igb.util
Class Windows2HeatMapSgr

java.lang.Object
  igb.util.Windows2HeatMapSgr

public class Windows2HeatMapSgr

extends java.lang.Object

Converts a text file (columns: chrom, start, stop, score) into a heat/block map specific sgr file for import into IGB.

Constructor Summary

Windows2HeatMapSgr(java.lang.String[] args)

Method Summary

static boolean	baseOverlapsWindow(int bp, igb.util.Windows2HeatMapSgr.Window win) Is a given base contained within the window?
double	highestScoringWindow(int base, int currentWindowIndex) Looks forward at overlapping windows, returns highest score for the given bp position.
static void	main(java.lang.String[] args)
void	makeBlockMapSgrFile(java.io.File file) Takes an array of Window
void	parseWindowFile(java.io.File file)
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles

Methods inherited from class java.lang.Object

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

Constructor Detail

Windows2HeatMapSgr

public Windows2HeatMapSgr(java.lang.String[] args)

Method Detail

makeBlockMapSgrFile

public void makeBlockMapSgrFile(java.io.File file)

Takes an array of Window

highestScoringWindow

public double highestScoringWindow(int base,
                                   int currentWindowIndex)

Looks forward at overlapping windows, returns highest score for the given bp position.

baseOverlapsWindow

public static boolean baseOverlapsWindow(int bp,
                                         igb.util.Windows2HeatMapSgr.Window win)

Is a given base contained within the window?

main

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

parseWindowFile

public void parseWindowFile(java.io.File file)

processArgs

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

This method will process each argument and assign any new varibles

printDocs

public static void printDocs()