void Network::addCompartment(int index, float _xmin, float _xmax, float _ymin, float _ymax, string _name){
//add in a compartment with all attributes specified.
if(index>=compartments->size())compartments->resize(index+1);
(*compartments)[index]=(Compartment(_xmin,_xmax,_ymin,_ymax,_name));
}
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;
}
void Network::addCompartment(int index, string _name){
//add in a compartment with _name specified (prefered in the algorithms).
if(index>=compartments->size())compartments->resize(index+1);
(*compartments)[index]=(Compartment(_name));
}
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;
}
