[Bioperl-l] validate_seq() in Bio::PrimarySeq

Hilmar Lapp hilmarl@yahoo.com
Fri, 30 Mar 2001 00:46:51 -0800

Ewan Birney wrote:
> >
> > I've added an implementation of validate_seq() to Bio::PrimarySeq
> > and Bio::Seq, and I added the method also to the interface
> > Bio::PrimarySeqI.
> >
> > I did these changes on the main trunk. In general I don't have a
> > principal problem with merging this to the branch, but first I'd
> > rather have some comments whether people think putting it into the
> > interface too may break backward-compatibility. I'm not even sure
> > it ought to be in the interface. Is anyone else?
> I do view validate_seq as more an internal method not part of the
> interface. Is there any reason to move this to the interface?

Not a strong one. Bio::LocatableSeq inherits off Bio::Seq (why not
PrimarySeq?), so it has to be both in Bio::PrimarySeq and

> If this clears up Peter's bug, then I think it is worth moving to the
> branch

It doesn't per se, it's only the foundation. Now validate_seq()
has to be overridden in LocatableSeq in order to allow for some
additional special characters. (BTW I still think LocatableSeq
should relocate to Bio::Seq::something, but that's main trunk

Hilmar Lapp                              email: hilmarl@yahoo.com
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757