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_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_Compartment_unsetSize()
{
C.setSize(0.2);
assertTrue(C.getSize() == 0.2);
assertEquals(true, C.isSetSize());
C.unsetSize();
assertEquals(false, C.isSetSize());
}
public void test_Compartment_setSize1()
{
int i = C.setSize(2.0);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(C.getSize() == 2.0);
i = C.unsetSize();
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
}
public void test_L3_Compartment_size()
{
double size = 0.2;
assertEquals(false, C.isSetSize());
assertEquals(true, isnan(C.getSize()));
C.setSize(size);
assertTrue(C.getSize() == size);
assertEquals(true, C.isSetSize());
C.unsetSize();
assertEquals(false, C.isSetSize());
assertEquals(true, isnan(C.getSize()));
}
public void test_Compartment_setSize2()
{
Compartment c = new Compartment(2, 2);
int i = c.setSize(4);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(c.getSize() == 4);
assertEquals(true, c.isSetSize());
i = c.unsetSize();
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertEquals(false, c.isSetSize());
c = null;
}
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_SBMLConvert_convertFromL3()
{
SBMLDocument d = new SBMLDocument(3, 1);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
c.setId(sid);
c.setSize(1.2);
c.setConstant(true);
c.setSpatialDimensions(3.4);
assertTrue(d.setLevelAndVersion(1, 1, true) == false);
assertTrue(d.setLevelAndVersion(1, 2, true) == false);
assertTrue(d.setLevelAndVersion(2, 1, true) == false);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.setLevelAndVersion(2, 4, true) == false);
assertTrue(d.setLevelAndVersion(3, 1, true) == true);
}
public void test_SBMLConvert_convertToL3_defaultUnits()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
c.setId(sid);
c.setSize(1.2);
c.setUnits("volume");
assertTrue(m.getNumUnitDefinitions() == 0);
assertTrue(d.setLevelAndVersion(3, 1, true) == true);
assertTrue(m.getNumUnitDefinitions() == 2);
UnitDefinition ud = m.getUnitDefinition(0);
assertTrue(ud != null);
assertTrue(("volume" == ud.getId()));
assertTrue(ud.getNumUnits() == 1);
Unit u = ud.getUnit(0);
assertTrue(u.getKind() == libsbml.UNIT_KIND_LITRE);
assertTrue(u.getExponent() == 1);
assertTrue(u.getMultiplier() == 1);
assertTrue(u.getScale() == 0);
ud = m.getUnitDefinition(1);
assertTrue(ud != null);
assertTrue(("area" == ud.getId()));
assertTrue(ud.getNumUnits() == 1);
u = ud.getUnit(0);
assertTrue(u.getKind() == libsbml.UNIT_KIND_METRE);
assertTrue(u.getExponent() == 2);
assertTrue(u.getMultiplier() == 1);
assertTrue(u.getScale() == 0);
assertTrue(("second" == m.getTimeUnits()));
d = null;
}
static void Main(string[] args)
{
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "fbc", 1);
SBMLDocument document = new SBMLDocument(sbmlns);
// create the Model
Model model = document.createModel();
// create the Compartment
Compartment compartment = model.createCompartment();
compartment.setId("compartment");
compartment.setConstant(true);
compartment.setSize(1);
// create the Species
Species species = model.createSpecies();
species.setId("Node1");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node2");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node3");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node4");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node5");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node6");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node7");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node8");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node0");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(true);
species = model.createSpecies();
species.setId("Node9");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(true);
Reaction reaction = model.createReaction();
reaction.setId("J0");
reaction.setReversible(false);
reaction.setFast(false);
SpeciesReference reactant = reaction.createReactant();
reactant.setSpecies("Node0");
reactant.setStoichiometry(1);
reactant.setConstant(true);
SpeciesReference product = reaction.createProduct();
product.setSpecies("Node1");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J1");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node1");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node2");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J2");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node2");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node3");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J3");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node1");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node4");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J4");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node4");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node3");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J5");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node3");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node5");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J6");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node5");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node6");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J7");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node6");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node7");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J8");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node5");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node8");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J9");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node8");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node7");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J10");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node7");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node9");
product.setStoichiometry(1);
product.setConstant(true);
//
// Get a FbcModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is SBasePlugin, and
// thus the value needs to be casted for the corresponding derived class.
//
FbcModelPlugin mplugin = (FbcModelPlugin)(model.getPlugin("fbc"));
FluxBound bound = mplugin.createFluxBound();
bound.setId("bound1");
bound.setReaction("J0");
bound.setOperation("equal");
bound.setValue(10);
Objective objective = mplugin.createObjective();
objective.setId("obj1");
objective.setType("maximize");
// mark obj1 as active objective
mplugin.setActiveObjectiveId("obj1");
FluxObjective fluxObjective = objective.createFluxObjective();
fluxObjective.setReaction("J8");
fluxObjective.setCoefficient(1);
libsbml.writeSBMLToFile(document, "fbc_example1.xml");
}
