FW: [Bioperl-l] Bio::Cluster

[shawnh@fugu-sg.org]

Looks good Hilmar. Thanks for polishing it up :)
I will follow  your framework and take up SequenceFamily.

A small question on bioperl convention, so if we don't have
implementation on interface objects, eg ClusterI then do we will
want to implement a Cluster.pm object for get/set methods like display_id
description etc ?   


shawn



On Fri, 25 Oct 2002, Hilmar Lapp wrote:

> 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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-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
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