Method read

src/openms/source/FORMAT/DATAACCESS/CsiFingerIdMzTabWriter.cpp:21–190

using namespace std;

void CsiFingerIdMzTabWriter::read(const std::vector<String>& sirius_output_paths,
                                  const String& original_input_mzml,
                                  const Size& top_n_hits,
                                  MzTab& result)
{

  CsiFingerIdMzTabWriter::CsiAdapterRun csi_result;

  for (const auto& it : sirius_output_paths)
  {
    // extract mz, rt of the precursor and the nativeID of the corresponding MS2 spectra in the spectrum.ms file
    SiriusMzTabWriter::SiriusSpectrumMSInfo info = SiriusMzTabWriter::extractSpectrumMSInfo(it);

    const std::string pathtocsicsv = it + "/structure_candidates.tsv";

    ifstream file(pathtocsicsv);

    if (file) 
    {
      CsvFile compounds(pathtocsicsv, '\t');
      const UInt rowcount = compounds.rowCount();

      if (rowcount > 1)
      {
        // correction if the rowcount is smaller than the number of hits used as parameter
        // rowcount-1 because the csv header will be skipped in the loop later on.
        int header = 1;
        const UInt top_n_hits_cor = (top_n_hits >= rowcount) ? rowcount-header : top_n_hits;

        // fill identification structure containing all candidate hits for a single spectrum
        CsiFingerIdMzTabWriter::CsiAdapterIdentification csi_id{};

        // extract scan_index from path
        OpenMS::String str = File::path(pathtocsicsv);
        int scan_index = SiriusMzTabWriter::extractScanIndex(str);
    
        // extract scan_number from string
        int scan_number = SiriusMzTabWriter::extractScanNumber(str);

        // extract feature_id from string
        String feature_id = SiriusMzTabWriter::extractFeatureId(str);

        // extract column name and index from header
        std::map< std::string, Size > columnname_to_columnindex = SiriusMzTabWriter::extract_columnname_to_columnindex(compounds);

        // j = 1 because of .csv file format (header)
        for (Size j = 1; j <= top_n_hits_cor; ++j)
        {
          StringList sl;
          compounds.getRow(j, sl);
          CsiFingerIdMzTabWriter::CsiAdapterHit csi_hit;
          csi_hit.inchikey2D = sl[columnname_to_columnindex.at("InChIkey2D")];
          csi_hit.inchi = sl[columnname_to_columnindex.at("InChI")];
          csi_hit.molecular_formula = sl[columnname_to_columnindex.at("molecularFormula")];
          csi_hit.rank = sl[columnname_to_columnindex.at("rank")].toInt();
          csi_hit.formula_rank = sl[columnname_to_columnindex.at("formulaRank")].toInt();
          csi_hit.adduct = sl[columnname_to_columnindex.at("adduct")];
          csi_hit.score = sl[columnname_to_columnindex.at("CSI:FingerIDScore")].toDouble();