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;
}