[Biojava-l] BlastLikeSearchBuilder and queryIDs

[Keith James]

>>>>> "Frank" == Frank Vernaillen <fr_ve at hotmail.com> writes:

[...]

    Frank> This way I end up with a Vector of
    Frank> SeqSimilaritySearchResults. The SeqSimilaritySearchResult
    Frank> interface offers a getQuerySequence() method, but it
    Frank> returns a SymbolList, not a Sequence. Now this is a
    Frank> problem, because I can't seem to obtain the *queryID* of
    Frank> the sequence anymore, only the sequence symbols
    Frank> themselves. Was this a deliberate design choice?

    Frank> Any ideas on how to elegantly obtain the queryIDs from the
    Frank> parsed Blast output?

Alrighty - I've made what should be the final change in this package
before the release. getQuerySequence now really does return a Sequence
which will be the same one as in your query sequence holder. If you
use a dummy query sequence holder (and therefore don't have access to
an instance of the query Sequence) the query Id is still available in
the Result annotation under the key "queryId".

There is also an interesting and elegant modular approach to parsing
the same output in demos/ssbind which doesn't rely on creating full
Result objects for every report. Useful of your data are absolutely
monstrous e.g. Gb of output.

This is in cvs and will make it into the next (pre) release.

cheers,

Keith

-- 

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