[Biojava-l] RichSequence.IOTools performance

[Khalil El Mazouari]

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" <ayates at ebi.ac.uk> 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/
>> 
>> 
>> 
>> 
>> 
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