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]> 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]> 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]> > 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]> > > 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]> > > >> wrote: > > >> > > > >> > On 20 Sep 2013, at 16:53, Andy Yates <[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] > > >> > http://lists.open-bio.org/mailman/listinfo/biojava-l > > >> > > >> _______________________________________________ > > >> Biojava-l mailing list - [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 > ----------------------------------------------------------------------- > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
