void checkSpeciesRefs(Model* model, ListOfSpeciesReferences* losr, set<string>& components, set<string>& tests, const map<string, vector<double> >& results)
{
for (unsigned int rp=0; rp<losr->size(); rp++) {
SpeciesReference* sr = static_cast<SpeciesReference*>(losr->get(rp));
if (sr->isSetStoichiometry() && sr->getStoichiometry() != 1) {
tests.insert("NonUnityStoichiometry");
}
if (sr->isSetStoichiometryMath()) {
tests.insert("NonUnityStoichiometry");
components.insert("StoichiometryMath");
if (variesIn(sr->getStoichiometryMath()->getMath(), model, results)) {
tests.insert("AssignedVariableStoichiometry");
}
else {
tests.insert("AssignedConstantStoichiometry");
}
}
else if (sr->isSetId()) {
double initialResult = 1;
if (results.find(sr->getId()) != results.end()) {
tests.insert("SpeciesReferenceOutput");
}
if (variesIn(sr->getId(), model, results)) {
tests.insert("AssignedVariableStoichiometry");
tests.insert("NonUnityStoichiometry");
}
else if (initialOverriddenIn(sr->getId(), model, results, tests)) {
tests.insert("AssignedConstantStoichiometry");
if (getInitialResultFor(sr->getId(), results, initialResult)) {
if (initialResult != 1) {
tests.insert("NonUnityStoichiometry");
}
}
else {
//Don't know what the actual initial result is, so we'll assume it's not 1.0.
tests.insert("NonUnityStoichiometry");
}
}
if (initialOverriddenIn(sr->getId(), model, results, tests)) {
tests.insert("InitialValueReassigned");
}
if (foundInMath(sr->getId(), model)) {
tests.insert("SpeciesReferenceInMath");
}
}
}
}
void dealWithAssigningL1Stoichiometry(Model & m, bool l2)
{
//char newid[15];
std::string id;
for (unsigned int i = 0; i < m.getNumReactions(); i++)
{
Reaction *r = m.getReaction(i);
unsigned int j;
for (j = 0; j < r->getNumReactants(); j++)
{
SpeciesReference *sr = r->getReactant(j);
// we do not get here unless the stoichiometryMath is an integer
// or a rational
if (l2 == true && sr->isSetStoichiometryMath() == true)
{
const ASTNode* ast = sr->getStoichiometryMath()->getMath();
if (ast->isInteger())
{
int num = ast->getInteger();
sr->setStoichiometry(num);
sr->setDenominator(1);
}
else
{
int num = ast->getNumerator();
int denom = ast->getDenominator();
sr->setStoichiometry(num);
sr->setDenominator(denom);
}
sr->unsetStoichiometryMath();
}
else
{
sr->setStoichiometry(sr->getStoichiometry());
sr->setDenominator(1);
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
SpeciesReference *sr = r->getProduct(j);
// we do not get here unless the stoichiometryMath is an integer
// or a rational
if (l2 == true && sr->isSetStoichiometryMath() == true)
{
const ASTNode* ast = sr->getStoichiometryMath()->getMath();
if (ast->isInteger())
{
int num = ast->getInteger();
sr->setStoichiometry(num);
sr->setDenominator(1);
}
else
{
int num = ast->getNumerator();
int denom = ast->getDenominator();
sr->setStoichiometry(num);
sr->setDenominator(denom);
}
sr->unsetStoichiometryMath();
}
else
{
sr->setStoichiometry(sr->getStoichiometry());
sr->setDenominator(1);
}
}
}
}
void dealWithL1Stoichiometry(Model & m, bool l2)
{
unsigned int idCount = 0;
char newid[15];
std::string id;
for (unsigned int i = 0; i < m.getNumReactions(); i++)
{
Reaction *r = m.getReaction(i);
unsigned int j;
for (j = 0; j < r->getNumReactants(); j++)
{
SpeciesReference *sr = r->getReactant(j);
if (sr->getDenominator() != 1)
{
long stoich = static_cast<long>(sr->getStoichiometry());
int denom = sr->getDenominator();
ASTNode *node = new ASTNode();
node->setValue(stoich, denom);
if (l2 == true)
{
StoichiometryMath * sm = sr->createStoichiometryMath();
sm->setMath(node);
}
else
{
sprintf(newid, "speciesRefId_%u", idCount);
id.assign(newid);
idCount++;
sr->setId(id);
InitialAssignment * ar = m.createInitialAssignment();
ar->setSymbol(id);
ar->setMath(node);
sr->unsetStoichiometry();
}
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
SpeciesReference *sr = r->getProduct(j);
if (sr->getDenominator() != 1)
{
long stoich = static_cast<long>(sr->getStoichiometry());
int denom = sr->getDenominator();
ASTNode *node = new ASTNode();
node->setValue(stoich, denom);
if (l2 == true)
{
StoichiometryMath * sm = sr->createStoichiometryMath();
sm->setMath(node);
}
else
{
sprintf(newid, "speciesRefId_%u", idCount);
id.assign(newid);
idCount++;
sr->setId(id);
InitialAssignment * ar = m.createInitialAssignment();
ar->setSymbol(id);
ar->setMath(node);
sr->unsetStoichiometry();
}
}
}
}
}