[Biojava-dev] ScoringMatrix interface/implementations

[Rahul Karnik]

mark.schreiber at group.novartis.com wrote:

> I like this approach. The only minor problem is what to do with 
> ambiguities that are not found in the matrix. Currently you through an 
> exception which is fine although you might also want another 
> implementation that more gracefully averages the match values of all the 
> possible sub-symbols of the ambiguity.

Thanks for the feedback. I am going to put off the averaging for 
ambiguities for now, mainly because ambiguous bases can also be added to 
the ScoringMatrix. As you say, it could be yet another implementation 
down the road.

Thanks,
Rahul