[Biojava-l] Substitution matices

[Matthew Pocock]

Schreiber, Mark wrote:
> Hi -
> 
> Does Biojava contain the concept of Substitution/ similarity matrices?
> 
> If not should we put in an Interface (probably in the dp package)?
> 
> Probably containing the method:
> 
>   double substitute(Symbol a, Symbol b) throws IllegalSymbolException;
> 
> Mark Schreiber
> Bioinformatics
> AgResearch Invermay
> PO Box 50034
> Mosgiel
> New Zealand
>  
> PH:   +64 3 489 9175
> FAX:  +64 3 489 3739


Hi Mark,

Yes and no. There is no explicit substitution matrix interface as such. 
However a Count or Distribution over (e.g.) proteinXprotein will have 
the desired properties. It is then a matter of interpreting the 
distribution to be a substitution matrix, or the count as being 
observations of substitutions.

Is there something (other than syntactic sugar) that isn't covered by 
this approach?

Matthew