[Bioc-devel] refactoring

James Bullard bullard at berkeley.edu
Fri Apr 11 21:47:23 CEST 2008

Hi All, I have a quick question about refactoring (mostly  
documentation). I have a set of classes which all have a method  
defined on them:

setClass("c1", representation(x = "numeric"))
setClass("c2", representation(x = "numeric"))
setClass("c3", representation(x = "numeric"))

setGeneric("m", def = function(klass) standardGeneric("m"))
setMethod("m", signature("c1"), function(klass) { klass at x^2 })
setMethod("m", signature("c2"), function(klass) { klass at x^3 })
setMethod("m", signature("c3"), function(klass) { klass at x^4 })

When I do promptClass on these classes I am happy and I get some  
boilerplate .Rd to fill in. However, if, once I have my nice .Rd files  
for the set of classes and I come along and make a new method I want  
to be able to add to the .Rd files the boilerplate for this new method  
so R CMD CHECK doesn't complain. Also, if I decide to export a method  
that was not exported previously then I have the same problem. I was  
wondering if people do particular things - it is not clear to me that  
any simple diff will work, but I was hoping that someone might have  
something because it is quite tedious to edit these files by hand,  
especially when you have a reasonable class hierarchy.

Why this question is posted to the bioc-devel list is that I was  
wondering also does bioc have any kind of document generation  
aspirations? I know that this has come up a number of times, but  
maintaining documentation is becoming too much of a burden and that  
generally means that I do a poor job. I didn't notice any discussion  
on: http://wiki.fhcrc.org/bioc/DeveloperPage#discussions, so maybe  
people are using other documentation utilities. I know that Henrik has  
his utilities, but I was hoping maybe there was a bioc standard and I  
could use that.

thanks in advance, jim

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