[Dynamite] Is this working now then?

[Ewan Birney]

On Mon, 6 Mar 2000, Guy Slater wrote:

> On Sun, 5 Mar 2000, Ian Holmes wrote:
> 
> > On Sun, 5 Mar 2000, Guy Slater wrote:
> > 
> > > I would have thought you wouldn't need any identifiers for the DP itself,
> > > but only for alignment display, database searching, etc.
> > > 
> > > Again, I think we need to have a list of all objects,
> > > to make it easier to mark out the territory of each of them ...
> > 
> > Maybe not a super-exact-final-ultimate-no_more_changes list, but 
> > definitely some discussion of the object boundaries.
> > 
> > Often what starts as one object can split into several very similar
> > objects (witness Sequence). With that caveat, I reckon we need the
> > following "objectoids": ("objectives"? "objections"?)
> > 
> > (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
> > 
> > (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)
> 
> No!  I'm v.against implementing everything as global and hacking in
> local alignments later.  Something like that needs to work from the start.

I am with Guy here actually. We will need global/local switches to be
nicely placed in the models.


> 
> You will be stuffed by the matrix-edge constraints
> when you try to implement semi-local aligments.
> 
> Also, these sort of distinctions need to be very clear
> in the object model for some optimisation strategies.
> 
> Guy.
> --
> 
> 
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