On Fri, Mar 18, 2016 at 2:53 PM, Hervé Pagès <hpa...@fredhutch.org> wrote:
> Hi,
>
> Short story
> -----------
>
> setClassUnion("ArrayLike", "array")
>
> showClass("ArrayLike") # no slot
>
> setClass("MyArrayLikeConcreteSubclass",
> contains="ArrayLike",
> representation(stuff="ANY")
> )
>
> showClass("MyArrayLikeConcreteSubclass") # 2 slots!!
>
> That doesn't seem right.
>
> Long story
> ----------
>
> S4 provides at least 3 ways to create a little class hierarchy
> like this:
>
> FooLike ............. virtual class with no slot
> ^ ^
> | |
> foo anotherfoo ..... 2 concrete subclasses
>
> (1) The "standard" way: define FooLike first, then foo and anotherfoo
> as subclasses of FooLike:
>
> setClass("FooLike")
>
> setClass("foo",
> contains="FooLike",
> representation(stuff="ANY")
> )
>
> setClass("anotherfoo",
> contains="FooLike",
> representation(stuff="ANY")
> )
>
> showClass("FooLike") # displays foo and anotherfoo as
> # known subclasses
>
> x1 <- new("foo")
> is(x1, "foo") # TRUE
> is(x1, "FooLike") # TRUE
> is(x1, "anotherfoo") # FALSE
>
> x2 <- new("anotherfoo")
> is(x2, "anotherfoo") # TRUE
> is(x2, "FooLike") # TRUE
> is(x2, "foo") # FALSE
>
> Everything works as expected.
>
> (2) Using a class union: define foo and anotherfoo first, then FooLike
> as the union of foo and anotherfoo:
>
> setClass("foo", representation(stuff="ANY"))
> setClass("anotherfoo", representation(stuff="ANY"))
> setClassUnion("FooLike", c("foo", "anotherfoo"))
>
> showClass("FooLike") # displays foo and anotherfoo as
> # known subclasses
>
> (3) Using a *unary* class union: define foo first, then FooLike as the
> (unary) union of foo, then anotherfoo as a subclass of FooLike:
>
> setClass("foo", representation(stuff="ANY"))
> setClassUnion("FooLike", "foo")
>
> showClass("FooLike") # displays foo as the only known subclass
>
> setClass("anotherfoo",
> contains="FooLike",
> representation(stuff="ANY")
> )
>
> showClass("FooLike") # now displays foo and anotherfoo as
> # known subclasses
>
> The 3 ways lead to the same hierarchy. However the 3rd way is
> interesting because it allows one to define the FooLike virtual
> class as the parent of an existing foo class that s/he doesn't
> control.
>
>
Why not use setIs() for this? Everything then behaves as expected. I don't
think it makes much sense to "contain" a class union. Rather, you just want
to establish the inheritance relationship.
> For example, to define an ArrayLike class:
>
> setClassUnion("ArrayLike", "array")
> showClass("ArrayLike") # displays array as a known subclass
>
> Note that ArrayLike is virtual with no slots (analog to a Java
> Interface), which is what is expected.
>
> setClass("MyArrayLikeConcreteSubclass",
> contains="ArrayLike",
> representation(stuff="ANY")
> )
>
> showClass("MyArrayLikeConcreteSubclass") # shows 2 slots!!
>
> What is the .Data slot doing here? I would expect to see that slot
> if MyArrayLikeConcreteSubclass was extending array but this is not
> the case here.
>
> a <- new("MyArrayLikeConcreteSubclass")
>
> is(a, "MyArrayLikeConcreteSubclass") # TRUE --> ok
> is(a, "ArrayLike") # TRUE --> ok
> is(a, "array") # FALSE --> ok
>
> But:
>
> is.array(a) # TRUE --> not ok!
>
> Is is.array() confused by the presence of the .Data slot?
>
>
It looks like the unary union somehow equates ArrayLike and array and thus
makes ArrayLike confer a dim attribute (and thus is.array(a) returns TRUE).
Since S4 objects cannot have attributes that are not slots, it must do this
via a data part, thus the .Data slot.
> I can fix it by defining an "is.array" method for
> MyArrayLikeConcreteSubclass objects:
>
> setMethod("is.array", "MyArrayLikeConcreteSubclass",
> function(x) FALSE
> )
>
> However, it feels that I shouldn't have to do this.
>
> Is the presence of the .Data slot in MyArrayLikeConcreteSubclass
> objects an unintended feature?
>
> Thanks,
> H.
>
> > sessionInfo()
> R Under development (unstable) (2016-01-07 r69884)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.4 LTS
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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