dynamically generated alignment annotation via built-in routines, web services and/or third party plugins

The Jalview 2 alignment annotation routines are hardcoded to generate alignment annotation with a specific name which is updated when ever the alignment or groups defined on the alignment is modified. Future versions of Jalview should allow a range of autogenerated annotation routines, and the software architecture should allow this set to be extended by third-party code executing within the same VM or via a webservice. The Jalview datamodel and and annotation IO formats (e.g. annotation files and project files) should allow the dynamically generated annotation to be stored and recovered (as dynamic annotation), along with any user-definable parameters needed to repeat any calculations performed.