trans.anno
Class IntersectRegions

java.lang.Object
  trans.anno.IntersectRegions

public class IntersectRegions

extends java.lang.Object

Performs an intersection analysis on binding region files (chr start stop (optional fraction gc)).

Constructor Summary

IntersectRegions(java.lang.String[] arguments)

Method Summary

static boolean	containedWithin(BindingRegion one, BindingRegion two) Returns true if two entirely contains one.
static BindingRegion[]	fetchChromosomeSpecificBRs(BindingRegion[] sortedBRs, java.lang.String chromosome) Given a sorted array of BindingRegion and a chromosome, returns the appropriate BindingRegions.
void	intersectBindingRegions()
void	intersectRandomBindingRegions(BindingRegion[] allTrialsOfSingleBR, BindingRegion[] chrOne) Assumes the same chromosome
void	intersectRandomRegions() Increments the hitsPerTrial int[].
static void	main(java.lang.String[] args)
static BindingRegion[]	makeBindingRegions(int[][] regions, java.lang.String chromosome) Given an array of start stops and a chromosome, makes BindingRegions.
RandomRegions	makeRandomRegions(java.lang.String chromosome)
static int	numberBases(BindingRegion[] brs)
static BindingRegion[]	parseIntervalFile(java.io.File intervalFile)
static BindingRegion[]	parseRegionsFile(java.io.File picksFile)
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles
double	pValue()
static double[]	statBindingRegionArray(BindingRegion[] brs)
static boolean	writeBindingRegions(BindingRegion[] brs, java.io.File file)

Methods inherited from class java.lang.Object

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

Constructor Detail

IntersectRegions

public IntersectRegions(java.lang.String[] arguments)

Method Detail

pValue

public double pValue()

intersectRandomRegions

public void intersectRandomRegions()

Increments the hitsPerTrial int[].

fetchChromosomeSpecificBRs

public static BindingRegion[] fetchChromosomeSpecificBRs(BindingRegion[] sortedBRs,
                                                         java.lang.String chromosome)

Given a sorted array of BindingRegion and a chromosome, returns the appropriate BindingRegions.

makeBindingRegions

public static BindingRegion[] makeBindingRegions(int[][] regions,
                                                 java.lang.String chromosome)

Given an array of start stops and a chromosome, makes BindingRegions.

makeRandomRegions

public RandomRegions makeRandomRegions(java.lang.String chromosome)

writeBindingRegions

public static boolean writeBindingRegions(BindingRegion[] brs,
                                          java.io.File file)

intersectRandomBindingRegions

public void intersectRandomBindingRegions(BindingRegion[] allTrialsOfSingleBR,
                                          BindingRegion[] chrOne)

Assumes the same chromosome

containedWithin

public static boolean containedWithin(BindingRegion one,
                                      BindingRegion two)

Returns true if two entirely contains one.

intersectBindingRegions

public void intersectBindingRegions()

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()

parseRegionsFile

public static BindingRegion[] parseRegionsFile(java.io.File picksFile)

parseIntervalFile

public static BindingRegion[] parseIntervalFile(java.io.File intervalFile)

statBindingRegionArray

public static double[] statBindingRegionArray(BindingRegion[] brs)

Returns:

double[2]{total bases,median length}.

numberBases

public static int numberBases(BindingRegion[] brs)

Returns:

total number of bases in the BindingRegion[], end-start+1.