code: public static List<Object> getAlignedUserCollection(String sequence) {
  		List<Object> aligned = new ArrayList<Object>(sequence.length());
  		for (char c : sequence.toCharArray()) {
  			aligned.add(Character.isUpperCase(c));
  		}
  		return aligned;
  	}
docs: Takes a protein sequence string with capital and lowercase letters and sets its {@link ProteinSequence#getUserCollection() user collection} to record which letters are uppercase (aligned) and which are lowercase (unaligned).
  @param sequence Make sure <em>not</em> to use {@link ProteinSequence#getSequenceAsString()} for this, as it won't preserve upper- and lower-case