[Bioperl-l] Re: Bio::Root::IOManager: used?

[Hilmar Lapp]

Ewan Birney wrote:
> 
> I realise that a little more consistency is a good thing here, so if we
> can collectively come to a decision about
> 
> (a) do we need Bio::Root::IOManager
> (b) how should we use it
> 
> that would be great. What are other people's views?
> 

My experience is that we are duplicating methods fh()/_filehandle()
(doing the same thing), _pushback(), _readline(), close() and DESTROY (to
close files upon garbage collection) all over the place, as well as code
in _initialize() to handle and set -file and -fh parameters.

It's not that any of these methods is complicated or substantial code,
but I don't think it's smart either.

So, I wouldn't expect fancy things, but just those little ones you in
fact need all the time.

> >
> > Finally, there is a similar question concerning network access and
> > URL-based queries: do people think that each module which needs it shall
> > implement it itself, or rather delegate to a yet to be created
> > Bio::Root::NetManager? This of course affects the proxy/firewall problem,
> > too (i.e., the place of where to solve it).
> >
> 
> See previous post by Chris. Perl again has a rich set of "standard" URL
> getting stuff. We should not need to rewrite things in my view..
> 

In my view the point is not to rewrite something, but rather delegation
of the guts. You already quote "standard", and the fact that the
Bio::DB::Gen* modules are not firewall compatible indicates that it may
not be as straightforward as it looks like.

So, I think your point of a little more consistency and a common decision
(like what do we recommend to use) are valid here as well.

	Hilmar

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Hilmar Lapp                                email: hlapp@gmx.net
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