[Bioc-devel] Making GenomicRanges::genome generic more generic ...
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.
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 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. Cheers, H.
Thanks, -steve
Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319