[Bioperl-l] remote blast update

[Hilmar Lapp]

"Chervitz, Steve" wrote:
> 
> 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.

Right. The from_searchResult() method in SimilarityPair was actually a
humble attempt to integrate the Tools::Blast objects at least a little
bit with the rest of Bioperl (i.e., this method allows you to turn
Blast objects into SeqFeatureI compliant objects). BPlite objects
already inherit from those SeqFeature classes and thereby do not need
such a method. (Obviously, BPlite objects don't implement interfaces
for hits and aligned regions either.)

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