[Bioperl-l] Re: issues with _rearrange

[Aaron J Mackey]

On Fri, 20 Sep 2002, Ewan Birney wrote:

> Can I propose an
>
>   (F) - Write a specific constructor, called like:
>
>    $feature = Bio::SeqFeature::Generic->seqio_direct_new($start,$end,$tag_hash_ref);

Certainly (this is another recasting of Matthew's actual idea, the one I
followed up on), and it's probably the easiest, "can do it right away"
thing to do.

Just to argue once more for option E (optimizer), the advantage is that
*every* call to _rearrange, no matter who/where/what get's optimized away;
no new speedy constructors needed.

> (caveat - how much stuff does Root::Object need intialised before it
> is happy, and if so... why...)

There does seem to be a lot of work going on to make sure that ->verbose()
can be overridden ...

-Aaron

P.S. with my now dead laptop unavailable for awhile, I'd really like some
list lurker to contact me about implementing some of these things; no
bioinformatics knowledge necessary!  Your chance to become a BioPerl hero!

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu