trans.main
Class MultiWindowIntervalMaker

java.lang.Object
  trans.main.MultiWindowIntervalMaker

public class MultiWindowIntervalMaker

extends java.lang.Object

Collapses arrays of Windows into an array of Interval based on scores and minimal number of windows that must pass.

Constructor Summary

MultiWindowIntervalMaker(java.lang.String[] args)

Method Summary

void	addIt()
Window	checkWindowScoresAndNumberOfOligos() Checks the scores and number of oligos in each window.
Window	fetchGoodWindow()
Window	findWindow(Window[] win)
static void	main(java.lang.String[] args)
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles
void	putLargestWindowArrayFirst() Puts longest window array first and it's associated minScore.

Methods inherited from class java.lang.Object

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

Constructor Detail

MultiWindowIntervalMaker

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

Method Detail

addIt

public void addIt()

fetchGoodWindow

public Window fetchGoodWindow()

checkWindowScoresAndNumberOfOligos

public Window checkWindowScoresAndNumberOfOligos()

Checks the scores and number of oligos in each window. Returns best one if they pass the minNumWindows and minScore cutoffs. Otherwise null is returned.

findWindow

public Window findWindow(Window[] win)

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

putLargestWindowArrayFirst

public void putLargestWindowArrayFirst()

Puts longest window array first and it's associated minScore.

printDocs

public static void printDocs()