[Biojava-l] issue with translating codons with N

[Andreas Prlic]

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...
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