trans.main
Class OverlappingWindowScoreExtractor

java.lang.Object
  trans.main.OverlappingWindowScoreExtractor

public class OverlappingWindowScoreExtractor

extends java.lang.Object

Finds the best overlapping Window for each region and prints that score with the region information. Built to associate a qPCR test result with the most overlapping window.

Constructor Summary

OverlappingWindowScoreExtractor(java.lang.String[] args)
For each validation region, finds the single test window that 'best' overlaps.

Method Summary

static void	main(java.lang.String[] args)
trans.main.OverlappingWindowScoreExtractor.QPCRWindow[]	makeQPCRWindows(Window[] ws)
static Window[]	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.
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles
static double	windowMidPoint(Window w)

Methods inherited from class java.lang.Object

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

Constructor Detail

OverlappingWindowScoreExtractor

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

For each validation region, finds the single test window that 'best' overlaps.

Method Detail

windowMidPoint

public static double windowMidPoint(Window w)

processArgs

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

This method will process each argument and assign any new varibles

printDocs

public static void printDocs()

main

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

makeQPCRWindows

public trans.main.OverlappingWindowScoreExtractor.QPCRWindow[] makeQPCRWindows(Window[] ws)

makeWindows

public static Window[] 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.