RemoveAllGlobalQuantityRowsCommand::RemoveAllGlobalQuantityRowsCommand(CQGlobalQuantityDM * pGlobalQuantityDM, const QModelIndex&)
{
mpGlobalQuantityDM = pGlobalQuantityDM;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
for (int i = 0; i != pGlobalQuantityDM->rowCount() - 1; ++i)
{
UndoGlobalQuantityData *data = new UndoGlobalQuantityData();
if (pModel->getModelValues()[i])
{
data->setName(pModel->getModelValues()[i]->getObjectName());
data->setStatus(pModel->getModelValues()[i]->getStatus());
if (pModel->getModelValues()[i]->getStatus() != CModelEntity::ASSIGNMENT)
{
data->setInitialValue(pModel->getModelValues()[i]->getInitialValue());
}
// set expression
if (pModel->getModelValues()[i]->getStatus() != CModelEntity::FIXED)
{
data->setExpression(pModel->getModelValues()[i]->getExpression());
}
// set initial expression
if (pModel->getModelValues()[i]->getStatus() != CModelEntity::ASSIGNMENT)
{
data->setInitialExpression(pModel->getModelValues()[i]->getInitialExpression());
}
setDependentObjects(pModel->getModelValues()[i]->getDeletedObjects());
data->setReactionDependencyObjects(getReactionData());
data->setSpecieDependencyObjects(getSpecieData());
data->setEventDependencyObjects(getEventData());
mpGlobalQuantityData.append(data);
}
}
mType = GLOBALQUANTITYREMOVEALL;
setEntityType("Global Quantity");
this->setText(removeAllGlobalQuantityRowsText());
}
DeleteSpecieCommand::DeleteSpecieCommand(CQSpeciesDetail *pSpecieDetail)
{
mpSpecieDetail = pSpecieDetail;
mFirstTime = true;
mpSpecieData = new UndoSpecieData();
mpReactionData = new QList <UndoReactionData*>();
mpGlobalQuantityData = new QList <UndoGlobalQuantityData*>();
mpEventData = new QList <UndoEventData*>();
std::string sName = mpSpecieDetail->mpMetab->getObjectName();
mpSpecieData->setName(sName);
mpSpecieData->setStatus(mpSpecieDetail->mpMetab->getStatus());
if (mpSpecieDetail->mpMetab->getStatus() != CModelEntity::ASSIGNMENT)
{
mpSpecieData->setIConc(mpSpecieDetail->mpMetab->getInitialConcentration());
}
if (mpSpecieDetail->mpMetab->getStatus() == CModelEntity::ASSIGNMENT || mpSpecieDetail->mpMetab->getStatus() == CModelEntity::ODE)
{
mpSpecieData->setExpression(mpSpecieDetail->mpMetab->getExpression());
}
// set initial expression
if (mpSpecieDetail->mpMetab->getStatus() != CModelEntity::ASSIGNMENT)
{
mpSpecieData->setInitialExpression(mpSpecieDetail->mpMetab->getInitialExpression());
}
//store to be deleted data
//QList<UndoReactionData*> *dependencyObjects = new QList<UndoReactionData*>();
setDependentObjects(mpSpecieDetail->mpMetab->getDeletedObjects());
mpSpecieData->setReactionDependencyObjects(getReactionData());
mpSpecieData->setGlobalQuantityDependencyObjects(getGlobalQuantityData());
mpSpecieData->setEventDependencyObjects(getEventData());
mType = SPECIEDELETE;
setEntityType("Species");
setName(sName);
this->setText(deleteSpecieText(sName));
}
RemoveCompartmentRowsCommand::RemoveCompartmentRowsCommand(QModelIndexList rows, CQCompartmentDM * pCompartmentDM, const QModelIndex&)
{
mpCompartmentDM = pCompartmentDM;
mRows = rows;
mFirstTime = true;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
CModel * pModel = pDataModel->getModel();
assert(pModel != NULL);
QModelIndexList::const_iterator i;
for (i = rows.begin(); i != rows.end(); ++i)
{
UndoCompartmentData *data = new UndoCompartmentData();
if (!pCompartmentDM->isDefaultRow(*i) && pModel->getCompartments()[(*i).row()])
{
mpSpecieData = new QList <UndoSpecieData*>();
mpReactionData = new QList <UndoReactionData*>();
mpGlobalQuantityData = new QList <UndoGlobalQuantityData*>();
mpEventData = new QList <UndoEventData*>();
data->setName(pModel->getCompartments()[(*i).row()]->getObjectName());
data->setStatus(pModel->getCompartments()[(*i).row()]->getStatus());
data->setInitialValue(pModel->getCompartments()[(*i).row()]->getInitialValue());
setDependentObjects(pModel->getCompartments()[(*i).row()]->getDeletedObjects());
data->setReactionDependencyObjects(getReactionData());
data->setSpecieDependencyObjects(getSpecieData());
data->setGlobalQuantityDependencyObjects(getGlobalQuantityData());
data->setEventDependencyObjects(getEventData());
mpCompartmentData.append(data);
}
}
this->setText(removeCompartmentRowsText());
mType = COMPARTMENTREMOVE;
setEntityType("Compartment");
}
DeleteGlobalQuantityCommand::DeleteGlobalQuantityCommand(CQModelValue *pModelValue)
{
mpModelValue = pModelValue;
mFirstTime = true;
mpGlobalQuantityData = new UndoGlobalQuantityData();
std::string sName = mpModelValue->mpModelValue->getObjectName();
mpGlobalQuantityData->setName(sName);
mpGlobalQuantityData->setStatus(mpModelValue->mpModelValue->getStatus());
if (mpModelValue->mpModelValue->getStatus() != CModelEntity::ASSIGNMENT)
{
mpGlobalQuantityData->setInitialValue(mpModelValue->mpModelValue->getInitialValue());
}
if (mpModelValue->mpModelValue->getStatus() != CModelEntity::FIXED)
{
mpGlobalQuantityData->setExpression(mpModelValue->mpModelValue->getExpression());
}
// set initial expression
if (mpModelValue->mpModelValue->getStatus() != CModelEntity::ASSIGNMENT)
{
mpGlobalQuantityData->setInitialExpression(mpModelValue->mpModelValue->getInitialExpression());
}
//store to be deleted data
setDependentObjects(mpModelValue->mpModelValue->getDeletedObjects());
mpGlobalQuantityData->setReactionDependencyObjects(getReactionData());
mpGlobalQuantityData->setSpecieDependencyObjects(getSpecieData());
mpGlobalQuantityData->setEventDependencyObjects(getEventData());
mType = GLOBALQUANTITYDELETE;
setEntityType("Global Quantity");
this->setText(deleteGlobalQuantityText(sName));
setName(sName);
}
void Transform::expand( CycleData& cyData, EventData& evData,
map< string, WaveformTable>& wftMap,
vector<string> pinList, double timescale) {
assert( timescale >= 0.0);
assert( timescale <= 1.0);
if(timescale == 0.0) {
//
// Calculate timescale
//
vector<double> res;
map<string, WaveformTable>::iterator iter;
for(iter = wftMap.begin(); iter != wftMap.end(); iter++) {
res.push_back( iter->second.getEventResolution());
}
double minRes = *(min_element( res.begin(), res.end()));
double exponent = ceil( log10(1/minRes));
timescale = pow( 10.0, -exponent);
//applog.debug << "Calculating timescale : " << timescale << endl;
//applog.debug << "minRes = " << minRes << " exponent = " << exponent << endl;
assert( timescale >= 0.0);
assert( timescale <= 1.0);
}
//if(debug)
//cyData.print( applog.debug);
SignalHeader signalHeader = cyData.getSignalHeader();
vector<string> pinNames;
for(unsigned int i=0; i < signalHeader.size(); i++) {
pinNames.push_back( signalHeader[i].name);
}
evData.setSignalHeader( signalHeader);
unsigned long numVectors = cyData.getNumVectors();
unsigned long long periodBeginTimestamp = 0;
unsigned long loopSum = 0;
for(unsigned long vecNum=0; vecNum < numVectors; vecNum++) {
CycleData::PeriodData periodData;
cyData.getPeriodData( periodData, vecNum);
// periodData.print( applog.debug);
WaveformTable wft = wftMap[periodData.wftRef];
double period = wft.period.value;
// Need my_round due to fractional error
unsigned long long periodTimestamp = (unsigned long long) my_round(period/timescale);
EventData periodEventData;
getEventData( periodData, wft, periodEventData, pinNames, timescale);
// periodEventData.print( applog.debug);
for(unsigned int i=0; i <= periodData.loopCount; i++) {
// append event data
//applog.debug << "Adding events at timestamp " << periodBeginTimestamp << endl;
evData.add( periodEventData, periodBeginTimestamp);
// periodBeginTimestamp = (unsigned long long) (((vecNum + 1 + loopSum + i)*period)/timescale);
periodBeginTimestamp = (unsigned long long) ((vecNum + 1 + loopSum + i)*periodTimestamp);
}
loopSum += periodData.loopCount;
}
evData.setTimescale( timescale);
}
