[Biojava-dev] NCBI Blast XML Parser update

[Andreas Prlic]

Hi Ali,

that's good news, can you send your patch to this list, so we can have
a look? At this stage it would be also great to provide a new Junit
test that makes sure that the parsing works ok and to demonstrate the
new feature. If you provide more patches in the future we can also set
up write access to the SVN repository.

Andreas

On Tue, Aug 19, 2008 at 6:10 AM, Muhammad Ali <talk2ali at gmail.com> wrote:
> 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 Also the javadocs for the BlastXMLParser seem to be outdated.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.
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>