code: public void apairs_from_idxlst(JointFragments jf) {
  		List<int[]> il = jf.getIdxlist();
  		//System.out.println("Alt Alig apairs_from_idxlst");
  
  		aligpath = new IndexPair[il.size()];
  		idx1 = new int[il.size()];
  		idx2 = new int[il.size()];
  		for (int i =0 ; i < il.size();i++) {
  			int[] p = il.get(i);
  			//System.out.print(" idx1 " + p[0] + " idx2 " + p[1]);
  			idx1[i] = p[0];
  			idx2[i] = p[1];
  			aligpath[i] = new IndexPair((short)p[0],(short)p[1]);
  
  		}
  		eqr0  = idx1.length;
  		//System.out.println("eqr " + eqr0);
  		gaps0 = count_gaps(idx1,idx2);
  
  	}
docs: Set apairs according to a list of (i,j) tuples.
  
  @param jf a JoingFragment