Modifications made so that StructAlign runs with some structures
missing, by essentially ignoring these leaves of the tree in the
structural likelihood computations. However, the sequences without
structures seem to end up unaligned to the other sequences, so either
there is an issue somewhere in the code, or perhaps there is a reason
why this formulation of the model favours unaligning the sequences that
do not have structural information (e.g. because the branch lengths end
up much larger).
StructAlign now works for cases where structures are only present for a
subset of the leaves, provided that there are at least two structures.

Also fixed a bug whereby the alphabet was set to null after removing a
sequence. 

Repeated addition of a sequence now updates the sequence rather than
creating duplicates (changes to RawSequences and PDBReader).