[Bioperl-l] Re: bioperl Registry

Lincoln Stein lstein at cshl.edu
Fri Nov 21 11:18:20 EST 2003


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
========================================================================




More information about the Bioperl-l mailing list