Bioperl: Bio::Species.pm: fixed bug #226

[Hilmar Lapp]

Hello all,

as encouraged by Jason, Ewan, and James, I've corrected the bug in Species.pm
mentioned in report #226, so far only on branch-06.

The fix involved a couple of changes, most noticeably a change of what
Bio::Species->classification() is expecting now when it is passed an argument.
The reason is that now all methods consistently access the same array, except
for common_name(). Bio::SeqIO::genbank.pm and Bio::SeqIO::embl.pm already
behaved as if Species.pm worked the way it does now, which triggered the bug.

See the doc quote at the end.

I'm wondering whether there's a point in fixing the main branch as well
immediately. A diff of Species.pm to the main-branch version showed a few
other, but minor, differences, which I think were not introduced by me. So it
seems to me that the two branches are not necessarily kept sync'ed even if the
changes do not introduce API changes or new features etc. Could someone let me
know whether I shall fix the main branch as well.

Regarding design, I have the impression that Bio::Species rather encapsulates
the source of a sequence (therefore the organelle() method) than a species
only, and that's exactly the point of interest with respect to seqs (like
organ, tissue, library etc). So, intuitively I'd call it something like
Bio::SeqSource or Bio::IsolationSource. Does anyone see a point in this? I
have no idea how much attention the list community pays to such issues, so
maybe someone can give me an idea whether this is just stupid and you leave
such things to the OO/Corba/Java domain.

In addition, Jason advised me to post these things (bug-fixes, discussion
stuff) here, but maybe I've misunderstood him and I'm too technical for this
list. If so, please let me know, I'm new to all this.

Cheers,

	Hilmar

Quoted from the updated documention:

=head2 classification

 Title   : classification
 Usage   : $self->classification(@class_array);
           @classification = $self->classification();
 Function: Fills or returns the classifcation list in
           the object.  The array provided must be in
           the order SUBSPECIES, SPECIES, GENUS ---> KINGDOM.
           The first and second element of the array, the subspecies and
           species, must be in lower case, and the rest in title
           case.  Only species must be present.

           Note that the format convention given above has changed after 
           release 0.60. Formerly, SUBSPECIES was not necessary. In order to
           break as few scripts as possible, the method tries to recognize
           whether or not the subspecies is provided, given that the rest
           is given in correct case. This is the reason that the example given
           below is still valid.
 Example : $obj->classification(qw( sapiens Homo Hominidae
           Catarrhini Primates Eutheria Mammalia Vertebrata
           Chordata Metazoa Eukaryota));
 Returns : Classification array
 Args    : Classification array

=cut

-- 
-----------------------------------------------------------------------
Hilmar Lapp                                      email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics                   phone: +43 1 86634 631
A-1235 Vienna                                      fax: +43 1 86634 727
ROI: Bioinformatics (arrays, expression, seqs), Programming, Databases,
     Mountain Biking (hard tail, hard fork: feel the trail)
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