code: public void  apairs_from_seed(int l,int i, int j){
  		aligpath = new IndexPair[l];
  		idx1 = new int[l];
  		idx2 = new int[l];
  		for (int x = 0 ; x < l ; x++) {
  			idx1[x]=i+x;
  			idx2[x]=j+x;
  			aligpath[x] = new IndexPair((short)(i+x),(short)(j+x));
  		}
  	}
docs: Set apairs according to a seed position.
  
  @param l
  @param i
  @param j