Thank you all for taking care of it so promptly! From: Nick England [mailto:[email protected]] Sent: Monday, September 23, 2013 8:00 AM To: Andreas Prlic Cc: [email protected]; 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 > <[email protected]<mailto:[email protected]>> 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 > > <[email protected]<mailto:[email protected]>> > 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 > >> <[email protected]<mailto:[email protected]>> > >> wrote: > >> > > >> > On 20 Sep 2013, at 16:53, Andy Yates > >> > <[email protected]<mailto:[email protected]>> 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 - > >> > [email protected]<mailto:[email protected]> > >> > http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > >> _______________________________________________ > >> Biojava-l mailing list - > >> [email protected]<mailto:[email protected]> > >> 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<tel:%28%2B1%29%20858.246.0526> ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected]<mailto:[email protected]> http://lists.open-bio.org/mailman/listinfo/biojava-l ________________________________ This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
