[Bioperl-l] remote blast update

Chervitz, Steve Steve_Chervitz@affymetrix.com
Mon, 16 Apr 2001 12:15:24 -0700

Hilmar Lapp [mailto:lapp@gnf.org] writes:
> "Chervitz, Steve" wrote:
> > 
> > 
> > I've seen Aaron's interfaces and think they're a good 
> start. It would be
> > great if your Similarity feature objects, for example, 
> could be constructed
> > based on such interfaces, and not be tied to any particular type of
> > similarity search result object, as they are now.
> Well, I thought they are not. If they are, I'd say it's a design bug.
> What in the design did you find tied to a particular type of search
> result? The SimilarityPair obviously is limited to a subject and a
> query, not many subjects.

The from_searchResult() method of SimilarityPair tests for and handles only
Bio::Tools::Blast::Sbjct or Bio::Tools::Blast::HSP objects, instead of some
generic interface type such as Bio::Search::Hit::HitI. You mention this
dependency in the docs for that method.

I'd say there is a design bug here, but your code is just a symptom of it.
The primary "illness" is that the Blast objects aren't implementing any
interfaces for hits and aligned regions.



> 	Hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp@gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------