/**
* Creates the simulations for SEDML.
*/
std::string CSEDMLExporter::createTimeCourseTask(CCopasiDataModel& dataModel, const std::string & modelId)
{
mpTimecourse = this->mpSEDMLDocument->createUniformTimeCourse();
mpTimecourse->setId(SEDMLUtils::getNextId("sim", mpSEDMLDocument->getNumSimulations()));
//presently SEDML only supports time course
CCopasiTask* pTask = (*dataModel.getTaskList())["Time-Course"];
CTrajectoryProblem* tProblem = static_cast<CTrajectoryProblem*>(pTask->getProblem());
mpTimecourse->setInitialTime(0.0);
mpTimecourse->setOutputStartTime(tProblem->getOutputStartTime());
mpTimecourse->setOutputEndTime(tProblem->getStepNumber()*tProblem->getStepSize());
mpTimecourse->setNumberOfPoints(tProblem->getStepNumber());
// set the correct KISAO Term
SedAlgorithm* alg = mpTimecourse->createAlgorithm();
if (pTask->getMethod()->getObjectName().find("Stochastic") != std::string::npos)
alg->setKisaoID("KISAO:0000241");
else
alg->setKisaoID("KISAO:0000019");
mpTimecourseTask = this->mpSEDMLDocument->createTask();
std::string taskId = SEDMLUtils::getNextId("task", mpSEDMLDocument->getNumTasks());
mpTimecourseTask->setId(taskId);
mpTimecourseTask->setSimulationReference(mpTimecourse->getId());
mpTimecourseTask->setModelReference(modelId);
return taskId;
}
void CQTSSAResultSubWidget::saveDataToFile()
{
C_INT32 Answer = QMessageBox::No;
QString fileName;
while (Answer == QMessageBox::No)
{
fileName =
CopasiFileDialog::getSaveFileName(this, "Save File Dialog",
"untitled.txt", "Text Files (*.txt)", "Save to");
if (fileName.isEmpty()) return;
// Checks whether the file exists
Answer = checkSelection(fileName);
if (Answer == QMessageBox::Cancel) return;
}
std::ofstream file(CLocaleString::fromUtf8(TO_UTF8(fileName)).c_str());
if (file.fail()) return;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiTask* mpTask =
dynamic_cast<CTSSATask *>((*(*CCopasiRootContainer::getDatamodelList())[0]->getTaskList())["Time Scale Separation Analysis"]);
if (!mpTask) return;
CCopasiProblem* mpProblem = mpTask->getProblem();
mpProblem->printResult(&file);
return;
}
void CMCAResultSubwidget::slotSave()
{
C_INT32 Answer = QMessageBox::No;
QString fileName;
while (Answer == QMessageBox::No)
{
fileName =
CopasiFileDialog::getSaveFileName(this, "Save File Dialog",
"untitled.txt", "TEXT Files (*.txt)", "Save to");
if (fileName.isEmpty()) return;
// Checks whether the file exists
Answer = checkSelection(fileName);
if (Answer == QMessageBox::Cancel) return;
}
std::ofstream file(CLocaleString::fromUtf8(TO_UTF8(fileName)).c_str());
if (file.fail())
return;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiTask* mpTask =
dynamic_cast<CMCATask *>((*(*CCopasiRootContainer::getDatamodelList())[0]->getTaskList())["Metabolic Control Analysis"]);
if (mpTask != NULL)
file << mpTask->getResult();
// mpTask->printResult(file);
return;
}
std::string Arguments::prepareModel() const
{
if (!isValid()) return "";
CCopasiDataModel* model = (*CCopasiRootContainer::getDatamodelList())[0];
model->loadModel(getFilename(), NULL);
if (mDisablePlots)
{
for (size_t index = 0; index < model->getPlotDefinitionList()->size(); ++index)
{
(*model->getPlotDefinitionList())[index]->setActive(false);
}
}
if (mClearTargets)
{
for (size_t index = 0; index < model->getTaskList()->size(); ++index)
{
(*model->getTaskList())[index]->getReport().setTarget("");
}
}
CCopasiTask *task = getTask();
if (task != NULL)
{
if (isGenerateOutput())
{
// calls initialize which is private
COutputAssistant::getListOfDefaultOutputDescriptions();
// generate the output
COutputAssistant::createDefaultOutput(mGenerateOutput, task, model);
}
if (haveReportFile())
task->getReport().setTarget(mReportFile);
COptTask* optTask = dynamic_cast<COptTask*>(task);
if (optTask != NULL)
{
COptProblem *problem = (COptProblem *)optTask->getProblem();
if (mSetSolutionStatistic)
optTask->setMethodType(CCopasiMethod::Statistics);
if (isDisableRandomizeStartValues())
problem->setRandomizeStartValues(false);
if (isDisableStatistic())
problem->setCalculateStatistics(false);
}
}
model->saveModel(getFilename() + ".view.cps", NULL, true);
return getFilename() + ".view.cps";
}
CCopasiTask* Arguments::getTaskForName(const std::string& name) const
{
CCopasiVectorN<CCopasiTask> &taskList = *(*CCopasiRootContainer::getDatamodelList())[0]->getTaskList();
for (size_t i = 0; i < taskList.size(); ++i)
{
CCopasiTask *current = taskList[i];
if (current->getObjectName() == name)
return current;
}
return NULL;
}
CCopasiTask* Arguments::getFirstScheduledTask()
{
CCopasiVectorN<CCopasiTask> &taskList = *(*CCopasiRootContainer::getDatamodelList())[0]->getTaskList();
for (size_t i = 0; i < taskList.size(); ++i)
{
CCopasiTask *current = taskList[i];
if (current->isScheduled())
return current;
}
return NULL;
}
/**
* Creates the simulations for SEDML.
*/
std::string CSEDMLExporter::createSteadyStateTask(CCopasiDataModel& dataModel, const std::string & modelId)
{
SedSteadyState *steady = this->mpSEDMLDocument->createSteadyState();
steady->setId(SEDMLUtils::getNextId("steady", mpSEDMLDocument->getNumSimulations()));
//presently SEDML only supports time course
CCopasiTask* pTask = (*dataModel.getTaskList())["Steady-State"];
CTrajectoryProblem* tProblem = static_cast<CTrajectoryProblem*>(pTask->getProblem());
// set the correct KISAO Term
SedAlgorithm* alg = steady->createAlgorithm();
alg->setKisaoID("KISAO:0000282");
SedTask *task = this->mpSEDMLDocument->createTask();
std::string taskId = SEDMLUtils::getNextId("task", mpSEDMLDocument->getNumTasks());
task->setId(taskId);
task->setSimulationReference(steady->getId());
task->setModelReference(modelId);
return taskId;
}
/*
* build the population tree
*/
void CCopasiSimpleSelectionTree::populateTree(const CModel * pModel,
const ObjectClasses & classes)
{
if (!pModel) return;
const CCopasiObject * pObject;
Q3ListViewItem * pItem;
// find all kinds of time
pObject = pModel->getObject(CCopasiObjectName("Reference=Time"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpTimeSubtree, "Model Time");
treeItems[pItem] = pObject;
}
pObject = pModel->getObject(CCopasiObjectName("Reference=Initial Time"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpTimeSubtree, "Model Initial Time");
treeItems[pItem] = pObject;
}
pObject = pModel->getObjectDataModel()->getObject(CCopasiObjectName("Timer=CPU Time"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpTimeSubtree, "CPU time");
treeItems[pItem] = pObject;
}
pObject = pModel->getObjectDataModel()->getObject(CCopasiObjectName("Timer=Wall Clock Time"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpTimeSubtree, "real time");
treeItems[pItem] = pObject;
}
removeEmptySubTree(&mpTimeSubtree);
// find all species (aka metabolites) and create items in the metabolite subtree
const CCopasiVector<CMetab>& metabolites = pModel->getMetabolites();
unsigned int counter;
unsigned int maxCount = metabolites.size();
for (counter = maxCount; counter != 0; --counter)
{
const CMetab* metab = metabolites[counter - 1];
std::string name = metab->getObjectName();
bool unique = isMetaboliteNameUnique(name, metabolites);
if (!unique)
{
const CCompartment* comp = metab->getCompartment();
if (comp)
{
name = name + "(" + comp->getObjectName() + ")";
}
}
pObject = metab->getObject(CCopasiObjectName("Reference=InitialParticleNumber"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteInitialNumberSubtree, FROM_UTF8(name + "(t=0)"));
treeItems[pItem] = pObject;
}
pObject = metab->getObject(CCopasiObjectName("Reference=ParticleNumber"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteTransientNumberSubtree, FROM_UTF8(name + "(t)"));
treeItems[pItem] = pObject;
}
if (metab->getStatus() != CModelEntity::ASSIGNMENT)
{
pObject = metab->getObject(CCopasiObjectName("Reference=ParticleNumberRate"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteRateNumberSubtree, FROM_UTF8("d(" + name + ")/dt"));
treeItems[pItem] = pObject;
}
}
name = "[" + name + "]"; // Concentration
pObject = metab->getObject(CCopasiObjectName("Reference=InitialConcentration"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteInitialConcentrationSubtree, FROM_UTF8(name + "(t=0)"));
treeItems[pItem] = pObject;
}
pObject = metab->getObject(CCopasiObjectName("Reference=Concentration"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteTransientConcentrationSubtree, FROM_UTF8(name + "(t)"));
treeItems[pItem] = pObject;
}
if (metab->getStatus() != CModelEntity::ASSIGNMENT)
{
pObject = metab->getObject(CCopasiObjectName("Reference=Rate"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpMetaboliteRateConcentrationSubtree, FROM_UTF8("d(" + name + ")/dt"));
treeItems[pItem] = pObject;
}
}
}
removeEmptySubTree(&mpMetaboliteInitialNumberSubtree);
removeEmptySubTree(&mpMetaboliteTransientNumberSubtree);
removeEmptySubTree(&mpMetaboliteRateNumberSubtree);
removeEmptySubTree(&mpMetaboliteInitialConcentrationSubtree);
removeEmptySubTree(&mpMetaboliteTransientConcentrationSubtree);
removeEmptySubTree(&mpMetaboliteRateConcentrationSubtree);
removeEmptySubTree(&mpMetaboliteSubtree);
// find all reactions and create items in the reaction subtree
const CCopasiVectorNS<CReaction>& reactions = pModel->getReactions();
maxCount = reactions.size();
for (counter = maxCount; counter != 0; --counter)
{
const CReaction* react = reactions[counter - 1];
std::string name = "flux(" + react->getObjectName() + ")";
pObject = react->getObject(CCopasiObjectName("Reference=Flux"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpReactionFluxConcentrationSubtree, FROM_UTF8(name));
treeItems[pItem] = pObject;
}
pObject = react->getObject(CCopasiObjectName("Reference=ParticleFlux"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpReactionFluxNumberSubtree, FROM_UTF8("particle " + name));
treeItems[pItem] = pObject;
}
// create items for the reaction parameters
pItem = new Q3ListViewItem(mpReactionParameterSubtree,
FROM_UTF8(react->getObjectName()));
const CCopasiParameterGroup & Parameters = react->getParameters();
unsigned int j;
unsigned int numParameters = Parameters.size();
for (j = numParameters; j != 0; --j)
{
const CCopasiParameter * pParameter = Parameters.getParameter(j - 1);
// We skip local parameters which ar covered by global parameters
if (!react->isLocalParameter(pParameter->getObjectName()))
continue;
pObject = pParameter->getObject(CCopasiObjectName("Reference=Value"));
if (filter(classes, pObject))
{
Q3ListViewItem * pParameterItem =
new Q3ListViewItem(pItem, FROM_UTF8(pParameter->getObjectName()));
treeItems[pParameterItem] = pObject;
}
}
removeEmptySubTree(&pItem);
}
removeEmptySubTree(&mpReactionFluxNumberSubtree);
removeEmptySubTree(&mpReactionFluxConcentrationSubtree);
removeEmptySubTree(&mpReactionParameterSubtree);
removeEmptySubTree(&mpReactionSubtree);
// find all global parameters (aka model values) variables
const CCopasiVector<CModelValue>& objects = pModel->getModelValues();
maxCount = objects.size();
for (counter = maxCount; counter != 0; --counter)
{
const CModelEntity* object = objects[counter - 1];
std::string name = object->getObjectName();
pObject = object->getObject(CCopasiObjectName("Reference=InitialValue"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpModelQuantityInitialValueSubtree, FROM_UTF8(name + "(t=0)"));
treeItems[pItem] = pObject;
}
pObject = object->getObject(CCopasiObjectName("Reference=Value"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpModelQuantityTransientValueSubtree, FROM_UTF8(name + "(t)"));
treeItems[pItem] = pObject;
}
if (object->getStatus() != CModelEntity::ASSIGNMENT)
{
pObject = object->getObject(CCopasiObjectName("Reference=Rate"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpModelQuantityRateSubtree, FROM_UTF8("d(" + name + ")/dt"));
treeItems[pItem] = pObject;
}
}
}
removeEmptySubTree(&mpModelQuantityRateSubtree);
removeEmptySubTree(&mpModelQuantityInitialValueSubtree);
removeEmptySubTree(&mpModelQuantityTransientValueSubtree);
removeEmptySubTree(&mpModelQuantitySubtree);
// find all compartments
const CCopasiVector<CCompartment>& objects2 = pModel->getCompartments();
maxCount = objects2.size();
for (counter = maxCount; counter != 0; --counter)
{
const CModelEntity* object = objects2[counter - 1];
std::string name = object->getObjectName();
pObject = object->getObject(CCopasiObjectName("Reference=InitialVolume"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpCompartmentInitialVolumeSubtree, FROM_UTF8(name + "(t=0)"));
treeItems[pItem] = pObject;
}
pObject = object->getObject(CCopasiObjectName("Reference=Volume"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpCompartmentTransientVolumeSubtree, FROM_UTF8(name + "(t)"));
treeItems[pItem] = pObject;
}
if (object->getStatus() != CModelEntity::ASSIGNMENT)
{
pObject = object->getObject(CCopasiObjectName("Reference=Rate"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(mpCompartmentRateSubtree, FROM_UTF8("d(" + name + ")/dt"));
treeItems[pItem] = pObject;
}
}
}
removeEmptySubTree(&mpCompartmentRateSubtree);
removeEmptySubTree(&mpCompartmentInitialVolumeSubtree);
removeEmptySubTree(&mpCompartmentTransientVolumeSubtree);
removeEmptySubTree(&mpCompartmentSubtree);
pObject = pModel->getObject(CCopasiObjectName("Reference=Avogadro Constant"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(this, "Avogadro Constant");
treeItems[pItem] = pObject;
}
pObject = pModel->getObject(CCopasiObjectName("Reference=Quantity Conversion Factor"));
if (filter(classes, pObject))
{
pItem = new Q3ListViewItem(this, "Quantity Conversion Factor");
treeItems[pItem] = pObject;
}
// find all model matrices
const CMatrix<C_FLOAT64> &StoiMatrix = pModel->getStoi();
if (StoiMatrix.array())
{
pObject = pModel->getObject(CCopasiObjectName("Array=Stoichiometry(ann)"));
if (filter(classes, pObject))
{
// pItem = new QListViewItem(matrixSubtree, "Stoichiometry(ann)");
pItem = new Q3ListViewItem(mpModelMatrixSubtree, FROM_UTF8(pObject->getObjectName()));
treeItems[pItem] = pObject;
}
}
const CMatrix<C_FLOAT64> &RedStoiMatrix = pModel->getRedStoi();
if (RedStoiMatrix.array())
{
pObject = pModel->getObject(CCopasiObjectName("Array=Reduced stoichiometry(ann)"));
if (filter(classes, pObject))
{
// pItem = new QListViewItem(matrixSubtree, "Reduced stoichiometry(ann)");
pItem = new Q3ListViewItem(mpModelMatrixSubtree, FROM_UTF8(pObject->getObjectName()));
treeItems[pItem] = pObject;
}
}
const CMatrix<C_FLOAT64> &LinkMatrix = pModel->getL0();
if (LinkMatrix.array())
{
pObject = pModel->getObject(CCopasiObjectName("Array=Link matrix(ann)"));
if (filter(classes, pObject))
{
// pItem = new QListViewItem(matrixSubtree, "Link matrix(ann)");
pItem = new Q3ListViewItem(mpModelMatrixSubtree, FROM_UTF8(pObject->getObjectName()));
treeItems[pItem] = pObject;
}
}
removeEmptySubTree(&mpModelMatrixSubtree);
// find all result matrices
// Metabolic Control Analysis
CCopasiTask *task;
assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
assert(pDataModel != NULL);
// MCA
task = dynamic_cast<CCopasiTask*>((*pDataModel->getTaskList())["Metabolic Control Analysis"]);
try
{
if (task && task->updateMatrices())
{
//for mca the result is in the method
CMCAMethod* pMethod = dynamic_cast<CMCAMethod *>(task->getMethod());
const CCopasiContainer::objectMap * pObjects = & pMethod->getObjects();
CCopasiContainer::objectMap::const_iterator its = pObjects->begin();
CArrayAnnotation *ann;
for (; its != pObjects->end(); ++its)
{
ann = dynamic_cast<CArrayAnnotation*>(its->second);
if (!ann) continue;
if (!ann->isEmpty() && filter(classes, ann))
{
pItem = new Q3ListViewItem(this->mpResultMCASubtree, FROM_UTF8(ann->getObjectName()));
treeItems[pItem] = ann;
}
}
}
}
catch (...)
{}
// Steady State
task = dynamic_cast<CCopasiTask *>((*pDataModel->getTaskList())["Steady-State"]);
try
{
if (task && task->updateMatrices())
{
//for steady state the results are in the task
const CCopasiContainer::objectMap * pObjects = & task->getObjects();
CCopasiContainer::objectMap::const_iterator its = pObjects->begin();
CArrayAnnotation *ann;
for (; its != pObjects->end(); ++its)
{
ann = dynamic_cast<CArrayAnnotation*>(its->second);
if (!ann) continue;
if (!ann->isEmpty() && filter(classes, ann))
{
pItem = new Q3ListViewItem(this->mpResultSteadyStateSubtree, FROM_UTF8(ann->getObjectName()));
treeItems[pItem] = ann;
}
}
}
}
catch (...)
{}
// Sensitivities
task = dynamic_cast<CCopasiTask *>((*pDataModel->getTaskList())["Sensitivities"]);
try
{
if (task && task->updateMatrices())
{
//for sensitivities the result is in the problem
CSensProblem *sens = dynamic_cast<CSensProblem *>(task->getProblem());
const CCopasiContainer::objectMap * pObjects = & sens->getObjects();
CCopasiContainer::objectMap::const_iterator its = pObjects->begin();
CArrayAnnotation *ann;
for (; its != pObjects->end(); ++its)
{
ann = dynamic_cast<CArrayAnnotation*>(its->second);
if (!ann) continue;
if (!ann->isEmpty() && filter(classes, ann))
{
pItem = new Q3ListViewItem(this->mpResultSensitivitySubtree, FROM_UTF8(ann->getObjectName()));
treeItems[pItem] = (CCopasiObject *) ann;
}
}
}
}
catch (...)
{}
removeEmptySubTree(&mpResultMCASubtree);
removeEmptySubTree(&mpResultSensitivitySubtree);
removeEmptySubTree(&mpResultSteadyStateSubtree);
removeEmptySubTree(&mpResultMatrixSubtree);
if (selectionMode() == Q3ListView::NoSelection)
{
// see if some objects are there, if yes set to single selection
Q3ListViewItemIterator it = Q3ListViewItemIterator(this);
while (it.current())
{
if (treeItems.find(it.current()) != treeItems.end())
{
setSelectionMode(Q3ListView::Single);
setCurrentItem(it.current());
it.current()->setSelected(true);
Q3ListViewItem* parent = it.current()->parent();
while (parent)
{
parent->setOpen(true);
parent = parent->parent();
}
break;
}
++it;
}
}
}
bool CExperimentSet::calculateStatistics()
{
mDependentObjectiveValues.resize(mDependentObjects.size());
mDependentObjectiveValues = 0.0;
mDependentRMS.resize(mDependentObjects.size());
mDependentRMS = 0.0;
mDependentErrorMean.resize(mDependentObjects.size());
mDependentErrorMean = 0.0;
mDependentErrorMeanSD.resize(mDependentObjects.size());
mDependentErrorMeanSD = 0.0;
mDependentDataCount.resize(mDependentObjects.size());
mDependentDataCount = 0;
mValidValueCount = 0;
// calculate the per experiment and per dependent value statistics.
std::vector< CExperiment * >::iterator it = mpExperiments->begin() + mNonExperiments;
std::vector< CExperiment * >::iterator end = mpExperiments->end();
size_t i, Count;
C_FLOAT64 Tmp;
for (; it != end; ++it)
{
(*it)->calculateStatistics();
const CObjectInterface ** ppObject = mDependentObjects.array();
const CObjectInterface ** ppEnd = ppObject + mDependentObjects.size();
for (i = 0; ppObject != ppEnd; ++ppObject, ++i)
{
Count = (*it)->getColumnValidValueCount(*ppObject);
if (Count)
{
mDependentObjectiveValues[i] += (*it)->getObjectiveValue(*ppObject);
Tmp = (*it)->getRMS(*ppObject);
mDependentRMS[i] += Tmp * Tmp * Count;
mDependentErrorMean[i] += (*it)->getErrorSum(*ppObject);
mDependentDataCount[i] += Count;
mValidValueCount += Count;
}
}
}
size_t imax = mDependentObjects.size();
for (i = 0; i != imax; i++)
{
Count = mDependentDataCount[i];
if (Count)
{
mDependentRMS[i] = sqrt(mDependentRMS[i] / Count);
mDependentErrorMean[i] /= Count;
}
else
{
mDependentRMS[i] = std::numeric_limits<C_FLOAT64>::quiet_NaN();
mDependentErrorMean[i] = std::numeric_limits<C_FLOAT64>::quiet_NaN();
}
}
it = mpExperiments->begin() + mNonExperiments;
// We need to loop again to calculate the std. deviation.
for (; it != end; ++it) //over experiments
{
const CObjectInterface ** ppObject = mDependentObjects.array();
const CObjectInterface ** ppEnd = ppObject + mDependentObjects.size();
for (i = 0; ppObject != ppEnd; ++ppObject, ++i)
{
Count = (*it)->getColumnValidValueCount(*ppObject);
if (Count)
mDependentErrorMeanSD[i] +=
(*it)->getErrorMeanSD(*ppObject, mDependentErrorMean[i]);
}
}
for (i = 0; i != imax; i++)
{
Count = mDependentDataCount[i];
if (Count)
mDependentErrorMeanSD[i] = sqrt(mDependentErrorMeanSD[i] / Count);
else
mDependentErrorMeanSD[i] = std::numeric_limits<C_FLOAT64>::quiet_NaN();
}
// This is the time to call the output handler to plot the fitted points.
for (it = mpExperiments->begin() + mNonExperiments, imax = 0; it != end; ++it)
imax = std::max(imax, (*it)->getDependentData().numRows());
CCopasiTask * pParentTask = dynamic_cast< CCopasiTask *>(getObjectAncestor("Task"));
assert(pParentTask != NULL);
for (i = 0; i < imax; i++)
{
for (it = mpExperiments->begin() + mNonExperiments; it != end; ++it)
(*it)->updateFittedPointValues(i, (*it)->getExperimentType() != CTaskEnum::Task::timeCourse); //false means without simulated data
pParentTask->output(COutputInterface::AFTER);
}
//now the extended time series
for (it = mpExperiments->begin() + mNonExperiments, imax = 0; it != end; ++it)
imax = std::max(imax, (*it)->extendedTimeSeriesSize());
for (i = 0; i < imax; i++)
{
for (it = mpExperiments->begin() + mNonExperiments; it != end; ++it)
{
if ((*it)->getExperimentType() == CTaskEnum::Task::timeCourse)
{
(*it)->updateFittedPointValuesFromExtendedTimeSeries(i);
}
}
pParentTask->output(COutputInterface::AFTER);
}
return true;
}