aroma.core (version 3.0.0)

AromaTabularBinaryFile: The AromaTabularBinaryFile class

Description

Package: aroma.core Class AromaTabularBinaryFile

Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFile ~~~~~~~~~~~~| ~~~~~~~~~~~~+--ColumnNamesInterface ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--GenericTabularFile ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile

Directly known subclasses: AromaCellCpgFile, AromaCellPositionFile, AromaCellSequenceFile, AromaCellTabularBinaryFile, AromaMicroarrayTabularBinaryFile, AromaUflFile, AromaUgcFile, AromaUgpFile, AromaUnitCallFile, AromaUnitChromosomeTabularBinaryFile, AromaUnitFracBCnBinaryFile, AromaUnitGcContentFile, AromaUnitGenotypeCallFile, AromaUnitPscnBinaryFile, AromaUnitSignalBinaryFile, AromaUnitTabularBinaryFile, AromaUnitTotalCnBinaryFile, AromaUnitTypesFile

public abstract static class AromaTabularBinaryFile extends FileCacheKeyInterface

A AromaTabularBinaryFile represents a file with a binary format. It has a well defined header, a data section, and a footer.

Usage

AromaTabularBinaryFile(...)

Arguments

...

Arguments passed to GenericTabularFile.

Fields and Methods

Methods:

	[
-
[<-	-
	colMeans
-
colSums	-
	getBytesPerColumn
-
getColClasses	-
	importFrom
-
nbrOfColumns	-
	nbrOfRows
-
readColumns	-
	readFooter
Reads the file footer in XML format into a named nested list.
subset	-
	summary
-
writeFooter	Writes a named nested list to the file footer in XML format.

Methods inherited from FileCacheKeyInterface: getCacheKey Methods inherited from CacheKeyInterface: getCacheKey Methods inherited from GenericTabularFile: [, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles Methods inherited from ColumnNamesInterface: appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames Methods inherited from GenericDataFile: as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName 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, objectSize, print, save, asThis

See Also

GenericDataFile.