Bioperl: Bioperl 0.6.1 release

[James Gilbert]

I've just committed changes to the 0.6 branch
which fix a number of parsing and printing bugs in
Bio::SeqIO::(embl|genbank|swiss).  

I've rationalised _read_FTHelper_EMBL and
_read_FTHelper_GenBank (and will do the same thing
to swissprot).  Looking at these three modules, we
have a number of near-identical subroutines, so we
should definitely be inheriting off a common base
class as Ewan suggests (but not in the 06 branch).

In addition, subspecies should now be correctly
parsed and printed.  I've added a sub_species
(should be "subspecies"?) method to Bio::Species,
and undone some of Hilmar's changes to
Bio::Species (sorry Hilmar).  classifiication()
now returns the same list as before, to preserve
backwards compatibility, but (thanks to Hilmar for
pointing this out) Genus is no longer duplicated
in the list when it comes from parsing
embl/genbank/swissprot.

I'm going to put an 0.6.1 release candidate on the
ftp site on Friday 12th, and do the release proper
next week.  Please scream now if there's a fix you
want to see in there which hasn't yet been done.

	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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