public void test_SBMLConvertStrict_convertL1ParamRule()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Parameter p = m.createParameter();
p.setId("p");
Parameter p1 = m.createParameter();
p1.setId("p1");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable("p1");
ar.setMath(math);
ar.setUnits("mole");
assertTrue(d.setLevelAndVersion(2, 1, true) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
Rule r1 = d.getModel().getRule(0);
assertTrue(r1.getUnits() == "");
d = null;
}
public void test_SBMLConvertStrict_convertNonStrictSBO()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
c.setConstant(false);
(c).setSBOTerm(64);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 1, true) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
Compartment c1 = d.getModel().getCompartment(0);
assertTrue((c1).getSBOTerm() == -1);
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
assertTrue(d.getLevel() == 1);
assertTrue(d.getVersion() == 2);
Compartment c2 = d.getModel().getCompartment(0);
assertTrue((c2).getSBOTerm() == -1);
d = 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;
}
protected override void Because()
{
var model = new Model(3, 1);
model.setName("TestModel");
model.setNotes("TestNotes");
model.setMetaId("TestMetaId");
sut.CreateEventsTopContainer();
sut.CreateTopContainer(model);
var compartment = new Compartment(3, 1);
compartment.setName("Compartment");
compartment.setId("c1");
compartment.setSpatialDimensions(1);
compartment.setSize(5);
var compartment2 = new Compartment(3, 1);
compartment2.setName("Compartment");
compartment2.setId("c2");
compartment2.setSpatialDimensions(2);
compartment2.setSize(5);
var compartment3 = new Compartment(3, 1);
compartment3.setName("Compartment");
compartment3.setId("c3");
compartment3.setSpatialDimensions(3);
compartment3.setSize(5);
_container = sut.CreateContainerFromCompartment(compartment);
_container2 = sut.CreateContainerFromCompartment(compartment2);
_container3 = sut.CreateContainerFromCompartment(compartment3);
sut.CreateSpatialStructureFromModel(sut._topContainer, model);
}
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_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_L3_Compartment_initDefaults()
{
Compartment c = new Compartment(3, 1);
c.setId("A");
assertEquals(true, c.isSetId());
assertEquals(false, c.isSetName());
assertEquals(false, c.isSetSize());
assertEquals(false, c.isSetVolume());
assertEquals(false, c.isSetUnits());
assertEquals(false, c.isSetConstant());
assertEquals(false, c.isSetSpatialDimensions());
c.initDefaults();
assertTrue(("A" == c.getId()));
assertTrue(c.getName() == "");
assertTrue(("litre" == c.getUnits()));
assertTrue(c.getSpatialDimensions() == 3);
assertTrue(c.getSize() == 1);
assertTrue(c.getConstant() == true);
assertEquals(true, c.isSetId());
assertEquals(false, c.isSetName());
assertEquals(false, c.isSetSize());
assertEquals(false, c.isSetVolume());
assertEquals(true, c.isSetUnits());
assertEquals(true, c.isSetConstant());
assertEquals(true, c.isSetSpatialDimensions());
c = null;
}
public void test_SBMLConvertStrict_convertToL1()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
(m).setMetaId("_m");
Compartment c = m.createCompartment();
c.setId("c");
(c).setSBOTerm(240);
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
assertTrue(d.getLevel() == 1);
assertTrue(d.getVersion() == 2);
Model m1 = d.getModel();
assertTrue((m1).getMetaId() == "");
Compartment c1 = m1.getCompartment(0);
assertTrue((c1).getSBOTerm() == -1);
Species s1 = m1.getSpecies(0);
assertTrue(s1.getHasOnlySubstanceUnits() == false);
d = null;
}
public void test_SBMLConvertStrict_convertNonStrictUnits()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
c.setConstant(false);
Parameter p = m.createParameter();
p.setId("p");
p.setUnits("mole");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable("c");
ar.setMath(math);
assertTrue(d.setLevelAndVersion(2, 1, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(1, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
d = null;
}
public void test_Model_addCompartment()
{
Compartment c = new Compartment(2, 4);
c.setId("c");
M.addCompartment(c);
assertTrue(M.getNumCompartments() == 1);
}
public void test_WriteL3SBML_Compartment()
{
string expected = "<compartment id=\"A\" constant=\"true\"/>";
Compartment c = D.createModel().createCompartment();
c.setId("A");
c.setConstant(true);
assertEquals(true, equals(expected, c.toSBML()));
}
public void test_Compartment_setId4()
{
Compartment c = new Compartment(2, 2);
int i = c.setId("");
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertEquals(false, c.isSetId());
c = null;
}
public void test_Compartment_setId2()
{
Compartment c = new Compartment(2, 2);
int i = c.setId("1cell");
assertTrue(i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE);
assertEquals(false, c.isSetId());
c = null;
}
public void test_Compartment()
{
Compartment c = new Compartment(2, 4);
assertEquals(false, (c.hasRequiredAttributes()));
c.setId("c");
assertEquals(true, c.hasRequiredAttributes());
c = null;
}
public void test_L3_Compartment_hasRequiredAttributes()
{
Compartment c = new Compartment(3, 1);
assertEquals(false, c.hasRequiredAttributes());
c.setId("id");
assertEquals(false, c.hasRequiredAttributes());
c.setConstant(false);
assertEquals(true, c.hasRequiredAttributes());
c = null;
}
static void testCreateSBML()
{
SBMLDocument d = new SBMLDocument(defLevel, defVersion);
Model m = d.createModel();
m.setId("testmodel");
Compartment c1 = m.createCompartment();
Compartment c2 = m.createCompartment();
c1.setId("c1");
c2.setId("c2");
Species s1 = m.createSpecies();
Species s2 = m.createSpecies();
string id1 = "s1";
string id2 = "s2";
// strings with non-ASCII characters (multibyte characters)
string n1 = "γ-lyase";
string n2 = "β-synthase";
s1.setId(id1);
s1.setName(n1);
s1.setCompartment("c1");
s2.setId(id2);
s2.setName(n2);
s2.setCompartment("c2");
string file = "test2.xml";
try
{
if (libsbml.writeSBML(d, file) == 0)
{
ERR("[CreateSBML] Error: cannot write " + file);
}
else
{
OK();
}
}
catch (Exception e)
{
ERR("[CreateSBML] (" + file + ") Error: Exception thrown : " + e.Message);
}
testReadSBMLFromFile(file);
}
public void test_Model_addCompartment3()
{
Model m = new Model(2, 2);
Compartment c = new Compartment(1, 2);
c.setId("c");
int i = m.addCompartment(c);
assertTrue(i == libsbml.LIBSBML_LEVEL_MISMATCH);
assertTrue(m.getNumCompartments() == 0);
c = null;
m = null;
}
public void test_WriteL3SBML_Compartment_spatialDimensions()
{
string expected = "<compartment id=\"A\" spatialDimensions=\"2.1\" " + "constant=\"false\"/>";
string expected1 = "<compartment id=\"A\" constant=\"false\"/>";
Compartment c = D.createModel().createCompartment();
c.setId("A");
c.setConstant(false);
c.setSpatialDimensions(2.1);
assertEquals(true, equals(expected, c.toSBML()));
c.unsetSpatialDimensions();
assertEquals(true, equals(expected1, c.toSBML()));
}
public void test_Model_addCompartment1()
{
Model m = new Model(2, 2);
Compartment c = new Compartment(2, 2);
int i = m.addCompartment(c);
assertTrue(i == libsbml.LIBSBML_INVALID_OBJECT);
c.setId("c");
i = m.addCompartment(c);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(m.getNumCompartments() == 1);
c = null;
m = null;
}
public void test_Compartment_parent_add()
{
Compartment c = new Compartment(2, 4);
c.setId("c");
Model m = new Model(2, 4);
m.addCompartment(c);
c = null;
ListOf lo = m.getListOfCompartments();
assertTrue(lo == m.getCompartment(0).getParentSBMLObject());
assertTrue(m == lo.getParentSBMLObject());
}
public void test_SBMLConvert_convertToL3_compartment()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
Compartment c1;
c.setId(sid);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
c1 = m.getCompartment(0);
assertTrue(c1.hasRequiredAttributes() == true);
d = null;
}
public void test_Model_getCompartmentById()
{
Compartment c1 = new Compartment(2, 4);
Compartment c2 = new Compartment(2, 4);
c1.setId("A");
c2.setId("B");
M.addCompartment(c1);
M.addCompartment(c2);
assertTrue(M.getNumCompartments() == 2);
assertTrue(M.getCompartment("A") != c1);
assertTrue(M.getCompartment("B") != c2);
assertTrue(M.getCompartment("C") == null);
}
public void test_L3_Compartment_id()
{
string id = "mitochondria";
assertEquals(false, C.isSetId());
C.setId(id);
assertTrue((id == C.getId()));
assertEquals(true, C.isSetId());
if (C.getId() == id)
{
;
}
{
}
}
public void test_Model_getCompartment()
{
Compartment c1 = new Compartment(2, 4);
Compartment c2 = new Compartment(2, 4);
c1.setId("A");
c2.setId("B");
M.addCompartment(c1);
M.addCompartment(c2);
assertTrue(M.getNumCompartments() == 2);
c1 = M.getCompartment(0);
c2 = M.getCompartment(1);
assertTrue(("A" == c1.getId()));
assertTrue(("B" == c2.getId()));
}
public void test_SBMLConvert_invalidLevelVersion()
{
SBMLDocument d = new SBMLDocument(2, 1);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
c.setId(sid);
c.setSize(1.2);
c.setUnits("volume");
assertTrue(d.setLevelAndVersion(1, 3, true) == false);
assertTrue(d.setLevelAndVersion(2, 7, true) == false);
assertTrue(d.setLevelAndVersion(3, 5, true) == false);
assertTrue(d.setLevelAndVersion(4, 1, true) == false);
}
public void test_Compartment_copyConstructor()
{
Compartment o1 = new Compartment(2, 4);
o1.setId("c");
o1.setOutside("c2");
assertTrue(o1.getId() == "c");
assertTrue(o1.getOutside() == "c2");
Compartment o2 = new Compartment(o1);
assertTrue(o2.getId() == "c");
assertTrue(o2.getOutside() == "c2");
assertTrue(o2.getParentSBMLObject() == o1.getParentSBMLObject());
o2 = null;
o1 = null;
}
public void test_Compartment_ancestor_add()
{
Compartment c = new Compartment(2, 4);
c.setId("C");
Model m = new Model(2, 4);
m.addCompartment(c);
c = null;
ListOf lo = m.getListOfCompartments();
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_SBMLConvert_convertToL1_Species_Amount()
{
SBMLDocument d = new SBMLDocument(2, 4);
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_Compartment_createWith()
{
Compartment c = new Compartment(2, 4);
c.setId("A");
assertTrue(c.getTypeCode() == libsbml.SBML_COMPARTMENT);
assertTrue(c.getMetaId() == "");
assertTrue(c.getNotes() == null);
assertTrue(c.getAnnotation() == null);
assertTrue(c.getName() == "");
assertTrue(c.getSpatialDimensions() == 3);
assertTrue(("A" == c.getId()));
assertTrue(c.getConstant() == true);
assertEquals(true, c.isSetId());
assertEquals(false, c.isSetName());
c = null;
}
public void test_Compartment_assignmentOperator()
{
Compartment o1 = new Compartment(2, 4);
o1.setId("c");
o1.setOutside("c2");
assertTrue(o1.getId() == "c");
assertTrue(o1.getOutside() == "c2");
Compartment o2 = new Compartment(2, 4);
o2 = o1;
assertTrue(o2.getId() == "c");
assertTrue(o2.getOutside() == "c2");
assertTrue(o2.getParentSBMLObject() == o1.getParentSBMLObject());
o2 = null;
o1 = null;
}
