public void test_Model_createCompartment()
{
Model m = new Model(2,2);
Compartment p = m.createCompartment();
assertTrue( m.getNumCompartments() == 1 );
assertTrue( (p).getLevel() == 2 );
assertTrue( (p).getVersion() == 2 );
m = null;
}
public void test_Model_L1V2()
{
Model m = new Model(1,2);
assertEquals( false, (m.hasRequiredElements()) );
m.createCompartment();
assertEquals( true, m.hasRequiredElements() );
m = null;
}
public void test_internal_consistency_check_99904_model()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
d.setLevelAndVersion(1,2,false);
Model m = new Model(2,4);
Compartment c = m.createCompartment();
c.setId("cc");
m.setMetaId("mmm");
d.setModel(m);
errors = d.checkInternalConsistency();
assertTrue( errors == 1 );
assertTrue( d.getError(0).getErrorId() == 20201 );
d = 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_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 createSystem(EcellObject anEml, Model aSBMLModel)
{
if ( anEml.LocalID == "SBMLParameter" || anEml.LocalID == "SBMLRule" )
return;
// create Compartment object
Compartment aCompartment = aSBMLModel.createCompartment();
// set ID ROOT System and Other System
string aCompartmentID = "";
if (anEml.LocalID == "/")
aCompartmentID = "default"; // Root system
else
aCompartmentID = anEml.LocalID;
// aCompartmentID = "default" + anEml.Key.Replace( "/", "__" );
ID_Namespace.Add( aCompartmentID );
if (aSBMLModel.getLevel() == 1)
aCompartment.setName( aCompartmentID );
else if (aSBMLModel.getLevel() == 2)
aCompartment.setId( aCompartmentID );
foreach(EcellObject child in anEml.Children)
{
if (!(child is EcellVariable))
continue;
// set Size and constant of Compartment
if( child.LocalID == "SIZE" )
{
double size = ((EcellSystem)anEml).SizeInVolume;
aCompartment.setSize(size);
EcellValue value = anEml.GetEcellValue("Fixed");
if(value != null)
aCompartment.setConstant(System.Convert.ToBoolean((int)value));
}
// set Dimensions of Compartment
else if( child.LocalID == "Dimensions" )
{
int dimension = (int)child.GetEcellValue("Value");
aCompartment.setSpatialDimensions(dimension);
}
}
// set Outside element of Compartment
if( anEml.ParentSystemID == "/" && anEml.LocalID != "")
{
aCompartment.setOutside( "default" );
}
else if (!string.IsNullOrEmpty(anEml.ParentSystemID))
{
aCompartment.setOutside(
getCurrentCompartment( anEml.ParentSystemID ));
}
}
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_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 );
}