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);
}
protected override void Context()
{
base.Context();
_sbmlModel = new Model(3, 1);
_sbmlInformation = new SBMLInformation();
//one compartment reaction
_reaction = _sbmlModel.createReaction();
_reaction.setId("r1");
//reaction partner
var s1 = _sbmlModel.createSpecies();
s1.setId("s1");
s1.setCompartment("default");
var s2 = _sbmlModel.createSpecies();
s2.setId("s2");
s2.setCompartment("default");
var m = new MoleculeInformation(s1);
var m2 = new MoleculeInformation(s2);
_sbmlInformation.MoleculeInformation.Add(m);
_sbmlInformation.MoleculeInformation.Add(m2);
//SRef
var s1Ref = _reaction.createReactant();
s1Ref.setSpecies("s1");
s1Ref.setStoichiometry(1);
var s2Ref = _reaction.createProduct();
s2Ref.setSpecies("s2");
s2Ref.setStoichiometry(2);
_reaction.addProduct(s2Ref);
//Modifier
var mod = _reaction.createModifier();
mod.setId("mod");
mod.setName("mod");
mod.setSpecies("s1");
//Kinetic Law
var kl = _reaction.createKineticLaw();
kl.setId("kl");
kl.setMath(libsbml.parseFormula("2*3"));
}
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 );
}
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_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_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_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_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_Reaction_copyConstructor()
{
Reaction o1 = new Reaction(2,4);
o1.setId("c");
assertTrue( o1.getId() == "c" );
KineticLaw kl = new KineticLaw(2,4);
kl.setMath(libsbml.parseFormula("1"));
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_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_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_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_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;
}
private static int Main(string[] args)
{
var retval = 0;
var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
var document = new SBMLDocument(sbmlns);
//Define the external model definition
var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
var extmod = compdoc.createExternalModelDefinition();
extmod.setId("ExtMod1");
extmod.setSource("enzyme_model.xml");
extmod.setModelRef("enzyme");
//Define the 'simple' model
var mod1 = compdoc.createModelDefinition();
mod1.setId("simple");
var comp = mod1.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
var spec = new Species(sbmlns);
//We have to construct it this way because we get the comp plugin from it later.
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
spec.setInitialConcentration(5);
mod1.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
mod1.addSpecies(spec);
var rxn = new Reaction(3, 1);
rxn.setReversible(true);
rxn.setFast(false);
rxn.setId("J0");
var sr = new SpeciesReference(3, 1);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(sr);
sr.setSpecies("D");
rxn.addProduct(sr);
mod1.addReaction(rxn);
var mod1plug = (CompModelPlugin)(mod1.getPlugin("comp"));
var port = new Port();
port.setId("S_port");
port.setIdRef("S");
mod1plug.addPort(port);
var port2 = mod1plug.createPort();
port2.setId("D_port");
port2.setIdRef("D");
port.setId("comp_port");
port.setIdRef("comp");
mod1plug.addPort(port);
port.setId("J0_port");
port.setIdRef("J0");
mod1plug.addPort(port);
// create the Model
var model = document.createModel();
model.setId("complexified");
// Set the submodels
var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("A");
submod1.setModelRef("ExtMod1");
var submod2 = mplugin.createSubmodel();
submod2.setId("B");
submod2.setModelRef("simple");
var del = submod2.createDeletion();
del.setPortRef("J0_port");
// Synchronize the compartments
var mcomp = model.createCompartment();
mcomp.setSpatialDimensions(3);
mcomp.setConstant(true);
mcomp.setId("comp");
mcomp.setSize(1L);
var compartplug = (CompSBasePlugin)(mcomp.getPlugin("comp"));
var re = new ReplacedElement();
re.setIdRef("comp");
re.setSubmodelRef("A");
compartplug.addReplacedElement(re);
re.setSubmodelRef("B");
re.unsetIdRef();
re.setPortRef("comp_port");
compartplug.addReplacedElement(re);
//Synchronize the species
spec.setId("S");
spec.setInitialConcentration(5);
var specplug = (CompSBasePlugin)(spec.getPlugin("comp"));
var sre = specplug.createReplacedElement();
sre.setSubmodelRef("A");
sre.setIdRef("S");
var sre2 = specplug.createReplacedElement();
sre2.setSubmodelRef("B");
sre2.setPortRef("S_port");
model.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
sre.setIdRef("D");
sre2.setPortRef("D_port");
model.addSpecies(spec);
libsbml.writeSBMLToFile(document, "spec_example3.xml");
document = libsbml.readSBMLFromFile("spec_example3.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
var stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "spec_example3_rt.xml");
}
return retval;
}
private static int Main(string[] args)
{
var retval = 0;
var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
var document = new SBMLDocument(sbmlns);
//Create our submodel
var compdoc = (CompSBMLDocumentPlugin) (document.getPlugin("comp"));
compdoc.setRequired(true);
var mod1 = compdoc.createModelDefinition();
mod1.setId("enzyme");
mod1.setName("enzyme");
var comp = mod1.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
var spec = new Species(3, 1);
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
mod1.addSpecies(spec);
spec.setId("E");
mod1.addSpecies(spec);
spec.setId("D");
mod1.addSpecies(spec);
spec.setId("ES");
mod1.addSpecies(spec);
var rxn = new Reaction(3, 1);
rxn.setReversible(true);
rxn.setFast(false);
var rxn2 = new Reaction(rxn);
rxn.setId("J0");
rxn2.setId("J1");
var sr = new SpeciesReference(3, 1);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(sr);
sr.setSpecies("E");
rxn.addReactant(sr);
rxn2.addProduct(sr);
sr.setSpecies("ES");
rxn.addProduct(sr);
rxn2.addReactant(sr);
sr.setSpecies("D");
rxn2.addProduct(sr);
mod1.addReaction(rxn);
mod1.addReaction(rxn2);
// create the Model
var model = document.createModel();
model.setId("aggregate");
// Create a submodel
var mplugin = (CompModelPlugin) (model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("submod1");
submod1.setModelRef("enzyme");
var submod2 = new Submodel();
submod2.setId("submod2");
submod2.setModelRef("enzyme");
mplugin.addSubmodel(submod2);
libsbml.writeSBMLToFile(document, "enzyme_model.xml");
document = libsbml.readSBMLFromFile("enzyme_model.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
var stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "enzyme_model_rt.xml");
}
return retval;
}
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_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_Reaction_clone()
{
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 = o1.clone();
assertTrue( o2.getId() == "c" );
assertTrue( o2.isSetKineticLaw() == true );
assertNotEquals(o2.getKineticLaw(),null);
assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() );
o2 = null;
o1 = null;
}