code: @SuppressWarnings("unused")
  	private static void displayAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException, StructureException {
  		Atom[] ca1clone = StructureTools.cloneAtomArray(ca1);
  		Atom[] ca2clone = StructureTools.cloneAtomArray(ca2);
  		if (! GuiWrapper.isGuiModuleInstalled()) {
  			System.err.println("The biojava-structure-gui and/or JmolApplet modules are not installed. Please install!");
  			// display alignment in console
  			System.out.println(afpChain.toCE(ca1clone, ca2clone));
  		} else {
  			Object jmol = GuiWrapper.display(afpChain,ca1clone,ca2clone);
  			GuiWrapper.showAlignmentImage(afpChain, ca1clone,ca2clone,jmol);
  		}
  	}
docs: TODO dmyersturnbull: This should probably be in structure-gui