Method main_

src/topp/MapAlignerSpectrum.cpp:100–172

  }

  ExitCodes main_(int, const char**) override
  {
    ExitCodes ret = checkParameters_();
    if (ret != EXECUTION_OK) return ret;

    MapAlignmentAlgorithmSpectrumAlignment algorithm;
    Param algo_params = getParam_().copy("algorithm:", true);
    algorithm.setParameters(algo_params);
    algorithm.setLogType(log_type_);

    StringList ins = getStringList_("in");
    StringList outs = getStringList_("out");
    StringList trafos = getStringList_("trafo_out");
    Param model_params = getParam_().copy("model:", true);
    String model_type = model_params.getValue("type").toString();
    model_params = model_params.copy(model_type + ":", true);
    std::vector<TransformationDescription> transformations;

    //-------------------------------------------------------------
    // perform peak alignment
    //-------------------------------------------------------------
    ProgressLogger progresslogger;
    progresslogger.setLogType(log_type_);

    // load input
    std::vector<PeakMap > peak_maps(ins.size());
    MzMLFile f;
    f.setLogType(log_type_);
    progresslogger.startProgress(0, ins.size(), "loading input files");
    for (Size i = 0; i < ins.size(); ++i)
    {
      progresslogger.setProgress(i);
      f.load(ins[i], peak_maps[i]);
    }
    progresslogger.endProgress();

    // try to align
    algorithm.align(peak_maps, transformations);
    if (model_type != "none")
    {
      for (TransformationDescription& tra : transformations)
      {
        tra.fitModel(model_type, model_params);
      }
    }

    // write output
    progresslogger.startProgress(0, outs.size(), "applying RT transformations and writing output files");
    for (Size i = 0; i < outs.size(); ++i)
    {
      progresslogger.setProgress(i);

      MapAlignmentTransformer::transformRetentionTimes(peak_maps[i], 
                                                       transformations[i]);
      // annotate output with data processing info
      addDataProcessing_(peak_maps[i], 
                         getProcessingInfo_(DataProcessing::ALIGNMENT));