Method main_

src/topp/ConsensusMapNormalizer.cpp:92–140

  }

  ExitCodes main_(int, const char **) override
  {
    String in = getStringOption_("in");
    String out = getStringOption_("out");
    String algo_type = getStringOption_("algorithm_type");
    String acc_filter = getStringOption_("accession_filter");
    String desc_filter = getStringOption_("description_filter");
    double ratio_threshold = getDoubleOption_("ratio_threshold");

    ConsensusXMLFile infile;
    infile.setLogType(log_type_);
    ConsensusMap map;
    infile.load(in, map);

    //map normalization
    if (algo_type == "robust_regression")
    {
      map.sortBySize();
      vector<double> results = ConsensusMapNormalizerAlgorithmThreshold::computeCorrelation(map, ratio_threshold, acc_filter, desc_filter);
      ConsensusMapNormalizerAlgorithmThreshold::normalizeMaps(map, results);
    }
    else if (algo_type == "median")
    {
      ConsensusMapNormalizerAlgorithmMedian::normalizeMaps(map, ConsensusMapNormalizerAlgorithmMedian::NM_SCALE, acc_filter, desc_filter);
    }
    else if (algo_type == "median_shift")
    {
      ConsensusMapNormalizerAlgorithmMedian::normalizeMaps(map, ConsensusMapNormalizerAlgorithmMedian::NM_SHIFT, acc_filter, desc_filter);
    }
    else if (algo_type == "quantile")
    {
      if (!acc_filter.empty() || !desc_filter.empty())
      {
        OPENMS_LOG_WARN << endl << "NOTE: Accession / description filtering is not supported in quantile normalization mode. Ignoring filters." << endl << endl;
      }
      ConsensusMapNormalizerAlgorithmQuantile::normalizeMaps(map);
    }
    else
    {
      cerr << "Unknown algorithm type  '" << algo_type.c_str() << "'." << endl;
      return ILLEGAL_PARAMETERS;
    }

    //annotate output with data processing info and save output file
    addDataProcessing_(map, getProcessingInfo_(DataProcessing::NORMALIZATION));
    infile.store(out, map);

    return EXECUTION_OK;
  }
};