[Bioperl-l] hash key for SeqFeatureI

[Jason Stajich]

actually it is not always a Location::Simple but instead is always a
Bio::LocationI object
Which can be
  Peter the (somewhat old) object diagram on the bioperl website might be
helpful.

Split locations won't have strands but will delegate to their internal
components which are a list of Bio::LocationI objects.

Fuzzy and Split locations will try and return a sensible summary value for
start/end/strand.

The method $location->to_FTstring() will return a string which should be
comparable (although sets of locations in different orders stored
in a SplitLocation will not be equivalent).

-j
On Thu, 25 Mar 2004, Chris Dwan (CCGB) wrote:

>
> > And related to this, where is the strandedness of Bioperl SeqFeatures
> > stored?
>
> Bio::SeqFeature::Generic has a member "location" which is a
> Bio::Location::Simple.  Bio::Location::Simple inherits the strand method
> from Bio::Location::Atomic.
>
> Really, under the hood, it's:
>   seqfeature->location()->{'_strand')}
>
> Which may be accessed as
>   seqfeature->strand()
>
> Allowed values are -1 (or '-'), 1 (or '+') and 0 (or '.').
>
> -Chris Dwan
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu