Method main_

src/topp/Decharger.cpp:105–168

  }

  ExitCodes main_(int, const char **) override
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    String infile = getStringOption_("in");
    String outfile_fm = getStringOption_("out_fm");
    String outfile_cm = getStringOption_("out_cm");
    String outfile_p = getStringOption_("outpairs");

    FeatureDeconvolution fdc;
    Param const & dc_param = getParam_().copy("algorithm:FeatureDeconvolution:", true);

    writeDebug_("Parameters passed to Decharger", dc_param, 3);

    fdc.setParameters(dc_param);

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------

    writeDebug_("Loading input file", 1);

    typedef FeatureMap FeatureMapType;
    FeatureMapType map_in, map_out;
    FileHandler().loadFeatures(infile, map_in);

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------
    ConsensusMap cm, cm2;
    StopWatch a;
    a.start();
    fdc.compute(map_in, map_out, cm, cm2);
    a.stop();
    //std::cerr << "took: " << a.getClockTime() << " seconds\n\n\n";

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------

    writeDebug_("Saving output files", 1);

    cm.getColumnHeaders()[0].filename = infile;
    cm2.getColumnHeaders()[0].filename = infile;

    //annotate output with data processing info
    addDataProcessing_(map_out, getProcessingInfo_(DataProcessing::CHARGE_DECONVOLUTION));
    addDataProcessing_(cm, getProcessingInfo_(DataProcessing::CHARGE_DECONVOLUTION));
    addDataProcessing_(cm2, getProcessingInfo_(DataProcessing::CHARGE_DECONVOLUTION));


    FileHandler().storeConsensusFeatures(outfile_cm, cm);

    if (!outfile_p.empty())
    {
      FileHandler().storeConsensusFeatures(outfile_p, cm2);
    }