[Biojava-l] Feature interface changes

[Matthew Pocock]

Hi all.

Since the 1.2 release is out, we can now start to think about some of 
the issues we have had with the current APIs. These changes would never 
be back-ported onto the release branch. We are commited to keeping the 
release branch APIs stable.

I think the Feature interface may be up for renewal. Here is my wish-list.

idea:
   - make the core properties of Feature and its sub-interfaces
   mutable
consequences:
   - get/set methods for things like location
   - changes must be propogated through our Feature projections
   - new code using getFoo will not be link-time compatable
   with old code
   - old code will be compatable with new API
severity:
   - i think we can live with this - we can fix the serialuid
   so that at least objects can be read/written from either
   model

idea:
   - replace the current Feture.Template instantiation system
   with an Annotation that conforms to the apropreate
   AnnotationType
consequences:
   - we could then instantiate features that inherit more than
   one feature interface e.g. Stranded & Framed
   - new code instantiating features would not be compatible
   with old code in either combination
   - possibility for much freer association of feature 'types'
   with interfaces, making ontologies of feature types more
   easily possible
severity:
   - this will break all feature instantiation code which
   will impact a reasonable number of files
   - most of the fixes can be located with search/replace

synergy:
   - the ChangeType instances that must be created for
   mutable features to be implemented can double up as
   property names in the Annotation bundles used to
   instantiate them
   - properties that can't be represented as feature
   properties due to a provider not implementing that
   interface can be stored under this key in the feature's
   annotation and this can be recognised by the annotation
   bundle's event forwarding code, providing a potentialy
   clean abstraction of the objects from their implementation.

All ideas, flames and dirty jokes greatfully recieved.

Matthew