trans.graphics
Class RankedSetAnalysis

java.lang.Object
  trans.graphics.RankedSetAnalysis

public class RankedSetAnalysis

extends java.lang.Object

Performs set analysis on genomic regions with a visual display.

Constructor Summary

RankedSetAnalysis(java.lang.String[] args)

Method Summary

static boolean	containsMatchedRankIntersect(GenomicRegion r, int testRank) Checks to see if among the hits to a particular GenomicRegion they have an equal or smaller rank.
double	fractionTotalIntersection(GenomicRegion[] r) Returns the total fraction of intersection.
org.jfree.chart.JFreeChart	getChart()
org.jfree.chart.ChartPanel	getChartPanel()
GenomicRegion[]	getRegionsOne()
GenomicRegion[]	getRegionsTwo()
java.io.File	getSetOneFile()
java.io.File	getSetTwoFile()
TextFrame	getTextFrame()
void	intersect()
boolean	intersectRegions() Loads regions with references to intersection partners.
boolean	isSavePngs()
static void	main(java.lang.String[] args)
void	makeRankedHitsGraph()
static GenomicRegion[]	parseGenomicRegionsFile(java.io.File f) Parses a regions file.
static void	printDocs()
void	printRankedIntersection(int[] hits) Prints to screen the results of rankedIntersection(GenomicRegion[] r).
void	printRankedIntersectionAll(GenomicRegion[] r) Rank analysis where each regions is check against the entire other list.
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles
static int[]	rankedIntersection(GenomicRegion[] r) Calculates the number of hits in the ranked matched list.
void	setChartPanel(org.jfree.chart.ChartPanel chartPanel)

Methods inherited from class java.lang.Object

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

Constructor Detail

RankedSetAnalysis

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

Method Detail

intersect

public void intersect()

makeRankedHitsGraph

public void makeRankedHitsGraph()

rankedIntersection

public static int[] rankedIntersection(GenomicRegion[] r)

Calculates the number of hits in the ranked matched list. As if one submitted a standard intersection analysis for every incremental rank.

printRankedIntersection

public void printRankedIntersection(int[] hits)

Prints to screen the results of rankedIntersection(GenomicRegion[] r).

containsMatchedRankIntersect

public static boolean containsMatchedRankIntersect(GenomicRegion r,
                                                   int testRank)

Checks to see if among the hits to a particular GenomicRegion they have an equal or smaller rank.

fractionTotalIntersection

public double fractionTotalIntersection(GenomicRegion[] r)

Returns the total fraction of intersection.

printRankedIntersectionAll

public void printRankedIntersectionAll(GenomicRegion[] r)

Rank analysis where each regions is check against the entire other list.

intersectRegions

public boolean intersectRegions()

Loads regions with references to intersection partners.

parseGenomicRegionsFile

public static GenomicRegion[] parseGenomicRegionsFile(java.io.File f)

Parses a regions file.

main

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

printDocs

public static void printDocs()

processArgs

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

This method will process each argument and assign any new varibles

getRegionsOne

public GenomicRegion[] getRegionsOne()

getRegionsTwo

public GenomicRegion[] getRegionsTwo()

getSetOneFile

public java.io.File getSetOneFile()

getSetTwoFile

public java.io.File getSetTwoFile()

getTextFrame

public TextFrame getTextFrame()

isSavePngs

public boolean isSavePngs()

getChartPanel

public org.jfree.chart.ChartPanel getChartPanel()

setChartPanel

public void setChartPanel(org.jfree.chart.ChartPanel chartPanel)

getChart

public org.jfree.chart.JFreeChart getChart()