void
UndoSpeciesData::fillObject(CModel *)
{
CMetab * pSpecies =
dynamic_cast<CMetab*>(CCopasiRootContainer::getKeyFactory()->get(mKey));
if (pSpecies == NULL) return;
if (getStatus() != CModelEntity::ASSIGNMENT)
{
pSpecies->setInitialConcentration(getIConc());
pSpecies->setInitialValue(getINumber());
}
if (getStatus() == CModelEntity::ODE || getStatus() == CModelEntity::ASSIGNMENT)
{
pSpecies->setExpression(getExpression());
}
// set initial expression
if (getStatus() != CModelEntity::ASSIGNMENT)
{
pSpecies->setInitialExpression(getInitialExpression());
}
}
const CModelParameter::CompareResult & CModelParameter::diff(const CModelParameter & other,
const CModelParameter::Framework & framework,
const bool & /* createMissing */)
{
if (mCompareResult == Missing ||
mCompareResult == Obsolete)
{
return mCompareResult;
}
switch (mType)
{
case Compartment:
case Species:
case ModelValue:
if (other.getObject() != NULL &&
mpObject != NULL &&
static_cast< CModelEntity *>(mpObject)->getStatus() == CModelEntity::ASSIGNMENT &&
(fabs(getValue(ParticleNumbers) - other.getValue(ParticleNumbers)) > 50 * (fabs(getValue(ParticleNumbers)) + fabs(other.getValue(ParticleNumbers))) * std::numeric_limits< C_FLOAT64 >::epsilon() ||
getInitialExpression() != ""))
{
mCompareResult = Conflict;
return mCompareResult;
}
break;
default:
break;
}
if (getInitialExpression() != other.getInitialExpression() ||
fabs(getValue(framework) - other.getValue(framework)) > 50 * (fabs(getValue(framework)) + fabs(other.getValue(framework))) * std::numeric_limits< C_FLOAT64 >::epsilon())
{
mCompareResult = Modified;
}
else
{
mCompareResult = Identical;
}
return mCompareResult;
}
bool CModelParameter::isReadOnly() const
{
if (mType == Reaction ||
mType == Group ||
mType == Set ||
(mType == Model && getModel()->isAutonomous()) ||
(mIsInitialExpressionValid && getInitialExpression() != ""))
{
return true;
}
return false;
}
// virtual
void CModelParameterReactionParameter::compile()
{
CModelParameter::compile();
mGlobalQuantityCN = std::string();
std::string Infix = getInitialExpression();
if (Infix.length() > 2)
{
// Infix: <CN,Reference=InitialValue> or <CN,Reference=Value>
CCopasiObjectName Tmp = Infix.substr(1, Infix.length() - 2);
std::string Separator = "";
for (; Tmp != ""; Tmp = Tmp.getRemainder())
{
CCopasiObjectName Primary = Tmp.getPrimary();
if (Primary.getObjectType() == "Reference")
{
break;
}
mGlobalQuantityCN += Separator + Primary;
Separator = ",";
}
setSimulationType(CModelEntity::ASSIGNMENT);
}
else
{
setSimulationType(CModelEntity::FIXED);
}
mpGlobalQuantity = this->getSet()->getModelParameter(mGlobalQuantityCN);
if (mpGlobalQuantity != NULL)
{
mValue = mpGlobalQuantity->getValue(ParticleNumbers);
}
std::vector< CCopasiContainer * > ListOfContainer;
CModel * pModel = getModel();
ListOfContainer.push_back(pModel);
mpReaction = static_cast< CReaction * >(pModel->getObjectDataModel()->ObjectFromName(ListOfContainer, mpParent->getCN()));
}
// 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;
}
