R.filesets: GenericDataFile – R documentation

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R.filesets

GenericDataFile

The abstract GenericDataFile class

Description

Package: R.filesets
Class GenericDataFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile

Directly known subclasses:
ChecksumFile, GenericTabularFile, RDataFile, RdsFile, TabularTextFile

public abstract static class GenericDataFile
extends FullNameInterface

A GenericDataFile is an object referring to a data file on a file system. Note that this class is abstract and can not be instantiated, but instead you have to use one of the subclasses or the generic *fromFile() method.

Usage

GenericDataFile(filename=NULL, path=NULL, mustExist=!is.na(filename), ...,
  .onUnknownArgs=c("error", "warning", "ignore"))

Arguments

`filename`	The filename of the file.
`path`	An optional path to the file.
`mustExist`	If `TRUE`, an exception is thrown if the file does not exists, otherwise not.
`...`	Not used.
`.onUnknownArgs`	A `character` string specifying what should occur if there are unknown arguments in `...`.

Fields and Methods

Methods:

	`compareChecksum`	Compares the file checksum with the value of the checksum file.
	`equals`	Checks if a file equals another.
	`getChecksum`	Gets the checksum of a file.
	`getChecksumFile`	-
	`getExtension`	Gets the filename extension.
	`getFileSize`	Gets the size of a file.
	`getFileType`	Gets the file type of a file.
	`getFilename`	Gets the filename of the file.
	`getPath`	Gets the path (directory) of the file.
	`getPathname`	Gets the pathname of the file.
	`is.na`	-
	`isFile`	Checks if this is an existing file.
	`validateChecksum`	Asserts that the file checksum matches the one of the checksum file.
	`writeChecksum`	Write the file checksum to a checksum file.

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Filename convention

The filename of an GenericDataFile is structured as follows:

filename: "sample001,a,b,c.CEL" (this follows the R convention, but not the Unix convention)
fullname: "sample001,a,b,c"
name: "sample001"
tags: c("a", "b", "c")
extension: "CEL"

Author(s)

Henrik Bengtsson