Bioperl: Boulderio 1.14 released

[Lincoln Stein]

 > >      1) Support for Boulder->XML and back again.
 > 
 > Cool. Much needed/wanted. Do you use your own parser, or are there XML::
 > dependencies?

You need XML::Parser to go from XML->Boulder, but not the other way.  

 > > Luca is currently working on the Java port of Boulder, which compiles
 > > on some systems and not on others (due to libdb incompatibilities),
 > > and on a LocusLink parser.  I am working on integrating Boulder with
 > > the main bioperl distribution, and finding it very hard to reconcile
 > > the data-oriented and object-oriented views of the world!
 > > 
 > 
 > I know this is tough! I thought it would be a challenge... 
 > 
 > My view on how to do this is that objects should subscribe to a
 > data-orientated interface that allows a data-orientated view of the
 > object. This interface should be defined somewhere off in Bio::Root::
 > stuff. 

I think there needs to be a self-describing schema, much the way that
the AcePerl implementation has an introspection mechanism for
interrogating the object to find out what tags and subtags are
available, and what their types and other constraints are.  People
will want support DTDs, RDFs, etc.  I'll try to work out some middle
ground which doesn't make it seem as if the data-oriented view is
taking over the object-oriented one.

Lincoln

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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