public void setUp() { string filename = "../../sbml/annotation/test/test-data/annotationL3.xml"; d = libsbml.readSBML(filename); m = d.getModel(); c = m.getCompartment(0); }
protected override void Import(Model sbmlModel) { CreateTopContainer(sbmlModel); CreateEventsTopContainer(); for (long i = 0; i < sbmlModel.getNumCompartments(); i++) { _topContainer.Add(CreateContainerFromCompartment(sbmlModel.getCompartment(i))); } CreateSpatialStructureFromModel(_topContainer, sbmlModel.getModel()); AddToProject(); }
/// <summary> /// Gets the dimension of the size Parameter of the container/compartment in which the given Species is located. /// </summary> private IDimension GetSizeDimensionFromCompartment(Species species, Model model) { var compartmentSizeUnit = model.getCompartment(species.getCompartment()).getUnits(); var sizeDimension = _moBiDimensionFactory.TryGetDimensionCaseInsensitive(compartmentSizeUnit); if (sizeDimension == OSPSuite.Core.Domain.Constants.Dimension.NO_DIMENSION) { return(sizeDimension); } if (_sbmlInformation.MobiDimension.ContainsKey(compartmentSizeUnit)) { sizeDimension = _sbmlInformation.MobiDimension[compartmentSizeUnit]; } if (_moBiDimensionFactory.Dimensions.All(dim => dim.Name != sizeDimension.Name)) { _moBiDimensionFactory.AddDimension(sizeDimension); } return(sizeDimension); }
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_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_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 ); }
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_ReadSBML_Compartment_L2() { Compartment c; string s = wrapSBML_L2v1("<listOfCompartments>" + " <compartment id='membrane' size='.3' spatialDimensions='2'" + " units='area' outside='tissue' constant='false'/>" + "</listOfCompartments>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M.getNumCompartments() == 1 ); c = M.getCompartment(0); assertEquals( true, c.isSetId() ); assertEquals( false, c.isSetName() ); assertEquals( true, c.isSetVolume() ); assertEquals( true, c.isSetSize() ); assertEquals( true, c.isSetUnits() ); assertEquals( true, c.isSetOutside() ); assertTrue(( "membrane" == c.getId() )); assertTrue(( "area" == c.getUnits() )); assertTrue(( "tissue" == c.getOutside() )); assertTrue( c.getSpatialDimensions() == 2 ); assertTrue( c.getSize() == .3 ); }
public void test_ReadSBML_Compartment_defaults_L2() { Compartment c; string s = wrapSBML_L2v1("<listOfCompartments> <compartment id='cell'/> </listOfCompartments>" ); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M.getNumCompartments() == 1 ); c = M.getCompartment(0); assertEquals( true, c.isSetId() ); assertEquals( false, c.isSetName() ); assertEquals( false, c.isSetSize() ); assertEquals( false, c.isSetUnits() ); assertEquals( false, c.isSetOutside() ); assertTrue(( "cell" == c.getId() )); assertTrue( c.getSpatialDimensions() == 3 ); assertTrue( c.getConstant() == true ); }
public void test_ReadSBML_Compartment_defaults() { Compartment c; string s = wrapSBML_L1v2("<listOfCompartments> <compartment name='cell'/> </listOfCompartments>" ); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M.getNumCompartments() == 1 ); c = M.getCompartment(0); assertEquals( true, c.isSetId() ); assertEquals( true, c.isSetVolume() ); assertEquals( false, c.isSetSize() ); assertEquals( false, c.isSetUnits() ); assertEquals( false, c.isSetOutside() ); assertTrue(( "cell" == c.getId() )); assertTrue( c.getVolume() == 1.0 ); }
public void test_ReadSBML_Compartment() { Compartment c; string s = wrapSBML_L1v2("<listOfCompartments>" + " <compartment name='mitochondria' volume='.0001' units='milliliters'" + " outside='cell'/>" + "</listOfCompartments>"); D = libsbml.readSBMLFromString(s); M = D.getModel(); assertTrue( M.getNumCompartments() == 1 ); c = M.getCompartment(0); assertTrue(( "mitochondria" == c.getId() )); assertTrue(( "milliliters" == c.getUnits() )); assertTrue(( "cell" == c.getOutside() )); assertTrue( c.getVolume() == .0001 ); assertEquals( true, c.isSetVolume() ); assertEquals( true, c.isSetSize() ); }