code: public static String flipAlignment(String xml) throws IOException,StructureException{
  		AFPChain[] afps = parseMultiXML( xml);
  		if ( afps.length < 1 )
  			return null;
  
  		if ( afps.length == 1) {
  			AFPChain newChain = AFPChainFlipper.flipChain(afps[0]);
  			if ( newChain.getAlgorithmName() == null) {
  				newChain.setAlgorithmName(DEFAULT_ALGORITHM_NAME);
  			}
  			return AFPChainXMLConverter.toXML(newChain);
  		}
  		throw new StructureException("not Implemented yet!");
  	}
docs: Takes an XML representation of the alignment and flips the positions of name1 and name2
  
  @param xml String representing the alignment
  @return XML representation of the flipped alignment