It hasn't been too long, but vamsas is now well under way. Initial
packaging can be found there:
http://svn.debian.org/viewsvn/pkg-java/trunk/libvamsas-client-java
svn://svn.debian.org/svn/pkg-java/trunk/libvamsas-client-java
I'll check now if the newer jalview builds and runs with it, and
I'll upload it then.
Cheers,
Vincent