[Dynamite] Is this working now then?

[Ewan Birney]

> Actually I wouldn't bet against you -- I was trying to say that even an
> AnonymousSeq should have a name. (This fits in nicely with the idea that
> everything should have a debugging display method.) But the other two
> names belong in the next level up (PrimarySeq in this case).

Interesting. A slight change from BioCorba. I might pass this idea 
on... ;)

> 
> No I think this is fine ;-)

:-) 'he shoots - he scores - the crowd goes wild'.

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

a-ok

> 
> 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.

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


This could be the first real code ... ;)