[Biojava-l] ambiguity fix

[Matthew Pocock]

Dear all,

I have checked in the new object model for ambiguities. The core symbol
classes/interfaces will not be touched now at all except for minor
bug-fixes. The demos work for me. Over time, there may be places where
we can restrict methods to only accepting AtomicSymbol instances, rather
than any Symbol. This will be done after 1.0, and as-and-when we notice.

AlphabetManager has become a place to put useful methods. It was
accessed by the instance() method, but this is a pain. This method has
been deprecated, and you can now access all of the AlphabetManager
methods as static members. This should affect no code, except for
producing occasional depricated warnings. It will also mean less typing.

I would like to welcome Gerald Loeffler to the development team, and
look forward to seeing  lots of @author tags with his name on.

Matthew

--
Joon: You're out of your tree
Sam:  It wasn't my tree
                                                 (Benny & Joon)