[Dynamite] Is this working now then?

[Guy Slater]

On Mon, 6 Mar 2000, Ewan Birney wrote:

> > 
> > ...OK, a couple of minor naming gripes ;-)
> > 
> > Can we rename "LightSeq_str" --> "LightSeq_momento" in accordance with
> > Gamma et al
> 
> a-ok

<PEDANTRY>
Gamma et al. use `memento' not `momento'.
</PEDANTRY>

> > I thought before that get_LightSeq_str() was wrongly located in the
> > LightSeq interface -- it belongs in the constructor of LightSeq_str.
> > However, I now realise it's not that straightforward because data-only
> > structures have no methods & hence there is no equivalent of a
> > "constructor" method in IDL. Hmmmmmmmm.
> 
> Hmmmm indeed. This is a good thing about CORBA - forces you to decide
> where to put the factory methods. 
> 
> > 
> > Finally can we please rename "primary_id" --> "implementation_id" because
> > I find "primary ID" confusing.
> 
> a-ok.
> 
> > 
> > OK but to some extent you will have to keep prodding me for it -- we've
> > tossed around a lot of ideas this morning, & I wouldn't have been able to
> > write half as much if we hadn't been able to throw around design patterns
> > jargon. (Of course you might think it'd be better if I hadn't written half
> > as much...)
> 
> It is just that until you write down the IDL there are usually some
> gotcha's in what you "say" in a sort of light and easy way.
> 
> > 
> > Here is my suggested revision of the sequence IDL
> > 
> > 
> > module Seq {
> >         
> >         struct LightSeq_momento {
> >                 string name;
> >                 string seq;
> >         };
> > 
> >         interface LightSeq {
> >                 attribute string name;
> >                 attribute string seq;
> >                 string get_subseq(in long start, in long end);
> >                 LightSeq_momento make_LightSeq_momento();
> >         };
> > 
> >         interface DatabaseSeq : LightSeq {
> >                 attribute string implementation_id; // implementation unique id
> >                 attribute string accession_number;  // biological unique id
> >         };
> > 
> > }
> > 
> 
> I am a-ok on this - just need to get Guy's thoughts on it.
> Guy - I am wondering to what extent we should coordinate this seq
> stuff with your fast-finder, and I think we should as much as possible.

Do you mean the overlap detection interface stuff for ensembl ?

They are different: the overlap detection stuff doesn't contain
the sequence itself, just references to it.

However, I think it would be trivial to move from one representation to
another.

> I am sort of hoping this is the last time I have to write a C sequence
> object in a long, long time...

;)
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