[Biojava-l] Trouble with parsing big Blast result raport

[Petri Pehkonen]

Hi,

It works now! I set the stack size value on hotspot-virtual machine
greater, and it goes through. I noticed that the stack of the parser
goes very big when parsing. I don't know if it's true but I suspect that
the endElement-method of my contenthandler is not executed every time it
should. So I have to check out if I have the newest versions of
biojava-components and the right version of Blast that suits with
BlastLikeSAXParser. Thanks for the help.

-Pete-



On Tue, 8 Jan 2002, Simon Brocklehurst wrote:

> Petri Pehkonen wrote:
> 
> > Hi,
> >
> > I'm using Java SDK Standard Edition 1.3.1 under Windows 2000. I tried to
> > change the virtual machine to "classic" but it didn't help and I got the
> > same error message. I wonder if anyone has made parsing with result files
> > as big as ours?
> 
> Hi,
> 
> I just tried the following test.
> 
> Run the application TutorialEx1 in the demos directory using an input file of
> around 28 MB  in size (I created this cat-ing together 3 copies of the c. 9 MB
> file - Massive.out - in the demos/files/ncbiblast directory of the biojava
> distribution).
> 
> I ran the program under J2SE 1.3.1_01, running under Solaris 8.
> 
> Everything seemed to work fine.
> 
> Should be trivial for someone who uses Win2K for their development environment to
> try this test.
> 
> S.
> --
> Simon M. Brocklehurst, Ph.D.
> Head of Bioinformatics & Advanced IS
> Cambridge Antibody Technology
> The Science Park, Melbourn, Cambridgeshire, UK
> http://www.CambridgeAntibody.com/
> mailto:simon.brocklehurst@CambridgeAntibody.com
> 
>