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 <[email protected]> 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); > > } > > } > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
