public void test_ListOf_append()
{
Model m = new Model(2,4);
m.createCompartment();
ListOf loc = m.getListOfCompartments();
assertTrue( loc.size() == 1 );
SBase c = new Compartment(2,4);
int i = loc.append(c);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( loc.size() == 2 );
SBase sp = new Species(2,4);
i = loc.append(sp);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
assertTrue( loc.size() == 2 );
m = null;
sp = 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_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_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_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() );
}
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 );
}
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_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_SBML_C_parseL3Formula_modelPresent3()
{
Model model = new Model(3,1);
Compartment p = model.createCompartment();
p.setId( "NaN");;
ASTNode r = libsbml.parseL3FormulaWithModel("NaN", model);
assertTrue( r.getType() == libsbml.AST_NAME );
assertTrue(( "NaN" == r.getName() ));
assertTrue( r.getNumChildren() == 0 );
r = null;
}
public void test_SBMLDocument_setModel2()
{
SBMLDocument d = new SBMLDocument(2,2);
Model m1 = new Model(1,2);
m1.createCompartment();
int i = d.setModel(m1);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( d.getModel() == null );
d = null;
}
public void test_SBMLDocument_clone()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(1,1,false);
Model m = new Model(1,1);
m.createCompartment();
m.createSpecies();
m.createReaction();
m.setId("foo");
o1.setModel(m);
assertTrue( o1.getLevel() == 1 );
assertTrue( o1.getVersion() == 1 );
assertTrue( o1.getModel().getId() == "foo" );
assertTrue( o1.getModel().getLevel() == 1 );
assertTrue( o1.getModel().getVersion() == 1 );
assertTrue( o1.getModel().getSBMLDocument() == o1 );
SBMLDocument o2 = o1.clone();
assertTrue( o2.getLevel() == 1 );
assertTrue( o2.getVersion() == 1 );
assertTrue( o2.getModel().getId() == "foo" );
assertTrue( o2.getModel().getLevel() == 1 );
assertTrue( o2.getModel().getVersion() == 1 );
assertTrue( o2.getModel().getSBMLDocument() == o2 );
o2 = null;
o1 = null;
}
