/// <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_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() );
}
public void test_Species_parent_add()
{
Species ia = new Species(2,4);
ia.setId("s");
ia.setCompartment("c");
Model m = new Model(2,4);
m.addSpecies(ia);
ia = null;
ListOf lo = m.getListOfSpecies();
assertTrue( lo == m.getSpecies(0).getParentSBMLObject() );
assertTrue( m == lo.getParentSBMLObject() );
}
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 );
}
public void test_Species_ancestor_add()
{
Species ia = new Species(2,4);
Model m = new Model(2,4);
ia.setId("s");
ia.setCompartment("c");
m.addSpecies(ia);
ia = null;
ListOf lo = m.getListOfSpecies();
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 );
}
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_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 );
}