// Return true if stoichiometry is defined for this species reference
static bool isStoichDefined(const SpeciesReference* s) {
if (!s)
// null ref
return false;
if (hasInitialAssignment(s) || hasAssignmentRule(s))
// stoich can be set by assignments
return true;
return s->isSetStoichiometry();
}
bool LLVMModelDataSymbols::isValidSpeciesReference(
const libsbml::SimpleSpeciesReference* ref, const std::string& reacOrProd)
{
string id = ref->getSpecies();
// can only define a reaction for a floating species
if (isIndependentFloatingSpecies(id))
{
return true;
}
else
{
string id = ref->getSpecies();
string err = "the species reference with id ";
err += string("\'" + ref->getId() + "\', ");
err += "which references species ";
string("\'" + id + "\', ");
err += "is NOT a valid " + reacOrProd + " reference, ";
// figure out what kind of thing we have and give a warning
if (hasAssignmentRule(id))
{
err += "it is defined by an assignment rule";
}
else if (hasRateRule(id))
{
err += "it is defined by rate rule";
}
else if (isIndependentBoundarySpecies(id))
{
err += "it is a boundary species";
}
else
{
err += "it is not a species";
}
err += ", it will be ignored.";
if (isIndependentBoundarySpecies(id))
{
// fairly common
Log(Logger::PRIO_DEBUG) << err;
}
else
{
// serious error
Log(Logger::PRIO_WARNING) << err;
}
return false;
}
}
