bool CEventAssignment::compile(CObjectInterface::ContainerList listOfContainer)
{
clearDirectDependencies();
bool success = true;
mpTarget = NULL;
CModelEntity * pEntity =
dynamic_cast< CModelEntity * >(CCopasiRootContainer::getKeyFactory()->get(getObjectName()));
// The entity type must not be an ASSIGNMENT
if (pEntity != NULL &&
pEntity->getStatus() != CModelEntity::ASSIGNMENT)
{
// We need use the virtual method getValueObject to retrieve the
// target value from the model entity
mpTarget = pEntity->getValueObject();
}
else if (pEntity != NULL &&
pEntity->getStatus() == CModelEntity::ASSIGNMENT)
{
CCopasiMessage(CCopasiMessage::WARNING, "Invalid EventAssignment for '%s': an Assignment Rule already exists", pEntity->getObjectName().c_str());
}
else if (pEntity == NULL)
{
CCopasiMessage(CCopasiMessage::WARNING, "Invalid EventAssignment for '%s': object does not exist.", getObjectName().c_str());
}
if (mpTarget == NULL)
{
success = false;
}
if (mpExpression != NULL)
{
success &= mpExpression->compile(listOfContainer);
setDirectDependencies(mpExpression->getDirectDependencies());
}
else
{
success = false;
}
return success;
}
void CModelExpansion::duplicateGlobalQuantity(const CModelValue* 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
CModelEntity* newObj;
std::ostringstream infix;
do
{
std::ostringstream name;
name << source->getObjectName() << infix.str() << index;
newObj = mpModel->createModelValue(name.str(), source->getInitialValue());
infix << "_";
}
while (!newObj);
//add duplicated object to the map
emap.add(source, newObj);
//status
newObj->setStatus(source->getStatus());
//expression (for assignment or ODE)
newObj->setExpression(source->getExpression());
updateExpression(newObj->getExpressionPtr(), index, sourceSet, emap);
//initial expression
newObj->setInitialExpression(source->getInitialExpression());
updateExpression(newObj->getInitialExpressionPtr(), index, sourceSet, emap);
newObj->setNotes(source->getNotes());
newObj->setMiriamAnnotation(source->getMiriamAnnotation(), newObj->getKey(), source->getKey());
}
void CQUpdatesWidget::loadObjectsTable(CModel* pModel)
{
if (!pModel) return;
mpTableObj->setColumnCount(5);
mpTableObj->setRowCount(0);
mpTableObj->setHorizontalHeaderItem(0, new QTableWidgetItem("User order"));
mpTableObj->setHorizontalHeaderItem(1, new QTableWidgetItem("status"));
mpTableObj->setHorizontalHeaderItem(2, new QTableWidgetItem(""));
mpTableObj->setHorizontalHeaderItem(3, new QTableWidgetItem("Reduced system"));
mpTableObj->setHorizontalHeaderItem(4, new QTableWidgetItem("status"));
size_t i, imax;
//metabolites
imax = pModel->getMetabolites().size();
if ((int) imax > mpTableObj->rowCount()) mpTableObj->setRowCount((int) imax);
for (i = 0; i < imax; ++i)
{
mpTableObj->setVerticalHeaderItem((int) i, new QTableWidgetItem(QString::number(i)));
CMetab* pM = pModel->getMetabolites()[i];
QColor c(100, 100, 100);
if (pM->getStatus() == CModelEntity::FIXED) c = QColor(150, 150, 150);
if (pM->getStatus() == CModelEntity::ASSIGNMENT) c = QColor(250, 150, 250);
if (pM->getStatus() == CModelEntity::REACTIONS) c = QColor(250, 250, 200);
if (pM->getStatus() == CModelEntity::ODE) c = QColor(150, 250, 250);
if (pM->getStatus() == CModelEntity::TIME) c = QColor(250, 150, 150);
mpTableObj->setItem((int) i, 0, new QTableWidgetItem(FROM_UTF8(pM->getObjectName())));
//mpTableObj->setText(i, 0, FROM_UTF8(pM->getObjectName()));
std::string tmpString = CModelEntity::StatusName[pM->getStatus()];
if (pM->isUsed())
tmpString += " (Used = true, ";
else
tmpString += " (Used = false, ";
mpTableObj->setItem((int) i, 1, new QTableWidgetItem(FROM_UTF8(tmpString)));
//mpTableObj->setText(i, 1, FROM_UTF8(tmpString));
}
mpTableObj->resizeColumnToContents(0);
mpTableObj->resizeColumnToContents(1);
mpTableObj->setColumnWidth(2, 10);
//metabolitesX
imax = pModel->getMetabolitesX().size();
if ((int) imax > mpTableObj->rowCount()) mpTableObj->setRowCount((int) imax);
for (i = 0; i < imax; ++i)
{
CMetab* pM = pModel->getMetabolitesX()[i];
QColor c(100, 100, 100);
if (pM->getStatus() == CModelEntity::FIXED) c = QColor(150, 150, 150);
if (pM->getStatus() == CModelEntity::ASSIGNMENT) c = QColor(250, 150, 250);
if (pM->getStatus() == CModelEntity::REACTIONS) c = QColor(250, 250, 200);
if (pM->getStatus() == CModelEntity::ODE) c = QColor(150, 250, 250);
if (pM->getStatus() == CModelEntity::TIME) c = QColor(250, 150, 150);
mpTableObj->setItem((int) i, 3, new QTableWidgetItem(FROM_UTF8(pM->getObjectName())));
//mpTableObj->setText(i, 3, FROM_UTF8(pM->getObjectName()));
std::string tmpString = CModelEntity::StatusName[pM->getStatus()];
if (pM->isUsed())
tmpString += " (Used = true, ";
else
tmpString += " (Used = false, ";
mpTableObj->setItem((int) i, 4, new QTableWidgetItem(FROM_UTF8(tmpString)));
}
mpTableObj->resizeColumnToContents(3);
mpTableObj->resizeColumnToContents(4);
//state
const CStateTemplate & st = pModel->getStateTemplate();
imax = st.size();
mpTableState->setRowCount(0);
mpTableState->setRowCount((int)(imax + 1));
mpTableState->setColumnCount(5);
mpTableState->setHorizontalHeaderItem(0, new QTableWidgetItem("Name"));
mpTableState->setHorizontalHeaderItem(1, new QTableWidgetItem("status"));
mpTableState->setHorizontalHeaderItem(2, new QTableWidgetItem(""));
mpTableState->setHorizontalHeaderItem(3, new QTableWidgetItem("ATol(1)"));
mpTableState->setHorizontalHeaderItem(4, new QTableWidgetItem("SS criterion(1)"));
for (i = 0; i < imax; ++i)
{
mpTableState->setVerticalHeaderItem((int) i, new QTableWidgetItem(QString::number(i)));
CModelEntity* pME = *(st.getEntities() + i);
//first column
QColor c(100, 100, 100);
if (dynamic_cast<CModel*>(pME)) c = QColor(250, 100, 100);
if (dynamic_cast<CMetab*>(pME)) c = QColor(250, 250, 150);
if (dynamic_cast<CCompartment*>(pME)) c = QColor(100, 250, 100);
if (dynamic_cast<CModelValue*>(pME)) c = QColor(100, 100, 250);
mpTableState->setItem((int) i, 0, new QTableWidgetItem(FROM_UTF8(pME->getObjectDisplayName())));
// mpTableState->setText(i, 0,FROM_UTF8(pME->getObjectDisplayName()));
//second column
std::string tmpString = CModelEntity::StatusName[pME->getStatus()];
if (pME->isUsed())
tmpString += " (Used = true, ";
else
tmpString += " (Used = false, ";
c = QColor(100, 100, 100);
if (pME->getStatus() == CModelEntity::FIXED) c = QColor(150, 150, 150);
if (pME->getStatus() == CModelEntity::ASSIGNMENT) c = QColor(250, 150, 250);
if (pME->getStatus() == CModelEntity::REACTIONS) c = QColor(250, 250, 200);
if (pME->getStatus() == CModelEntity::ODE) c = QColor(150, 250, 250);
if (pME->getStatus() == CModelEntity::TIME) c = QColor(250, 150, 150);
mpTableState->setItem((int) i, 1, new QTableWidgetItem(FROM_UTF8(tmpString)));
//mpTableState->setText(i, 1, FROM_UTF8(tmpString));
}
QColor c(200, 250, 250);
for (i = st.beginIndependent() - st.getEntities(); i < (size_t)(st.endIndependent() - st.getEntities()); ++i)
mpTableState->setItem((int) i, 2, new QTableWidgetItem(""));
c = QColor(250, 200, 250);
for (i = st.beginDependent() - st.getEntities(); i < (size_t)(st.endDependent() - st.getEntities()); ++i)
mpTableState->setItem((int) i, 2, new QTableWidgetItem(""));
c = QColor(200, 200, 200);
for (i = st.beginFixed() - st.getEntities(); i < (size_t)(st.endFixed() - st.getEntities()); ++i)
mpTableState->setItem((int) i, 2, new QTableWidgetItem(""));
int tmpint = st.beginIndependent() - st.getEntities();
mpTableState->setItem(tmpint, 2, new QTableWidgetItem("beginIndependent "));
tmpint = st.endIndependent() - st.getEntities();
mpTableState->setItem(tmpint, 2, new QTableWidgetItem(mpTableState->item(tmpint, 2)->text() + "endIndependent "));
tmpint = st.beginDependent() - st.getEntities();
mpTableState->setItem(tmpint, 2, new QTableWidgetItem(mpTableState->item(tmpint, 2)->text() + "beginDependent "));
tmpint = st.endDependent() - st.getEntities();
mpTableState->setItem(tmpint, 2, new QTableWidgetItem(mpTableState->item(tmpint, 2)->text() + "endDependent "));
tmpint = st.beginFixed() - st.getEntities();
mpTableState->setItem(tmpint, 2, new QTableWidgetItem(mpTableState->item(tmpint, 2)->text() + "beginFixed "));
tmpint = st.endFixed() - st.getEntities();
mpTableState->setItem(tmpint, 2, new QTableWidgetItem("endFixed "));
//add absolute Tolerances to table
CVector< C_FLOAT64 > atolv = pModel->initializeAtolVector(1, false);
tmpint = st.beginIndependent() - st.getEntities();
for (i = 0; i < atolv.size(); ++i)
{
mpTableState->setItem((int) i + tmpint, 3, new QTableWidgetItem(QString::number(atolv[i])));
CModelEntity* pME = *(st.getEntities() + i + 1);
C_FLOAT64 tmp = std::min(atolv[i], std::max(100.0 * std::numeric_limits< C_FLOAT64 >::min(), fabs(pME->getInitialValue())));
mpTableState->setItem((int) i + tmpint, 4, new QTableWidgetItem(QString::number(tmp)));
}
mpTableState->resizeColumnToContents(0);
mpTableState->resizeColumnToContents(1);
mpTableState->resizeColumnToContents(2);
mpTableState->resizeColumnToContents(3);
mpTableState->resizeColumnToContents(4);
}
// virtual
bool CModelParameter::refreshFromModel(const bool & modifyExistence)
{
bool success = true;
if (modifyExistence)
{
if (mCompareResult == CModelParameter::Obsolete)
{
delete this;
return true;
}
if (mCompareResult == CModelParameter::Missing)
{
mCompareResult = CModelParameter::Identical;
}
if (mType != ReactionParameter &&
mpObject != NULL)
{
mSimulationType = static_cast< CModelEntity * >(mpObject)->getStatus();
}
}
if (mpObject != NULL)
{
switch (mType)
{
case Model:
{
CModel * pModel = static_cast< CModel * >(mpObject);
if (!pModel->isAutonomous())
{
mValue = pModel->getInitialValue();
}
else
{
mValue = 0.0;
}
}
break;
case Compartment:
case Species:
case ModelValue:
{
CModelEntity * pEntity = static_cast< CModelEntity * >(mpObject);
mValue = pEntity->getInitialValue();
}
break;
case ReactionParameter:
{
CCopasiParameter * pParameter = static_cast< CCopasiParameter * >(mpObject);
mValue = * pParameter->getValue().pDOUBLE;
// We need to update the mapping
// Check whether this refers to a global quantity.
const CReaction * pReaction = static_cast< CModelParameterReactionParameter * >(this)->getReaction();
if (pReaction != NULL)
{
if (pReaction->isLocalParameter(getName()))
{
mSimulationType = CModelEntity::FIXED;
static_cast< CModelParameterReactionParameter * >(this)->setGlobalQuantityCN("");
}
else
{
mSimulationType = CModelEntity::ASSIGNMENT;
const std::vector<std::string> ModelValue = pReaction->getParameterMapping(getName());
assert(ModelValue.size() == 1);
CModelValue * pModelValue = static_cast< CModelValue * >(CCopasiRootContainer::getKeyFactory()->get(ModelValue[0]));
static_cast< CModelParameterReactionParameter * >(this)->setGlobalQuantityCN(pModelValue->getInitialValueReference()->getCN());
}
}
CCopasiObjectName GlobalQuantityCN = static_cast< CModelParameterReactionParameter * >(this)->getGlobalQuantityCN();
if (GlobalQuantityCN != "")
{
CModelParameter * pGlobalQuantity = getSet()->getModelParameter(GlobalQuantityCN);
if (pGlobalQuantity != NULL)
{
mValue = pGlobalQuantity->getValue(ParticleNumbers);
}
}
}
break;
default:
success = false;
break;
}
}
return success;
}
// 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;
}
bool CQRDFTreeView::enterProtected()
{
clear();
CCopasiObject *pObject = dynamic_cast< CCopasiObject * >(CCopasiRootContainer::getKeyFactory()->get(mKey));
if (pObject != NULL)
{
CModelEntity * pEntity = NULL;
CEvent * pEvent = NULL;
CReaction * pReaction = NULL;
CFunction * pFunction = NULL;
const std::string * pMiriamAnnotation = NULL;
if ((pEntity = dynamic_cast< CModelEntity * >(pObject)) != NULL)
pMiriamAnnotation = &pEntity->getMiriamAnnotation();
else if ((pEvent = dynamic_cast< CEvent * >(pObject)) != NULL)
pMiriamAnnotation = &pEvent->getMiriamAnnotation();
else if ((pReaction = dynamic_cast< CReaction * >(pObject)) != NULL)
pMiriamAnnotation = &pReaction->getMiriamAnnotation();
else if ((pFunction = dynamic_cast< CFunction * >(pObject)) != NULL)
pMiriamAnnotation = &pFunction->getMiriamAnnotation();
if (pMiriamAnnotation && *pMiriamAnnotation != "")
mpGraph = CRDFParser::graphFromXml(*pMiriamAnnotation);
}
CCopasiMessage::clearDeque();
if (CCopasiMessage::size() != 0)
{
QString Message = FROM_UTF8(CCopasiMessage::getAllMessageText());
CQMessageBox::warning(this, QString("RDF Warning"), Message,
QMessageBox::Ok, QMessageBox::Ok);
}
if (mpGraph == NULL)
mpGraph = new CRDFGraph;
// We make sure that we always have an about node.
mpGraph->createAboutNode(mKey);
// We iterate of all triplets
std::set< CRDFTriplet >::const_iterator it = mpGraph->getTriplets().begin();
std::set< CRDFTriplet >::const_iterator end = mpGraph->getTriplets().end();
for (; it != end; ++it)
{
CQRDFTreeViewItem * pSubjectItem = find(it->pSubject);
if (pSubjectItem == NULL)
{
pSubjectItem = new CQRDFTreeViewItem(mpTreeWidget, NULL);
insert(it->pSubject, pSubjectItem);
// Display the subject information
const CRDFSubject & Subject = it->pSubject->getSubject();
switch (Subject.getType())
{
case CRDFSubject::RESOURCE:
pSubjectItem->setText(COL_SUBJECT, FROM_UTF8(Subject.getResource()));
break;
case CRDFSubject::BLANK_NODE:
pSubjectItem->setText(COL_SUBJECT, FROM_UTF8(Subject.getBlankNodeID()));
break;
}
}
CQRDFTreeViewItem * pObjectItem = NULL;
if (it->Predicate.getURI() == "http://www.w3.org/1999/02/22-rdf-syntax-ns#subject")
{
pObjectItem = new CQRDFTreeViewItem(pSubjectItem, NULL);
insert(it->pObject, pObjectItem);
}
else
pObjectItem = find(it->pObject);
if (pObjectItem == NULL)
{
pObjectItem = new CQRDFTreeViewItem(pSubjectItem, NULL);
insert(it->pObject, pObjectItem);
}
else
{
QTreeWidgetItem * pParent = pObjectItem->parent();
if (pParent == NULL)
{
mpTreeWidget->invisibleRootItem()->removeChild(pObjectItem);
pSubjectItem->addChild(pObjectItem);
}
else
{
pParent->removeChild(pObjectItem);
pSubjectItem->addChild(pObjectItem);
}
}
pObjectItem->setTriplet(*it);
}
mpTreeWidget->setFocus();
return true;
}