//static
void SBMLUtils::collectIds(Model* pModel, std::map<std::string, const SBase*>& ids, std::map<std::string, const SBase*>& metaIds)
{
if (pModel != NULL)
{
// the model itself
SBase* pSBase = NULL;
std::string id;
if (pModel->isSetId())
{
id = pModel->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pModel->isSetMetaId())
{
id = pModel->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// ListOfFunctionDefinitions
pSBase = pModel->getListOfFunctionDefinitions();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// all FunctionDefinitions
unsigned int i, iMax = pModel->getListOfFunctionDefinitions()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getListOfFunctionDefinitions()->get(i);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfUnitDefinition
pSBase = pModel->getListOfUnitDefinitions();
if (pSBase != NULL)
{
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// all UnitDefinitions
// for each UnitDefinition: ListOfUnits, each Unit in ListOfUnits
unsigned int i, iMax = pModel->getListOfUnitDefinitions()->size();
for (i = 0; i < iMax; ++i)
{
/* UnitDefinitions have their ids in a different namespace
so we only consider meta ids.
*/
UnitDefinition* pUDef = pModel->getUnitDefinition(i);
assert(pUDef != NULL);
if (pUDef->isSetMetaId())
{
id = pUDef->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pUDef));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
ListOf* pList = pUDef->getListOfUnits();
if (pList != NULL)
{
if (pList->isSetMetaId())
{
id = pList->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pList));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned j, jMax = pList->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pList->get(j);
assert(pSBase != NULL);
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
}
}
// ListOfCompartmentTypes
pSBase = pModel->getListOfCompartmentTypes();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each compartment type
unsigned int i, iMax = pModel->getListOfCompartmentTypes()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getCompartmentType(i);
assert(pSBase != NULL);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfSpeciesTypes
pSBase = pModel->getListOfSpeciesTypes();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each species type
unsigned int i, iMax = pModel->getListOfSpeciesTypes()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getSpeciesType(i);
assert(pSBase != NULL);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfCompartments
pSBase = pModel->getListOfCompartments();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// all compartments
unsigned int i, iMax = pModel->getListOfCompartments()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getCompartment(i);
assert(pSBase != NULL);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfSpecies
pSBase = pModel->getListOfSpecies();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// all species
unsigned int i, iMax = pModel->getListOfSpecies()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getSpecies(i);
assert(pSBase != NULL);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfParameters
pSBase = pModel->getListOfParameters();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each parameter
unsigned int i, iMax = pModel->getListOfParameters()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getParameter(i);
assert(pSBase != NULL);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfInitialAssignments
pSBase = pModel->getListOfInitialAssignments();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each initial assignment
unsigned int i, iMax = pModel->getListOfInitialAssignments()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getInitialAssignment(i);
assert(pSBase != NULL);
// initial assignments have no ids
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfRules
pSBase = pModel->getListOfRules();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each rule
unsigned int i, iMax = pModel->getListOfRules()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getRule(i);
assert(pSBase != NULL);
// rules don't have ids
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfConstraints
pSBase = pModel->getListOfConstraints();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each constraint
unsigned int i, iMax = pModel->getListOfConstraints()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getConstraint(i);
assert(pSBase != NULL);
// constraints don't have ids
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfReactions
pSBase = pModel->getListOfReactions();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// all reactions
unsigned int i, iMax = pModel->getListOfReactions()->size();
for (i = 0; i < iMax; ++i)
{
Reaction* pReaction = pModel->getReaction(i);
assert(pReaction != NULL);
if (pReaction->isSetId())
{
id = pReaction->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pReaction));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pReaction->isSetMetaId())
{
id = pReaction->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pReaction));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// for each reaction: ListOfSubstrates, each substrate, ListOfProducts, each
// Product, ListOfModifieres, each modifier, KineticLaw, ListOfparameters,
// each parameter
if (pReaction->getListOfReactants() != NULL)
{
pSBase = pReaction->getListOfReactants();
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned int j, jMax = pReaction->getListOfReactants()->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pReaction->getReactant(j);
assert(pSBase != NULL);
// since L2V2 species references can have ids
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
if (pReaction->getListOfProducts() != NULL)
{
pSBase = pReaction->getListOfProducts();
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned int j, jMax = pReaction->getListOfProducts()->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pReaction->getProduct(j);
assert(pSBase != NULL);
// since L2V2 species references can have ids
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
if (pReaction->getListOfModifiers() != NULL)
{
pSBase = pReaction->getListOfModifiers();
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned int j, jMax = pReaction->getListOfModifiers()->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pReaction->getModifier(j);
assert(pSBase != NULL);
// since L2V2 species references can have ids
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
KineticLaw* pKLaw = pReaction->getKineticLaw();
if (pKLaw != NULL)
{
if (pKLaw->isSetMetaId())
{
id = pKLaw->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pKLaw));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
pSBase = pKLaw->getListOfParameters();
if (pSBase != NULL)
{
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned int j, jMax = pKLaw->getListOfParameters()->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pKLaw->getParameter(j);
assert(pSBase != NULL);
// local parameters have their ids in a
// different namespace
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
}
}
}
// ListOfEvents
pSBase = pModel->getListOfEvents();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each event
unsigned int i, iMax = pModel->getListOfEvents()->size();
for (i = 0; i < iMax; ++i)
{
Event* pEvent = pModel->getEvent(i);
assert(pEvent != NULL);
if (pEvent->isSetId())
{
id = pEvent->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pEvent));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pEvent->isSetMetaId())
{
id = pEvent->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pEvent));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// in each event Trigger,Delay,ListOfEventAssignments, each event assignment
if (pEvent->isSetTrigger())
{
pSBase = pEvent->getTrigger();
assert(pSBase != NULL);
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
if (pEvent->isSetDelay())
{
pSBase = pEvent->getDelay();
assert(pSBase != NULL);
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
if (pEvent->getListOfEventAssignments() != NULL)
{
pSBase = pEvent->getListOfEventAssignments();
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned int j, jMax = pEvent->getListOfEventAssignments()->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pEvent->getEventAssignment(j);
assert(pSBase != NULL);
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
}
}
}
}
void
CompIdBase::checkId (const Reaction& x)
{
if (x.isSetId()) doCheckId(x.getId(), x);
}
void SbmlReader::createReaction(const map< string, Id > &molSidcmptMIdMap ) {
Reaction* reac;
map< string,double > rctMap;
map< string,double >::iterator rctMap_iter;
map< string,double >prdMap;
map< string,double >::iterator prdMap_iter;
map< string,EnzymeInfo >enzInfoMap;
for ( unsigned int r = 0; r < model_->getNumReactions(); r++ ) {
Id reaction_;
reac = model_->getReaction( r );
noOfsub_ = 0;
noOfprd_ = 0;
std:: string id; //=reac->getId();
if ( reac->isSetId() )
id = reac->getId();
std::string name;
if ( reac->isSetName() ) {
name = reac->getName();
name = nameString(name);
}
if (name.empty()) {
if (id.empty())
assert("Reaction id and name is empty");
else
name = id;
}
string grpname = getAnnotation( reac,enzInfoMap );
if ( (grpname != "") && (enzInfoMap[grpname].stage == 3) ) {
setupEnzymaticReaction( enzInfoMap[grpname],grpname ,molSidcmptMIdMap,name);
}
//if (grpname != "")
// {
//cout << "\n enz matic reaction " << enzInfoMap[grpname].stage;
//setupEnzymaticReaction( enzInfoMap[grpname],grpname ,molSidcmptMIdMap);
//}
else if ( grpname == "" ) {
if (reac->getNumModifiers() > 0)
setupMMEnzymeReaction( reac,id,name ,molSidcmptMIdMap);
else {
bool rev=reac->getReversible();
bool fast=reac->getFast();
if ( fast ) {
cout<<"warning: for now fast attribute is not handled"<<endl;
errorFlag_ = true;
}
int numRcts = reac->getNumReactants();
int numPdts = reac->getNumProducts();
if ( numRcts == 0 && numPdts != 0 ) {
cout << "Reaction with zero Substrate is not possible but exist in this model";
const SpeciesReference* pdt = reac->getProduct( 0 );
std::string spName = pdt->getSpecies();
Id parent = molSidcmptMIdMap.find( spName )->second; //gives compartment of spName
cout << " \n \t ################################# Sub = 0 and prd != 0 need to the reac ############### ";
const SpeciesReference* rect=reac->getReactant(0);
std::string sp=rect->getSpecies();
Id comptRef = molSidcmptMIdMap.find(sp)->second; //gives compartment of sp
Id meshEntry = Neutral::child( comptRef.eref(), "mesh" );
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
reaction_ = shell->doCreate("Reac", meshEntry, name, 1);
//shell->doAddMsg( "Single", meshEntry, "remeshReacs", reaction_, "remesh");
//Get Substrate
addSubPrd(reac,reaction_,"prd");
} //if numRcts == 0
else {
const SpeciesReference* rect=reac->getReactant(0);
std::string sp=rect->getSpecies();
Id comptRef = molSidcmptMIdMap.find(sp)->second; //gives compartment of sp
Id meshEntry = Neutral::child( comptRef.eref(), "mesh" );
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
reaction_ = shell->doCreate("Reac", comptRef, name, 1);
//shell->doAddMsg( "Single", meshEntry, "remeshReacs", reaction_, "remesh");
//Get Substrate
addSubPrd(reac,reaction_,"sub");
//Get Product
addSubPrd(reac,reaction_,"prd");
}
if ( reac->isSetKineticLaw() ) {
KineticLaw * klaw=reac->getKineticLaw();
//vector< double > rate = getKLaw( klaw,rev );
vector< double > rate;
rate.clear();
getKLaw( klaw,rev,rate );
if ( errorFlag_ )
return;
else if ( !errorFlag_ ) {
//cout << " Reaction name " << name << " kf " << rate[0] << " kb " << rate[1]<<endl;
Field < double > :: set( reaction_, "Kf", rate[0] );
Field < double > :: set( reaction_, "Kb", rate[1] );
/*if (numRcts > 1)
rate[0] = rate[0]*pow(1e3,1.0);
cout << "Reaction " << id << " " << name << " " << rate[0] << " " << rate[1]<<endl;
Field < double > :: set( reaction_, "Kf", rate[0] );
Field < double > :: set( reaction_, "Kb", rate[1] );
*/
}
} //issetKineticLaw
} //else
} // else grpname == ""
}//for unsigned
} //reaction