Mussa aligned sequence view seems to work

Mussa aligned sequence view seems to work
I added a "normalizedIndexes" to the ConservedPath classes to return
vectors which don't have any negative path values.

I also think the use of menu entries is a bit annoying as it wont extend
well to large numbers of selected paths. Additionally, deselecting an
alignment doesnt seem to do much as I suspect there's a fair amount of
overlap betwen the various alignments.

But i was eventually able to make them all go away.