code: private static List<ConnectionNotation> hybridizationWithLengthFromStart(PolymerNotation one, PolymerNotation two,
  			String senseAnalogSeq, String antisenseAnalogSeq, int lengthFromStart) throws NotationException {
  		List<ConnectionNotation> connections = new ArrayList<ConnectionNotation>();
  		ConnectionNotation connection;
  		for (int i = 0; i < lengthFromStart; i++) {
  			int ssPos = i * 3 + 2;
  			int asPos = (lengthFromStart - 1 - i) * 3 + 2;
  			String ssChar = String.valueOf(senseAnalogSeq.charAt(i));
  			String asChar = String.valueOf(antisenseAnalogSeq.charAt(lengthFromStart - 1 - i));
  			if (complementMap.get(ssChar).equalsIgnoreCase(asChar)) {
  				String details = ssPos + ":pair-" + asPos + ":pair";
  				connection = new ConnectionNotation(one.getPolymerID(), two.getPolymerID(), details);
  				connections.add(connection);
  			}
  
  		}
  		return connections;
  	}
docs: method to generate a List of ConnectionNotations given the two
  PolymerNotations and the sequences and the start point
  
  @param one
  PolymerNotation
  @param two
  PolymerNotation
  @param senseAnalogSeq
  sense Sequence
  @param antisenseAnalogSeq
  antisense Sequence
  @param lengthFromStart
  start position
  @return List of ConnectionNotations
  @throws NotationException
  if notation is not valid