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);

	}
public void apairs_from_idxlst ( JointFragments jf ) { List < int [ ] > il = jf . getIdxlist ( ) ; 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 ) ; idx1 [ i ] = p [ 0 ] ; idx2 [ i ] = p [ 1 ] ; aligpath [ i ] = new IndexPair ( ( short ) p [ 0 ] , ( short ) p [ 1 ] ) ; } eqr0 = idx1 . length ; gaps0 = count_gaps ( idx1 , idx2 ) ; }
Set apairs according to a list of (i,j) tuples.

@param jf a JoingFragment