JAL-3878 Separate gui elements from operations.

JAL-3878 Separate gui elements from operations.

Separation went well for alignment operation but not so much
for the annotations. GUI progress bar needs to be moved outside
the operation and be controlled by the worker listener.
Addition of the results to the frame needs to be moved out from
the #done method, but it's strongly wired to the align frame
code and cannot be nicely packed into AnnotationResult object.