code: @Override
  	public double getPercentageOfIdentity(boolean countGaps) {
  		double seqid = getNumIdenticals();
  		double length = getLength();
  		if (!countGaps) {
  			length = length - getAlignedSequence(1).getNumGapPositions()
  					- getAlignedSequence(2).getNumGapPositions();
  		}
  		return seqid / length;
  	}
docs: Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
  
  @param countGaps
  If true, gap positions are counted as mismatches, i.e., the percentage is normalized by the alignment length.
  If false, gap positions are not counted, i.e. the percentage is normalized by the number of aligned residue pairs.
  See May (2004). "Percent sequence identity: the need to be explicit."
  @return the percentage of sequence identity as a fraction in [0,1]