[Bioperl-l] SearchIO speed up

Chris Fields cjfields at uiuc.edu
Thu Aug 17 17:34:52 EDT 2006


I suppose you could do it that way.  What I was thinking would be having
hit() and query() methods directly in HSPI (no inheritance), so I guess you
wouldn't really be 'implementing' them.  

They would return Bio::SeqFeature::Similarity objects directly.  Though I
don't really know if it's possible, and also don't really see the purpose
here if the speedup is marginal.
 
Chris

> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: Thursday, August 17, 2006 4:17 PM
> To: Chris Fields
> Cc: 'Sendu Bala'; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] SearchIO speed up
> 
> You mean you maintain inheritance but re-implement the methods to
> override the inherited ones?
> 
> On Aug 17, 2006, at 4:49 PM, Chris Fields wrote:
> 
> > 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
> >
> 
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 




More information about the Bioperl-l mailing list