[Biojava-l] StructurePairAligner

[Andreas Prlic]

Hi Jay,

What is the goal of what you want to do with this? The
StructurePairAligner is  historically the oldest of the various
structure alignment algorithms that are coming with biojava. The
events that you are pointing out allow to trace what is going on in
this implementation. However because they are quite specific to this
algorithm, this did not get used when we were working later on the ce
and fatcat implementations. If you want to work on derived algorithms,
I recommend implementing the StructureAlignment interface and use
CeMain.java (and others) as a template...

I am not sure what you mean with pair aligner gui. There are some
examples in the demo package in biojava3-structure-gui. E.g.
DemoAlignmentGui ..

Hope that helps,

Andreas




On Fri, Jun 10, 2011 at 11:30 AM, Jay Vyas <jayunit100 at gmail.com> wrote:
>   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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