Method main_

src/topp/IDScoreSwitcher.cpp:67–100

  }

  ExitCodes main_(int, const char**) override
  {
    switcher_.setParameters(getParam_().copySubset(switcher_.getParameters()));
    String in = getStringOption_("in"), out = getStringOption_("out");
    bool do_proteins_ = getFlag_("proteins"); // from full param of IDScoreSwitcherAlgorithm

    vector<ProteinIdentification> proteins;
    vector<PeptideIdentification> peptides;

    IdXMLFile().load(in, proteins, peptides);

    Size counter = 0;
    if (do_proteins_)
    {
      for (auto& pid : proteins)
      {
        switcher_.switchScores<ProteinIdentification>(pid, counter);
      }
    }
    else
    {
      for (auto& pepid : peptides)
      {
        switcher_.switchScores<PeptideIdentification>(pepid, counter);
      }
    }

    IdXMLFile().store(out, proteins, peptides);

    OPENMS_LOG_INFO << "Successfully switched " << counter << " "
             << (do_proteins_ ? "protein" : "PSM") << " scores." << endl;

    return EXECUTION_OK;
  }

};