END_TEST
START_TEST (test_Compartment_setId)
{
const char *id = "mitochondria";
Compartment_setId(C, id);
fail_unless( !strcmp(Compartment_getId(C), id) );
fail_unless( Compartment_isSetId(C) );
if (Compartment_getId(C) == id)
{
fail("Compartment_setId(...) did not make a copy of string.");
}
/* Reflexive case (pathological) */
Compartment_setId(C, Compartment_getId(C));
fail_unless( !strcmp(Compartment_getId(C), id) );
Compartment_setId(C, NULL);
fail_unless( !Compartment_isSetId(C) );
if (Compartment_getId(C) != NULL)
{
fail("Compartment_setId(C, NULL) did not clear string.");
}
}
END_TEST
START_TEST (test_SBMLConvert_convertFromL3)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, sid );
Compartment_setSize ( c, 1.2 );
Compartment_setConstant( c, 1);
Compartment_setSpatialDimensionsAsDouble(c, 3.4);
fail_unless(SBMLDocument_setLevelAndVersion(d, 1, 1) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 1, 2) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 1) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 2) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 3) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 4) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 3, 1) == 1);
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertSBO)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t * m = SBMLDocument_createModel(d);
/* create a compartment with SBO */
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
SBase_setSBOTerm((SBase_t *) (c), 240);
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 3) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 3, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
/* check that sbo term has been removed */
Compartment_t *c1 = Model_getCompartment(SBMLDocument_getModel(d), 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_Compartment_initDefaults)
{
Compartment_t *c = Compartment_create(2, 4);
Compartment_setId(c, "A");
Compartment_initDefaults(c);
fail_unless( !strcmp(Compartment_getId (c), "A"));
fail_unless( Compartment_getName (c) == NULL );
fail_unless( Compartment_getUnits (c) == NULL );
fail_unless( Compartment_getOutside(c) == NULL );
fail_unless( Compartment_getSpatialDimensions(c) == 3 );
fail_unless( Compartment_getVolume (c) == 1.0 );
fail_unless( Compartment_getConstant (c) == 1 );
fail_unless( Compartment_isSetId (c) );
fail_unless( !Compartment_isSetName (c) );
fail_unless( !Compartment_isSetSize (c) );
fail_unless( !Compartment_isSetVolume (c) );
fail_unless( !Compartment_isSetUnits (c) );
fail_unless( !Compartment_isSetOutside(c) );
fail_unless( Compartment_isSetSpatialDimensions(c) );
fail_unless( Compartment_isSetConstant(c) );
Compartment_free(c);
}
END_TEST
/* since the setId function has been used as an
* alias for setName we cant require it to only
* be used on a L2 model
START_TEST (test_Compartment_setId1)
{
int i = Compartment_setId(C, "cell");
fail_unless( i == LIBSBML_UNEXPECTED_ATTRIBUTE );
fail_unless( !Compartment_isSetId(C) );
}
END_TEST
*/
START_TEST (test_Compartment_setId2)
{
Compartment_t *c =
Compartment_create(2, 2);
int i = Compartment_setId(c, "1cell");
fail_unless( i == LIBSBML_INVALID_ATTRIBUTE_VALUE );
fail_unless( !Compartment_isSetId(c) );
Compartment_free(c);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL1_Species_Amount)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c = Compartment_create(2, 4);
Species_t *s = Species_create(2, 4);
Compartment_setId ( c, sid );
Model_addCompartment( m, c );
Species_setCompartment ( s, sid );
Species_setInitialAmount( s, 2.34 );
Model_addSpecies ( m, s );
fail_unless( SBMLDocument_setLevelAndVersion(d, 1, 2) == 1, NULL );
fail_unless( Species_getInitialAmount(s) == 2.34, NULL );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLDocument_setLevelAndVersion_UnitsError)
{
SBMLDocument_t *d = SBMLDocument_create();
SBMLDocument_setLevelAndVersionNonStrict(d, 2, 4);
Model_t *m1 = SBMLDocument_createModel(d);
Compartment_t *c = Model_createCompartment(m1);
Compartment_setId(c, "c");
Parameter_t *p = Model_createParameter(m1);
Parameter_setId(p, "p");
Parameter_setUnits(p, "mole");
Rule_t * r = Model_createAssignmentRule(m1);
Rule_setVariable(r, "c");
Rule_setFormula(r, "p*p");
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,2,2) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,2,3) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,1,2) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,1,1) == 0);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_Compartment_createWith)
{
Compartment_t *c = Compartment_create(2, 4);
Compartment_setId(c, "A");
fail_unless( SBase_getTypeCode ((SBase_t *) c) == SBML_COMPARTMENT );
fail_unless( SBase_getMetaId ((SBase_t *) c) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) c) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) c) == NULL );
fail_unless( Compartment_getName(c) == NULL );
fail_unless( Compartment_getSpatialDimensions(c) == 3 );
fail_unless( !strcmp( Compartment_getId (c), "A" ) );
fail_unless( Compartment_getConstant(c) == 1 );
fail_unless( Compartment_isSetId (c) );
fail_unless( !Compartment_isSetName (c) );
Compartment_free(c);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_defaultUnits)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, sid );
Compartment_setSize ( c, 1.2 );
Compartment_setUnits( c, "volume");
fail_unless(Model_getNumUnitDefinitions(m) == 0);
fail_unless( SBMLDocument_setLevelAndVersion(d, 3, 1) == 1, NULL);
fail_unless(Model_getNumUnitDefinitions(m) == 2);
UnitDefinition_t *ud = Model_getUnitDefinition(m, 0);
fail_unless (ud != NULL);
fail_unless (!strcmp(UnitDefinition_getId( ud), "volume"));
fail_unless(UnitDefinition_getNumUnits(ud) == 1);
Unit_t * u = UnitDefinition_getUnit(ud, 0);
fail_unless(Unit_getKind(u) == UNIT_KIND_LITRE);
fail_unless(Unit_getExponent(u) == 1);
fail_unless(Unit_getMultiplier(u) == 1);
fail_unless(Unit_getScale(u) == 0);
ud = Model_getUnitDefinition(m, 1);
fail_unless (ud != NULL);
fail_unless (!strcmp(UnitDefinition_getId( ud), "time"));
fail_unless(UnitDefinition_getNumUnits(ud) == 1);
u = UnitDefinition_getUnit(ud, 0);
fail_unless(Unit_getKind(u) == UNIT_KIND_SECOND);
fail_unless(Unit_getExponent(u) == 1);
fail_unless(Unit_getMultiplier(u) == 1);
fail_unless(Unit_getScale(u) == 0);
fail_unless(!strcmp(Model_getTimeUnits(m), "time"));
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_Compartment_setId4)
{
Compartment_t *c =
Compartment_create(2, 2);
int i = Compartment_setId(c, NULL);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Compartment_isSetId(c) );
Compartment_free(c);
}
END_TEST
START_TEST (test_Compartment_setId3)
{
Compartment_t *c =
Compartment_create(2, 2);
int i = Compartment_setId(c, "cell");
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Compartment_isSetId(c) );
fail_unless( !strcmp(Compartment_getId(c), "cell" ));
Compartment_free(c);
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertNonStrictSBO)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t * m = SBMLDocument_createModel(d);
/* create a compartment with SBO */
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
Compartment_setConstant(c, 0);
SBase_setSBOTerm((SBase_t *) (c), 64);
/* conversion to L2V3 and L2V2 should fail due to bad SBO
* but to L2V1 and L1 should pass as sbo terms not applicable
*/
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 3) == 0 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 4, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 2) == 0 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 4, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 1) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 1, NULL );
/* check that sbo term has been removed */
Compartment_t *c1 = Model_getCompartment(SBMLDocument_getModel(d), 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 1, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 1, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
/* check that sbo term has been removed */
Compartment_t *c2 = Model_getCompartment(SBMLDocument_getModel(d), 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c2)) == -1, NULL );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_L3_Compartment_hasRequiredAttributes )
{
Compartment_t *c = Compartment_create (3, 1);
fail_unless ( !Compartment_hasRequiredAttributes(c));
Compartment_setId(c, "id");
fail_unless ( !Compartment_hasRequiredAttributes(c));
Compartment_setConstant(c, 0);
fail_unless ( Compartment_hasRequiredAttributes(c));
Compartment_free(c);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL1_Species_Concentration)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c =
Compartment_create(2, 1);
Species_t *s =
Species_create(2, 1);
Compartment_setId ( c, sid );
Compartment_setSize ( c, 1.2 );
Model_addCompartment( m, c );
Species_setId ( s, "s" );
Species_setCompartment ( s, sid );
Species_setInitialConcentration( s, 2.34 );
Model_addSpecies ( m, s );
fail_unless( SBMLDocument_setLevelAndVersion(d, 1, 2) == 1, NULL);
/**
* These tests will fail under Cygwin because of a minimal
* setlocale() implementation (see setlocale manpage).
*/
#ifndef CYGWIN
fail_unless( Species_getInitialAmount(Model_getSpecies(m, 0)) == 2.808, NULL );
#endif
Species_t * s1 = Model_getSpecies(m, 0);
fail_unless (s1 != NULL);
fail_unless (!strcmp(Species_getCompartment(s1), "C"));
fail_unless(Compartment_getSize(Model_getCompartmentById(m, "C")) == 1.2);
fail_unless(Species_getInitialConcentration(s1) == 2.34);
fail_unless(Species_isSetInitialConcentration(s1) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_L3_Compartment_id)
{
const char *id = "mitochondria";
fail_unless( !Compartment_isSetId(C) );
Compartment_setId(C, id);
fail_unless( !strcmp(Compartment_getId(C), id) );
fail_unless( Compartment_isSetId(C) );
if (Compartment_getId(C) == id)
{
fail("Compartment_setId(...) did not make a copy of string.");
}
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertToL1)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
/* create model with metaid */
Model_t * m = SBMLDocument_createModel(d);
SBase_setMetaId((SBase_t *) (m), "_m");
/* create a compartment with sbo*/
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
SBase_setSBOTerm((SBase_t *) (c), 240);
/* create a species with hasOnlySubstanceUnits = true*/
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Species_setHasOnlySubstanceUnits(s, 1);
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 1, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 1, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
///* check that attributes that are no longer valid have been removed */
Model_t * m1 = SBMLDocument_getModel(d);
fail_unless (SBase_getMetaId((SBase_t *) (m1)) == NULL);
Compartment_t *c1 = Model_getCompartment(m1, 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
Species_t *s1 = Model_getSpecies(m1, 0);
fail_unless (Species_getHasOnlySubstanceUnits(s1) == 0);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_stoichiometryMath)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, "c" );
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Reaction_t * r = Model_createReaction(m);
SpeciesReference_t *sr = Reaction_createReactant(r);
SpeciesReference_setSpecies(sr, "s");
StoichiometryMath_t *sm = SpeciesReference_createStoichiometryMath(sr);
ASTNode_t * ast = SBML_parseFormula("c*2");
StoichiometryMath_setMath(sm, ast);
fail_unless(Model_getNumRules(m) == 0);
fail_unless(SpeciesReference_isSetId(sr) == 0);
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1);
m = SBMLDocument_getModel(d);
r = Model_getReaction(m, 0);
sr = Reaction_getReactant(r, 0);
fail_unless(Model_getNumRules(m) == 1);
fail_unless(SpeciesReference_isSetId(sr) == 1);
Rule_t *rule = Model_getRule(m, 0);
fail_unless( strcmp(SpeciesReference_getId(sr), Rule_getVariable(rule)) == 0 );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_invalidLevelVersion)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, sid );
Compartment_setSize ( c, 1.2 );
Compartment_setUnits( c, "volume");
fail_unless(SBMLDocument_setLevelAndVersion(d, 1, 3) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 5) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 3, 2) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 4, 1) == 0);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_localParameters)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2);
Model_t *m = SBMLDocument_createModel(d);
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, "c" );
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Reaction_t * r = Model_createReaction(m);
SpeciesReference_t *sr = Reaction_createReactant(r);
SpeciesReference_setSpecies(sr, "s");
KineticLaw_t *kl = Reaction_createKineticLaw(r);
KineticLaw_setFormula(kl, "s*k");
Parameter_t *p = KineticLaw_createParameter(kl);
Parameter_setId(p, "k");
fail_unless(KineticLaw_getNumLocalParameters(kl) == 0);
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1 );
m = SBMLDocument_getModel(d);
r = Model_getReaction(m,0);
kl = Reaction_getKineticLaw(r);
fail_unless(KineticLaw_getNumLocalParameters(kl) == 1);
LocalParameter_t *lp = KineticLaw_getLocalParameter(kl, 0);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_compartment)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c = Model_createCompartment(m);
Compartment_t *c1;
Compartment_setId ( c, sid );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);
c1 = Model_getCompartment(m, 0);
fail_unless(Compartment_hasRequiredAttributes(c1) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertL1ParamRule)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2);
Model_t * m = SBMLDocument_createModel(d);
/* create a compartment */
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
/* create a parameter */
Parameter_t * p = Model_createParameter(m);
Parameter_setId(p, "p");
Parameter_t * p1 = Model_createParameter(m);
Parameter_setId(p1, "p1");
/* create a math element */
ASTNode_t *math = SBML_parseFormula("p");
/* create an assignment rule */
Rule_t *ar = Model_createAssignmentRule(m);
Rule_setVariable(ar, "p1");
Rule_setMath(ar, math);
Rule_setUnits(ar, "mole");
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 1) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 1, NULL );
Rule_t * r1 = Model_getRule(SBMLDocument_getModel(d), 0);
fail_unless (Rule_getUnits(r1) == NULL );
SBMLDocument_free(d);
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
int retval = 0;
XMLNamespaces_t * fbc;
SBMLNamespaces_t * sbmlns;
SBMLDocument_t * doc;
Compartment_t * compartment;
Species_t * species;
Reaction_t * reaction;
SpeciesReference_t *reactant;
SpeciesReference_t *product;
Model_t * model;
SBMLDocumentPlugin_t * docPlug;
SBasePlugin_t * modelPlug;
FluxBound_t * fluxBound;
Objective_t * objective;
FluxObjective_t * fluxObjective;
/* get fbc registry entry */
SBMLExtension_t *sbmlext = SBMLExtensionRegistry_getExtension("fbc");
/* create the sbml namespaces object with fbc */
fbc = XMLNamespaces_create();
XMLNamespaces_add(fbc, SBMLExtension_getURI(sbmlext, 3, 1, 1), "fbc");
sbmlns = SBMLNamespaces_create(3, 1);
SBMLNamespaces_addNamespaces(sbmlns, fbc);
/* create the document */
doc = SBMLDocument_createWithSBMLNamespaces(sbmlns);
/* set the fbc reqd attribute to false */
docPlug = (SBMLDocumentPlugin_t*)(SBase_getPlugin((SBase_t*)(doc), "fbc"));
SBMLDocumentPlugin_setRequired(docPlug, 0);
// create the Model
model = SBMLDocument_createModel(doc);
// create the Compartment
compartment = Model_createCompartment(model);
Compartment_setId(compartment, "compartment");
Compartment_setConstant(compartment, 1);
Compartment_setSize(compartment, 1);
// create the Species
species = Model_createSpecies(model);
Species_setId(species, "Node1");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node2");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node3");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node4");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node5");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node6");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node7");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node8");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node0");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 1);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node9");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 1);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
// create the Reactions
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J0");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node0");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node1");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J1");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node1");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node2");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J2");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node2");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node3");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J3");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node1");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node4");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J4");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node4");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node3");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J5");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node3");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node5");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J6");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node5");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node6");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J7");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node6");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node7");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J8");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node5");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node8");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J9");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node8");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node7");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J10");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node7");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node9");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
// Get a SBasePlugin_t object plugged in the model object.
modelPlug = SBase_getPlugin((SBase_t *)(model), "fbc");
// create the fluxBound object and add it to model plugin
fluxBound = FluxBound_create(3, 1, 1);
FluxBound_setId(fluxBound, "bound1");
FluxBound_setReaction(fluxBound, "J0");
FluxBound_setOperation(fluxBound, "equal");
FluxBound_setValue(fluxBound, 10);
FbcModelPlugin_addFluxBound(modelPlug, fluxBound);
// create the objective object and add it to model plugin
objective = Objective_create(3, 1, 1);
Objective_setId(objective, "obj1");
Objective_setType(objective, "maximize");
fluxObjective = Objective_createFluxObjective(objective);
FluxObjective_setReaction(fluxObjective, "J8");
FluxObjective_setCoefficient(fluxObjective, 1);
FbcModelPlugin_addObjective(modelPlug, objective);
// mark obj1 as active objective
FbcModelPlugin_setActiveObjectiveId(modelPlug, "obj1");
/* write the file */
writeSBMLToFile(doc, "fbc_example1.xml");
return retval;
}
int main(int argc,char** argv)
{
int retval = 0;
XMLNamespaces_t * groups;
SBMLNamespaces_t * sbmlns;
SBMLDocument_t * doc;
Compartment_t * compartment;
Species_t * species;
Model_t * model;
SBMLDocumentPlugin_t * docPlug;
SBasePlugin_t * modelPlug;
Group_t * group;
Member_t * member;
/* get groups registry entry */
SBMLExtension_t *sbmlext = SBMLExtensionRegistry_getExtension("groups");
/* create the sbml namespaces object with groups */
groups = XMLNamespaces_create();
XMLNamespaces_add(groups, SBMLExtension_getURI(sbmlext, 3, 1, 1), "groups");
sbmlns = SBMLNamespaces_create(3, 1);
SBMLNamespaces_addNamespaces(sbmlns, groups);
/* create the document */
doc = SBMLDocument_createWithSBMLNamespaces(sbmlns);
/* set the groups reqd attribute to false */
docPlug = (SBMLDocumentPlugin_t*)(SBase_getPlugin((SBase_t*)(doc), "groups"));
SBMLDocumentPlugin_setRequired(docPlug, 0);
// create the Model
model = SBMLDocument_createModel(doc);
// create the Compartment
compartment = Model_createCompartment(model);
Compartment_setId(compartment, "cytosol");
Compartment_setConstant(compartment, 1);
Compartment_setSize(compartment, 1);
compartment = Model_createCompartment(model);
Compartment_setId(compartment, "mitochon");
Compartment_setConstant(compartment, 1);
Compartment_setSize(compartment, 1);
// create the Species
species = Model_createSpecies(model);
Species_setId(species, "ATPc");
Species_setCompartment(species, "cytosol");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "ATPm");
Species_setCompartment(species, "mitochon");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
// create the Groups
// Get a SBasePlugin_t object plugged in the model object.
modelPlug = SBase_getPlugin((SBase_t *)(model), "groups");
// create the group object and add it to model plugin
group = Group_create(3, 1, 1);
Group_setId(group, "ATP");
Group_setKind(group, GROUP_KIND_CLASSIFICATION);
SBase_setSBOTerm(group, 252);
member = Group_createMember(group);
Member_setIdRef(member, "ATPc");
member = Group_createMember(group);
Member_setIdRef(member, "ATPm");
// we need a function here
GroupsModelPlugin_addGroup((GroupsModelPlugin_t*)(modelPlug), group);
/* write the file */
writeSBMLToFile(doc, "groups_example1.xml");
return retval;
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
int retval = 0;
XMLNamespaces_t * comp;
SBMLNamespaces_t * sbmlns;
SBMLDocument_t * doc;
Compartment_t * c;
Species_t * s1;
Species_t * s2;
Species_t * s3;
Species_t * s4;
Reaction_t * r1;
Reaction_t * r2;
SpeciesReference_t *sr1;
SpeciesReference_t *sr2;
SpeciesReference_t *sr3;
SpeciesReference_t *sr4;
SpeciesReference_t *sr5;
SpeciesReference_t *sr6;
Model_t * model;
CompSBMLDocumentPlugin_t * docPlug;
CompModelPlugin_t *modelPlug;
Submodel_t * sub1;
Submodel_t * sub2;
ModelDefinition_t * modDef;
/* get comp registry entry */
SBMLExtension_t *sbmlext = SBMLExtensionRegistry_getExtension("comp");
/* create the sbml namespaces object with comp */
comp = XMLNamespaces_create();
XMLNamespaces_add(comp, SBMLExtension_getURI(sbmlext, 3, 1, 1), "comp");
sbmlns = SBMLNamespaces_create(3, 1);
SBMLNamespaces_addNamespaces(sbmlns, comp);
/* create the document */
doc = SBMLDocument_createWithSBMLNamespaces(sbmlns);
/* set the comp reqd attribute to true */
docPlug = (CompSBMLDocumentPlugin_t * )(SBase_getPlugin((SBase_t*)(doc), "comp"));
SBMLDocumentPlugin_setRequired((SBMLDocumentPlugin_t*)(docPlug), 1);
/* create the submodel */
modDef = CompSBMLDocumentPlugin_createModelDefinition(docPlug);
Model_setId((Model_t*)(modDef), "enzyme");
Model_setName((Model_t*)(modDef), "enzyme");
c = Model_createCompartment((Model_t*)(modDef));
Compartment_setId(c, "comp");
Compartment_setConstant(c, 1);
Compartment_setSize(c, 1.0);
Compartment_setSpatialDimensions(c, 3);
s1 = Model_createSpecies((Model_t*)(modDef));
Species_setId(s1, "S");
Species_setCompartment(s1, "comp");
Species_setHasOnlySubstanceUnits(s1, 0);
Species_setBoundaryCondition(s1, 0);
Species_setConstant(s1, 0);
s2 = Model_createSpecies((Model_t*)(modDef));
Species_setId(s2, "E");
Species_setCompartment(s2, "comp");
Species_setHasOnlySubstanceUnits(s2, 0);
Species_setBoundaryCondition(s2, 0);
Species_setConstant(s2, 0);
s3 = Model_createSpecies((Model_t*)(modDef));
Species_setId(s3, "D");
Species_setCompartment(s3, "comp");
Species_setHasOnlySubstanceUnits(s3, 0);
Species_setBoundaryCondition(s3, 0);
Species_setConstant(s3, 0);
s4 = Model_createSpecies((Model_t*)(modDef));
Species_setId(s4, "ES");
Species_setCompartment(s4, "comp");
Species_setHasOnlySubstanceUnits(s4, 0);
Species_setBoundaryCondition(s4, 0);
Species_setConstant(s4, 0);
r1 = Model_createReaction((Model_t*)(modDef));
Reaction_setId(r1, "J0");
Reaction_setReversible(r1, 1);
Reaction_setFast(r1, 0);
sr1 = Reaction_createReactant(r1);
SpeciesReference_setSpecies(sr1, "S");
SpeciesReference_setStoichiometry(sr1, 1.0);
SpeciesReference_setConstant(sr1, 1);
sr2 = Reaction_createReactant(r1);
SpeciesReference_setSpecies(sr2, "E");
SpeciesReference_setStoichiometry(sr2, 1.0);
SpeciesReference_setConstant(sr2, 1);
sr3 = Reaction_createProduct(r1);
SpeciesReference_setSpecies(sr3, "ES");
SpeciesReference_setStoichiometry(sr3, 1.0);
SpeciesReference_setConstant(sr3, 1);
r2 = Model_createReaction((Model_t*)(modDef));
Reaction_setId(r2, "J1");
Reaction_setReversible(r2, 1);
Reaction_setFast(r2, 0);
sr4 = Reaction_createProduct(r2);
SpeciesReference_setSpecies(sr4, "E");
SpeciesReference_setStoichiometry(sr4, 1.0);
SpeciesReference_setConstant(sr4, 1);
sr5 = Reaction_createReactant(r2);
SpeciesReference_setSpecies(sr5, "ES");
SpeciesReference_setStoichiometry(sr5, 1.0);
SpeciesReference_setConstant(sr5, 1);
sr6 = Reaction_createProduct(r2);
SpeciesReference_setSpecies(sr6, "D");
SpeciesReference_setStoichiometry(sr6, 1.0);
SpeciesReference_setConstant(sr6, 1);
/* create the model */
model = SBMLDocument_createModel(doc);
Model_setId(model, "aggregate");
/* add the submodels*/
modelPlug = (CompModelPlugin_t*)(SBase_getPlugin((SBase_t *)(model), "comp"));
sub1 = CompModelPlugin_createSubmodel(modelPlug);
Submodel_setId(sub1, "submod1");
Submodel_setModelRef(sub1, "enzyme");
sub2 = CompModelPlugin_createSubmodel(modelPlug);
Submodel_setId(sub2, "submod2");
Submodel_setModelRef(sub2, "enzyme");
/* write the file */
writeSBMLToFile(doc, "enzyme_model.xml");
return retval;
}
