[Biojava-l] RNATools bug

[Cox, Greg]

When converting a DNA strand to an RNA strand, RNATools has a hardcoded T ->
U and returns the symbol otherwise.  This breaks if an ambiguous nucleotide
is passed in, since they don't trip the T check.  I looked in the alphabet
XML file, and there are no ambiguous RNA symbols.  

The use case I'm facing is translating a DNA sequence.  The translation in
BioJava goes through an RNA sequence, so ambiguous residues foul it up.

So, I propose one of the following solutions:

* Introduce ambiguous RNA symbols that are analogous to the DNA symbols.  

* Introduce one ambiguous RNA symbol that all ambigous DNA symbols map to.

* Break the biological parallel and translate DNA directly to amino acids.

If I don't hear from anyone, I'll do the third.

Greg