[Biojava-dev] NCBI Blast XML Parser update

[Muhammad Ali]

Hello,

The current version of the BlastXMLParser (used for parsing NCBI BLAST
output files) is not handling multiple Iteration entries in the file
correctly. It lumps them all together, resulting in a loss of
search-specific parameters. The end result is a single
SeqSimilaritySearchResult object. The expected output should be one
SeqSimilaritySearchResult for each Iteration entry in the file.

I've fixed this issue on my locally checked out copy by modifying a
few files in the  org.biojava.bio.program.sax.blastxml package. I'm
interested in submitting the updated code back to the main repository.
Can someone tell me how I can go about doing so?

Also the javadocs for the BlastXMLParser seem to be outdated. They
mention malformed XML being generated by NCBI, but that doesn't seem
to be the case anymore.

Thanks,
Ali.