biolockj.module.report.taxa

Class LogTransformTaxaTables

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.taxa.TaxaCountModule

biolockj.module.report.taxa.NormalizeTaxaTables

biolockj.module.report.taxa.LogTransformTaxaTables

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class LogTransformTaxaTables
extends NormalizeTaxaTables

This utility is used to log-transform the raw OTU counts on Log10 or Log-e scales.

GUI Module Name

Log Transform Taxa Tables

Field Summary

Fields inherited from class biolockj.module.report.taxa.NormalizeTaxaTables

LOG_10, LOG_E

Fields inherited from class biolockj.module.JavaModuleImpl

BLJ_OPTIONS

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.ScriptModule

SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
LogTransformTaxaTables()

Method Summary

Modifier and Type	Method and Description
protected void	transform(File otuTable) Log transform the data

Methods inherited from class biolockj.module.report.taxa.NormalizeTaxaTables

checkDependencies, filterZeroSampleIDs, findAllZeroIndex, getLogBase, getOtuNames, getSummary, runModule, writeDataToFile

Methods inherited from class biolockj.module.report.taxa.TaxaCountModule

filterByProcessLevel, getInputFiles, getPreRequisiteModules, isTaxaModule, isValidInputModule

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getSource, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init, toString, validateFileNameUnique

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

cleanUp, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init

Constructor Detail

LogTransformTaxaTables

public LogTransformTaxaTables()

Method Detail

transform

protected void transform(File otuTable)
                  throws Exception

Log transform the data

Overrides:

transform in class NormalizeTaxaTables

Parameters:

otuTable - OTU raw count table

Throws:

Exception - if unable to construct LogTransformTaxaTables