[Dynamite] Is this working now then?

[Ian Holmes]

On Mon, 6 Mar 2000, Ewan Birney wrote:

> > Revised:
> > 
> > > module Seq {
> > >         
> > >         struct LightSeqMomento {
> > >                 string name;
> > >                 string seq;
> > >         };
> > > 
> > >         interface LightSeq {
> > >                 string name();

actually now i think the name should be an attribute after all.
oh well -- i'll change it when the wiki's up... :)

> > >                 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);
> };

How about

  interface SequentialAccessDatabase {
    DatabaseSeqIterator make_DatabaseSeqIterator();
  }

  interface RandomAccessDatabase : SequentialAccessDatabase {
    DatabaseSeq get_DatabaseSeq_from_id(in string implementation_id);
    sequence<string> all_implementation_ids();   // (perhaps)
  }

...so we can e.g. stream through a FASTA file without worrying about
building an index.

Ian