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

[Ewan Birney]

On Fri, 30 Mar 2001, Hilmar Lapp wrote:

> Peter Schattner wrote:
> > > > Ideally Bio::PrimarySeq
> > > > (or maybe better Bio::PrimarySeqI?) has a method boolean
> > > > validate_seq(), and depending on its return value seq() throws an
> > > > exception. So, in your deriving implementation you'd only have to
> > > > override validate_seq(). (As a matter of fact, there is no
> > > > validate_seq() right now :|
> > >
> > > Yup. The refinement here is that Alignments use LocatableSeq so that's the
> > > place to put it (perhaps LocatableSeq should migrate to AlignedSeq...)
> > 
> > Do you guys envision
> > implementing these enhancements (eg validate_seq() method) in 0.7.1 or
> > only in 0.8?
> 
> 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?


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


BTW Hilmar - nice cleaning up on the buglist/branch areas...



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