[Biocorba-l] Annotation and anys

[Juha Muilu]

Ewan Birney wrote:
> 
> The lack of any's is a good thing. Thanks for being flexible on this Juha.
> 
> I still don't like too much SeqFeature inherieting from Annotation -
> SeqFeature is 90% of the time a very small, compact set of information
> which people have lots of (100,000 or so). Although the interface does not
> mean that the data behind the interface has to be there at all, it does
> mean that systems that are tyring to handle - say - storing of seq
> features have a real challenge.

Actually when the SeqFeature inherits from the AbstractAnnotation we do
not have to bring anything extra to SeqFeature what is already in
bioCORBA 0.2

interface AbstractAnnotation { 
   string name ;
   short the_basis ; /* we may remove this if not needed here */
}

interface SeqFeature : AbstractAnnotation { 

   unsigned long start;
   unsigned long  end;
   short strand;
   AnonymousSequence owner_sequence; /* or what ever */
 
   stringList qualifiers ;

}

we can then have another subclass for annotated seq feature if needed.
Is this what you meant:

  interface AnnotatedSeqFeature : SeqFeature, Annotatable { 

  }

We may end up having lot of layers (lasagne code) but perhaps it is not
problem

> 
> Could we split this up into:
> 
>     SimpleSeqFeatureI
> 
>     AnnotatedSeqFeatureI : SimpleSeqFeatureI
> 
> I believe the restriction to the more simple type will be very useful for
> both clients and servers to indicate that they have "just" got a
> seqfeature.


> 
> I'll need to read again the whole IDL but I think we are iterating down to
> the last serious points ;)
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
> -----------------------------------------------------------------
> 
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