Thanks Martin, it's clearer now.
Indeed things get a bit dirty with replace methods. I'm wondering if
it's a bug, a normal behaviour or if there is nothing to do about it?
I think it's because the replace method of A into B is not called after
replacing an object's slot. I imagine this would be done in method
'slot<-', wouldn't it?
See messages with the following code:
setIs("B", "A",
test=function(object){ message("Test if B is A"); TRUE},
coerce=function(object){ message("Coerce B into A"); slot(object,
"obj")},
replace=function(object, value) {
message("Replace slot A in B")
slot(object, "obj") <- value
object
})
setGeneric("number<-", function(object, value) standardGeneric("number<-"))
setReplaceMethod("number", "A", function(object, value) {
message("Replace number in A")
slot(object, "number") <- value
object
})
objB <- new('B', obj=new('A', number=10))
number(objB) <- 20
Martin Morgan wrote:
Hi Renaud --
Renaud Gaujoux <ren...@mancala.cbio.uct.ac.za> writes:
Hi list,
I've got a class B that contains a slot obj of class A. I'd like to be
able to call all the methods of class A directly on objects of class B
as if I had called the method on slot obj. This without overloading
all methods of class A to work on class B.
I don't define B as an extension of A, because I want class B to also
work with objects of classes that inherit from class A and that I
don't know the names.
So I tried to dispatch the methods of class A to slot obj using
function setAs as follows:
setClass('A', representation(number='numeric'))
setGeneric('getNumber', function(object) standardGeneric('getNumber'))
setMethod('getNumber', 'A', function(object) obj...@number)
setClass('B', representation(obj='A', extra='list'))
setAs('B', 'A', def= function(from) f...@obj )
objB <- new('B', obj=new('A', number=10))
getNumber(objB)
But get the error:
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "getNumber", for
signature "B"
I thought the dispatch procedure in S4 would try to find a way to
coerce objects of class 'B' into the closest class usable with the
given method (in that case into an object of class 'A'). I expected it
to internally do:
getNumber(as(objB, 'A'))
Am I thinking wrong or do I need to do another thing to make it work?
setAs defines a method for coercing from one object to another,
without defining an inheritance.
You can use 'setIs'
setClass('A', representation(number='numeric'))
setGeneric('number', function(object) standardGeneric('number'))
setMethod('number', 'A', function(object) obj...@number)
setClass('B', representation(obj='A', extra='list'))
setIs("B", "A",
test=function(object) TRUE,
coerce=function(object) slot(object, "obj"),
replace=function(object, value) {
slot(object, "obj") <- value
object
})
to define an inheritance relationship:
objB <- new('B', obj=new('A', number=10))
number(objB)
[1] 10
This is not something I usually do (are all A methods appropriate for
B's slot 'obj'?) and at least in my hands there seem to be some rough
edges
setGeneric("number<-",
function(object, value) standardGeneric("number<-"))
setReplaceMethod("number", "A", function(object, value) {
slot(object, "number") <- value
object
})
number(objB) <- 20
is(objB, "B")
[1] FALSE
Martin
Thanks
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