Move alphabet type into SeqString

Move alphabet type into SeqString
This is another large patch.
This moves alphabet_ref from Sequence to SeqString.

I still need to deal with a better way of handling reverse complementing
especially given my attempts to keep everything in reference counted
structures.

Also this patch and the previous:
Store Sequence sequence location in a shared_ptr class
have broken the display of motifs in mussa.

(I used to be using shared_ptr<Sequences> for everything,
but now since there's a couple of seperate objects updating
the motifs in one doesn't really help so much for the other.

so warning, these two patches and the next few that I make
are going to be unstable.
**END OF DESCRIPTION***

Place the long patch description above the ***END OF DESCRIPTION*** marker.
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This patch contains the following changes:

M ./alg/CMakeLists.txt +1
M ./alg/alphabet.cpp +35
M ./alg/alphabet.hpp -1 +14
M ./alg/motif_parser.cpp -3 +4
A ./alg/seq.cpp
M ./alg/seq.hpp -3 +17
M ./alg/seq_span.cpp -6 +3
M ./alg/seq_span.hpp -1 +4
M ./alg/sequence.cpp -82 +26
M ./alg/sequence.hpp -15 +10
M ./alg/test/CMakeLists.txt +1
M ./alg/test/test_alphabet.cpp +5
A ./alg/test/test_seq.cpp
M ./alg/test/test_seq_span.cpp +9
M ./alg/test/test_sequence.cpp -43 +43
M ./qui/motif_editor/MotifElement.cpp -2 +2