[Bioperl-l] SeqIO parsing

[Heikki Lehvaslaiho]

On Tue, 2002-09-24 at 17:01, Ewan Birney wrote:
> 
>   this scheme in my mind has one *SERIOUS* gotcha. People *have* to write 
> their @ISA's with their implementation tree *first* and their interface 
> inheritance second. Is this ok with people?

That is how it should be. I checked the bioperl-live an found only the
following cases:

./Bio/Annotation/Comment.pm:51: 
	@ISA = qw(Bio::AnnotationI Bio::Root::Root);
./Bio/Annotation/Reference.pm:60: 
	@ISA = qw(Bio::AnnotationI Bio::Annotation::DBLink);
./Bio/DB/Universal.pm:114: 
	@ISA = qw(Bio::DB::RandomAccessI Bio::Root::Root);
./Bio/DB/Fasta.pm:397: @ISA = qw(Bio::DB::SeqI Bio::Root::Root);
./Bio/DB/BioFetch.pm:97: @ISA = qw(Bio::DB::WebDBSeqI Bio::Root::Root);

in all other cases the interfaces are after implementing classes.
Most of these are "inteface" classes are these "decorated inteface"
which actually implement methods.


is it time  we get rid of them?

	-heikki



 
> The nice thing about (a) is that it should give speed ups across the 
> entire system, not just SeqIO. 
> 
> 
> Jason/Hilmar - is there a hidden gotcha here somewhere?
> 
> 
> 
> 
>   (b) Making a new Bio::Seq::SeqFactory with privledged access to 
> functions in Bio::Seq and Bio::PrimarySeq to make fast access objects, eg, 
> not going through a second alphabet on setting seq.
> 
> 
> 
> (b) is SeqIO specific so I want to do this second.
> 
> 
> 
> 
> 
> BTW - I think I can cut the object creation time by a factor of 6 in my 
> tests if I get this written right ;)
> 
> 
> 
> 
> 
>         
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      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
___ _/_/_/_/_/________________________________________________________