Method main_

src/topp/OpenSwathFeatureXMLToTSV.cpp:377–491

  }

  ExitCodes main_(int, const char **) override
  {
    StringList file_list = getStringList_("in");
    String tr_file = getStringOption_("tr");
    String out = getStringOption_("out");
    //String main_var_name = getStringOption_("main_var_name");
    String best_scoring = getStringOption_("best_scoring_peptide");
    bool short_format = getFlag_("short_format");

    setLogType(log_type_);

    TargetedExperiment transition_exp;
    TraMLFile().load(tr_file, transition_exp);

    startProgress(0, transition_exp.getTransitions().size(), "indexing transitions peaks");
    for (Size i = 0; i < transition_exp.getTransitions().size(); i++)
    {
      setProgress(i);
      const ReactionMonitoringTransition *transition = &transition_exp.getTransitions()[i];

      {
        peptide_transition_map[transition->getPeptideRef()].push_back(&transition_exp.getTransitions()[i]);
      }
    }
    endProgress();

    std::ofstream os(out.c_str());
    //set high precision for writing of floating point numbers
    os.precision(writtenDigits(double()));
    if (!os)
    {
      throw Exception::UnableToCreateFile(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, out);
    }

    // write the csv header (we need to know which parameters are in the map to do that)
    if (file_list.empty())
    {
      throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "No input files given ");
    }
    FeatureMap feature_map;
    FeatureXMLFile feature_file;
    feature_file.setLogType(log_type_);
    // feature_file.load() resets the locale to the user's (Don't know where, maybe QT or Xerces)
    // Somehow even our variable OpenMS::Internal::OpenMS_locale is overwritten
    // Create copy here and reset it later. TODO this needs to be fixed more thouroughly.
    String locale_before = String(OpenMS::Internal::OpenMS_locale);
    feature_file.load(file_list[0], feature_map);
    setlocale(LC_ALL, locale_before.c_str());
    if (feature_map.getIdentifier().empty())
    {
      feature_map.setIdentifier("run0");
    }
    std::vector<String> meta_value_names;

    if (feature_map.empty() && file_list.size() > 1)
    {
      throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Feature map " + file_list[0] + " is empty.");
    }