[Bioperl-l] Re: issues with _rearrange

[Hilmar Lapp]

On Thursday, September 19, 2002, at 11:57 AM, Steve Chervitz wrote:

>
> Another thing to try is exporting _rearrange from RootI so that it 
> can be used
> as a class method, instead of an instance method, i.e., call it as 
> _rearrange(
> ... ) rather than $self->_rearrange( ... ). This should improve 
> performance.
>

This sounds like an excellent idea to me. I don't know of any place 
in bioperl where it is overridden, or where overriding it would be 
useful, or where we would want someone to override it.

> I've always been concerned about all of the overhead from 
> _rearrange calls, so
> Aaron's suggestion seems reasonable to me. _rearrange is 
> convenient, but maybe
> it's a little *too* convenient. Allowing this much flexibility in 
> specifying
> method arguments is probably not necessary as many programmers and 
> users are
> accustomed to precisely defined arg lists.

The problem is not so much that people are or are not used to the 
flexibility. It's rather that all constructors behave extremely 
consistent in what flexibility they allow and which they don't, so 
if have been used to some style from one part of bioperl I can be 
sure it works exactly the same way in another part.

The exported _re_arrange would maintain that centralization.

	-hilmar
--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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