[Bioperl-l] SearchIO speed up

Chris Fields cjfields at uiuc.edu
Thu Aug 17 16:49:15 EDT 2006


I have to agree.  If there was a way to get around this by having the change
behind the scenes in HSPI then I wouldn't see a problem. 

Hence my suggestion of implementing hit() and other
SeqFeature::SimilarityPair methods directly in Bio::Search::HSP::HSPI (i.e.
no SimilarityPair inheritance) to return Bio::SeqFeature::Similarity objects
directly.

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: Thursday, August 17, 2006 3:20 PM
> To: Sendu Bala
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] SearchIO speed up
> 
> 
> On Aug 17, 2006, at 4:07 PM, Sendu Bala wrote:
> 
> > The entire test suite is happy except for t/SimilarityPair (it tests
> > that a HSP is a SimilarityPair, which it obviously isn't anymore)
> 
> This is a sure sign that the change should not be made. There are
> numerous possible applications that may need to rely on this being a
> SeqFeature::SimilarityPair, for instance OR mappers.
> 
> A change like this is pretty drastic. Making it in a well-traveled
> interface like SearchIO and friends would need to be justified by the
> previous design being clearly very poor or too limiting (or both), or
> by an at least equally drastic speed-up. Any speed-up would have to
> be more than an order of magnitude to count as drastic.
> 
> 	-hilmar
> 
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list