Method storeIdentifiedSequences_

src/openms/source/FORMAT/OMSFileStore.cpp:835–896

  void OMSFileStore::storeIdentifiedSequences_(const IdentificationData& id_data)
  {
    if (id_data.getIdentifiedPeptides().empty() &&
        id_data.getIdentifiedOligos().empty()) return;

    if (!db_->tableExists("ID_IdentifiedMolecule"))
    {
      createTableIdentifiedMolecule_();
    }
    auto& query = *prepared_queries_["ID_IdentifiedMolecule"];

    bool any_parent_matches = false;
    // identified compounds get stored earlier and use the same key range as peptides/oligos:
    Key id = id_data.getIdentifiedCompounds().size() + 1;
    // store peptides:
    query.bind(":molecule_type_id", int(ID::MoleculeType::PROTEIN) + 1);
    for (const ID::IdentifiedPeptide& peptide : id_data.getIdentifiedPeptides())
    {
      if (!peptide.parent_matches.empty()) any_parent_matches = true;
      query.bind(":id", id);
      query.bind(":identifier", peptide.sequence.toString());
      execWithExceptionAndReset(query, 1, __LINE__, OPENMS_PRETTY_FUNCTION, "error inserting data");

      identified_peptide_keys_[&peptide] = id;
      ++id;
    }
    storeScoredProcessingResults_(id_data.getIdentifiedPeptides(), "ID_IdentifiedMolecule",
                                  identified_peptide_keys_);
    // store RNA oligos:
    query.bind(":molecule_type_id", int(ID::MoleculeType::RNA) + 1);
    for (const ID::IdentifiedOligo& oligo : id_data.getIdentifiedOligos())
    {
      if (!oligo.parent_matches.empty()) any_parent_matches = true;
      query.bind(":id", id); // use address as primary key
      query.bind(":identifier", oligo.sequence.toString());
      execWithExceptionAndReset(query, 1, __LINE__, OPENMS_PRETTY_FUNCTION, "error inserting data");

      identified_oligo_keys_[&oligo] = id;
      ++id;
    }
    storeScoredProcessingResults_(id_data.getIdentifiedOligos(), "ID_IdentifiedMolecule",
                                  identified_oligo_keys_);

    if (any_parent_matches)
    {
      createTableParentMatches_();
      for (const ID::IdentifiedPeptide& peptide : id_data.getIdentifiedPeptides())
      {
        if (!peptide.parent_matches.empty())
        {
          storeParentMatches_(peptide.parent_matches, identified_peptide_keys_[&peptide]);
        }
      }
      for (const ID::IdentifiedOligo& oligo : id_data.getIdentifiedOligos())
      {
        if (!oligo.parent_matches.empty())
        {
          storeParentMatches_(oligo.parent_matches, identified_oligo_keys_[&oligo]);