GenericDataFileSet: The GenericDataFileSet class

In R.filesets: Easy Handling of and Access to Files Organized in Structured Directories

The GenericDataFileSet class

Description

Package: R.filesets
Class GenericDataFileSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet

Directly known subclasses:
ChecksumFileSet, GenericTabularFileSet, RDataFileSet, RdsFileSet, TabularTextFileSet

public static class GenericDataFileSet
extends FullNameInterface

A GenericDataFileSet object represents a set of GenericDataFiles.

Usage

GenericDataFileSet(files=NULL, tags="*", depth=NULL, ...,
  .onUnknownArgs=c("error", "warning", "ignore"))

Arguments

files	A list of GenericDataFile:s or a GenericDataFileSet.
tags	A character vector of tags to be used for this file set. The string "*" indicates that it should be replaced by the tags part of the file set pathname.
depth	An non-negative integer.
...	Not used.
.onUnknownArgs	A character string specifying what should occur if there are unknown arguments in ....

Fields and Methods

Methods:

	anyDuplicated	-
	anyNA	-
	append	-
	appendFiles	-
	as.list	-
	byName	-
	byPath	-
	duplicated	-
	equals	-
	extract	-
	getChecksum	-
	getChecksumFileSet	-
	getDefaultFullName	-
	getFile	-
	getFileClass	-
	getFileSize	-
	getFullNames	-
	getNames	-
	getOneFile	-
	getPath	-
	getPathnames	-
	gunzip	-
	gzip	-
	hasFile	-
	indexOf	-
	is.na	-
	sortBy	-
	unique	-
	validate	-

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

Author(s)

Henrik Bengtsson

Examples

# Setup a file set
path <- system.file(package="R.filesets")
ds <- GenericDataFileSet$byPath(path)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cat("Path of data set:\n")
print(getPath(ds))

cat("Fullname of data set:\n")
print(getFullName(ds))


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Data files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cat("Pathnames:\n")
print(getPathnames(ds))

cat("Filenames:\n")
print(sapply(ds, getFilename))

cat("Extensions:\n")
print(sapply(ds, getExtension))


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Subsetting
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
n <- length(ds)
ds2 <- extract(ds, 1:n)
print(ds2)

ds3 <- extract(ds, n:1)
print(ds3)

stopifnot(identical(rev(getPathnames(ds3)), getPathnames(ds2)))

idxs <- c(1,2,NA,n,NA)
ds4 <- extract(ds, idxs, onMissing="NA")
print(ds4)
print(getFullNames(ds4))
print(getFiles(ds4))

stopifnot(identical(is.na(idxs), unname(is.na(getPathnames(ds4)))))

R.filesets documentation built on May 29, 2024, 9:10 a.m.