trans.main
Class IntervalReportPrinter

java.lang.Object
  trans.main.IntervalReportPrinter

public class IntervalReportPrinter

extends java.lang.Object

Prints all things contained within an interval to a spreadsheet or a report card.

Constructor Summary

IntervalReportPrinter(java.lang.String[] args)

Method Summary

static double	aveMedianAbsDiffSubWinControl(Interval i) Calculate maximum median absolute diff of SubWindow control values
static double	calculateMeanNumberOligoMatches(Oligo[] oligos) Calculates the average number of oligo matches to the genome.
java.lang.String	fetchIntervalLine(Interval i, int intervalNumber)
java.lang.String	fetchIntervalReport(Interval i, int intervalNumber)
void	generateIntervalStats(Interval interval) Calculate stats on oligos from best window.
static void	main(java.lang.String[] args)
static double	maxMedianAbsDiffSubWinTreatment(Interval i) Calculate maximum median absolute diff of SubWindow treatment values
static double	medianRatioSubWindow(Interval i) Calculate Median ratio of SubWindow where the treatments are averaged, and the controls are averaged
static void	printDocs()
void	printRatios(Interval interval) Used when making mock Intervals from which you want to calculate various oligo based measurements.
void	printReport()
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

IntervalReportPrinter

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

Method Detail

printReport

public void printReport()

generateIntervalStats

public void generateIntervalStats(Interval interval)

Calculate stats on oligos from best window.

calculateMeanNumberOligoMatches

public static double calculateMeanNumberOligoMatches(Oligo[] oligos)

Calculates the average number of oligo matches to the genome.

printRatios

public void printRatios(Interval interval)

Used when making mock Intervals from which you want to calculate various oligo based measurements.

fetchIntervalLine

public java.lang.String fetchIntervalLine(Interval i,
                                          int intervalNumber)

fetchIntervalReport

public java.lang.String fetchIntervalReport(Interval i,
                                            int intervalNumber)

printDocs

public static void printDocs()

processArgs

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

This method will process each argument and assign any new varibles

main

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

medianRatioSubWindow

public static double medianRatioSubWindow(Interval i)

Calculate Median ratio of SubWindow where the treatments are averaged, and the controls are averaged

maxMedianAbsDiffSubWinTreatment

public static double maxMedianAbsDiffSubWinTreatment(Interval i)

Calculate maximum median absolute diff of SubWindow treatment values

aveMedianAbsDiffSubWinControl

public static double aveMedianAbsDiffSubWinControl(Interval i)

Calculate maximum median absolute diff of SubWindow control values