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

[Ewan Birney]

On Fri, 30 Mar 2001, Hilmar Lapp wrote:

> 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
> Bio::Seq.

Aha. LocatableSeq inherieting off Bio::Seq is cruft.

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

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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