On Sat, Mar 19, 2016 at 12:10 AM, Hervé Pagès <hpa...@fredhutch.org> wrote:
> On 03/18/2016 03:28 PM, Michael Lawrence wrote: > >> >> On Fri, Mar 18, 2016 at 2:53 PM, Hervé Pagès <hpa...@fredhutch.org >> <mailto: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? >> > > > setClass("ArrayLike") > > setIs("array", "ArrayLike") > Error in setIs("array", "ArrayLike") : > class “array” is sealed; new superclasses can not be defined, except > by 'setClassUnion' > > How do you define a virtual class as the parent of an existing class > with setIs? > > You can only do that with setClassUnion(). But the new classes should use setIs() to inherit from the union. So it's: setClassUnion("ArrayLike", "array") setClass("MyArrayLike") setIs("MyArrayLike", "ArrayLike") > Everything then behaves as expected. I >> don't think it makes much sense to "contain" a class union. >> > > Why is that? A class union is just a virtual class with no slot > that is the parent of the classes that are in the union. All the > classes in the union contain their parent. What's interesting is that > this union is actually open to new members: when I later define a new > class that contains the class union, I'm just adding a new member to > the union. > > Rather, you >> just want to establish the inheritance relationship. >> > > Isn't what I'm doing when I define a new class that contains the > class union? > Containing does two things: establishes the is() relationship and adds slots to the class. These slots are comprised of the slots of the contained class, and as a special case the "array" class and other native types confer a data part that comes from the prototype of the class. The "array" class has a double vector with a dim attribute as its prototype. That is all well understood. What is surprising is that "ArrayLike" has the same prototype as "array". That happens via setIs(doComplete=TRUE), called by setClassUnion(). When a class gains its first non-virtual child, the parent assumes the prototype of its child. I'm not sure why, but the logic is very explicit and I've come to just accept it as a "feature". I ran into this some months ago when defining my own ArrayLike when working on a very similar package to the one you are developing ;) > >> 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 >> > > Clearly the unary union makes ArrayLike a parent of array, as it should > be. This can be confirmed by extends(): > > > extends("array", "ArrayLike") > [1] TRUE > > extends("ArrayLike", "array") > [1] FALSE > > The results for is(a, "ArrayLike") (TRUE) and is(a, "array") (FALSE) > on a MyArrayLikeConcreteSubclass instance are consistent with this. > > So the little 3-class hierarchy I end up with in the above example > is exactly how expected: > > ArrayLike > ^ ^ > | | > array MyArrayLikeConcreteSubclass > > What is not expected is that MyArrayLikeConcreteSubclass has a .Data > slot and that is.array(a) returns TRUE on a MyArrayLikeConcreteSubclass > object. > > H. > > 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 <mailto:hpa...@fredhutch.org> >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >> >> ______________________________________________ >> R-devel@r-project.org <mailto:R-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> >> > -- > 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 > > [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
