[Biojava-l] issue with translating codons with N

[Michael Heuer]

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...
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