S4 method setClass prototype definition question

I think you didn't type what you meant to type (see below.)

Sourcing in your class descriptions with 1.7.1, I get what you expected.
new("Annotation1")
An object of class "Annotation1"
Slot "x":
NULL

Slot "y":
NULL

Slot "catId":
[1] -1

Slot "isResolved":
[1] FALSE

Slot "resolve":
logical(0)

Slot "valid":
[1] TRUE
Dear list,

this is not a problem report -- I would like to ask for advise what the
recommended and safe way to perform the following is or what problems might
arise in doing it differently.

The question is:  What is the recommended way of providing a default value in a
prototype statement for a derived class for a slot provided from a parent class?
I have first consulted the methods package reference but am still unclear to as
this point.

The following is a bit length example + variations thereof taken from a real
project.

I would appreciate any comments and insights shared.

Best regards,

   Matthias

##
##  R 1.7.1 on Debian Linux (compiled with gcc 3.2.2)
 > version
          _
platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    1
minor    7.1
year     2003
month    06
day      16
language R

##  define a base class (virtual) without prototype
   setClass("IDataType",
            representation("VIRTUAL",
                           valid="logical"),
            validity=NULL,
            sealed=TRUE)

##  same now with prototype definition
   setClass("IDataType1",
            representation("VIRTUAL",
                           valid="logical"),
            prototype=list(valid=TRUE),
            validity=NULL,
            sealed=TRUE)

## and now the derived class in question
## the slot under investigatin is 'valid'
    setClass("Annotation",
             representation ("IDataType",
                             x="vector",
                             y="vector",
                             catId="integer",
                             isResolved="logical",
                             resolve="logical"),
             prototype(isResolved=FALSE,
                       catId=as.integer(-1)),
             validity=NULL,
             sealed=TRUE)

##  instantiate an object an
an<-new("Annotation")
 > an
An object of class "Annotation"
Slot "x":
NULL

Slot "y":
NULL

Slot "catId":
[1] -1

Slot "isResolved":
[1] FALSE

Slot "resolve":
logical(0)

Slot "valid":
logical(0)

##  which is what I expected. Now in order to set a default for
##  the 'valid' slot (provided by the parent class 'IDataType') in the
##  Annotation class I tried

setClass("Annotation1",
             representation ("IDataType",
                             x="vector",
                             y="vector",
                             catId="integer",
                             isResolved="logical",
                            resolve="logical"),
             prototype(isResolved=FALSE,
                       catId=as.integer(-1),
                       valid=TRUE),
             validity=NULL,
             sealed=TRUE)

##  instantiate an object an1
 > an1<-new("Annotation")
Sorry, naming it an1 still leaves it an object of class "Annotation", as
the printed output tells you.
 > an1
An object of class "Annotation"
Slot "x":
NULL

Slot "y":
NULL

Slot "catId":
[1] -1

Slot "isResolved":
[1] FALSE

Slot "resolve":
logical(0)

Slot "valid":
logical(0)

##  now this is NOT what I had expected; my prediction would have been to see
##  slot 'valid' set to TRUE

##  ok, so this is an alternative to get what I aimed at, i.e. use the 2nd
##  virtual base class IDataType1 with prototype definition
  setClass("Annotation2",
             representation ("IDataType1",
                             x="vector",
                             y="vector",
                             catId="integer",
                             isResolved="logical",
                             resolve="logical"),
             prototype(isResolved=FALSE,
                       catId=as.integer(-1)),
             validity=NULL,
             sealed=TRUE)
[1] "Annotation2"
 > an2<-new("Annotation2")
 > an2
An object of class "Annotation2"
Slot "x":
NULL

Slot "y":
NULL

Slot "catId":
[1] -1

Slot "isResolved":
[1] FALSE

Slot "resolve":
logical(0)

Slot "valid":
[1] TRUE

##  so this does what I aimed at but surprises me as I thought it would
##  not make sense
##  to provide a prototype for a virtual class

## reading further in the methods package reference manual
## (refman.pdf: The Methods Package)
## I conclude that setAs

##  use IDataType class w prototype and explicit contains statement
 >  setClass("Annotation3",
            representation ("IDataType1",
                            x="vector",
                            y="vector",
                            catId="integer",
                            isResolved="logical",
                            resolve="logical"),
            prototype(isResolved=FALSE,
                      catId=as.integer(-1)),
            contains=as.character("IDataType1"),
            validity=NULL,
            sealed=TRUE)

[1] "Annotation3"
 > an3<-new("Annotation3")
 > an3
An object of class "Annotation3"
Slot "x":
NULL

Slot "y":
NULL

Slot "catId":
[1] -1

Slot "isResolved":
[1] FALSE

Slot "resolve":
logical(0)

Slot "valid":
[1] TRUE

##  so this works aswell
##  and yet another alternative:
##  use IDataType class w/o prototype but explicitly use
##  contain=as.character("IDataType")
##  statement and set slot 'valid' prototype
 >   setClass("Annotation4",
             representation ("IDataType",
                             x="vector",
                             y="vector",
                             catId="integer",
                             isResolved="logical",
                             resolve="logical"),
             prototype(isResolved=FALSE,
                       catId=as.integer(-1),
                       valid=TRUE),
             contains=as.character("IDataType"),
             validity=NULL,
             sealed=TRUE)

[1] "Annotation4"

 > an4<-new("Annotation4")
 > an4
An object of class "Annotation4"
Slot "x":
NULL

Slot "y":
NULL

Slot "catId":
[1] -1

Slot "isResolved":
[1] FALSE

Slot "resolve":
logical(0)

Slot "valid":
[1] TRUE

##  This also works as expected.

##  So what is the recommended way of providing a default in a prototype
##  statement for a
##  slot provided from a parent class?

--
Matthias Burger

Bioinformatics R&D
Epigenomics AG                      www.epigenomics.com
Kleine Pr?sidentenstra?e 1          fax:   +49-30-24345-555
10178 Berlin Germany                phone: +49-30-24345-0

______________________________________________
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John M. Chambers                  jmc@bell-labs.com
Bell Labs, Lucent Technologies    office: (908)582-2681
700 Mountain Avenue, Room 2C-282  fax:    (908)582-3340
Murray Hill, NJ  07974            web: http://www.cs.bell-labs.com/~jmc
I think you didn't type what you meant to type (see below.)

Sourcing in your class descriptions with 1.7.1, I get what you expected.

You are of course correct! Thanks for pointing this out. I should have looked 
more carefully!

[...]

Still the answer to the question on what is the recommended programming style 
for setClass definitions is not clear to me. For what purpose or in which 
circumstances should one use the 'contains' argument?
See the example code below. What side effects has it or what difference is there 
between the two versions (if any).

I would be very happy for any help gaining a clearer understanding of that 
mechanism.

Regards,

    Matthias

setClass("IDataType",
          representation("VIRTUAL",
                         valid="logical"),
          validity=NULL,
          sealed=TRUE)

##  define the parent class dependency in representation
setClass("Annotation1",
          representation ("IDataType",
                          x="vector",
                          y="vector",
                          catId="integer",
                          isResolved="logical",
                          resolve="logical"),
          prototype(isResolved=FALSE,
                    catId=as.integer(-1),
                    valid=TRUE),
          validity=NULL,
          sealed=TRUE)

##  define the dependency via a contains statement
setClass("Annotation2",
          representation (x="vector",
                          y="vector",
                          catId="integer",
                          isResolved="logical",
                          resolve="logical"),
          prototype(isResolved=FALSE,
                    catId=as.integer(-1),
                    valid=TRUE),
          contains=as.character("IDataType"),
          validity=NULL,
          sealed=TRUE)

 > an1 <- new("Annotation1")
 > an1
An object of class "Annotation1"
Slot "x":
NULL

Slot "y":
NULL

Slot "catId":
[1] -1

Slot "isResolved":
[1] FALSE

Slot "resolve":
logical(0)

Slot "valid":
[1] TRUE

 > an2 <- new("Annotation2")
 > an2
An object of class "Annotation2"
Slot "x":
NULL

Slot "y":
NULL

Slot "catId":
[1] -1

Slot "isResolved":
[1] FALSE

Slot "resolve":
logical(0)

Slot "valid":
[1] TRUE

 > all.equal(an1,an2)
[1] "Attributes: < Component 2: 1 string mismatches >"

So I conclude that appart from the class name those two objects are the same, 
and accordingly they will behave the same in all situations, won't they?
Matthias Burger

Bioinformatics R&D
Epigenomics AG                      www.epigenomics.com
Kleine Pr?sidentenstra?e 1          fax:   +49-30-24345-555
10178 Berlin Germany                phone: +49-30-24345-0