Hi,
I am having a problem parsing huge blast results. Basically I am parsing the blast results pretty much the same way as in "Biojava in Anger", with as only difference that I use the setModeLazy() of the BlastLikeSAXParser, since I am using NCBI Blast version 2.2.4 and that version is not recognised by the parser yet. Besides that the only difference lays in the things I do with the data. The problem is that when I parse a blast result that is a few hundred MB, for example 300MB, the java application is ballooning up to around 1.6GB of memory. Sometimes the application even crashes because I only have got 2GB to play with. Does anyone know what's causing this? Is it because I set the lazy mode? Is there any way to work around it? Kind regards, Frans Verhoef Bioinformatics Specialist Genome Institute of Singapore Genome, #02-01, 60 Biopolis Street, Singapore 138672 Tel: +65 6478 8000 DID: +65 6478 8060 HP: +65 9848 4325 Email: [EMAIL PROTECTED]
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