trans.main
Class Interval

java.lang.Object
  extended bytrans.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, int sizeOfOligo)
           
 
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()
           
 SubWindow getBestSubWindow()
           
 java.lang.String getBestSubWindowSequence()
           
 Window getBestWindow()
           
 java.lang.String getBestWindowSequence()
           
 BindingPeak[] getBindingPeaks()
           
 java.io.File[] getCelFiles()
           
 java.lang.String getChromosome()
           
 double[] getFractionIntersections()
           
 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[] getRegionNames()
           
 java.lang.String getSequence()
           
 int getSizeOfOligoMinusOne()
           
 double getSortBy()
           
 int getStart1stOligo()
           
 int getStartLastOligo()
           
 boolean isBestWindowScored()
           
 void setBaseScores(double[] baseScores)
           
 void setBestSubWindow(SubWindow bestSubWindow)
           
 void setBestWindow(Window bestWindow)
           
 void setBestWindowScored(boolean bestAIDWindowScored)
           
 void setBindingPeaks(BindingPeak[] bindingPeaks)
           
 void setCelFiles(java.io.File[] celFiles)
           
 void setChromosome(java.lang.String string)
           
 void setFractionIntersections(double[] percentIntersections)
           
 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 setRegionNames(java.lang.String[] repeatNames)
           
 void setSequence(java.lang.String sequence)
           
 void setSizeOfOligoMinusOne(int sizeOfOligoMinusOne)
           
 void setSortBy(double sortBy)
           
 void setStart1stOligo(int i)
           
 void setStartLastOligo(int i)
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Interval

public Interval(Window window,
                int sizeOfOligo)
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()

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.


getBestWindowSequence

public java.lang.String getBestWindowSequence()

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)

getOligos

public Oligo[] getOligos()

setOligos

public void setOligos(Oligo[] oligos)

getBestWindow

public Window getBestWindow()

setBestWindow

public void setBestWindow(Window bestWindow)

getCelFiles

public java.io.File[] getCelFiles()

setCelFiles

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

getSizeOfOligoMinusOne

public int getSizeOfOligoMinusOne()

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)

isBestWindowScored

public boolean isBestWindowScored()

setBestWindowScored

public void setBestWindowScored(boolean bestAIDWindowScored)

getBindingPeaks

public BindingPeak[] getBindingPeaks()

setBindingPeaks

public void setBindingPeaks(BindingPeak[] bindingPeaks)

getFractionIntersections

public double[] getFractionIntersections()

setFractionIntersections

public void setFractionIntersections(double[] percentIntersections)

getRegionNames

public java.lang.String[] getRegionNames()

setRegionNames

public void setRegionNames(java.lang.String[] repeatNames)

setSizeOfOligoMinusOne

public void setSizeOfOligoMinusOne(int sizeOfOligoMinusOne)