Method preparePin_

src/openms/source/FORMAT/PercolatorInfile.cpp:268–456

  TextFile PercolatorInfile::preparePin_(
    const vector<PeptideIdentification>& peptide_ids, 
    const StringList& feature_set, 
    const std::string& enz, 
    int min_charge, 
    int max_charge)
  {
    TextFile txt;  
    txt.addLine(ListUtils::concatenate(feature_set, '\t'));
    if (peptide_ids.empty()) 
    {
      OPENMS_LOG_WARN << "No identifications provided. Creating empty percolator input." << endl;
      return txt;
    }

    // extract native id (usually in spectrum_reference)
    const String sid = getScanIdentifier(peptide_ids[0], 0);

    // determine RegEx to extract scan/index number
    boost::regex scan_regex = boost::regex(SpectrumLookup::getRegExFromNativeID(sid));

    // keep track of errors
    size_t missing_meta_value_count{};
    set<String> missing_meta_values;

    size_t index = 0;
    for (const PeptideIdentification& pep_id : peptide_ids)
    {
      index++;
      // try to make a file and scan unique identifier
      String scan_identifier = getScanIdentifier(pep_id, index);
      String file_identifier = pep_id.getMetaValue("file_origin", String());

      file_identifier += (String)pep_id.getMetaValue("id_merge_index", String());

      Int scan_number = SpectrumLookup::extractScanNumber(scan_identifier, scan_regex, true);
      
      double exp_mass = pep_id.getMZ();
      double retention_time = pep_id.getRT();
      for (const PeptideHit& psm : pep_id.getHits())
      {
        if (psm.getPeptideEvidences().empty())
        {
          OPENMS_LOG_WARN << "PSM (PeptideHit) without protein reference found. "
                  << "This may indicate incomplete mapping during PeptideIndexing (e.g., wrong enzyme settings)." 
                  << "Will skip this PSM." << endl;
          continue;
        }
        PeptideHit hit(psm); // make a copy of the hit to store temporary features
        hit.setMetaValue("SpecId", file_identifier + scan_identifier);
        hit.setMetaValue("ScanNr", scan_number);
        
        if (!hit.metaValueExists("target_decoy") 
          || hit.getMetaValue("target_decoy").toString().empty()) 
        {
          continue;
        }