Method main_

src/topp/PeakPickerHiRes.cpp:186–258

  }

  ExitCodes main_(int, const char **) override
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    in = getStringOption_("in");
    out = getStringOption_("out");
    String process_option = getStringOption_("processOption");

    Param pepi_param = getParam_().copy("algorithm:", true);
    writeDebug_("Parameters passed to PeakPickerHiRes", pepi_param, 3);

    PeakPickerHiRes pp;
    pp.setLogType(log_type_);
    pp.setParameters(pepi_param);

    if (process_option == "lowmemory")
    {
      return doLowMemAlgorithm(pp);
    }

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------
    MzMLFile mz_data_file;
    mz_data_file.setLogType(log_type_);
    PeakMap ms_exp_raw;
    mz_data_file.load(in, ms_exp_raw);

    if (ms_exp_raw.empty() && ms_exp_raw.getChromatograms().empty())
    {
      OPENMS_LOG_WARN << "The given file does not contain any conventional peak data, but might"
                  " contain chromatograms. This tool currently cannot handle them, sorry.";
      return INCOMPATIBLE_INPUT_DATA;
    }

    //check if spectra are sorted
    for (Size i = 0; i < ms_exp_raw.size(); ++i)
    {
      if (!ms_exp_raw[i].isSorted())
      {
        writeLogError_("Error: Not all spectra are sorted according to peak m/z positions. Use FileFilter to sort the input!");
        return INCOMPATIBLE_INPUT_DATA;
      }
    }

    //check if chromatograms are sorted
    for (Size i = 0; i < ms_exp_raw.getChromatograms().size(); ++i)
    {
      if (!ms_exp_raw.getChromatogram(i).isSorted())
      {
        writeLogError_("Error: Not all chromatograms are sorted according to peak m/z positions. Use FileFilter to sort the input!");
        return INCOMPATIBLE_INPUT_DATA;
      }
    }

    //-------------------------------------------------------------