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

[Jason Stajich]

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....

-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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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/