Method main_

src/topp/OpenSwathRTNormalizer.cpp:140–298

  }

  ExitCodes main_(int, const char **) override
  {

    ///////////////////////////////////
    // Read input files and parameters
    ///////////////////////////////////
    StringList file_list = getStringList_("in");
    String tr_file_str = getStringOption_("tr");
    String out = getStringOption_("out");
    double min_rsq = getDoubleOption_("min_rsq");
    double min_coverage = getDoubleOption_("min_coverage");
    bool estimateBestPeptides = getFlag_("estimateBestPeptides");
    const char * tr_file  = tr_file_str.c_str();

    MapType all_xic_maps; // all XICs from all files
    OpenSwath::LightTargetedExperiment targeted_exp;

    std::cout << "Loading TraML file" << std::endl;
    {
      TargetedExperiment transition_exp_;
      TraMLFile().load(tr_file, transition_exp_);
      OpenSwathDataAccessHelper::convertTargetedExp(transition_exp_, targeted_exp);
    }

    Param pepEstimationParams = getParam_().copy("peptideEstimation:", true);
    Param RTNormParams = getParam_().copy("RTNormalization:", true);
    String outlier_method = RTNormParams.getValue("outlierMethod").toString();

    // 1. Estimate the retention time range of the whole experiment
    std::pair<double,double> RTRange = OpenSwathHelper::estimateRTRange(targeted_exp);
    std::cout << "Detected retention time range from " << RTRange.first << " to " << RTRange.second << std::endl;

    // 2. Store the peptide retention times in an intermediate map
    std::map<std::string, double> PeptideRTMap;
    for (Size i = 0; i < targeted_exp.getCompounds().size(); i++)
    {
      PeptideRTMap[targeted_exp.getCompounds()[i].id] = targeted_exp.getCompounds()[i].rt; 
    }

    MzMLFile f;
    f.setLogType(log_type_);
    TransformationXMLFile trafoxml;
    TransformationDescription trafo;

    // If we have a transformation file, trafo will transform the RT in the
    // scoring according to the model. If we don't have one, it will apply the
    // null transformation.
    if (!getStringOption_("rt_norm").empty())
    {
      String trafo_in = getStringOption_("rt_norm");
      String model_type = "linear"; //getStringOption_("model:type");
      trafoxml.load(trafo_in, trafo);
    }

    ///////////////////////////////////
    // Start computation
    ///////////////////////////////////