trans.main
Class IntervalMaker

java.lang.Object
  trans.main.IntervalMaker

public class IntervalMaker

extends java.lang.Object

Collapses an array of Window into and array of Interval based on scores.

Constructor Summary

IntervalMaker(java.io.File windowFile, Window[] windows, double[] cutoffs, int sizeOfOligo, int scoreIndex, int maxGap, int minimumNumberOfOligos)

IntervalMaker(java.lang.String[] args)

Method Summary

void	addIt()
boolean	checkScoreAndNumOligos(Window win)
Window	fetchGoodWindow()
static void	invertScores(Window[] windows) Multiplies all of the Window[] scores by -1
static void	main(java.lang.String[] args)
void	makeIntervals(java.io.File windowFile)
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

IntervalMaker

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

IntervalMaker

public IntervalMaker(java.io.File windowFile,
                     Window[] windows,
                     double[] cutoffs,
                     int sizeOfOligo,
                     int scoreIndex,
                     int maxGap,
                     int minimumNumberOfOligos)

Method Detail

makeIntervals

public void makeIntervals(java.io.File windowFile)

addIt

public void addIt()

invertScores

public static void invertScores(Window[] windows)

Multiplies all of the Window[] scores by -1

fetchGoodWindow

public Window fetchGoodWindow()

checkScoreAndNumOligos

public boolean checkScoreAndNumOligos(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

printDocs

public static void printDocs()