code: private int count_gaps(int[] i1, int[] i2){
  
  		int i0 = i1[0];
  		int j0 = i2[0];
  		int gaps = 0;
  		for (int i =1 ; i<i1.length;i++ ){
  			if ( Math.abs(i1[i]-i0) != 1 ||
  					( Math.abs(i2[i]-j0) != 1)){
  				gaps +=1;
  			}
  			i0 = i1[i];
  			j0 = i2[i];
  		}
  
  		return gaps;
  	}
docs: Count the number of gaps in an alignment represented by idx1,idx2.
  
  @param i1
  @param i2
  @return the number of gaps in this alignment