[R] How to: initialize, setValidity, copy-constructor

[Renaud Gaujoux]

Thanks Martin,

I'll try that. One question about memory though, just to be sure. When 
one does:

# create new instance of A
a <- new('A', ...)
# create new instance of B based on a
b <- new('B', a, b=...)

Will two instances of A be created (using twice the memory) or will 
there be a single instance and a reference to it (own by b the instance 
of B)?

Thanks.

Martin Morgan wrote:
> 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.
>>     
>
>