public void setUp() { C = new Compartment(2,4); if (C == null); { } }
public void setUp() { string filename = "../../sbml/annotation/test/test-data/annotationL3.xml"; d = libsbml.readSBML(filename); m = d.getModel(); c = m.getCompartment(0); }
public void test_Compartment() { Compartment c = new Compartment(2,4); assertEquals( false, (c.hasRequiredAttributes()) ); c.setId("c"); assertEquals( true, c.hasRequiredAttributes() ); c = null; }
public void test_Model_addCompartment2() { Model m = new Model(2,2); Compartment c = new Compartment(2,1); c.setId( "c"); int i = m.addCompartment(c); assertTrue( i == libsbml.LIBSBML_VERSION_MISMATCH ); assertTrue( m.getNumCompartments() == 0 ); c = null; m = null; }
public void test_Compartment_setCompartmentType2() { Compartment c = new Compartment(2,2); int i = c.setCompartmentType( "1cell"); assertTrue( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE ); assertEquals( false, c.isSetCompartmentType() ); i = c.unsetCompartmentType(); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertEquals( false, c.isSetCompartmentType() ); c = null; }
public void test_Model_addCompartment1() { Model m = new Model(2,2); Compartment c = new Compartment(2,2); int i = m.addCompartment(c); assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT ); c.setId( "c"); i = m.addCompartment(c); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( m.getNumCompartments() == 1 ); c = null; m = null; }
public void test_Compartment_assignmentOperator() { Compartment o1 = new Compartment(2,4); o1.setId("c"); o1.setOutside("c2"); assertTrue( o1.getId() == "c" ); assertTrue( o1.getOutside() == "c2" ); Compartment o2 = new Compartment(2,4); o2 = o1; assertTrue( o2.getId() == "c" ); assertTrue( o2.getOutside() == "c2" ); assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() ); o2 = null; o1 = null; }
public void test_Compartment_createWith() { Compartment c = new Compartment(2,4); c.setId( "A"); assertTrue( c.getTypeCode() == libsbml.SBML_COMPARTMENT ); assertTrue( c.getMetaId() == "" ); assertTrue( c.getNotes() == null ); assertTrue( c.getAnnotation() == null ); assertTrue( c.getName() == "" ); assertTrue( c.getSpatialDimensions() == 3 ); assertTrue(( "A" == c.getId() )); assertTrue( c.getConstant() == true ); assertEquals( true, c.isSetId() ); assertEquals( false, c.isSetName() ); c = null; }
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_Compartment_initDefaults() { Compartment c = new Compartment(2,4); c.setId( "A"); c.initDefaults(); assertTrue(( "A" == c.getId() )); assertTrue( c.getName() == "" ); assertTrue( c.getUnits() == "" ); assertTrue( c.getOutside() == "" ); assertTrue( c.getSpatialDimensions() == 3 ); assertTrue( c.getVolume() == 1.0 ); assertTrue( c.getConstant() == true ); assertEquals( true, c.isSetId() ); assertEquals( false, c.isSetName() ); assertEquals( false, c.isSetSize() ); assertEquals( false, c.isSetVolume() ); assertEquals( false, c.isSetUnits() ); assertEquals( false, c.isSetOutside() ); assertEquals( true, c.isSetSpatialDimensions() ); assertEquals( true, c.isSetConstant() ); c = null; }
public void test_internal_consistency_check_99903() { SBMLDocument d = new SBMLDocument(2,4); long errors; Compartment c = new Compartment(2,4); d.setLevelAndVersion(1,2,false); Model m = d.createModel(); c.setConstant(true); c.setId("c"); m.addCompartment(c); Rule r = m.createAssignmentRule(); r.setVariable("c"); r.setFormula("2*3"); errors = d.checkInternalConsistency(); assertTrue( errors == 3 ); d = null; }
public void test_SBMLConvert_convertToL1_Species_Amount() { SBMLDocument d = new SBMLDocument(2,4); Model m = d.createModel(); string sid = "C"; Compartment c = new Compartment(2,4); Species s = new Species(2,4); c.setId(sid); m.addCompartment(c); s.setCompartment(sid); s.setInitialAmount(2.34); m.addSpecies(s); assertTrue( d.setLevelAndVersion(1,2,true) == true ); assertTrue( s.getInitialAmount() == 2.34 ); 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_Model_getCompartmentById() { Compartment c1 = new Compartment(2,4); Compartment c2 = new Compartment(2,4); c1.setId( "A" ); c2.setId( "B" ); M.addCompartment(c1); M.addCompartment(c2); assertTrue( M.getNumCompartments() == 2 ); assertTrue( M.getCompartment( "A" ) != c1 ); assertTrue( M.getCompartment( "B" ) != c2 ); assertTrue( M.getCompartment( "C" ) == null ); }
public void test_Compartment_parent_add() { Compartment c = new Compartment(2,4); c.setId("c"); Model m = new Model(2,4); m.addCompartment(c); c = null; ListOf lo = m.getListOfCompartments(); assertTrue( lo == m.getCompartment(0).getParentSBMLObject() ); assertTrue( m == lo.getParentSBMLObject() ); }
public void test_Compartment_createWithNS() { XMLNamespaces xmlns = new XMLNamespaces(); xmlns.add( "http://www.sbml.org", "testsbml"); SBMLNamespaces sbmlns = new SBMLNamespaces(2,1); sbmlns.addNamespaces(xmlns); Compartment c = new Compartment(sbmlns); assertTrue( c.getTypeCode() == libsbml.SBML_COMPARTMENT ); assertTrue( c.getMetaId() == "" ); assertTrue( c.getNotes() == null ); assertTrue( c.getAnnotation() == null ); assertTrue( c.getLevel() == 2 ); assertTrue( c.getVersion() == 1 ); assertTrue( c.getNamespaces() != null ); assertTrue( c.getNamespaces().getLength() == 2 ); assertTrue( c.getName() == "" ); assertTrue( c.getSpatialDimensions() == 3 ); assertTrue( c.getConstant() == true ); c = null; }
public void test_Compartment() { Compartment c = new Compartment(2,4); assertEquals( true, c.hasRequiredElements() ); c = null; }
public void test_Model_addCompartment5() { Model m = new Model(2,2); Compartment c = new Compartment(2,2); c.setId( "c"); Compartment c1 = new Compartment(2,2); c1.setId( "c"); int i = m.addCompartment(c); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( m.getNumCompartments() == 1 ); i = m.addCompartment(c1); assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID ); assertTrue( m.getNumCompartments() == 1 ); c = null; c1 = null; m = null; }
public void tearDown() { C = null; }
public void test_RDFAnnotation_parseCVTerms() { XMLNode node = RDFAnnotationParser.parseCVTerms(m.getCompartment(0)); assertTrue( node.getNumChildren() == 1 ); XMLNode rdf = node.getChild(0); assertTrue(( "RDF" == rdf.getName() )); assertTrue(( "rdf" == rdf.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI() )); assertTrue( rdf.getNumChildren() == 1 ); XMLNode desc = rdf.getChild(0); assertTrue(( "Description" == desc.getName() )); assertTrue(( "rdf" == desc.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI() )); assertTrue( desc.getNumChildren() == 1 ); XMLNode is1 = desc.getChild(0); assertTrue(( "is" == is1.getName() )); assertTrue(( "bqbiol" == is1.getPrefix() )); assertTrue( is1.getNumChildren() == 1 ); XMLNode Bag = is1.getChild(0); assertTrue(( "Bag" == Bag.getName() )); assertTrue(( "rdf" == Bag.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI() )); assertTrue( Bag.getNumChildren() == 4 ); XMLNode li = Bag.getChild(0); assertTrue(( "li" == li.getName() )); assertTrue(( "rdf" == li.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI() )); assertTrue( li.getNumChildren() == 0 ); XMLNode li1 = Bag.getChild(1); assertTrue(( "li" == li1.getName() )); assertTrue(( "rdf" == li1.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI() )); assertTrue( li1.getNumChildren() == 0 ); XMLNode li2 = Bag.getChild(2); assertTrue(( "li" == li2.getName() )); assertTrue(( "rdf" == li2.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI() )); assertTrue( li2.getNumChildren() == 0 ); XMLNode li3 = Bag.getChild(3); assertTrue(( "li" == li3.getName() )); assertTrue(( "rdf" == li3.getPrefix() )); assertTrue(( "http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI() )); assertTrue( li3.getNumChildren() == 0 ); node = null; XMLNode node1 = RDFAnnotationParser.parseCVTerms(null); assertTrue( node1 == null ); node1 = RDFAnnotationParser.createCVTerms(null); assertTrue( node1 == null ); node1 = RDFAnnotationParser.parseCVTerms(m.getCompartment(2)); assertTrue( node1 == null ); node1 = RDFAnnotationParser.createCVTerms(m.getCompartment(2)); assertTrue( node1 == null ); node1 = RDFAnnotationParser.parseCVTerms(m); assertTrue( node1 == null ); node1 = RDFAnnotationParser.createCVTerms(m); assertTrue( node1 == null ); Compartment c = new Compartment(3,1); c.setMetaId("_002"); node1 = RDFAnnotationParser.parseCVTerms(c); assertTrue( node1 == null ); node1 = RDFAnnotationParser.createCVTerms(c); assertTrue( node1 == null ); CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType(23); cv.addResource("http://myres"); c.addCVTerm(cv); node1 = RDFAnnotationParser.createCVTerms(c); assertTrue( node1 == null ); c = null; Model m1 = new Model(3,1); m1.setMetaId("_002"); cv = new CVTerm(libsbml.MODEL_QUALIFIER); cv.setModelQualifierType(23); cv.addResource("http://myres"); m1.addCVTerm(cv); node1 = RDFAnnotationParser.createCVTerms(m1); assertTrue( node1 == null ); }
/** * Copy constructor; creates a copy of a Compartment. * * @param orig the Compartment instance to copy. * * @throws @if python ValueError @else SBMLConstructorException @endif * Thrown if the argument @p orig is @c null. */ public Compartment(Compartment orig) : this(libsbmlPINVOKE.new_Compartment__SWIG_2(Compartment.getCPtr(orig)), true) { if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve(); }
internal static HandleRef getCPtrAndDisown(Compartment obj) { HandleRef ptr = new HandleRef(null, IntPtr.Zero); if (obj != null) { ptr = obj.swigCPtr; obj.swigCMemOwn = false; } return ptr; }
internal static HandleRef getCPtr(Compartment obj) { return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr; }
public void test_Model_addCompartment() { Compartment c = new Compartment(2,4); c.setId( "c"); M.addCompartment(c); assertTrue( M.getNumCompartments() == 1 ); }
public void test_internal_consistency_check_99904() { SBMLDocument d = new SBMLDocument(2,4); long errors; Compartment c = new Compartment(2,4); d.setLevelAndVersion(1,2,false); Model m = d.createModel(); c.setId("c"); c.setMetaId("mmm"); m.addCompartment(c); errors = d.checkInternalConsistency(); assertTrue( errors == 1 ); assertTrue( d.getError(0).getErrorId() == 10103 ); d = null; }
public void test_Compartment_ancestor_add() { Compartment c = new Compartment(2,4); c.setId("C"); Model m = new Model(2,4); m.addCompartment(c); c = null; ListOf lo = m.getListOfCompartments(); 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 ); }
/** * Adds a copy of the given Compartment object to this Model. * * @param c the Compartment object to add * * @return integer value indicating success/failure of the * function. The possible values * returned by this function are: * @li @link libsbml#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink * @li @link libsbml#LIBSBML_LEVEL_MISMATCH LIBSBML_LEVEL_MISMATCH@endlink * @li @link libsbml#LIBSBML_VERSION_MISMATCH LIBSBML_VERSION_MISMATCH@endlink * @li @link libsbml#LIBSBML_DUPLICATE_OBJECT_ID LIBSBML_DUPLICATE_OBJECT_ID@endlink * @li @link libsbml#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT@endlink * @li @link libsbml#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink * * * @note This method should be used with some caution. The fact that this * method @em copies the object passed to it means that the caller will be * left holding a physically different object instance than the one contained * inside this object. Changes made to the original object instance (such as * resetting attribute values) will <em>not affect the instance in this * object</em>. In addition, the caller should make sure to free the * original object if it is no longer being used, or else a memory leak will * result. Please see other methods on this class (particularly a * corresponding method whose name begins with the word <code>create</code>) * for alternatives that do not lead to these issues. * * * * @see createCompartment() */ public int addCompartment(Compartment c) { int ret = libsbmlPINVOKE.Model_addCompartment(swigCPtr, Compartment.getCPtr(c)); return ret; }
public void test_SBase_setSBOTerm1() { SBase c = new Compartment(1,2); int i = c.setSBOTerm(2); assertTrue( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE ); assertEquals( false, c.isSetSBOTerm() ); c = null; }
public void test_Compartment_constructor() { SBase s; try { s = new Compartment(1,1); s = new Compartment(1,2); s = new Compartment(2,1); s = new Compartment(2,2); s = new Compartment(2,3); s = new Compartment(2,4); s = new Compartment(3,1); s = new Compartment(SN11); s = new Compartment(SN12); s = new Compartment(SN21); s = new Compartment(SN22); s = new Compartment(SN23); s = new Compartment(SN24); s = new Compartment(SN31); } catch (SBMLConstructorException e) { s = null; } assertTrue(s != null); string msg = ""; try { s = new Compartment(9,9); } catch (SBMLConstructorException e) { msg = e.Message; } assertTrue(msg == ErrMsg); msg = ""; try { s = new Compartment(SN99); } catch (SBMLConstructorException e) { msg = e.Message; } assertTrue(msg == ErrMsg); msg = ""; try { s = new Compartment(SN99); } catch (SBMLConstructorException e) { msg = e.Message; } assertTrue(msg == ErrMsg); }
public void test_Model_getCompartment() { Compartment c1 = new Compartment(2,4); Compartment c2 = new Compartment(2,4); c1.setId( "A"); c2.setId( "B"); M.addCompartment(c1); M.addCompartment(c2); assertTrue( M.getNumCompartments() == 2 ); c1 = M.getCompartment(0); c2 = M.getCompartment(1); assertTrue(( "A" == c1.getId() )); assertTrue(( "B" == c2.getId() )); }