Thank you guys!
I now have a great looking solution which is lean and fast.
I am definitely a biojava fan.
Regards,
Frans
___
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
Hi,
Thanks for the suggestions. I am quite new in the world of Biojava and
basically what I did was copy the example in Biojava in anger and adapt
it to my needs. It seems I now have to adapt it a little more.
One more question. If the blast output is already in XML, how would you
go about it in
> " " == VERHOEF Frans <[EMAIL PROTECTED]> writes:
> Hi Keith, Thanks for your response. I did paste the method
> that's doing the parsing somewhere below. I also ran just now
> this method trying to parse a blast output file with a size of
> approximately 350mb. The output
iption + "\n");
out.flush();
hitAnno = null;description = null;hit=null;
System.gc();
}
out.close();
hits = null; out=null; outFile=null; bsetting=null; lib=null;
database=null; queryID=null; anno=null; result=null;
System.gc();
out.flush();
hitAnno = null;description = null;hit=null;
System.gc();
}
out.close();
hits = null; out=null; outFile=null; bsetting=null; lib=null;
database=null; queryID=null; anno=null; result=null;
System.gc();
}
file.de
> "FV" == VERHOEF Frans <[EMAIL PROTECTED]> writes:
FV> Hi, I am having a problem parsing huge blast
FV> results. Basically I am parsing the blast results pretty much
FV> the same way as in "Biojava in Anger", with as only difference
FV> that I use the setModeLazy() of the Blas
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 rec
