[Biojava-l] Change to SimpleTranslationTable

[Thomas Down]

On Mon, Oct 22, 2001 at 10:52:41AM -0400, Cox, Greg wrote:
> Working with ambiguous nucleotides, I've had to add a method to
> SimpleTranslationTable;
> 
> public void setTranslation(Symbol from, Symbol to)
> 	throws IllegalSymbolException
> 
> This supplements setTranslation(AtomicSymbol, AtomicSymbol).  Will this
> cause problems for anyone if I commit it?

Sorry if I'm being dense here, but are there actually any
cases we're interested in where:

  trans([x y]) != [trans(x) trans(y)]

(where "trans" is the operator represented by some translation
table and [] represents an ambiguity set).

If so, then go for it.  But in general, I think it's good
to keep ambiguity handling as automagic as possible, otherwise
it's liable to come back and bother us at regular intervals.

Anyone else?

     Thomas.