trans.main
Class PeakPicker

java.lang.Object
  trans.main.PeakPicker

public class PeakPicker

extends java.lang.Object

Finds peaks in Intervals, both flat topped or peaks with sloping sides.

Constructor Summary

PeakPicker()

Method Summary

double	averageWindowScores(int start, int stop) Averages the smoothed oligo scores, stop is inclusive.
boolean	checkWidth(int leftIndex, int peakIndex, int rightIndex)
boolean	expandFlatTopPeak() Attempts to expand the leftIndex and rightIndex
int	findFlatTopPeak()
int	findHighestScore()
int	findPeak()
int	findPeakBp(int peakIndex)
Interval	getInterval()
int	getLeftIndex()
int	getMaxNumPeaks()
int	getMinBpSides()
double	getMinPercent()
int	getMinRun()
int	getNumOligos()
Oligo[]	getOligos()
int	getPeakBp()
int	getPeakIndex()
int	getRightIndex()
double	getScoreCutOff()
int	growLeft(int index) Uses the idea of a local window, counts the number of pos slopes within the window, if > minPercent, keeps advancing.
int	growRight(int index) Uses the idea of a local window, counts the number of neg slopes within the window, if > minPercent, keeps advancing.
void	mask(int start, int stop)
void	pickPeaks(Interval[] intervals)
void	setInterval(Interval interval)
void	setLeftIndex(int leftIndex)
void	setMakeFlattops(boolean makeFlattops)
void	setMaxBpGap(int maxBpGap)
void	setMaxNumPeaks(int maxNumPeaks)
void	setMaxScoreFractionDrop(double maxScoreFractionDrop)
void	setMinBpSides(int minBpSides)
void	setMinPercent(double minPercent)
void	setMinRun(int minRun)
void	setNumOligos(int numOligos)
void	setOligos(Oligo[] oligos)
void	setPeakBp(int peakBp)
void	setPeakIndex(int peakIndex)
void	setRightIndex(int rightIndex)
void	setScoreCutOff(double scoreCutOff)
boolean	setSubWindowScoreAsMinScore() Averages the smoothed scores in the best sub window.
void	slopeOligos()

Methods inherited from class java.lang.Object

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

Constructor Detail

PeakPicker

public PeakPicker()

Method Detail

expandFlatTopPeak

public boolean expandFlatTopPeak()

Attempts to expand the leftIndex and rightIndex

averageWindowScores

public double averageWindowScores(int start,
                                  int stop)

Averages the smoothed oligo scores, stop is inclusive.

setSubWindowScoreAsMinScore

public boolean setSubWindowScoreAsMinScore()

Averages the smoothed scores in the best sub window. and sets this * maxScoreFractionDrop as the scoreCutOff.

pickPeaks

public void pickPeaks(Interval[] intervals)

mask

public void mask(int start,
                 int stop)

findFlatTopPeak

public int findFlatTopPeak()

findPeak

public int findPeak()

checkWidth

public boolean checkWidth(int leftIndex,
                          int peakIndex,
                          int rightIndex)

findPeakBp

public int findPeakBp(int peakIndex)

growRight

public int growRight(int index)

Uses the idea of a local window, counts the number of neg slopes within the window, if > minPercent, keeps advancing.

growLeft

public int growLeft(int index)

Uses the idea of a local window, counts the number of pos slopes within the window, if > minPercent, keeps advancing.

findHighestScore

public int findHighestScore()

slopeOligos

public void slopeOligos()

getInterval

public Interval getInterval()

setInterval

public void setInterval(Interval interval)

getLeftIndex

public int getLeftIndex()

setLeftIndex

public void setLeftIndex(int leftIndex)

getMinBpSides

public int getMinBpSides()

setMinBpSides

public void setMinBpSides(int minBpSides)

getMinPercent

public double getMinPercent()

setMinPercent

public void setMinPercent(double minPercent)

getMinRun

public int getMinRun()

setMinRun

public void setMinRun(int minRun)

getNumOligos

public int getNumOligos()

setNumOligos

public void setNumOligos(int numOligos)

getOligos

public Oligo[] getOligos()

setOligos

public void setOligos(Oligo[] oligos)

getPeakBp

public int getPeakBp()

setPeakBp

public void setPeakBp(int peakBp)

getPeakIndex

public int getPeakIndex()

setPeakIndex

public void setPeakIndex(int peakIndex)

getRightIndex

public int getRightIndex()

setRightIndex

public void setRightIndex(int rightIndex)

getScoreCutOff

public double getScoreCutOff()

setScoreCutOff

public void setScoreCutOff(double scoreCutOff)

getMaxNumPeaks

public int getMaxNumPeaks()

setMaxNumPeaks

public void setMaxNumPeaks(int maxNumPeaks)

setMakeFlattops

public void setMakeFlattops(boolean makeFlattops)

setMaxBpGap

public void setMaxBpGap(int maxBpGap)

setMaxScoreFractionDrop

public void setMaxScoreFractionDrop(double maxScoreFractionDrop)