[Bioperl-l] how to determine if SeqFeature is attached to Sequence

[Ewan Birney]

On Wed, 20 Jun 2001, Jason Stajich wrote:

> Ewan's suggestion looks good - couple of other comments after perusing the
> code:
> 
> a) Should Bio::LocationI seq_id should return the sequence id of the
>    sequence it is attached to.  I know we create locations explicitly
>    with seq_id when parsing a seq file that has a location which
>    refers to another sequence, but should the default return the seq_id
>    for the current seq?
> 
>    Bio::SeqFeature::attach_seq doesn't touch the location object.   
> 
> b) seqname doesn't appear to get set when attach_seq is called - should
>    it?  This would be a less computational way than testing if
>    entire_seq() or seq() is null....

seqname can be set with entire_seq being null. I think. 


> 
> -Jason
> 
> On Wed, 20 Jun 2001, Mark Wilkinson wrote:
> 
> > Hi Group!
> > 
> > Is there a "right way" to ask a SeqFeature if it has been attached to a
> > Sequence by $Seq->add_SeqFeature?
> > 
> > Given that it is possible to create standaone SeqFeature::Generic's, I
> > now find myself needing to ask individual features whether they have
> > been added to a Sequence object or if they are still orphans.
> > 
> > >>sigh<<    the trials and tribulations of GUI's   ;-)
> > 
> > Any advice appreciated!
> > 
> > M
> > 
> > --
> > --------------------------------
> > "Speed is subsittute fo accurancy."
> > ________________________________
> > 
> > Dr. Mark Wilkinson
> > Bioinformatics Group
> > National Research Council of Canada
> > Plant Biotechnology Institute
> > 110 Gymnasium Place
> > Saskatoon, SK
> > Canada
> > 
> > 
> > 
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
> 
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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