[Bioperl-l] Re: [Bioperl-guts-l] bioperl commit

Hilmar Lapp hlapp at gmx.net
Wed Aug 11 12:02:06 EDT 2004

Well the thing is by definition they always have an underlying 
PrimarySeq. And, almost all flat attributes do delegate to the 
PrimarySeq. See the constructor.

If there is to be a Seq w/o an underlying PrimarySeq we'll have to do 
some serious re-thinking of how we do things. Just as an example, when 
you attach features to a Seq object, the method will attach the 
PrimarySeq to the feature.


On Wednesday, August 11, 2004, at 04:51  AM, Aaron J. Mackey wrote:

> On Aug 11, 2004, at 3:27 AM, Hilmar Lapp wrote:
>> Log Message:
>> Made primary_id() to delegate. Yes, always. Also, added a Seq test to 
>> make
>> sure glaring inconsistencies don't happen again.
> I'm not going to argue vociferously, but I imagine that the issue 
> might be Seq.pm's that don't actually have underlying PrimarySeq's 
> associated with them ... perhaps your delegation can check to see 
> whether there's actually something to delegate to?
> -Aaron
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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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