CCopasiObject::DataObjectSet CMetab::getDeletedObjects() const
{
CCopasiObject::DataObjectSet Deleted = CModelEntity::getDeletedObjects();
Deleted.insert(mpIConcReference);
Deleted.insert(mpConcReference);
Deleted.insert(mpConcRateReference);
Deleted.insert(mpTTReference);
return Deleted;
}
bool CQUnitDM::removeRows(QModelIndexList rows, const QModelIndex&)
{
if (rows.isEmpty())
return false;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = &CCopasiRootContainer::getDatamodelList()->operator[](0);
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
if (pModel == NULL)
return false;
// Build the list of pointers to items to be deleted
// before actually deleting any item.
QList <CUnitDefinition *> pUnitDefQList;
QModelIndexList::const_iterator i;
CUnitDefinition * pUnitDef;
for (i = rows.begin(); i != rows.end(); ++i)
{
if (!isDefaultRow(*i) &&
(pUnitDef = &CCopasiRootContainer::getUnitList()->operator[](i->row())) != NULL &&
pModel->getUnitSymbolUsage(pUnitDef->getSymbol()).empty() &&
!pUnitDef->isReadOnly())//Don't delete built-ins or used units
pUnitDefQList.append(&CCopasiRootContainer::getUnitList()->operator[](i->row()));
}
for (QList <CUnitDefinition *>::const_iterator j = pUnitDefQList.begin(); j != pUnitDefQList.end(); ++j)
{
size_t delRow =
CCopasiRootContainer::getUnitList()->CCopasiVector< CUnitDefinition >::getIndex(*j);
if (delRow != C_INVALID_INDEX)
{
CCopasiObject::DataObjectSet DeletedObjects;
DeletedObjects.insert(*j);
QMessageBox::StandardButton choice =
CQMessageBox::confirmDelete(NULL, "unit",
FROM_UTF8((*j)->getObjectName()),
DeletedObjects);
if (choice == QMessageBox::Ok)
removeRow((int) delRow);
}
}
return true;
}
// static
bool CCopasiObject::compare(const CCopasiObject * lhs, const CCopasiObject * rhs)
{
if (lhs != rhs)
{
CCopasiObject::DataObjectSet Candidates;
CCopasiObject::DataObjectSet VerifiedSet;
Candidates.insert(lhs);
if (rhs->hasCircularDependencies(Candidates, VerifiedSet))
return true;
}
return false;
}
// virtual
bool CCopasiObject::mustBeDeleted(const CCopasiObject::DataObjectSet & deletedObjects) const
{
bool MustBeDeleted = false;
DataObjectSet::const_iterator it = mDependencies.begin();
DataObjectSet::const_iterator end = mDependencies.end();
for (; it != end; ++it)
{
if (deletedObjects.find(*it) != deletedObjects.end())
{
MustBeDeleted = true;
break;
}
}
return MustBeDeleted;
}
void CMetab::compileIsInitialConcentrationChangeAllowed()
{
// We check whether changing the initial concentration will lead to circular
// dependencies in the system.
// These circular dependencies must always involve the initial particle number, i.e.,
// it suffices to check whether the initial particle number has circular dependencies when the
// concentration is changes.
CCopasiObject::DataObjectSet Candidates;
CCopasiObject::DataObjectSet Verified;
CCopasiObject::DataObjectSet Context;
Context.insert(this->mpIConcReference);
mIsInitialConcentrationChangeAllowed = !mpIValueReference->hasCircularDependencies(Candidates, Verified, Context);
return;
}
// virtual
bool CEvent::mustBeDeleted(const CCopasiObject::DataObjectSet & deletedObjects) const
{
bool MustBeDeleted = false;
CCopasiObject::DataObjectSet ChildObjects;
if (mpTriggerExpression != NULL)
{
ChildObjects.insert(mpTriggerExpression);
}
if (mpDelayExpression != NULL)
{
ChildObjects.insert(mpDelayExpression);
}
if (mpPriorityExpression != NULL)
{
ChildObjects.insert(mpPriorityExpression);
}
// We need to add all assignment targets and expressions
CCopasiVector< CEventAssignment >::const_iterator itAssignment = mAssignments.begin();
CCopasiVector< CEventAssignment >::const_iterator endAssignment = mAssignments.end();
for (; itAssignment != endAssignment; ++itAssignment)
{
if (itAssignment->getTargetObject() != NULL)
{
ChildObjects.insert(itAssignment->getTargetObject());
}
if (itAssignment->getExpressionPtr() != NULL)
{
ChildObjects.insert(itAssignment->getExpressionPtr());
}
}
DataObjectSet::const_iterator it = ChildObjects.begin();
DataObjectSet::const_iterator end = ChildObjects.end();
for (; it != end; ++it)
{
if ((*it)->mustBeDeleted(deletedObjects))
{
MustBeDeleted = true;
break;
}
}
return MustBeDeleted;
}
bool CCopasiObject::hasCircularDependencies(CCopasiObject::DataObjectSet & candidates,
CCopasiObject::DataObjectSet & verified,
const CCopasiObject::DataObjectSet & context) const
{
bool hasCircularDependencies = false;
if (verified.count(this) != 0)
return hasCircularDependencies;
const CCopasiObject::DataObjectSet & DirectDependencies = getDirectDependencies(context);
CCopasiObject::DataObjectSet::const_iterator it = DirectDependencies.begin();
CCopasiObject::DataObjectSet::const_iterator end = DirectDependencies.end();
std::pair<CCopasiObject::DataObjectSet::iterator, bool> Inserted;
// Dual purpose insert
Inserted = candidates.insert(this);
// Check whether the insert was successful, if not
// the object "this" was among the candidates. Thus we have a detected
// a circular dependency
if (Inserted.second)
{
for (; it != end && !hasCircularDependencies; ++it)
{
hasCircularDependencies = (*it)->hasCircularDependencies(candidates, verified, context);
}
// Remove the inserted object this from the candidates to avoid any
// side effects.
candidates.erase(this);
}
else
hasCircularDependencies = true;
// The element has been checked and does not need to be checked again.
verified.insert(this);
return hasCircularDependencies;
}
void CCopasiObject::getAllDependencies(CCopasiObject::DataObjectSet & dependencies,
const CCopasiObject::DataObjectSet & context) const
{
const CCopasiObject::DataObjectSet & DirectDependencies = getDirectDependencies(context);
CCopasiObject::DataObjectSet::const_iterator it = DirectDependencies.begin();
CCopasiObject::DataObjectSet::const_iterator end = DirectDependencies.end();
std::pair<CCopasiObject::DataObjectSet::iterator, bool> Inserted;
for (; it != end; ++it)
{
// Dual purpose insert
Inserted = dependencies.insert(*it);
// The direct dependency *it was among the dependencies
// we assume also its dependencies have been added already.
if (!Inserted.second) continue;
// Add all the dependencies of the direct dependency *it.
(*it)->getAllDependencies(dependencies, context);
}
}
//static
std::vector< Refresh * >
CCopasiObject::buildUpdateSequence(const CCopasiObject::DataObjectSet & objects,
const CCopasiObject::DataObjectSet & uptoDateObjects,
const CCopasiObject::DataObjectSet & context)
{
CCopasiObject::DataObjectSet DependencySet;
CCopasiObject::DataObjectSet VerifiedSet;
CCopasiObject::DataObjectSet::const_iterator itSet;
CCopasiObject::DataObjectSet::const_iterator endSet = objects.end();
std::pair<CCopasiObject::DataObjectSet::iterator, bool> InsertedObject;
assert(objects.count(NULL) == 0);
// Check whether we have any circular dependencies
for (itSet = objects.begin(); itSet != endSet; ++itSet)
if ((*itSet)->hasCircularDependencies(DependencySet, VerifiedSet, context))
CCopasiMessage(CCopasiMessage::EXCEPTION, MCObject + 1, (*itSet)->getCN().c_str());
// Build the complete set of dependencies
for (itSet = objects.begin(); itSet != endSet; ++itSet)
{
// At least the object itself needs to be up to date.
InsertedObject = DependencySet.insert(*itSet);
// Add all its dependencies
if (InsertedObject.second)
(*itSet)->getAllDependencies(DependencySet, context);
}
// Remove all objects which do not have any refresh method as they will
// be ignored anyway, i.e., no need to sort them.
for (itSet = DependencySet.begin(), endSet = DependencySet.end(); itSet != endSet;)
if ((*itSet)->getRefresh() == NULL ||
((dynamic_cast< const CParticleReference * >(*itSet) != NULL ||
dynamic_cast< const CConcentrationReference * >(*itSet) != NULL) &&
(*itSet)->getDirectDependencies(context).size() == 0))
{
const CCopasiObject * pObject = *itSet;
++itSet;
DependencySet.erase(pObject);
}
else
++itSet;
// Build the list of all up to date objects
CCopasiObject::DataObjectSet UpToDateSet;
for (itSet = uptoDateObjects.begin(), endSet = uptoDateObjects.end(); itSet != endSet; ++itSet)
{
// At least the object itself is up to date.
InsertedObject = UpToDateSet.insert(*itSet);
// Add all its dependencies too
if (InsertedObject.second)
(*itSet)->getAllDependencies(UpToDateSet, context);
}
// Now remove all objects in the dependency set which are up to date
for (itSet = UpToDateSet.begin(), endSet = UpToDateSet.end(); itSet != endSet; ++itSet)
DependencySet.erase(*itSet);
// Create a properly sorted list.
std::list< const CCopasiObject * > SortedList =
sortObjectsByDependency(DependencySet.begin(), DependencySet.end(), context);
std::list< const CCopasiObject * >::iterator itList;
std::list< const CCopasiObject * >::iterator endList;
// Build the vector of pointers to refresh methods
Refresh * pRefresh;
std::vector< Refresh * > UpdateVector;
std::vector< Refresh * >::const_iterator itUpdate;
std::vector< Refresh * >::const_iterator endUpdate;
itList = SortedList.begin();
endList = SortedList.end();
for (; itList != endList; ++itList)
{
pRefresh = (*itList)->getRefresh();
itUpdate = UpdateVector.begin();
endUpdate = UpdateVector.end();
while (itUpdate != endUpdate && !(*itUpdate)->isEqual(pRefresh)) ++itUpdate;
if (itUpdate == endUpdate)
UpdateVector.push_back(pRefresh);
}
return UpdateVector;
}
void CMetab::setStatus(const CModelEntity::Status & status)
{
Status OldStatus = getStatus();
CModelEntity::setStatus(status);
if (status == OldStatus) return;
CCopasiObject::DataObjectSet Dependencies;
const CCopasiObject * pVolumeReference = NULL;
if (mpCompartment)
pVolumeReference = mpCompartment->getValueReference();
switch (getStatus())
{
case FIXED:
break;
case ASSIGNMENT:
Dependencies.insert(mpConcReference);
if (pVolumeReference)
Dependencies.insert(pVolumeReference);
mpValueReference->setDirectDependencies(Dependencies);
mpConcReference->setDirectDependencies(mpExpression->getDirectDependencies());
// The dependencies and refresh of the rate are correct (see CModelEntity::setStatus).
mpConcRateReference->setDirectDependencies(mpRateReference->getDirectDependencies());
break;
case ODE:
mpValueReference->setDirectDependencies(Dependencies);
Dependencies.insert(mpValueReference);
if (pVolumeReference)
Dependencies.insert(pVolumeReference);
mpConcReference->setDirectDependencies(Dependencies);
Dependencies.clear();
Dependencies.insert(mpConcRateReference);
if (pVolumeReference)
Dependencies.insert(pVolumeReference);
mpRateReference->setDirectDependencies(Dependencies);
mpConcRateReference->setDirectDependencies(mpExpression->getDirectDependencies());
break;
case REACTIONS:
mpValueReference->setDirectDependencies(Dependencies);
if (pVolumeReference)
Dependencies.insert(pVolumeReference);
Dependencies.insert(mpValueReference);
mpConcReference->setDirectDependencies(Dependencies);
Dependencies.clear();
if (pVolumeReference)
Dependencies.insert(pVolumeReference);
Dependencies.insert(mpRateReference);
mpConcRateReference->setDirectDependencies(Dependencies);
break;
default:
break;
}
if (mpModel && mpCompartment) refreshConcentration();
}