Package org.biojava.bio.seq.projection

Code for projecting Feature objects and systematically altering their properties.

Feature Projection is the BioJava system whereby a feature hierarchy can be transformed into a similar hierarchy with feature properties systematically modified. For example, projection may translate all features by 120 residues, or add an annotation property to all features.

This package contains the underlying `engine' code for feature projection. ProjectedFeatureHolder uses a ProjectionContext to project a set of features. ProjectionEngine does the actual magic of gluing the projected features through a ProjectionContext to the underlying features.

There are several implementations of ProjectionContext provided here for your convenience. They do standard things like translate or flip features, and graft them into another feature hierarchy.

To develop your own projections, implement ProjectionContext and provide the necessary projection methods. ReparentContext is a really good base-class to use for deriving your custom projections (belive me, getting the basics of an implementation right are not simple) and will handle both the re-rooting of the feature hierarchy and also any event wiring needed.

ProjectionContext does deep voodoo involving introspeciton and class generation. If you don't really want to know the gory details, we strongly suggest that you don't take a peek inside.

Interface Summary

Interface	Description
Projection	Interface implemented by all projected feature objects.
ProjectionContext	Interface that defines the projection between original features and projected features.
ProjectionEngine.Instantiator	Internal helper class.
ProjectionEngine.TemplateProjector	This is an interface for things that project feature templates.

Class Summary

Class	Description
ProjectedFeature	Internal class used by ProjectionEngine to wrap Feature objects.
ProjectedFeatureHolder	Helper class for projecting Feature objects into an alternative coordinate system.
ProjectionEngine	Factory for proxy objects which project BioJava features into alternate coordinate systems.
ProjectionUtils	Some common things you want to do while projecting features.
ReparentContext	A good base class to implement ProjectionContext from.
TranslateFlipContext	A ProjectionContext that translates and optionaly flips features.