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(...)
Fields and Methods
Methods:
rll{
[ -
[<- -
colMeans -
colMedians -
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:
dim, extractMatrix, nbrOfRows, readColumns, readDataFrame
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, appendColumnNamesTranslatorByNULL, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
getParentName, as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFilename, getFilenameExtension, getFileSize, getFileType, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, isFile, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save