[Biojava-l] Packed DNA Symbol List

[David Huen]

I've written a packed version of a DNA symbol list (4 bits per symbol, 8 
times cheaper than the current). Surprisingly, the performance seems OK -
I expected it to be abysmal.  Its constructor can take and return data in
a byte array so data can be serialised from/to a database.

The drawback is that it uses its own AlphabetIndex because I could not 
make the ones in the package take ambiguity tokens for whatever reason.
Most likely I am missing some thing here.  My main concern is that if I
were to use this class in a persistent implementation and the Alphabet
Index for this class needed to be  changed later, it would scramble
these objects so the necessity to get it right now.

Any suggestions as to solutions before I consider committing it to
development trunk?

Regards,
David Huen