[Bioperl-l] Re: bioperl Registry

[Lincoln Stein]

Hi Heikki,

It's not the same functionality, though.  Your version returned undef if the 
sequence is undef even though "start" might be defined.

Lincoln

On Friday 21 November 2003 10:03 am, Heikki Lehvaslaiho wrote:
> Lincoln,
>
> The code you wrote below gives the same functionality than my previous
> version but is easier to understand. Let's use it. I'll commit it.
>
> 	-Heikki
>
> On Friday 21 Nov 2003 TT:02, Lincoln Stein wrote:
> > In fact I would be happy with this:
> >
> > 	return $self->{'start'};
> >
> > The GFF code is correctly setting the 'start' key in this case.  The || 1
> > was residual because I didn't understand what the intent of the code was.
> > Perhaps the logic you are looking for is:
> >
> > 	return $self->{'start'} if defined $self->{'start'};
> > 	return 1                   if $self->seq;
> > 	return;
> >
> > ???
> >
> > Lincoln
> >
> > > I happy to accept this but would like to understand why before I change
> > > the t/Locatable.t.
> > >
> > > 	-Heikki
> > >
> > > > Lincoln
> > > >
> > > > On Thursday 20 November 2003 09:16 pm, Lincoln Stein wrote:
> > > > > I've got perl 5.8.2 installed now and can partially reproduce the
> > > > > problem. I am working on it now.
> > > > >
> > > > > Lincoln
> > > > >
> > > > > On Thursday 20 November 2003 08:19 am, Heikki Lehvaslaiho wrote:
> > > > > > Michele & Lincoln,
> > > > > >
> > > > > > Could I bother either of you two to have a look at the bioperl
> > > > > > live Registry/ Bio::DB::Flat modules. There is something wrong in
> > > > > > the BerkeleyDB version of flatdb and I can not get my head around
> > > > > > it.
> > > > > >
> > > > > > Brian has been  working on it but everything works under his
> > > > > > cygwin system so he is stuck. I isolated the BDB tests from
> > > > > > t/Registry.t into an other file and put it into bugzilla:
> > > > > > http://bugzilla.bioperl.org/show_bug.cgi?id=1562
> > > > > >
> > > > > > The tests fail in both Mandrake Linux 9.2+cooker (Perl 5.8.2) and
> > > > > > RedHat Linux 9 (Perl 5.8.1), so it is definitely not just my
> > > > > > system's problem.
> > > > > >
> > > > > > Cheers,
> > > > > > 		-Heikki

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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