trans.anno
Class IntersectKeyWithRegions

java.lang.Object
  trans.anno.IntersectKeyWithRegions

public class IntersectKeyWithRegions

extends java.lang.Object

Takes a key from a spike in experiment and sorted lists of regions to calculate TPR, FPR, and FDR for every threshold

Constructor Summary

IntersectKeyWithRegions(java.lang.String[] args)

Method Summary

void	calculateAndPrintStats(Region[] r)
int	intersectsKey(Region region) Returns 1 if bpInt <= maxGap and the particular key hasn't been hit, 0 not in key, -1 hits a key that has already been counted.
static void	main(java.lang.String[] args)
void	parseRegionFiles()
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles

Methods inherited from class java.lang.Object

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

Constructor Detail

IntersectKeyWithRegions

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

Method Detail

calculateAndPrintStats

public void calculateAndPrintStats(Region[] r)

intersectsKey

public int intersectsKey(Region region)

Returns 1 if bpInt <= maxGap and the particular key hasn't been hit, 0 not in key, -1 hits a key that has already been counted.

parseRegionFiles

public void parseRegionFiles()

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()