StructurePairAligner

   Hi Guys : I am trying to adopt the StructurePairAligner.java program
which Andreas wrote, which is available online.   I noticed that
"startingAlignment" "calculatedFragmentPairs" and "jointFragments" are not
in the AlignmentProfressListener class.  Is there an updated version of the
pair aligner gui ?


private void notifyStartingAlignment(String name1, Atom[] ca1, String name2,
Atom[] ca2){

           for (AlignmentProgressListener li : listeners){

              li.startingAlignment(name1, ca1, name2, ca2);

           }

        }


        private void notifyFragmentListeners(List<FragmentPair> fragments){


           for (AlignmentProgressListener li : listeners){

              li.calculatedFragmentPairs(fragments);

           }


        }


        private void notifyJointFragments(JointFragments[] fragments){

           for (AlignmentProgressListener li : listeners){

              li.jointFragments(fragments);

           }

        }
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