[Bioperl-l] PrimarySeq POD changes

Chris Fields cjfields at uiuc.edu
Thu Sep 28 00:15:23 UTC 2006


Looks like it did accept named arguments at one point.  Aaron added the
'alphabet' argument at rev 1.52, which initially used _rearrange().  Ewan
changed it to a straight two-argument version on rev 1.71 (no _rearrange()
call), but it looks like the change was mainly for returning the sequence
string if no arguments were passed.  This was leading up to the 1.2 release.

It could be Ensembl-related; I think they still use bioperl 1.2.3.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: Wednesday, September 27, 2006 7:01 PM
> To: Chris Fields
> Cc: 'Sendu Bala'; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] PrimarySeq POD changes
> On Sep 27, 2006, at 7:47 PM, Chris Fields wrote:
> > Anyway, I believe the POD signaled an intent to do something like
> > this that
> > was never brought to fruition.
> I don't have the time right now to check this but maybe you guys can
> while you're at it - if my memory doesn't betray me and Jason's
> message reinforces my belief that at least in this case it doesn't
> then at some point the method *did* take named arguments, but that
> was later changed. (I do not recall why.)
> 	-hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================

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