[Bioperl-l] somethin' strange about RootI?

Hilmar Lapp lapp@gnf.org
Fri, 01 Dec 2000 15:17:16 -0800

Mark Wilkinson wrote:
> Hi Group,
> Is there something about the RootI that has changed to prevent these
> lines from
> working properly? (This routine was working until I cvs-updated my
> bioperl "live" folder this afternoon...)
> my $SelectedSeq = Bio::PrimarySeq->new(-seq => (join '',@SelectedSeqs),
> -moltype => 'dna');
> my $SelectedTrans = $SelectedSeq->translate()->seq;
> I get the following error (in both Windows and Linux):
> -------------------- EXCEPTION --------------------
> MSG:
> SCRIPT: Workbench2.pl
> Bio::Root::RootI::new(82)

Hm. The only thing I can say right now is that RootI::new() actually
shouldn't be called, because it is meant to be absent (and eventually it
will be or throw an exception). If this is the reason,
PrimarySeqI::translate seems to create an object from an interface or a
class that does not implement new() itself (which now every class is
supposed to do), or chains back to the inherited (unlikely).

As a general comment to the list, it is probably not a good idea to check
out the main trunk for those people who aren't involved in the
RootI-transition until we've settled this. It's a really a development-only
trunk at the moment. If you're eager to get the newest version for the
latest features, you better wait 1-2 weeks or maybe even a bit more.

Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757