trans.main
Class WindowBlockMakerTwoColor

java.lang.Object
  trans.main.WindowBlockMakerTwoColor

public class WindowBlockMakerTwoColor

extends java.lang.Object

Converts a Window[] into a heat map specific bar 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. Note, this will place at the 0 and 1 base two values to maintain symetry in the values.

Constructor Summary

WindowBlockMakerTwoColor(int sizeOfOligo, java.lang.String genomeVersion, double minWindowFilter, double maxWindowFilter)

WindowBlockMakerTwoColor(java.lang.String[] args)

Method Summary

void	add(int base, float value) Adds a gr line to the global ArrayLists for later burning to bar.
void	addHeatMapBlocks(int startIndex, int stopIndex) Make a heatmap blocks from given window indexes, stop not included.
void	assembleHeatMapBlocks()
void	balanceValues()
Window[]	filterWindows(Window[] windows) Tosses any windows within the min max filter range.
double	getMaxWindowFilter()
double	getMinWindowFilter()
static void	main(java.lang.String[] args)
void	makeHeatMapBarFiles(Window[] windows) Makes a stair step heat map from an array of windows in bar format.
void	makeHeatMapBarFiles(Window[] windows, java.io.File barDirectory, int scoreIndex)
boolean	overlapOrAbut(Window left, Window right) Assumes right window is to right of left or abuts or doesn't overlap.
static void	printDocs()
void	printSgrLines()
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles
void	setBarDirectory(java.io.File barDirectory)
void	setMaxWindowFilter(double maxWindowFilter)
void	setMinWindowFilter(double minWindowFilter)

Methods inherited from class java.lang.Object

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

Constructor Detail

WindowBlockMakerTwoColor

public WindowBlockMakerTwoColor(int sizeOfOligo,
                                java.lang.String genomeVersion,
                                double minWindowFilter,
                                double maxWindowFilter)

WindowBlockMakerTwoColor

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

Method Detail

makeHeatMapBarFiles

public void makeHeatMapBarFiles(Window[] windows,
                                java.io.File barDirectory,
                                int scoreIndex)

filterWindows

public Window[] filterWindows(Window[] windows)

Tosses any windows within the min max filter range.

makeHeatMapBarFiles

public void makeHeatMapBarFiles(Window[] windows)

Makes a stair step heat map from an array of windows in bar format. One per chromosome. Don't forget to set the barDirectory and score Index!!!!!!!

balanceValues

public void balanceValues()

printSgrLines

public void printSgrLines()

assembleHeatMapBlocks

public void assembleHeatMapBlocks()

addHeatMapBlocks

public void addHeatMapBlocks(int startIndex,
                             int stopIndex)

Make a heatmap blocks from given window indexes, stop not included.

add

public void add(int base,
                float value)

Adds a gr line to the global ArrayLists for later burning to bar.

main

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

overlapOrAbut

public boolean overlapOrAbut(Window left,
                             Window right)

Assumes right window is to right of left or abuts or doesn't overlap.

processArgs

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

This method will process each argument and assign new varibles

printDocs

public static void printDocs()

setBarDirectory

public void setBarDirectory(java.io.File barDirectory)

getMaxWindowFilter

public double getMaxWindowFilter()

setMaxWindowFilter

public void setMaxWindowFilter(double maxWindowFilter)

getMinWindowFilter

public double getMinWindowFilter()

setMinWindowFilter

public void setMinWindowFilter(double minWindowFilter)