[Bioperl-l] Bio::FeatureHolderI interface confusion

Steve Mathias smathias at unm.edu
Wed Jun 18 10:54:36 EDT 2003

>>>>> "Chris" == Chris Mungall <cjm at fruitfly.org> writes:


Chris> Personally, I would much rather see the swarm of interfaces and
Chris> objects stopped and rolled back.


>>>>> "Hilmar" == Hilmar Lapp <hlapp at gnf.org> writes:


Hilmar> Why don't you make a proposal, state how much that's going to
Hilmar> destroy backward compatibility, list what we would gain from it
Hilmar> in exchange, identify who's going to refactor the codebase
Hilmar> accordingly, and then we vote on it.

Hilmar> Otherwise I'm having difficulty seeing the point.

While I do not wish to put words in anyone's mouth, and at the risk of
diverting the discussion somewhat, I will offer my perspective on what
the point is.  

The point is that unless you have the bioperl object model ingrained in
your mind and/or use bioperl every day, it can be extremely difficult to
to use as a toolkit.  It's a fair point if Chris' application is pushing
the boundries of what bioperl was designed to do.  My point is that it
can be very difficult to ascertain this without investing a significant
amount of time to (re)learn bioperl and the bioperl object model.  It
might be a different story if the documentation was complete and in-sync
with the code.  But it's not, and I often find myself spending too much
time trying to figure out what class is returned by
get_special_sub_seq_features(), what "interfaces"
Bio::SeqFeature::ReturnedByGetSpecialMethods objects implement, etc.
It's too often easier to just roll my own solution to the problem at

But my point is not to criticize.  I think bioperl is a great project
and phenomenon and I have been using it intermittently since the
Bio::PreSeq (yeah Cherverator!) days.  Rather, I just think the
perpective of a, perhaps infrequent, user of bioperl can be considerably
different than that of a core developer.

I doubt there is a way to make a library with the richness and
complexity of bioperl intuitive to use for all programmers.  Certainly
not all bioinformatics programmers, computational biologists, or
whatever we call ourselves.  My conclusion is that the only hope is to
try to make it simple.

>>>>> "Nat" == Nathan \(Nat\) Goodman <Nathan> writes:


Nat> But it sure would be nice to have a cleaned up, slimmed down
Nat> version whose architecture made it easy to understand what's going
Nat> on instead of obfuscating the obvious :) Oh well.  In another life
Nat> maybe...

It sure would be nice.  Maybe it doesn't have to be in another life.  I
would certainly contribute my time and effort to making it happen.

(    Stephen L. Mathias, Ph.D.                     (                    (
 )   Office of Biocomputing                         )  s m a t h i a s   )
(    University of New Mexico School of Medicine   (   @ p o b l a n o  (
 )   MSC08 4560                                     )  . h e a l t h .   )
(    915 Camino de Salud, NE                       (   u n m . e d u    (
 )   Albuquerque, NM 87131-5196                     )                    )

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