[Dynamite] update

[Guy Slater]

On Mon, 24 Apr 2000, Ian Holmes wrote:

> I have to stop work on this for a few days (visiting Paracel tomorrow) so
> here is what I've done on Telegraph so far. I have just kind of pushed
> ahead with the Perl thing, because it made so much sense to me.
> 
> This is not a working prototype yet, but it does support a couple of
> tests. You can find them in the directory "Telegraph/t" (of course). Make
> sure that the root directory "Telegraph" is located in a directory that is
> in your $PERL5LIB path.
> 
> I'm just posting them so y'all know roughly where we're at.

I had a go, and the tests ran fine ... looks good.

There seem to be lots of files ending in ~  Is that an emacs thing ?

Is this still supposed to correspond to the idl in the wiki,
or has that been put aside for the moment ?
Browsing the code, I can't see the correspondance.

Is this stuff in the cvs now ?  Ewan - afaik, I don't have a bioperl
account - can you set one up so I can have access to thre repository, please.

> =====
> 
> The tests:
> 	alphabet-test.pl
> 		constructs a few Alphabets and works them out
> 
> 	param-test.pl
> 		constructs a few Params (substitution matrices and the
> 		like) from string identifiers; assigns Values to them;
> 		writes the Values out and reads them back in
> 
> Untested/incomplete modules:
> 
> 	Group, Space, DirichletMixture
> 		...training modules for specifying the
> 		probabilistic structure of a Param space
> 		& corresponding Dirichlet pseudocounts
> 
> 	Element, AlgebraicTerm, AlgebraicProduct
> 		...modules for specifying mappings between Param spaces
> 		and parsing expressions like:
> 
> RNA_match[n](UCC) = Protein_match[n](S) * RNA_null(U) * RNA_null(C) / (RNA_null(U) * RNA_null(C) + RNA_null(A) * RNA_null(G) + (RNA_null(U) + RNA_null(C)));
> 
> 
> 	PolymerPairModel, Transition
> 		...modules for specifying PolymerPairModels
> 		(these are the most hardcore models so I decided to do
> 		them first)
> 
> =====
> 
> So - good news is I reckon we'll definitely have something by ISMB...
> 
> Ian
> 

--
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