S4: inheritance of validity methods?

Vitalie S. wrote:

On Tue, 18 Aug 2009 15:42:48 +0200, Martin Morgan <mtmorgan at fhcrc.org>
wrote:

"Vitalie S." <vitosmail at rambler.ru> writes:

Dear Developers,

In current implementation of validity method, objects are first
coerced to  superclass (slots are striped). Thus, it is not possible
to write validity  method which would perform some checks on children
slots.

Say, I want to check if number of slots in a class is equal to "n":

setClass("A", representation(a="numeric", n="integer"),
          prototype=list(a=12, n=1L),
          validity=function(object){
              if(length(slotNames(object))!=object at n+1) paste("Number
              of  slots must be ", object at n)
              else TRUE
          })


setClass("B", representation(b="numeric"), contains="A",
          prototype=list(a=12, b=14, n=2L))


new("B", a=11, b=33)
Error in validObject(.Object) :
   invalid class "B" object: Number of slots must be  2

Error, because an object of class "A" is passed to validObject with
one  slot "b" removed and n=2.

Is were a work around for this, or I am just doomed to write the same
validity method for each children class?

I think you're doomed, but checking the number of slots in an instance
seems like a very unusual validity method -- isn't this the job of the
methods package, not your implementation of particular classes?

Perhaps I was too quick in saying you were doomed. First, if A is
VIRTUAL then the class seen by its validity method is, as implied by ?as,

  the object will be from the closest actual class, in particular the
  original object, if that class extends the virtual class directly

so

  .validity <- function(object) {
      cat(class(object), "\n")
      TRUE
  }

  setClass("A",
           representation(a="numeric", n="integer", "VIRTUAL"),
           validity=.validity)

  setClass("B", representation(b="numeric"), contains="A")

leads to

res <- new("B", b=1)

B

This seems to require some careful thought about how derived classes are
to behave.

  setClass("C", representation(c="numeric"), contains="B")

 res <- new("C", c=1)

Another approach, probably obvious and which does not really bring
anything 'automatic', is to define a helper function that can be called
in each validity method, or itself used as the validity method.

  .validity <- function(object) {
     # TRUE or message
  }

  setClass("A", representation(a="numeric", n="integer"))
  setClass("B", representation(b="numeric"), contains="A",
           validity=.validity)
  setClass("C", representation(c="numeric"), contains="A",
           validity=function(object) .validity(object))

one might make .validity generic, so that one gets inheritance &
dispatch in the validity methods.

 setGeneric(".validity")
 setClass("A", representation(a="numeric", n="integer"))
 setClass("B", representation("A", b="numeric"), validity=.validity)
 setMethod(.validity, "A", function(object) {
    cat(class(object), "\n")
    TRUE
 })

 tb <- new("B", b=2)

 tc <- new("C", c=3)

 tb <- new("B", b=2, n=2L)

That was a toy example. In fact that I need is to ensure that some
specific slots have the same length. Names of these slots are kept in
separate slot (@atributes).

I think it's not an insane idea to require a predefined relationship to
hold between "future" children's slots.

To be honest, I find it hard to think of a compelling reason to convert
the object before testing the validity. What can possibly go wrong if
children slots are kept in place?

I guess this is reflected in 'setIs' / 'setAs', which allow for derived
classes to have and interpret their representation in a way that is
completely different from parent classes.

Martin

Vitalie.

Martin

Many thanks,
Vitalie.