Bioperl: Bioperl 0.6.1 release

[James Gilbert]

> classifiication() now returns the same list as before, to preserve
> backwards compatibility, but (thanks to Hilmar for
> 
>      Backward compatibility is generally a good thing, but shouldn't dominate
>      design, at least IMHO.

>      I think a method for set/get that does not return
>      the same array as it requires is not well designed.
Yes, but this doesn't happen.

>      So, I think either
>      subspecies must be set through sub_species($subspecies) only, or if it
>      allowed to be passed to classification(), it
>      should be returned there as well.

I decided that it was cleaner to get and set
subspecies (which is only occasionally available)  
through the sub_species() method, and keep species
and genus as the first and second elements of the
classification() array (since these are almost
always available).

	James

James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919

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