[Bioperl-l] UniGene modules now in CVS

[Lincoln Stein]

We should follow the principle of Fewest Surprises.  If you feel
strongly that next_seq() is redundant, then let's change Bio::SeqIO to
recognize next(), and deprecate next_seq() (but still allow it).  I
believe there's a next_feature() in SeqFeatureI that should be
modified as well.

Lincoln

Heikki Lehvaslaiho writes:
 > Lincoln Stein wrote:
 > 
 > >  > which is somewhat redundant. A more generic way would be:
 > >  >
 > >  > $io = Bio::ClusterIO::IO->new(-file=>'myfile',
 > >  >                                -format=>'unigene');
 > >  > $clu = $str->next();
 > > 
 > > Yes, but Bio::SeqIO uses next_seq().
 > 
 > I know, but in my opinion it should be next(). Attaching the object type to
 > the method name is again that kind of redundancy, I'd like not to have.
 > Having a generic method name makes it easier to inherit and use the classes. 
 > 
 > I've done this already in Bio::Variation::IO which inherits a lot from
 > Bio::SeqIO a but uses read() and write().
 > 
 > 
 > We could add read() and write() as an alternative to SeqIO so that all IO
 > classes could use the same method names.
 > 	-Heikki
 > 
 > -- 
 > ______ _/      _/_____________________________________________________
 >       _/      _/                      http://www.ebi.ac.uk/mutations/
 >      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
 >     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
 >    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
 >   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
 >      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
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