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

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

    IndexedMzMLFileLoader loader; 

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------
    OnDiscPeakMap exp;
    loader.load(in, exp);

    // We could write out this warning in the constructor if no spectra have come our way ...
    /*
    if (ms_exp_raw.empty() && ms_exp_raw.getChromatograms().size() == 0)
    {
      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;
    }
    */

    // We could check with the first spectrum that we process whether it fulfills the requirements
    // check for peak type (profile data required)
    /*
    if (!ms_exp_raw.empty() && PeakTypeEstimator().estimateType(ms_exp_raw[0].begin(), ms_exp_raw[0].end()) == SpectrumSettings::CENTROID)
    {
      writeLog_("Warning: OpenMS peak type estimation indicates that this is not profile data!");
    }
    */

    // We can check each spectrum and throw an error if it is not sorted
    // check if spectra are sorted
    /*
    for (Size i = 0; i < ms_exp_raw.size(); ++i)
    {
      if (!ms_exp_raw[i].isSorted())
      {
        writeLog_("Error: Not all spectra are sorted according to peak m/z positions. Use FileFilter to sort the input!");
        return INCOMPATIBLE_INPUT_DATA;
      }
    }
    */

    // We can check each chromatogram and throw an error if it is not sorted
    //check if chromatograms are sorted
    /*
    for (Size i = 0; i < ms_exp_raw.getChromatograms().size(); ++i)
    {
      if (!ms_exp_raw.getChromatogram(i).isSorted())
      {
        writeLog_("Error: Not all chromatograms are sorted according to peak m/z positions. Use FileFilter to sort the input!");
        return INCOMPATIBLE_INPUT_DATA;
      }
    }
    */

    //-------------------------------------------------------------
    // pick
    //-------------------------------------------------------------
    PeakMap ms_exp_peaks;

    ///////////////////////////////////
    // Create PeakPickerHiRes and hand it to the PPHiResMzMLConsumer
    ///////////////////////////////////
    Param pepi_param = getParam_().copy("algorithm:", true);
    writeDebug_("Parameters passed to LowMemPeakPickerHiRes", pepi_param, 3);

    PeakPickerHiRes pp;
    pp.setLogType(log_type_);
    pp.setParameters(pepi_param);
    pp.pickExperiment(exp, ms_exp_peaks);

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------
    //annotate output with data processing info
    addDataProcessing_(ms_exp_peaks, getProcessingInfo_(DataProcessing::PEAK_PICKING));

    MzMLFile mz_data_file;
    mz_data_file.setLogType(log_type_);
    mz_data_file.store(out, ms_exp_peaks);

    return EXECUTION_OK;
  }
Beispiel #2
0
  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().size() == 0)
    {
      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())
      {
        writeLog_("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())
      {
        writeLog_("Error: Not all chromatograms are sorted according to peak m/z positions. Use FileFilter to sort the input!");
        return INCOMPATIBLE_INPUT_DATA;
      }
    }

    //-------------------------------------------------------------
    // pick
    //-------------------------------------------------------------
    PeakMap ms_exp_peaks;
    bool check_spectrum_type = !getFlag_("force");
    pp.pickExperiment(ms_exp_raw, ms_exp_peaks, check_spectrum_type);

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------
    //annotate output with data processing info
    addDataProcessing_(ms_exp_peaks, getProcessingInfo_(DataProcessing::PEAK_PICKING));
    mz_data_file.store(out, ms_exp_peaks);

    return EXECUTION_OK;
  }