Method main_

src/topp/NoiseFilterGaussian.cpp:141–225

  }

  ExitCodes main_(int, const char **) override
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    in = getStringOption_("in");
    out = getStringOption_("out");
    String process_option = getStringOption_("processOption");

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

    GaussFilter gauss;
    gauss.setLogType(log_type_);
    gauss.setParameters(filter_param);

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

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

    if (exp.empty() && exp.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 for peak type (profile data required)
    if (!exp.empty() && exp[0].getType(true) == SpectrumSettings::CENTROID)
    {
      writeLogWarn_("Warning: OpenMS peak type estimation indicates that this is not profile data!");
    }

    //check if spectra are sorted
    for (Size i = 0; i < exp.size(); ++i)
    {
      if (!exp[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 < exp.getChromatograms().size(); ++i)
    {
      if (!exp.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;