public void test_KineticLaw_getParameterById()
{
Parameter k1 = new Parameter(2,4);
Parameter k2 = new Parameter(2,4);
k1.setId( "k1");
k2.setId( "k2");
k1.setValue(3.14);
k2.setValue(2.72);
M.addParameter(k1);
M.addParameter(k2);
Reaction r1 = new Reaction(2,4);
r1.setId( "reaction_1" );
KineticLaw kl = new KineticLaw(2,4);
kl.setFormula( "k1 * X0");
Parameter k3 = new Parameter(2,4);
Parameter k4 = new Parameter(2,4);
k3.setId( "k1");
k4.setId( "k2");
k3.setValue(2.72);
k4.setValue(3.14);
kl.addParameter(k3);
kl.addParameter(k4);
r1.setKineticLaw(kl);
M.addReaction(r1);
KineticLaw kl1 = M.getReaction(0).getKineticLaw();
assertNotEquals(kl1.getParameter( "k1" ),k3);
assertNotEquals(kl1.getParameter( "k1" ),k1);
assertNotEquals(kl1.getParameter( "k2" ),k4);
assertEquals(kl1.getParameter( "k3" ),null);
}
public void test_Model_addReaction5()
{
Model m = new Model(2,2);
Reaction r = new Reaction(2,2);
r.setId( "r");
Reaction r1 = new Reaction(2,2);
r1.setId( "r");
int i = m.addReaction(r);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumReactions() == 1 );
i = m.addReaction(r1);
assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID );
assertTrue( m.getNumReactions() == 1 );
r = null;
r1 = null;
m = null;
}
public void test_Model_addReaction3()
{
Model m = new Model(2,2);
Reaction r = new Reaction(1,2);
r.setId( "r");
int i = m.addReaction(r);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( m.getNumReactions() == 0 );
r = null;
m = null;
}
public void test_Model_addReaction1()
{
Model m = new Model(2,2);
Reaction r = new Reaction(2,2);
int i = m.addReaction(r);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
r.setId( "r");
i = m.addReaction(r);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumReactions() == 1 );
r = null;
m = null;
}
public void test_internal_consistency_check_99911_react()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Model m = d.createModel();
Reaction r = new Reaction(2,4);
d.setLevelAndVersion(2,1,false);
r.setId("r");
r.setSBOTerm(2);
m.addReaction(r);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99904_react()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Reaction r = new Reaction(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("cc");
r.setId("r");
r.setMetaId("mmm");
m.addReaction(r);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_Reaction_copyConstructor()
{
Reaction o1 = new Reaction(2,4);
o1.setId("c");
assertTrue( o1.getId() == "c" );
KineticLaw kl = new KineticLaw(2,4);
o1.setKineticLaw(kl);
kl = null;
assertTrue( o1.isSetKineticLaw() == true );
assertNotEquals(o1.getKineticLaw(),null);
Reaction o2 = new Reaction(o1);
assertTrue( o2.getId() == "c" );
assertTrue( o2.isSetKineticLaw() == true );
assertNotEquals(o2.getKineticLaw(),null);
assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() );
o2 = null;
o1 = null;
}
public void test_L3_Reaction_hasRequiredAttributes()
{
Reaction r = new Reaction(3,1);
assertEquals( false, r.hasRequiredAttributes() );
r.setId( "id");
assertEquals( false, r.hasRequiredAttributes() );
r.setFast(false);
assertEquals( false, r.hasRequiredAttributes() );
r.setReversible(false);
assertEquals( true, r.hasRequiredAttributes() );
r = null;
}
public void test_Model_getSpeciesReferenceById()
{
Reaction r1 = new Reaction(2,4);
r1.setId( "r1");
SpeciesReference sr = r1.createReactant();
sr.setId( "s1");
M.addReaction(r1);
assertTrue( M.getNumReactions() == 1 );
assertNotEquals(M.getSpeciesReference( "s1" ),sr);
}
public void test_Model_getReactionById()
{
Reaction r1 = new Reaction(2,4);
Reaction r2 = new Reaction(2,4);
r1.setId( "reaction_1" );
r2.setId( "reaction_2" );
M.addReaction(r1);
M.addReaction(r2);
assertTrue( M.getNumReactions() == 2 );
assertNotEquals(M.getReaction( "reaction_1" ),r1);
assertNotEquals(M.getReaction( "reaction_2" ),r2);
assertEquals(M.getReaction( "reaction_3" ),null);
}
public void test_Model_getReaction()
{
Reaction r1 = new Reaction(2,4);
Reaction r2 = new Reaction(2,4);
r1.setId( "reaction_1");
r2.setId( "reaction_2");
M.addReaction(r1);
M.addReaction(r2);
assertTrue( M.getNumReactions() == 2 );
r1 = M.getReaction(0);
r2 = M.getReaction(1);
assertTrue(( "reaction_1" == r1.getId() ));
assertTrue(( "reaction_2" == r2.getId() ));
}
public void test_Model_addReaction()
{
Reaction r = new Reaction(2,4);
r.setId( "r");
M.addReaction(r);
assertTrue( M.getNumReactions() == 1 );
}
public void test_Reaction_parent_add()
{
Reaction ia = new Reaction(2,4);
Model m = new Model(2,4);
ia.setId("k");
m.addReaction(ia);
ia = null;
ListOf lo = m.getListOfReactions();
assertTrue( lo == m.getReaction(0).getParentSBMLObject() );
assertTrue( m == lo.getParentSBMLObject() );
}
public void test_Reaction()
{
Reaction r = new Reaction(2,4);
assertEquals( false, (r.hasRequiredAttributes()) );
r.setId("r");
assertEquals( true, r.hasRequiredAttributes() );
r = null;
}
public void test_Reaction_ancestor_add()
{
Reaction ia = new Reaction(2,4);
Model m = new Model(2,4);
ia.setId("k");
m.addReaction(ia);
ia = null;
ListOf lo = m.getListOfReactions();
Reaction obj = m.getReaction(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 );
}