public void test_L3_SpeciesReference_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1);
sbmlns.addNamespaces(xmlns);
SpeciesReference sr = new SpeciesReference(sbmlns);
assertTrue(sr.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE);
assertTrue(sr.getMetaId() == "");
assertTrue(sr.getNotes() == null);
assertTrue(sr.getAnnotation() == null);
assertTrue(sr.getLevel() == 3);
assertTrue(sr.getVersion() == 1);
assertTrue(sr.getNamespaces() != null);
assertTrue(sr.getNamespaces().getLength() == 2);
assertTrue(sr.getId() == "");
assertTrue(sr.getName() == "");
assertTrue(sr.getSpecies() == "");
assertEquals(true, isnan(sr.getStoichiometry()));
assertTrue(sr.getConstant() == false);
assertEquals(false, sr.isSetId());
assertEquals(false, sr.isSetName());
assertEquals(false, sr.isSetSpecies());
assertEquals(false, sr.isSetStoichiometry());
assertEquals(false, sr.isSetConstant());
sr = null;
}
public void test_SBMLConvert_convertToL3_stoichiometryMath()
{
SBMLDocument d = new SBMLDocument(2, 1);
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");
StoichiometryMath sm = sr.createStoichiometryMath();
ASTNode ast = libsbml.parseFormula("c*2");
sm.setMath(ast);
assertTrue(m.getNumRules() == 0);
assertTrue(sr.isSetId() == false);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
m = d.getModel();
r = m.getReaction(0);
sr = r.getReactant(0);
assertTrue(m.getNumRules() == 1);
assertTrue(sr.isSetId() == true);
Rule rule = m.getRule(0);
assertTrue((rule.getVariable() == sr.getId()));
d = null;
}
public void test_SpeciesReference()
{
SpeciesReference sr = new SpeciesReference(2, 4);
assertEquals(true, sr.hasRequiredElements());
sr = 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;
}
/// <summary>
/// Creates a MoBi ReactionPartner by a given SBML Species Reference
/// </summary>
private IReactionPartnerBuilder CreateReactionPartner(SpeciesReference speciesReference, Model model)
{
var molecule = _sbmlInformation.GetMoleculeBySBMLId(speciesReference.getSpecies());
if (molecule == null)
{
return(null);
}
IReactionPartnerBuilder productBuilder = new ReactionPartnerBuilder
{
MoleculeName = molecule.Name,
};
if (speciesReference.isSetStoichiometryMath())
{
CreateStoichiometryErrorMsg(speciesReference.getSpecies());
}
productBuilder.StoichiometricCoefficient = speciesReference.isSetStoichiometry() ? speciesReference.getStoichiometry() : SBMLConstants.SBML_STOICHIOMETRY_DEFAULT;
var species = GetSpeciesById(speciesReference.getSpecies(), model);
if (species == null)
{
return(productBuilder);
}
if (species.getConstant() && species.getBoundaryCondition() == false)
{
productBuilder.StoichiometricCoefficient = 0;
}
return(productBuilder);
}
public void test_SpeciesReference_setStoichiometryMath7()
{
SpeciesReference sr1 = new SpeciesReference(1, 2);
int i = sr1.unsetStoichiometryMath();
assertTrue(i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE);
sr1 = null;
}
public void test_SpeciesReference_setName3()
{
SpeciesReference c = new SpeciesReference(2, 1);
int i = c.setName("cell");
assertTrue(i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE);
assertEquals(false, c.isSetName());
c = null;
}
public void test_SpeciesReference_setDenominator2()
{
SpeciesReference c = new SpeciesReference(2, 2);
int i = c.setDenominator(4);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(c.getDenominator() == 4);
c = null;
}
public void test_SpeciesReference_setStoichiometry2()
{
SpeciesReference c = new SpeciesReference(2, 2);
int i = c.setStoichiometry(4);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(c.getStoichiometry() == 4.0);
c = null;
}
public void test_SpeciesReference_setSpecies2()
{
SpeciesReference c = new SpeciesReference(2, 2);
int i = c.setSpecies("1cell");
assertTrue(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE);
assertEquals(false, c.isSetSpecies());
c = null;
}
public void test_SpeciesReference()
{
SpeciesReference sr = new SpeciesReference(2, 4);
assertEquals(false, (sr.hasRequiredAttributes()));
sr.setSpecies("sr");
assertEquals(true, sr.hasRequiredAttributes());
sr = null;
}
public void setUp()
{
sr = new SpeciesReference(2, 4);
if (sr == null)
{
;
}
{
}
}
public void test_Reaction_createReactant()
{
Reaction m = new Reaction(2, 2);
SpeciesReference p = m.createReactant();
assertTrue(m.getNumReactants() == 1);
assertTrue((p).getLevel() == 2);
assertTrue((p).getVersion() == 2);
m = null;
}
public void test_Reaction_addReactant4()
{
Reaction m = new Reaction(2, 2);
SpeciesReference p = null;
int i = m.addReactant(p);
assertTrue(i == libsbml.LIBSBML_OPERATION_FAILED);
assertTrue(m.getNumReactants() == 0);
m = null;
}
public void test_SpeciesReference_setSpecies3()
{
SpeciesReference c = new SpeciesReference(2, 2);
int i = c.setSpecies("mole");
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(("mole" == c.getSpecies()));
assertEquals(true, c.isSetSpecies());
c = null;
}
public void setUp()
{
SR = new SpeciesReference(3, 1);
if (SR == null)
{
;
}
{
}
}
public void test_SpeciesReference_Reactant_parent_create()
{
Reaction r = new Reaction(2, 4);
SpeciesReference sr = r.createReactant();
ListOf lo = r.getListOfReactants();
assertTrue(lo == r.getReactant(0).getParentSBMLObject());
assertTrue(lo == sr.getParentSBMLObject());
assertTrue(r == lo.getParentSBMLObject());
}
public void test_WriteL3SBML_SpeciesReference()
{
string expected = "<speciesReference species=\"s\"" + " stoichiometry=\"3\" constant=\"true\"/>";
SpeciesReference sr = D.createModel().createReaction().createReactant();
sr.setSpecies("s");
sr.setStoichiometry(3);
sr.setConstant(true);
assertEquals(true, equals(expected, sr.toSBML()));
}
public void test_Model_createReactant()
{
Model m = new Model(2, 2);
Reaction p = m.createReaction();
SpeciesReference sr = m.createReactant();
assertTrue(p.getNumReactants() == 1);
assertTrue((sr).getLevel() == 2);
assertTrue((sr).getVersion() == 2);
m = null;
}
public void test_SpeciesReference_Product_parent_create_model()
{
Model m = new Model(2, 4);
Reaction r = m.createReaction();
SpeciesReference sr = m.createProduct();
ListOf lo = r.getListOfProducts();
assertTrue(lo == r.getProduct(0).getParentSBMLObject());
assertTrue(lo == sr.getParentSBMLObject());
assertTrue(r == lo.getParentSBMLObject());
}
public void test_L3_SpeciesReference_hasRequiredAttributes()
{
SpeciesReference sr = new SpeciesReference(3, 1);
assertEquals(false, sr.hasRequiredAttributes());
sr.setSpecies("id");
assertEquals(false, sr.hasRequiredAttributes());
sr.setConstant(false);
assertEquals(true, sr.hasRequiredAttributes());
sr = null;
}
public void test_Reaction_addReactant()
{
SpeciesReference sr = new SpeciesReference(2, 4);
sr.setSpecies("s");
R.addReactant(sr);
assertTrue(R.getNumReactants() == 1);
assertTrue(R.getNumProducts() == 0);
assertTrue(R.getNumModifiers() == 0);
sr = null;
}
public void test_StoichiometryMath_parent_add()
{
StoichiometryMath m = new StoichiometryMath(2, 4);
m.setMath(libsbml.parseFormula("1"));
SpeciesReference sr = new SpeciesReference(2, 4);
sr.setStoichiometryMath(m);
m = null;
assertTrue(sr == sr.getStoichiometryMath().getParentSBMLObject());
sr = 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_SpeciesReference_copyConstructor()
{
SpeciesReference o1 = new SpeciesReference(2, 4);
o1.setId("c");
assertTrue(o1.getId() == "c");
SpeciesReference o2 = new SpeciesReference(o1);
assertTrue(o2.getId() == "c");
assertTrue(o2.getParentSBMLObject() == o1.getParentSBMLObject());
o2 = null;
o1 = null;
}
public void test_SpeciesReference_Reactant_parent_add()
{
SpeciesReference sr = new SpeciesReference(2, 4);
Reaction r = new Reaction(2, 4);
sr.setSpecies("s");
r.addReactant(sr);
sr = null;
ListOf lo = r.getListOfReactants();
assertTrue(lo == r.getReactant(0).getParentSBMLObject());
assertTrue(r == lo.getParentSBMLObject());
}
public void test_Reaction_addProduct2()
{
Reaction m = new Reaction(2, 2);
SpeciesReference p = new SpeciesReference(2, 1);
p.setSpecies("k");
int i = m.addProduct(p);
assertTrue(i == libsbml.LIBSBML_VERSION_MISMATCH);
assertTrue(m.getNumProducts() == 0);
p = null;
m = null;
}
public void test_Reaction_addReactant3()
{
Reaction m = new Reaction(2, 2);
SpeciesReference p = new SpeciesReference(1, 2);
p.setSpecies("k");
int i = m.addReactant(p);
assertTrue(i == libsbml.LIBSBML_LEVEL_MISMATCH);
assertTrue(m.getNumReactants() == 0);
p = null;
m = null;
}
public void test_SBMLConvert_convertToL3_reactant()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
SpeciesReference sr1;
sr.setSpecies("s");
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
sr1 = m.getReaction(0).getReactant(0);
assertTrue(sr1.hasRequiredAttributes() == true);
d = null;
}
public void setSpeciesReference(int linkNumber, ComponentLinkType linkType, SpeciesReference reference)
{
switch (linkType)
{
case ComponentLinkType.Input:
reactants[linkNumber] = reference;
break;
case ComponentLinkType.Output:
products[linkNumber] = reference;
break;
}
}
public void SpeciesReferenceElement(Hashtable attrs)
{
String speciesId;
Species species;
try
{
speciesId = (String)attrs["species"];
species = (Species)this.model.findObject(speciesId);
// find out if it is a list of reactants or products
if (((String)elementStack.Pop()) == "listOfReactants")
{
SpeciesReference speciesRef;
List<SpeciesReference> reactantsList = (List<SpeciesReference>)elementStack.Peek();
if (attrs.Contains("stoichiometry"))
{
speciesRef = new SpeciesReference(this.model, species,
(double)(Double.Parse((String)attrs["stoichiometry"])));
}
else
{
speciesRef = new SpeciesReference(this.model, species);
}
reactantsList.Add(speciesRef);
elementStack.Push("listOfReactants");
}
else
// list of products instead
{
SpeciesReference speciesRef;
List<SpeciesReference> productsList = (List<SpeciesReference>)elementStack.Peek();
if (attrs.Contains("stoichiometry"))
{
speciesRef = new SpeciesReference(this.model, species,
(double)(Double.Parse((String)attrs["stoichiometry"])));
}
else
{
speciesRef = new SpeciesReference(this.model, species);
}
productsList.Add(speciesRef);
elementStack.Push("listOfProducts");
}
}
catch (ArgumentNullException e)
{
Console.WriteLine("speciesReference element missing required attribute 'species'");
throw (e);
}
}