[Dynamite] Is this working now then?

[Ewan Birney]

> 
> (1) Model descriptors
> 
> - SingleHMM, PairHMM, PolymerHMM
>    ... these specify the topology of the models
> 
> - SingleParameters, PairParameters, PolymerParameters
>    ... these specify the parameterisations of the models
>    ... these should probably be interfaces rather than data structures,
>    ... so that we can e.g. provide a wrapper class that maps "gap_open"
>    ... & "gap_extend" to the appropriate transitions in a Needleman-Wunsch
>    ... model

Ok. I *really* can't see how you get the parameters separated from the
model easily. Can you give me some IDL to persuade me one way or the
other?

> 
> (NB I think all alignment algorithms should be global at the minute. Doing
> local alignment is effectively an optimisation step, equivalent to saying
> that some cells are zero throughout the matrix)

Fine...

> 
> (2) DP algorithms & results
> 
> - SingleViterbiAlgorithm, PairViterbiAlgorithm, PolymerViterbiAlgorithm
>    ... these return an alignment & a log-likelihood
>    ... my feeling on alignments is much the same as my feeling on
>    ... sequences: the base alignment class should be VERY simple,
>    ... probably just a sequence<int> describing the state path through the
>    ... HMM. We can get additional functionality by inheriting.

Alignment data structure - is going to be fun. I want to call it

"traceback" not "alignment" so people don't think it is an alignment
in the way that they think MSF is an alignment. 

> 
> - SingleForwardBackwardAlgorithm, etc.
> 
> - SingleCounts, PairCounts, PolymerCounts
>    [and possibly SingleDerivatives, PairDerivatives, PolymerDerivatives?]
>    ... these are datastructures returned by the Forward-Backward algorithm

Right. We have too many things that want to go into the model stuff
for me
	model
	parameters
	counts
	derivatives

so I guess - Ian - if you can come up with a way of pulling these
things apart and putting them back together again I would be delighted
to see it. 


Got to be some magic here...

> 
> Ian
> 
> 
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