[Biojava-l] issue with translating codons with N

[Nick England]

Hi

I've updated to that 3.0.7-SNAPSHOT and can confirm the issue has been
resolved for me too.

Thanks for fixing it so quickly!

Nick


On 23 September 2013 02:38, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi,
>
> I believe this is fixed  now according to Andy's suggestion. Can somebody
> else please verify? Then I can push out 3.0.7 shortly.
>
> https://github.com/biojava/biojava/issues/53
>
> Cruisecontrol has already pushed out the latest snapshot builds into our
> maven repository, so anybody who is using 3.0.7-SNAPSHOT as a dependency
> should be able to get it by doing a mvn -U  (force update).
>
> Andreas
>
>
>
>
>
>
> On Fri, Sep 20, 2013 at 10:10 AM, Michael Heuer <heuermh at gmail.com> wrote:
>
> > That is reasonable, though the sequencing module already has a
> > dependency on guava.
> >
> > Does this issue only apply to biojava3 or is biojava-legacy affected
> > as well?  If so I should be able to do the release there.
> >
> >    michael
> >
> >
> > On Fri, Sep 20, 2013 at 11:53 AM, Andreas Prlic <andreas at sdsc.edu>
> wrote:
> > > Hi,
> > >
> > > I'd prefer to keep the -core free of external dependencies.
> > >
> > > I filed this as a ticket on github and added the code snippets that
> were
> > > shared on this thread. Who will take this one on?
> > >
> > > I will make a quick BioJava release once this has been fixed and
> > verified.
> > >
> > > Andreas
> > >
> > >
> > >
> > >
> > > On Fri, Sep 20, 2013 at 9:16 AM, Michael Heuer <heuermh at gmail.com>
> > wrote:
> > >>
> > >> You might also want to performance compare against Guava's
> ImmutableMap
> > >>
> > >>
> > >>
> >
> http://docs.guava-libraries.googlecode.com/git/javadoc/com/google/common/collect/ImmutableMap.html
> > >>
> > >> keeping in mind the javadoc note about caching hashCodes in the
> > >> elements if calculating them is slow.
> > >>
> > >>    michael
> > >>
> > >>
> > >> On Fri, Sep 20, 2013 at 11:05 AM, LAW Andy <andy.law at roslin.ed.ac.uk>
> > >> wrote:
> > >> >
> > >> > On 20 Sep 2013, at 16:53, Andy Yates <ayates at ebi.ac.uk> wrote:
> > >> >
> > >> >> Hi Nick,
> > >> >>
> > >> >> It depends on the number of translations you're doing. We did some
> > >> >> quite large performance testing Pjotr Prins for his chapter in
> > Evolutionary
> > >> >> Genomics book and those changes where a direct result of that *. I
> > think the
> > >> >> right solution is to revert to using the map already available in
> > the class
> > >> >>
> > >> >> Andy
> > >> >>
> > >> >> * I wish I still had the stats from before & after this change to
> > show
> > >> >> what the performance impact was.
> > >> >>
> > >> >
> > >> > I'm surprised at that, given that the lookup is essentially from a
> > >> > small, finite set. But then again, the quicker version seems to have
> > been
> > >> > giving the wrong answer so that's probably not a trade off one would
> > want to
> > >> > consider :o{
> > >> >
> > >> > Later,
> > >> >
> > >> > Andy
> > >> > --------
> > >> > Yada, yada, yada...
> > >> >
> > >> > Disclaimer: This e-mail and any attachments are confidential and
> > >> > intended solely for the use of the recipient(s) to whom they are
> > addressed.
> > >> > If you have received it in error, please destroy all copies and
> > inform the
> > >> > sender.
> > >> >
> > >> >
> > >> >
> > >> >
> > >> > --
> > >> > The University of Edinburgh is a charitable body, registered in
> > >> > Scotland, with registration number SC005336.
> > >> >
> > >> >
> > >> > _______________________________________________
> > >> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > >> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >>
> > >> _______________________________________________
> > >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >
> > >
> > >
> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>