Update note.
Add todo note.
Use blank_copy.
Move Construct implementation into a class.
Stop translating branches to nodes during construction.
Add notes.
Add new class homology_matrix
Access the alignment through an accessor function.
Add new get_alignment( ) function.
Add accessor method to get the sequences.
Add some infrastructure for recomputing the alignment.
Don't forget to initialize seqs.
Remove some uses of A_.modify()
Recalulate the alignment immediately.
Remove cases of P.A_.modify().
Add note.