eu.isas.peptideshaker.scoring.targetdecoy

Class TargetDecoySeries

java.lang.Object

eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries

public class TargetDecoySeries
extends Object

This class will contain the PEP, FDR and FNR values of a target decoy map directly available for plotting.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
TargetDecoySeries(HashMap<Double,TargetDecoyPoint> hitMap) Constructor.

Method Summary

Modifier and Type	Method and Description
double[]	getBenefit() Returns the benefit series.
double[]	getConfidence() Returns the confidence series.
double[]	getConfidenceLog() Returns the confidence log series.
void	getConfidenceResults(TargetDecoyResults targetDecoyResults) Completes the results at the desired confidence threshold.
double[]	getFDR() Returns the FDR series.
void	getFDRResults(TargetDecoyResults targetDecoyResults) Completes the results at the desired FDR threshold.
double[]	getFNR() Returns the probabilistic FNR series.
void	getFNRResults(TargetDecoyResults targetDecoyResults) Completes the results at the desired FNR threshold.
double[]	getnDecoy() Returns the decoy series of the target decoy histogram.
double[]	getnTarget() Returns the target series of the target decoy histogram.
double[]	getPEP() Returns the score series.
double[]	getScores() Returns the score series.
double[]	getScoresLog() Returns the log score series.
double[]	getTdBins() Returns the target decoy bins to use for the histogram.

Methods inherited from class java.lang.Object

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

Constructor Detail

TargetDecoySeries

public TargetDecoySeries(HashMap<Double,TargetDecoyPoint> hitMap)

Constructor.

Parameters:

hitMap - a map as present in target decoy maps

Method Detail

getFDRResults

public void getFDRResults(TargetDecoyResults targetDecoyResults)

Completes the results at the desired FDR threshold.

Parameters:

targetDecoyResults - the results containing the threshold

getConfidenceResults

public void getConfidenceResults(TargetDecoyResults targetDecoyResults)

Completes the results at the desired confidence threshold.

Parameters:

targetDecoyResults - the results containing the threshold

getFNRResults

public void getFNRResults(TargetDecoyResults targetDecoyResults)

Completes the results at the desired FNR threshold.

Parameters:

targetDecoyResults - the results containing the threshold

getTdBins

public double[] getTdBins()

Returns the target decoy bins to use for the histogram.

Returns:

the target decoy bins to use for the histogram

getnTarget

public double[] getnTarget()

Returns the target series of the target decoy histogram.

Returns:

the target series of the target decoy histogram

getnDecoy

public double[] getnDecoy()

Returns the decoy series of the target decoy histogram.

Returns:

the decoy series of the target decoy histogram

getFDR

public double[] getFDR()

Returns the FDR series.

Returns:

the FDR series

getConfidence

public double[] getConfidence()

Returns the confidence series.

Returns:

the confidence series

getConfidenceLog

public double[] getConfidenceLog()

Returns the confidence log series.

Returns:

the confidence log series

getBenefit

public double[] getBenefit()

Returns the benefit series.

Returns:

the benefit series

getFNR

public double[] getFNR()

Returns the probabilistic FNR series.

Returns:

the probabilistic FNR series

getScores

public double[] getScores()

Returns the score series.

Returns:

the score series

getScoresLog

public double[] getScoresLog()

Returns the log score series.

Returns:

the log score series

getPEP

public double[] getPEP()

Returns the score series.

Returns:

the score series