// virtual
CXMLHandler * ReactionGlyphHandler::processStart(const XML_Char * pszName,
const XML_Char ** papszAttrs)
{
CXMLHandler * pHandlerToCall = NULL;
switch (mCurrentElement.first)
{
case ReactionGlyph:
{
//workload
const char * key;
const char * name;
const char * reaction;
key = mpParser->getAttributeValue("key", papszAttrs);
name = mpParser->getAttributeValue("name", papszAttrs);
reaction = mpParser->getAttributeValue("reaction", papszAttrs, false);
mpData->pReactionGlyph = new CLReactionGlyph(name);
const char * objectRole = mpParser->getAttributeValue("objectRole", papszAttrs, false);
if (objectRole != NULL && objectRole[0] != 0)
{
mpData->pReactionGlyph->setObjectRole(objectRole);
}
if (reaction && reaction[0])
{
CReaction * pReaction = dynamic_cast< CReaction * >(mpData->mKeyMap.get(reaction));
if (!pReaction)
{
CCopasiMessage(CCopasiMessage::WARNING, MCXML + 19, "ReactionGlyph" , key);
}
else
{
mpData->pReactionGlyph->setModelObjectKey(pReaction->getKey());
}
}
mpData->pCurrentLayout->addReactionGlyph(mpData->pReactionGlyph);
addFix(key, mpData->pReactionGlyph);
}
break;
case BoundingBox:
case Curve:
case ListOfMetaboliteReferenceGlyphs:
pHandlerToCall = getHandler(mCurrentElement.second);
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return pHandlerToCall;
}
void UndoDependentData::restoreDependentObjects(CModel *pModel, QList<UndoReactionData *> *reactionData)
{
if (pModel == NULL || reactionData == NULL || reactionData->empty())
return;
QList <UndoReactionData *>::const_iterator j;
for (j = reactionData->begin(); j != reactionData->end(); ++j)
{
UndoReactionData * rData = *j;
//need to make sure reaction doesn't exist in the model already
if (pModel->getReactions().getIndex(rData->getName()) != C_INVALID_INDEX)
continue;
CReaction *pRea = rData->restoreObjectIn(pModel);
rData->restoreDependentObjects(pModel);
updateGUI(ListViews::REACTION, ListViews::ADD, pRea->getKey());
}
}
void CModelExpansion::duplicateReaction(const CReaction* source, const std::string & index, const SetOfModelElements & sourceSet, ElementsMap & emap)
{
//if the source object has already been duplicated: do nothing
if (emap.exists(source))
return;
//try creating the object until we find a name that is not yet used
CReaction* newObj;
std::ostringstream infix;
do
{
std::ostringstream name;
name << source->getObjectName() << infix.str() << index;
newObj = mpModel->createReaction(name.str());
infix << "_";
}
while (!newObj);
//add duplicated object to the map
emap.add(source, newObj);
//now copy the chemical equation
size_t i;
for (i = 0; i < source->getChemEq().getSubstrates().size(); ++i)
{
const CChemEqElement * sourceElement = source->getChemEq().getSubstrates()[i];
const CMetab* pMetab = NULL;
if (sourceSet.contains(sourceElement->getMetabolite()))
{
if (!emap.exists(sourceElement->getMetabolite()))
duplicateMetab(sourceElement->getMetabolite(), index, sourceSet, emap);
pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
}
else //add the original metab
{
pMetab = sourceElement->getMetabolite();
}
if (pMetab)
newObj->addSubstrate(pMetab->getKey(), sourceElement->getMultiplicity());
}
for (i = 0; i < source->getChemEq().getProducts().size(); ++i)
{
const CChemEqElement * sourceElement = source->getChemEq().getProducts()[i];
const CMetab* pMetab = NULL;
if (sourceSet.contains(sourceElement->getMetabolite()))
{
if (!emap.exists(sourceElement->getMetabolite()))
duplicateMetab(sourceElement->getMetabolite(), index, sourceSet, emap);
pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
}
else //add the original metab
{
pMetab = sourceElement->getMetabolite();
}
if (pMetab)
newObj->addProduct(pMetab->getKey(), sourceElement->getMultiplicity());
}
for (i = 0; i < source->getChemEq().getModifiers().size(); ++i)
{
const CChemEqElement * sourceElement = source->getChemEq().getModifiers()[i];
const CMetab* pMetab = NULL;
if (sourceSet.contains(sourceElement->getMetabolite()))
{
if (!emap.exists(sourceElement->getMetabolite()))
duplicateMetab(sourceElement->getMetabolite(), index, sourceSet, emap);
pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
}
else //add the original metab
{
pMetab = sourceElement->getMetabolite();
}
if (pMetab)
newObj->addModifier(pMetab->getKey());
}
newObj->setReversible(source->isReversible());
//set the kinetic function
newObj->setFunction(const_cast<CFunction*>(source->getFunction()));
//mapping and local parameters
for (i = 0; i < newObj->getFunctionParameters().size(); ++i)
{
switch (newObj->getFunctionParameters()[i]->getUsage())
{
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
case CFunctionParameter::MODIFIER:
{
bool isVector = (newObj->getFunctionParameters()[i]->getType() == CFunctionParameter::VFLOAT64);
if (isVector)
newObj->clearParameterMapping(i);
size_t k;
for (k = 0; k < source->getParameterMappings()[i].size(); ++k)
{
//we assume that by now the metab was copied if necessary.
//therefore we only need to check the map.
std::string targetKey;
if (emap.exists(source->getParameterMappings()[i][k]))
targetKey = emap.getDuplicateKey(source->getParameterMappings()[i][k]);
else
targetKey = source->getParameterMappings()[i][k];
if (isVector)
newObj->addParameterMapping(i, targetKey);
else
newObj->setParameterMapping(i, targetKey);
}
}
break;
case CFunctionParameter::TIME:
newObj->setParameterMapping(i, source->getParameterMappings()[i][0]);
break;
case CFunctionParameter::VOLUME:
if (sourceSet.contains(source->getParameterMappings()[i][0]))
{
if (!emap.exists(source->getParameterMappings()[i][0]))
{
const CCompartment* pSource = dynamic_cast<const CCompartment*>(
(CCopasiRootContainer::getKeyFactory()->get(source->getParameterMappings()[i][0])));
duplicateCompartment(pSource, index, sourceSet, emap);
}
newObj->setParameterMapping(i, emap.getDuplicateKey(source->getParameterMappings()[i][0]));
}
else //add the original metab
{
newObj->setParameterMapping(i, source->getParameterMappings()[i][0]);
}
break;
case CFunctionParameter::PARAMETER:
if (newObj->isLocalParameter(i))
{
//just copy the value
newObj->setParameterValue(newObj->getFunctionParameters()[i]->getObjectName(),
source->getParameterValue(newObj->getFunctionParameters()[i]->getObjectName()));
}
else
{
if (sourceSet.contains(source->getParameterMappings()[i][0]))
{
if (!emap.exists(source->getParameterMappings()[i][0]))
{
const CModelValue* pSource = dynamic_cast<const CModelValue*>(
(CCopasiRootContainer::getKeyFactory()->get(source->getParameterMappings()[i][0])));
duplicateGlobalQuantity(pSource, index, sourceSet, emap);
}
newObj->setParameterMapping(i, emap.getDuplicateKey(source->getParameterMappings()[i][0]));
}
else //add the original global quantity
{
newObj->setParameterMapping(i, source->getParameterMappings()[i][0]);
}
}
break;
default:
break;
}
}
newObj->setNotes(source->getNotes());
newObj->setMiriamAnnotation(source->getMiriamAnnotation(), newObj->getKey(), source->getKey());
}
void CQCompartment::addCompartment(UndoCompartmentData *pSData)
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
//reinsert all the Compartments
CCompartment *pCompartment = pModel->createCompartment(pSData->getName());
pCompartment->setInitialValue(pSData->getInitialValue());
pCompartment->setStatus(pSData->getStatus());
std::string key = pCompartment->getKey();
protectedNotify(ListViews::COMPARTMENT, ListViews::ADD, key);
//restore all the dependencies
//reinsert all the species
QList <UndoSpecieData *> *pSpecieData = pSData->getSpecieDependencyObjects();
QList <UndoSpecieData *>::const_iterator i;
for (i = pSpecieData->begin(); i != pSpecieData->end(); ++i)
{
UndoSpecieData * data = *i;
// beginInsertRows(QModelIndex(), 1, 1);
CMetab *pSpecie = pModel->createMetabolite(data->getName(), data->getCompartment(), data->getIConc(), data->getStatus());
protectedNotify(ListViews::METABOLITE, ListViews::ADD, pSpecie->getKey());
//endInsertRows();
}
//reinsert the dependency reaction
QList <UndoReactionData *> *pReactionData = pSData->getReactionDependencyObjects();
QList <UndoReactionData *>::const_iterator j;
for (j = pReactionData->begin(); j != pReactionData->end(); ++j)
{
//UndoReactionData * rData = dynamic_cast<UndoReactionData*>(*j);
UndoReactionData * rData = *j;
//TODO check if reaction already exist in the model, better idea may be implemented in the future
bool exist = false;
for (int ii = 0; ii < (int)pModel->getReactions().size(); ++ii)
{
if (pModel->getReactions()[ii]->getObjectName() == rData->getName())
{
exist = true;
ii = ii + pModel->getReactions().size() + 1; //jump out of the loop reaction exist already
}
else
{
exist = false;
}
}
if (!exist)
{
protectedNotify(ListViews::METABOLITE, ListViews::ADD, ""); //Refresh all dependency species.
CReaction *pRea = pModel->createReaction(rData->getName());
rData->getRi()->writeBackToReaction(pRea);
protectedNotify(ListViews::REACTION, ListViews::ADD, pRea->getKey());
}
}
mpListView->switchToOtherWidget(C_INVALID_INDEX, key);
}
