trans.main
Class Interval
java.lang.Object
trans.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
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Interval
public Interval(Window window,
int sizeOfOligo)
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)