Method store

src/openms/source/FORMAT/MzTabFile.cpp:2878–2978

stream IDs to file

  }
    // stream IDs to file
  void MzTabFile::store(
        const String& filename,
        const std::vector<ProteinIdentification>& protein_identifications,
        const std::vector<PeptideIdentification>& peptide_identifications,
        bool first_run_inference_only,
        bool export_empty_pep_ids,
        bool export_all_psms,
        const String& title)
  {
    if (!(FileHandler::hasValidExtension(filename, FileTypes::MZTAB) || FileHandler::hasValidExtension(filename, FileTypes::TSV)))
    {
      throw Exception::UnableToCreateFile(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename, "invalid file extension, expected '"
      + FileTypes::typeToName(FileTypes::MZTAB) + "' or '" + FileTypes::typeToName(FileTypes::TSV) + "'");
    }

    vector<const PeptideIdentification*> pep_ids_ptr;
    pep_ids_ptr.reserve(peptide_identifications.size());
    for (const PeptideIdentification& pi : peptide_identifications) { pep_ids_ptr.push_back(&pi); }

    vector<const ProteinIdentification*> prot_ids_ptr;
    prot_ids_ptr.reserve(protein_identifications.size());
    for (const ProteinIdentification& pi : protein_identifications) { prot_ids_ptr.push_back(&pi); }

    ofstream tab_file;
    tab_file.open(filename, ios::out | ios::trunc);

    MzTab::IDMzTabStream s(
      prot_ids_ptr,
      pep_ids_ptr,
      filename,
      first_run_inference_only,
      export_empty_pep_ids,
      export_all_psms,
      title);      

    // generate full meta data section and write to file
    MzTabMetaData meta_data = s.getMetaData();

    {
      StringList out;
      generateMzTabMetaDataSection_(meta_data, out);
      for (const String & line : out) { tab_file << line << "\n"; }
    }
   
    Size n_best_search_engine_score = meta_data.protein_search_engine_score.size();

    {
      MzTabProteinSectionRow row;
      bool first = true;
      size_t n_header_columns = 0;
      while (s.nextPRTRow(row))
      {
        if (first)
        { // add header
          tab_file << "\n" << generateMzTabProteinHeader_(
            row,
            n_best_search_engine_score,
            s.getProteinOptionalColumnNames(),