bool CExperimentObjectMap::elevateChildren()
{
bool success = true;
elements::iterator itColumn = beginIndex();
elements::iterator endColumn = endIndex();
if (itColumn != endColumn &&
dynamic_cast< CCopasiParameterGroup * >(*itColumn) == NULL) // We have an old data format.
{
CCopasiParameterGroup New(getObjectName());
for (; itColumn != endColumn; ++itColumn)
{
CCopasiParameterGroup * pGroup = New.assertGroup((*itColumn)->getObjectName());
pGroup->assertParameter("Object CN", CCopasiParameter::CN, (*itColumn)->getValue< CRegisteredObjectName >());
}
clear();
operator=(New);
}
for (itColumn = beginIndex(); itColumn != endColumn; ++itColumn)
if (((*itColumn) = elevate<CDataColumn, CCopasiParameterGroup>(*itColumn)) == NULL)
success = false;
return success;
}
// virtual
QModelIndex CQTaskMethodParametersDM::index(int row, int column, const QModelIndex & parent) const
{
CCopasiParameterGroup * pParent = static_cast< CCopasiParameterGroup * >(nodeFromIndex(parent));
if (pParent == NULL &&
mMethods.size() > 0)
{
QVector< CCopasiMethod * >::const_iterator it = mMethods.constBegin();
QVector< CCopasiMethod * >::const_iterator end = mMethods.constEnd();
int Row = row;
for (; it != end; ++it)
if (Row < (int)(*it)->size())
{
return createIndex(row, column, *((*it)->beginIndex() + Row));
}
else
{
Row -= (int)(*it)->size();
}
return QModelIndex();
}
if (pParent != NULL && row < (int) pParent->size())
return createIndex(row, column, *(pParent->beginIndex() + row));
else
return QModelIndex();
}
bool CExperimentObjectMap::elevateChildren()
{
bool success = true;
std::vector<CCopasiParameter *>::iterator itColumn = mValue.pGROUP->begin();
std::vector<CCopasiParameter *>::iterator endColumn = mValue.pGROUP->end();
if (itColumn != endColumn &&
dynamic_cast< CCopasiParameterGroup * >(*itColumn) == NULL) // We have an old data format.
{
CCopasiParameterGroup New(getObjectName());
for (; itColumn != endColumn; ++itColumn)
{
CCopasiParameterGroup * pGroup = New.assertGroup((*itColumn)->getObjectName());
pGroup->assertParameter("Object CN", CCopasiParameter::CN, *(*itColumn)->getValue().pCN);
}
clear();
*this = New;
}
for (itColumn = mValue.pGROUP->begin(); itColumn != endColumn; ++itColumn)
if (((*itColumn) = elevate<CDataColumn, CCopasiParameterGroup>(*itColumn)) == NULL)
success = false;
return success;
}
C_FLOAT64 CExperimentObjectMap::CDataColumn::getDefaultScale() const
{
if (mpObjectCN == NULL)
return std::numeric_limits<C_FLOAT64>::quiet_NaN();
CCopasiParameterGroup *pGroup =
dynamic_cast< CCopasiParameterGroup * >(getObjectParent());
if (pGroup == NULL)
return std::numeric_limits<C_FLOAT64>::quiet_NaN();
const CExperiment *pExperiment =
dynamic_cast<const CExperiment * >(pGroup->getObjectParent());
if (pExperiment == NULL)
return std::numeric_limits<C_FLOAT64>::quiet_NaN();
CObjectInterface::ContainerList ListOfContainer;
ListOfContainer.push_back(getObjectDataModel());
const CCopasiObject * pObject = CObjectInterface::DataObject(CObjectInterface::GetObjectFromCN(ListOfContainer, *mpObjectCN));
if (pObject == NULL)
return std::numeric_limits<C_FLOAT64>::quiet_NaN();
return pExperiment->getDefaultScale(pObject);
}
void CQParameterGroupView::slotPushButtonClicked(const QModelIndex & index)
{
QModelIndex Source = index;
while (Source.model()->inherits("QSortFilterProxyModel"))
{
Source = static_cast< const QSortFilterProxyModel *>(Source.model())->mapToSource(index);
}
if (this->itemDelegateForRow(Source.row()) != mpPushButtonDelegate) return;
CCopasiParameter * pParameter = CQParameterGroupDM::nodeFromIndex(Source);
if (pParameter->getType() != CCopasiParameter::Type::GROUP) return;
CCopasiParameterGroup * pGroup = static_cast< CCopasiParameterGroup * >(pParameter);
CCopasiParameterGroup::elements::const_iterator it = pGroup->getElementTemplates().beginIndex();
CCopasiParameterGroup::elements::const_iterator end = pGroup->getElementTemplates().endIndex();
for (; it != end; ++it)
{
switch ((*it)->getType())
{
case CCopasiParameter::Type::CN:
modifySelectCNs(*pGroup, **it);
break;
default:
break;
}
}
}
C_FLOAT64 CExperimentObjectMap::CDataColumn::getDefaultScale() const
{
if (mpObjectCN == NULL)
return std::numeric_limits<C_FLOAT64>::quiet_NaN();
CCopasiParameterGroup *pGroup =
dynamic_cast< CCopasiParameterGroup * >(getObjectParent());
if (pGroup == NULL)
return std::numeric_limits<C_FLOAT64>::quiet_NaN();
const CExperiment *pExperiment =
dynamic_cast<const CExperiment * >(pGroup->getObjectParent());
if (pExperiment == NULL)
return std::numeric_limits<C_FLOAT64>::quiet_NaN();
const CCopasiDataModel* pDataModel = getObjectDataModel();
assert(pDataModel != NULL);
const CCopasiObject * pObject = pDataModel->getDataObject(*mpObjectCN);
if (pObject == NULL)
return std::numeric_limits<C_FLOAT64>::quiet_NaN();
return pExperiment->getDefaultScale(pObject);
}
int CQTaskMethodParametersDM::getRow(const CCopasiParameter * pNode) const
{
if (pNode == NULL)
{
return -1;
}
CCopasiParameterGroup * pParent = static_cast< CCopasiParameterGroup * >(pNode->getObjectParent());
if (pParent == NULL)
{
return 0;
}
if (isMethod(pParent))
{
QVector< CCopasiMethod * >::const_iterator itMethod = mMethods.constBegin();
QVector< CCopasiMethod * >::const_iterator endMethod = mMethods.constEnd();
int i = 0;
for (; itMethod != endMethod; ++itMethod)
{
CCopasiParameterGroup::index_iterator it = pParent->beginIndex();
CCopasiParameterGroup::index_iterator end = pParent->endIndex();
for (; it != end; ++it, ++i)
if (*it == pNode)
{
return i;
}
}
}
else
{
int i = 0;
CCopasiParameterGroup::index_iterator it = pParent->beginIndex();
CCopasiParameterGroup::index_iterator end = pParent->endIndex();
for (; it != end; ++it, ++i)
if (*it == pNode)
{
return i;
}
}
return -1;
}
bool CScanWidgetRandom::saveToScanItem(CScanProblem * pg) const
{
CScanProblem::Type type = CScanProblem::SCAN_RANDOM;
unsigned C_INT32 steps = 1;
CCopasiParameterGroup* tmp = pg->createScanItem(type, steps, mpObject);
assert(tmp);
tmp->setValue("Distribution type", (unsigned C_INT32)comboBoxType->currentItem());
tmp->setValue("Minimum", lineEditMin->text().toDouble());
tmp->setValue("Maximum", lineEditMax->text().toDouble());
tmp->setValue("log", checkBoxLog->isChecked());
return true;
}
void CQParameterGroupView::modifySelectCNs(CCopasiParameterGroup & group, const CCopasiParameter & cnTemplate)
{
// OpenSelectionDialog
std::vector< const CDataObject * > Selection;
CObjectInterface::ContainerList ContainerList;
ContainerList.push_back(group.getObjectDataModel());
// Create the current selection
CCopasiParameterGroup::elements::iterator it = group.beginIndex();
CCopasiParameterGroup::elements::iterator end = group.endIndex();
for (; it != end; ++it)
{
const CDataObject * pObject = CObjectInterface::DataObject(CObjectInterface::GetObjectFromCN(ContainerList, (*it)->getValue< CCommonName >()));
if (pObject != NULL)
{
Selection.push_back(pObject);
}
}
CModel * pModel = group.getObjectDataModel()->getModel();
std::vector<const CDataObject * > ValidObjects;
const std::vector< std::pair < CCommonName, CCommonName > > & ValidValues = cnTemplate.getValidValues< CCommonName >();
std::vector< std::pair < CCommonName, CCommonName > >::const_iterator itValidValues = ValidValues.begin();
std::vector< std::pair < CCommonName, CCommonName > >::const_iterator endValidValues = ValidValues.end();
for (; itValidValues != endValidValues; ++itValidValues)
{
CObjectLists::ListType ListType = toEnum(itValidValues->first, CObjectLists::ListTypeName, CObjectLists::EMPTY_LIST);
std::vector<const CDataObject * > Tmp = CObjectLists::getListOfConstObjects(ListType, pModel);
ValidObjects.insert(ValidObjects.end(), Tmp.begin(), Tmp.end());
}
std::vector< const CDataObject * > NewSelection = CCopasiSelectionDialog::getObjectVector(this, ValidObjects, &Selection);
// Modify group parameters;
mpParameterGroupDM->beginResetModel();
group.clear();
std::vector< const CDataObject * >::const_iterator itNew = NewSelection.begin();
std::vector< const CDataObject * >::const_iterator endNew = NewSelection.end();
for (; itNew != endNew; ++itNew)
{
group.addParameter("Reaction", CCopasiParameter::Type::CN, (*itNew)->getCN());
}
mpParameterGroupDM->endResetModel();
}
bool CFitProblem::elevateChildren()
{
// This call is necessary since CFitProblem is derived from COptProblem.
if (!COptProblem::elevateChildren()) return false;
// Due to a naming conflict the following parameters may have been overwritten during
// the load of a CopasiML file we replace them with default values if that was the case.
mpParmSteadyStateCN =
assertParameter("Steady-State", CCopasiParameter::CN, CCopasiObjectName(""))->getValue().pCN;
mpParmTimeCourseCN =
assertParameter("Time-Course", CCopasiParameter::CN, CCopasiObjectName(""))->getValue().pCN;
CCopasiVectorN< CCopasiTask > * pTasks = NULL;
CCopasiDataModel* pDataModel = getObjectDataModel();
if (pDataModel)
pTasks = pDataModel->getTaskList();
if (pTasks == NULL)
pTasks = dynamic_cast<CCopasiVectorN< CCopasiTask > *>(getObjectAncestor("Vector"));
if (pTasks)
{
unsigned C_INT32 i, imax = pTasks->size();
if (!mpParmSteadyStateCN->compare(0, 5 , "Task_") ||
*mpParmSteadyStateCN == "")
for (i = 0; i < imax; i++)
if ((*pTasks)[i]->getType() == CCopasiTask::steadyState)
{
*mpParmSteadyStateCN = (*pTasks)[i]->getCN();
break;
}
if (!mpParmTimeCourseCN->compare(0, 5 , "Task_") ||
*mpParmTimeCourseCN == "")
for (i = 0; i < imax; i++)
if ((*pTasks)[i]->getType() == CCopasiTask::timeCourse)
{
*mpParmTimeCourseCN = (*pTasks)[i]->getCN();
break;
}
}
std::map<std::string, std::string> ExperimentMap;
CCopasiParameterGroup * pGroup;
CExperiment * pExperiment;
std::vector<CCopasiParameter *> * pExperiments =
getGroup("Experiment Set")->CCopasiParameter::getValue().pGROUP;
std::vector<CCopasiParameter *>::iterator itExp;
std::vector<CCopasiParameter *>::iterator endExp;
for (itExp = pExperiments->begin(), endExp = pExperiments->end(); itExp != endExp; ++itExp)
if ((pGroup = dynamic_cast< CCopasiParameterGroup * >(*itExp)) != NULL &&
pGroup->getParameter("Key") != NULL)
ExperimentMap[*pGroup->getValue("Key").pKEY] = (*itExp)->getObjectName();
mpExperimentSet =
elevate<CExperimentSet, CCopasiParameterGroup>(getGroup("Experiment Set"));
if (!mpExperimentSet) return false;
std::map<std::string, std::string>::iterator itMap;
std::map<std::string, std::string>::iterator endMap;
for (itMap = ExperimentMap.begin(), endMap = ExperimentMap.end(); itMap != endMap; ++itMap)
{
pExperiment = mpExperimentSet->getExperiment(itMap->second);
itMap->second = pExperiment->CCopasiParameter::getKey();
pExperiment->setValue("Key", itMap->second);
}
std::vector<COptItem * >::iterator it = mpOptItems->begin();
std::vector<COptItem * >::iterator end = mpOptItems->end();
for (; it != end; ++it)
{
if (!((*it) = elevate<CFitItem, COptItem>(*it)))
return false;
pExperiments =
(*it)->getParameter("Affected Experiments")->getValue().pGROUP;
for (itExp = pExperiments->begin(), endExp = pExperiments->end(); itExp != endExp; ++itExp)
(*itExp)->setValue(ExperimentMap[*(*itExp)->getValue().pKEY]);
}
it = mpConstraintItems->begin();
end = mpConstraintItems->end();
for (; it != end; ++it)
{
if (!((*it) = elevate<CFitConstraint, COptItem>(*it)))
return false;
pExperiments =
(*it)->getParameter("Affected Experiments")->getValue().pGROUP;
for (itExp = pExperiments->begin(), endExp = pExperiments->end(); itExp != endExp; ++itExp)
(*itExp)->setValue(ExperimentMap[*(*itExp)->getValue().pKEY]);
}
return true;
}
/**
* Creates the simulations for SEDML.
*/
std::string CSEDMLExporter::createScanTask(CCopasiDataModel& dataModel, const std::string & modelId)
{
// need L1V2 to export repeated tasks
if (mpSEDMLDocument->getVersion() != 2) return "";
CScanTask* pTask = dynamic_cast<CScanTask*>((*dataModel.getTaskList())["Scan"]);
if (pTask == NULL) return "";
CScanProblem* pProblem = dynamic_cast<CScanProblem*>(pTask->getProblem());
size_t numItems = pProblem->getNumberOfScanItems();
if (numItems == 0)
return "";
if (pProblem->getSubtask() != CCopasiTask::steadyState &&
pProblem->getSubtask() != CCopasiTask::timeCourse)
{
CCopasiMessage(CCopasiMessage::WARNING, "This version of COPASI only allows the export of time course or steady state scans.");
return "";
}
std::string subTaskId;
if (pProblem->getSubtask() == CCopasiTask::steadyState)
{
subTaskId = createSteadyStateTask(dataModel, modelId);
}
else
{
subTaskId = mpTimecourseTask->getId();
}
SedRepeatedTask* task = mpSEDMLDocument->createRepeatedTask();
std::string taskId = SEDMLUtils::getNextId("task", mpSEDMLDocument->getNumTasks());
task->setId(taskId);
task->setResetModel(!pProblem->getContinueFromCurrentState());
// craete ranges / changes
for (size_t i = 0; i < numItems; ++i)
{
CCopasiParameterGroup* current = pProblem->getScanItem(i);
CScanProblem::Type type = (CScanProblem::Type)(*current->getParameter("Type")->getValue().pUINT);
// ignore random items
if (type == CScanProblem::SCAN_RANDOM)
{
CCopasiMessage(CCopasiMessage::WARNING, "This version of COPASI cannot export random scan items, they will be ignored.");
continue;
}
int numSteps = (*current->getParameter("Number of steps")->getValue().pUINT);
// handle repeats
if (type == CScanProblem::SCAN_REPEAT)
{
SedUniformRange *range = task->createUniformRange();
range->setId(SEDMLUtils::getNextId("range", task->getNumRanges()));
range->setStart(0);
range->setEnd(numSteps);
range->setNumberOfPoints(numSteps);
range->setType("linear");
if (task->isSetRangeId())
task->setRangeId(range->getId());
continue;
}
// handle scans
if (type == CScanProblem::SCAN_LINEAR)
{
double min = (*current->getParameter("Minimum")->getValue().pDOUBLE);
double max = (*current->getParameter("Maximum")->getValue().pDOUBLE);
bool log = (*current->getParameter("log")->getValue().pBOOL);
SedUniformRange *range = task->createUniformRange();
range->setId(SEDMLUtils::getNextId("range", task->getNumRanges()));
range->setStart(min);
range->setEnd(max);
range->setNumberOfPoints(numSteps);
range->setType(log ? "log" : "linear");
const CRegisteredObjectName& cn = (*current->getParameter("Object")->getValue().pCN);
std::string xpath = SEDMLUtils::getXPathForObject(*static_cast<const CCopasiObject*>(dataModel.getObject(cn)));
if (xpath.empty())
{
CCopasiMessage(CCopasiMessage::WARNING, "This version of COPASI cannot export the selected scan object, it will be ignored.");
continue;
}
SedSetValue *change = task->createTaskChange();
change->setModelReference(modelId);
if (xpath == SEDML_TIME_URN)
{
change->setSymbol(xpath);
}
else
{
change->setTarget(xpath);
}
change->setRange(range->getId());
change->setMath(SBML_parseFormula(range->getId().c_str()));
continue;
}
}
if (!task->isSetRangeId() && task->getNumRanges() > 0)
task->setRangeId(task->getRange(0)->getId());
// create subtask
SedSubTask* subTask = task->createSubTask();
subTask->setOrder(1);
subTask->setTask(subTaskId);
return taskId;
}
CExperimentSet::CExperimentSet(const CCopasiParameterGroup & group,
const CDataContainer * pParent):
CCopasiParameterGroup(group, static_cast< const CDataContainer * >((pParent != NULL) ? pParent : group.getObjectDataModel())),
mpExperiments(NULL),
mNonExperiments(0),
mDependentObjects(0),
mDependentObjectiveValues(0),
mDependentRMS(0),
mDependentErrorMean(0),
mDependentErrorMeanSD(0),
mDependentDataCount(0),
mValidValueCount(0)
{initializeParameter();}