'Zoom' PAE annotation Y axis to show just the visible positions in the alignment

Currently the only way to zoom in on the PAE is by increasing its height, but this is problematic when examining substructure interactions after hiding columns of the alignment, because the Y axis of the PAE still shows all positions regardless of their visibility.

By default it may be better to always exclude hidden positions when showing PAEs. This is already done when looking at sub sequences, and here there is the opposite problem, where one may want to view the full PAE (or another specific part).