[Biocorba-l] Part II - Annotations on a Seq

[Ewan Birney]

On Mon, 12 Feb 2001, Alan Robinson wrote:

> 
> 
> 2) At the moment, you cannot attach general annotations to an entire
>    sequence; only SeqFeature's that include a specific location upon the
>    sequence.
> 
> Solution 1: Specify that an annotation that applies to the whole sequence
> has start=1 and end='length of sequence'
> 
> Solution 2: Have an interface 'Annotation' that takes the location
> independent stuff out of SeqFeature. Then SeqFeature inherits from
> Annotation:
> 
>   interface Annotation : GNOME::Unknown 
>   {
>     string type();
>     string source();
>     string seq_primary_id();
>     NameValueSet qualifiers();
>   };
> 
>   interface SeqFeature : Annotation 
>   {
>    // Everything else that was in SeqFeature previously.
>   };
> 
> 
> To the 'Seq' interface add a method to return the Annotation objects. This
> would also require the addition of an AnnotationVector and
> AnnotationIterator interfaces [unless we want to handle this as a simple
> CORBA sequence with 'typedef sequence<Annotation> AnnotationList'?]:
> 
>   interface Seq : PrimarySeq 
>   {
>     // ...
>     AnnotationVector annotations();
>   };
> 
> 
>   interface AnnotationVector : GNOME::Unknown 
>   {
>     long size();
>     Annotation elementAt(in long index)
>       raises (OutOfRange);
>     AnnotationIterator iterator();
>   };
> 
>   interface AnnotationIterator : GNOME::Unknown 
>   {
>     Annotation next()
>       raises (EndOfStream);
>     boolean has_more();
>   };


I like this basic model and it jives well with bioperl. Jason?


> 
> 
> --
> ============================================================
> Alan J. Robinson, D.Phil.             Tel:+44-(0)1223 494444
> European Bioinformatics Institute     Fax:+44-(0)1223 494468
> EMBL Outstation - Hinxton             Email:  alan@ebi.ac.uk
> Wellcome Trust Genome Campus
> Hinxton, Cambridge
> CB10 1SD, UK                http://industry.ebi.ac.uk/~alan/
> ============================================================
> 
> 
> 
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> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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