Method getFullProteins_

src/openms/source/FORMAT/OSWFile.cpp:509–581

    }

    void OSWFile::getFullProteins_(OSWData& swath_result, Size index)
    {
      String protein_subselect;
      if (index == ALL_PROTEINS)
      {
        swath_result.clearProteins();
        protein_subselect = "PROTEIN";
      }
      else
      { //  do not use accession to filter -- its as slow as full query
        protein_subselect = "(select * from PROTEIN  where ID = " + String(swath_result.getProteins().at(index).getID()) + ") as PROTEIN";
      }
     

      // check of SCORE_MS2 table is available (for OSW files which underwent pyProphet)
      // set q_value to -1 if missing
      String MS2_select = (has_SCOREMS2_ ? "SCORE_MS2.QVALUE as qvalue" : "-1 as qvalue");
      String MS2_join = (has_SCOREMS2_ ? "inner join(select * from SCORE_MS2) as SCORE_MS2 on SCORE_MS2.FEATURE_ID = FEATURE.ID" : "");

      // assemble the protein-PeptidePrecursor-Feature hierarchy
      // note: when changing the query, make sure to keep the indices in ColProteinSelect in sync!!!
      String select_sql = "select PROTEIN.ID as prot_id, PROTEIN_ACCESSION as prot_accession, PROTEIN.DECOY as decoy, "
                          "       PEPTIDE.MODIFIED_SEQUENCE as modified_sequence,"
                          "       PRECURSOR.ID as prec_id, PRECURSOR.PRECURSOR_MZ as pc_mz, PRECURSOR.CHARGE as pc_charge,"
                          "       FEATURE.ID as feat_id, FEATURE.EXP_RT as rt_experimental, FEATURE.DELTA_RT as rt_delta, FEATURE.LEFT_WIDTH as rt_left_width, FEATURE.RIGHT_WIDTH as rt_right_width,"
                          "       FeatTrMap.TRANSITION_ID as tr_id, " +
        MS2_select +
        " FROM " + protein_subselect +
        " inner join(select* FROM PEPTIDE_PROTEIN_MAPPING) as PepProtMap on PepProtMap.PROTEIN_ID = PROTEIN.ID "
        " inner join(select ID, MODIFIED_SEQUENCE FROM PEPTIDE) as PEPTIDE on PEPTIDE.ID = PepProtMap.PEPTIDE_ID "
        " inner join(select * FROM PRECURSOR_PEPTIDE_MAPPING) as PrePepMap on PrePepMap.PEPTIDE_ID = PEPTIDE.ID "
        " inner join(select * from PRECURSOR) as PRECURSOR on PRECURSOR.ID = PrePepMap.PRECURSOR_ID "
        " inner join(select * from FEATURE) as FEATURE on FEATURE.PRECURSOR_ID = PRECURSOR.ID "
        " inner join(select * from FEATURE_TRANSITION) as FeatTrMap on FeatTrMap.FEATURE_ID = FEATURE.ID " +
        MS2_join +
        " order by prot_id, prec_id, feat_id, qvalue, tr_id ";


      sqlite3_stmt* stmt;
      conn_.prepareStatement(&stmt, select_sql);

      Sql::SqlState rc = Sql::nextRow(stmt);
      if (sqlite3_column_count(stmt) != SIZE_OF_ColProteinSelect)
      {
        throw Exception::SqlOperationFailed(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Query was changed! Please report this bug!");
      }

      if (rc == Sql::SqlState::SQL_DONE)
      { // no data
        return;
      }

      LineState current_line;
      initLine(current_line, stmt);
      OSWProtein prot;

      if (index == ALL_PROTEINS)
      {