[Bioperl-l] Bio::*Taxonomy* changes

[Chris Fields]

Makes sense to me.  From my previous post the only bioperl class that used
it was Bio::Expression::Platform, and that only for grabbing Node objects
from Bio::DB::Taxonomy::entrez (so, change it to use whatever object
Bio::DB::Taxonomy returns).  

I couldn't find anything else in the core outside of the Bio::DB::Taxonomy
and Bio::Taxonomy classes and tests that use them.  There aren't even any
scripts or examples.

If you implement Bio::Root::RootI (and pretty much everything does), you
could use warn() or deprecated() for these easily:

...
 Title   : warn
 Usage   : $object->warn("Warning message");
 Function: Places a warning. What happens now is down to the
           verbosity of the object  (value of $obj->verbose) 
            verbosity 0 or not set => small warning
            verbosity -1 => no warning
            verbosity 1 => warning with stack trace
            verbosity 2 => converts warnings into throw

...

 Title   : deprecated
 Usage   : $obj->deprecated("Method X is deprecated");
 Function: Prints a message about deprecation 
           unless verbose is < 0 (which means be quiet)
 Returns : none
 Args    : Message string to print to STDERR
...


Chris


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: Thursday, July 27, 2006 11:39 AM
> To: Sendu Bala
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Bio::*Taxonomy* changes
> 
> That's what I said could be possible here on much shorter notice that
> we'd do usually due to the low usage.
> 
> Eventually deprecated modules should also be physically removed, so
> you want to prepare for that. (removing a module breaks scripts that
> used it; issuing a warning alerts to this being forthcoming.)
> 
> 	-hilmar
> 
> On Jul 27, 2006, at 12:30 PM, Sendu Bala wrote:
> 
> > Hilmar Lapp wrote:
> >> How do you mean 'process'? You create a new module, and then you
> >> deprecate the ones you're phasing out. If possible you rewrite the
> >> implementation to use the new module.
> >>
> >> Not sure this answers your question?
> >
> > I guess. I was thinking of just making Bio::Taxonomy::Node isa
> > Bio::Taxon and then simply removing all the code from Node, leaving
> > just
> > some perldoc that said it had been renamed?
> >
> > Or should there be some methods that issue a warning and then call
> > SUPER?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l