trans.main
Class T2

java.lang.Object
  trans.main.T2

public class T2

extends java.lang.Object

Runs entire TiMAT2 suite based on a parameter file.

Constructor Summary

T2(java.lang.String[] args)

Method Summary

void	convertCelFiles()
void	deleteSplitNormalizedFiles()
void	filterIntervals() Creates set number of intervals.
java.lang.String[]	findChromPairs() Attempts to join smallest chromosomes together so long as the combine file doesn't exceed the size of the biggest.
void	findSubBindingRegions() Creates set number of intervals.
void	launchCelNormalization(java.io.File[] celaFiles, java.util.ArrayList generalCmd, java.io.File clusterName)
void	launchJQSub(java.util.ArrayList args, int memory)
void	loadIntervalArrays() Creates set number of intervals.
static void	main(java.lang.String[] args)
void	makeAndMoveIntervals() File management for intervals.
void	makeChromosomeSets()
void	makeChromSet(java.io.File[][] setRep, boolean treatmentSet)
void	mergeWindows() Creats one or two window merged window arrays containing all of the chromosomes.
void	normalizeCelFiles()
int	numberOfIntervalsToMake() Returns the number of intervals that remain to be made.
int	numberReplicasToMake()
static void	printDocs()
void	printIntervalGraphs() Prints interval bed and sgr files via IntervalGraphPrinter.
void	printSpreadSheets() Prints interval reports in a spread sheet via IntervalReportPrinter.
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles
void	scanChromosomes()
void	setNumberIntervalMaker() Creates set number of intervals.
void	splitChromSetArray() Pulls and places replica directories to this.

Methods inherited from class java.lang.Object

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

Constructor Detail

T2

public T2(java.lang.String[] args)

Method Detail

numberOfIntervalsToMake

public int numberOfIntervalsToMake()

Returns the number of intervals that remain to be made.

makeAndMoveIntervals

public void makeAndMoveIntervals()

File management for intervals.

setNumberIntervalMaker

public void setNumberIntervalMaker()

Creates set number of intervals.

loadIntervalArrays

public void loadIntervalArrays()

Creates set number of intervals.

findSubBindingRegions

public void findSubBindingRegions()

Creates set number of intervals.

printSpreadSheets

public void printSpreadSheets()

Prints interval reports in a spread sheet via IntervalReportPrinter.

printIntervalGraphs

public void printIntervalGraphs()

Prints interval bed and sgr files via IntervalGraphPrinter.

filterIntervals

public void filterIntervals()

Creates set number of intervals.

mergeWindows

public void mergeWindows()

Creats one or two window merged window arrays containing all of the chromosomes.

splitChromSetArray

public void splitChromSetArray()

Pulls and places replica directories to this.

scanChromosomes

public void scanChromosomes()

findChromPairs

public java.lang.String[] findChromPairs()

Attempts to join smallest chromosomes together so long as the combine file doesn't exceed the size of the biggest.

deleteSplitNormalizedFiles

public void deleteSplitNormalizedFiles()

makeChromSet

public void makeChromSet(java.io.File[][] setRep,
                         boolean treatmentSet)

numberReplicasToMake

public int numberReplicasToMake()

makeChromosomeSets

public void makeChromosomeSets()

normalizeCelFiles

public void normalizeCelFiles()

launchCelNormalization

public void launchCelNormalization(java.io.File[] celaFiles,
                                   java.util.ArrayList generalCmd,
                                   java.io.File clusterName)

convertCelFiles

public void convertCelFiles()

launchJQSub

public void launchJQSub(java.util.ArrayList args,
                        int memory)

main

public static void main(java.lang.String[] args)

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign new varibles

printDocs

public static void printDocs()