Package 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 Description
    TargetDecoyResults()
    Constructor.

  • Method Summary

    Modifier and Type Method 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 Details

  • Method Details

    • 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