FW: [Bioperl-l] Bio::Cluster

[Hilmar Lapp]

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
-- 
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Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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