eu.isas.peptideshaker.scoring.targetdecoy

Class TargetDecoyResults

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults

All Implemented Interfaces:

Serializable

public class TargetDecoyResults
extends com.compomics.util.experiment.personalization.ExperimentObject
implements Serializable

This class will compile Target/decoy results of a certain target/decoy map according to user's validation criteria

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor and Description
TargetDecoyResults() Constructor.

Method Summary

Modifier and Type	Method and Description
double	getConfidenceLimit() Returns the confidence limit.
double	getFdrLimit() Returns the FDR limit.
double	getFnrLimit() Returns the FNR limit.
int	getInputType() Returns the type of input.
double	getLogScoreLimit() Returns the score limit obtained with the current validation settings.
double	getN() Returns the number of retained hits.
double	getnFP() Returns the estimated number of false positives.
double	getnTP() Returns the estimated number of retained True positives.
double	getnTPTotal() Returns the estimated total number of True positives.
double	getScoreLimit() Returns the score limit obtained with the current validation settings.
double	getUserInput() Returns the user input.
boolean	noValidated() Returns a boolean indicating that everything was validated.
void	setConfidenceLimit(double confidenceLimit) Sets the confidence limit.
void	setFdrLimit(double fdrLimit) Sets the FDR limit.
void	setFnrLimit(double fnrLimit) Sets the FNR limit.
void	setInputType(int inputType) Sets the type of input.
void	setn(double n) Sets the number of retained hits.
void	setnFP(double nFP) Sets the estimated number of false positives.
void	setNoValidated(boolean validateAll) Sets whether everything was validated.
void	setnTPTotal(double nTPTotal) Sets the estimated total number of True positives.
void	setScoreLimit(double scoreLimit) Sets the score limit obtained with the current validation settings.
void	setUserInput(double userInput) Sets the user input.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

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

Constructor Detail

TargetDecoyResults

public TargetDecoyResults()

Constructor.

Method Detail

getConfidenceLimit

public double getConfidenceLimit()

Returns the confidence limit.

Returns:

the confidence limit

setConfidenceLimit

public void setConfidenceLimit(double confidenceLimit)

Sets the confidence limit.

Parameters:

confidenceLimit - the confidence limit

getFdrLimit

public double getFdrLimit()

Returns the FDR limit.

Returns:

the FDR limit

setFdrLimit

public void setFdrLimit(double fdrLimit)

Sets the FDR limit.

Parameters:

fdrLimit - the FDR limit

getFnrLimit

public double getFnrLimit()

Returns the FNR limit.

Returns:

the FNR limit

setFnrLimit

public void setFnrLimit(double fnrLimit)

Sets the FNR limit.

Parameters:

fnrLimit - the FNR limit

getnFP

public double getnFP()

Returns the estimated number of false positives.

Returns:

the estimated number of false positives

setnFP

public void setnFP(double nFP)

Sets the estimated number of false positives.

Parameters:

nFP - the estimated number of false positives

getnTP

public double getnTP()

Returns the estimated number of retained True positives.

Returns:

the estimated number of retained True positives

setn

public void setn(double n)

Sets the number of retained hits.

Parameters:

n - the estimated number of retained True positives

getnTPTotal

public double getnTPTotal()

Returns the estimated total number of True positives.

Returns:

the estimated total number of True positives

setnTPTotal

public void setnTPTotal(double nTPTotal)

Sets the estimated total number of True positives.

Parameters:

nTPTotal - the estimated total number of True positives

getN

public double getN()

Returns the number of retained hits.

Returns:

the number of retained hits

getScoreLimit

public double getScoreLimit()

Returns the score limit obtained with the current validation settings.

Returns:

the score limit obtained with the current validation settings

getLogScoreLimit

public double getLogScoreLimit()

Returns the score limit obtained with the current validation settings.

Returns:

the score limit obtained with the current validation settings

setScoreLimit

public void setScoreLimit(double scoreLimit)

Sets the score limit obtained with the current validation settings.

Parameters:

scoreLimit - the score limit obtained with the current validation settings

noValidated

public boolean noValidated()

Returns a boolean indicating that everything was validated.

Returns:

a boolean indicating that everything was validated

setNoValidated

public void setNoValidated(boolean validateAll)

Sets whether everything was validated.

Parameters:

validateAll - a boolean indicating whether everything should be validated

getInputType

public int getInputType()

Returns the type of input. 0 > confidence 1 > FDR 2 > FNR.

Returns:

the type of input

setInputType

public void setInputType(int inputType)

Sets the type of input.

Parameters:

inputType - the input type

getUserInput

public double getUserInput()

Returns the user input.

Returns:

the user input

setUserInput

public void setUserInput(double userInput)

Sets the user input.

Parameters:

userInput - the user input