Method storeIdentifiedCompounds_

src/openms/source/FORMAT/OMSFileStore.cpp:787–832

  void OMSFileStore::storeIdentifiedCompounds_(const IdentificationData& id_data)
  {
    if (id_data.getIdentifiedCompounds().empty()) return;

    if (!db_->tableExists("ID_IdentifiedMolecule"))
    {
      createTableIdentifiedMolecule_();
    }
    auto& query_molecule = *prepared_queries_["ID_IdentifiedMolecule"];
    query_molecule.bind(":molecule_type_id", int(ID::MoleculeType::COMPOUND) + 1);

    createTable_(
      "ID_IdentifiedCompound",
      "molecule_id INTEGER UNIQUE NOT NULL , "                          \
      "formula TEXT, "                                                  \
      "name TEXT, "                                                     \
      "smile TEXT, "                                                    \
      "inchi TEXT, "                                                    \
      "FOREIGN KEY (molecule_id) REFERENCES ID_IdentifiedMolecule (id)");
    SQLite::Statement query_compound(*db_, "INSERT INTO ID_IdentifiedCompound VALUES (" \
                           ":molecule_id, "                             \
                           ":formula, "                                 \
                           ":name, "                                    \
                           ":smile, "                                   \
                           ":inchi)");
    Key id = 1;
    for (const ID::IdentifiedCompound& compound : id_data.getIdentifiedCompounds())
    {
      query_molecule.bind(":id", id);
      query_molecule.bind(":identifier", compound.identifier);
      execWithExceptionAndReset(query_molecule, 1, __LINE__, OPENMS_PRETTY_FUNCTION, "error inserting data");

      query_compound.bind(":molecule_id", id);
      query_compound.bind(":formula", compound.formula.toString());
      query_compound.bind(":name", compound.name);
      query_compound.bind(":smile", compound.name);
      query_compound.bind(":inchi", compound.inchi);
      execWithExceptionAndReset(query_compound, 1, __LINE__, OPENMS_PRETTY_FUNCTION, "error inserting data");


      identified_compound_keys_[&compound] = id;
      ++id;
    }
    storeScoredProcessingResults_(id_data.getIdentifiedCompounds(), "ID_IdentifiedMolecule",
                                  identified_compound_keys_);
  }


  void OMSFileStore::storeIdentifiedSequences_(const IdentificationData& id_data)