Uses of Class
trans.main.Window

Packages that use Window

trans.anno	For associating intervals, binding regions, and binding peaks with GFF annotation.
trans.main	Principle classes and scripts used in TiMAT2 analysis.
trans.misc	Rough working scripts.

Uses of Window in trans.anno

Methods in trans.anno with parameters of type Window

boolean

Region.intersect(Window window, int sizeOligo, double fractionAcceptibleCoverage) Returns true only if region contains or is contained or is covered by >= fractionAcceptibleCoverage by a window.

Uses of Window in trans.main

Methods in trans.main that return Window

Window[]	WindowBlockMakerTwoColor.filterWindows(Window[] windows) Tosses any windows within the min max filter range.
Window	SetNumberIntervalMaker.fetchGoodWindow(double minScoreInt)
Window[]	ScanChromosomes.getWindows()
static Window[]	OverlappingWindowScoreExtractor.makeWindows(java.io.File txtFile) Converts a tab delimited txt file of chr, start, stop, scores (multiple permitted or none) into an array of Windows.
Window	MultiWindowIntervalMaker.fetchGoodWindow()
Window	MultiWindowIntervalMaker.checkWindowScoresAndNumberOfOligos() Checks the scores and number of oligos in each window.
Window	MultiWindowIntervalMaker.findWindow(Window[] win)
Window[]	MergeWindowArrays.filter(Window[] win)
Window	IntervalMaker.fetchGoodWindow()
Window	Interval.getBestWindow()

Methods in trans.main with parameters of type Window

void	WindowBlockMakerTwoColor.makeHeatMapBarFiles(Window[] windows, java.io.File barDirectory, int scoreIndex)
Window[]	WindowBlockMakerTwoColor.filterWindows(Window[] windows) Tosses any windows within the min max filter range.
void	WindowBlockMakerTwoColor.makeHeatMapBarFiles(Window[] windows) Makes a stair step heat map from an array of windows in bar format.
boolean	WindowBlockMakerTwoColor.overlapOrAbut(Window left, Window right) Assumes right window is to right of left or abuts or doesn't overlap.
void	WindowBlockMaker.makeHeatMapGrFiles(Window[] windows, java.io.File directory) Be sure to set the scoreIndex, defaults to 0.
void	WindowBlockMaker.makeHeatMapSgrFile(Window[] windows, java.io.File file, boolean zipCompressIt) Be sure to set the scoreIndex, defaults to 0.
void	WindowBlockMaker.makeHeatMapBarFiles(Window[] windows, java.io.File directory) Be sure to set the scoreIndex, defaults to 0.
boolean	WindowBlockMaker.baseOverlapsWindow(int bp, Window win) Is a given base contained within the window?
boolean	Window.overlap(Window other)
void	ScanChromosomes.makeBarFiles(Window[] windows, java.io.File directory, int scoreIndex) Makes xxx.bar.zip files from a Window[], one per chromosome.
void	ScanChromosomes.importScores(Window[] windows, java.io.File importFile) Reads in a file of scores from a qvalue output file Also makes gr files for the qValues.
void	ScanChip.importScores(Window[] windows, java.io.File importFile) Reads in a file of scores from a qvalue output file Also writes and zips an .sgr file for the qValues.
void	ScanChip.makeSgrFile(Window[] windows, java.io.File sgrFile, int scoreIndex) Makes a xxx.sgr.zip file from a sorted Window[].
static double	OverlappingWindowScoreExtractor.windowMidPoint(Window w)
trans.main.OverlappingWindowScoreExtractor.QPCRWindow[]	OverlappingWindowScoreExtractor.makeQPCRWindows(Window[] ws)
Window	MultiWindowIntervalMaker.findWindow(Window[] win)
Window[]	MergeWindowArrays.filter(Window[] win)
static void	IntervalMaker.invertScores(Window[] windows) Multiplies all of the Window[] scores by -1
boolean	IntervalMaker.checkScoreAndNumOligos(Window win)
void	Interval.setBestWindow(Window bestWindow)
int	FDRWindowConverter.thresholdWindows(Window[] w, double score, int startingIndex)
void	FDRWindowConverter.setScoreAndSort(Window[] w)

Constructors in trans.main with parameters of type Window

IntervalMaker(java.io.File windowFile, Window[] windows, double[] cutoffs, int sizeOfOligo, int scoreIndex, int maxGap, int minimumNumberOfOligos)

Interval(Window window, int sizeOfOligo)

Uses of Window in trans.misc

Methods in trans.misc that return Window

static Window[]	Util.removeLowOligoWindows(Window[] win, int minNumberOligos) Removes windows that contain < minNumberOligos.
static Window[][]	Util.splitWindowsByChromosome(Window[] win)

Methods in trans.misc with parameters of type Window

static double[]	Util.minMaxWindowScores(Window[] win, int scoreIndex) Finds min max score
static double[]	Util.minMaxWindowArray(Window[] win, int scoreIndex) Returns the min and max values of a given score index in a Window[].
static Window[]	Util.removeLowOligoWindows(Window[] win, int minNumberOligos) Removes windows that contain < minNumberOligos.
static Window[][]	Util.splitWindowsByChromosome(Window[] win)