Re: RichSequence.IOTools performance
Andy Yates <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Makes a lot of sense. There's no way of knowing if a stream is buffered unless the top level object given was an instance of BufferedOutputStream. Does this mean that by some fluke we could buffer a buffered stream? TBH I'm more glad that we've got the speed back :). Andy On 30 Mar 2011, at 20:38, Scooter Willis wrote: > Khalil > > For BioJava3 FastaWriter was simply using an OutputStream where its > use was wrapped by FastaWriterHelper which was not using a > BufferedOutputStream. I made changes to FastaWriter to check if the > OutputStream is an instance of BufferedOutputStream and if not create > one locally and the close when returning. The writing of 10,000 > sequences or 4.5MB of data went from 15 seconds to .6 seconds. I > checked in the code change if you wanted to test using your code. > > Thanks > > Scooter > > On Tue, Mar 29, 2011 at 5:47 PM, Khalil El Mazouari > <[email protected]> wrote: >> 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]... >> >> -- 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] http://lists.open-bio.org/mailman/listinfo/biojava-l