bool CReportDefinition::preCompileTable(const std::vector< CCopasiContainer * > & listOfContainer)
{
bool success = true;
mHeaderVector.clear();
mBodyVector.clear();
mFooterVector.clear();
std::vector<CRegisteredObjectName>::const_iterator it = mTableVector.begin();
std::vector<CRegisteredObjectName>::const_iterator end = mTableVector.end();
CCopasiDataModel* pDataModel = getObjectDataModel();
CCopasiObject * pObject;
for (; it != end; ++it)
{
pObject = pDataModel->ObjectFromName(listOfContainer, *it);
if (pObject != NULL)
{
addTableElement(pObject);
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCCopasiTask + 6, it->c_str());
}
}
return success;
}
bool CFitProblem::initialize()
{
mHaveStatistics = false;
if (!COptProblem::initialize())
{
while (CCopasiMessage::peekLastMessage().getNumber() == MCOptimization + 5 ||
CCopasiMessage::peekLastMessage().getNumber() == MCOptimization + 7)
CCopasiMessage::getLastMessage();
if (CCopasiMessage::getHighestSeverity() > CCopasiMessage::WARNING &&
CCopasiMessage::peekLastMessage().getNumber() != MCCopasiMessage + 1)
return false;
}
std::vector< CCopasiContainer * > ContainerList;
ContainerList.push_back(getObjectAncestor("Vector"));
CCopasiDataModel* pDataModel = getObjectDataModel();
assert(pDataModel != NULL);
mpSteadyState =
dynamic_cast< CSteadyStateTask * >(pDataModel->ObjectFromName(ContainerList, *mpParmSteadyStateCN));
if (mpSteadyState == NULL)
mpSteadyState =
static_cast<CSteadyStateTask *>((*pDataModel->getTaskList())["Steady-State"]);
// We only need to initialize the steady-state task if steady-state data is present.
if (mpExperimentSet->hasDataForTaskType(CCopasiTask::steadyState))
{
mpSteadyState->initialize(CCopasiTask::NO_OUTPUT, NULL, NULL);
}
mpTrajectory =
dynamic_cast< CTrajectoryTask * >(pDataModel->ObjectFromName(ContainerList, *mpParmTimeCourseCN));
if (mpTrajectory == NULL)
mpTrajectory =
static_cast<CTrajectoryTask *>((*pDataModel->getTaskList())["Time-Course"]);
// We only need to initialize the trajectory task if time course data is present.
if (mpExperimentSet->hasDataForTaskType(CCopasiTask::timeCourse))
{
mpTrajectory->initialize(CCopasiTask::NO_OUTPUT, NULL, NULL);
}
ContainerList.clear();
ContainerList.push_back(mpModel);
CFitTask * pTask = dynamic_cast<CFitTask *>(getObjectParent());
if (pTask)
{
ContainerList.push_back(pTask);
ContainerList.push_back(mpSteadyState);
ContainerList.push_back(mpTrajectory);
}
if (!mpExperimentSet->compile(ContainerList)) return false;
// Build a matrix of experiment and experiment local items.
mExperimentUpdateMethods.resize(mpExperimentSet->getExperimentCount(),
mpOptItems->size());
mExperimentUpdateMethods = NULL;
mExperimentInitialRefreshes.resize(mpExperimentSet->getExperimentCount());
std::vector< std::set< const CCopasiObject * > > ObjectSet;
ObjectSet.resize(mpExperimentSet->getExperimentCount());
std::vector<COptItem * >::iterator it = mpOptItems->begin();
std::vector<COptItem * >::iterator end = mpOptItems->end();
std::vector<COptItem * >::iterator itTmp;
CFitItem * pItem;
unsigned C_INT32 i, imax;
unsigned C_INT32 j;
unsigned C_INT32 Index;
imax = mSolutionVariables.size();
mFisher.resize(imax, imax);
mpFisherMatrix->resize();
mCorrelation.resize(imax, imax);
mpCorrelationMatrix->resize();
for (j = 0; it != end; ++it, j++)
{
pItem = static_cast<CFitItem *>(*it);
pItem->updateBounds(mpOptItems->begin());
std::string Annotation = pItem->getObjectDisplayName();
imax = pItem->getExperimentCount();
if (imax == 0)
{
for (i = 0, imax = mpExperimentSet->getExperimentCount(); i < imax; i++)
{
mExperimentUpdateMethods(i, j) = pItem->COptItem::getUpdateMethod();
ObjectSet[i].insert(pItem->getObject());
}
}
else
{
Annotation += "; {" + pItem->getExperiments() + "}";
for (i = 0; i < imax; i++)
{
if ((Index = mpExperimentSet->keyToIndex(pItem->getExperiment(i))) == C_INVALID_INDEX)
return false;
mExperimentUpdateMethods(Index, j) = pItem->COptItem::getUpdateMethod();
ObjectSet[Index].insert(pItem->getObject());
};
}
mpFisherMatrix->setAnnotationString(0, j, Annotation);
mpFisherMatrix->setAnnotationString(1, j, Annotation);
mpCorrelationMatrix->setAnnotationString(0, j, Annotation);
mpCorrelationMatrix->setAnnotationString(1, j, Annotation);
}
for (i = 0, imax = mpExperimentSet->getExperimentCount(); i < imax; i++)
mExperimentInitialRefreshes[i] = mpModel->buildInitialRefreshSequence(ObjectSet[i]);
// Build a matrix of experiment and constraint items;
mExperimentConstraints.resize(mpExperimentSet->getExperimentCount(),
mpConstraintItems->size());
mExperimentConstraints = NULL;
mExperimentConstraintRefreshes.resize(mpExperimentSet->getExperimentCount());
ObjectSet.clear();
ObjectSet.resize(mpExperimentSet->getExperimentCount());
it = mpConstraintItems->begin();
end = mpConstraintItems->end();
CFitConstraint * pConstraint;
std::set< const CCopasiObject * >::const_iterator itDepend;
std::set< const CCopasiObject * >::const_iterator endDepend;
for (j = 0; it != end; ++it, j++)
{
pConstraint = static_cast<CFitConstraint *>(*it);
itDepend = pConstraint->getDirectDependencies().begin();
endDepend = pConstraint->getDirectDependencies().end();
imax = pConstraint->getExperimentCount();
if (imax == 0)
{
for (i = 0, imax = mpExperimentSet->getExperimentCount(); i < imax; i++)
{
mExperimentConstraints(i, j) = pConstraint;
ObjectSet[i].insert(itDepend, endDepend);
}
}
else
{
for (i = 0; i < imax; i++)
{
if ((Index = mpExperimentSet->keyToIndex(pConstraint->getExperiment(i))) == C_INVALID_INDEX)
return false;
mExperimentConstraints(Index, j) = pConstraint;
ObjectSet[Index].insert(itDepend, endDepend);
};
}
}
for (i = 0, imax = mpExperimentSet->getExperimentCount(); i < imax; i++)
mExperimentConstraintRefreshes[i] = CCopasiObject::buildUpdateSequence(ObjectSet[i], mpModel->getUptoDateObjects());
mExperimentDependentValues.resize(mpExperimentSet->getDataPointCount());
if (!mpSteadyState)
{
mpSteadyState =
dynamic_cast< CSteadyStateTask * >((*pDataModel->getTaskList())["Steady-State"]);
if (mpSteadyState == NULL) fatalError();
setValue("Steady-State", mpSteadyState->getKey());
mpSteadyState->initialize(CCopasiTask::NO_OUTPUT, NULL, NULL);
ContainerList.push_back(mpSteadyState);
}
if (!mpTrajectory)
{
mpTrajectory =
dynamic_cast< CTrajectoryTask * >((*pDataModel->getTaskList())["Time-Course"]);
if (mpTrajectory == NULL) fatalError();
setValue("Time-Course", mpTrajectory->getKey());
mpTrajectory->initialize(CCopasiTask::NO_OUTPUT, NULL, NULL);
ContainerList.push_back(mpTrajectory);
}
pdelete(mpTrajectoryProblem);
mpTrajectoryProblem =
new CTrajectoryProblem(*static_cast<CTrajectoryProblem *>(mpTrajectory->getProblem()));
static_cast<CTrajectoryProblem *>(mpTrajectory->getProblem())->setStepNumber(1);
pdelete(mpInitialState);
mpInitialState = new CState(mpModel->getInitialState());
return true;
}
