Uses of Class
trans.main.Interval

Packages that use Interval

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

Uses of Interval in trans.anno

Methods in trans.anno with parameters of type Interval

boolean	Region.intersect(Interval interval)
int	Region.overlap(Interval interval) Returns -1 for no overlap, or a positive int for the # bases of overlap.

Constructors in trans.anno with parameters of type Interval

BindingRegion(Interval interval, int rank)

Uses of Interval in trans.graphics

Methods in trans.graphics with parameters of type Interval

void	IntervalDrawFrame.makePanel(Interval interval, int intervalNumber, TextFrame textFrame, boolean showPSPM)

Constructors in trans.graphics with parameters of type Interval

IntervalDrawPanel(Interval interval, int intervalNumber, TextFrame textFrame, boolean showPSPM)

IntervalDrawFrame(Interval interval, int intervalNumber, TextFrame textFrame, boolean showPSPM)

Uses of Interval in trans.main

Methods in trans.main that return Interval

Interval	PosRegion.getClosestInterval()
Interval	PeakPicker.getInterval()
static Interval[]	OverlapCounter.subtractIntervals(Interval[] bigger, Interval[] smaller) Returns the difference between two interval arrays, be sure to get bigger and smaller correct.

Methods in trans.main with parameters of type Interval

void	ScoreIntervals.setGenomicSequenceParams(Interval interval) Loads up the fasta file for a particular chromosome and sets some params.
void	PosRegion.setClosestInterval(Interval closestInterval)
void	PeakPicker.pickPeaks(Interval[] intervals)
void	PeakPicker.setInterval(Interval interval)
void	OverlapCounter.findClosestPeaks(Interval[] one, Interval[] two, java.io.File fileOne, java.io.File fileTwo)
int	OverlapCounter.overlapPeaks(Interval one, Interval two) Returns distance between top peaks.
static int	OverlapCounter.findPeak(Interval i) Returns base position of highest scoring peak, if no peak uses middle of sub window if no sub window uses middle of interval
boolean	OverlapCounter.overlap(Interval one, Interval two) checks to see if intervals overlap by the minimum maxGap, can set maxGap negative to require an overlap.
java.lang.String	OverlapCounter.testOverlap(Interval[] one, Interval[] two, java.io.File fileOne, java.io.File fileTwo) Returns the average % intersection.
static Interval[]	OverlapCounter.subtractIntervals(Interval[] bigger, Interval[] smaller) Returns the difference between two interval arrays, be sure to get bigger and smaller correct.
static void	LoadIntervalOligoInfo.sortIntervalsByChromosome(Interval[] intervals) Ugly, ugly, ugly, use a Comparator!
void	IntervalReportPrinter.generateIntervalStats(Interval interval) Calculate stats on oligos from best window.
void	IntervalReportPrinter.printRatios(Interval interval) Used when making mock Intervals from which you want to calculate various oligo based measurements.
java.lang.String	IntervalReportPrinter.fetchIntervalLine(Interval i, int intervalNumber)
java.lang.String	IntervalReportPrinter.fetchIntervalReport(Interval i, int intervalNumber)
static double	IntervalReportPrinter.medianRatioSubWindow(Interval i) Calculate Median ratio of SubWindow where the treatments are averaged, and the controls are averaged
static double	IntervalReportPrinter.maxMedianAbsDiffSubWinTreatment(Interval i) Calculate maximum median absolute diff of SubWindow treatment values
static double	IntervalReportPrinter.aveMedianAbsDiffSubWinControl(Interval i) Calculate maximum median absolute diff of SubWindow control values
static void	IntervalGraphPrinter.printScores(Interval[] intervals, java.io.File file, boolean printRatios) Prints to a File a line for every Oligo in each Interval.
java.lang.String	IntervalGraphPrinter.convertToSGR(Interval[] intervals) Converts an array of Interval to a .sgr String format.
java.lang.String	IntervalGraphPrinter.convertToBED(Interval[] intervals) Converts an array of Interval to a .bed String format.
static void	IntervalGFFPrinter.gff(Oligo o, Interval i, java.lang.String name, int oligoNumber, java.lang.StringBuffer s) Appends a GFF3 line for an Oligo.
static void	IntervalGFFPrinter.gff(BindingPeak peak, Interval i, java.lang.String name, int peakNumber, java.lang.StringBuffer s) Appends a GFF3 line for a BindingPeak
static void	IntervalGFFPrinter.gff(SubWindow sub, Interval i, java.lang.String name, java.lang.StringBuffer s) Appends a GFF3 line for a SubWindow.
void	IntervalGFFPrinter.gff(Interval i, int rank, java.lang.String name, java.lang.StringBuffer s) Appends a GFF3 line for an Interval.
void	IntervalGFFPrinter.gff(Interval i, java.lang.String name, java.lang.StringBuffer s) Appends a GFF3 line for a Window.
void	ExportIntervalData.loadBestWindowOligoIntensities(Interval interval) Loads the treatment and control intensity arrays for a particular interval.

Uses of Interval in trans.misc

Methods in trans.misc with parameters of type Interval

static void

Util.sortIntervalsBySubWindowMedianRatio(Interval[] intervals) Sorts an array of Interval by the median ratio of the best SubWindow.