com.compomics.util.preferences
Class PTMScoringPreferences

java.lang.Object
  extended by com.compomics.util.preferences.PTMScoringPreferences
All Implemented Interfaces:
Serializable

public class PTMScoringPreferences
extends Object
implements Serializable

This class contains the PTM scoring preferences.

Author:
Marc Vaudel
See Also:
Serialized Form

Constructor Summary
PTMScoringPreferences()
          Constructor.
 
Method Summary
 boolean aScoreCalculation()
          Returns a boolean indicating whether the A-score should be calculated.
 double getFlrThreshold()
          Returns the FLR threshold.
 boolean isaScoreNeutralLosses()
          Indicates whether the A-score calculation should take neutral losses into account.
 void setaScoreCalculation(boolean aScoreCalculation)
          Sets whether the A-score should be calculated.
 void setaScoreNeutralLosses(boolean aScoreNeutralLosses)
          Sets whether the A-score calculation should take neutral losses into account.
 void setFlrThreshold(double flr)
          Sets the FLR threshold.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PTMScoringPreferences

public PTMScoringPreferences()
Constructor.

Method Detail

aScoreCalculation

public boolean aScoreCalculation()
Returns a boolean indicating whether the A-score should be calculated.

Returns:
a boolean indicating whether the A-score should be calculated

setaScoreCalculation

public void setaScoreCalculation(boolean aScoreCalculation)
Sets whether the A-score should be calculated.

Parameters:
aScoreCalculation - a boolean indicating whether the A-score should be calculated

isaScoreNeutralLosses

public boolean isaScoreNeutralLosses()
Indicates whether the A-score calculation should take neutral losses into account.

Returns:
a boolean indicating whether the A-score calculation should take neutral losses into account

setaScoreNeutralLosses

public void setaScoreNeutralLosses(boolean aScoreNeutralLosses)
Sets whether the A-score calculation should take neutral losses into account.

Parameters:
aScoreNeutralLosses - a boolean indicating whether the A-score calculation should take neutral losses into account

getFlrThreshold

public double getFlrThreshold()
Returns the FLR threshold.

Returns:
the FLR threshold

setFlrThreshold

public void setFlrThreshold(double flr)
Sets the FLR threshold.

Parameters:
flr - the FLR threshold


Copyright © 2013. All Rights Reserved.