JAL-2428: NJTree refactoring
Just a tidy up, not functional change:
Separate loading tree from file, from computing a tree.
Make 3 NJ-specific methods overloads in a subclass instead of an if-else choice.
Use BitSet instead of int for Cluster and 'done' field.
Add Javadoc, tests, as time permits.
Branches in review
Issues Raised From Comments