path: Accessing the path of an object

In Bioconductor/BiocGenerics: S4 generic functions used in Bioconductor

Accessing the path of an object

Description

Get or set the path of an object.

Usage

path(object, ...)
path(object, ...) <- value

basename(path, ...)
basename(path, ...) <- value

dirname(path, ...)
dirname(path, ...) <- value

## The purpose of the following methods is to make the basename() and
## dirname() getters work out-of-the-box on any object for which the
## path() getter works.

## S4 method for signature 'ANY'
basename(path, ...)

## S4 method for signature 'ANY'
dirname(path, ...)

## The purpose of the following replacement methods is to make the
## basename() and dirname() setters work out-of-the-box on any object
## for which the path() getter and setter work.

## S4 replacement method for signature 'character'
basename(path, ...) <- value

## S4 replacement method for signature 'ANY'
basename(path, ...) <- value

## S4 replacement method for signature 'character'
dirname(path, ...) <- value

## S4 replacement method for signature 'ANY'
dirname(path, ...) <- value

Arguments

object	An object containing paths. Even though it will typically contain a single path, object can actually contain an arbitrary number of paths.
...	Additional arguments, for use in specific methods.
value	For path<-, the paths to set on object. For basename<- or dirname<-, the basenames or dirnames to set on path.
path	A character vector or an object containing paths.

Value

A character vector for path(object), basename(path), and dirname(path). Typically of length 1 but not necessarily. Possibly with names on it for path(object).

See Also

• base::basename for the functions the basename and dirname generics are based on.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• path,RsamtoolsFile-method in the Rsamtools package for an example of a specific path method (defined for RsamtoolsFile objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

## ---------------------------------------------------------------------
## GENERIC FUNCTIONS AND DEFAULT METHODS
## ---------------------------------------------------------------------

path
showMethods("path")

`path<-`
showMethods("path<-")

basename
showMethods("basename")

`basename<-`
showMethods("basename<-")

dirname
showMethods("dirname")

`dirname`
showMethods("dirname<-")


## Default basename() and dirname() getters:
selectMethod("basename", "ANY")
selectMethod("dirname", "ANY")

## Default basename() and dirname() setters:
selectMethod("basename<-", "character")
selectMethod("basename<-", "ANY")
selectMethod("dirname<-", "character")
selectMethod("dirname<-", "ANY")

## ---------------------------------------------------------------------
## OBJECTS CONTAINING PATHS
## ---------------------------------------------------------------------

## Let's define a simple class to represent objects that contain paths:
setClass("A", slots=c(stuff="ANY", path="character"))

a <- new("A", stuff=runif(5),
              path=c(one="path/to/file1", two="path/to/file2"))

## path() getter:
setMethod("path", "A", function(object) object@path)

path(a)

## Because the path() getter works on 'a', now the basename() and
## dirname() getters also work:
basename(a)
dirname(a)

## path() setter:
setReplaceMethod("path", "A",
    function(object, ..., value)
    {
        if (length(list(...)) != 0L) {
            dots <- match.call(expand.dots=FALSE)[[3L]]
            stop(BiocGenerics:::unused_arguments_msg(dots))
        }
        object@path <- value
        object
    }
)

a <- new("A", stuff=runif(5))
path(a) <- c(one="path/to/file1", two="path/to/file2")
path(a)

## Because the path() getter and setter work on 'a', now the basename()
## and dirname() setters also work:
basename(a) <- toupper(basename(a))
path(a)
dirname(a) <- "~/MyDataFiles"
path(a)

Bioconductor/BiocGenerics documentation built on Nov. 5, 2023, 6:10 a.m.