[Bioperl-l] GCG MSF format alignments

[Peter Schattner]

> > I actually like the exception being thrown there, even though I bumped
> > into this several times, too. However, it always indicated a bug.
> >
> > I'd actually prefer this being solved by creating a specialized class
> > that specifically allows for additional characters as they are used in
> > e.g. alignments. This should go under Bio::Seq::<AlignedSeq>.pm
> > (replace <...> with whatever you like better). 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...)

Well, I'm clearly out-voted.  That's fine by me.  Do you guys envision
implementing these enhancements (eg validate_seq() method) in 0.7.1 or
only in 0.8?  In the latter case I'll submit a documentation-bug fix
removing the statement that alignments can be read in with "~" or
similar strange characters and fixed later.  

Cheers

Peter