nix.affy.main
Class Interval

java.lang.Object
  nix.affy.main.Interval

All Implemented Interfaces:

java.lang.Comparable, java.io.Serializable

public class Interval

extends java.lang.Object

implements java.lang.Comparable, java.io.Serializable

Container for holding information about a potential enriched region: windows, oligos, sub windows, binding peaks....

See Also:

Serialized Form

Constructor Summary

Interval(Window window, java.lang.String intensityScoreUsed)

Method Summary

int	compareTo(java.lang.Object obj)
Oligo[]	extractSubRegionOligos(int start, int end) Given a bp start and bp end as well as a larger Oligo[] returns a sub array of the oligos flanking and including the start and end.
double[]	getBaseScores()
java.lang.String	getBestStatWindowSequence()
SubWindow	getBestSubWindow()
java.lang.String	getBestSubWindowSequence()
java.lang.String	getBestWindowIntensityTestSequence()
Window	getBestWinIntTest()
Window	getBestWinStatTest()
BindingPeak[]	getBindingPeaks()
java.io.File[]	getCelFiles()
java.lang.String	getChromosome()
java.lang.String	getIntensityScoreUsed()
int	getMaxCluster()
double	getMotifHitSum() Sums the logged motif hit values using the best AID window or the entire interval.
int	getNumberControlIntensities()
int	getNumberMotifHits()
int	getNumberOfWindows()
int	getNumberTreatmentIntensities()
Oligo[]	getOligos()
java.lang.String	getSequence()
int	getSizeOfOligo()
double	getSortBy()
int	getStart1stOligo()
int	getStartLastOligo()
boolean	isBestAIDWindowScored()
void	setBaseScores(double[] baseScores)
void	setBestAIDWindowScored(boolean bestAIDWindowScored)
void	setBestSubWindow(SubWindow bestSubWindow)
void	setBestWinIntTest(Window bestWinIntTest)
void	setBestWinStatTest(Window bestWinStatTest)
void	setBindingPeaks(BindingPeak[] bindingPeaks)
void	setCelFiles(java.io.File[] celFiles)
void	setChromosome(java.lang.String string)
void	setIntensityScoreUsed(java.lang.String intensityScoreUsed)
void	setMaxCluster(int maxCluster)
void	setNumberControlIntensities(int numberControlIntensities)
void	setNumberMotifHits(int motifHits)
void	setNumberOfWindows(int numberOfWindows)
void	setNumberTreatmentIntensities(int numberTreatmentIntensities)
void	setOligos(Oligo[] oligos)
void	setSequence(java.lang.String sequence)
void	setSizeOfOligo(int sizeOfOligo)
void	setSortBy(double sortBy)
void	setStart1stOligo(int i)
void	setStartLastOligo(int i)
java.lang.String	toString() Returns chromosome, start first oligo, start last oligo, number of observations used in calculating statistical score, statistical score, aveIntDiff, (if these WindowIntervals were scored using the ScoreWindowIntervals program then these additional catagories will be returned) max cluster, number motif hits, sequence

Methods inherited from class java.lang.Object

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

Constructor Detail

Interval

public Interval(Window window,
                java.lang.String intensityScoreUsed)

Method Detail

compareTo

public int compareTo(java.lang.Object obj)

Specified by:

compareTo in interface java.lang.Comparable

getMotifHitSum

public double getMotifHitSum()

Sums the logged motif hit values using the best AID window or the entire interval. This is equivalent to the product of the probabilities.

toString

public java.lang.String toString()

Returns chromosome, start first oligo, start last oligo, number of observations used in calculating statistical score, statistical score, aveIntDiff, (if these WindowIntervals were scored using the ScoreWindowIntervals program then these additional catagories will be returned) max cluster, number motif hits, sequence

extractSubRegionOligos

public Oligo[] extractSubRegionOligos(int start,
                                      int end)

Given a bp start and bp end as well as a larger Oligo[] returns a sub array of the oligos flanking and including the start and end.

getBestWindowIntensityTestSequence

public java.lang.String getBestWindowIntensityTestSequence()

getBestStatWindowSequence

public java.lang.String getBestStatWindowSequence()

getBestSubWindowSequence

public java.lang.String getBestSubWindowSequence()

getChromosome

public java.lang.String getChromosome()

getStartLastOligo

public int getStartLastOligo()

getStart1stOligo

public int getStart1stOligo()

setChromosome

public void setChromosome(java.lang.String string)

setStartLastOligo

public void setStartLastOligo(int i)

setStart1stOligo

public void setStart1stOligo(int i)

getNumberMotifHits

public int getNumberMotifHits()

setNumberMotifHits

public void setNumberMotifHits(int motifHits)

getSequence

public java.lang.String getSequence()

setSequence

public void setSequence(java.lang.String sequence)

getMaxCluster

public int getMaxCluster()

setMaxCluster

public void setMaxCluster(int maxCluster)

setSortBy

public void setSortBy(double sortBy)

getSortBy

public double getSortBy()

getNumberOfWindows

public int getNumberOfWindows()

setNumberOfWindows

public void setNumberOfWindows(int numberOfWindows)

setSizeOfOligo

public void setSizeOfOligo(int sizeOfOligo)

getOligos

public Oligo[] getOligos()

setOligos

public void setOligos(Oligo[] oligos)

getBestWinIntTest

public Window getBestWinIntTest()

setBestWinIntTest

public void setBestWinIntTest(Window bestWinIntTest)

getBestWinStatTest

public Window getBestWinStatTest()

setBestWinStatTest

public void setBestWinStatTest(Window bestWinStatTest)

getCelFiles

public java.io.File[] getCelFiles()

setCelFiles

public void setCelFiles(java.io.File[] celFiles)

getSizeOfOligo

public int getSizeOfOligo()

getNumberControlIntensities

public int getNumberControlIntensities()

setNumberControlIntensities

public void setNumberControlIntensities(int numberControlIntensities)

getNumberTreatmentIntensities

public int getNumberTreatmentIntensities()

setNumberTreatmentIntensities

public void setNumberTreatmentIntensities(int numberTreatmentIntensities)

getBaseScores

public double[] getBaseScores()

setBaseScores

public void setBaseScores(double[] baseScores)

getBestSubWindow

public SubWindow getBestSubWindow()

setBestSubWindow

public void setBestSubWindow(SubWindow bestSubWindow)

isBestAIDWindowScored

public boolean isBestAIDWindowScored()

setBestAIDWindowScored

public void setBestAIDWindowScored(boolean bestAIDWindowScored)

getBindingPeaks

public BindingPeak[] getBindingPeaks()

setBindingPeaks

public void setBindingPeaks(BindingPeak[] bindingPeaks)

getIntensityScoreUsed

public java.lang.String getIntensityScoreUsed()

setIntensityScoreUsed

public void setIntensityScoreUsed(java.lang.String intensityScoreUsed)