[Bioperl-l] 0.7 release: SeqIO

[Jason Stajich]

I would first say I like Ewan's proposal for SeqFeature handling.

I have been working with the SeqIO code - attempting to extract
Bio::Root::Object dependance.  It appears we should certainly
include the routines verbose and _initialize in Bio::Root::RootI
interface as they are everywhere.  I am moving to an every module has a
'new'. The implementation I am messing with has chained _initialize calls.
Debates with this? 

Questions:

1. For my edification - (Ewan/Elia?) What is this for? (in
                         genbank,embl,swiss _initialize)
   # hash for functions for decoding keys.
   $self->{'_func_ftunit_hash'} = {}; 

2. Brad Marshall or other bioxmlers - can you provide some example
   code and/or test for Bio::SeqIO::bioxml so I can bring it up to
   these standards.  It would be helpful to have a test written for
   it.

3. I would like to think can we add fuzzy feature support by January
   following Ewan's proposal. I would like to work towards it so we can
   have the tools necessary to support the latest (0.2) biocorba idl
   proposal as well.  I'd like to get this on the main branch before we
   fork at 0.7 because it will probably be an involved process.

Jason Stajich
jason@chg.mc.duke.edu
http://galton.mc.duke.edu/~jason/
(919)684-1806 (office) 
(919)684-2275 (fax) 
Center for Human Genetics - Duke University Medical Center
http://wwwchg.mc.duke.edu/