[Biojava-l] parse blast results

[Keith James]

>>>>> "Howard" == Howard Ungar <howard_ungar@yahoo.com> writes:

[...]

    Howard> Keith, I think I tried to get the QueryId from the
    Howard> RawOutput, but the parser was not starting to include data
    Howard> until later in the Blast Report file.  I don't think my
    Howard> changes will fit into the current DTD as you described it.
    Howard> I could modify what I did to create these attributes in
    Howard> the rawOutput element if you would like me to.  Or would
    Howard> it be better to consider modifying the DTD (and risk
    Howard> breaking existing code).  Either way, please take a look
    Howard> at what I did and provide some feedback about how you
    Howard> would like me to proceed.

Hi Howard,

Your code gave me the incentive to sort this out. As your patch
produced XML which contained the query ID, but didn't comply with the
Biojava DTD, I haven't applied it.

Instead I have added support for the QueryId and DatabaseId elements
described in the DTD and the BlastSAXParser now emits these elements
for Blast (but not HMMER).

Your BlastHandler should now be able to get the query ID from its
stack in the same way as it does for all the other elements.

thanks for reminding us about this,

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK