END_TEST START_TEST (test_FbcExtension_read_L3V1V1_defaultNS) { char *filename = safe_strcat(TestDataDirectory, "fbc_example1_defaultNS.xml"); SBMLDocument *document = readSBMLFromFile(filename); fail_unless(document->getPackageName() == "core"); Model *model = document->getModel(); fail_unless(model != NULL); fail_unless(model->getPackageName() == "core"); fail_unless(document->getNumErrors() == 0); // get the fbc plugin FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc")); fail_unless(mplugin != NULL); fail_unless(mplugin->getNumObjectives() == 1); fail_unless(mplugin->getListOfObjectives()->getPackageName() == "fbc"); Objective* objective = mplugin->getObjective(0); fail_unless(objective->getId() == "obj1"); fail_unless(objective->getType() == "maximize"); fail_unless(objective->getNumFluxObjectives() == 1); fail_unless(objective->getPackageName() == "fbc"); fail_unless(objective->getListOfFluxObjectives()->getPackageName() == "fbc"); FluxObjective* fluxObjective = objective->getFluxObjective(0); fail_unless(fluxObjective->getReaction() == "J8"); fail_unless(fluxObjective->getPackageName() == "fbc"); fail_unless(fluxObjective->getCoefficient() == 1); fail_unless(mplugin->getNumFluxBounds() == 1); fail_unless(mplugin->getListOfFluxBounds()->getPackageName() == "fbc"); FluxBound* bound = mplugin->getFluxBound(0); fail_unless(bound->getId() == "bound1"); fail_unless(bound->getPackageName() == "fbc"); fail_unless(bound->getReaction() == "J0"); fail_unless(bound->getOperation() == "equal"); fail_unless(bound->getValue() == 10); delete document; }
void setObjectiveCoefficient(FbcModelPlugin* plugin, Model* model) { if (plugin == NULL || model == NULL) return; Objective* obj = plugin->getActiveObjective(); if (obj == NULL) return; for (unsigned int i = 0; i < obj->getNumFluxObjectives(); ++i) { FluxObjective* fluxObj = obj->getFluxObjective(i); if (fluxObj == NULL) continue; Reaction* reaction = model->getReaction(fluxObj->getReaction()); if (reaction == NULL) continue; KineticLaw* law = reaction->getKineticLaw(); if (law == NULL) continue; LocalParameter* param = law->getLocalParameter("OBJECTIVE_COEFFICIENT"); param->setValue(fluxObj->getCoefficient()); } }
LIBSBML_CPP_NAMESPACE_USE int main(int argc,char** argv) { SBMLNamespaces sbmlns(3,1,"fbc",1); // create the document SBMLDocument *document = new SBMLDocument(&sbmlns); document->setPackageRequired("fbc", false); // create the Model Model* model=document->createModel(); // create the Compartment Compartment* compartment = model->createCompartment(); compartment->setId("compartment"); compartment->setConstant(true); compartment->setSize(1); // create the Species Species* species = model->createSpecies(); species->setId("Node1"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species->setConstant(false); species->setHasOnlySubstanceUnits(false); species = model->createSpecies(); species->setId("Node2"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species->setConstant(false); species->setHasOnlySubstanceUnits(false); species = model->createSpecies(); species->setId("Node3"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species->setConstant(false); species->setHasOnlySubstanceUnits(false); species = model->createSpecies(); species->setId("Node4"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species->setConstant(false); species->setHasOnlySubstanceUnits(false); species = model->createSpecies(); species->setId("Node5"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species->setConstant(false); species->setHasOnlySubstanceUnits(false); species = model->createSpecies(); species->setId("Node6"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species->setConstant(false); species->setHasOnlySubstanceUnits(false); species = model->createSpecies(); species->setId("Node7"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species->setConstant(false); species->setHasOnlySubstanceUnits(false); species = model->createSpecies(); species->setId("Node8"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species->setConstant(false); species->setHasOnlySubstanceUnits(false); species = model->createSpecies(); species->setId("Node0"); species->setCompartment("compartment"); species->setBoundaryCondition(true); species->setConstant(false); species->setHasOnlySubstanceUnits(false); species = model->createSpecies(); species->setId("Node9"); species->setCompartment("compartment"); species->setBoundaryCondition(true); species->setConstant(false); species->setHasOnlySubstanceUnits(false); Reaction* reaction = model->createReaction(); reaction->setId("J0"); reaction->setReversible(false); reaction->setFast(false); SpeciesReference* reactant = reaction->createReactant(); reactant->setSpecies("Node0"); reactant->setStoichiometry(1); reactant->setConstant(true); SpeciesReference* product = reaction->createProduct(); product->setSpecies("Node1"); product->setStoichiometry(1); product->setConstant(true); reaction = model->createReaction(); reaction->setId("J1"); reaction->setReversible(false); reaction->setFast(false); reactant = reaction->createReactant(); reactant->setSpecies("Node1"); reactant->setStoichiometry(1); reactant->setConstant(true); product = reaction->createProduct(); product->setSpecies("Node2"); product->setStoichiometry(1); product->setConstant(true); reaction = model->createReaction(); reaction->setId("J2"); reaction->setReversible(false); reaction->setFast(false); reactant = reaction->createReactant(); reactant->setSpecies("Node2"); reactant->setStoichiometry(1); reactant->setConstant(true); product = reaction->createProduct(); product->setSpecies("Node3"); product->setStoichiometry(1); product->setConstant(true); reaction = model->createReaction(); reaction->setId("J3"); reaction->setReversible(false); reaction->setFast(false); reactant = reaction->createReactant(); reactant->setSpecies("Node1"); reactant->setStoichiometry(1); reactant->setConstant(true); product = reaction->createProduct(); product->setSpecies("Node4"); product->setStoichiometry(1); product->setConstant(true); reaction = model->createReaction(); reaction->setId("J4"); reaction->setReversible(false); reaction->setFast(false); reactant = reaction->createReactant(); reactant->setSpecies("Node4"); reactant->setStoichiometry(1); reactant->setConstant(true); product = reaction->createProduct(); product->setSpecies("Node3"); product->setStoichiometry(1); product->setConstant(true); reaction = model->createReaction(); reaction->setId("J5"); reaction->setReversible(false); reaction->setFast(false); reactant = reaction->createReactant(); reactant->setSpecies("Node3"); reactant->setStoichiometry(1); reactant->setConstant(true); product = reaction->createProduct(); product->setSpecies("Node5"); product->setStoichiometry(1); product->setConstant(true); reaction = model->createReaction(); reaction->setId("J6"); reaction->setReversible(false); reaction->setFast(false); reactant = reaction->createReactant(); reactant->setSpecies("Node5"); reactant->setStoichiometry(1); reactant->setConstant(true); product = reaction->createProduct(); product->setSpecies("Node6"); product->setStoichiometry(1); product->setConstant(true); reaction = model->createReaction(); reaction->setId("J7"); reaction->setReversible(false); reaction->setFast(false); reactant = reaction->createReactant(); reactant->setSpecies("Node6"); reactant->setStoichiometry(1); reactant->setConstant(true); product = reaction->createProduct(); product->setSpecies("Node7"); product->setStoichiometry(1); product->setConstant(true); reaction = model->createReaction(); reaction->setId("J8"); reaction->setReversible(false); reaction->setFast(false); reactant = reaction->createReactant(); reactant->setSpecies("Node5"); reactant->setStoichiometry(1); reactant->setConstant(true); product = reaction->createProduct(); product->setSpecies("Node8"); product->setStoichiometry(1); product->setConstant(true); reaction = model->createReaction(); reaction->setId("J9"); reaction->setReversible(false); reaction->setFast(false); reactant = reaction->createReactant(); reactant->setSpecies("Node8"); reactant->setStoichiometry(1); reactant->setConstant(true); product = reaction->createProduct(); product->setSpecies("Node7"); product->setStoichiometry(1); product->setConstant(true); reaction = model->createReaction(); reaction->setId("J10"); reaction->setReversible(false); reaction->setFast(false); reactant = reaction->createReactant(); reactant->setSpecies("Node7"); reactant->setStoichiometry(1); reactant->setConstant(true); product = reaction->createProduct(); product->setSpecies("Node9"); product->setStoichiometry(1); product->setConstant(true); // // Get a FbcModelPlugin object plugged in the model object. // // The type of the returned value of SBase::getPlugin() function is // SBasePlugin*, and thus the value needs to be casted for the // corresponding derived class. // FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc")); FluxBound* bound= mplugin->createFluxBound(); bound->setId("bound1"); bound->setReaction("J0"); bound->setOperation("equal"); bound->setValue(10); Objective* objective = mplugin->createObjective(); objective->setId("obj1"); objective->setType("maximize"); // mark obj1 as active objective mplugin->setActiveObjectiveId("obj1"); FluxObjective* fluxObjective = objective->createFluxObjective(); fluxObjective->setReaction("J8"); fluxObjective->setCoefficient(1); writeSBML(document,"fbc_example1.xml"); delete document; }
END_TEST START_TEST(test_FbcExtension_create_and_write_new_geneassociation ) { FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 2); // create the document SBMLDocument document(sbmlns); document.setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false); document.setConsistencyChecks(LIBSBML_CAT_MODELING_PRACTICE, false); // create the Model Model* model = document.createModel(); // create the Compartment Compartment* compartment = model->createCompartment(); compartment->setId("compartment"); compartment->setConstant(true); compartment->setSize(1); // create the Species Species* species = model->createSpecies(); species->setId("Node1"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species = model->createSpecies(); species->setId("Node2"); species->setCompartment("compartment"); species->setBoundaryCondition(false); Reaction* reaction = model->createReaction(); reaction->setId("J0"); reaction->setReversible(false); SpeciesReference* reactant = reaction->createReactant(); reactant->setSpecies("Node0"); reactant->setStoichiometry(1); SpeciesReference* product = reaction->createProduct(); product->setSpecies("Node1"); product->setStoichiometry(1); // use fbc FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc")); fail_unless(mplugin != NULL); FluxBound* bound = mplugin->createFluxBound(); bound->setId("bound1"); bound->setReaction("J0"); bound->setOperation("equal"); bound->setValue(10); Objective* objective = mplugin->createObjective(); objective->setId("obj1"); objective->setType("maximize"); FluxObjective* fluxObjective = objective->createFluxObjective(); fluxObjective->setReaction("J0"); fluxObjective->setCoefficient(1); FbcReactionPlugin* rplug = dynamic_cast<FbcReactionPlugin*>(reaction->getPlugin("fbc")); fail_unless(rplug != NULL); GeneProductAssociation * ga = rplug->createGeneProductAssociation(); ga->setId("ga1"); ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079"); fail_unless(ga->getAssociation() != NULL); fail_unless(mplugin->getNumGeneProducts() == 5); ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079"); fail_unless(ga->getAssociation() != NULL); fail_unless(mplugin->getNumGeneProducts() == 5); delete sbmlns; }
END_TEST START_TEST(test_FbcExtension_create_and_write_L3V1V1) { FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 1); // create the document SBMLDocument *document = new SBMLDocument(sbmlns); delete sbmlns; // create the Model Model* model = document->createModel(); // create the Compartment Compartment* compartment = model->createCompartment(); compartment->setId("compartment"); compartment->setConstant(true); compartment->setSize(1); // create the Species Species* species = model->createSpecies(); species->setId("Node1"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species = model->createSpecies(); species->setId("Node2"); species->setCompartment("compartment"); species->setBoundaryCondition(false); Reaction* reaction = model->createReaction(); reaction->setId("J0"); reaction->setReversible(false); SpeciesReference* reactant = reaction->createReactant(); reactant->setSpecies("Node0"); reactant->setStoichiometry(1); SpeciesReference* product = reaction->createProduct(); product->setSpecies("Node1"); product->setStoichiometry(1); // use fbc FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc")); fail_unless(mplugin != NULL); FluxBound* bound = mplugin->createFluxBound(); bound->setId("bound1"); bound->setReaction("J0"); bound->setOperation("equal"); bound->setValue(10); Objective* objective = mplugin->createObjective(); objective->setId("obj1"); objective->setType("maximize"); FluxObjective* fluxObjective = objective->createFluxObjective(); fluxObjective->setReaction("J0"); fluxObjective->setCoefficient(1); string s1 = writeSBMLToStdString(document); // check clone() SBMLDocument* document2 = document->clone(); string s2 = writeSBMLToStdString(document2); fail_unless(s1 == s2); // check operator= Model m = *(document->getModel()); document2->setModel(&m); s2 = writeSBMLToStdString(document2); fail_unless(s1 == s2); delete document2; delete document; }