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_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_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_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_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_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_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_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; }
private static int Main(string[] args) { var retval = 0; var sbmlns = new SBMLNamespaces(3, 1, "comp", 1); // create the document var document = new SBMLDocument(sbmlns); //Define the external model definition var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp")); compdoc.setRequired(true); var extmod = compdoc.createExternalModelDefinition(); extmod.setId("ExtMod1"); extmod.setSource("enzyme_model.xml"); extmod.setModelRef("enzyme"); //Define the 'simple' model var mod1 = compdoc.createModelDefinition(); mod1.setId("simple"); var comp = mod1.createCompartment(); comp.setSpatialDimensions(3); comp.setConstant(true); comp.setId("comp"); comp.setSize(1L); var spec = new Species(sbmlns); //We have to construct it this way because we get the comp plugin from it later. spec.setCompartment("comp"); spec.setHasOnlySubstanceUnits(false); spec.setConstant(false); spec.setBoundaryCondition(false); spec.setId("S"); spec.setInitialConcentration(5); mod1.addSpecies(spec); spec.setId("D"); spec.setInitialConcentration(10); mod1.addSpecies(spec); var rxn = new Reaction(3, 1); rxn.setReversible(true); rxn.setFast(false); rxn.setId("J0"); var sr = new SpeciesReference(3, 1); sr.setConstant(true); sr.setStoichiometry(1); sr.setSpecies("S"); rxn.addReactant(sr); sr.setSpecies("D"); rxn.addProduct(sr); mod1.addReaction(rxn); var mod1plug = (CompModelPlugin)(mod1.getPlugin("comp")); var port = new Port(); port.setId("S_port"); port.setIdRef("S"); mod1plug.addPort(port); var port2 = mod1plug.createPort(); port2.setId("D_port"); port2.setIdRef("D"); port.setId("comp_port"); port.setIdRef("comp"); mod1plug.addPort(port); port.setId("J0_port"); port.setIdRef("J0"); mod1plug.addPort(port); // create the Model var model = document.createModel(); model.setId("complexified"); // Set the submodels var mplugin = (CompModelPlugin)(model.getPlugin("comp")); var submod1 = mplugin.createSubmodel(); submod1.setId("A"); submod1.setModelRef("ExtMod1"); var submod2 = mplugin.createSubmodel(); submod2.setId("B"); submod2.setModelRef("simple"); var del = submod2.createDeletion(); del.setPortRef("J0_port"); // Synchronize the compartments var mcomp = model.createCompartment(); mcomp.setSpatialDimensions(3); mcomp.setConstant(true); mcomp.setId("comp"); mcomp.setSize(1L); var compartplug = (CompSBasePlugin)(mcomp.getPlugin("comp")); var re = new ReplacedElement(); re.setIdRef("comp"); re.setSubmodelRef("A"); compartplug.addReplacedElement(re); re.setSubmodelRef("B"); re.unsetIdRef(); re.setPortRef("comp_port"); compartplug.addReplacedElement(re); //Synchronize the species spec.setId("S"); spec.setInitialConcentration(5); var specplug = (CompSBasePlugin)(spec.getPlugin("comp")); var sre = specplug.createReplacedElement(); sre.setSubmodelRef("A"); sre.setIdRef("S"); var sre2 = specplug.createReplacedElement(); sre2.setSubmodelRef("B"); sre2.setPortRef("S_port"); model.addSpecies(spec); spec.setId("D"); spec.setInitialConcentration(10); sre.setIdRef("D"); sre2.setPortRef("D_port"); model.addSpecies(spec); libsbml.writeSBMLToFile(document, "spec_example3.xml"); document = libsbml.readSBMLFromFile("spec_example3.xml"); if (document == null) { Console.WriteLine("Error reading back in file."); retval = -1; } else { document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false); document.checkConsistency(); if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 || document.getErrorLog().getNumFailsWithSeverity(3) > 0) { var stream = new OStringStream(); document.printErrors(stream); Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" + stream.str()); retval = -1; } libsbml.writeSBMLToFile(document, "spec_example3_rt.xml"); } return retval; }
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; }
private static int Main(string[] args) { var retval = 0; var sbmlns = new SBMLNamespaces(3, 1, "comp", 1); // create the document var document = new SBMLDocument(sbmlns); //Create our submodel var compdoc = (CompSBMLDocumentPlugin) (document.getPlugin("comp")); compdoc.setRequired(true); var mod1 = compdoc.createModelDefinition(); mod1.setId("enzyme"); mod1.setName("enzyme"); var comp = mod1.createCompartment(); comp.setSpatialDimensions(3); comp.setConstant(true); comp.setId("comp"); comp.setSize(1L); var spec = new Species(3, 1); spec.setCompartment("comp"); spec.setHasOnlySubstanceUnits(false); spec.setConstant(false); spec.setBoundaryCondition(false); spec.setId("S"); mod1.addSpecies(spec); spec.setId("E"); mod1.addSpecies(spec); spec.setId("D"); mod1.addSpecies(spec); spec.setId("ES"); mod1.addSpecies(spec); var rxn = new Reaction(3, 1); rxn.setReversible(true); rxn.setFast(false); var rxn2 = new Reaction(rxn); rxn.setId("J0"); rxn2.setId("J1"); var sr = new SpeciesReference(3, 1); sr.setConstant(true); sr.setStoichiometry(1); sr.setSpecies("S"); rxn.addReactant(sr); sr.setSpecies("E"); rxn.addReactant(sr); rxn2.addProduct(sr); sr.setSpecies("ES"); rxn.addProduct(sr); rxn2.addReactant(sr); sr.setSpecies("D"); rxn2.addProduct(sr); mod1.addReaction(rxn); mod1.addReaction(rxn2); // create the Model var model = document.createModel(); model.setId("aggregate"); // Create a submodel var mplugin = (CompModelPlugin) (model.getPlugin("comp")); var submod1 = mplugin.createSubmodel(); submod1.setId("submod1"); submod1.setModelRef("enzyme"); var submod2 = new Submodel(); submod2.setId("submod2"); submod2.setModelRef("enzyme"); mplugin.addSubmodel(submod2); libsbml.writeSBMLToFile(document, "enzyme_model.xml"); document = libsbml.readSBMLFromFile("enzyme_model.xml"); if (document == null) { Console.WriteLine("Error reading back in file."); retval = -1; } else { document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false); document.checkConsistency(); if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 || document.getErrorLog().getNumFailsWithSeverity(3) > 0) { var stream = new OStringStream(); document.printErrors(stream); Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" + stream.str()); retval = -1; } libsbml.writeSBMLToFile(document, "enzyme_model_rt.xml"); } return retval; }
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_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_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_internal_consistency_check_99904_species() { 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.setCompartment("c"); s.setId("s"); s.setMetaId("mmm"); m.addSpecies(s); errors = d.checkInternalConsistency(); assertTrue( errors == 0 ); d = 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_Model_addSpecies() { Species s = new Species(2,4); s.setId( "s"); s.setCompartment( "c"); M.addSpecies(s); assertTrue( M.getNumSpecies() == 1 ); }
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 ); }
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_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_ListOf_copyConstructor() { ListOf o1 = new ListOf(2,1); 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; }