Method loadIdentifiedSequences_

src/openms/source/FORMAT/OMSFileLoad.cpp:590–660

  void OMSFileLoad::loadIdentifiedSequences_(IdentificationData& id_data)
  {
    if (!db_->tableExists("ID_IdentifiedMolecule")) return;

    SQLite::Statement query(*db_, "SELECT * FROM ID_IdentifiedMolecule "          \
                            "WHERE molecule_type_id = :molecule_type_id");
    // @TODO: can we combine handling of meta info and applied processing steps?
    SQLite::Statement subquery_info(*db_, "");
    bool have_meta_info = prepareQueryMetaInfo_(subquery_info,
                                                "ID_IdentifiedMolecule");
    SQLite::Statement subquery_step(*db_, "");
    bool have_applied_steps =
      prepareQueryAppliedProcessingStep_(subquery_step,
                                         "ID_IdentifiedMolecule");
    SQLite::Statement subquery_parent(*db_, "");
    bool have_parent_matches = db_->tableExists(
                                            "ID_ParentMatch");
    if (have_parent_matches)
    {
      subquery_parent = SQLite::Statement(*db_, "SELECT * FROM ID_ParentMatch " \
                              "WHERE molecule_id = :id");
    }

    // load peptides:
    query.bind(":molecule_type_id", int(ID::MoleculeType::PROTEIN) + 1);
    while (query.executeStep())
    {
      Key id = query.getColumn("id").getInt64();
      String sequence = query.getColumn("identifier").getString();
      ID::IdentifiedPeptide peptide(AASequence::fromString(sequence));
      if (have_meta_info)
      {
        handleQueryMetaInfo_(subquery_info, peptide, id);
      }
      if (have_applied_steps)
      {
        handleQueryAppliedProcessingStep_(subquery_step, peptide, id);
      }
      if (have_parent_matches)
      {
        handleQueryParentMatch_(subquery_parent, peptide.parent_matches, id);
      }
      ID::IdentifiedPeptideRef ref = id_data.registerIdentifiedPeptide(peptide);
      identified_molecule_vars_[id] = ref;
    }
    query.reset(); // get ready for new executeStep()

    // load RNA oligos:
    query.bind(":molecule_type_id", int(ID::MoleculeType::RNA) + 1);
    while (query.executeStep())
    {
      Key id = query.getColumn("id").getInt64();
      String sequence = query.getColumn("identifier").getString();
      ID::IdentifiedOligo oligo(NASequence::fromString(sequence));
      if (have_meta_info)
      {
        handleQueryMetaInfo_(subquery_info, oligo, id);
      }