[Bioperl-l] 0.7 release: Bio::Root::* classes

[Jason Stajich]

On Mon, 13 Nov 2000, Ewan Birney wrote:

> On Mon, 13 Nov 2000, Hilmar Lapp wrote:
> 
> > Ewans proposal was to get rid of Bio::Root::Object.
> > 
> > Personally, I can't comment much on this subject. After looking at what
> > Bio::Root::Object actually implements, it seems that everything I used so
> > far (initialization, _rearrange(), throw(), warn()) in fact were things
> > provided by Bio::Root::RootI.
> 
> This is why I made RootI (notice it doesn't give you the _initialize
> routine, and there is still a dependency I belive on Root:;Objecct from
> the warn method we need to remove).
> 
> I originally made RootI because there are a large number of cases where
> you want to use the nice ->throw or ->warn syntax but don't want to have a
> Root::Object (ie, a perl hash with particular properties) around. Classic
> examples are C extension objects.
> 
> Having used RootI for a while, I can't imagine using anything from the 
> Root::Object call. The only thing I have heard of being useful is hte
> ->clone call. However, ->clone is a hard thing to implement once you are
> outside the world of "well behaved" perl objects (eg, C objects, CORBA
> stuff) and I don't think it is healthy to mandate that every bioperl
> object should be "cloneable".

I think using RootI compliance is a very reasonable goal for 0.7 and
volunteer to help on this front.  I think there may be some instances that
require a bit of work, but will also help us really go through and look at
every bioperl module before the release.

> 
> 
>  > 
> > So, what are the arguments for abandoning Bio::Root::Object? Does anyone
> > object to deprecate using it?
> 
> 
> I don't ;)
> 
> Steve or Peter vh might do though....
> 
> 
> > 
> > 
> > 	Hilmar
> > 
> > -- 
> > -----------------------------------------------------------------
> > Hilmar Lapp                                email: hlapp@gmx.net
> > GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
> > -----------------------------------------------------------------
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> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
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Jason Stajich
jason@chg.mc.duke.edu
http://galton.mc.duke.edu/~jason/
(919)684-1806 (office) 
(919)684-2275 (fax) 
Center for Human Genetics - Duke University Medical Center
http://wwwchg.mc.duke.edu/