[Bioperl-l] printing UnivAlgn

[Ewan Birney]

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...


> 
> the diffs are attached.
> 
> By the way, I found it useful to modify AlignIO::clustalw a bit to make
> sure that the sequence name does not exceed the space allocated to it in
> the printed alignment. diffs for this is attached as well.
> 
> Regards,
> 
> Peter Schattner wrote:
> > 
> > Murad Nayal wrote:
> > 
> > > is UnivAln being phased out?
> > 
> > It would be nice if UnivAln were phased out.  But since it still has lots of
> > features that some people may be using this doesn't seem likely to happen very
> > soon.
> > 
> > > if not then maybe it is worth it to make
> > > UnivAln conform to 'the SimpleAlign interface'. I am guessing this is
> > > probably a simple thing to do
> > 
> > Well it didn't seem simple to me, but take a look at it and if you can see a
> > simple way of doing it, do let me know (or better yet,  implement it!  :-)
> > 
> > - Peter
> 
> -- 
> 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

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