alignment/sequence analysis UI model which does not unnecessarily create new windows

Currently, analysis' performed on an alignment nearly always create a new window, regardless of whether it is necessary to do so. When an analysis is performed on an alignment that only creates new annotation, then it could simply open a new view on the same alignment rather than create a whole new alignment window in order to display the results.

Note: if the user has modified the alignment after the analysis has been started, then Jalview should open a new window regardless, but allow the user to easily transfer the resulting annotation onto their modified alignment if they so desire.