void CModelExpansion::replaceInMetab(CMetab* pX, const ElementsMap & emap)
{
replaceInModelEntity(pX, emap);
//is the metab in a compartment that needs to be replaced?
if (emap.exists(pX->getCompartment()))
{
//move the metab to the new compartment
CCompartment* oldComp = const_cast<CCompartment*>(pX->getCompartment());
CCompartment* newComp = dynamic_cast<CCompartment*>(emap.getDuplicatePtr(pX->getCompartment()));
bool success = false;
do
{
success = newComp->addMetabolite(pX);
if (success)
{
oldComp->getMetabolites().remove(pX->getObjectName());
mpModel->setCompileFlag();
mpModel->initializeMetabolites();
}
else
{
//rename the metab so that it can be added to the new compartment
pX->setObjectName(pX->getObjectName() + "_");
//TODO: check if the renaming actually worked
}
}
while (!success);
}
}
// virtual
CXMLHandler * MetaboliteHandler::processStart(const XML_Char * pszName,
const XML_Char ** papszAttrs)
{
CXMLHandler * pHandlerToCall = NULL;
CCompartment * pCompartment = NULL;
const char * Name;
const char * simulationType;
CModelEntity::Status SimulationType;
const char reactions[] = "reactions";
const char * Compartment;
bool AddNoise;
switch (mCurrentElement.first)
{
case Metabolite:
mKey = mpParser->getAttributeValue("key", papszAttrs);
Name = mpParser->getAttributeValue("name", papszAttrs);
simulationType = mpParser->getAttributeValue("simulationType", papszAttrs, false);
// We need to handle old files which used the attribute status.
if (!simulationType)
{
simulationType = mpParser->getAttributeValue("status", papszAttrs, false);
if (!simulationType) // status and simulationType are both missing
simulationType = mpParser->getAttributeValue("simulationType", papszAttrs);
else if (!strcmp(simulationType, "variable")) // reactions was named variable
simulationType = reactions;
}
SimulationType = toEnum(simulationType, CModelEntity::XMLStatus, CModelEntity::REACTIONS);
Compartment = mpParser->getAttributeValue("compartment", papszAttrs);
AddNoise = mpParser->toBool(mpParser->getAttributeValue("addNoise", papszAttrs, "false"));
mpMetabolite = new CMetab();
addFix(mKey, mpMetabolite);
mpMetabolite->setObjectName(Name);
mpMetabolite->setStatus(SimulationType);
mpMetabolite->setAddNoise(AddNoise);
pCompartment =
dynamic_cast< CCompartment* >(mpData->mKeyMap.get(Compartment));
if (!pCompartment) fatalError();
pCompartment->addMetabolite(mpMetabolite);
mpData->pModel->getMetabolites().add(mpMetabolite, false);
break;;
case MiriamAnnotation:
case Comment:
case Expression:
case InitialExpression:
case NoiseExpression:
pHandlerToCall = getHandler(mCurrentElement.second);
break;
case ListOfUnsupportedAnnotations:
mpData->mUnsupportedAnnotations.clear();
pHandlerToCall = getHandler(mCurrentElement.second);
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return pHandlerToCall;
}
