Re: RichSequence.IOTools performance
Khalil El Mazouari <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Hi I am using netbeans profiler. The total exec time was ± 20s (macbook pro i7, 4GB, SSD) for ± 10.000 seq. By writing the RichSequence object to ByteArrayOutputStream -> FileChannel, where appropriate, the total exec time dropped to 7s. Huge improvement, for the app I am developing. The app will be used to analyze ± 100,000 sequence per run. Regards, khalil On 29 Mar 2011, at 22:13, Scooter Willis wrote: > Instead of percentage metrics can you get the time before and after the write execution for comparison without profiling. What profiler are you using? > > >> On Mar 28, 2011 5:39 PM, "Andy Yates" <[email protected]> wrote: >> >> Dang Rich :). >> >> At the moment we've not done anything WRT Genbank outputting but would accept anything to help us out with this. >> >> As for the performance difference between BJ3 & BJ what happens if you use the writer objects directly with a BufferedOutputStream writer? Have you got any profiling results? It would be very interesting to see where we've lost the performance ... >> >> Andy >> >> On 28 Mar 2011, at 18:23, Richard Holland wrote: >> >> > In which case you've got little option but to r... >> >> -- >> Andrew Yates Ensembl Genomes Engineer >> EMBL-EBI Tel: +44-(0)1223-492538 >> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 >> Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/ >> >> >> >> >> >> _______________________________________________ >> Biojava-l mailing list - [email protected]... >> > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l