Class "fcReference" and its subclasses

Description

Classes and methods to provide reference-based semantics for flow cytometry workflows.

Usage

fcReference(ID=paste("genericRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcTreeReference(ID=paste("treeRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcAliasReference(ID=paste("aliasRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcDataReference(ID=paste("dataRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcActionReference(ID=paste("actionRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcViewReference(ID=paste("viewRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcFilterResultReference(ID=paste("fresRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcFilterReference(ID=paste("filterRef", guid(), sep="_"), env=new.env(parent=emptyenv()))

fcCompensateReference(ID=paste("compRef",
                                           guid(), sep="_"),
                                  env=new.env(parent=emptyenv()))

fcNormalizationReference(ID=paste("normRef",
                                           guid(), sep="_"),
                                  env=new.env(parent=emptyenv()))

fcSubsettingReference(ID=paste("subRef",
                                           guid(), sep="_"),
                                  env=new.env(parent=emptyenv()))

fcTransformReference(ID=paste("transRef",
                                          guid(), sep="_"),
                                 env=new.env(parent=emptyenv()))

fcNullReference(...)


assign(x, value, pos = -1, envir = as.environment(pos), inherits = FALSE, 
    immediate = TRUE)

## S4 method for signature 'fcReference,missing,missing'
get(x, pos = -1, envir = as.environment(pos), mode = "any", 
    inherits = TRUE)

isNull(f)

Rm(symbol, envir, subSymbol, ...)

Arguments

Details

These classes provide references to objects within an R environment and allow for method dispatch based on the nature of the referenced object. The parent fcReference class is used for references to all R objects, unless there exists a more specific subclass. fcTreeReference, fcViewReference, and fcActionReference are used to reference to graphNEL, view, and actionItem objects, respectively. fcDataReference should be used for flowFrame or flowSet objects, whereas fcFilterResultReference, fcFilterReference, fcTransformReference, fcCompensateReference, and fcNormalizationReference link to filterResult, filter, transform and compensation objects. fsStructureReference only exists to jointly dispatch on certain subgroups of references.

Value

An object of class fcReference or one of its subclasses for the assign constructor.

The object referenced to for the get method.

A character string of the object symbol for the identifier method.

A logical scalar for the isNull method.

Extends

fcStructureReference:

Class "fcReference", directly.

fcTreeReference:

Class "fcStructureReference", directly. Class "fcReference", by class "fcStructureReference", distance 2.

fcAliasReference:

Class "fcStructureReference", directly. Class "fcReference", by class "fcStructureReference", distance 2.

fcDataReference:

Class "fcReference", directly.

fcActionReference:

Class "fcStructureReference", directly. Class "fcReference", by class "fcStructureReference", distance 2.

fcViewReference:

Class "fcStructureReference", directly. Class "fcReference", by class "fcStructureReference", distance 2.

fcFilterResultReference:

Class "fcReference", directly.

fcFilterReference:

Class "fcReference", directly.

fcCompensateReference:

Class "fcReference", directly.

fcTransformReference:

Class "fcReference", directly.

fcNormalizationReference:

Class "fcReference", directly.

fcNullReference:

Class "fcDataReference", directly. Class "fcActionReference", directly. Class "fcViewReference", directly. Class "fcFilterResultReference", directly. Class "fcFilterReference", directly. Class "fcCompensateReference", directly. Class "fcTransformReference", directly. Class "fcNormalizationReference", directly. Class "fcTreeReference", directly. Class "fcAliasReference", directly. Class "fcReference", by class "fcDataReference", distance2. Class "fcStructureReference", by class "fcActionReference", distance 2. Class "fcReference", by class "fcActionReference", distance 3. Class "fcStructureReference", by class "fcViewReference", distance 2. Class "fcReference", by class "fcViewReference", distance3. Class "fcReference", by class "fcFilterResultReference", distance 2. Class "fcReference", by class "fcFilterReference", distance 2. Class "fcReference", by class "fcCompensateReference", distance 2. Class "fcReference", by class "fcTransformReference", distance 2. Class "fcStructureReference", by class "fcTreeReference", distance 2. Class "fcReference", by class "fcTreeReference", distance 3.

Objects from the Class

Objects should be created via the assign constructor. Whenever an object is assigned to a workFlow using the assign method, an appropriate instance of class fcReference or one of its subclasses is returned. In addition, there are the usual constructor functions of same names as the classes that can be used for object instantiation without assignment. Note that this might lead to unresolvable references unless the object referenced to is available in the environment.

Slots

ID:

Object of class "character" The name of the object in env referenced to.

env:

Object of class "environment" An environment that contains the referenced objects. Usually, this will be the environment that's part of a workFlow object.

Methods

get

signature(x = "fcReference", pos = "missing", envir = "missing", mode = "missing", inherits = "missing"): Resolve the reference, i.e., get the object from the environment.

get

signature(x = "fcNullReference", pos = "missing", envir = "missing", mode = "missing", inherits = "missing"): Resolve the reference. This always returns NULL.

identifier

signature(object = "fcReference"): Return a character string of the object name.

isNull

signature(f = "fcReference"): Check whether a fcReference is a NULL reference. Note that this is different from a unresolvable reference.

Rm

signature(symbol = "fcReference", envir = "missing", subSymbol = "character"): Remove the object referenced to by a fcReference from its environment. The argument subSymbol will be automatically set by the generic and should never be provided by the user.

Rm

signature(symbol = "fcReference", envir = "workFlow", subSymbol = "character"): Remove the object referenced to by a fcReference from a workFlow. The argument subSymbol will be automatically set by the generic and should never be provided by the user.

Rm

signature(symbol = "fcNullReference", envir = "missing", subSymbol = "character"): Essentially, this doesn't do anything since there is no object referenced to.

show

signature(object = "fcReference"): Print details about the object.

show

signature(object = "fcNullReference"): Print details about the object.

Author(s)

Florian Hahne

See Also

workFlow

Examples

showClass("fcReference")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(flowCore)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowCore/fcReference-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fcReference-class
> ### Title: Class "fcReference" and its subclasses
> ### Aliases: fcReference-class fcReference fcStructureReference-class
> ###   fcTreeReference-class fcTreeReference fcAliasReference-class
> ###   fcAliasReference fcDataReference-class fcDataReference
> ###   fcActionReference-class fcActionReference fcViewReference-class
> ###   fcViewReference fcFilterResultReference-class fcFilterResultReference
> ###   fcFilterReference-class fcFilterReference fcCompensateReference-class
> ###   fcCompensateReference fcTransformReference-class fcTransformReference
> ###   fcNormalizationReference-class fcNormalizationReference
> ###   fcNullReference-class fcSubsettingReference
> ###   fcSubsettingReference-class assign fcNullReference
> ###   get,fcReference,missing,missing-method
> ###   get,fcNullReference,missing,missing-method
> ###   identifier,fcReference-method isNull isNull,fcReference-method Rm
> ###   Rm,fcReference,missing,character-method
> ###   Rm,fcReference,workFlow,character-method
> ###   Rm,fcNullReference,missing,character-method show,fcReference-method
> ###   show,fcNullReference-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("fcReference")
Class "fcReference" [package "flowCore"]

Slots:
                              
Name:           ID         env
Class:   character environment

Known Subclasses: 
Class "fcStructureReference", directly
Class "fcDataReference", directly
Class "fcFilterResultReference", directly
Class "fcFilterReference", directly
Class "fcCompensateReference", directly
Class "fcTransformReference", directly
Class "fcNormalizationReference", directly
Class "fcSubsettingReference", directly
Class "fcTreeReference", by class "fcStructureReference", distance 2
Class "fcJournalReference", by class "fcStructureReference", distance 2
Class "fcAliasReference", by class "fcStructureReference", distance 2
Class "fcActionReference", by class "fcStructureReference", distance 2
Class "fcViewReference", by class "fcStructureReference", distance 2
Class "fcNullReference", by class "fcDataReference", distance 2
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>