[Dynamite] ...getting started...

[Guy Slater]

On Fri, 3 Mar 2000, Ewan Birney wrote:

> 
> 
> This is really just to get us started on this. We have alot of
> decisions to make, but the only way we are going to get there
> is by sending IDL to each other.... ;)

Should we have some sort of list of interfaces/objects first ?

The stuff below looks like a *lot* for an alphabet,
what else will there be for substitutions, sequence types etc ?

> typedef sequence<float> WeightVector;
> 
> interface Alphabet
> {
>   // every symbol in the alphabet corresponds to a non-negative integer 0,1,2...(size-1)
>   // negative integers represent ambiguous symbols, e.g. "N" "Y" "R" for DNA, "X" for proteins, and wildcards "*"
>   //  -1 is always 'N' and -2 is always '*'
>   // these ambiguities can be represented by a weighted sum over the real symbols in the alphabet
>   //  e.g. "Y" = 0.5 * "C" + 0.5 * "T"
>   //       "*" = "A" + "C" + "G" + "T" 
>   //  (NB this is not a probability distribution, as it doesn't sum to one, although in general ambiguous characters are probabilistic)
>   // such weighted sums are represented by WeightVectors
>   //

I don't like this bit - I think it could be confusing
because everyone else uses "*" for stop codons.

Guy.
--