BaseFile: The BaseFile class

In HenrikBengtsson/aroma.Base: A generic R plugin dispatcher for BASE

Description

Package: aroma.Base
Class BaseFile

Object
~~|
~~+--BaseFile

Directly known subclasses:

public static class BaseFile
extends Object

Usage

BaseFile(sections=NULL, ...)

Arguments

sections	A list BaseFileSection objects.
...	Not used.

Fields and Methods

Methods:

	appendSection	Adds a section to this BASE file structure.
	as.character	Gets a string description of object.
	as.list	Gets a list representation of object.
	equals	Checks if this object equals another.
	getAllDataFiles	Gets the names of a external data files used by a BASE file.
	getSection	Gets one section of this BASE file structure.
	getSections	Gets a subset or all BASE sections.
	hasSerialBioAssaySets	Checks if the bioassay sets have data in serial format.
	isSerial	Checks if a BASE file is in serial format or not.
	length	-
	nbrOfSections	Gets the number of sections in this BASE file structure.
	read	Static method to read a BASE file structure.
	removeAllDataFiles	Removes all external data files used by a BASE file structure.
	removeSection	Removes a section from a BASE file structure.
	replaceSection	Replaces a section in a BASE file structure.
	seq	Gets an index sequence for the sections in this BASE file structure.
	write	Writes this BASE file structure.

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

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

Examples

# Read a simple BASE file structure (adopted from [2])
filename <- system.file("data-ex", "baseExample.base", package="aroma.Base")
base <- BaseFile$read(filename)
print(base)

# Write it back to file
tmpfile <- tempfile()
write(base, tmpfile)

# Read the newly create file
base2 <- BaseFile$read(tmpfile)
file.remove(tmpfile)

# Compare with the original structure
stopifnot(equals(base, base2))

HenrikBengtsson/aroma.Base documentation built on May 7, 2019, 1:51 a.m.