[Biojava-l] BLAST/Java interface

[Keith James]

>>>>> "Mark" == Schreiber, Mark <mark.schreiber@agresearch.co.nz> writes:

    Mark> Matthew and Keith, Might this be a case for encapsulation of
    Mark> some of the common parsing tasks in a single easy to use
    Mark> object or tools class.

[...]

That's a good idea. Unfortunately my plate is full right now with
documenting other peoples' code (you know who you are ;P) and updating
the parser & tests to support NCBI Blast 2.2.3 in strict mode.

    Mark> Is it possible to have a class that contains an internal
    Mark> Process object that points to the blast binary(s) (whose
    Mark> path could be passed as a File reference). This object could
    Mark> then take seach strings as an InputStream and return results
    Mark> as an OutputStream abstracting away the need to understand
    Mark> whats happening under the hood.

Maybe this should be more generic - I can imagine programs other than
Blast being run (HMMER, Fasta etc). Also good idea, though.

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -