trans.main
Class IntervalGraphPrinter

java.lang.Object
  trans.main.IntervalGraphPrinter

public class IntervalGraphPrinter

extends java.lang.Object

Prints an array of Interval as an '.sgr' file for import into IGB.

Constructor Summary

IntervalGraphPrinter(java.lang.String[] args)

Method Summary

java.lang.String	convertToBED(Interval[] intervals) Converts an array of Interval to a .bed String format.
java.lang.String	convertToSGR(Interval[] intervals) Converts an array of Interval to a .sgr String format.
static void	main(java.lang.String[] args)
static void	printDocs()
void	printSaveIntervalScoreGraphFiles() Prints and saves a Affy .sgr file
static void	printScores(Interval[] intervals, java.io.File file, boolean printRatios) Prints to a File a line for every Oligo in each Interval.
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles
void	sortIntervals() Sorts Interval[] based on subWindow if present, if not, then uses best window

Methods inherited from class java.lang.Object

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

Constructor Detail

IntervalGraphPrinter

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

Method Detail

processArgs

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

This method will process each argument and assign any new varibles

printSaveIntervalScoreGraphFiles

public void printSaveIntervalScoreGraphFiles()

Prints and saves a Affy .sgr file

printScores

public static void printScores(Interval[] intervals,
                               java.io.File file,
                               boolean printRatios)

Prints to a File a line for every Oligo in each Interval. Tab delimited: Chromosome, Start of the oligo, the log2(aveT/ aveC ratio).

convertToSGR

public java.lang.String convertToSGR(Interval[] intervals)

Converts an array of Interval to a .sgr String format.

convertToBED

public java.lang.String convertToBED(Interval[] intervals)

Converts an array of Interval to a .bed String format.

sortIntervals

public void sortIntervals()

Sorts Interval[] based on subWindow if present, if not, then uses best window

main

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

printDocs

public static void printDocs()