org.fhcrc.cpl.viewer.mrm
Class BasicLowIntensityElutionCurveStrategy

java.lang.Object
  org.fhcrc.cpl.viewer.mrm.ElutionCurveStrategy
      org.fhcrc.cpl.viewer.mrm.BasicLowIntensityElutionCurveStrategy

public class BasicLowIntensityElutionCurveStrategy
extends ElutionCurveStrategy

Created by IntelliJ IDEA. User: tholzman Date: May 27, 2008 Time: 10:07:49 AM To change this template use File | Settings | File Templates.

Field Summary

protected int	minPointsInACurve
protected double	minSignal
protected double	noisePctOfHighestPeak
protected int	noiseSearchWindowWidth

Fields inherited from class org.fhcrc.cpl.viewer.mrm.ElutionCurveStrategy

bestDaughterCurve, bestParentCurve, daughter, daughterCurves, parent, parentCurves

Constructor Summary

BasicLowIntensityElutionCurveStrategy()

BasicLowIntensityElutionCurveStrategy(MRMTransition p, MRMDaughter d)

Method Summary

ElutionCurve	bestParentCurve(double noiseFloor, PlotDataSupplier pds)
void	calculateAUC(ElutionCurve ec)
void	calculateBestCurves()
java.util.List<ElutionCurve>	calculateDaughterElutionCurves(PlotDataSupplier pds)
java.util.List<ElutionCurve>	calculateElutionCurves(PlotDataSupplier pds)
java.util.List<ElutionCurve>	calculateParentElutionCurves(PlotDataSupplier pds)
ElutionCurve	getBestDaughterCurve()
ElutionCurve	getBestParentCurve()
MRMDaughter	getDaughter()
java.util.List<ElutionCurve>	getDaughterCurves()
int	getMinPointsInACurve()
double	getMinSignal()
double	getNoisePctOfHighestPeak()
int	getNoiseSearchWindowWidth()
MRMTransition	getParent()
java.util.List<ElutionCurve>	getParentCurves()
double	highestPeak(PlotDataSupplier pds)
boolean	isATeePee(java.util.ArrayList<org.jfree.data.xy.XYDataItem> data, int curpoint)
boolean	isBestDaughterCurve(ElutionCurve ec)
boolean	isBestParentCurve(ElutionCurve ec)
ElutionCurve	maxAUC(java.util.List<ElutionCurve> curves)
double	meanWindow(java.util.ArrayList<org.jfree.data.xy.XYDataItem> data, int startAt)
double	noiseLevel(PlotDataSupplier pds)
void	setBestDaughterCurve(ElutionCurve ec)
void	setBestParentCurve(ElutionCurve ec)
void	setDaughter(MRMDaughter d)
void	setDaughterCurves(java.util.List<ElutionCurve> dc)
void	setMinPointsInACurve(int minPointsInACurve)
void	setMinSignal(double minSignal)
void	setNoisePctOfHighestPeak(double noisePctOfHighestPeak)
void	setNoiseSearchWindowWidth(int noiseSearchWindowWidth)
void	setParent(MRMTransition p)
void	setParentCurves(java.util.List<ElutionCurve> pc)

Methods inherited from class org.fhcrc.cpl.viewer.mrm.ElutionCurveStrategy

getInstance

Methods inherited from class java.lang.Object

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

Field Detail

noiseSearchWindowWidth

protected int noiseSearchWindowWidth

noisePctOfHighestPeak

protected double noisePctOfHighestPeak

minPointsInACurve

protected int minPointsInACurve

minSignal

protected double minSignal

Constructor Detail

BasicLowIntensityElutionCurveStrategy

public BasicLowIntensityElutionCurveStrategy(MRMTransition p,
                                             MRMDaughter d)

BasicLowIntensityElutionCurveStrategy

public BasicLowIntensityElutionCurveStrategy()

Method Detail

getBestParentCurve

public ElutionCurve getBestParentCurve()

Specified by:

getBestParentCurve in class ElutionCurveStrategy

getBestDaughterCurve

public ElutionCurve getBestDaughterCurve()

Specified by:

getBestDaughterCurve in class ElutionCurveStrategy

setBestParentCurve

public void setBestParentCurve(ElutionCurve ec)

Specified by:

setBestParentCurve in class ElutionCurveStrategy

setBestDaughterCurve

public void setBestDaughterCurve(ElutionCurve ec)

Specified by:

setBestDaughterCurve in class ElutionCurveStrategy

isBestParentCurve

public boolean isBestParentCurve(ElutionCurve ec)

Overrides:

isBestParentCurve in class ElutionCurveStrategy

isBestDaughterCurve

public boolean isBestDaughterCurve(ElutionCurve ec)

Overrides:

isBestDaughterCurve in class ElutionCurveStrategy

getParent

public MRMTransition getParent()

Specified by:

getParent in class ElutionCurveStrategy

setParent

public void setParent(MRMTransition p)

Specified by:

setParent in class ElutionCurveStrategy

getDaughter

public MRMDaughter getDaughter()

Specified by:

getDaughter in class ElutionCurveStrategy

setDaughter

public void setDaughter(MRMDaughter d)

Specified by:

setDaughter in class ElutionCurveStrategy

getParentCurves

public java.util.List<ElutionCurve> getParentCurves()

Specified by:

getParentCurves in class ElutionCurveStrategy

setParentCurves

public void setParentCurves(java.util.List<ElutionCurve> pc)

Specified by:

setParentCurves in class ElutionCurveStrategy

getDaughterCurves

public java.util.List<ElutionCurve> getDaughterCurves()

Specified by:

getDaughterCurves in class ElutionCurveStrategy

setDaughterCurves

public void setDaughterCurves(java.util.List<ElutionCurve> dc)

Specified by:

setDaughterCurves in class ElutionCurveStrategy

getNoiseSearchWindowWidth

public int getNoiseSearchWindowWidth()

Specified by:

getNoiseSearchWindowWidth in class ElutionCurveStrategy

setNoiseSearchWindowWidth

public void setNoiseSearchWindowWidth(int noiseSearchWindowWidth)

Specified by:

setNoiseSearchWindowWidth in class ElutionCurveStrategy

getMinSignal

public double getMinSignal()

setMinSignal

public void setMinSignal(double minSignal)

getMinPointsInACurve

public int getMinPointsInACurve()

setMinPointsInACurve

public void setMinPointsInACurve(int minPointsInACurve)

getNoisePctOfHighestPeak

public double getNoisePctOfHighestPeak()

setNoisePctOfHighestPeak

public void setNoisePctOfHighestPeak(double noisePctOfHighestPeak)

noiseLevel

public double noiseLevel(PlotDataSupplier pds)

Specified by:

noiseLevel in class ElutionCurveStrategy

highestPeak

public double highestPeak(PlotDataSupplier pds)

Specified by:

highestPeak in class ElutionCurveStrategy

meanWindow

public double meanWindow(java.util.ArrayList<org.jfree.data.xy.XYDataItem> data,
                         int startAt)

isATeePee

public boolean isATeePee(java.util.ArrayList<org.jfree.data.xy.XYDataItem> data,
                         int curpoint)

calculateElutionCurves

public java.util.List<ElutionCurve> calculateElutionCurves(PlotDataSupplier pds)

calculateParentElutionCurves

public java.util.List<ElutionCurve> calculateParentElutionCurves(PlotDataSupplier pds)

Specified by:

calculateParentElutionCurves in class ElutionCurveStrategy

calculateDaughterElutionCurves

public java.util.List<ElutionCurve> calculateDaughterElutionCurves(PlotDataSupplier pds)

Specified by:

calculateDaughterElutionCurves in class ElutionCurveStrategy

bestParentCurve

public ElutionCurve bestParentCurve(double noiseFloor,
                                    PlotDataSupplier pds)

maxAUC

public ElutionCurve maxAUC(java.util.List<ElutionCurve> curves)

calculateBestCurves

public void calculateBestCurves()

Specified by:

calculateBestCurves in class ElutionCurveStrategy

calculateAUC

public void calculateAUC(ElutionCurve ec)

Specified by:

calculateAUC in class ElutionCurveStrategy