[Bioperl-l] Bio::FeatureHolderI interface confusion

[Hilmar Lapp]

On Wednesday, June 18, 2003, at 03:37  PM, Lincoln Stein wrote:

> Oy vey.  As far as I can see, this is all the propagation of a POD  
> typo.
> Look here at the top of the FeatureHolderI file:
>
>   Popular feature-holders are for instance L<Bio::Seq> objects. Since
>   L<Bio::SeqFeatureI> defines a sub_SeqFeature() method, most
>   Bio::SeqFeatureI implementations like L<Bio::SeqFeature::Generic>  
> will
>   implement the feature holder interface as well.
>
> This isn't true; it's called get_SeqFeatures() in Bio::SeqFeatureI.
>

It was called sub_SeqFeature() before. Obviously after making the  
change I forgot to change the doc in FeatureHolderI accordingly. Sorry  
'bout that.


> Then below (still in FeatureHolderI):
>
>  =head2 get_SeqFeatures
>
>   Title   : get_SeqFeatures
>   Usage   :
>   Function: Get the feature objects held by this feature holder.
>   Example :
>   Returns : an array of Bio::SeqFeatureI implementing objects
>   Args    : none
>
>  At some day we may want to expand this method to allow for a feature
>  filter to be passed in.
>
>  =cut
>
>  sub get_SeqFeatures{
>      shift->throw_not_implemented();
>  }
>
> Clearly the right brain didn't know what the left was doing.

Well, I didn't paint one on canvas and typed the other on the keyboard  
... it's the same half of the brain, but at different times.

>   Then in
> Bio::Seqfeature::Generic:
>
>   # we revamped the feature containing property to implementing
>   # Bio::FeatureHolderI
>   *sub_SeqFeature = \&get_SeqFeatures;
>   *add_sub_SeqFeature = \&add_SeqFeature;
>
>> Step 4 would not be a contract violation if Bio::SeqFeatureI inherited
>> from Bio::FeatureHolderI - it does not.
>>
>> Yes, I can do a test:
>>
>>   if ($sf->isa("Bio::FeatureHolderI")) {
>>     $sf->add_SeqFeature($foo);
>>   }
>>   else {
>>     $self->throw("feature does not have ability to hold subfeatures");
>>   }
>
> This is yuck.  Bio::SeqI implements get_SeqFeatures().  Always has,  
> always
> will.

Yes the latter, no the former. It used to be called all_SeqFeature()  
and top_SeqFeature() before 1.2.x (which actually caused my brain to  
tie up in a knot).


>
> sub_SeqFeature() must die!
>

I emphatically agree.

	-hilmar


> Lincoln
>
> --  
> ======================================================================= 
> =
> Lincoln D. Stein                           Cold Spring Harbor  
> Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> ======================================================================= 
> =
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------