MeSH terms in bioperl RE: [Bioperl-l] (no subject)

[Hilmar Lapp]

On Tuesday, July 29, 2003, at 05:13  AM, Heikki Lehvaslaiho wrote:

>>
>> BTW just for consistent style, we said a while ago that we'd deprecate
>> the each_XXX style in favor of get_XXXXs()/add_XXXX()/remove_XXXXs().
>
> I missed that discussion. Could you point me to it, please.
>

With the limited mailing list searches that work right now, here's what  
I can point you to and comment.

- fall last year I refactored all array accessors in Bio::SeqI and  
Bio::SeqFeatureI and its implementors to adhere to the  
get_XXXXs()/add_XXXX()/remove_XXXXs() convention. If you check out  
those modules you'll find that the each_XXXX() methods are only  
synonyms anymore for backward compatibility. This was discussed to on  
the mailing list before.

- the bioperl.lisp configuration for emacs provides templates for array  
accessors that follow this convention (since a couple months already)

- here are a few mailing list links that I can ht:dig up right now:

http://portal.open-bio.org/mailman/htdig/bioperl-l/2002-September/ 
009473.html
http://portal.open-bio.org/mailman/htdig/bioperl-l/2002-October/ 
009725.html
http://portal.open-bio.org/mailman/htdig/bioperl-l/2002-September/ 
009494.html

Supposedly there should be more, like where I announce the addition to  
the template, but I can't seem to find that.

	-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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