[Bioperl-l] printing UnivAlgn

[Murad Nayal]

Ewan Birney wrote:
> 
> On Sat, 16 Dec 2000, Murad Nayal wrote:
> 
> >
> >
> > Hi Peter,
> >
> > Ok, so implementing all of SimpleAlign interface in UnivAln is not the
> > most straightforward thing in the world. for one the internal
> > representation of sequences in the two are very different. nonetheless
> > you only use three functions in AlignIO to output the alignment (at
> > least in AlignIO::clustalw and a couple of other classes). I implemented
> > these functions in UnivAln (in terms of UnivAln interface) and it seems
> > to allow AlignIO to print out UnivAln as you would expect. While I was
> > at it I implemented a function to get a SimpleAlign from UnivAln. these
> > new functions, getSimpleAlign() and eachSeq(), are inefficient, they
> > create brand new LocatableSeqs every time they're called. but to augment
> > UnivAln and have it maintain a permanent set of LocatableSeqs needs some
> > substantial effort to ensure consistency between these sequences and the
> > UnivAln->{seq} array, which is too much work for tonight! :-)
> 
> I am impressed! It sounds like you need to get a cvs login...
> 


Thanks Ewan, that would be very cool! :-). 






-- 
Murad Nayal M.D. Ph.D.
Department of Biochemistry and Molecular Biophysics
College of Physicians and Surgeons of Columbia University
630 West 168th Street. New York, NY 10032
Tel: 212-305-6884	Fax: 212-305-6926