public void test_Species_parent_add()
{
Species ia = new Species(2,4);
ia.setId("s");
ia.setCompartment("c");
Model m = new Model(2,4);
m.addSpecies(ia);
ia = null;
ListOf lo = m.getListOfSpecies();
assertTrue( lo == m.getSpecies(0).getParentSBMLObject() );
assertTrue( m == lo.getParentSBMLObject() );
}
public void test_Model_addSpecies5()
{
Model m = new Model(2,2);
Species s = new Species(2,2);
s.setId( "s");
s.setCompartment( "c");
Species s1 = new Species(2,2);
s1.setId( "s");
s1.setCompartment( "c");
int i = m.addSpecies(s);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumSpecies() == 1 );
i = m.addSpecies(s1);
assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID );
assertTrue( m.getNumSpecies() == 1 );
s = null;
s1 = null;
m = null;
}
public void test_Species_ancestor_add()
{
Species ia = new Species(2,4);
Model m = new Model(2,4);
ia.setId("s");
ia.setCompartment("c");
m.addSpecies(ia);
ia = null;
ListOf lo = m.getListOfSpecies();
Species obj = m.getSpecies(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_Model_addSpecies2()
{
Model m = new Model(2,2);
Species s = new Species(2,1);
s.setId( "s");
s.setCompartment( "c");
int i = m.addSpecies(s);
assertTrue( i == libsbml.LIBSBML_VERSION_MISMATCH );
assertTrue( m.getNumSpecies() == 0 );
s = null;
m = null;
}
public void test_Model_addSpecies3()
{
Model m = new Model(2,2);
Species s = new Species(1,2);
s.setId( "s");
s.setCompartment( "c");
s.setInitialAmount(2);
int i = m.addSpecies(s);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( m.getNumSpecies() == 0 );
s = null;
m = null;
}
public void test_Species_L1()
{
Species s = new Species(1,2);
assertEquals( false, (s.hasRequiredAttributes()) );
s.setId("s");
assertEquals( false, (s.hasRequiredAttributes()) );
s.setCompartment("c");
assertEquals( false, (s.hasRequiredAttributes()) );
s.setInitialAmount(2);
assertEquals( true, s.hasRequiredAttributes() );
s = null;
}
public void test_Model_getSpeciesById()
{
Species s1 = new Species(2,4);
Species s2 = new Species(2,4);
s1.setId( "Glucose" );
s2.setId( "Glucose_6_P" );
s1.setCompartment( "c");
s2.setCompartment( "c");
M.addSpecies(s1);
M.addSpecies(s2);
assertTrue( M.getNumSpecies() == 2 );
assertTrue( M.getSpecies( "Glucose" ) != s1 );
assertTrue( M.getSpecies( "Glucose_6_P") != s2 );
assertTrue( M.getSpecies( "Glucose2" ) == null );
}
public void test_Model_addSpecies()
{
Species s = new Species(2,4);
s.setId( "s");
s.setCompartment( "c");
M.addSpecies(s);
assertTrue( M.getNumSpecies() == 1 );
}
public void test_Model_getNumSpeciesWithBoundaryCondition()
{
Species s1 = new Species(2,4);
Species s2 = new Species(2,4);
Species s3 = new Species(2,4);
s1.setId( "s1");
s2.setId( "s2");
s3.setId( "s3");
s1.setCompartment( "c1");
s2.setCompartment( "c2");
s3.setCompartment( "c3");
s1.setBoundaryCondition(true);
s2.setBoundaryCondition(false);
s3.setBoundaryCondition(true);
assertTrue( M.getNumSpecies() == 0 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 0 );
M.addSpecies(s1);
assertTrue( M.getNumSpecies() == 1 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 1 );
M.addSpecies(s2);
assertTrue( M.getNumSpecies() == 2 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 1 );
M.addSpecies(s3);
assertTrue( M.getNumSpecies() == 3 );
assertTrue( M.getNumSpeciesWithBoundaryCondition() == 2 );
}
public void test_internal_consistency_check_99916_rule()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Species s = new Species(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
s.setId("s");
s.setCompartment("c");
s.setConstant(true);
m.addSpecies(s);
Rule r = m.createAssignmentRule();
r.setVariable("s");
r.setFormula("2");
errors = d.checkInternalConsistency();
assertTrue( errors == 2 );
d = null;
}
public void test_internal_consistency_check_99904_species()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Species s = new Species(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
s.setCompartment("c");
s.setId("s");
s.setMetaId("mmm");
m.addSpecies(s);
errors = d.checkInternalConsistency();
assertTrue( errors == 0 );
d = null;
}
public void test_internal_consistency_check_99916_reaction()
{
SBMLDocument d = new SBMLDocument(2,4);
long errors;
Species s = new Species(2,4);
d.setLevelAndVersion(1,2,false);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Reaction r = m.createReaction();
r.setId("r");
SpeciesReference sr = r.createReactant();
s.setId("s");
s.setCompartment("c");
s.setConstant(true);
sr.setSpecies("s");
m.addSpecies(s);
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_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_Model_getSpecies()
{
Species s1 = new Species(2,4);
Species s2 = new Species(2,4);
s1.setId( "Glucose" );
s2.setId( "Glucose_6_P" );
s1.setCompartment( "c");
s2.setCompartment( "c");
M.addSpecies(s1);
M.addSpecies(s2);
assertTrue( M.getNumSpecies() == 2 );
s1 = M.getSpecies(0);
s2 = M.getSpecies(1);
assertTrue(( "Glucose" == s1.getId() ));
assertTrue(( "Glucose_6_P" == s2.getId() ));
}
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_Species_hasRequiredAttributes()
{
Species s = new Species(3,1);
assertEquals( false, s.hasRequiredAttributes() );
s.setId( "id");
assertEquals( false, s.hasRequiredAttributes() );
s.setCompartment( "cell");
assertEquals( false, s.hasRequiredAttributes() );
s.setHasOnlySubstanceUnits(false);
assertEquals( false, s.hasRequiredAttributes() );
s.setBoundaryCondition(false);
assertEquals( false, s.hasRequiredAttributes() );
s.setConstant(false);
assertEquals( true, s.hasRequiredAttributes() );
s = null;
}