Method main_

src/topp/MetaProSIP.cpp:2900–3603

  }

  ExitCodes main_(int, const char**) override
  {
    String file_extension_ = getStringOption_("plot_extension");
    Int debug_level = getIntOption_("debug");
    String in_mzml = getStringOption_("in_mzML");
    String in_features = getStringOption_("in_featureXML");
    double mz_tolerance_ppm_ = getDoubleOption_("mz_tolerance_ppm");
    double rt_tolerance_s = getDoubleOption_("rt_tolerance_s");

    double weight_merge_window_ = getDoubleOption_("weight_merge_window");
    double intensity_threshold_ = getDoubleOption_("intensity_threshold");
    double decomposition_threshold = getDoubleOption_("decomposition_threshold");

    Size min_consecutive_isotopes = (Size)getIntOption_("min_consecutive_isotopes");

    String qc_output_directory = getStringOption_("qc_output_directory");

    Size n_heatmap_bins = getIntOption_("heatmap_bins");
    double score_plot_y_axis_min = getDoubleOption_("score_plot_yaxis_min");

    String tmp_path = File::getTempDirectory();
    tmp_path.substitute('\\', '/');

    // Do we want to create a qc report?
    if (!qc_output_directory.empty())
    {
      QString executable = getStringOption_("r_executable").toQString();
      // convert path to absolute path
      QDir qc_dir(qc_output_directory.toQString());
      qc_output_directory = String(qc_dir.absolutePath());

      // trying to create qc_output_directory if not present
      if (!qc_dir.exists())
      {
        qc_dir.mkpath(qc_output_directory.toQString());
      }
      // check if R and dependencies are installed
      StringList package_names;
      package_names.push_back("gplots");

      bool R_is_working = RIntegration::checkRDependencies(tmp_path, package_names, executable);
      if (!R_is_working)
      {
        OPENMS_LOG_INFO << "There was a problem detecting one of the required R libraries." << endl;
        return EXTERNAL_PROGRAM_ERROR;
      }
    }

    String out_csv = getStringOption_("out_csv");
    ofstream out_csv_stream(out_csv.c_str());
    out_csv_stream << fixed << setprecision(4);

    String out_peptide_centric_csv = getStringOption_("out_peptide_centric_csv");
    ofstream out_peptide_csv_stream(out_peptide_centric_csv.c_str());
    out_peptide_csv_stream << fixed << setprecision(4);

    String labeling_element = getStringOption_("labeling_element");