code: private int mapRawNumToInternalScanNum(int rawScanNum) throws FileParsingException {
      MZXMLIndexElement byRawNum = index.getByRawNum(rawScanNum);
      if (byRawNum == null) {
        String msg = String.format("Could not find a mapping from spectrum index"
                + " ref to an internal scan number for"
                + "\n\t file: %s"
                + "\n\t raw scan num searched for: #%d"
                + "\n\t raw scan num of the spectrum in which the error occured: #%d"
            , source.getPath(), rawScanNum, vars.scanNumRaw);
        throw new FileParsingException(msg);
      }
      return byRawNum.getNumber();
    }
docs: Given a scan internal number (spectrum index) goes to the index and tries to find a mapping.
  
  @param rawScanNum the number as is in the scan tag