FW: [Bioperl-l] Bio::Cluster

[Hilmar Lapp]

All done, except that annotation() isn't on the interface 
Bio::ClusterI yet. (Also, I haven't yet implemented IdentifiableI 
and DescribableI in Cluster::SequenceFamily. Any volunteers are 
welcome to do that ...)

What about defining an interface Bio::AnnotatableI with currently 
one method annotation()? Right now there's not much difference to 
querying $obj->can('annotation'), but this may change in the future 
as we may want to stick more methods onto AnnotatableI.

	-hilmar


On Thursday, October 24, 2002, at 03:16 PM, Hilmar Lapp wrote:

> I'm more or less through this.
>
> I also added a method display_id() in Bio::ClusterI. unigene_id() 
> and family_id() in Cluster::UniGene and Cluster::SequenceFamily, 
> resp., alias to this.
>
> My feeling is many cluster implementions will want to be or are 
> naturally IdentifiableI. Would anyone have a problem with me 
> implementing IdentifiableI and DescribableI in Cluster::UniGene. 
> I'm not so sure regarding Cluster::SequenceFamily, but my gut 
> feeling says 'you too.'
>
> I'm also going to implement Bio::ClusterI in Bio::Cluster::UniGene 
> (it wasn't so far).
>
> Last but not least I'd propose to add annotation() to 
> Bio::ClusterI. Things like gene() etc in Cluster::UniGene could 
> then come off the annotation collection. Alternatively I could 
> write an adaptor like I did for Seqfeature tag/value pairs that 
> would give me a AnnotationCollectionI view on Cluster::UniGene.
>
> Comments/suggestions more than welcome.
>
> 	-hilmar
>
> -----Original Message-----
> From: Hilmar Lapp
> Sent: Thursday, October 24, 2002 12:20 PM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Bio::Cluster
>
>
> The modules and interfaces in Bio::ClusterI and Bio::Cluster::* 
> deviate in
> a couple aspects from the rest of bioperl (or at least from how the 
> rest
> of bioperl should be :) , namely
>
> - interfaces traditionally do not have any implementation (I know there
> are exceptions, but there are usually good - or not so good - 
> reasons for
> it)
> - as a consequence, there is no new() in interfaces
> - array accessors or iterators don't exhaust their arrays
>
> I'm going to fix those things as I come across them, unless anyone has
> objections.
>
> 	-hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp@gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
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--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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