[Biojava-l] Stop condition for blast parser

Marcel Huntemann marcel.huntemann at gmail.com
Sat Mar 7 00:55:35 UTC 2009


Hi!

I followed the example in
http://biojava.org/wiki/BioJava:CookBook:Blast:Echo to create my own blast
parser.
I've the problem that I am often only interested in the hits of a certain
query. Is there a way to tell the blast parser via my customized
SearchContentHandler to stop parsing after it found this certain queryId?
Because often the wanted queryId will be in the beginning of the blast
file and I don't want the parser to run over the really, really long rest
of the file, even if it doesn't do much during that. I just want the
parser to stop then. Can I implement that somehow in my customized
SearchContentHandler or do I've to change the source code of biojava
somewhere for that?

Thanks,
Marcel



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