bool variesIn(string id, Model* model, const map<string, vector<double> >& results)
{
if (variesIn(id, results)) return true;
Rule* rule = model->getRule(id);
if (rule != NULL) {
if (rule->getTypeCode() == SBML_RATE_RULE) return true;
return variesIn(rule->getMath(), model, results);
}
if (!getConstant(id, model, results)) {
//The variable might be set by an algebraic rule
for (unsigned long r=0; r<model->getNumRules(); r++) {
if (model->getRule(r)->getTypeCode() == SBML_ALGEBRAIC_RULE) {
if (appearsIn(id, model->getRule(r)->getMath()) &&
variesBesides(id, model->getRule(r)->getMath(), model, results)) return true;
}
}
}
for (unsigned long e=0; e<model->getNumEvents(); e++) {
Event* event = model->getEvent(e);
for (unsigned long ea=0; ea<event->getNumEventAssignments(); ea++) {
if (event->getEventAssignment(ea)->getVariable() == id) return true;
}
}
Species* species = model->getSpecies(id);
if (species==NULL) return false;
if (species->isSetBoundaryCondition() && species->getBoundaryCondition()==true) return false;
for (unsigned long r=0; r<model->getNumReactions(); r++) {
Reaction* rxn = model->getReaction(r);
if (variesIn(id, rxn->getListOfReactants(), results)) return true;
if (variesIn(id, rxn->getListOfProducts(), results)) return true;
}
return false;
}
void checkSpecies(Model* model, set<string>& components, set<string>& tests, const map<string, vector<double> >& results, int type)
{
//Must call this after 'checkCompartments' because we look in 'tests' for 'NonUnityCompartment'.
if (model->getNumSpecies() > 0) {
components.insert("Species");
if (type==0) {
tests.insert("Amount||Concentration");
}
else if (type==2) {
tests.insert("Amount");
}
set<string> compartments;
for (unsigned int s=0; s<model->getNumSpecies(); s++) {
Species* species = model->getSpecies(s);
if (species->isSetBoundaryCondition() && species->getBoundaryCondition()) {
tests.insert("BoundaryCondition");
}
if (species->getConstant()) {
tests.insert("ConstantSpecies");
}
if (species->isSetConversionFactor()) {
tests.insert("ConversionFactors");
}
if (species->isSetHasOnlySubstanceUnits() && species->getHasOnlySubstanceUnits()) {
tests.insert("HasOnlySubstanceUnits");
}
if (!species->isSetInitialAmount() && !species->isSetInitialConcentration()) {
tests.insert("InitialValueReassigned");
}
else if (species->isSetId() && initialOverriddenIn(species->getId(), model, results, tests)) {
tests.insert("InitialValueReassigned");
}
if (species->isSetCompartment()) {
compartments.insert(species->getCompartment());
}
}
if (tests.find("MultiCompartment") != tests.end() && compartments.size()==1 && model->getNumSpecies() > 1) {
cerr << "Error: multiple compartments discovered, but all species are in a single compartment." << endl;
tests.insert("ERRORMultiCompartment");
}
}
}