[Bioperl-l] GenericHSP methods

[Paul Boutros]

And it is always possible to reach through to contained elements?  I had
assumed that access methods would be protected and not accessible.


On Tue, 1 Oct 2002, Jason Stajich wrote:

> Look at the ISA hierarchy -
> HSPI is-a Bio::SimilarityPair which contains 2 Bio::SimilarityPair objects.
> 
> 
> 
> On Tue, 1 Oct 2002, Paul Boutros wrote:
> 
> > Excellent!
> >
> > Let me see if I understand this, then:
> > GenericHSP objects contain two LocatableSeq objects -- query and hit.  We
> > can reach through GenericHSP to call LocatableSeq methods directly.  Is
> > that what's goign on here?
> >
> > Thanks,
> > Paul
> >
> > On Tue, 1 Oct 2002, Wiepert, Mathieu wrote:
> >
> > > Try:
> > >
> > > > Is there anyway currently to get the:
> > > > -query_start
> > >
> > > print "\t\tQuery Start: ", $hsp->query->start(), "\n";
> > >
> > > > -query_end
> > >
> > > print "\t\tQuery End: ", $hsp->query->end(), "\n";
> > >
> > > > -hit_start
> > >
> > > print "\t\tHSP Hit Start: ",$hsp->hit->start(), "\n";
> > >
> > > > -hit_end
> > >
> > > print "\t\tHSP Hit End: ",$hsp->hit->end(), "\n";
> > >
> > >
> > >
> > > I can send you a test script as well if you like,
> > >
> > > -Mat
> > >
> > >
> > >
> >
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> >
> 
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>