code: protected int mapIdRefToInternalScanNum(CharArray id) throws FileParsingException {
      String idStr = id.toString();
      MZMLIndexElement byId = index.getById(idStr);
      if (byId == null) {
        String msg = String.format("Could not find a mapping from spectrum id"
            + " ref to an internal scan number for"
            + "\n\t file: %s"
            + "\n\t spectrum index of the spectrum in which the error occured: #%d"
            + "\n\t idRef searched for: %s", source.getPath(), vars.spectrumIndex, idStr);
        throw new FileParsingException(msg);
      }
      return byId.getNumber();
    }
docs: Given a scan ID goes to the index and tries to find a mapping.
  
  @throws umich.ms.fileio.exceptions.FileParsingException in case the mapping can't be done