Method main_

src/topp/MRMMapper.cpp:121–152

  }

  ExitCodes main_(int, const char **) override
  {
    String in = getStringOption_("in");
    String tr_file = getStringOption_("tr");
    String out = getStringOption_("out");

    OpenMS::TargetedExperiment targeted_exp;
    OpenMS::PeakMap chromatogram_map;
    OpenMS::PeakMap output;

    TraMLFile().load(tr_file, targeted_exp);
    MzMLFile().load(in, chromatogram_map);

    Param param = getParam_().copy("algorithm:", true);

    MRMMapping mrmm;
    mrmm.setParameters(param);
    mrmm.mapExperiment(chromatogram_map, targeted_exp, output);

    // add all data processing information to all the chromatograms
    DataProcessing dp_ = getProcessingInfo_(DataProcessing::FORMAT_CONVERSION);
    DataProcessingPtr dp = boost::shared_ptr<DataProcessing>(new DataProcessing(dp_));
    std::vector<MSChromatogram > chromatograms = output.getChromatograms();
    for (Size i=0; i<chromatograms.size(); ++i)
    {
      chromatograms[i].getDataProcessing().push_back(dp);
    }
    output.setChromatograms(chromatograms);

    MzMLFile().store(out, output);
    return EXECUTION_OK;
  }

};