trans.main
Class OverlappingWindowScoreExtractor

java.lang.Object
  extended bytrans.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.