C++ CCopasiDataModel::getPlotDefinitionList方法代码示例

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";
}

void CQPlotsWidget::slotBtnDeactivateAllClicked()
{
  CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
  assert(pDataModel != NULL);

  if (!pDataModel->getModel())
    return;

  for (size_t i = 0; i < pDataModel->getPlotDefinitionList()->size(); i++)
    {
      CPlotSpecification *pPS = static_cast<CPlotSpecification *>(pDataModel->getPlotDefinitionList()->operator[](i));
      pPS->setActive(false);
    }

  mpTblPlots->doItemsLayout();
}

void CSEDMLExporter::createSEDMLDocument(CCopasiDataModel& dataModel, std::string modelRef)
{
  const SedDocument* pOldSEDMLDocument = NULL; //dataModel.getCurrentSEDMLDocument();
  const CModel* pModel = dataModel.getModel();
  COutputDefinitionVector *plotDef = dataModel.getPlotDefinitionList();
  assert(plotDef != NULL); //need to emit a message
  assert(pModel != NULL);

  if (pOldSEDMLDocument == NULL)
    {
      this->mpSEDMLDocument = new SedDocument(mSEDMLLevel, mSEDMLVersion);
    }
  else
    {
      this->mpSEDMLDocument = dynamic_cast<SedDocument*>(pOldSEDMLDocument->clone());
    }

  if (this->mpSEDMLDocument == NULL) fatalError();

  createModels(dataModel, modelRef);
  createTasks(dataModel,  modelRef);
}

/**
 * Creates the data generators for SEDML.
 */
void CSEDMLExporter::createDataGenerators(CCopasiDataModel & dataModel, std::string & taskId)
{
  const CModel* pModel = dataModel.getModel();
  std::vector<std::string> stringsContainer; //split string container

  if (pModel == NULL)
    CCopasiMessage(CCopasiMessage::ERROR, "No model for this SEDML document. An SBML model must exist for every SEDML document.");

  SedPlot2D* pPSedPlot;
  SedCurve* pCurve; // = pPSedPlot->createCurve();

  //create generator for special varibale time
  const CCopasiObject* pTime = static_cast<const CCopasiObject *>(dataModel.getModel()->getObject(CCopasiObjectName("Reference=Time")));
  SedDataGenerator *pTimeDGenp = this->mpSEDMLDocument->createDataGenerator();
  pTimeDGenp->setId("time");
  pTimeDGenp->setName(pTime->getObjectName());
  SedVariable *pTimeVar = pTimeDGenp->createVariable();
  pTimeVar->setId("var_time");
  pTimeVar->setTaskReference(taskId);
  pTimeVar->setSymbol(SEDML_TIME_URN);
  pTimeDGenp->setMath(SBML_parseFormula(pTimeVar->getId().c_str()));

  size_t i, imax = dataModel.getPlotDefinitionList()->size();
  SedDataGenerator *pPDGen;

  if (!imax)
    CCopasiMessage(CCopasiMessage::ERROR, "No plot definition for this SEDML document.");

  for (i = 0; i < imax; i++)
    {
      pPSedPlot = this->mpSEDMLDocument->createPlot2D();
      const CPlotSpecification* pPlot = (*dataModel.getPlotDefinitionList())[i];
      std::string plotName = pPlot->getObjectName();

      SEDMLUtils::removeCharactersFromString(plotName, "[]");

      pPSedPlot->setId(SEDMLUtils::getNextId("plot", mpSEDMLDocument->getNumOutputs()));
      pPSedPlot->setName(plotName);

      size_t j, jmax = pPlot->getItems().size();

      for (j = 0; j < jmax; j++)
        {
          const CPlotItem* pPlotItem = pPlot->getItems()[j];

          CCopasiObject *objectX, *objectY;

          if (pPlotItem->getChannels().size() >= 1)
            objectX = dataModel.getDataObject(pPlotItem->getChannels()[0]);

          bool xIsTime = objectX->getCN() == pTime->getCN();

          if (pPlotItem->getChannels().size() >= 2)
            objectY = dataModel.getDataObject(pPlotItem->getChannels()[1]);

          const std::string& type = objectY->getObjectName();
          std::string yAxis = objectY->getObjectDisplayName();
          std::string targetXPathString = SEDMLUtils::getXPathAndName(yAxis, type,
                                          pModel, dataModel);

          if (targetXPathString.empty())
            {
              continue;
            }

          pPDGen = createDataGenerator(
                     this->mpSEDMLDocument,
                     yAxis,
                     targetXPathString,
                     taskId,
                     i,
                     j
                   );

          pCurve = pPSedPlot->createCurve();
          std::ostringstream idCurveStrStream;
          idCurveStrStream << "p";
          idCurveStrStream << i + 1;
          idCurveStrStream << "_curve_";
          idCurveStrStream << j + 1;
          pCurve->setId(idCurveStrStream.str());
          pCurve->setLogX(pPlot->isLogX());
          pCurve->setLogY(pPlot->isLogY());
          pCurve->setYDataReference(pPDGen->getId());

          if (xIsTime)
            {
              pCurve->setXDataReference(pTimeDGenp->getId());
            }
          else
            {
              const std::string& typeX = objectX->getObjectName();
              std::string xAxis = objectX->getObjectDisplayName();
              std::string targetXPathStringX = SEDMLUtils::getXPathAndName(xAxis, typeX,
                                               pModel, dataModel);

              pPDGen = createDataGenerator(
//.........这里部分代码省略.........

/**
 * Creates the data generators for SEDML.
 */
void CSEDMLExporter::createDataGenerators(CCopasiDataModel & dataModel,
    std::string & taskId,
    CCopasiTask* task)
{
  const CModel* pModel = dataModel.getModel();
  std::vector<std::string> stringsContainer; //split string container

  if (pModel == NULL)
    CCopasiMessage(CCopasiMessage::ERROR, "SED-ML: No model for this SED-ML document. An SBML model must exist for every SED-ML document.");

  SedPlot2D* pPSedPlot;
  SedCurve* pCurve; // = pPSedPlot->createCurve();

  //create generator for special varibale time
  const CCopasiObject* pTime = static_cast<const CCopasiObject *>(dataModel.getModel()->getObject(CCopasiObjectName("Reference=Time")));
  SedDataGenerator *pTimeDGenp = this->mpSEDMLDocument->createDataGenerator();
  pTimeDGenp->setId("time");
  pTimeDGenp->setName(pTime->getObjectName());
  SedVariable *pTimeVar = pTimeDGenp->createVariable();
  pTimeVar->setId("var_time");
  pTimeVar->setTaskReference(taskId);
  pTimeVar->setSymbol(SEDML_TIME_URN);
  pTimeDGenp->setMath(SBML_parseFormula(pTimeVar->getId().c_str()));

  size_t i, imax = dataModel.getPlotDefinitionList()->size();
  SedDataGenerator *pPDGen;

  if (imax == 0 && (task == NULL || task->getReport().getTarget().empty()))
    CCopasiMessage(CCopasiMessage::ERROR, "SED-ML: No plot/report definition for this SED-ML document.");

  // export report
  if (task != NULL && !task->getReport().getTarget().empty())
    {
      CReportDefinition* def = task->getReport().getReportDefinition();

      if (def != NULL)
        {
          SedReport* pReport = mpSEDMLDocument->createReport();
          std::string name = def->getObjectName();
          SEDMLUtils::removeCharactersFromString(name, "[]");
          //
          pReport->setId(SEDMLUtils::getNextId("report", mpSEDMLDocument->getNumOutputs()));
          pReport->setName(name);

          std::vector<CRegisteredObjectName> header = *def->getHeaderAddr();
          std::vector<CRegisteredObjectName> body =
            def->isTable() ? *def->getTableAddr() :
            *def->getBodyAddr();

          int dsCount = 0;

          for (size_t i = 0; i < body.size(); ++i)
            {
              CRegisteredObjectName& current = body[i];

              if (current == def->getSeparator().getCN()) continue;

              CCopasiObject *object = dataModel.getDataObject(current);

              if (object == NULL) continue;

              const std::string& typeX = object->getObjectName();
              std::string xAxis = object->getObjectDisplayName();

              std::string targetXPathStringX = SEDMLUtils::getXPathAndName(xAxis, typeX,
                                               pModel, dataModel);

              if (object->getCN() == pTime->getCN())
                pPDGen = pTimeDGenp;
              else
                pPDGen = createDataGenerator(
                           this->mpSEDMLDocument,
                           xAxis,
                           targetXPathStringX,
                           taskId,
                           i,
                           0
                         );

              SedDataSet* pDS = pReport->createDataSet();
              pDS->setId(SEDMLUtils::getNextId("ds", ++dsCount));

              if (def->isTable())
                {
                  CCopasiObject *headerObj = NULL;

                  if (header.size() > i)
                    headerObj = dataModel.getDataObject(header[i]);
                  else
                    headerObj = dataModel.getDataObject(body[i]);

                  if (headerObj != NULL)
                    pDS->setLabel(headerObj->getObjectDisplayName());
                  else
                    pDS->setLabel(xAxis);
                }
              else
//.........这里部分代码省略.........