[Bioperl-l] GenericHSP methods

[Jason Stajich]

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