|
public getCompartment ( long n ) : |
||
| n | long | |
| return | ||
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() );
}
