org.expasy.mzjava.stats.statscores

Class ScoreStatistics

java.lang.Object

org.expasy.mzjava.stats.statscores.ScoreStatistics

Direct Known Subclasses:

FirstRankScoreStatistics, FitDecoyScoreStatistics

public abstract class ScoreStatistics
extends Object

Version:

0.0

Author:

Markus Muller, Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ScoreStatistics.SortAction

Field Summary

Fields

Modifier and Type	Field and Description
protected float[]	decoyScores
protected float[]	fdrValues
protected float[]	qValues
protected float[]	targetScores

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ScoreStatistics()
	ScoreStatistics(double[] targetScores, double[] decoyScores)
	ScoreStatistics(double[] targetScores, double[] decoyScores, ScoreStatistics.SortAction sortAction)
	ScoreStatistics(float[] targetScores, float[] decoyScores)
	ScoreStatistics(float[] targetScores, float[] decoyScores, ScoreStatistics.SortAction sortAction)
	ScoreStatistics(gnu.trove.list.TDoubleList targetScores, gnu.trove.list.TDoubleList decoyScores)
	ScoreStatistics(gnu.trove.list.TDoubleList targetScores, gnu.trove.list.TDoubleList decoyScores, ScoreStatistics.SortAction sortAction)
	ScoreStatistics(gnu.trove.list.TFloatList targetScores, gnu.trove.list.TFloatList decoyScores)
	ScoreStatistics(gnu.trove.list.TFloatList targetScores, gnu.trove.list.TFloatList decoyScores, ScoreStatistics.SortAction sortAction)

Method Summary

Methods

Modifier and Type	Method and Description
protected abstract void	calculateFDR()
protected void	calculateQValue()
gnu.trove.list.TFloatList	getDecoyScores()
int	getNrDecoyScores(float score)
int	getNrTargetScores(float score)
float	getQValue(float score)
float	getScoreForQValue(float qValue)
gnu.trove.list.TFloatList	getTargetScores()

Methods inherited from class java.lang.Object

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

Field Detail

targetScores

protected float[] targetScores

decoyScores

protected float[] decoyScores

fdrValues

protected float[] fdrValues

qValues

protected float[] qValues

Constructor Detail

ScoreStatistics

protected ScoreStatistics()

ScoreStatistics

public ScoreStatistics(float[] targetScores,
               float[] decoyScores)

ScoreStatistics

public ScoreStatistics(float[] targetScores,
               float[] decoyScores,
               ScoreStatistics.SortAction sortAction)

ScoreStatistics

public ScoreStatistics(double[] targetScores,
               double[] decoyScores)

ScoreStatistics

public ScoreStatistics(double[] targetScores,
               double[] decoyScores,
               ScoreStatistics.SortAction sortAction)

ScoreStatistics

public ScoreStatistics(gnu.trove.list.TFloatList targetScores,
               gnu.trove.list.TFloatList decoyScores)

ScoreStatistics

public ScoreStatistics(gnu.trove.list.TFloatList targetScores,
               gnu.trove.list.TFloatList decoyScores,
               ScoreStatistics.SortAction sortAction)

ScoreStatistics

public ScoreStatistics(gnu.trove.list.TDoubleList targetScores,
               gnu.trove.list.TDoubleList decoyScores)

ScoreStatistics

public ScoreStatistics(gnu.trove.list.TDoubleList targetScores,
               gnu.trove.list.TDoubleList decoyScores,
               ScoreStatistics.SortAction sortAction)

Method Detail

getScoreForQValue

public float getScoreForQValue(float qValue)

getQValue

public float getQValue(float score)

calculateQValue

protected void calculateQValue()

getNrTargetScores

public int getNrTargetScores(float score)

getNrDecoyScores

public int getNrDecoyScores(float score)

getTargetScores

public gnu.trove.list.TFloatList getTargetScores()

getDecoyScores

public gnu.trove.list.TFloatList getDecoyScores()

calculateFDR

protected abstract void calculateFDR()