public void test_Model_createSpecies()
{
Model m = new Model(2,2);
Species p = m.createSpecies();
assertTrue( m.getNumSpecies() == 1 );
assertTrue( (p).getLevel() == 2 );
assertTrue( (p).getVersion() == 2 );
m = null;
}
public void test_Model_L1V1()
{
Model m = new Model(1,1);
assertEquals( false, (m.hasRequiredElements()) );
m.createCompartment();
assertEquals( false, (m.hasRequiredElements()) );
m.createSpecies();
assertEquals( false, (m.hasRequiredElements()) );
m.createReaction();
assertEquals( true, m.hasRequiredElements() );
m = null;
}
public void test_Species_parent_create()
{
Model m = new Model(2,4);
Species s = m.createSpecies();
ListOf lo = m.getListOfSpecies();
assertTrue( lo == s.getParentSBMLObject() );
assertTrue( lo == m.getSpecies(0).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_create_l1v1_units()
{
SBMLDocument d;
Model m;
Compartment c;
KineticLaw kl;
Parameter p;
Reaction r;
Species s;
SpeciesReference sr;
Unit u;
UnitDefinition ud;
d = new SBMLDocument();
m = new Model(2,4);
d.setModel(m);
ud = m.createUnitDefinition();
ud.setName( "substance");
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_MOLE);
u.setScale(-3);
ud = m.createUnitDefinition();
ud.setName( "mls");
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_MOLE);
u.setScale(-3);
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_LITER);
u.setExponent(-1);
u = m.createUnit();
u.setKind(libsbml.UNIT_KIND_SECOND);
u.setExponent(-1);
c = m.createCompartment();
c.setName( "cell");
s = m.createSpecies();
s.setName( "x0");
s.setCompartment( "cell");
s.setInitialAmount(1);
s = m.createSpecies();
s.setName( "x1");
s.setCompartment( "cell");
s.setInitialAmount(1);
s = m.createSpecies();
s.setName( "s1");
s.setCompartment( "cell");
s.setInitialAmount(1);
s = m.createSpecies();
s.setName( "s2");
s.setCompartment( "cell");
s.setInitialAmount(1);
p = m.createParameter();
p.setName( "vm");
p.setUnits( "mls");
p.setValue(2);
p = m.createParameter();
p.setName( "km");
p.setValue(2);
r = m.createReaction();
r.setName( "v1");
sr = m.createReactant();
sr.setSpecies( "x0");
sr = m.createProduct();
sr.setSpecies( "s1");
kl = m.createKineticLaw();
kl.setFormula( "(vm * s1)/(km + s1)");
r = m.createReaction();
r.setName( "v2");
sr = m.createReactant();
sr.setSpecies( "s1");
sr = m.createProduct();
sr.setSpecies( "s2");
kl = m.createKineticLaw();
kl.setFormula( "(vm * s2)/(km + s2)");
r = m.createReaction();
r.setName( "v3");
sr = m.createReactant();
sr.setSpecies( "s2");
sr = m.createProduct();
sr.setSpecies( "x1");
kl = m.createKineticLaw();
kl.setFormula( "(vm * s1)/(km + s1)");
d = null;
}
public void test_Species_ancestor_create()
{
Model m = new Model(2,4);
Species s = m.createSpecies();
ListOf lo = m.getListOfSpecies();
assertTrue( s.getAncestorOfType(libsbml.SBML_MODEL) == m );
assertTrue( s.getAncestorOfType(libsbml.SBML_LIST_OF) == lo );
assertTrue( s.getAncestorOfType(libsbml.SBML_DOCUMENT) == null );
assertTrue( s.getAncestorOfType(libsbml.SBML_EVENT) == null );
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 );
}
