Bioperl: Re: Bioperl-guts: Possible Seq.pm reimplementation

[Aaron J Mackey]

yes Yes YES ... I've always found it fascinating that our "lightweight"
sequence object takes the longest to load into cperl-mode in my emacs
editor.

On Thu, 29 Jul 1999, Ewan Birney wrote:

> This page is about the possible reimplementation of Seq.pm. I
> (Ewan) strongly feel this should happen because: 
> 
>      There is too much code in Seq.pm, some useful, some not 

Or, rather, some not so useful to what Seq.pm purports to be.

>      The design of the object is not that clean 
>                
>      There is no clear interface definition for the object to
> allow other implementations 

I continue to fail to understand this overreaching design philosophy.  I
could have sworn we were BioPerl not BioJava.  I have always thought the
idea was to make the perfect wheel so that everyone else would stop
recreating the wheel and use ours, not to specify what the perfect wheel
should look like so that everyone can make perfect wheels that all work
the same.

I think I understand where abstraction and inheritance fit into a general
OO scheme of things, but all these BioObjectI.pm's that are just
documentation copies of BioObject.pm don't make any sense to me, but, as
always, that's just me.  Perhaps (hopefully) someone in Hiedelberg will
enlighten me and I can sleep again.

>      We need to seriously deprecate the IO handling of Seq.pm to
> using the SeqIO system. 

I agree.  SeqIO is just the niftiest thing since sliced bread and
(currently) is what I feel is BioPerl's strongest allure.  Especially once
we get AnnSeqIO going.

-Aaron

-- 
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