[Dynamite] Is this working now then?

[Guy Slater]

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.

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.
--