[BioPerl] Re: [Bioperl-l] ->alphabet documentation wrong here
there and everywhere :-)
markw at illuminae.com
Sat Jan 10 16:13:06 EST 2004
But... surely the documentation for the modules that DO implement it
this way should reflect that... or? As it stands, all implementers have
simply copy/pasted the documentation from the interface module, even
though their implementation adds this functionality.
On Sat, 2004-01-10 at 13:12, Jason Stajich wrote:
> The documentation is correct we cannot assume that all implementers of the
> interface will be mutable.
> An interface does not assume that you can set value while a implementation
> may choose to allow it. Consider a DBPrimarySeq which is a read-only
> representation of the db - it implements the PrimarySeqI interface but
> does not allow alphabet to be updated while Bio::PrimarySeq does.
> On Fri, 9 Jan 2004, Mark Wilkinson wrote:
> > Does anyone object to me fixing the documentation for PrimarySeqI et al.
> > with respect to the 'alphabet' function? It claims to not accept any
> > arguments, but every implementation of it that I can find in the
> > sequence hierarchy actually does, so... the docs are wrong all over the
> > place.
> > Alternately, I could leave the Interface documentation alone, and simply
> > update the documentation for all of the implementing objects who
> > actually DO allow you to set the alphabet explicitly after Seq object
> > creation...
> > Which do you prefer? Was it intentional that the ->alphabet interface
> > not be get/set, or is that historical cruft?
> > Mark
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
Mark Wilkinson <markw at illuminae.com>
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