On 07/07/2010 08:09 AM, james.fo...@diamond.ac.uk wrote:
>
>
> Dear R developers,
> I have a new class, which I called "Molecule", and have tried to define =
> a "+" operation for 2 objects of this class.
> This is what I have written so far, although the method is not complete =
> (I'm trying to look at it at intermediate stages):
>
> setMethod(
> f=3D"+",
> signature(x=3D"Molecule",y=3D"Molecule"),
> definition=3Dfunction(x,y,...)
> {
> # Check both objects are correct
> checkMolecule(x)
> checkMolecule(y)
>
> # Extract chains information
> ch1 <- getMoleculeChains(x)
> ch2 <- getMoleculeChains(y)
> union_ch <- unique(c(ch1,ch2))
> not_used <- .ALPHABET
> for (i in seq(along =3D union_ch))
> {
> idx <- which(not_used !=3D union_ch[i])
> if (length(idx) !=3D 0) not_used <- not_used[idx]
> }
>
> return(not_used)
> }
> )
>
>
> The definition of class Molecule is included earlier in the same file. =
> When I source it, I get the following error message:
>
> Error in match.call(fun, fcall) :=20
> unused argument(s) (x =3D "Molecule", y =3D "Molecule")
If I
> getGeneric("+")
standardGeneric for "+" defined from package "base"
belonging to group(s): Arith
function (e1, e2)
standardGeneric("+", .Primitive("+"))
<environment: 0xb432f8>
Methods may be defined for arguments: e1, e2
Use showMethods("+") for currently available ones.
I see that the generic is defined to take two arguments e1 and e2. So
setMethod("+", c("Molecule", "Molecule"), function(e1, e2) {
## ...
})
but actually here it might often pay to discover ?GroupGenericFunctions
and end up with something like
setClass("A", representation=representation(x="numeric"))
setMethod("Arith", c("A", "A"), function(e1, e2) {
new(class(e1), x=callGeneric(e1...@x, e2...@x))
})
and then
> new("A", x=1:5) + new("A", x=5:1)
An object of class "A"
Slot "x":
[1] 6 6 6 6 6
but also
> new("A", x=1:5) * new("A", x=5:1)
An object of class "A"
Slot "x":
[1] 5 8 9 8 5
Martin
>
>
> I can't see what's wrong in my method definition. Can anyone help me =
> with this?
>
> J
>
> Dr James Foadi PhD
> Membrane Protein Laboratory (MPL)
> Diamond Light Source Ltd
> Diamond House
> Harewell Science and Innovation Campus
> Chilton, Didcot
> Oxfordshire OX11 0DE
>
> Email : james.fo...@diamond.ac.uk
> Alt Email: j.fo...@imperial.ac.uk
>
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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