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

//.........这里部分代码省略.........
    }
  else
    {
      std::cerr << "Invalid method type. Valid options are:" << std::endl;
      std::cerr << "    stochastic" << std::endl;
      std::cerr << "    directMethod" << std::endl;
      std::cerr << "    tauLeap" << std::endl;
    }

  if (endTime == 0.0)
    {
      std::cerr << "Invalid endtime " << pEndTime << std::endl;
      exit(1);
    }

  if (stepNumber == 0.0)
    {
      std::cerr << "Invalid step number " << pStepNumber << std::endl;
      exit(1);
    }

  for (i = NUMARGS; i < iMax; ++i)
    {
      pSBMLSpeciesIds[i - NUMARGS] = argv[i];
      //std::cout << "Copying pointer to " <<  argv[i]  << "." << std::endl;
    }

  try
    {
      // Create the global data model.
      CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();

      // Import the SBML File
      pDataModel->importSBML(pSBMLFilename);

      //pDataModel->getModel()->forceCompile();

      // create a report with the correct filename and all the species against
      // time.
      CReportDefinitionVector* pReports = pDataModel->getReportDefinitionList();
      CReportDefinition* pReport = pReports->createReportDefinition("Report", "Output for stochastic testsuite run");
      pReport->setTaskType(CCopasiTask::timeCourse);
      pReport->setIsTable(false);

      CCopasiReportSeparator Separator(std::string(","));
      pReport->setSeparator(Separator);

      std::vector<CRegisteredObjectName> * pHeader = pReport->getHeaderAddr();
      std::vector<CRegisteredObjectName> * pBody = pReport->getBodyAddr();

      // Add time column
      pHeader->push_back(CCopasiStaticString("time").getCN());
      pBody->push_back(CCopasiObjectName(pDataModel->getModel()->getCN() + ",Reference=Time"));

      iMax = iMax - NUMARGS;
      const CCopasiVector<CMetab>& metabolites = pDataModel->getModel()->getMetabolites();

      for (i = 0; i < iMax; ++i)
        {
          pHeader->push_back(Separator.getCN());
          pBody->push_back(Separator.getCN());

          unsigned int j, jMax = metabolites.size();

          std::string SBMLId = unQuote(pSBMLSpeciesIds[i]);

int main(int argc, char *argv[])
{
  // Parse the commandline options
  // first argument is the SBML filename
  // second argument is the endtime
  // third argument is the step number
  // fourth argument is the filename where the results are to be written
  // fifth argument is the tmp directory (this is not needed)
  // the rest of the arguments are species names for the result
  try
    {
      // Create the root container.
      CCopasiRootContainer::init(0, NULL, false);
    }

  catch (copasi::autoexcept &e)
    {}

  catch (copasi::option_error &e)
    {}

  if (argc < 5)
    {
      std::cout << "Usage: semantic-test-suite SBMLFILENAME ENDTIME STEPNUMBER OUTFILENAME TMPDIR SPECIESID1 SPECIESID2 ..." << std::endl;
      exit(1);
    }

  char* pSBMLFilename = argv[1];
  const char* pEndTime = argv[2];
  const char* pStepNumber = argv[3];
  char* pOutputFilename = argv[4];
  //char* pTmpDirectory=argv[5];
  char** pSBMLSpeciesIds = new char * [argc - 6];
  unsigned int i, iMax = argc;
  CTrajectoryTask* pTrajectoryTask = NULL;

  std::string CWD = COptions::getPWD();
  double endTime = strToDouble(pEndTime, &pEndTime);
  double stepNumber = strToDouble(pStepNumber, &pStepNumber);

  if (endTime == 0.0)
    {
      std::cerr << "Invalid endtime " << pEndTime << std::endl;
      exit(1);
    }

  if (stepNumber == 0.0)
    {
      std::cerr << "Invalid step number " << pStepNumber << std::endl;
      exit(1);
    }

  for (i = 6; i < iMax; ++i)
    {
      pSBMLSpeciesIds[i - 6] = argv[i];
      //std::cout << "Copying pointer to " <<  argv[i]  << "." << std::endl;
    }

  try
    {
      // Create the global data model.
      CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();

      // Import the SBML File
      pDataModel->importSBML(pSBMLFilename);

      //pDataModel->getModel()->forceCompile();

      // create a report with the correct filename and all the species against
      // time.
      CReportDefinitionVector* pReports = pDataModel->getReportDefinitionList();
      CReportDefinition* pReport = pReports->createReportDefinition("Report", "Output for SBML testsuite run");
      pReport->setTaskType(CCopasiTask::timeCourse);
      pReport->setIsTable(true);

      std::vector<CRegisteredObjectName>* pTable = pReport->getTableAddr();
      pTable->push_back(CCopasiObjectName(pDataModel->getModel()->getCN() + ",Reference=Time"));
      iMax = iMax - 6;
      const CCopasiVector<CMetab>& metabolites = pDataModel->getModel()->getMetabolites();

      for (i = 0; i < iMax; ++i)
        {
          unsigned int j, jMax = metabolites.size();

          for (j = 0; j < jMax; ++j)
            {
              if (metabolites[j]->getSBMLId() == pSBMLSpeciesIds[i])
                {
                  pTable->push_back(metabolites[j]->getObject(CCopasiObjectName("Reference=Concentration"))->getCN());
                  //std::cout << "adding metabolite " << metabolites[j]->getObjectName() << " to report." << std::endl;
                  break;
                }
            }

          if (j == jMax)
            {
              std::cerr << "Could not find a metabolite for the SBML id " << pSBMLSpeciesIds[i] << std::endl;
              exit(1);
            }
        }
//.........这里部分代码省略.........

int main(int argc, char** argv)
{
  // initialize the backend library
  CCopasiRootContainer::init(argc, argv);
  assert(CCopasiRootContainer::getRoot() != NULL);
  // create a new datamodel
  CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();
  assert(CCopasiRootContainer::getDatamodelList()->size() == 1);

  // the only argument to the main routine should be the name of an SBML file
  if (argc == 2)
    {
      std::string filename = argv[1];

      try
        {
          // load the model without progress report
          pDataModel->importSBML(filename, NULL);
        }
      catch (...)
        {
          std::cerr << "Error while importing the model from file named \"" << filename << "\"." << std::endl;
          CCopasiRootContainer::destroy();
          return 1;
        }

      CModel* pModel = pDataModel->getModel();
      assert(pModel != NULL);
      // create a report with the correct filename and all the species against
      // time.
      CReportDefinitionVector* pReports = pDataModel->getReportDefinitionList();
      // create a new report definition object
      CReportDefinition* pReport = pReports->createReportDefinition("Report", "Output for timecourse");
      // set the task type for the report definition to timecourse
      pReport->setTaskType(CTaskEnum::timeCourse);
      // we don't want a table
      pReport->setIsTable(false);
      // the entries in the output should be seperated by a ", "
      pReport->setSeparator(", ");

      // we need a handle to the header and the body
      // the header will display the ids of the metabolites and "time" for
      // the first column
      // the body will contain the actual timecourse data
      std::vector<CRegisteredObjectName>* pHeader = pReport->getHeaderAddr();
      std::vector<CRegisteredObjectName>* pBody = pReport->getBodyAddr();
      pBody->push_back(CCopasiObjectName(pDataModel->getModel()->getCN() + ",Reference=Time"));
      pBody->push_back(CRegisteredObjectName(pReport->getSeparator().getCN()));
      pHeader->push_back(CCopasiStaticString("time").getCN());
      pHeader->push_back(pReport->getSeparator().getCN());

      size_t i, iMax = pModel->getMetabolites().size();

      for (i = 0; i < iMax; ++i)
        {
          CMetab* pMetab = &pModel->getMetabolites()[i];
          assert(pMetab != NULL);

          // we don't want output for FIXED metabolites right now
          if (pMetab->getStatus() != CModelEntity::FIXED)
            {
              // we want the concentration oin the output
              // alternatively, we could use "Reference=Amount" to get the
              // particle number
              pBody->push_back(pMetab->getObject(CCopasiObjectName("Reference=Concentration"))->getCN());
              // after each entry, we need a seperator
              pBody->push_back(pReport->getSeparator().getCN());

              // add the corresponding id to the header
              pHeader->push_back(CCopasiStaticString(pMetab->getSBMLId()).getCN());
              // and a seperator
              pHeader->push_back(pReport->getSeparator().getCN());
            }
        }

      if (iMax > 0)
        {
          // delete the last separator
          // since we don't need one after the last element on each line
          if ((*pBody->rbegin()) == pReport->getSeparator().getCN())
            {
              pBody->erase(--pBody->end());
            }

          if ((*pHeader->rbegin()) == pReport->getSeparator().getCN())
            {
              pHeader->erase(--pHeader->end());
            }
        }

      // get the task list
      CCopasiVectorN< CCopasiTask > & TaskList = * pDataModel->getTaskList();

      // get the trajectory task object
      CTrajectoryTask* pTrajectoryTask = dynamic_cast<CTrajectoryTask*>(&TaskList["Time-Course"]);

      // if there isn't one
      if (pTrajectoryTask == NULL)
        {
          // remove any existing trajectory task just to be sure since in
//.........这里部分代码省略.........