[Bioperl-l] GenericHSP methods

[Jason Stajich]

On Tue, 1 Oct 2002, Paul Boutros wrote:

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

If they are public methods they are accessible, public methods are
functions which don't start with a leading '_'.

Two rules: If the method starts with _ it is private, and don't expect
private data ($obj->{'_hashkey'}) to be valid when inheriting or even
between versions of the toolkit (unless you know exactly what you are
doing).

-jason
>
> 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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> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu