[Bioperl-l] Re: [Bioperl-guts-l] [Bug 1742] New: GFF parser messes attributes (fwd)

[Hilmar Lapp]

On Monday, January 31, 2005, at 04:56  PM, Allen Day wrote:

> This bug isn't coming from SeqFeature::Annotated, it's from the 
> refactor
> of SeqFeatureI to inherit from AnnotatableI.  Meaning get_tag_values() 
> and
> similar functions are now get/setting attributes to a
> Bio::AnnotationColleciton store.  Simple strings passed in are turned 
> into
> objects when added to the store, and given back in object form.
>
> It was never specified in Bio::SeqFeatureI, even before refactoring, 
> that
> the returned values of annotation tags should be strings.  Code using 
> the
> interface just assumed this was the case, and it wasn't a bad 
> assumption
> given that Bio::SeqFeature::Generic was the only instantiable class and
> did use strings as values rather than objects.

If it wasn't a bad assumption and if everybody made that assumption, 
what's so great about breaking that?

What SeqFeatureI stated was:

  Title   : get_tag_values
  Usage   : @values = $self->get_tag_values('some_tag')
  Function:
  Returns : An array comprising the values of the specified tag.
  Args    : a string

So you might say the term 'values' does not say it must be a string, 
yet in the synopsis that's exactly how the method is demonstrated.

I think it's fair to say that implicitly by usage pattern the contract 
has become you have to return a string here, and I think breaking this 
so as to return objects may be a great idea and a great change but in a 
bioperl-2.0 only.

Otherwise, you demand that all current and future Bio::AnnotationI 
implementations are properly stringification-overloaded, and that 
people are perfectly aware that $annvalue and "$annvalue" are two very 
different things.


	-hilmar

-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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