bool CQGlobalQuantityDM::removeRows(int position, int rows)
{
if (rows <= 0)
return true;
beginRemoveRows(QModelIndex(), position, position + rows - 1);
std::vector< std::string > DeletedKeys;
DeletedKeys.resize(rows);
std::vector< std::string >::iterator itDeletedKey;
std::vector< std::string >::iterator endDeletedKey = DeletedKeys.end();
CCopasiVector< CModelValue >::const_iterator itRow = mpGlobalQuantities->begin() + position;
for (itDeletedKey = DeletedKeys.begin(); itDeletedKey != endDeletedKey; ++itDeletedKey, ++itRow)
{
*itDeletedKey = itRow->getKey();
}
for (itDeletedKey = DeletedKeys.begin(); itDeletedKey != endDeletedKey; ++itDeletedKey)
{
mpDataModel->getModel()->removeModelValue(*itDeletedKey);
emit notifyGUI(ListViews::MODELVALUE, ListViews::DELETE, *itDeletedKey);
emit notifyGUI(ListViews::MODELVALUE, ListViews::DELETE, ""); //Refresh all as there may be dependencies.
}
endRemoveRows();
return true;
}
bool CQSpecieDM::insertRows(int position, int rows, const QModelIndex&)
{
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
if (pDataModel->getModel()->getCompartments().size() == 0)
{
pDataModel->getModel()->createCompartment("compartment");
emit notifyGUI(ListViews::COMPARTMENT, ListViews::ADD, pDataModel->getModel()->getCompartments()[0]->getKey());
}
beginInsertRows(QModelIndex(), position, position + rows - 1);
for (int row = 0; row < rows; ++row)
{
mpSpecies =
pDataModel->getModel()->createMetabolite(TO_UTF8(createNewName("species", COL_NAME_SPECIES)), "", 1.0, CModelEntity::REACTIONS);
if (mNotify)
{
emit notifyGUI(ListViews::METABOLITE, ListViews::ADD, mpSpecies->getKey());
}
}
endInsertRows();
return true;
}
bool CQSpecieDM::removeRows(int position, int rows, const QModelIndex&)
{
if (rows <= 0)
return true;
beginRemoveRows(QModelIndex(), position, position + rows - 1);
CModel * pModel = (*CCopasiRootContainer::getDatamodelList())[0]->getModel();
std::vector< std::string > DeletedKeys;
DeletedKeys.resize(rows);
std::vector< std::string >::iterator itDeletedKey;
std::vector< std::string >::iterator endDeletedKey = DeletedKeys.end();
CCopasiVector< CMetab >::const_iterator itRow = pModel->getMetabolites().begin() + position;
for (itDeletedKey = DeletedKeys.begin(); itDeletedKey != endDeletedKey; ++itDeletedKey, ++itRow)
{
*itDeletedKey = (*itRow)->getKey();
}
for (itDeletedKey = DeletedKeys.begin(); itDeletedKey != endDeletedKey; ++itDeletedKey)
{
pModel->removeMetabolite(*itDeletedKey);
emit notifyGUI(ListViews::METABOLITE, ListViews::DELETE, *itDeletedKey);
emit notifyGUI(ListViews::METABOLITE, ListViews::DELETE, ""); //Refresh all as there may be dependencies.
}
endRemoveRows();
return true;
}
QList <UndoSpeciesData *> CQSpecieDM::insertNewSpecieRow(int position, int rows, const QModelIndex&index, const QVariant& value)
{
QList <UndoSpeciesData *> result;
GET_MODEL_OR(pModel, return result);
bool createdCompartment = false;
if (pModel->getCompartments().size() == 0)
{
CCompartment* pComp = pModel->createCompartment("compartment");
createdCompartment = true;
if (mNotify)
{
emit notifyGUI(ListViews::COMPARTMENT, ListViews::ADD, pComp->getKey());
}
}
beginInsertRows(QModelIndex(), position, position + rows - 1);
int column = index.column();
for (int row = 0; row < rows; ++row)
{
QString name = createNewName(index.isValid() && column == COL_NAME_SPECIES ? value.toString() : "species", COL_NAME_SPECIES);
QString compartment = index.isValid() && column == COL_COMPARTMENT ? value.toString() : "";
double initial = index.isValid() && column == COL_ICONCENTRATION ? value.toDouble() : 1.0;
CModelEntity::Status status = index.isValid() && column == COL_TYPE_SPECIES ?
(CModelEntity::Status) mItemToType[value.toInt()] : CModelEntity::REACTIONS;
mpSpecies =
pModel->createMetabolite(TO_UTF8(name), TO_UTF8(compartment), initial, status);
if (mpSpecies == NULL)
continue;
if (mNotify)
{
emit notifyGUI(ListViews::METABOLITE, ListViews::ADD, mpSpecies->getKey());
}
UndoSpeciesData* data = new UndoSpeciesData(mpSpecies);
data->setCreatedCompartment(row == 0 && createdCompartment);
result.append(data);
}
endInsertRows();
return result;
}
bool CQParameterSetsDM::removeRows(int position, int rows, const QModelIndex&)
{
if (rows <= 0) return true;
if (mpListOfParameterSets == NULL) return false;
beginRemoveRows(QModelIndex(), position, position + rows - 1);
std::vector< CModelParameterSet * > DeletedModelParameterSets;
DeletedModelParameterSets.resize(rows);
std::vector< CModelParameterSet * >::iterator itDeletedModelParameterSet;
std::vector< CModelParameterSet * >::iterator endDeletedModelParameterSet = DeletedModelParameterSets.end();
CCopasiVectorN< CModelParameterSet >::const_iterator itRow = mpListOfParameterSets->begin() + position;
for (itDeletedModelParameterSet = DeletedModelParameterSets.begin(); itDeletedModelParameterSet != endDeletedModelParameterSet; ++itDeletedModelParameterSet, ++itRow)
{
*itDeletedModelParameterSet = *itRow;
}
for (itDeletedModelParameterSet = DeletedModelParameterSets.begin(); itDeletedModelParameterSet != endDeletedModelParameterSet; ++itDeletedModelParameterSet)
{
std::string Key = (*itDeletedModelParameterSet)->getKey();
pdelete(*itDeletedModelParameterSet);
emit notifyGUI(ListViews::MODELPARAMETERSET, ListViews::DELETE, Key);
}
endRemoveRows();
return true;
}
bool CQReportDM::setData(const QModelIndex &index, const QVariant &value,
int role)
{
if (index.isValid() && role == Qt::EditRole)
{
bool defaultRow = isDefaultRow(index);
if (defaultRow)
{
if (index.data() != value)
{
mNewName = (index.column() == COL_NAME_REPORTS) ? value.toString() : "report";
insertRow(rowCount(), index);
}
else
return false;
}
CReportDefinition *pRepDef = &mpDataModel->getReportDefinitionList()->operator[](index.row());
if (index.column() == COL_NAME_REPORTS)
pRepDef->setObjectName(TO_UTF8(value.toString()));
emit dataChanged(index, index);
emit notifyGUI(ListViews::REPORT, ListViews::CHANGE, pRepDef->getKey());
}
return true;
}
bool CQModifiedDM::setData(const QModelIndex &index, const QVariant &value,
int role)
{
if (index.isValid() && role == Qt::EditRole)
{
if (isDefaultRow(index))
{
if (index.data() != value)
insertRow(rowCount(), index);
else
return false;
}
switch (index.column())
{
case COL_DATE_MODIFIED:
mpMIRIAMInfo->getModifications()[index.row()].setDate(TO_UTF8(value.toDateTime().toString(Qt::ISODate)));
break;
}
emit dataChanged(index, index);
emit notifyGUI(ListViews::MIRIAM, ListViews::CHANGE, "");
return true;
}
return false;
}
bool CQGlobalQuantityDM::insertGlobalQuantityRows(QList <UndoGlobalQuantityData *>& pData)
{
//reinsert all the GlobalQuantities
QList <UndoGlobalQuantityData *>::const_iterator i;
for (i = pData.begin(); i != pData.end(); ++i)
{
UndoGlobalQuantityData * data = *i;
if (mpGlobalQuantities->getIndex(data->getName()) != C_INVALID_INDEX)
continue;
beginInsertRows(QModelIndex(), 1, 1);
CModelValue *pGlobalQuantity = data->restoreObjectIn(mpDataModel->getModel());
if (pGlobalQuantity != NULL)
emit notifyGUI(ListViews::MODELVALUE, ListViews::ADD, pGlobalQuantity->getKey());
endInsertRows();
}
switchToWidget(CCopasiUndoCommand::GLOBALQUANTITYIES);
return true;
}
void CQGlobalQuantityDM::insertNewGlobalQuantityRow(int position, int rows, const QModelIndex& index, const QVariant& value)
{
beginInsertRows(QModelIndex(), position, position + rows - 1);
int column = index.column();
for (int row = 0; row < rows; ++row)
{
QString name = createNewName(index.isValid() && column == COL_NAME_GQ ? value.toString() : "quantity", COL_NAME_GQ);
double initial = index.isValid() && column == COL_INITIAL_GQ ? value.toDouble() : 0.0;
CModelValue *pGQ = mpDataModel->getModel()->createModelValue(TO_UTF8(name), initial);
if (pGQ == NULL) continue;
if (index.isValid() && column == COL_TYPE_GQ)
{
pGQ->setStatus((CModelEntity::Status) mItemToType[value.toInt()]);
}
emit notifyGUI(ListViews::MODELVALUE, ListViews::ADD, pGQ->getKey());
}
endInsertRows();
}
void CQSpecieDM::deleteSpecieRow(UndoSpeciesData *pSpecieData)
{
GET_MODEL_OR_RETURN(pModel);
switchToWidget(CCopasiUndoCommand::SPECIES);
CMetab * pSpecies = dynamic_cast< CMetab * >(pSpecieData->getObject(pModel));
if (pSpecies == NULL) return;
size_t Index = pModel->getMetabolites().getIndex(pSpecies);
removeRow((int) Index);
if (!pSpecieData->getCreatedCompartment()) return;
Index = pModel->getCompartments().getIndex(pSpecieData->getCompartment());
if (Index == C_INVALID_INDEX) return;
CCompartment* pComp = &pModel->getCompartments()[Index];
if (pComp == NULL) return;
std::string key = pComp->getKey();
pModel->removeCompartment(Index);
emit notifyGUI(ListViews::COMPARTMENT, ListViews::DELETE, key);
}
bool CQReferenceDM::setData(const QModelIndex &index, const QVariant &value,
int role)
{
if (index.isValid() && role == Qt::EditRole)
{
if (isDefaultRow(index))
{
if (index.data() != value)
insertRow(rowCount(), index);
else
return false;
}
switch (index.column())
{
case COL_RESOURCE_REFERENCE:
mpMIRIAMInfo->getReferences()[index.row()].setResource(TO_UTF8(value.toString()));
break;
case COL_ID_REFERENCE:
mpMIRIAMInfo->getReferences()[index.row()].setId(TO_UTF8(value.toString()));
break;
case COL_DESCRIPTION:
mpMIRIAMInfo->getReferences()[index.row()].setDescription(TO_UTF8(value.toString()));
break;
}
emit dataChanged(index, index);
emit notifyGUI(ListViews::MIRIAM, ListViews::CHANGE, "");
return true;
}
return false;
}
bool CQUnitDM::setData(const QModelIndex &index, const QVariant &value,
int role)
{
if (index.isValid() && role == Qt::EditRole)
{
bool defaultRow = isDefaultRow(index);
if (defaultRow)
{
if (index.data() != value)
insertRow(rowCount(), index);
else
return false;
}
CUnitDefinition *pUnitDef = &CCopasiRootContainer::getUnitList()->operator[](index.row());
if (pUnitDef == NULL)
return false;
if (index.column() == COL_NAME_UNITS)
pUnitDef->setObjectName(TO_UTF8(value.toString()));
else if (index.column() == COL_SYMBOL_UNITS)
{
if (!pUnitDef->setSymbol(TO_UTF8(value.toString())))
{
QString msg;
msg = "Unable set Symbol of Unit '" + FROM_UTF8(pUnitDef->getObjectName()) + "'\n"
+ "to '" + value.toString() + "' since a Unit with that symbol already exists.\n";
CQMessageBox::information(NULL,
"Unable set Symbol",
msg,
QMessageBox::Ok, QMessageBox::Ok);
}
}
else if (index.column() == COL_EXPRESSION_UNITS)
{
if (index.data() != value)
{
QString msg;
msg = "Expression must not be changed for '" + FROM_UTF8(pUnitDef->getObjectName()) + "'.\n";
CQMessageBox::information(NULL,
"Unable to change Unit Expression",
msg,
QMessageBox::Ok, QMessageBox::Ok);
}
}
if (defaultRow && this->index(index.row(), COL_SYMBOL_UNITS).data().toString() == "unit")
pUnitDef->setObjectName(TO_UTF8(createNewName("unit", COL_SYMBOL_UNITS)));
emit dataChanged(index, index);
emit notifyGUI(ListViews::UNIT, ListViews::CHANGE, pUnitDef->getKey());
}
return true;
}
bool CQFunctionDM::removeRows(int position, int rows, const QModelIndex & parent)
{
if (rows <= 0)
return true;
std::vector< std::string > DeletedKeys;
DeletedKeys.resize(rows);
std::vector< std::string >::iterator itDeletedKey;
std::vector< std::string >::iterator endDeletedKey = DeletedKeys.end();
CDataVector< CFunction >::const_iterator itRow =
CRootContainer::getFunctionList()->loadedFunctions().begin() + position;
int row = 0;
for (itDeletedKey = DeletedKeys.begin(), row = 0; itDeletedKey != endDeletedKey; ++itDeletedKey, ++itRow, ++row)
{
if (isFunctionReadOnly(this->index(position + row, 0)))
{
*itDeletedKey = "";
}
else
{
*itDeletedKey = itRow->getCN();
}
}
beginRemoveRows(parent, position, position + row - 1);
for (itDeletedKey = DeletedKeys.begin(), row = 0; itDeletedKey != endDeletedKey; ++itDeletedKey, ++row)
{
if (*itDeletedKey != "")
{
CRootContainer::getFunctionList()->removeFunction(*itDeletedKey);
emit notifyGUI(ListViews::ObjectType::FUNCTION, ListViews::DELETE, *itDeletedKey);
emit notifyGUI(ListViews::ObjectType::FUNCTION, ListViews::DELETE, std::string()); //Refresh all as there may be dependencies.
}
}
endRemoveRows();
return true;
}
void CQGlobalQuantityDM::addGlobalQuantityRow(UndoGlobalQuantityData *pGlobalQuantityData)
{
switchToWidget(CCopasiUndoCommand::GLOBALQUANTITYIES);
beginInsertRows(QModelIndex(), 1, 1);
CModelValue *pGlobalQuantity = pGlobalQuantityData->restoreObjectIn(mpDataModel->getModel());
if (pGlobalQuantity != NULL)
emit notifyGUI(ListViews::MODELVALUE, ListViews::ADD, pGlobalQuantity->getKey());
endInsertRows();
}
bool CQCreatorDM::insertRows(int position, int rows, const QModelIndex&)
{
beginInsertRows(QModelIndex(), position, position + rows - 1);
for (int row = 0; row < rows; ++row)
{
mpMIRIAMInfo->createCreator("");
}
endInsertRows();
emit notifyGUI(ListViews::MIRIAM, ListViews::ADD, "");
return true;
}
void CQSpecieDM::addSpecieRow(UndoSpeciesData *pSpecieData)
{
GET_MODEL_OR_RETURN(pModel);
switchToWidget(CCopasiUndoCommand::SPECIES);
CMetab *species = pSpecieData->restoreObjectIn(pModel);
if (species == NULL)
return;
beginInsertRows(QModelIndex(), 1, 1);
emit notifyGUI(ListViews::METABOLITE, ListViews::ADD, species->getKey());
endInsertRows();
}
bool CQModifiedDM::insertRows(int position, int rows, const QModelIndex&)
{
beginInsertRows(QModelIndex(), position, position + rows - 1);
for (int row = 0; row < rows; ++row)
{
//mpMIRIAMInfo->createModification(TO_UTF8(QDateTime::currentDateTime().toString(Qt::ISODate)));
mpMIRIAMInfo->createModification("");
}
endInsertRows();
emit notifyGUI(ListViews::MIRIAM, ListViews::ADD, "");
return true;
}
bool CQUnitDM::insertRows(int position, int rows, const QModelIndex&)
{
beginInsertRows(QModelIndex(), position, position + rows - 1);
for (int row = 0; row < rows; ++row)
{
CUnitDefinition *pUnitDef;
CCopasiRootContainer::getUnitList()->add(pUnitDef = new CUnitDefinition(TO_UTF8(createNewName("unit", COL_NAME_UNITS)), CCopasiRootContainer::getUnitList()), true);
emit notifyGUI(ListViews::UNIT, ListViews::ADD, pUnitDef->getKey());
}
endInsertRows();
return true;
}
bool CQReportDM::removeRows(int position, int rows)
{
if (rows <= 0)
return true;
if (mpDataModel == NULL)
return false;
CCopasiVector< CReportDefinition > * pReportList = mpDataModel->getReportDefinitionList();
if (pReportList == NULL)
return false;
beginRemoveRows(QModelIndex(), position, position + rows - 1);
for (int row = 0; row < rows; ++row)
{
CReportDefinition * pReport = &pReportList->operator[](position);
if (pReport == NULL)
continue;
std::set< const CCopasiObject * > Tasks;
std::set< const CCopasiObject * > DeletedObjects;
DeletedObjects.insert(pReport);
if (mpDataModel->appendDependentTasks(DeletedObjects, Tasks))
{
std::set< const CCopasiObject * >::iterator it = Tasks.begin();
std::set< const CCopasiObject * >::iterator end = Tasks.end();
for (; it != end; ++it)
{
const CCopasiTask * pTask = static_cast< const CCopasiTask *>(*it);
const_cast< CCopasiTask * >(pTask)->getReport().setReportDefinition(NULL);
}
}
std::string deletedKey = pReport->getKey();
pReportList->remove(pReport);
emit notifyGUI(ListViews::REPORT, ListViews::DELETE, deletedKey);
}
endRemoveRows();
return true;
}
bool CQParameterSetsDM::insertRows(int position, int rows, const QModelIndex&)
{
if (mpListOfParameterSets == NULL) return false;
if (position + rows > (int) mpListOfParameterSets->size()) return false;
beginInsertRows(QModelIndex(), position, position + rows - 1);
for (int row = 0; row < rows; ++row)
{
emit notifyGUI(ListViews::LAYOUT, ListViews::ADD, (*mpListOfParameterSets)[position + row]->getKey());
}
endInsertRows();
return true;
}
bool CQCreatorDM::removeRows(int position, int rows, const QModelIndex&)
{
if (rows <= 0)
return true;
beginRemoveRows(QModelIndex(), position, position + rows - 1);
for (int row = 0; row < rows; ++row)
{
mpMIRIAMInfo->removeCreator(position);
}
endRemoveRows();
emit notifyGUI(ListViews::MIRIAM, ListViews::DELETE, "");
return true;
}
bool CQReportDM::insertRows(int position, int rows, const QModelIndex & source)
{
beginInsertRows(QModelIndex(), position, position + rows - 1);
for (int row = 0; row < rows; ++row)
{
QString Name = createNewName(mNewName, COL_NAME_REPORTS);
CReportDefinition *pRepDef = mpDataModel->getReportDefinitionList()->createReportDefinition(TO_UTF8(Name), "");
emit notifyGUI(ListViews::REPORT, ListViews::ADD, pRepDef->getKey());
}
endInsertRows();
mNewName = "report";
return true;
}
bool CQGlobalQuantityDM::globalQuantityDataChange(const QModelIndex &index, const QVariant &value, int role)
{
assert((size_t)index.row() < mpGlobalQuantities->size());
if (!index.isValid() || role != Qt::EditRole)
return false;
bool defaultRow = isDefaultRow(index);
if (defaultRow)
{
if (index.column() == COL_TYPE_GQ)
{
if (index.data().toString() != QString(FROM_UTF8(CModelEntity::StatusName[mItemToType[value.toInt()]])))
insertRow(rowCount(), index);
else
return false;
}
else if (index.data() != value)
insertRow(rowCount(), index);
else
return false;
}
switchToWidget(CCopasiUndoCommand::GLOBALQUANTITYIES);
CModelValue & GQ = mpGlobalQuantities->operator [](index.row());
if (index.column() == COL_NAME_GQ)
GQ.setObjectName(TO_UTF8(value.toString()));
else if (index.column() == COL_TYPE_GQ)
GQ.setStatus((CModelEntity::Status) mItemToType[value.toInt()]);
else if (index.column() == COL_INITIAL_GQ)
GQ.setInitialValue(value.toDouble());
if (defaultRow && this->index(index.row(), COL_NAME_GQ).data().toString() == "quantity")
GQ.setObjectName(TO_UTF8(createNewName("quantity", COL_NAME_GQ)));
emit dataChanged(index, index);
emit notifyGUI(ListViews::MODELVALUE, ListViews::CHANGE, GQ.getKey());
return true;
}
bool CQFunctionDM::insertRows(int position, int rows, const QModelIndex & parent)
{
beginInsertRows(parent, position, position + rows - 1);
for (int row = 0; row < rows; ++row)
{
CFunction *pFunc;
QString Name = createNewName(mNewName, COL_NAME_FUNCTIONS);
CRootContainer::getFunctionList()->add(pFunc = new CKinFunction(TO_UTF8(Name)), true);
emit notifyGUI(ListViews::ObjectType::FUNCTION, ListViews::ADD, pFunc->getCN());
}
endInsertRows();
mNewName = "function";
return true;
}
bool CQUnitDM::removeRows(int position, int rows)
{
if (rows <= 0)
return true;
std::vector< std::string > DeletedKeys;
DeletedKeys.resize(rows);
std::vector< std::string >::iterator itDeletedKey;
std::vector< std::string >::iterator endDeletedKey = DeletedKeys.end();
CCopasiVector< CUnitDefinition >::const_iterator itRow =
CCopasiRootContainer::getUnitList()->begin() + position;
int row = 0;
for (itDeletedKey = DeletedKeys.begin(), row = 0; itDeletedKey != endDeletedKey; ++itDeletedKey, ++itRow, ++row)
{
*itDeletedKey = itRow->getKey();
}
beginRemoveRows(QModelIndex(), position, position + row - 1);
for (itDeletedKey = DeletedKeys.begin(), row = 0; itDeletedKey != endDeletedKey; ++itDeletedKey, ++row)
{
if (*itDeletedKey != "")
{
CCopasiObject * pUnitDef = CCopasiRootContainer::getKeyFactory()->get(*itDeletedKey);
if (pUnitDef != NULL) delete pUnitDef;
emit notifyGUI(ListViews::UNIT, ListViews::DELETE, *itDeletedKey);
}
}
endRemoveRows();
return true;
}
bool CQCreatorDM::setData(const QModelIndex &index, const QVariant &value,
int role)
{
if (index.isValid() && role == Qt::EditRole)
{
if (isDefaultRow(index))
{
if (index.data() != value)
insertRow();
else
return false;
}
switch (index.column())
{
case COL_FAMILY_NAME:
mpMIRIAMInfo->getCreators()[index.row()]->setFamilyName(TO_UTF8(value.toString()));
break;
case COL_GIVEN_NAME:
mpMIRIAMInfo->getCreators()[index.row()]->setGivenName(TO_UTF8(value.toString()));
break;
case COL_EMAIL:
mpMIRIAMInfo->getCreators()[index.row()]->setEmail(TO_UTF8(value.toString()));
break;
case COL_ORG:
mpMIRIAMInfo->getCreators()[index.row()]->setORG(TO_UTF8(value.toString()));
break;
}
emit dataChanged(index, index);
emit notifyGUI(ListViews::MIRIAM, ListViews::CHANGE, "");
return true;
}
return false;
}
bool CQSpecieDM::specieDataChange(
UndoSpeciesData *pUndoSpeciesData,
const QVariant &value,
int column)
{
switchToWidget(CCopasiUndoCommand::SPECIES);
GET_MODEL_OR(pModel, return false);
mpSpecies =
dynamic_cast<CMetab*>(pUndoSpeciesData->getObject(pModel));
if (mpSpecies == NULL)
return false;
const CCompartment * pCompartment = NULL;
if (column == COL_COMPARTMENT ||
column == COL_ICONCENTRATION ||
column == COL_INUMBER)
{
try
{
pCompartment = mpSpecies->getCompartment();
}
catch (...) {}
}
if (column == COL_NAME_SPECIES)
{
mpSpecies->setObjectName(TO_UTF8(value.toString()));
pUndoSpeciesData->setCN(mpSpecies->getCN());
}
else if (column == COL_COMPARTMENT)
{
// This must be set first for setInitialConcentration and
// setInitialNumber to work correctly.
std::string Compartment(TO_UTF8(value.toString()));
if (Compartment != pCompartment->getObjectName())
{
std::string CompartmentToRemove = mpSpecies->getCompartment()->getObjectName();
if (!(pModel->getCompartments()[Compartment].addMetabolite(mpSpecies)))
{
QString msg;
msg = "Unable to move species '" + FROM_UTF8(mpSpecies->getObjectName()) + "'\n"
+ "from compartment '" + FROM_UTF8(CompartmentToRemove) + "' to compartment '" + FROM_UTF8(Compartment) + "'\n"
+ "since a species with that name already exist in the target compartment.";
CQMessageBox::information(NULL,
"Unable to move Species",
msg,
QMessageBox::Ok, QMessageBox::Ok);
return false;
}
else
{
pModel->getCompartments()[CompartmentToRemove].getMetabolites().remove(mpSpecies->getObjectName());
pModel->setCompileFlag();
pModel->initializeMetabolites();
if (mpSpecies && pCompartment)
{
C_FLOAT64 Factor = 1.0 / pCompartment->getInitialValue();
Factor *= pCompartment->getInitialValue();
mpSpecies->setInitialValue(Factor * pUndoSpeciesData->getINumber());
mpSpecies->setValue(Factor * mpSpecies->getValue());
}
emit notifyGUI(ListViews::METABOLITE, ListViews::CHANGE, mpSpecies->getKey());
emit notifyGUI(ListViews::COMPARTMENT, ListViews::CHANGE, pCompartment->getKey());
}
}
}
else if (column == COL_TYPE_SPECIES)
mpSpecies->setStatus((CModelEntity::Status) mItemToType[value.toInt()]);
else if (column == COL_ICONCENTRATION)
{
if (mFlagConc)
mpSpecies->setInitialConcentration(value.toDouble());
if (mpSpecies && pCompartment)
{
const C_FLOAT64 initialValue =
CMetab::convertToNumber(pUndoSpeciesData->getIConc(),
*pCompartment,
*pModel);
mpSpecies->setInitialValue(initialValue);
}
}
else if (column == COL_INUMBER)
{
if (!mFlagConc)
mpSpecies->setInitialValue(value.toDouble());
if (mpSpecies && pCompartment)
{
mpSpecies->setInitialConcentration(
CMetab::convertToConcentration(pUndoSpeciesData->getINumber(),
*pCompartment,
*pModel)
);
}
}
//Save Key
std::string key = mpSpecies->getKey();
// ask for refresh this may change the key!
QModelIndex index = getIndexFor(mpSpecies, column);
emit dataChanged(index, index);
if (column == COL_NAME_SPECIES)
{
emit notifyGUI(ListViews::METABOLITE, ListViews::RENAME, key);
}
else
{
emit notifyGUI(ListViews::METABOLITE, ListViews::CHANGE, key);
}
return true;
}
bool CQSpecieDM::setData(const QModelIndex &index, const QVariant &value,
int role)
{
if (index.isValid() && role == Qt::EditRole)
{
bool defaultRow = isDefaultRow(index);
if (defaultRow)
{
if (index.column() == COL_TYPE_SPECIES)
{
if (index.data().toString() == QString(FROM_UTF8(CModelEntity::StatusName[mItemToType[value.toInt()]])))
return false;
}
else if (index.column() == COL_COMPARTMENT && value == "")
{
return false;
}
else if (index.data() == value)
{
return false;
}
mNotify = false;
insertRow();
mNotify = true;
}
else
{
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
mpSpecies = (*CCopasiRootContainer::getDatamodelList())[0]->getModel()->getMetabolites()[index.row()];
}
const CCompartment * pCompartment = NULL;
if (index.column() == COL_COMPARTMENT ||
index.column() == COL_ICONCENTRATION ||
index.column() == COL_INUMBER)
{
try
{
pCompartment = mpSpecies->getCompartment();
}
catch (...) {}
}
if (index.column() == COL_NAME_SPECIES)
mpSpecies->setObjectName(TO_UTF8(value.toString()));
else if (index.column() == COL_COMPARTMENT)
{
// This must be set first for setInitialConcentration and
// setInitialNumber to work correctly.
std::string Compartment(TO_UTF8(value.toString()));
if (Compartment != pCompartment->getObjectName())
{
std::string CompartmentToRemove = mpSpecies->getCompartment()->getObjectName();
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
if (!(*CCopasiRootContainer::getDatamodelList())[0]->getModel()->getCompartments()[Compartment]->addMetabolite(mpSpecies))
{
QString msg;
msg = "Unable to move species '" + FROM_UTF8(mpSpecies->getObjectName()) + "'\n"
+ "from compartment '" + FROM_UTF8(CompartmentToRemove) + "' to compartment '" + FROM_UTF8(Compartment) + "'\n"
+ "since a species with that name already exist in the target compartment.";
CQMessageBox::information(NULL,
"Unable to move Species",
msg,
QMessageBox::Ok, QMessageBox::Ok);
return false;
}
else
{
(*CCopasiRootContainer::getDatamodelList())[0]->getModel()->getCompartments()[CompartmentToRemove]->getMetabolites().remove(mpSpecies->getObjectName());
(*CCopasiRootContainer::getDatamodelList())[0]->getModel()->setCompileFlag();
(*CCopasiRootContainer::getDatamodelList())[0]->getModel()->initializeMetabolites();
if (mpSpecies && pCompartment)
{
C_FLOAT64 Factor = 1.0 / pCompartment->getInitialValue();
Factor *= pCompartment->getInitialValue();
mpSpecies->setInitialValue(Factor * this->index(index.row(), COL_INUMBER).data().toDouble());
mpSpecies->setValue(Factor * this->index(index.row(), COL_NUMBER).data().toDouble());
}
emit notifyGUI(ListViews::METABOLITE, ListViews::CHANGE, mpSpecies->getKey());
emit notifyGUI(ListViews::COMPARTMENT, ListViews::CHANGE, pCompartment->getKey());
}
}
}
else if (index.column() == COL_TYPE_SPECIES)
mpSpecies->setStatus((CModelEntity::Status) mItemToType[value.toInt()]);
else if (index.column() == COL_ICONCENTRATION)
{
if (mFlagConc)
mpSpecies->setInitialConcentration(value.toDouble());
if (mpSpecies && pCompartment)
{
const C_FLOAT64 initialValue =
CMetab::convertToNumber(this->index(index.row(), COL_ICONCENTRATION).data().toDouble(),
*pCompartment,
*(*CCopasiRootContainer::getDatamodelList())[0]->getModel());
mpSpecies->setInitialValue(initialValue);
}
}
else if (index.column() == COL_INUMBER)
{
if (!mFlagConc)
mpSpecies->setInitialValue(value.toDouble());
if (mpSpecies && pCompartment)
{
mpSpecies->setInitialConcentration(
CMetab::convertToConcentration(this->index(index.row(), COL_INUMBER).data().toDouble(),
*pCompartment,
*(*CCopasiRootContainer::getDatamodelList())[0]->getModel())
);
}
}
if (defaultRow && this->index(index.row(), COL_NAME_SPECIES).data().toString() == "species")
mpSpecies->setObjectName(TO_UTF8(createNewName("species", COL_NAME_SPECIES)));
//Save Key
std::string key = mpSpecies->getKey();
emit dataChanged(index, index);
if (defaultRow)
{
emit notifyGUI(ListViews::METABOLITE, ListViews::ADD, key);
}
else
{
emit notifyGUI(ListViews::METABOLITE, ListViews::CHANGE, key);
}
}
return true;
}
bool CQFunctionDM::setData(const QModelIndex &index, const QVariant &value,
int role)
{
if (index.isValid() && role == Qt::EditRole)
{
bool defaultRow = isDefaultRow(index);
if (defaultRow)
{
if (index.data() != value)
{
mNewName = (index.column() == COL_NAME_FUNCTIONS) ? value.toString() : "function";
insertRow(rowCount(), index);
}
else
return false;
}
CEvaluationTree *pFunc = &CRootContainer::getFunctionList()->loadedFunctions()[index.row()];
if (pFunc == NULL)
return false;
if (index.column() == COL_NAME_FUNCTIONS)
pFunc->setObjectName(TO_UTF8(value.toString()));
else if (index.column() == COL_TYPE_FUNCTIONS)
{
if (index.data() != value)
{
QString msg;
msg = "Type must not be changed for '" + FROM_UTF8(pFunc->getObjectName()) + "'.\n";
CQMessageBox::information(NULL,
"Unable to change Function Type",
msg,
QMessageBox::Ok, QMessageBox::Ok);
}
}
else if (index.column() == COL_MATH_DESC_FUNCTIONS)
{
if (index.data() != value)
{
if (!pFunc->setInfix(TO_UTF8(value.toString())))
{
QString msg;
msg = "Incorrect mathematical description'" + FROM_UTF8(pFunc->getObjectName()) + "'.\n";
CQMessageBox::information(NULL,
"Unable to change mathematical description",
msg,
QMessageBox::Ok, QMessageBox::Ok);
}
}
}
emit dataChanged(index, index);
emit notifyGUI(ListViews::ObjectType::FUNCTION, ListViews::CHANGE, pFunc->getCN());
}
return true;
}
void iozoneThread::run()
{
callFlag = new QSystemSemaphore("notify", 0, QSystemSemaphore::Create);
waitFlag = new QSystemSemaphore("wait", 1, QSystemSemaphore::Create);
shm = NULL;
int argc = DEFAULT_ARGC;
int i = 0;
char *argv[DEFAULT_ARGV];
for( ; i<DEFAULT_ARGV; ++i)
argv[i] = new char[DEFAULT_ARG_CHAR];
/* 格式化设备并挂载 */
QString qsCommand;
QStringList args;
if ( param->bFlagMnt == true )
{ /* 格式化设备 */
qsCommand = "mkfs";
args.append("-t");
args.append(param->qsFsType);
args.append(param->qsDevDir);
QProcess::execute(qsCommand, args);
}
if ( param->bFlagMnt == true )
{ /* 挂载文件系统 */
qsCommand = "mount";
args.clear();
args.append("-t");
args.append(param->qsFsType);
args.append(param->qsDevDir);
args.append(param->qsMntDir);
QProcess::execute(qsCommand, args);
}
if ( param->bFlagShell == true )
{ /* 执行shell 以"sh ./shell fstype mount"格式 */
qsCommand = "sh";
args.clear();
args << param->qsShellDir << param->qsFsType << "mount";
QProcess::execute( qsCommand, args );
}
sleep(1);/* 给时间完成以上工作 */
//获取系统时间并设置显示格式
QDateTime currentDateTime = QDateTime::currentDateTime();
QString tagDateTime = currentDateTime.toString("yyyyMMddhhmmss");
/*生成字符串数组argv*/
i = 0;
strcpy(argv[i++], "./iozone");
if(param->bFlaga)
strcpy(argv[i++], "-a");
if(param->bFlags) {
strcpy(argv[i++], "-s");
sprintf(argv[i++], "%dm", param->iFileSize);
}
if(param->bFlagi0){
strcpy(argv[i++], "-i");
strcpy(argv[i++], "0");
}
if(param->bFlagi1){
strcpy(argv[i++], "-i");
strcpy(argv[i++], "1");
}
if(param->bFlagi2){
strcpy(argv[i++], "-i");
strcpy(argv[i++], "2");
}
strcpy(argv[i++], "-f");
strcpy(argv[i], param->qsFileName.toStdString().c_str() );
strcat(argv[i++], tagDateTime.toStdString().c_str());
argc = i;
iozoneThread *p = this;
pid_t pid;
i = 0;
goFork:
if((pid = fork())==0){
/* 子进程 */
callFlag = new QSystemSemaphore("notify", 0, QSystemSemaphore::Open);
waitFlag = new QSystemSemaphore("wait", 1, QSystemSemaphore::Open);
/* 共享内存 */
shmid = shmget( ftok(".", 1), sizeof(struct shmNotify), 0666|IPC_CREAT);
if(shmid == -1)
{
_exit(EXIT_FAILURE);
}
shm = shmat(shmid, (void*)0, 0);
if(shm == (void*)-1)
{
_exit(EXIT_FAILURE);
}
qDebug()<<"Child Memory attached at "<<shm<<endl;
pShmNotify = (struct shmNotify*)shm;
pShmNotify->notifyFlag = 0;
/* 调用iozone主函数 */
iozoneMain(p, argc, argv);
/* 一轮测试结束 */
waitFlag->acquire();/* 若父进程等待 */
pShmNotify->notifyFlag = -1;/* 结束标志 */
callFlag->release();/* 子进程已发出通知 */
/* 把共享内存从当前进程中分离 */
if(shmdt(pShmNotify) == -1)
{
qDebug()<<"shmdt failed"<<endl;
_exit(EXIT_FAILURE);
}
_exit(0);
/*-----子进程结束-----*/
}
else if(pid>0){
/* 父进程中 */
++i;
/* 共享内存 */
shmid = shmget( ftok(".", 1), sizeof(struct shmNotify), 0666|IPC_CREAT);
if(shmid == -1)
{
exit(EXIT_FAILURE);
}
shm = shmat(shmid, (void*)0, 0);
if(shm == (void*)-1)
{
exit(EXIT_FAILURE);
}
qDebug()<<"Father Memory attached at "<<shm<<endl;
pShmNotify = (struct shmNotify*)shm;
/* 等待处理子进程的通知直到子进程发出结束标志 */
while(1)
{
callFlag->acquire();/* 若子进程已发出通知 */
if(pShmNotify->notifyFlag == 1)
{ /* 若子进程通知传数据,父进程创建事件对象传给主窗口 */
notifyGUI(pShmNotify->type, pShmNotify->kb, pShmNotify->reclen, pShmNotify->speed);
pShmNotify->notifyFlag = 0;/* 标志位置为已接收 */
waitFlag->release();/* 父进程等待 */
continue;
}
else if(pShmNotify->notifyFlag == -1)
{ /* 若子进程通知一轮测试已结束 */
pShmNotify->notifyFlag = 0;/* 将标志位置为已接收 */
waitFlag->release();/* 父进程等待 */
break;
}
}
waitpid(pid, NULL, 0);/* 等待子进程 */
/* 把共享内存从当前进程分离 */
if(shmdt(pShmNotify) == -1)
{
qDebug()<<"shmdt failed"<<endl;
exit(EXIT_FAILURE);
}
/* 释放对象 */
delete callFlag;
delete waitFlag;
/* 判断测试轮数是否达到要求,没有达到的话再fork一次 */
if ( i < param->iTestTimes )
{ /* 下次fork之前恢复初始状态 否则会出错 */
callFlag = new QSystemSemaphore("notify", 0, QSystemSemaphore::Create);
waitFlag = new QSystemSemaphore("wait", 1, QSystemSemaphore::Create);
goto goFork;
}
/* 判断是否需要取消挂载 */
if ( param->bFlagMnt == true )
{ /* 取消挂载 */
qsCommand = "umount";
args.clear();
args.append(param->qsMntDir);
QProcess::execute(qsCommand, args);
}
if ( param->bFlagShell == true )
{ /* 执行shell 以"sh ./shell fstype mount"格式 */
qsCommand = "sh";
args.clear();
args << param->qsShellDir << param->qsFsType << "umount";
QProcess::execute( qsCommand, args );
}
/* 测试结束 */
//*(param->pbFlagRun) = false; 在iozonewidget中修改
/* 释放内存 */
for ( i = 0; i < DEFAULT_ARGV; ++i)
{
delete argv[i];
}
delete this->param;/* 在点击start按钮时getparam()中new的 */
this->quit();
}
}
