In which case you've got little option but to rewrite the GenbankFormat module to use NIO or other alternative methods for writing files. However before you do that I suggest you investigate the recent BioJava3 developments to see if they've already done anything in this area - Andy Yates is your man there.
On 28 Mar 2011, at 18:11, Khalil El Mazouari wrote: > Sequences objects are all in-memory. > I agree, 10000 seq in ± 20 sec is not bad. However, scientists will processes > 100,000 seqs in each run, and IO is a real bottleneck. So, I am trying, as > far as I can, to fine tune the app. > > Regards, > > khalil > > On 28 Mar 2011, at 18:15, Richard Holland wrote: > >> I would have thought 10,000 seqs written out in full Genbank format in 20 >> seconds was pretty good! However, the key to speeding it up would be to >> modify the OutputStream interactions to use faster things such as NIO. Also >> it would depend on the source of your sequence objects - if they are all >> in-memory then this isn't an issue, but if they are being read from a >> database using lazy or dynamic loading then that could be a bottleneck too. >> >> >> On 28 Mar 2011, at 17:07, Khalil El Mazouari wrote: >> >>> Hi, >>> >>> I am developing a sequence annotation app. It should handle ± 100.000 >>> sequence per run. >>> >>> When profiling the app (with 10.000 seq), the total execution time was ± 20 >>> seconds, of which 57% was used for RichSequence.IOTools.writeGenbak!! >>> >>> How one could improve the RichSequence.IOTools performance? >>> >>> Thanks. >>> >>> khalil >>> _______________________________________________ >>> Biojava-l mailing list - [email protected] >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> -- >> Richard Holland, BSc MBCS >> Operations and Delivery Director, Eagle Genomics Ltd >> T: +44 (0)1223 654481 ext 3 | E: [email protected] >> http://www.eaglegenomics.com/ >> > -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: [email protected] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
