TODO/Bugs

- Conditional highlight overlay

- Sync path graph display with pairwise and alignment information.

- Sync create alignment with displays.

- Highlight filters in path graph display.

- Fix Save Alignment Set so that is saves created alignments as well.

- Make create filters, alignments, highlight dialogs non-modal.

- Fetched annotations do not align correctly when subsequences are used.  

- Sync feature check boxes when turning on/off and editing annotations.
