Refactor Alignment

[rbouckaert]

Currently, the Alignment class does not allow editing of the actual alignment. Also, it does not allow continuous values. However, BEAUti relies on the Alignment class to define partitions, so it is fundamental to the user interface.

A workaround to get non-standard tree associated data into BEAUti is to derive from Aligment, e.g. beastclassic.evolution.alignment.AlignmentFromTraitMap, and suppress all kinds of options, like stateCount and methods.

A cleaner approach is to have a base class for Alignment -- say TreeData-- make BEAUti aware of that, and have the other classes currently deriving from Alignment derive from the TreeData class. The main work probably will be making BEAUti compatible with this.