code: private final static List<String> generateIDForNucleotide(MonomerNotationUnitRNA object, String existingMonomerID,
  			String newMonomerID) throws MonomerLoadingException, ChemistryException, CTKException {
  		List<String> result = new ArrayList<String>();
  		String hasChanged = null;
  		StringBuilder sb = new StringBuilder();
  		String id = "";
  		for (MonomerNotation element : object.getContents()) {
  			if (element.getUnit().equals(existingMonomerID)) {
  				hasChanged = "";
  				id = generateIDRNA(newMonomerID, element.getCount(), element.getAnnotation());
  			} else {
  				id = generateIDRNA(element.getUnit(), element.getCount(), element.getAnnotation());
  			}
  			sb.append(id);
  		}
  		try {
  			if (!(Integer.parseInt(object.getCount()) == 1)) {
  				sb.append("'" + object.getCount() + "'");
  			}
  		} catch (NumberFormatException e) {
  			sb.append("'" + object.getCount() + "'");
  		}
  		if (object.getAnnotation() != null) {
  			sb.append("\"" + object.getAnnotation() + "\"");
  		}
  		result.add(sb.toString());
  		result.add(hasChanged);
  		return result;
  	}
docs: method to replace the MonomerNotationUnitRNA having the MonomerID with
  the new MonomerID
  
  @param object
  MonomerNotationUnitRNA
  @param existingMonomerID
  @param newMonomerID
  @return List of MonomerNotationUnitRNA in String format and the
  information if the MonomerNotationUnitRNA has to be changed
  @throws MonomerLoadingException
  @throws ChemistryException
  @throws CTKException