code: public void setIdxlist(List<int[]> idxs) {
  			Iterator<int[]> iter = idxs.iterator();
  			while (iter.hasNext()){
  				int[] e = iter.next();
  				idxlist.add(e);
  			}
  		}
docs: Stores the alignment between the residues of several fragments.
  Each int[] stores the residue numbers of several equivalent residues.