[Bioperl-l] FeaturePair:length

[Jason Stajich]

further digging:

We pass in -querylength, -sbjctlength to BPlite::HSP constructor and never
use it.

Will add a hsplength method to HSP object for now to see if it can
capture what we need.  Adding more tests to BPlite to handle this.

Also adding Kris V's gap methods which are much appreciated!

-jason
 
On Fri, 27 Jul 2001, Ewan Birney wrote:

> On Fri, 27 Jul 2001, Jason Stajich wrote:
> 
> > I think that fundamentally we are doing something wrong with SimilarityPairs.
> > 
> > Right now, for a feature pair (SimilarityPair isa FeaturePair) $fp->length
> > is calculated from ($fp->end - $fp->start). $fp->start is really an alias
> > for $fp->feature1->start so the length of the pair is really only relative
> > to feature1 of the feature pair.  This causes problems for similarity
> > paris where gaps can be occuring.
> 
> I think this is the right semantics for length (remember it has to honor
> the seqfeature interface, which views the SimilarityPair from one "side" -
> this case being feature1).
> 
> 
> I agree we need a hsplength sort of call. What it gives... is another
> question (think BLASTX results...)
> 
> 
> > 
> > I'm adding the method hsplength to the BPlite::HSP object to at least
> > handle this for BPlite results, but we may want think about storing length
> > on the SimilarityPair object rather than delegating it to feature1 (what
> > we do right now).
> > 
> > Perhaps this can all go into a  more generalized HSP/Search objects which
> > has been an idea kicking around for a little while now.  Probably would be
> > a full rewrite of what Aaron started in Bio::Search::* but wouldn't mind
> > keeping that namespace.  (*project possibility*).
> > 
> > -jason
> > Jason Stajich
> > jason@chg.mc.duke.edu
> > Center for Human Genetics
> > Duke University Medical Center 
> > http://www.chg.duke.edu/ 
> > 
> > 
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> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
> 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/