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
