R help - Jul 2009 - How to: initialize, setValidity, copy-constructor

Hello list,

I'm having troubles setting up a basic calss hierarchy with S4.
Here is a simplified schema of what I'd like to do:

- Two classes: A and B that extends A
- Ensure that the slots added by B are consistent with the slots of A
- Let A initialize itself (I'm not supposed to know the internal cooking 
of A)
- By default set the slots of B based on the slots that A initialized

Another question is: what is the recommended way of implementing a 
copy-constructor in R?

I know that all of this is easily done in C++. The constructor of each 
class is called recursively back-up to the root class. Validity checks 
can be performed after/during associated initialization. 
Copy-constructor are basics in C++.

Here below is a piece of code that I thought would work (but it does 
not... therefore my post), what's wrong with it?
I think the main issue is when is the validity check performed: why is 
it performed before the end of the initialize method?

Thank you for your help.
Renaud

# define class A with a single numeric slot
setClass('A', representation(a='numeric'))

# define class B that extends class A, adding another numeric slot
setClass('B', representation('A', b='numeric'))
# we want for example to ensure that slots a and b have the same length
setValidity('B',
function(object){
cat("*** B::validate ***\n")
print(object)
cat("*****************\n")
if( length(object at a) != length(object at b) ) return('Inconsistent
lengths')
TRUE
}
)
# As a default behaviour if b is not provided, we want slot b to be 
equal to slot a
setMethod('initialize', 'B',
function(.Object, b, ...){
cat("*** B::initialize ***\n")
print(.Object)

# Let the superclass (A) initialize itself via callNextMethod
# I thought it would only do that: initialize and optionnaly validate 
the class A part of the object
#But it generates an ERROR: apparently it calls the validation method of B,
# before leaving me a chance to set slot b to a valid value
.Object <- callNextMethod(.Object, ...)

# now deal with the class B part of the object
cat("*** Test missing b ***\n")
if( missing(b) ){
cat("*** b is MISSING ***\n")
b <- .Object at a
}

# set slot b
.Object at b <- b

.Object
}
)

### Testing

# empty A: OK
aObj <- new('A')
aObj

# class A with some data: OK
aObj <- new('A', a=c(1,2) )
aObj

# empty B: OK
bObj <- new('B')
bObj

# initialize B setting the slot of class A: ERROR
bObj <- new('B', a=c(1,2))

# initialize B setting only the slot class B: OK!! Whereas it produces a 
non valid object.
bObj <- new('B', b=c(1,2))
bObj

######### RESULTS:

 > # empty A: OK
 > aObj <- new('A')
 > aObj
An object of class ?A?
Slot "a":
numeric(0)

 >
 > # class A with some data: OK
 > aObj <- new('A', a=c(1,2) )
 > aObj
An object of class ?A?
Slot "a":
[1] 1 2

 >
 > # empty B: OK
 > bObj <- new('B')
*** B::initialize ***
An object of class ?B?
Slot "b":
numeric(0)

Slot "a":
numeric(0)

*** Test missing b ***
*** b is MISSING ***
 > bObj
An object of class ?B?
Slot "b":
numeric(0)

Slot "a":
numeric(0)

 >
 > # initialize B setting the slot of class A: ERROR
 > bObj <- new('B', a=c(1,2))
*** B::initialize ***
An object of class ?B?
Slot "b":
numeric(0)

Slot "a":
numeric(0)

*** B::validate ***
An object of class ?B?
Slot "b":
numeric(0)

Slot "a":
[1] 1 2

*****************
Error in validObject(.Object) :
invalid class "B" object: Inconsistent lengths
 >
 > # initialize B setting only the slot class B: OK!! Whereas it creates 
a non valid object.
 > bObj <- new('B', b=c(1,2))
*** B::initialize ***
An object of class ?B?
Slot "b":
numeric(0)

Slot "a":
numeric(0)

*** Test missing b ***
 > bObj
An object of class ?B?
Slot "b":
[1] 1 2

Slot "a":
numeric(0)



-----------------------------
 > sessionInfo()
R version 2.9.1 (2009-06-26)
x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_ZA.UTF-8;LC_NUMERIC=C;LC_TIME=en_ZA.UTF-8;LC_COLLATE=en_ZA.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_ZA.UTF-8;LC_PAPER=en_ZA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_ZA.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices datasets utils methods base

other attached packages:
[1] Biobase_2.4.1

Hi Renaud --

Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> writes:
> Hello list,
>
> I'm having troubles setting up a basic calss hierarchy with S4.
> Here is a simplified schema of what I'd like to do:
>
> - Two classes: A and B that extends A
> - Ensure that the slots added by B are consistent with the slots of A
> - Let A initialize itself (I'm not supposed to know the internal
>   cooking of A)
> - By default set the slots of B based on the slots that A initialized
>
> Another question is: what is the recommended way of implementing a
> copy-constructor in R?
>
> I know that all of this is easily done in C++. The constructor of each
> class is called recursively back-up to the root class. Validity checks
> can be performed after/during associated
> initialization. Copy-constructor are basics in C++.
>
> Here below is a piece of code that I thought would work (but it does
> not... therefore my post), what's wrong with it?
> I think the main issue is when is the validity check performed: why is
> it performed before the end of the initialize method?
loosely, new("B", ...) calls initialize(prototypeOfB, ...).
initialize,B-method uses callNextMethod(), so initialize,A-method sees
as .Object the value prototypeOfB.  If initialize,A-method is
well-behaved, it'll call initialize,ANY-method, which also sees
prototypeOfB. You'll see that, when the ... argument is not empty

  getMethod(initialize, "ANY")

eventually calls validObject, in this case on prototypeOfB. Hence what
you are seeing, an 'early' check on the validity of B.

There are many creative ways around this in initialize,B-method, e.g.,
assigning B slots before callNextMethod(), or explicitly creating a
new instance of A from appropriate supplied arguments (in
initialize,B-method, name arguments meant to initialize B slots and
pass ... to the A constructor) and using that to initialize B, etc.

The approach I find most palatable (not meant to be real code) is to
have a constructor

  B <- function(x, y, z, ...) {
     # do all the work to map x, y, z into slots of A, B (or an
     # instance of A and slots of B), then...
     new("B", a=, b=, ...) # or new("B", instanceOfA, b=,
...)
  }

and avoid writing explicit initialize methods. 

Oddly enough, this solution leads to a copy constructor, viz.,

  initialize(instanceOfB, b=)

I'm not sure that this really does anything more than move the
'pattern' from the initialize method to the constructor.

Martin
> Thank you for your help.
> Renaud
>
> # define class A with a single numeric slot
> setClass('A', representation(a='numeric'))
>
> # define class B that extends class A, adding another numeric slot
> setClass('B', representation('A', b='numeric'))
> # we want for example to ensure that slots a and b have the same length
> setValidity('B',
> function(object){
> cat("*** B::validate ***\n")
> print(object)
> cat("*****************\n")
> if( length(object at a) != length(object at b) ) return('Inconsistent
lengths')
> TRUE
> }
> )
> # As a default behaviour if b is not provided, we want slot b to be
>   equal to slot a
> setMethod('initialize', 'B',
> function(.Object, b, ...){
> cat("*** B::initialize ***\n")
> print(.Object)
>
> # Let the superclass (A) initialize itself via callNextMethod
> # I thought it would only do that: initialize and optionnaly validate
>   the class A part of the object
> #But it generates an ERROR: apparently it calls the validation method of B,
> # before leaving me a chance to set slot b to a valid value
> .Object <- callNextMethod(.Object, ...)
>
> # now deal with the class B part of the object
> cat("*** Test missing b ***\n")
> if( missing(b) ){
> cat("*** b is MISSING ***\n")
> b <- .Object at a
> }
>
> # set slot b
> .Object at b <- b
>
> .Object
> }
> )
>
> ### Testing
>
> # empty A: OK
> aObj <- new('A')
> aObj
>
> # class A with some data: OK
> aObj <- new('A', a=c(1,2) )
> aObj
>
> # empty B: OK
> bObj <- new('B')
> bObj
>
> # initialize B setting the slot of class A: ERROR
> bObj <- new('B', a=c(1,2))
>
> # initialize B setting only the slot class B: OK!! Whereas it produces
>   a non valid object.
> bObj <- new('B', b=c(1,2))
> bObj
>
> ######### RESULTS:
>
>  > # empty A: OK
>  > aObj <- new('A')
>  > aObj
> An object of class ?A?
> Slot "a":
> numeric(0)
>
>  >
>  > # class A with some data: OK
>  > aObj <- new('A', a=c(1,2) )
>  > aObj
> An object of class ?A?
> Slot "a":
> [1] 1 2
>
>  >
>  > # empty B: OK
>  > bObj <- new('B')
> *** B::initialize ***
> An object of class ?B?
> Slot "b":
> numeric(0)
>
> Slot "a":
> numeric(0)
>
> *** Test missing b ***
> *** b is MISSING ***
>  > bObj
> An object of class ?B?
> Slot "b":
> numeric(0)
>
> Slot "a":
> numeric(0)
>
>  >
>  > # initialize B setting the slot of class A: ERROR
>  > bObj <- new('B', a=c(1,2))
> *** B::initialize ***
> An object of class ?B?
> Slot "b":
> numeric(0)
>
> Slot "a":
> numeric(0)
>
> *** B::validate ***
> An object of class ?B?
> Slot "b":
> numeric(0)
>
> Slot "a":
> [1] 1 2
>
> *****************
> Error in validObject(.Object) :
> invalid class "B" object: Inconsistent lengths
>  >
>  > # initialize B setting only the slot class B: OK!! Whereas it
>      creates a non valid object.
>  > bObj <- new('B', b=c(1,2))
> *** B::initialize ***
> An object of class ?B?
> Slot "b":
> numeric(0)
>
> Slot "a":
> numeric(0)
>
> *** Test missing b ***
>  > bObj
> An object of class ?B?
> Slot "b":
> [1] 1 2
>
> Slot "a":
> numeric(0)
>
>
>
> -----------------------------
>  > sessionInfo()
> R version 2.9.1 (2009-06-26)
> x86_64-pc-linux-gnu
>
> locale:
>
LC_CTYPE=en_ZA.UTF-8;LC_NUMERIC=C;LC_TIME=en_ZA.UTF-8;LC_COLLATE=en_ZA.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_ZA.UTF-8;LC_PAPER=en_ZA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_ZA.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
> other attached packages:
> [1] Biobase_2.4.1
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
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