trans.main
Class WindowBlockMaker

java.lang.Object
  trans.main.WindowBlockMaker

public class WindowBlockMaker

extends java.lang.Object

Converts a Window[] into a heat map specific sgr file for import into IGB. Assumes windows are sorted by chromosome and start position Score index is the index to use when fetching a score for a window from it's double[] of scores see ScanChip or ScanChromosomes for current score indexes.

Constructor Summary

WindowBlockMaker(int sizeOfOligo)

WindowBlockMaker(int sizeOfOligo, java.lang.String genomeVersion)

WindowBlockMaker(java.lang.String[] args)

Method Summary

boolean	baseOverlapsWindow(int bp, Window win) Is a given base contained within the window?
float	getBaseScore()
int	getScoreIndex()
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	makeHeatMapBarFiles(Window[] windows, java.io.File directory) Be sure to set the scoreIndex, defaults to 0.
void	makeHeatMapGrFiles(Window[] windows, java.io.File directory) Be sure to set the scoreIndex, defaults to 0.
void	makeHeatMapSgrFile(Window[] windows, java.io.File file, boolean zipCompressIt) Be sure to set the scoreIndex, defaults to 0.
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles
void	setBaseScore(float baseScore)
void	setScoreIndex(int scoreIndex)

Methods inherited from class java.lang.Object

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

Constructor Detail

WindowBlockMaker

public WindowBlockMaker(int sizeOfOligo)

WindowBlockMaker

public WindowBlockMaker(int sizeOfOligo,
                        java.lang.String genomeVersion)

WindowBlockMaker

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

Method Detail

makeHeatMapGrFiles

public void makeHeatMapGrFiles(Window[] windows,
                               java.io.File directory)

Be sure to set the scoreIndex, defaults to 0. Automatically zips them

makeHeatMapSgrFile

public void makeHeatMapSgrFile(Window[] windows,
                               java.io.File file,
                               boolean zipCompressIt)

Be sure to set the scoreIndex, defaults to 0.

makeHeatMapBarFiles

public void makeHeatMapBarFiles(Window[] windows,
                                java.io.File directory)

Be sure to set the scoreIndex, defaults to 0. Automatically zips them

highestScoringWindow

public double highestScoringWindow(int base,
                                   int currentWindowIndex)

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

baseOverlapsWindow

public boolean baseOverlapsWindow(int bp,
                                  Window win)

Is a given base contained within the window?

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()

getScoreIndex

public int getScoreIndex()

setScoreIndex

public void setScoreIndex(int scoreIndex)

getBaseScore

public float getBaseScore()

setBaseScore

public void setBaseScore(float baseScore)