code: public void addAlignedSequence(S sequence){
  		if(length == null){
  			length = sequence.getLength();
  		}
  		if(sequence.getLength() != length){
  			throw new IllegalArgumentException(sequence.getAccession() + " length = " + sequence.getLength() +
  					" not equal to MSA length = " + length);
  		}
  		sequences.add(sequence);
  	}
docs: A sequence that has been aligned to other sequences will have inserts.
  @param sequence