public void test_L3_Species_hasRequiredAttributes()
{
Species s = new Species(3,1);
assertEquals( false, s.hasRequiredAttributes() );
s.setId( "id");
assertEquals( false, s.hasRequiredAttributes() );
s.setCompartment( "cell");
assertEquals( false, s.hasRequiredAttributes() );
s.setHasOnlySubstanceUnits(false);
assertEquals( false, s.hasRequiredAttributes() );
s.setBoundaryCondition(false);
assertEquals( false, s.hasRequiredAttributes() );
s.setConstant(false);
assertEquals( true, s.hasRequiredAttributes() );
s = 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_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_internal_consistency_check_99919()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Species s = new Species(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
s.setId("s");
s.setCompartment("c");
s.setHasOnlySubstanceUnits(true);
m.addSpecies(s);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = 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_internal_consistency_check_99916_reaction()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Species s = new Species(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Reaction r = m.createReaction();
r.setId("r");
SpeciesReference sr = r.createReactant();
s.setId("s");
s.setCompartment("c");
s.setConstant(true);
sr.setSpecies("s");
m.addSpecies(s);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99916_rule()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Species s = new Species(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
s.setId("s");
s.setCompartment("c");
s.setConstant(true);
m.addSpecies(s);
Rule r = m.createAssignmentRule();
r.setVariable("s");
r.setFormula("2");
errors = d.checkInternalConsistency();
assertTrue( errors == 2 );
d = null;
}
public void test_SBMLConvert_convertToL1_Species_Amount()
{
SBMLDocument d = new SBMLDocument(2,1);
Model m = d.createModel();
string sid = "C";
Compartment c = new Compartment(2,4);
Species s = new Species(2,4);
c.setId(sid);
m.addCompartment(c);
s.setCompartment(sid);
s.setInitialAmount(2.34);
m.addSpecies(s);
assertTrue( d.setLevelAndVersion(1,2,true) == true );
assertTrue( s.getInitialAmount() == 2.34 );
d = null;
}
public void test_SBMLConvert_convertToL1_Species_Concentration()
{
SBMLDocument d = new SBMLDocument(2,1);
Model m = d.createModel();
string sid = "C";
Compartment c = new Compartment(2,1);
Species s = new Species(2,1);
c.setId(sid);
c.setSize(1.2);
m.addCompartment(c);
s.setId( "s" );
s.setCompartment(sid);
s.setInitialConcentration(2.34);
m.addSpecies(s);
assertTrue( d.setLevelAndVersion(1,2,true) == true );
Species s1 = m.getSpecies(0);
assertTrue( s1 != null );
assertTrue(( "C" == s1.getCompartment() ));
assertTrue( m.getCompartment( "C").getSize() == 1.2 );
assertTrue( s1.getInitialConcentration() == 2.34 );
assertTrue( s1.isSetInitialConcentration() == true );
d = null;
}
public void test_Model_getSpecies()
{
Species s1 = new Species(2,4);
Species s2 = new Species(2,4);
s1.setId( "Glucose" );
s2.setId( "Glucose_6_P" );
s1.setCompartment( "c");
s2.setCompartment( "c");
M.addSpecies(s1);
M.addSpecies(s2);
assertTrue( M.getNumSpecies() == 2 );
s1 = M.getSpecies(0);
s2 = M.getSpecies(1);
assertTrue(( "Glucose" == s1.getId() ));
assertTrue(( "Glucose_6_P" == s2.getId() ));
}
public void test_Model_getSpeciesById()
{
Species s1 = new Species(2,4);
Species s2 = new Species(2,4);
s1.setId( "Glucose" );
s2.setId( "Glucose_6_P" );
s1.setCompartment( "c");
s2.setCompartment( "c");
M.addSpecies(s1);
M.addSpecies(s2);
assertTrue( M.getNumSpecies() == 2 );
assertTrue( M.getSpecies( "Glucose" ) != s1 );
assertTrue( M.getSpecies( "Glucose_6_P") != s2 );
assertTrue( M.getSpecies( "Glucose2" ) == null );
}
public void test_Model_getNumSpeciesWithBoundaryCondition()
{
Species s1 = new Species(2,4);
Species s2 = new Species(2,4);
Species s3 = new Species(2,4);
s1.setId( "s1");
s2.setId( "s2");
s3.setId( "s3");
s1.setCompartment( "c1");
s2.setCompartment( "c2");
s3.setCompartment( "c3");
s1.setBoundaryCondition(true);
s2.setBoundaryCondition(false);
s3.setBoundaryCondition(true);
assertTrue( M.getNumSpecies() == 0 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 0 );
M.addSpecies(s1);
assertTrue( M.getNumSpecies() == 1 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 1 );
M.addSpecies(s2);
assertTrue( M.getNumSpecies() == 2 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 1 );
M.addSpecies(s3);
assertTrue( M.getNumSpecies() == 3 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 2 );
}
public void test_Model_addSpecies()
{
Species s = new Species(2,4);
s.setId( "s");
s.setCompartment( "c");
M.addSpecies(s);
assertTrue( M.getNumSpecies() == 1 );
}
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_L1()
{
Species s = new Species(1,2);
assertEquals( false, (s.hasRequiredAttributes()) );
s.setId("s");
assertEquals( false, (s.hasRequiredAttributes()) );
s.setCompartment("c");
assertEquals( false, (s.hasRequiredAttributes()) );
s.setInitialAmount(2);
assertEquals( true, s.hasRequiredAttributes() );
s = 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 );
}