Is there some place that lists all the keys that are stored in Annotations for various
types of reports that are parsed (specifically BLAST in my case)? Or are we stuck with
manually going in,?
listing them all and "seeing before trying". Say it ain't so! :)
Also, I've been getting inconsistent errors when parsing Blast reports. Specifically,
I get an error when I try parsing a BLAST report using the BlastParser program given
in Biojava in Anger (nice title BTW) while the Blast2HTML parser in the demos
directory (also using the BlastLikeSaxParser) runs perfectly fine. So the problem is
probably actually in the ContentHandler or the SeqSimilarityAdapter. Anyway, the
error that the BlastParser program returns is:
-----------------------------
"org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.6 is not supported by the
biojava blast-like parsing framework
at
org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:241)
at
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160)
at BlastParser.main(BlastParser.java:43)"
-------------------------
Any help is greatly appreciated!
Thanks,
DeAngelo Lampkin
Scientific Programmer
Xencor
626 - 737 - 8083
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