[Bioperl-l] Naming consistency and Bioperl future search result parsing

[Jason Stajich]

In an effort to make bioperl approachable to new developers and users
alike we are trying to establish some consistency for naming of things.
In the first wave of these changes I am working on the Search objects and
the assorted supporting cast.

Ewan, Steve, and I have talked about Steve's new Search objects and I'd
like to go with his nomeclature:

Query - the query input to a db search or the first item in a pairwise
        alignment
Hit   - a database search 'hit' (formerly a 'subject') or 2nd item in a
        pairwise alignment
HSP   - a component of a Hit that is an alignment between the query and
        subject - in most cases the best local alignment(s).
Result - a database or pairwise alignment search run (formerly 'report').
        Report can be used to refer to a

My plan is to migrate calls to 'hit' from subject and deprecate the
Bio::SeqFeature::SimilarityPair method 'subject' in favor of a new method
'hit'.

The Bio::Search and Bio::SearchIO classes and directories will be
reorganized to only contain Query, Hit, HSP, & Result in the API.

Bio::Tools::Blast is to be deprecated in 1.0 and eventually removed from
the bioperl distribution in favor of the new Bio::SearchIO system.  It is
unclear how we will proceed wrt to the Blast-Parsing Lite system (BPlite,
BPpsilite, BPbl2seq) they will certainly be part of the 1.0 release and it
remains to be seen if we will want to continue to support 2 frameworks.

Bioperl 1.0 should contain a robust event based parsing framework for
search results.  We will focus on providing simple access to report data
in the SearchIO system in a standard API for multiple search result
formats.

Additionally groundwork has been laid by Steve C to provide lazy parsing
for those with specific performance and flexibilty needs.  I am still
sifting through the options here, but I think we can meet the both goals
of supporting power users and not confusing new users or developers.

I hope to have this transition finished in the next few weeks, any
comments, volunteers, or ideas are welcomed, but unless you can help
code I intend to take the course outlined above.  This will be our 3rd
generation parsing system (3G ;) ) and work will continue to be done to
improve and integrate this system with bioperl and support future formats.

-jason

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu