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_KineticLaw()
{
KineticLaw kl = new KineticLaw(2, 4);
assertEquals(true, kl.hasRequiredAttributes());
kl = null;
}
public void test_Reaction_parent_NULL()
{
SBMLDocument d = new SBMLDocument();
Model m = d.createModel();
Reaction c = m.createReaction();
SpeciesReference sr = c.createReactant();
KineticLaw kl = c.createKineticLaw();
assertTrue(c.getAncestorOfType(libsbml.SBML_MODEL) == m);
assertEquals(c.getSBMLDocument(), d);
assertTrue(sr.getAncestorOfType(libsbml.SBML_REACTION) == c);
assertTrue(kl.getAncestorOfType(libsbml.SBML_REACTION) == c);
Reaction c1 = c.clone();
d = null;
assertTrue(c1.getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(c1.getParentSBMLObject() == null);
assertEquals(c1.getSBMLDocument(), null);
SpeciesReference sr1 = c1.getReactant(0);
assertTrue(sr1.getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(sr1.getAncestorOfType(libsbml.SBML_REACTION) == c1);
assertEquals(sr1.getSBMLDocument(), null);
assertTrue(c1.getKineticLaw().getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(c1.getKineticLaw().getAncestorOfType(libsbml.SBML_REACTION) == c1);
assertEquals(c1.getKineticLaw().getSBMLDocument(), null);
c1 = null;
}
public void test_SBMLConvert_convertToL3_localParameters()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies("s");
KineticLaw kl = r.createKineticLaw();
kl.setFormula("s*k");
Parameter p = kl.createParameter();
p.setId("k");
assertTrue(kl.getNumLocalParameters() == 0);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
m = d.getModel();
r = m.getReaction(0);
kl = r.getKineticLaw();
assertTrue(kl.getNumLocalParameters() == 1);
LocalParameter lp = kl.getLocalParameter(0);
d = null;
}
public void test_KineticLaw_Parameter_ancestor_create_model()
{
Model m = new Model(2, 4);
Reaction r = m.createReaction();
KineticLaw kl = m.createKineticLaw();
Parameter p = m.createKineticLawParameter();
assertTrue(kl.getNumParameters() == 1);
ListOfParameters lop = kl.getListOfParameters();
assertTrue(p.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl);
assertTrue(p.getAncestorOfType(libsbml.SBML_LIST_OF) == lop);
assertTrue(p.getAncestorOfType(libsbml.SBML_REACTION) == r);
assertTrue(p.getAncestorOfType(libsbml.SBML_MODEL) == m);
assertTrue(p.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(p.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
Parameter obj = kl.getParameter(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lop);
assertTrue(obj.getAncestorOfType(libsbml.SBML_REACTION) == r);
assertTrue(obj.getAncestorOfType(libsbml.SBML_MODEL) == m);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
kl = null;
}
public void test_KineticLaw_parent_create()
{
Reaction r = new Reaction(2, 4);
KineticLaw kl = r.createKineticLaw();
assertTrue(r == kl.getParentSBMLObject());
r = null;
}
public void test_KineticLaw()
{
KineticLaw kl = new KineticLaw(2, 4);
assertEquals(false, (kl.hasRequiredElements()));
kl.setMath(libsbml.parseFormula("kl"));
assertEquals(true, kl.hasRequiredElements());
kl = null;
}
public void test_KineticLaw_setTimeUnits4()
{
KineticLaw kl1 = new KineticLaw(1, 2);
int i = kl1.setTimeUnits("");
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertEquals(false, kl1.isSetTimeUnits());
kl1 = null;
}
public void test_KineticLaw_L1()
{
KineticLaw kl = new KineticLaw(1, 2);
assertEquals(false, (kl.hasRequiredAttributes()));
kl.setFormula("kl");
assertEquals(true, kl.hasRequiredAttributes());
kl = null;
}
public void setUp()
{
KL = new KineticLaw(3, 1);
if (KL == null)
{
;
}
{
}
}
public void test_KineticLaw_createParameter()
{
KineticLaw kl = new KineticLaw(2, 2);
Parameter p = kl.createParameter();
assertTrue(kl.getNumParameters() == 1);
assertTrue((p).getLevel() == 2);
assertTrue((p).getVersion() == 2);
kl = null;
}
public void test_KineticLaw_addParameter4()
{
KineticLaw kl = new KineticLaw(2, 2);
Parameter p = null;
int i = kl.addParameter(p);
assertTrue(i == libsbml.LIBSBML_OPERATION_FAILED);
assertTrue(kl.getNumParameters() == 0);
kl = null;
}
public void setUp()
{
kl = new KineticLaw(2, 4);
if (kl == null)
{
;
}
{
}
}
public void test_KineticLaw_parent_create_model()
{
Model m = new Model(2, 4);
Reaction r = m.createReaction();
KineticLaw kl = r.createKineticLaw();
assertTrue(r == kl.getParentSBMLObject());
assertTrue(r == r.getKineticLaw().getParentSBMLObject());
r = null;
}
public void test_Reaction_createKineticLaw()
{
Reaction r = new Reaction(2, 2);
KineticLaw kl = r.createKineticLaw();
assertTrue(r.isSetKineticLaw() == true);
assertTrue((kl).getLevel() == 2);
assertTrue((kl).getVersion() == 2);
r = null;
}
public void test_KineticLaw_parent_add()
{
KineticLaw kl = new KineticLaw(2, 4);
kl.setMath(libsbml.parseFormula("1"));
Reaction r = new Reaction(2, 4);
r.setKineticLaw(kl);
assertTrue(r == r.getKineticLaw().getParentSBMLObject());
r = null;
}
public void test_Model_createKineticLaw()
{
Model m = new Model(2, 2);
Reaction p = m.createReaction();
KineticLaw kl = m.createKineticLaw();
assertTrue(p.isSetKineticLaw() == true);
assertTrue((kl).getLevel() == 2);
assertTrue((kl).getVersion() == 2);
m = null;
}
public void test_Reaction_setKineticLaw3()
{
KineticLaw kl = new KineticLaw(1, 2);
kl.setMath(libsbml.parseFormula("1"));
int i = R.setKineticLaw(kl);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertEquals(true, R.isSetKineticLaw());
kl = null;
}
public void test_Reaction_setKineticLaw2()
{
KineticLaw kl = new KineticLaw(1, 1);
kl.setMath(libsbml.parseFormula("1"));
int i = R.setKineticLaw(kl);
assertTrue(i == libsbml.LIBSBML_VERSION_MISMATCH);
assertEquals(false, R.isSetKineticLaw());
kl = null;
}
public void test_KineticLaw_setTimeUnits3()
{
KineticLaw kl1 = new KineticLaw(1, 2);
int i = kl1.setTimeUnits("1second");
assertTrue(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE);
assertEquals(false, kl1.isSetTimeUnits());
i = kl1.unsetTimeUnits();
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertEquals(false, kl1.isSetTimeUnits());
kl1 = null;
}
public void test_KineticLaw_setSubstanceUnits2()
{
KineticLaw kl1 = new KineticLaw(1, 2);
int i = kl1.setSubstanceUnits("mole");
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertEquals(true, kl1.isSetSubstanceUnits());
i = kl1.unsetSubstanceUnits();
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertEquals(false, kl1.isSetSubstanceUnits());
kl1 = null;
}
public void test_KineticLaw_Parameter_parent_create()
{
KineticLaw kl = new KineticLaw(2, 4);
Parameter p = kl.createParameter();
assertTrue(kl.getNumParameters() == 1);
ListOfParameters lop = kl.getListOfParameters();
assertTrue(kl == lop.getParentSBMLObject());
assertTrue(lop == p.getParentSBMLObject());
assertTrue(lop == kl.getParameter(0).getParentSBMLObject());
kl = null;
}
public void test_Model_createKineticLawParameters()
{
Model m = new Model(2, 2);
Reaction r = m.createReaction();
KineticLaw kl = m.createKineticLaw();
Parameter p = m.createKineticLawParameter();
assertTrue(r.isSetKineticLaw() == true);
assertTrue(kl.getNumParameters() == 1);
assertTrue((p).getLevel() == 2);
assertTrue((p).getVersion() == 2);
m = null;
}
public void test_KineticLaw_addParameter3()
{
KineticLaw kl = new KineticLaw(2, 2);
Parameter p = new Parameter(1, 2);
p.setId("p");
int i = kl.addParameter(p);
assertTrue(i == libsbml.LIBSBML_LEVEL_MISMATCH);
assertTrue(kl.getNumParameters() == 0);
p = null;
kl = null;
}
public void test_KineticLaw_addParameter1()
{
KineticLaw kl = new KineticLaw(2, 2);
Parameter p = new Parameter(2, 2);
int i = kl.addParameter(p);
assertTrue(i == libsbml.LIBSBML_INVALID_OBJECT);
p.setId("p");
i = kl.addParameter(p);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(kl.getNumParameters() == 1);
p = null;
kl = null;
}
public void test_WriteL3SBML_KineticLaw_ListOfParameters()
{
string expected = "<kineticLaw>\n" +
" <listOfLocalParameters>\n" +
" <localParameter id=\"n\" value=\"1.2\"/>\n" +
" </listOfLocalParameters>\n" +
"</kineticLaw>";
KineticLaw kl = D.createModel().createReaction().createKineticLaw();
LocalParameter p = kl.createLocalParameter();
p.setId("n");
p.setValue(1.2);
assertEquals(true, equals(expected, kl.toSBML()));
}
public void test_KineticLaw_ancestor_add()
{
KineticLaw kl = new KineticLaw(2, 4);
kl.setMath(libsbml.parseFormula("1"));
Reaction r = new Reaction(2, 4);
r.setKineticLaw(kl);
KineticLaw obj = r.getKineticLaw();
assertTrue(obj.getAncestorOfType(libsbml.SBML_REACTION) == r);
assertTrue(obj.getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
r = null;
}
public void test_KineticLaw_Parameter_parent_create_model()
{
Model m = new Model(2, 4);
Reaction r = m.createReaction();
KineticLaw kl = m.createKineticLaw();
Parameter p = m.createKineticLawParameter();
assertTrue(kl.getNumParameters() == 1);
ListOfParameters lop = kl.getListOfParameters();
assertTrue(r == kl.getParentSBMLObject());
assertTrue(kl == lop.getParentSBMLObject());
assertTrue(lop == p.getParentSBMLObject());
assertTrue(lop == kl.getParameter(0).getParentSBMLObject());
kl = null;
}
public void test_KineticLaw_Parameter_parent_add()
{
KineticLaw kl = new KineticLaw(2, 4);
Parameter p = new Parameter(2, 4);
p.setId("jake");
kl.addParameter(p);
p = null;
assertTrue(kl.getNumParameters() == 1);
assertTrue(kl.getParameter(0).getId() == "jake");
ListOfParameters lop = kl.getListOfParameters();
assertTrue(kl == lop.getParentSBMLObject());
assertTrue(lop == kl.getParameter(0).getParentSBMLObject());
kl = null;
}
public void test_KineticLaw_parent_NULL()
{
Reaction r = new Reaction(2, 4);
KineticLaw kl = r.createKineticLaw();
Parameter p = kl.createParameter();
assertTrue(r == kl.getParentSBMLObject());
assertTrue(r == p.getAncestorOfType(libsbml.SBML_REACTION));
assertTrue(kl == p.getAncestorOfType(libsbml.SBML_KINETIC_LAW));
KineticLaw kl1 = kl.clone();
assertTrue(kl1.getParentSBMLObject() == null);
assertTrue(kl1.getParameter(0).getAncestorOfType(libsbml.SBML_REACTION) == null);
assertTrue(kl1 == kl1.getParameter(0).getAncestorOfType(libsbml.SBML_KINETIC_LAW));
r = null;
}
public void KineticLawElement(Hashtable attrs)
{
Reaction reaction = (Reaction)elementStack.Peek();
KineticLaw kLaw = new KineticLaw(this.model);
reaction.kineticLaw = kLaw;
elementStack.Push(kLaw);
}
