[Dynamite] Is this working now then?

[Ewan Birney]

On Sun, 5 Mar 2000, Ian Holmes wrote:

> Just spotted a gotcha in this...
> 
> 
> These two should be methods & not attributes I think.
> Also I reckon we need a length() method so we don't have to retrieve the
> whole sequence (which might, as Ewan pointed out, be a behemoth spanning
> several contigs) to find this.
> 

Right. Good stuff.

> Revised:
> 
> > module Seq {
> >         
> >         struct LightSeqMomento {
> >                 string name;
> >                 string seq;
> >         };
> > 
> >         interface LightSeq {
> >                 string name();
> >                 string seq();
> >                 int    length();    // need a length method because we might not want to retrieve the whole seq()
> >                 string subseq(in long start, in long end);
> >                 LightSeqMomento make_LightSeqMomento();
> >         };
> > 
> >         interface DatabaseSeq : LightSeq {
> >                 attribute string implementation_id; // implementation unique id
> >                 attribute string accession_number;  // biological unique id
> >         };
> > 
> > }
> 

Ok.

Now we need something like....

interface DatabaseSeqIterator {
	DatabaseSeq next();
	boolean at_end();
};

// even if we are in module 'Seq', Database might be a little
// too generic a name
interface Database {
	DatabaseSeqIterator make_DatabaseSeqIterator();
	DatabaseSeq get_DatabaseSeq_from_id(in string implementation_id);
};

And we are done for sequences

(except - where does this fecking alphabet shit go?)