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

[Hilmar Lapp]

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?

	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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