[Bioperl-l] removing Seq features

[Ewan Birney]

On Wed, 18 Oct 2000 hilmar.lapp@pharma.Novartis.com wrote:

> 
> 
> Interesting. For Generic features there is I think a flush_sub_SeqFeature()
> or something similar, but it turns out to be absent from Seq. I guess this
> has something to do with the supposed immutability of Seq objects, right
> Ewan? Otherwise it's a bug.

A missing feature ;)

> 
> We had a discussion some time ago about seq mutability. Given your context
> of users dropping or adding features, you clearly need Seq objects as
> mutable objects. I don't know how strongly Seq objects are supposed to be
> immutable in BioPerl. Not least as you can change the sequence legally ...
> 

Yes. If you notice the mutability of the sequence object is *not*
guarenteed by the interface definition.

Possibly we could have a Bio::MutableSeqI interface and a Bio::SeqI
interface (MutableSeqI isa SeqI). This might save us some tears later
on...



>      Hilmar
> 
> 
> 
> 
> 
> Mark Wilkinson <mwilkinson@gene.pbi.nrc.ca>@bioperl.org on 18.10.2000
> 17:59:14
> 
> Sent by:  bioperl-l-admin@bioperl.org
> 
> 
> To:   bioperl-l@bioperl.org
> cc:
> Subject:  [Bioperl-l] removing Seq features
> 
> 
> hi group,
> 
> is there a 'formal' way to remove features from a Seq object?  I see
> that there is an add_SeqFeature method for the Seq object, but there
> appears to be no equlivalent remove_SeqFeature method.
> 
> If not, I presume it is sufficient just to delete this feature from the
> hash 'by force'?  ...or?
> 
> Any advice appreciated!
> 
> Mark
> 
> --
> ---
> Dr. Mark Wilkinson
> Bioinformatics Group
> National Research Council of Canada
> Plant Biotechnology Institute
> 110 Gymnasium Place
> Saskatoon, SK
> Canada
> 
> 
> 
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> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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