[Biojava-l] Problems with SAX parsing

[Simon Brocklehurst]

Alexander Churbanov wrote:
>    Hello Matthew or Thomas,
> 
>    I just use SAX BLAST parser to parse a massive of
> BLAST output. Unfortunately this package does a really
> poor job in a batch mode. It runs out of memory
> because of the recursive self-calls which adversely
> affects the heap.
>    I know that you have borrowed this from another
> team, but are there any ways to fix it, outherwise I
> run into strange situation while parsing 18,000 Blast
> runs.

We've heard of this before - this *may* be due to an old bug that was 
*supposed* to have been fixed in the biojava code base long ago i.e. 
something not getting popped of a stack when it should be.  Should be 
easy to fix if this bug is somehow still in the biojava code.

If could e-mail the code of the ContentHandler you are using it would be 
helpful. It would be useful to confirm that the problem you are 
experiencing is nothing to do with object creation *outside* of the SAX 
driver itself.

An obvious work around for your problem is to split the blast output 
into smaller chunks.

Simon
-- 
Dr Simon M. Brocklehurst, Ph.D.
Director of Informatics & Robotics

Cambridge Antibody Technology
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