[Bioperl-l] Re: [BioSQL-l] seqfeature.display_id

[Hilmar Lapp]

Hi Lincoln,

from what I've seen in your code you're using display_id() to 
implement PrimarySeqI's display_id(). Unless I missed something, I 
understood you implement SeqI and SeqFeatureI in the same module 
(Bio::Graphics::Feature). So since you're flattening SeqFeatureI and 
SeqI, display_id() and seqname() will probably be the same in your 
implementation (but not in Bio::SeaFeature::Generic).

Correct me if I missed something.

	-hilmar


On Tuesday, October 1, 2002, at 04:22 AM, Lincoln Stein wrote:

> Was there any further discussion on this?  I do use display_id() in the
> Bio::Graphics module, and am confused about the distinction between
> display_id() and seqname().
>
> Lincoln
>
> On Thursday 26 September 2002 04:15 pm, Hilmar Lapp wrote:
>> It turns out the definition in Bio::SeqFeatureI does state that it
>> is a name for the feature,  _not_ the sequence. So the
>> implementation is in contradiction to the interface definition and
>> to intuition.
>>
>> 	-hilmar
>>
>> On Thursday, September 26, 2002, at 01:04 PM, Hilmar Lapp wrote:
>>> I just realized that display_id() in SeqFeature::Generic is just an
>>> alias for seqname(). I thought it's a genuine feature attribute.
>>>
>>> This is really bad IMO, because seqname() clearly refers to the
>>> attached sequence, whereas display_id is easily mistaken for being
>>> a genuine property of the feature (in fact, it may even be useful
>>> to have a 'human-readable' name of a feature - but 'display_name'
>>> or something similar may be better suited names).
>>>
>>> I vote for removing display_id() from SeqFeature::Generic. Who
>>> needs to have it named display_id, and cannot call it as seqname()?
>>>
>>> 	-hilmar
>>> --
>>> -------------------------------------------------------------
>>> Hilmar Lapp                            email: lapp at gnf.org
>>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>>> -------------------------------------------------------------
>>>
>>> _______________________________________________
>>> BioSQL-l mailing list
>>> BioSQL-l@open-bio.org
>>> http://open-bio.org/mailman/listinfo/biosql-l
>
> --
> Lincoln Stein
> lstein@cshl.org
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------