C++ CCopasiDataModel::getObject方法代码示例

bool CScanWidgetRandom::initFromScanItem(CCopasiParameterGroup * pg, const CModel* model)
{
  if (!model) return false;

  mpModel = model;

  unsigned C_INT32 * tmp;

  if (!(tmp = pg->getValue("Type").pUINT)) return false;

  if (*(CScanProblem::Type *) tmp != CScanProblem::SCAN_RANDOM)
    return false;

  std::string *pString;

  if (!(pString = pg->getValue("Object").pSTRING)) return false;

  if (*pString == "")
    mpObject = NULL;
  else
    {
      assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
      CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
      assert(pDataModel != NULL);
      mpObject = pDataModel->getObject(*pString);
    }

  if (mpObject)
    lineEditObject->setText(FROM_UTF8(mpObject->getObjectDisplayName()));
  else
    lineEditObject->setText("");

  if (!(tmp = pg->getValue("Distribution type").pUINT)) return false;

  comboBoxType->setCurrentItem(*tmp);
  changeType();

  lineEditMin->setText(getParameterValue(pg, "Minimum"));
  lineEditMax->setText(getParameterValue(pg, "Maximum"));

  bool * pBool;

  if (!(pBool = pg->getValue("log").pBOOL)) return false;

  checkBoxLog->setChecked(* pBool);

  return true;
}

bool
CQSpectogramWidget::LoadFromCurveSpec(const CPlotItem * pCurve)
{
  if (!pCurve)
    {
      // We need to reset the widget to defaults
      mpEditTitle->setText("");

      mpObjectX = mpObjectY = mpObjectZ = NULL;

      mpEditX->setText("");
      mpEditY->setText("");
      mpEditZ->setText("");

      mpCheckBefore->setChecked(false);
      mpCheckDuring->setChecked(true);
      mpCheckAfter->setChecked(false);

      return true;
    }

  if (pCurve->getType() != CPlotItem::spectogram) return false;

  //if (pCurve->getChannels().getSize != 3) return false;

  mpEditTitle->setText(FROM_UTF8(pCurve->getTitle()));

  //TODO: check if objects exist....
  assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
  CCopasiDataModel* pDataModel = &CCopasiRootContainer::getDatamodelList()->operator[](0);
  assert(pDataModel != NULL);
  mpObjectX = mpObjectY = mpObjectZ = NULL;

  if (pCurve->getChannels().size() >= 1)
    mpObjectX = dynamic_cast<const CCopasiObject*>(pDataModel->getObject(pCurve->getChannels()[0]));

  if (pCurve->getChannels().size() >= 2)
    mpObjectY = dynamic_cast<const CCopasiObject*>(pDataModel->getObject(pCurve->getChannels()[1]));

  if (pCurve->getChannels().size() >= 3)
    {
      mpObjectZ = dynamic_cast<const CCopasiObject*>(pDataModel->getObject(pCurve->getChannels()[2]));

      if ((mpObjectZ->getObjectDisplayName() == "(CN)Root") && mpObjectY)
        mpObjectZ = mpObjectY;  // as long as we haven't a second Y-axis chooser, this has to suffice.
    }

  if (mpObjectX)
    mpEditX->setText(FROM_UTF8(mpObjectX->getObjectDisplayName()));
  else
    mpEditX->clear();

  if (mpObjectY)
    mpEditY->setText(FROM_UTF8(mpObjectY->getObjectDisplayName()));
  else
    mpEditY->clear();

  if (mpObjectZ)
    mpEditZ->setText(FROM_UTF8(mpObjectZ->getObjectDisplayName()));
  else
    mpEditZ->clear();

  CPlotItem* pItem = const_cast<CPlotItem*>(pCurve);

  mpLogZ->setChecked(*pItem->assertParameter("logZ", CCopasiParameter::BOOL, false));
  mpBilinear->setChecked(*pItem->assertParameter("bilinear", CCopasiParameter::BOOL, true));
  std::string *contours = pItem->assertParameter("contours", CCopasiParameter::STRING, std::string(""));
  mpContours->setText(FROM_UTF8(*contours));
  std::string *maxZ = pItem->assertParameter("maxZ", CCopasiParameter::STRING, std::string(""));
  mpMaxZ->setText(FROM_UTF8(*maxZ));
  std::string *colorMap = pItem->assertParameter("colorMap", CCopasiParameter::STRING, std::string("Default"));
  mpColorMap->setCurrentIndex(mpColorMap->findText(FROM_UTF8(*colorMap)));

  mpCheckBefore->setChecked(pCurve->getActivity() & COutputInterface::BEFORE);
  mpCheckDuring->setChecked(pCurve->getActivity() & COutputInterface::DURING);
  mpCheckAfter->setChecked(pCurve->getActivity() & COutputInterface::AFTER);

  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)
            {
//.........这里部分代码省略.........

bool
BandedGraphWidget::LoadFromCurveSpec(const CPlotItem * pCurve)
{
  if (!pCurve)
    {
      // We need to reset the widget to defaults
      mpEditTitle->setText("");

      mpObjectX = mpObjectYone = mpObjectYtwo = NULL;

      mpEditX->setText("");
      mpEditYone->setText("");
      mpEditYtwo->setText("");

      mpCheckBefore->setChecked(false);
      mpCheckDuring->setChecked(true);
      mpCheckAfter->setChecked(false);

      return true;
    }

  if (pCurve->getType() != CPlotItem::bandedGraph) return false;

  //if (pCurve->getChannels().getSize != 3) return false;

  mpEditTitle->setText(FROM_UTF8(pCurve->getTitle()));

  CCopasiDataModel* pDataModel = pCurve->getObjectDataModel();
  assert(pDataModel != NULL);

  mpObjectX = mpObjectYone = mpObjectYtwo = NULL;

  if (pCurve->getChannels().size() >= 1)
    mpObjectX = dynamic_cast<const CCopasiObject*>(pDataModel->getObject(pCurve->getChannels()[0]));

  if (pCurve->getChannels().size() >= 2)
    mpObjectYone = dynamic_cast<const CCopasiObject*>(pDataModel->getObject(pCurve->getChannels()[1]));

  if (pCurve->getChannels().size() >= 3)
    {
      mpObjectYtwo = dynamic_cast<const CCopasiObject*>(pDataModel->getObject(pCurve->getChannels()[2]));

      if ((mpObjectYtwo->getObjectDisplayName() == "(CN)Root") && mpObjectYone)
        mpObjectYtwo = mpObjectYone;  // as long as we haven't a second Y-axis chooser, this has to suffice.
    }

  if (mpObjectX)
    mpEditX->setText(FROM_UTF8(mpObjectX->getObjectDisplayName()));
  else
    mpEditX->clear();

  if (mpObjectYone)
    mpEditYone->setText(FROM_UTF8(mpObjectYone->getObjectDisplayName()));
  else
    mpEditYone->clear();

  if (mpObjectYtwo)
    mpEditYtwo->setText(FROM_UTF8(mpObjectYtwo->getObjectDisplayName()));
  else
    mpEditYtwo->clear();

  mpCheckBefore->setChecked(pCurve->getActivity() & COutputInterface::BEFORE);
  mpCheckDuring->setChecked(pCurve->getActivity() & COutputInterface::DURING);
  mpCheckAfter->setChecked(pCurve->getActivity() & COutputInterface::AFTER);

  return true;
}

void CQFittingResult::slotSave(void)
{
  C_INT32 Answer = QMessageBox::No;
  QString fileName;

  while (Answer == QMessageBox::No)
    {
      fileName =
        CopasiFileDialog::getSaveFileName(this, "Save File Dialog",
                                          QString::null, "TEXT Files (*.txt);;All Files (*.*);;", "Save to");

      if (fileName.isEmpty()) return;

      if (!fileName.endsWith(".txt") &&
          !fileName.endsWith(".")) fileName += ".txt";

      fileName = fileName.remove(QRegExp("\\.$"));

      Answer = checkSelection(fileName);

      if (Answer == QMessageBox::Cancel) return;
    }

  std::ofstream file(utf8ToLocale(TO_UTF8(fileName)).c_str());

  if (file.fail()) return;

  unsigned C_INT32 i, imax;

  // The global result and statistics
  file << "Objective Value\tRoot Mean Square\tStandard Deviation" << std::endl;
  file << mpProblem->getSolutionValue() << "\t";
  file << mpProblem->getRMS() << "\t";
  file << mpProblem->getStdDeviation() << std::endl;

  file << "Function Evaluations\tCPU Time [s]\tEvaluations/second [1/s]" << std::endl;
  const unsigned C_INT32 & FunctionEvaluations = mpProblem->getFunctionEvaluations();
  const C_FLOAT64 & ExecutionTime = mpProblem->getExecutionTime();
  file << FunctionEvaluations << "\t";
  file << ExecutionTime << "\t";
  file << FunctionEvaluations / ExecutionTime << std::endl;

  // Set up the parameters table
  file << std::endl << "Parameters:" << std::endl;
  file << "Parameter\tValue\tStd. Deviation\tCoeff. of Variation [%]\tGradient" << std::endl;

  // Loop over the optimization items
  const std::vector< COptItem * > & Items = mpProblem->getOptItemList();
  const CVector< C_FLOAT64 > & Solutions = mpProblem->getSolutionVariables();
  const CVector< C_FLOAT64 > & StdDeviations = mpProblem->getVariableStdDeviations();
  const CVector< C_FLOAT64 > & Gradients = mpProblem->getVariableGradients();

  imax = Items.size();

  if (mpProblem->getFunctionEvaluations() == 0)
    imax = 0;

  assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
  CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
  assert(pDataModel != NULL);

  for (i = 0; i != imax; i++)
    {
      const CCopasiObject *pObject =
        pDataModel->getObject(Items[i]->getObjectCN());

      if (pObject)
        {
          std::string Experiments =
            static_cast<CFitItem *>(Items[i])->getExperiments();

          if (Experiments != "")
            Experiments = "; {" + Experiments + "}";

          file << pObject->getObjectDisplayName() << Experiments << "\t";
        }
      else
        file << "Not Found\t";

      const C_FLOAT64 & Solution = Solutions[i];
      file << Solution << "\t";
      const C_FLOAT64 & StdDeviation = StdDeviations[i];
      file << StdDeviation << "\t";
      file << fabs(100.0 * StdDeviation / Solution) << "\t";
      file << Gradients[i] << std::endl;
    }

  // Set up the experiments table
  file << std::endl << "Experiments:" << std::endl;
  file << "Experiment\tObjective Value\tRoot Mean Square\tError Mean\tError Mean Std. Deviation" << std::endl;

  // Loop over the experiments
  const CExperimentSet & Experiments = mpProblem->getExperiementSet();

  imax = Experiments.getExperimentCount();

  if (mpProblem->getFunctionEvaluations() == 0)
    imax = 0;

  for (i = 0; i != imax; i++)
//.........这里部分代码省略.........

bool CQFittingResult::enterProtected()
{
  assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
  CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
  assert(pDataModel != NULL);
  mpTask =
    dynamic_cast<CFitTask *>((*pDataModel->getTaskList())["Parameter Estimation"]);

  if (!mpTask) return false;

  mpProblem = dynamic_cast<const CFitProblem *>(mpTask->getProblem());

  if (!mpProblem) return false;

  mpMain->load(mpProblem);

  unsigned C_INT32 i, imax;

  // Loop over the optimization items
  const std::vector< COptItem * > & Items = mpProblem->getOptItemList();
  const CVector< C_FLOAT64 > & Solutions = mpProblem->getSolutionVariables();
  const CVector< C_FLOAT64 > & StdDeviations = mpProblem->getVariableStdDeviations();
  const CVector< C_FLOAT64 > & Gradients = mpProblem->getVariableGradients();

  imax = Items.size();

  if (mpProblem->getFunctionEvaluations() == 0)
    imax = 0;

  mpParameters->setNumRows(imax);

  for (i = 0; i != imax; i++)
    {
      const CCopasiObject *pObject =
        pDataModel->getObject(Items[i]->getObjectCN());

      if (pObject)
        {
          std::string Experiments =
            static_cast<CFitItem *>(Items[i])->getExperiments();

          if (Experiments != "")
            Experiments = "; {" + Experiments + "}";

          mpParameters->setText(i, 0, FROM_UTF8(pObject->getObjectDisplayName() + Experiments));
        }
      else
        mpParameters->setText(i, 0, "Not Found");

      const C_FLOAT64 & Solution = Solutions[i];
      mpParameters->setText(i, 1, QString::number(Solution));
      const C_FLOAT64 & StdDeviation = StdDeviations[i];
      mpParameters->setText(i, 2, QString::number(StdDeviation));
      mpParameters->setText(i, 3, QString::number(fabs(100.0 * StdDeviation / Solution)));
      mpParameters->setText(i, 4, QString::number(Gradients[i]));
    }

  for (i = 0, imax = mpParameters->numCols(); i != imax; i++)
    mpParameters->adjustColumn(i);

  // Loop over the experiments
  const CExperimentSet & Experiments = mpProblem->getExperiementSet();

  imax = Experiments.getExperimentCount();

  if (mpProblem->getFunctionEvaluations() == 0)
    imax = 0;

  mpExperiments->setNumRows(imax);

  for (i = 0; i != imax; i++)
    {
      const CExperiment & Experiment = * Experiments.getExperiment(i);
      mpExperiments->setText(i, 0, FROM_UTF8(Experiment.getObjectName()));
      mpExperiments->setText(i, 1, QString::number(Experiment.getObjectiveValue()));
      mpExperiments->setText(i, 2, QString::number(Experiment.getRMS()));

      mpExperiments->setText(i, 3, QString::number(Experiment.getErrorMean()));
      mpExperiments->setText(i, 4, QString::number(Experiment.getErrorMeanSD()));
    }

  for (i = 0, imax = mpExperiments->numCols(); i != imax; i++)
    mpExperiments->adjustColumn(i);

  // Loop over the dependent objects
  imax = Experiments.getDependentObjects().size();

  if (mpProblem->getFunctionEvaluations() == 0)
    imax = 0;

  mpValues->setNumRows(imax);

  for (i = 0; i != imax; i++)
    {
      const CCopasiObject * pObject = Experiments.getDependentObjects()[i];

      if (pObject)
        mpValues->setText(i, 0, FROM_UTF8(pObject->getObjectDisplayName()));
      else
        mpValues->setText(i, 0, "Not Found");
//.........这里部分代码省略.........