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Reference classes OOP

Reference classes are a Java-like class system (no generics!) implementation in R.

Reference classes use pass-by-reference logic that is different from the usual pass-by-value logic R uses. This means when we assign a=b both a and b point to the same object, and changing a will also modify b and vica versa.

Creating classes

Similar syntax as S4, but now slots are called fields, and setRefClass returns a constructor object.

Seq <- setRefClass("Seq",
                   fields = list(
                     name = "character",
                     alphabet = "character",
                     sequence = "character"))

We then use the constuctor to create objects:

a = Seq(name="My seq", alphabet=c("A", "T"), sequence="ATTTTAAAAAA")
a

## Reference class object of class "Seq"
## Field "name":
## [1] "My seq"
## Field "alphabet":
## [1] "A" "T"
## Field "sequence":
## [1] "ATTTTAAAAAA"

Defining methods

Methods are defined either with the class, or later by modifying the constructor object.

Seq <- setRefClass("Seq",
                   fields = list(
                     name = "character",
                     alphabet = "character",
                     sequence = "character"),
                   methods = list(
                     comp = function() {
                       "Complements the (DNA) sequence" ## inline docs
                       sequence <<- chartr("ACGT","TGCA",.self$sequence)
                       name <<- paste(.self$name, "-- complemented")                     
                     }
                     ## there can be more, of course
                     ))

A couple of things to note here:

  • accessing fields and calling methods is done with the $ operator.
  • the current object can be referred to in a method by the reserved name .self.
  • Changing fields of an object within methods needs to be done with the <<- operator.

Calling a method on the object will modify it:

s <- Seq$new(name="foo", sequence="GATCATCA")
s

## Reference class object of class "Seq"
## Field "name":
## [1] "foo"
## Field "alphabet":
## character(0)
## Field "sequence":
## [1] "GATCATCA"

s$sequence

## [1] "GATCATCA"

s$comp()
s$sequence

## [1] "CTAGTAGT"

Objects are copied by reference and not value:

s2 = s
s$sequence

## [1] "CTAGTAGT"

s2$sequence

## [1] "CTAGTAGT"

s$sequence = "ATTTA"
s$sequence

## [1] "ATTTA"

s2$sequence

## [1] "ATTTA"

Summary

Reference classes are suitable for objects that are dynamically tracked by all the code: GUI components, read-only access to files (streams, data bases), internet resources, editing facilities, ... Because they are passed by reference they are never copied, which means they are never duplicated in memory.

Because of their pass-by-reference semantics they are not appropriate as a replacement for S3 and S4 as this would lead to a lot of unanticipated side effects.