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

Ewan Birney birney@ebi.ac.uk
Sun, 24 Sep 2000 12:01:24 +0100 (BST)

On Sun, 24 Sep 2000, Hilmar Lapp wrote:

> Dear all,
> there is a module Bio::Root::IOManager, which seems to be supposed to
> take over all those tasks related to file opening, closing, file handles,
> reading (well, not yet) etc. Nevertheless, all modules concerned with
> handling files (i.e., all parsers, SeqIO/*, LargePrimarySeq, AlignIO)
> appear to deal with this on their own.
> Is there a common sense that we should stay away from delegating file
> handling to Bio::Root::IOManager? Likewise, is there a common sense that
> modules accessing files should rather duplicate the according code
> instead of delegating this to a central module?

So - you are seeing a difference between me coding and stevec's coding. My
view is that Bio::Root::IOManager is pointless. Perl has a rich set of IO
objects, able to do nearly anything you like, and extendable. I see
no point in having Bio::Root::IOManager (I don't like modules second
guessing gzip filenames etc.) 

Steve obviously likes it. ;)

It would annoy me if we had to do everything through Bio::Root::IOManager;
actualy, if we could *remove* it that would be ok for me.

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?

> 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..

> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
> A-1235 Vienna                                fax: +43 1 86634 727
> -----------------------------------------------------------------

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420