code: public static final List<Integer> getEQRAlignmentPos(AFPChain afpChain){
  		List<Integer> lst = new ArrayList<Integer>();
  
  		char[] s1 = afpChain.getAlnseq1();
  		char[] s2 = afpChain.getAlnseq2();
  		char[] symb = afpChain.getAlnsymb();
  		boolean isFatCat = afpChain.getAlgorithmName().startsWith("jFatCat");
  
  		for ( int i =0 ; i< s1.length; i++){
  			char c1 = s1[i];
  			char c2 = s2[i];
  
  			if ( isAlignedPosition(i,c1,c2,isFatCat, symb)) {
  				lst.add(i);
  			}
  
  		}
  		return lst;
  
  	}
docs: TODO: same as getEqrPos??? !!!