[Bioperl-l] printing UnivAlgn

Murad Nayal murad@godel.bioc.columbia.edu
Sat, 16 Dec 2000 09:47:50 +0100

Ewan Birney wrote:
> On Fri, 15 Dec 2000, Murad Nayal wrote:
> >
> >
> > is UnivAln being phased out? 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 and would make at least AlignIO able to
> > print either alignment object in all formats etc.
> Feel free to jump in and sort this out! (whoever codes it, wins the
> argument...)
> I agree with Peter tht we should focus efforts on one of them, which seems
> to be SimpleAlign and move functionality into it. What do you use UnivAln
> for?

Hi Ewan

that's how I feel too. maintaining them as separate classes with
incompatible interfaces is 'inelegant' I feel as they represent a single
concept. I like SimpleAlign better because it maintains the
encapsulation of the sequence idea internally (as LocatableSeq), while
UnivAln essentially reimplements the Seq object. that makes its code
more complicated than it probably needs to be.

I actually haven't needed to use UnivAln specialized facilities yet. I
had to deal with it because it is the Alignment object that
Tools::Blast::HSP builds out of Blast reports!