// virtual
bool CModelParameter::updateModel()
{
bool success = true;
if (mpObject != NULL)
{
switch (mType)
{
case Model:
{
CModel * pModel = static_cast< CModel * >(mpObject);
if (!pModel->isAutonomous())
{
pModel->setInitialValue(mValue);
}
else
{
pModel->setInitialValue(0.0);
}
}
break;
case Compartment:
case Species:
case ModelValue:
{
CModelEntity * pEntity = static_cast< CModelEntity * >(mpObject);
if (pEntity->getStatus() != CModelEntity::ASSIGNMENT)
{
pEntity->setInitialValue(mValue);
if (mIsInitialExpressionValid)
{
pEntity->setInitialExpression(getInitialExpression());
}
}
}
break;
case ReactionParameter:
{
CCopasiParameter * pParameter = static_cast< CCopasiParameter * >(mpObject);
CReaction * pReaction = static_cast< CReaction * >(mpObject->getObjectAncestor("Reaction"));
if (mIsInitialExpressionValid &&
getInitialExpression() != "")
{
CModel * pModel = mpParent->getModel();
assert(pModel != NULL);
std::vector< CCopasiContainer * > ListOfContainer;
ListOfContainer.push_back(pModel);
CCopasiObjectName CN = static_cast< CEvaluationNodeObject * >(mpInitialExpression->getRoot())->getObjectCN();
CCopasiObject * pObject = pModel->getObjectDataModel()->ObjectFromName(ListOfContainer, CN);
assert(pObject != NULL);
// We assign the object value
pParameter->setValue(* (C_FLOAT64 *) pObject->getValuePointer());
// We map the parameter to the global quantity
pReaction->setParameterMapping(pParameter->getObjectName(), pObject->getObjectParent()->getKey());
}
else
{
pParameter->setValue(mValue);
// We need to remove the existing mapping to a global quantity1.
pReaction->setParameterMapping(pParameter->getObjectName(), pParameter->getKey());
}
}
break;
default:
success = false;
break;
}
}
return success;
}
std::string CODEExporterC::KineticFunction2ODEmember(const CReaction *reac)
{
std::ostringstream equation;
if (reac->getFunction()->getType() != CEvaluationTree::MassAction)
{
const CFunctionParameters & params = reac->getFunctionParameters();
size_t k, params_size = params.size();
const std::vector<std::vector<std::string> > & keyMap = reac->getParameterMappings();
std::string name;
equation << NameMap[reac->getFunction()->getKey()] << "(";
for (k = 0; k < params_size; ++k)
{
CFunctionParameter::Role role = params[k]->getUsage();
CCopasiObject * obj = CCopasiRootContainer::getKeyFactory()->get(keyMap[k][0]);
if ((role == CFunctionParameter::SUBSTRATE)
|| (role == CFunctionParameter::PRODUCT)
|| (role == CFunctionParameter::MODIFIER))
{
if (obj)
name = NameMap[obj->getKey()];
else
name = "unknown";
}
if (role == CFunctionParameter::PARAMETER)
{
if (!(reac->isLocalParameter(k)))
{
CModelValue* modval;
modval = dynamic_cast< CModelValue * >(obj);
name = NameMap[modval->getKey()];
}
else
{
CCopasiParameter* param;
param = dynamic_cast< CCopasiParameter * >(obj);
name = NameMap[param->getKey()];
}
}
if (role == CFunctionParameter::VOLUME)
{
CCompartment* comp;
comp = dynamic_cast< CCompartment * >(obj);
name = NameMap[comp->getKey()];
}
if (role == CFunctionParameter::TIME)
{
name = "T";
}
if (name.empty())
{
std::string message = "Could not export C code, since one of the arguments could not be resolved. Please consider filing a bug with the COPASI tracker: http://www.copasi.org/tracker";
CCopasiMessage(CCopasiMessage::EXCEPTION, message.c_str());
}
equation << name;
if (k != params_size - 1)
equation << ", ";
}
equation << ")";
}
else
{
const CCopasiVector<CChemEqElement> & substrs = reac->getChemEq().getSubstrates();
const CCopasiVector<CChemEqElement> & prods = reac->getChemEq().getProducts();
const std::vector<std::vector<std::string> > & keyMap = reac->getParameterMappings();
CCopasiObject * obj;
size_t substrs_size = substrs.size(), prods_size = prods.size();
size_t k, m, mult;
const CChemEqElement* substr;
const CChemEqElement* prod;
const CMassAction & cMassAction = *static_cast<const CMassAction*>(reac->getFunction());
equation << "(";
obj = CCopasiRootContainer::getKeyFactory()->get(keyMap[0][0]);
if (!(reac->isLocalParameter(0)))
{
CModelValue* modval;
modval = dynamic_cast< CModelValue * >(obj);
equation << NameMap[modval->getKey()];
}
else
{
CCopasiParameter* param;
param = dynamic_cast< CCopasiParameter * >(obj);
equation << NameMap[param->getKey()];
}
for (k = 0; k < substrs_size; ++k)
{
substr = &substrs[k];
mult = (size_t) substr->getMultiplicity();
assert(substr->getMetabolite());
equation << " * " << NameMap[substr->getMetabolite()->getKey()];
if (mult > 1)
for (m = 1; m < mult; ++m)
equation << " * " << NameMap[substr->getMetabolite()->getKey()];
}
if (cMassAction.isReversible() == TriTrue)
{
equation << " - ";
obj = CCopasiRootContainer::getKeyFactory()->get(keyMap[2][0]);
if (!(reac->isLocalParameter(2)))
{
CModelValue* modval;
modval = dynamic_cast< CModelValue * >(obj);
equation << NameMap[modval->getKey()];
}
else
{
CCopasiParameter* param;
param = dynamic_cast< CCopasiParameter * >(obj);
equation << NameMap[param->getKey()];
}
for (k = 0; k < prods_size; ++k)
{
prod = &prods[k];
mult = (size_t) prod->getMultiplicity();
assert(prod->getMetabolite());
equation << " * " << NameMap[prod->getMetabolite()->getKey()];
if (mult > 1)
for (m = 1; m < mult; ++m)
equation << " * " << NameMap[prod->getMetabolite()->getKey()];
}
}
equation << ") ";
}
return equation.str();
}
