[Bioc-devel] Making GenomicRanges::genome generic more generic ...

Hi Herve&  Michael:

2011/11/4 Michael Lawrence<lawrence.michael at gene.com>:

2011/11/4 Herv? Pag?s<hpages at fhcrc.org>

Hi Steve,

On 11-11-04 02:02 PM, Steve Lianoglou wrote:

Hi all,

It looks like the `genome` generic function from rtracklayer has moved
to GenomicRanges in the 2.9 release train, and subsequently lost its
`...` param.

I moved it, together with the `genome<-` generic, and dropped the `...`
arg from `genome` because (1) I couldn't find any method in BioC
that uses this arg, (2) `genome` (getter) and `genome<-` (setter)
are aimed to be accessors and it's unusual to have `...` in an
accessor, (3) it was a little bit ackward to have `...` in the getter
but not in the setter.

I guess we share different opinions of what "awkward" means :-)

Going backwards: is it possible to have `...` in a setter anyway? I
mean, I guess I don't see where `...` would go in:

something(object)<- 'something'

though I do see `...` in the def for `setReplaceMethod` ... hmm.

anyway, with respect to (1) I'd argue that it's better err on the side
of things that "might be" (even if they don't yet exist in the
bioc-universe). Especially with functions as "generic" (excuse the
overloaded term -- here I mean non-specificly named) as a function
named "genome" (vs. "exonsByOverlaps") ... not that I'm arguing
anything, it seems like you're open to adding it back in to devel
(which is fine by me).

Would anybody mind if I add the `...` back to the genome function now
defined in GenomicRanges? I'll be careful to update the setMethods
where appropriate in GenomicRanges, but I guess other packages will
also need to update (rtracklayer) that I can't commit to.

In devel? Sure. It's a perfect time to break things ;-) I'm not so sure
about release though. What other people think?

I'm fine w/ only adding it to devel if that's ok w/ everyone.

And Michael:

Do we really need to modify every method? I think changing the generic is
all that is really necessary.

I wasn't sure if packages would pass checks if the generic defines a
function to take `...` but a setMethod() didn't include the `...` If
it's not necessary, then I wouldn't suggest modifying every method, I
was just anticipating the worst.

I was `importFrom(rtracklayer, genome)`-ing the genome function in one
of my packages ... switching it to importFrom GenomicRanges isn't a
problem, but I use the `...`

(here's another post that touches on the "need" for a centralized
BiocGenerics (or whatever) package that pops up from time to time).

Not every generic is going to make it to BiocGenerics. Also a generic
function is not just a name, there are also some expectations about what
kind of operation its methods should do.

I see ... not sure what exactly you mean by that, but perhaps I missed
a relevant thread discussing the expectations of a generics
operations?

-steve