END_TEST
START_TEST (test_AssignmentRule_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(2,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Rule_t *object =
Rule_createAssignmentWithNS(sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) object) == SBML_ASSIGNMENT_RULE );
fail_unless( SBase_getMetaId ((SBase_t *) object) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) object) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) object) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) object) == 2 );
fail_unless( SBase_getVersion ((SBase_t *) object) == 1 );
fail_unless( Rule_getNamespaces (object) != NULL );
fail_unless( XMLNamespaces_getLength(Rule_getNamespaces(object)) == 2 );
Rule_free(object);
}
END_TEST
START_TEST (test_Parameter_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(2,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Parameter_t *object =
Parameter_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) object) == SBML_PARAMETER );
fail_unless( SBase_getMetaId ((SBase_t *) object) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) object) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) object) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) object) == 2 );
fail_unless( SBase_getVersion ((SBase_t *) object) == 1 );
fail_unless( Parameter_getNamespaces (object) != NULL );
fail_unless( XMLNamespaces_getLength(
Parameter_getNamespaces(object)) == 2 );
Parameter_free(object);
}
END_TEST
START_TEST (test_ModifierSpeciesReference_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(2,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
ModifierSpeciesReference_t *object = ModifierSpeciesReference_createWithNS(sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) object) == SBML_MODIFIER_SPECIES_REFERENCE );
fail_unless( SBase_getMetaId ((SBase_t *) object) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) object) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) object) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) object) == 2 );
fail_unless( SBase_getVersion ((SBase_t *) object) == 1 );
fail_unless( SpeciesReference_getNamespaces ((SpeciesReference_t *) object) != NULL );
const XMLNamespaces_t *n = SpeciesReference_getNamespaces((SpeciesReference_t *) object);
fail_unless( XMLNamespaces_getLength( n ) == 2 );
ModifierSpeciesReference_free(object);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_Compartment_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(2,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Compartment_t *c =
Compartment_createWithNS (sbmlns);
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( SBase_getLevel ((SBase_t *) c) == 2 );
fail_unless( SBase_getVersion ((SBase_t *) c) == 1 );
fail_unless( Compartment_getNamespaces (c) != NULL );
fail_unless( XMLNamespaces_getLength(Compartment_getNamespaces(c)) == 2 );
fail_unless( Compartment_getName(c) == NULL );
fail_unless( Compartment_getSpatialDimensions(c) == 3 );
fail_unless( Compartment_getConstant(c) == 1 );
Compartment_free(c);
}
END_TEST
START_TEST (test_InitialAssignment_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(2,3);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
InitialAssignment_t *object =
InitialAssignment_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) object) == SBML_INITIAL_ASSIGNMENT );
fail_unless( SBase_getMetaId ((SBase_t *) object) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) object) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) object) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) object) == 2 );
fail_unless( SBase_getVersion ((SBase_t *) object) == 3 );
fail_unless( InitialAssignment_getNamespaces (object) != NULL );
fail_unless( XMLNamespaces_getLength(
InitialAssignment_getNamespaces(object)) == 2 );
InitialAssignment_free(object);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_L3_Species_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Species_t *s =
Species_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) s) == SBML_SPECIES );
fail_unless( SBase_getMetaId ((SBase_t *) s) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) s) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) s) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) s) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) s) == 1 );
fail_unless( Species_getNamespaces (s) != NULL );
fail_unless( XMLNamespaces_getLength(Species_getNamespaces(s)) == 2 );
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( Species_getSubstanceUnits (s) == NULL );
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( !Species_isSetSubstanceUnits (s) );
fail_unless( !Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( !Species_isSetBoundaryCondition(s) );
fail_unless( !Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_free(s);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_L3_Model_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Model_t *m =
Model_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) m) == SBML_MODEL );
fail_unless( SBase_getMetaId ((SBase_t *) m) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) m) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) m) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) m) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) m) == 1 );
fail_unless( Model_getNamespaces (m) != NULL );
fail_unless( XMLNamespaces_getLength(Model_getNamespaces(m)) == 2 );
fail_unless( Model_getId (m) == NULL );
fail_unless( Model_getName (m) == NULL );
fail_unless( Model_getSubstanceUnits(m) == NULL );
fail_unless( Model_getTimeUnits(m) == NULL );
fail_unless( Model_getVolumeUnits(m) == NULL );
fail_unless( Model_getAreaUnits(m) == NULL );
fail_unless( Model_getLengthUnits(m) == NULL );
fail_unless( Model_getConversionFactor(m) == NULL );
fail_unless( !Model_isSetId (m) );
fail_unless( !Model_isSetName (m) );
fail_unless( !Model_isSetSubstanceUnits(m) );
fail_unless( !Model_isSetTimeUnits(m) );
fail_unless( !Model_isSetVolumeUnits(m) );
fail_unless( !Model_isSetAreaUnits(m) );
fail_unless( !Model_isSetLengthUnits(m) );
fail_unless( !Model_isSetConversionFactor(m) );
Model_free(m);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_L3_SpeciesReference_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
SpeciesReference_t *sr =
SpeciesReference_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) sr) == SBML_SPECIES_REFERENCE );
fail_unless( SBase_getMetaId ((SBase_t *) sr) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) sr) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) sr) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) sr) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) sr) == 1 );
fail_unless( SpeciesReference_getNamespaces (sr) != NULL );
fail_unless( XMLNamespaces_getLength(SpeciesReference_getNamespaces(sr)) == 2 );
fail_unless( SpeciesReference_getId (sr) == NULL );
fail_unless( SpeciesReference_getName (sr) == NULL );
fail_unless( SpeciesReference_getSpecies (sr) == NULL );
fail_unless( util_isNaN(SpeciesReference_getStoichiometry (sr)) );
fail_unless( SpeciesReference_getConstant(sr) == 0 );
fail_unless( !SpeciesReference_isSetId (sr) );
fail_unless( !SpeciesReference_isSetName (sr) );
fail_unless( !SpeciesReference_isSetSpecies (sr) );
fail_unless( !SpeciesReference_isSetStoichiometry (sr) );
fail_unless( !SpeciesReference_isSetConstant(sr) );
SpeciesReference_free(sr);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_L3_Parameter_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Parameter_t *p =
Parameter_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) p) == SBML_PARAMETER );
fail_unless( SBase_getMetaId ((SBase_t *) p) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) p) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) p) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) p) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) p) == 1 );
fail_unless( Parameter_getNamespaces (p) != NULL );
fail_unless( XMLNamespaces_getLength(Parameter_getNamespaces(p)) == 2 );
fail_unless( Parameter_getId (p) == NULL );
fail_unless( Parameter_getName (p) == NULL );
fail_unless( Parameter_getUnits (p) == NULL );
fail_unless( isnan(Parameter_getValue(p)));
fail_unless( Parameter_getConstant(p) == 1 );
fail_unless( !Parameter_isSetId (p) );
fail_unless( !Parameter_isSetName (p) );
fail_unless( !Parameter_isSetValue (p) );
fail_unless( !Parameter_isSetUnits (p) );
fail_unless( !Parameter_isSetConstant(p) );
Parameter_free(p);
}
END_TEST
START_TEST (test_L3_Unit_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Unit_t *u =
Unit_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) u) == SBML_UNIT );
fail_unless( SBase_getMetaId ((SBase_t *) u) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) u) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) u) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) u) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) u) == 1 );
fail_unless( Unit_getNamespaces (u) != NULL );
fail_unless( XMLNamespaces_getLength(Unit_getNamespaces(u)) == 2 );
fail_unless( Unit_getKind (u) == UNIT_KIND_INVALID );
fail_unless( isnan(Unit_getExponentAsDouble (u)) );
fail_unless( isnan(Unit_getMultiplier (u)) );
// fail_unless( isnan((double)(Unit_getScale (u))) );
fail_unless( !Unit_isSetKind (u) );
fail_unless( !Unit_isSetExponent (u) );
fail_unless( !Unit_isSetMultiplier (u) );
fail_unless( !Unit_isSetScale (u) );
Unit_free(u);
}
END_TEST
START_TEST (test_L3_Event_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Event_t *e =
Event_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) e) == SBML_EVENT );
fail_unless( SBase_getMetaId ((SBase_t *) e) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) e) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) e) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) e) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) e) == 1 );
fail_unless( Event_getNamespaces (e) != NULL );
fail_unless( XMLNamespaces_getLength(Event_getNamespaces(e)) == 2 );
fail_unless( Event_getId (e) == NULL );
fail_unless( Event_getName (e) == NULL );
fail_unless( Event_getUseValuesFromTriggerTime(e) == 1 );
fail_unless( !Event_isSetId (e) );
fail_unless( !Event_isSetName (e) );
fail_unless( !Event_isSetUseValuesFromTriggerTime(e) );
Event_free(e);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_SyntaxChecker_validXHTML)
{
SBMLNamespaces_t *NS24 = SBMLNamespaces_create(2,4);
SBMLNamespaces_t *NS31 = SBMLNamespaces_create(3,1);
XMLTriple_t * toptriple = XMLTriple_createWith("notes", "", "");
XMLTriple_t * triple = XMLTriple_createWith("p", "", "");
XMLAttributes_t * att = XMLAttributes_create ();
XMLNamespaces_t *ns = XMLNamespaces_create();
XMLNamespaces_add(ns, "http://www.w3.org/1999/xhtml", "");
XMLToken_t *tt = XMLToken_createWithText("This is my text");
XMLNode_t *n1 = XMLNode_createFromToken(tt);
XMLToken_t *toptoken = XMLToken_createWithTripleAttr(toptriple, att);
XMLNode_t *topnode = XMLNode_createFromToken(toptoken);
XMLToken_t *token = XMLToken_createWithTripleAttrNS(triple, att, ns);
XMLNode_t *node = XMLNode_createFromToken(token);
XMLNode_addChild(node, n1);
XMLNode_addChild(topnode, node);
fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NULL) == 1 );
fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS24) == 1 );
fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS31) == 1 );
XMLTriple_free(triple);
XMLToken_free(token);
XMLNode_free(node);
triple = XMLTriple_createWith("html", "", "");
token = XMLToken_createWithTripleAttrNS(triple, att, ns);
node = XMLNode_createFromToken(token);
XMLNode_addChild(node, n1);
XMLNode_free(XMLNode_removeChild(topnode, 0));
XMLNode_addChild(topnode, node);
fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NULL) == 1 );
fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS24) == 0 );
fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS31) == 1 );
XMLTriple_free(triple);
triple = XMLTriple_createWith("html", "", "");
XMLNamespaces_clear(ns);
XMLToken_free(token);
XMLNode_free(node);
token = XMLToken_createWithTripleAttrNS(triple, att, ns);
node = XMLNode_createFromToken(token);
XMLNode_addChild(node, n1);
XMLNode_free(XMLNode_removeChild(topnode, 0));
XMLNode_addChild(topnode, node);
fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NULL) == 0 );
fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS24) == 0 );
fail_unless( SyntaxChecker_hasExpectedXHTMLSyntax(topnode, NS31) == 0 );
SBMLNamespaces_free(NS24);
SBMLNamespaces_free(NS31);
XMLTriple_free(toptriple);
XMLTriple_free(triple);
XMLAttributes_free(att);
XMLNamespaces_free(ns);
XMLToken_free(tt);
XMLNode_free(n1);
XMLToken_free(toptoken);
XMLNode_free(topnode);
XMLToken_free(token);
XMLNode_free(node);
}
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;
}
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;
}
END_TEST
//START_TEST (test_RateRule_createWithFormula)
//{
// const ASTNode_t *math;
// char *formula;
//
// Rule_t *ar = Rule_createRateWithVariableAndFormula("s", "1 + 1");
//
//
// fail_unless( SBase_getTypeCode ((SBase_t *) ar) == SBML_RATE_RULE );
// fail_unless( SBase_getMetaId ((SBase_t *) ar) == NULL );
// fail_unless( !strcmp(Rule_getVariable(ar), "s") );
//
// math = Rule_getMath((Rule_t *) ar);
// fail_unless(math != NULL);
//
// formula = SBML_formulaToString(math);
// fail_unless( formula != NULL );
// fail_unless( !strcmp(formula, "1 + 1") );
//
// fail_unless( !strcmp(Rule_getFormula((Rule_t *) ar), formula) );
//
// Rule_free(ar);
// safe_free(formula);
//}
//END_TEST
//START_TEST (test_RateRule_createWithMath)
//{
// ASTNode_t *math = SBML_parseFormula("1 + 1");
//
// Rule_t *ar = Rule_createRateWithVariableAndMath("s", math);
//
//
// fail_unless( SBase_getTypeCode ((SBase_t *) ar) == SBML_RATE_RULE );
// fail_unless( SBase_getMetaId ((SBase_t *) ar) == NULL );
// fail_unless( !strcmp(Rule_getVariable(ar), "s") );
// fail_unless( !strcmp(Rule_getFormula((Rule_t *) ar), "1 + 1") );
// fail_unless( Rule_getMath((Rule_t *) ar) != math );
//
// Rule_free(ar);
//}
//END_TEST
START_TEST (test_RateRule_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(2,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Rule_t *object =
Rule_createRateWithNS(sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) object) == SBML_RATE_RULE );
fail_unless( SBase_getMetaId ((SBase_t *) object) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) object) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) object) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) object) == 2 );
fail_unless( SBase_getVersion ((SBase_t *) object) == 1 );
fail_unless( Rule_getNamespaces (object) != NULL );
fail_unless( XMLNamespaces_getLength(Rule_getNamespaces(object)) == 2 );
Rule_free(object);
}
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;
}