| public getCompartment ( long n ) : Compartment | ||
| n | long | |
| return | Compartment | |
public void setUp()
{
string filename = "../../annotation/test/test-data/annotationL3.xml";
d = libsbml.readSBML(filename);
m = d.getModel();
c = m.getCompartment(0);
}
/// <summary>
/// [ CompartmentStruct ]
/// [[ Id , Name , SpatialDimension , Size , Volume , Unit , Ouside , Constant ]]
/// </summary>
/// <param name="aSBMLmodel"></param>
/// <returns></returns>
public static List<CompartmentStruct> getCompartment(Model aSBMLmodel)
{
List<CompartmentStruct> list = new List<CompartmentStruct>();
ListOfCompartments compartments = aSBMLmodel.getListOfCompartments();
for (int i = 0; i < compartments.size(); i++ )
{
Compartment item = aSBMLmodel.getCompartment(i);
string anId = item.getId();
string aName = item.getName();
long aSpatialDimension = item.getSpatialDimensions();
double aSize = GetCompartmentSize(item);
double aVolume = GetCompartmentVolume(item);
string anUnit = item.getUnits();
string anOutside = item.getOutside();
bool aConstant = item.getConstant();
CompartmentStruct compartment = new CompartmentStruct(
anId,
aName,
aSpatialDimension,
aSize,
aVolume,
anUnit,
anOutside,
aConstant);
list.Add(compartment);
}
return list;
}
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() );
}
private static void createSpecies(EcellObject anEml, Model aSBMLModel)
{
string aCurrentCompartment = getCurrentCompartment( anEml.ParentSystemID );
Compartment aCurrentCompartmentObj = aSBMLModel.getCompartment( aCurrentCompartment );
if( aCurrentCompartment == "SBMLParameter" )
{
// ------------------------
// create Parameter object
// ------------------------
Parameter aParameter = aSBMLModel.createParameter();
string aParameterID;
if ( ID_Namespace.Contains(anEml.LocalID) == false )
aParameterID = anEml.LocalID;
else
aParameterID = "SBMLParamter__" + anEml.LocalID;
// set Paramter ID to Id namespace
ID_Namespace.Add( aParameterID );
// set Parameter ID
if (aSBMLModel.getLevel() == 1)
aParameter.setName( aParameterID );
else if (aSBMLModel.getLevel() == 2)
aParameter.setId( aParameterID );
// set Parameter Name, Value and Constant
foreach(EcellData aProperty in anEml.Value)
{
string aFullPN = anEml.FullID + ":" + aProperty.Name;
// set Parameter Name
if ( aProperty.Name == "Name" )
{
if (aSBMLModel.getLevel() == 1)
{
}
if (aSBMLModel.getLevel() == 2)
{
aParameter.setName( (string)aProperty.Value );
}
}
// set Parameter Value
else if ( aProperty.Name == "Value" )
{
aParameter.setValue( (double)aProperty.Value );
}
// set Constant
else if ( aProperty.Name == "Fixed" )
{
aParameter.setConstant(System.Convert.ToBoolean((int)aProperty.Value));
}
else
{
Trace.WriteLine("Unrepresentable property; " + aFullPN);
//throw new EcellException("Unrepresentable property; " + aFullPN);
}
}
}
else
{
if( anEml.LocalID != "SIZE" && anEml.LocalID != "Dimensions" )
{
// create Species object
Species aSpecies = aSBMLModel.createSpecies();
// set Species ID
string aSpeciesID;
if ( ID_Namespace.Contains( anEml.LocalID) == false )
aSpeciesID = anEml.LocalID;
else
{
if ( !anEml.ParentSystemID.Equals("/") )
aSpeciesID = anEml.LocalID;
else
aSpeciesID = anEml.LocalID;
}
ID_Namespace.Add( aSpeciesID );
if (aSBMLModel.getLevel() == 1)
aSpecies.setName( aSpeciesID );
if (aSBMLModel.getLevel() == 2)
aSpecies.setId( aSpeciesID );
// set Compartment of Species
if( aCurrentCompartment == "" )
aSpecies.setCompartment( "default" );
else
aSpecies.setCompartment( aCurrentCompartment );
// set Species Name, Value and Constant
foreach(EcellData aProperty in anEml.Value)
{
string aFullPN = anEml.FullID + ":" + aProperty.Name;
// set Species Name
if ( aProperty.Name == "Name" )
{
if (aSBMLModel.getLevel() == 1)
{
}
else if (aSBMLModel.getLevel() == 2)
{
aSpecies.setName( (string)aProperty.Value );
}
}
// set Species Value
else if ( aProperty.Name == "Value" )
{
// aMolarValue = convertToMoleUnit(
// anEml.getEntityProperty( aFullPN )[0] )
aSpecies.setInitialAmount( (double)aProperty.Value / 6.0221367e+23 );
}
// set Species Constant
else if ( aProperty.Name == "Fixed" )
{
aSpecies.setConstant(System.Convert.ToBoolean((int)aProperty.Value));
}
// set Concentration by rule
else if ( aProperty.Name == "MolarConc" )
{
// XXX: units are just eventually correct here, because
// SBML falls back to mole and liter for substance and
// volume of the species if these are unspecified.
if (aSBMLModel.getLevel() == 1)
{
double compVol;
if (aCurrentCompartmentObj != null)
compVol = aCurrentCompartmentObj.getVolume();
else
compVol = 1.0;
double propValue = (double)aProperty.Value;
aSpecies.setInitialAmount( compVol * propValue );
}
else // SBML lv.2
{
aSpecies.setInitialConcentration( (double)aProperty.Value );
}
}
else
{
Trace.WriteLine("Unrepresentable property; " + aFullPN);
//throw new EcellException("Unrepresentable property: " + aFullPN);
}
}
}
}
}
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_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_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() );
}
