trans.graphics
Class AggregatePlots

java.lang.Object
  trans.graphics.AggregatePlots

public class AggregatePlots

extends java.lang.Object

For each region finds the underlying scores from the chromosome specific bar files. Converts the bps to zero coordinates and centers all of the scores relative to the largest region. Generates aggregate plots.

Constructor Summary

AggregatePlots(java.lang.String[] args)

Method Summary

void	loadChromosomeBarFile()
static void	loadRegions(Sgr sgr, Positive[] pos) Checks to see if an sgr object is in the positives, if so, adds the sgr object to the positive.
static void	main(java.lang.String[] args)
static int	maxLength(Positive[] regions) Finds max length of the Region[], stop-start+1
void	plot()
static void	printArray(float[][] scores) Prints x as row, y as column with row index, float[y][x]
static void	printDocs()
static void	printEachArray(float[][] scores) Prints x as row, y as column with row index, float[y][x]
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

AggregatePlots

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

Method Detail

plot

public void plot()

printArray

public static void printArray(float[][] scores)

Prints x as row, y as column with row index, float[y][x]

printEachArray

public static void printEachArray(float[][] scores)

Prints x as row, y as column with row index, float[y][x]

maxLength

public static int maxLength(Positive[] regions)

Finds max length of the Region[], stop-start+1

loadChromosomeBarFile

public void loadChromosomeBarFile()

loadRegions

public static void loadRegions(Sgr sgr,
                               Positive[] pos)

Checks to see if an sgr object is in the positives, if so, adds the sgr object to the positive.

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()