[Bioperl-l] a littlet bit inconsistency in Bio::SeqFeature::Generic

[Hilmar Lapp]

Yes, that's one of the embarrassing inconsistencies. The thing to 
fix though is the parameter names, not the method names. In order 
not to break backward compatibility, both flavors have to be 
recognized though. If you have a patch doing this send it along, or 
do it right in the repository if you can -- but make *absolutely 
sure* then that all tests pass ...

And BTW the hash keys are supposed to be hidden -- if you do 
something with them directly you're on your own.

	-hilmar

On Thursday, December 12, 2002, at 09:39 AM, Xiao Juguang wrote:

> Hi all,
>
> As a very beginner of bioperl, my mind is fixed on the rule that if 
> there is a key in the hash of 'new' method of a bioperl object, 
> then there is, generally, a getter/setter method for this field 
> with the same name as the key name without prefix '-', as well, the 
> key for the internal hash is named from this getter/setter method 
> name with the prefix '_'
>
> However, 2 guys in Bio::SeqFeature::Generic do not follow it. There 
> are 'primary' and 'source'. Their getter/setter name are 
> 'primary_tag' and 'source_tag' respectively. Same names as their 
> siblings from Bio::EnsEMBL::SeqFeature. So I suspected they're 
> written by ensembl guys. ;)
>
> Should we make them consistent, with a second effort? :)
>
> Juguang.
>
>
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--
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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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