[Biojava-l] Re: Symbol change

[Matthew Pocock]

Matthew Pocock wrote:

> Hi all,
>
> I am gearing up to commit the new Symbol code. I sudgest that you take a
> CVS snapshot now to work from as the code I check in may be buggy. I
> will try to commit tommorow noon UK time. Hopefuly once this is in and
> working, nobody will notice, and we will be able to have ambiguity
> symbols that represent arbitrary collections of codons (all stop codons,
> or all PHE codons etc.).

This has all been checked in now (25 hrs later than planned due to
plumbers). I have got some basic examples to work for me, but I realy don't
know what hidden bugs are lieing arround in there. Please, assume that any
symbol/alphabet related exceptions are due to bugs in BioJava and report
them, rather than trying to find workarounds or to fix your code. All
examples of when things don't work are greatfully recieved. Also, if you
feel brave (or realy bored), could you read through AlphabetManager, Symbol,
BasisSymbol and AtomicSymbol, along with the implementations and Alphabet
implementations? This code realy does need more eyes.

Thanks for your patience.

Matthew