TargetDecoyMap (PeptideShaker 2.2.2 API)

java.lang.Object
- com.compomics.util.experiment.personalization.ExperimentObject
- - eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

All Implemented Interfaces:

Serializable
```
public class TargetDecoyMap
extends com.compomics.util.experiment.personalization.ExperimentObject
```
This map contains the information of a target/decoy strategy.

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

TargetDecoyMap()
Constructor.

TargetDecoyMap(Integer minDecoysInBin)
Constructor.

Constructors
Constructor and Description
`TargetDecoyMap()` Constructor.
`TargetDecoyMap(Integer minDecoysInBin)` Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAll(TargetDecoyMap anOtherMap)` Adds all the points from another target/decoy map.
`void`	`cleanUp()` Removes empty points and clears dependent metrics if needed.
`TargetDecoyPoint`	`createTargetDecoyPoint(double score)` Creates the target decoy point of the map at the given score if no other thread has done it before.
`void`	`estimateProbabilities(com.compomics.util.waiting.WaitingHandler waitingHandler)` Estimates the posterior error probabilities in this map.
`int`	`getMapSize()` Returns the size of the map.
`double`	`getMinFdr()` Returns the minimal FDR which can be achieved in this dataset.
`int`	`getNDecoy(double score)` Returns the number of decoy hits found at the given score.
`int`	`getnMax()` Returns the Nmax metric.
`int`	`getNTarget(double score)` Returns the number of target hits found at the given score.
`Integer`	`getnTargetOnly()` Returns the number of target hits before the first decoy hit.
`double`	`getProbability(double score)` Returns the posterior error probability estimated at the given score.
`double`	`getResolution()` Returns the minimal detectable PEP variation in percent.
`ArrayList<Double>`	`getScores()` Returns the sorted scores implemented in this map.
`TargetDecoyResults`	`getTargetDecoyResults()` Returns the current target decoy results.
`TargetDecoySeries`	`getTargetDecoySeries()` Returns the target decoy series.
`int`	`getWindowSize()` Returns the window size used for pep estimation.
`void`	`put(double score, boolean isDecoy)` Puts a new point in the target/decoy map at the given score.
`void`	`remove(double score, boolean isDecoy)` Removes a point in the target/decoy map at the given score.
`void`	`setWindowSize(int windowSize)` Sets the window size used for pep estimation.
`boolean`	`suspiciousInput(double initialFDR)` Returns a boolean indicating if a suspicious input was detected.

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
  - TargetDecoyMap
```
public TargetDecoyMap()
```
    Constructor.
  - TargetDecoyMap
```
public TargetDecoyMap(Integer minDecoysInBin)
```
    Constructor.
    
    Parameters:
    
    minDecoysInBin - the number of decoy matches to include in the first bin to set the bin size
- Method Detail
  - getProbability
```
public double getProbability(double score)
```
    Returns the posterior error probability estimated at the given score.
    
    Parameters:
    
    score - the given score
    
    Returns:
    
    the estimated posterior error probability
  - getNTarget
```
public int getNTarget(double score)
```
    Returns the number of target hits found at the given score.
    
    Parameters:
    
    score - the given score
    
    Returns:
    
    the number of target hits found at the given score
  - getNDecoy
```
public int getNDecoy(double score)
```
    Returns the number of decoy hits found at the given score.
    
    Parameters:
    
    score - the given score
    
    Returns:
    
    the number of decoy hits found at the given score
  - put
```
public void put(double score,
                boolean isDecoy)
```
    Puts a new point in the target/decoy map at the given score.
    
    Parameters:
    
    score - The given score
    
    isDecoy - boolean indicating whether the hit is decoy
  - createTargetDecoyPoint
```
public TargetDecoyPoint createTargetDecoyPoint(double score)
```
    Creates the target decoy point of the map at the given score if no other thread has done it before.
    
    Parameters:
    
    score - the score of interest
    
    Returns:
    
    the target decoy point of the map at the given score
  - remove
```
public void remove(double score,
                   boolean isDecoy)
```
    Removes a point in the target/decoy map at the given score. Note: it is necessary to run cleanUp() afterwards to clean up the map.
    
    Parameters:
    
    score - the given score
    
    isDecoy - boolean indicating whether the hit is decoy
  - cleanUp
```
public void cleanUp()
```
    Removes empty points and clears dependent metrics if needed.
  - estimateProbabilities
```
public void estimateProbabilities(com.compomics.util.waiting.WaitingHandler waitingHandler)
```
    Estimates the posterior error probabilities in this map.
    
    Parameters:
    
    waitingHandler - the handler displaying feedback to the user
  - getnMax
```
public int getnMax()
```
    Returns the Nmax metric.
    
    Returns:
    
    the Nmax metric
  - getMinFdr
```
public double getMinFdr()
```
    Returns the minimal FDR which can be achieved in this dataset.
    
    Returns:
    
    the minimal FDR which can be achieved in this dataset
  - getResolution
```
public double getResolution()
```
    Returns the minimal detectable PEP variation in percent.
    
    Returns:
    
    the minimal detectable PEP variation in percent
  - getnTargetOnly
```
public Integer getnTargetOnly()
```
    Returns the number of target hits before the first decoy hit.
    
    Returns:
    
    the number of target hits before the first decoy hit
  - getScores
```
public ArrayList<Double> getScores()
```
    Returns the sorted scores implemented in this map.
    
    Returns:
    
    the sorted scores implemented in this map.
  - addAll
```
public void addAll(TargetDecoyMap anOtherMap)
```
    Adds all the points from another target/decoy map.
    
    Parameters:
    
    anOtherMap - another target/decoy map
  - suspiciousInput
```
public boolean suspiciousInput(double initialFDR)
```
    Returns a boolean indicating if a suspicious input was detected.
    
    Parameters:
    
    initialFDR - the minimal FDR requested for a group
    
    Returns:
    
    a boolean indicating if a suspicious input was detected
  - getTargetDecoyResults
```
public TargetDecoyResults getTargetDecoyResults()
```
    Returns the current target decoy results.
    
    Returns:
    
    the current target decoy results
  - getTargetDecoySeries
```
public TargetDecoySeries getTargetDecoySeries()
```
    Returns the target decoy series.
    
    Returns:
    
    the target decoy series
  - getWindowSize
```
public int getWindowSize()
```
    Returns the window size used for pep estimation.
    
    Returns:
    
    the window size used for pep estimation
  - setWindowSize
```
public void setWindowSize(int windowSize)
```
    Sets the window size used for pep estimation.
    
    Parameters:
    
    windowSize - the window size used for pep estimation
  - getMapSize
```
public int getMapSize()
```
    Returns the size of the map.
    
    Returns:
    
    the size of the map

Class TargetDecoyMap

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Constructor Detail

TargetDecoyMap

TargetDecoyMap

Method Detail

getProbability

getNTarget

getNDecoy

put

createTargetDecoyPoint

remove

cleanUp

estimateProbabilities

getnMax

getMinFdr

getResolution

getnTargetOnly

getScores

addAll

suspiciousInput

getTargetDecoyResults

getTargetDecoySeries

getWindowSize

setWindowSize

getMapSize