Method loadAndCleanupIDFile_

src/topp/ProteomicsLFQ.cpp:772–938

  }

  ExitCodes loadAndCleanupIDFile_(
    const String& id_file_abs_path,
    const String& mz_file,
    const String& in_db,
    const Size& fraction_group,
    const Size& fraction,
    vector<ProteinIdentification>& protein_ids, 
    vector<PeptideIdentification>& peptide_ids,
    set<String>& fixed_modifications,  // adds to
    set<String>& variable_modifications) // adds to
  {

    const String& mz_file_abs_path = File::absolutePath(mz_file);
    IdXMLFile().load(id_file_abs_path, protein_ids, peptide_ids);

    ExitCodes e = checkSingleRunPerID_(protein_ids, id_file_abs_path);
    if (e != EXECUTION_OK) return e;

    // Re-index
    if (!in_db.empty())
    {
      PeptideIndexing indexer;
      Param param_pi = indexer.getParameters();
      param_pi.setValue("missing_decoy_action", "silent");
      param_pi.setValue("write_protein_sequence", "true");
      param_pi.setValue("write_protein_description", "true");
      indexer.setParameters(param_pi);

      // stream data in fasta file
      FASTAContainer<TFI_File> fasta_db(in_db);
      PeptideIndexing::ExitCodes indexer_exit = indexer.run(fasta_db, protein_ids, peptide_ids);

      picked_decoy_string_ = indexer.getDecoyString();
      picked_decoy_prefix_ = indexer.isPrefix();
      if ((indexer_exit != PeptideIndexing::EXECUTION_OK) &&
          (indexer_exit != PeptideIndexing::PEPTIDE_IDS_EMPTY))
      {
        if (indexer_exit == PeptideIndexing::DATABASE_EMPTY)
        {
          return INPUT_FILE_EMPTY;
        }
        else if (indexer_exit == PeptideIndexing::UNEXPECTED_RESULT)
        {
          return UNEXPECTED_RESULT;
        }
        else
        {
          return UNKNOWN_ERROR;
        }
      }
    }

    e = switchScoreType_(peptide_ids, id_file_abs_path);
    if (e != EXECUTION_OK) return e;
  
    // TODO we could think about removing this limitation but it gets complicated quickly
    IDFilter::keepBestPeptideHits(peptide_ids, false); // strict = false