" == sb.getMetaId() )); sb = r.getProduct(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "sr2" == sb.getMetaId() )); sb = r.getListOfModifiers(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lom" == sb.getMetaId() )); sb = r.getModifier(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "msr" == sb.getMetaId() )); sb = r.getKineticLaw(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "kl" == sb.getMetaId() )); }
public void test_ReadSBML_metaid_ListOf() { SBase sb; string s = wrapSBML_L2v1("<listOfFunctionDefinitions metaid='lofd'/>" + "<listOfUnitDefinitions metaid='loud'/>" + "<listOfCompartments metaid='loc'/>" + "<listOfSpecies metaid='los'/>" + "<listOfParameters metaid='lop'/>" + "<listOfRules metaid='lor'/>" + "<listOfReactions metaid='lorx'/>" + "<listOfEvents metaid='loe'/>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M != null ); sb = M.getListOfFunctionDefinitions(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lofd" == sb.getMetaId() )); sb = M.getListOfUnitDefinitions(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "loud" == sb.getMetaId() )); sb = M.getListOfCompartments(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "loc" == sb.getMetaId() )); sb = M.getListOfSpecies(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "los" == sb.getMetaId() )); sb = M.getListOfParameters(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lop" == sb.getMetaId() )); sb = M.getListOfRules(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lor" == sb.getMetaId() )); sb = M.getListOfReactions(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "lorx" == sb.getMetaId() )); sb = M.getListOfEvents(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "loe" == sb.getMetaId() )); }
public void test_ReadSBML_metaid_Event() { SBase sb; Event e; string s = wrapSBML_L2v1("<listOfEvents>" + " <event metaid='e'>" + " <listOfEventAssignments metaid='loea'>" + " <eventAssignment metaid='ea'/>" + " </listOfEventAssignments>" + " </event>" + "</listOfEvents>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M != null ); e = M.getEvent(0); sb = e; assertEquals( true, sb.isSetMetaId() ); assertTrue(( "e" == sb.getMetaId() )); sb = e.getListOfEventAssignments(); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "loea" == sb.getMetaId() )); sb = e.getEventAssignment(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "ea" == sb.getMetaId() )); }
public void test_ReadSBML_metaid() { SBase sb; string s = wrapSBML_L2v1("<listOfFunctionDefinitions>" + " <functionDefinition metaid='fd'/>" + "</listOfFunctionDefinitions>" + "<listOfUnitDefinitions>" + " <unitDefinition metaid='ud'/>" + "</listOfUnitDefinitions>" + "<listOfCompartments>" + " <compartment metaid='c'/>" + "</listOfCompartments>" + "<listOfSpecies>" + " <species metaid='s'/>" + "</listOfSpecies>" + "<listOfParameters>" + " <parameter metaid='p'/>" + "</listOfParameters>" + "<listOfRules>" + " <rateRule metaid='rr'/>" + "</listOfRules>" + "<listOfReactions>" + " <reaction metaid='rx'/>" + "</listOfReactions>" + "<listOfEvents>" + " <event metaid='e'/>" + "</listOfEvents>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M != null ); sb = M.getFunctionDefinition(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "fd" == sb.getMetaId() )); sb = M.getUnitDefinition(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "ud" == sb.getMetaId() )); sb = M.getCompartment(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "c" == sb.getMetaId() )); sb = M.getSpecies(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "s" == sb.getMetaId() )); sb = M.getParameter(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "p" == sb.getMetaId() )); sb = M.getRule(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "rr" == sb.getMetaId() )); sb = M.getReaction(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "rx" == sb.getMetaId() )); sb = M.getEvent(0); assertEquals( true, sb.isSetMetaId() ); assertTrue(( "e" == sb.getMetaId() )); }
public void test_SBMLConvertStrict_convertToL1() { SBMLDocument d = new SBMLDocument(2,4); Model m = d.createModel(); (m).setMetaId( "_m"); Compartment c = m.createCompartment(); c.setId( "c"); (c).setSBOTerm(240); Species s = m.createSpecies(); s.setId( "s"); s.setCompartment( "c"); s.setHasOnlySubstanceUnits(true); assertTrue( d.setLevelAndVersion(1,2,true) == true ); assertTrue( d.getLevel() == 1 ); assertTrue( d.getVersion() == 2 ); Model m1 = d.getModel(); assertTrue( (m1).getMetaId() == "" ); Compartment c1 = m1.getCompartment(0); assertTrue( (c1).getSBOTerm() == -1 ); Species s1 = m1.getSpecies(0); assertTrue( s1.getHasOnlySubstanceUnits() == false ); d = null; }
public void test_ReadSBML_notes_ListOf() { SBase sb; string s = wrapSBML_L2v1("<listOfFunctionDefinitions>" + " <notes>My Functions</notes>" + " <functionDefinition/>" + "</listOfFunctionDefinitions>" + "<listOfUnitDefinitions>" + " <notes>My Units</notes>" + " <unitDefinition/>" + "</listOfUnitDefinitions>" + "<listOfCompartments>" + " <notes>My Compartments</notes>" + " <compartment/>" + "</listOfCompartments>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M != null ); sb = M.getListOfFunctionDefinitions(); assertEquals( true, sb.isSetNotes() ); string notes = sb.getNotes().getChild(0).getCharacters(); assertTrue( ( "My Functions" != notes ) == false ); sb = M.getListOfUnitDefinitions(); assertEquals( true, sb.isSetNotes() ); notes = sb.getNotes().getChild(0).getCharacters(); assertTrue( ( "My Units" != notes ) == false ); sb = M.getListOfCompartments(); assertEquals( true, sb.isSetNotes() ); notes = sb.getNotes().getChild(0).getCharacters(); assertTrue( ( "My Compartments" != notes ) == false ); }
public void test_ReadSBML_AlgebraicRule() { Rule ar; string s = wrapSBML_L1v2("<listOfRules>" + " <algebraicRule formula='x + 1'/>" + "</listOfRules>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M.getNumRules() == 1 ); ar = M.getRule(0); assertTrue(( "x + 1" == ar.getFormula() )); }
public void test_ReadSBML_notes_xmlns() { string s = wrapSBML_L2v3("<notes>" + " <body xmlns=\"http://www.w3.org/1999/xhtml\">Some text.</body>" + "</notes>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M.getNotes() != null ); XMLNamespaces ns = M.getNotes().getChild(0).getNamespaces(); assertTrue( ns.getLength() == 1 ); assertTrue(( "http://www.w3.org/1999/xhtml" == ns.getURI(0) )); string notes = M.getNotes().getChild(0).getChild(0).getCharacters(); assertTrue( ( "Some text." != notes ) == false ); }
public void test_SBMLDocument_setModel2() { SBMLDocument d = new SBMLDocument(2,2); Model m1 = new Model(1,2); int i = d.setModel(m1); assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH ); assertTrue( d.getModel() == null ); d = null; }
public void test_ReadSBML_Parameter() { Parameter p; string s = wrapSBML_L1v2("<listOfParameters>" + " <parameter name='Km1' value='2.3' units='second'/>" + "</listOfParameters>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M.getNumParameters() == 1 ); p = M.getParameter(0); assertTrue(( "Km1" == p.getId() )); assertTrue(( "second" == p.getUnits() )); assertTrue( p.getValue() == 2.3 ); assertTrue( p.isSetValue() == true ); }
public void test_SBMLDocument_clone() { SBMLDocument o1 = new SBMLDocument(); o1.setLevelAndVersion(1,1,false); Model m = new Model(1,1); 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; }
public void test_ReadSBML_ParameterRule() { Rule pr; string s = wrapSBML_L1v2("<listOfRules>" + " <parameterRule name='k' formula='k3/k2'/>" + "</listOfRules>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M.getNumRules() == 1 ); pr = M.getRule(0); assertEquals( true, pr.isParameter() ); assertTrue(( "k" == pr.getVariable() )); assertTrue(( "k3/k2" == pr.getFormula() )); assertTrue( pr.getType() == libsbml.RULE_TYPE_SCALAR ); }
public void test_SBMLConvert_convertToL3_localParameters() { SBMLDocument d = new SBMLDocument(1,2); Model m = d.createModel(); Compartment c = m.createCompartment(); c.setId( "c" ); Species s = m.createSpecies(); s.setId( "s"); s.setCompartment( "c"); Reaction r = m.createReaction(); SpeciesReference sr = r.createReactant(); sr.setSpecies( "s"); KineticLaw kl = r.createKineticLaw(); kl.setFormula( "s*k"); Parameter p = kl.createParameter(); p.setId( "k"); assertTrue( kl.getNumLocalParameters() == 0 ); assertTrue( d.setLevelAndVersion(3,1,false) == true ); m = d.getModel(); r = m.getReaction(0); kl = r.getKineticLaw(); assertTrue( kl.getNumLocalParameters() == 1 ); LocalParameter lp = kl.getLocalParameter(0); d = null; }
public void test_Model_ancestor_add() { SBMLDocument d = new SBMLDocument(2,4); Model m = new Model(2,4); d.setModel(m); assertTrue( d == d.getModel().getAncestorOfType(libsbml.SBML_DOCUMENT) ); d = null; }
public void setUp() { string filename = "../../annotation/test/test-data/annotation2.xml"; d2 = libsbml.readSBML(filename); m2 = d2.getModel(); }
public void test_ReadSBML_KineticLaw_Parameter() { Reaction r; KineticLaw kl; Parameter p; string s = wrapSBML_L1v2("<listOfReactions>" + " <reaction name='J1'>" + " <kineticLaw formula='k1*X0'>" + " <listOfParameters>" + " <parameter name='k1' value='0'/>" + " </listOfParameters>" + " </kineticLaw>" + " </reaction>" + "</listOfReactions>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M.getNumReactions() == 1 ); r = M.getReaction(0); kl = r.getKineticLaw(); assertTrue(( "k1*X0" == kl.getFormula() )); assertTrue( kl.getNumParameters() == 1 ); p = kl.getParameter(0); assertTrue(( "k1" == p.getId() )); assertTrue( p.getValue() == 0 ); }