code: public int getAlignPos(int[][] alignList)
  	{
  		int     i = B1;
  		int     j = B2;
  		int     s = 0;
  		int     a = 0;
  		int     op;
  		while(i <= E1 && j <= E2)       {
  			op = sapp0[s ++];
  
  			if (op == 0)    {
  				alignList[0][a] = i - 1; //i - 1
  				alignList[1][a] = j - 1;
  				a ++;
  				i ++;
  				j ++;
  			}
  			else if (op > 0) {
  				j += op;
  			}
  			else {
  				i -= op;
  			}
  		}
  		return a;
  	}
docs: record the aligned pairs in alignList[][0], alignList[][1];
  return the number of aligned pairs
  @param alignList
  @return the number of aligned pairs