/// <summary>
/// Gets a SBML species by it's Id.
/// </summary>
private Species GetSpeciesById(string speciesId, Model model)
{
for (long i = 0; i < model.getNumSpecies(); i++)
{
if (model.getSpecies(i).getId() == speciesId)
{
return(model.getSpecies(i));
}
}
return(null);
}
protected override void Import(Model model)
{
CreateMoleculeBuildingBlock();
for (long i = 0; i < model.getNumSpecies(); i++)
{
CreateMoleculeFromSpecies(model.getSpecies(i));
}
CheckMoleculeNameContainer();
CreateDummySpecies();
CreateMoleculeStartValueBuildingBlock(model);
SetMoleculeStartValues(model);
SetDummyMSVs();
AddToProject();
}
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_addSpecies5()
{
Model m = new Model(2,2);
Species s = new Species(2,2);
s.setId( "s");
s.setCompartment( "c");
Species s1 = new Species(2,2);
s1.setId( "s");
s1.setCompartment( "c");
int i = m.addSpecies(s);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumSpecies() == 1 );
i = m.addSpecies(s1);
assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID );
assertTrue( m.getNumSpecies() == 1 );
s = null;
s1 = null;
m = null;
}
public void test_Model_addSpecies4()
{
Model m = new Model(2,2);
Species s = null;
int i = m.addSpecies(s);
assertTrue( i == libsbml.LIBSBML_OPERATION_FAILED );
assertTrue( m.getNumSpecies() == 0 );
m = null;
}
public void test_Model_addSpecies3()
{
Model m = new Model(2,2);
Species s = new Species(1,2);
s.setId( "s");
s.setCompartment( "c");
s.setInitialAmount(2);
int i = m.addSpecies(s);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( m.getNumSpecies() == 0 );
s = null;
m = null;
}
public void test_Model_addSpecies2()
{
Model m = new Model(2,2);
Species s = new Species(2,1);
s.setId( "s");
s.setCompartment( "c");
int i = m.addSpecies(s);
assertTrue( i == libsbml.LIBSBML_VERSION_MISMATCH );
assertTrue( m.getNumSpecies() == 0 );
s = null;
m = null;
}
public void test_ReadSBML_Specie_defaults()
{
Species sp;
string s = wrapSBML_L1v1("<listOfSpecie>" +
" <specie name='Glucose' compartment='cell' initialAmount='1.0'/>" +
"</listOfSpecie>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumSpecies() == 1 );
sp = M.getSpecies(0);
assertTrue(( "Glucose" == sp.getId() ));
assertTrue(( "cell" == sp.getCompartment() ));
assertTrue( sp.getInitialAmount() == 1.0 );
assertTrue( sp.getBoundaryCondition() == false );
assertTrue( sp.isSetInitialAmount() == true );
assertTrue( sp.isSetCharge() == false );
}
public void test_ReadSBML_Species_L2_defaults()
{
Species sp;
string s = wrapSBML_L2v1("<listOfSpecies>" +
" <species id='Glucose_6_P' compartment='cell'/>" +
"</listOfSpecies>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumSpecies() == 1 );
sp = M.getSpecies(0);
assertEquals( true, sp.isSetId() );
assertEquals( false, sp.isSetName() );
assertEquals( true, sp.isSetCompartment() );
assertEquals( false, sp.isSetInitialAmount() );
assertEquals( false, sp.isSetInitialConcentration() );
assertEquals( false, sp.isSetSubstanceUnits() );
assertEquals( false, sp.isSetSpatialSizeUnits() );
assertEquals( false, sp.isSetCharge() );
assertTrue(( "Glucose_6_P" == sp.getId() ));
assertTrue(( "cell" == sp.getCompartment() ));
assertTrue( sp.getHasOnlySubstanceUnits() == false );
assertTrue( sp.getBoundaryCondition() == false );
assertTrue( sp.getConstant() == false );
}
public void test_ReadSBML_Species_L2_1()
{
Species sp;
string s = wrapSBML_L2v1("<listOfSpecies>" +
" <species id='Glucose' compartment='cell' initialConcentration='4.1'" +
" substanceUnits='item' spatialSizeUnits='volume'" +
" boundaryCondition='true' charge='6' constant='true'/>" +
"</listOfSpecies>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumSpecies() == 1 );
sp = M.getSpecies(0);
assertEquals( true, sp.isSetId() );
assertEquals( false, sp.isSetName() );
assertEquals( true, sp.isSetCompartment() );
assertEquals( false, sp.isSetInitialAmount() );
assertEquals( true, sp.isSetInitialConcentration() );
assertEquals( true, sp.isSetSubstanceUnits() );
assertEquals( true, sp.isSetSpatialSizeUnits() );
assertEquals( true, sp.isSetCharge() );
assertTrue(( "Glucose" == sp.getId() ));
assertTrue(( "cell" == sp.getCompartment() ));
assertTrue(( "item" == sp.getSubstanceUnits() ));
assertTrue(( "volume" == sp.getSpatialSizeUnits() ));
assertTrue( sp.getInitialConcentration() == 4.1 );
assertTrue( sp.getHasOnlySubstanceUnits() == false );
assertTrue( sp.getBoundaryCondition() == true );
assertTrue( sp.getCharge() == 6 );
assertTrue( sp.getConstant() == true );
}
public void test_ReadSBML_Species()
{
Species sp;
string s = wrapSBML_L1v2("<listOfSpecies>" +
" <species name='Glucose' compartment='cell' initialAmount='4.1'" +
" units='volume' boundaryCondition='false' charge='6'/>" +
"</listOfSpecies>");
D = libsbml.readSBMLFromString(s);
M = D.getModel();
assertTrue( M.getNumSpecies() == 1 );
sp = M.getSpecies(0);
assertTrue(( "Glucose" == sp.getId() ));
assertTrue(( "cell" == sp.getCompartment() ));
assertTrue(( "volume" == sp.getUnits() ));
assertTrue( sp.getInitialAmount() == 4.1 );
assertTrue( sp.getBoundaryCondition() == false );
assertTrue( sp.getCharge() == 6 );
assertTrue( sp.isSetInitialAmount() == true );
assertTrue( sp.isSetCharge() == true );
}