trans.main
Class T2Parameter

java.lang.Object
  trans.main.T2Parameter

public class T2Parameter

extends java.lang.Object

Container with info related to runing multiple T2 programs.

Constructor Summary

T2Parameter(java.io.File paramFile)

Method Summary

boolean	checkNumberOfReplicas(java.io.File[][] files)
boolean	fetchBoolean(java.lang.String key)
java.io.File	fetchFile(java.lang.String key)
java.io.File[][]	fetchNumberedFiles(java.lang.String prepended, java.io.File directory)
java.io.File[]	fetchNumberedOneFile(java.lang.String prepended, java.io.File directory)
java.lang.String	fetchPossibleValue(java.lang.String key)
java.lang.String	fetchValue(java.lang.String key)
java.io.File	getAppsDirectory()
java.io.File[][]	getControlCelFiles()
java.io.File	getGenomeFastaDirectory()
java.lang.String	getGenomeVersion()
java.io.File	getJava()
java.io.File	getLogFile()
int	getMaxGap()
int	getMaxMemory()
int	getMaxNumberPeaks()
int	getMinimumNumberOfOligos()
int	getMinNumberOligosInSubWin()
java.io.File[]	getNormalizedControlReplicas()
java.io.File[]	getNormalizedTreatmentReplicas()
java.lang.String	getNumberOfIntervals()
int	getNumberOfRandomPermutations()
int	getPeakPickerWindowSize()
java.io.File	getRApp()
java.io.File[]	getRepeatRegionFiles()
java.io.File	getResultsDirectory()
java.lang.String	getResultsName()
int	getSizeOfOligo()
int	getSubWindowSize()
java.io.File	getSymmetricNullApp()
int	getTargetMedian()
java.io.File[]	getTpmapFiles()
java.io.File[][]	getTreatmentCelFiles()
int	getWindowSize()
boolean	isMakeReducedWindows()
boolean	isMedianScaleUsingControlSeqs()
boolean	isQuantileNormalizeAll()
boolean	isUsePseudoMedian()
boolean	isUseRandomPermutation()
boolean	isUseSymmetricNull()
void	loadApps()
void	loadGeneral()
void	loadMapsAndRawCelFiles()
void	renameCelFiles() Replaces the File pointers to the converted xxx.cela files preserving the input structure.
java.io.File[][]	renameToACels(java.io.File[][] f)
void	setNormalizedControlReplicas(java.io.File[] normalizedControlReplicas)
void	setNormalizedTreatmentReplicas(java.io.File[] normalizedTreatmentReplicas)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

T2Parameter

public T2Parameter(java.io.File paramFile)

Method Detail

renameCelFiles

public void renameCelFiles()

Replaces the File pointers to the converted xxx.cela files preserving the input structure.

renameToACels

public java.io.File[][] renameToACels(java.io.File[][] f)

loadApps

public void loadApps()

loadGeneral

public void loadGeneral()

loadMapsAndRawCelFiles

public void loadMapsAndRawCelFiles()

checkNumberOfReplicas

public boolean checkNumberOfReplicas(java.io.File[][] files)

fetchNumberedFiles

public java.io.File[][] fetchNumberedFiles(java.lang.String prepended,
                                           java.io.File directory)

fetchNumberedOneFile

public java.io.File[] fetchNumberedOneFile(java.lang.String prepended,
                                           java.io.File directory)

fetchValue

public java.lang.String fetchValue(java.lang.String key)

fetchPossibleValue

public java.lang.String fetchPossibleValue(java.lang.String key)

fetchFile

public java.io.File fetchFile(java.lang.String key)

fetchBoolean

public boolean fetchBoolean(java.lang.String key)

getControlCelFiles

public java.io.File[][] getControlCelFiles()

getLogFile

public java.io.File getLogFile()

getResultsDirectory

public java.io.File getResultsDirectory()

getResultsName

public java.lang.String getResultsName()

getSizeOfOligo

public int getSizeOfOligo()

getTpmapFiles

public java.io.File[] getTpmapFiles()

getTreatmentCelFiles

public java.io.File[][] getTreatmentCelFiles()

getTargetMedian

public int getTargetMedian()

getAppsDirectory

public java.io.File getAppsDirectory()

getMaxMemory

public int getMaxMemory()

getNormalizedControlReplicas

public java.io.File[] getNormalizedControlReplicas()

setNormalizedControlReplicas

public void setNormalizedControlReplicas(java.io.File[] normalizedControlReplicas)

getNormalizedTreatmentReplicas

public java.io.File[] getNormalizedTreatmentReplicas()

setNormalizedTreatmentReplicas

public void setNormalizedTreatmentReplicas(java.io.File[] normalizedTreatmentReplicas)

getMinimumNumberOfOligos

public int getMinimumNumberOfOligos()

getNumberOfRandomPermutations

public int getNumberOfRandomPermutations()

getRApp

public java.io.File getRApp()

getSymmetricNullApp

public java.io.File getSymmetricNullApp()

isUsePseudoMedian

public boolean isUsePseudoMedian()

isUseRandomPermutation

public boolean isUseRandomPermutation()

isUseSymmetricNull

public boolean isUseSymmetricNull()

getWindowSize

public int getWindowSize()

getGenomeVersion

public java.lang.String getGenomeVersion()

isMakeReducedWindows

public boolean isMakeReducedWindows()

getNumberOfIntervals

public java.lang.String getNumberOfIntervals()

getMaxGap

public int getMaxGap()

getGenomeFastaDirectory

public java.io.File getGenomeFastaDirectory()

getMaxNumberPeaks

public int getMaxNumberPeaks()

getMinNumberOligosInSubWin

public int getMinNumberOligosInSubWin()

getPeakPickerWindowSize

public int getPeakPickerWindowSize()

getSubWindowSize

public int getSubWindowSize()

getRepeatRegionFiles

public java.io.File[] getRepeatRegionFiles()

getJava

public java.io.File getJava()

isQuantileNormalizeAll

public boolean isQuantileNormalizeAll()

isMedianScaleUsingControlSeqs

public boolean isMedianScaleUsingControlSeqs()