[Rd] how to define method for "+" function in a new class
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")
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
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Re: [Rd] how to define method for "+" function in a new class
I don't know why a "3D" appears instead of a "(".
Please, interpret a "( whenever you see a "3D".
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
-Original Message-
From: r-devel-boun...@r-project.org on behalf of james.fo...@diamond.ac.uk
Sent: Wed 07/07/2010 16:09
To: r-devel@r-project.org
Subject: [Rd] how to define method for "+" function in a new class
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")
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
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Re: [Rd] how to define method for "+" function in a new class
Thank you, Martin! Very clear.
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
-Original Message-
From: Martin Morgan [mailto:mtmor...@fhcrc.org]
Sent: Wed 07/07/2010 16:43
To: Foadi, James (Imperial Coll.,RAL,DIA)
Cc: r-devel@r-project.org
Subject: Re: [Rd] how to define method for "+" function in a new class
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("+"))
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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[Rd] method using several (and different) arguments in turn
Dear R-developers community, I have the following generic:
setGeneric(
name="newsample",
def=function(x,y,z,a,b,c,...){standardGeneric("newsample")}
And I can build several methods for this generic. One useful thing is to use
"newsample"
with only one of the 6 arguments listed. At the moment this is what I do:
setMethod(
f="newsample",
signature=c("missing","missing","numeric","missing","missing","missing"),
function(x,y,z,a,b,c,...)
{
..
..
}
)
This would be used when the single argument is z:
newsample(z=12.5)
To use newsample with another argument (say x) I should implement the same as
before,
but with signature
c("numeric","missing","missing","missing","missing","missing").
Is there another shorter and easier way to do this?
J
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Re: [Rd] method using several (and different) arguments in turn
Dear Martin,
I could not entirely follow your suggestion.
I can see how you define two classes inheriting from TypeOfSample, and how
these two
classes have two associated methods (incidentally, I'm unfamiliar with the:
function(type,x=numeric(),...)to do.
J
expression. What is type?
But then I'm lost. I wouldn't know how to carry on from here.
I don't know if I have explained the key point clear enough before. For the
person using
"newsample" it makes sense which name (x or y or z, etc) is used.
newsample(x=12.4) would
give something different from newsample(y=12.4); and yet another result would
be obtained if
using a combination, like newsample(x=12.4,y=12.4).
I wanted to use a simple function with default values at first, but I'm in the
middle of developing
a package using S4 formalism. I'm not sure this would be a wise thing
Sent: 14 February 2012 17:00
To: Foadi, James (Imperial Coll.,RAL,DIA)
Cc: r-devel@r-project.org
Subject: Re: [Rd] method using several (and different) arguments in turn
On 02/14/2012 08:43 AM, james.fo...@diamond.ac.uk wrote:
> Dear R-developers community, I have the following generic:
>
> setGeneric(
> name="newsample",
>
> def=function(x,y,z,a,b,c,...){standardGeneric("newsample")}
>
> And I can build several methods for this generic. One useful thing is to use
> "newsample"
> with only one of the 6 arguments listed. At the moment this is what I do:
>
> setMethod(
> f="newsample",
>
> signature=c("missing","missing","numeric","missing","missing","missing"),
> function(x,y,z,a,b,c,...)
> {
> ..
> ..
>
> }
> )
>
> This would be used when the single argument is z:
>
> newsample(z=12.5)
>
> To use newsample with another argument (say x) I should implement the same as
> before,
> but with signature
> c("numeric","missing","missing","missing","missing","missing").
> Is there another shorter and easier way to do this?
Hi James --
A matter of opinion, but multiple dispatch like this can be very
complicated, e.g., figuring out the 'next' method when dispatching on
two or more arguments; I'd really discourage it.
A different approach, assuming that x, y, z, ... are all numeric() but
that the sample to be drawn differs, is to define a small class
hierarchy to be used for dispatch.
setClass("TypeOfSample")
setClass("XSample", contains="TypeOfSample")
XSample <- new("XSample") ## a 'singleton', used for dispatch
setClass("YSample", contains="TypeOfSample")
YSample <- new("YSample")
and then
setGeneric("newsample",
function(type, x=numeric(), ...) standardGeneric("newsample"),
signature="type")
setMethod("newsample", "XSample", function(type, x=numeric(), ...) {
"XSample"
})
setMethod("newsample", "YSample", function(type, x=numeric(), ...) {
"YSample"
})
One could implement a default method on "TypeOfSample", and use
callNextMethod() after initial transformation, if that were the pattern.
To use:
newsample(XSample, x=1:100)
Martin
>
>
> J
>
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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