[Biojava-l] Any memory-optimised blast parser available ?[Scanned]

[Jolyon Holdstock]

Can you use the -Xmx flag to add more memory to the JRE?

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Benoit
VARVENNE
Sent: 13 November 2006 10:54
To: biojava-l
Subject: [Biojava-l] Any memory-optimised blast parser available
?[Scanned]

Hello,

I'm trying to parse blast result files from a remote blast on NCBI
databases.
In order to do so, i'm using biojava XML parser like this :

-----------
      InputStream is = new FileInputStream(blastFile);
      BlastXMLParserFacade parser = new BlastXMLParserFacade();
      SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();

      parser.setContentHandler(adapter);

      List results = new ArrayList();

      SearchContentHandler builder = new BlastLikeSearchBuilder(results,
          new DummySequenceDB("queries"), new
DummySequenceDBInstallation());

      adapter.setSearchContentHandler(builder);

// Here is the method that throws 'OutOfMemoryException'
      parser.parse(new InputSource(is));
-----------

While blasting a genomic sequence (i've tried with 50Kb long sequences
max),
I've got an OutOfMemory exception.

Does anyone know a way to resolve this ? (this aim is not to dividde my
genomic locus in too many parts, 50Kb is a quarter of my genomic...)

Thanks,
Regards,

Benoit


-- 
Benoit Varvenne,
Bioinformatics pearson in charge,
GenOway - Lyon (France)

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