[Biojava-l] issue with translating codons with N

[Hara Dilley]

Thank you all for taking care of it so promptly!

From: Nick England [mailto:nickengland at gmail.com]
Sent: Monday, September 23, 2013 8:00 AM
To: Andreas Prlic
Cc: biojava-l at biojava.org; Hara Dilley
Subject: Re: [Biojava-l] issue with translating codons with N

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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:andy.law at roslin.ed.ac.uk>>
> >> wrote:
> >> >
> >> > On 20 Sep 2013, at 16:53, Andy Yates <ayates at ebi.ac.uk<mailto: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...
> >> >
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> >> >
> >> >
> >> >
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> >> >
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> >
>


--
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526<tel:%28%2B1%29%20858.246.0526>
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