code: private double checkScore()
  	{
  		int     i, j, op, s;
  		double  sco;
  
  		sco = 0;
  		op = 0;
  		s = 0;
  
  		i = B1;
  		j = B2;
  		while (i <= E1 && j <= E2) {
  			op = sapp0[s ++];
  			if (op == 0)    {
  				sco += sij[i - 1][j - 1];
  				//if (debug)
  					//System.err.println(String.format("%d-%d %f\n", i - 1, j - 1, sij[i - 1][j - 1]));
  				i ++;
  				j ++;
  			}
  			else if (op > 0) {
  				sco -= g+op*h;
  				j = j+op;
  			}
  			else {
  				sco -= g-op*h;
  				i = i-op;
  			}
  		}
  		return(sco);
  	}
docs: checkscore - return the score of the alignment stored in sapp