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 > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
