[Biojava-l] question about ambiguous symbols

[Thomas Down]

On Wed, Feb 05, 2003 at 03:52:03PM +0000, Keith James wrote:
>
> I got bitten by this too, when porting some of the code. If you look
> in biojava-live/resources/org/biojava/bio/symbol/AlphabetManager.xml
> you will see that the default RNA alphabet contains only
> agcu-~. i.e. no ambiguity symbols at all.
> 
> I haven't tested this, but you could hack your AlphabetManager.xml to
> include
> 
>    <ambiguityMapping token="n">
>     <symbolref name="guanine" />
> 	<symbolref name="adenine" />
> 	<symbolref name="cytosine" />
> 	<symbolref name="uracil" />
>    </ambiguityMapping>
> 
> as in the DNA alphabet. Not sure if this is the best solution - I'm
> sure someone will say if it's not.

Yes, I think it is the right solution.  In fact, I thought someone
checked it in last time this issue came up, but evidently not.
I've added it in CVS now.  Not sure what to do about other
possible RNA ambiguities -- does anyone use them?

     Thomas.