Method main_

src/topp/SimpleSearchEngine.cpp:91–123

    }

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

      ProgressLogger progresslogger;
      progresslogger.setLogType(log_type_);

      vector<ProteinIdentification> protein_ids;
      vector<PeptideIdentification> peptide_ids;

      SimpleSearchEngineAlgorithm sse;
      sse.setParameters(getParam_().copy("Search:", true));
      //TODO ??? Why not use the TOPPBase ExitCodes?
      // same for OpenPepXL etc. Otherwise please write a proper mapping.
      SimpleSearchEngineAlgorithm::ExitCodes e = sse.search(in, database, protein_ids, peptide_ids);
      if (e != SimpleSearchEngineAlgorithm::ExitCodes::EXECUTION_OK)
      {
        return TOPPBase::ExitCodes::INTERNAL_ERROR;
      }

      // MS path already set in algorithm. Overwrite here so we get something testable
      if (getFlag_("test"))
      {
        // if test mode set, add file without path so we can compare it
        protein_ids[0].setPrimaryMSRunPath({"file://" + File::basename(in)});
      }

      IdXMLFile().store(out, protein_ids, peptide_ids);

      return EXECUTION_OK;
    }

};