Method main_

src/topp/SpectraMerger.cpp:87–166

  }

  ExitCodes main_(int, const char **) override
  {
    //-------------------------------------------------------------
    // parsing parameters
    //-------------------------------------------------------------
    String in(getStringOption_("in"));
    String out(getStringOption_("out"));
    String merging_method(getStringOption_("merging_method"));

    //-------------------------------------------------------------
    // reading input
    //-------------------------------------------------------------

    FileHandler fh;
    FileTypes::Type in_type = fh.getType(in);

    PeakMap exp;
    fh.loadExperiment(in, exp, in_type, log_type_);
    exp.sortSpectra();
    exp.updateRanges();

    auto levels = exp.getMSLevels();
    if (levels.empty()) throw Exception::InvalidSize(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, levels.size());
    int min_ms_level = levels.front();
    int max_ms_level = levels.back();
    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------

    SpectraMerger merger;
    merger.setLogType(log_type_);
    merger.setParameters(getParam_().copy("algorithm:", true));
    if (merging_method == "precursor_method")
    {
      merger.mergeSpectraPrecursors(exp);
    }
    else if (merging_method == "block_method")
    {
      merger.mergeSpectraBlockWise(exp);
    }
    else if (merging_method == "average_gaussian")
    {
      int ms_level = merger.getParameters().getValue("average_gaussian:ms_level");
      if (ms_level == 0)
      {
        for (int tmp_ms_level = min_ms_level; tmp_ms_level <= max_ms_level; tmp_ms_level++)
        {
          merger.average(exp, "gaussian", tmp_ms_level);
        }
      }
      else
      {
        merger.average(exp, "gaussian", ms_level);
      }
    }
    else if (merging_method == "average_tophat")
    {
      int ms_level = merger.getParameters().getValue("average_tophat:ms_level");