com.compomics.util.preferences
Class ProcessingPreferences

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

public class ProcessingPreferences
extends Object
implements Serializable

This class groups the user preferences for the initial PeptideShaker processing.

Author:
Marc Vaudel
See Also:
Serialized Form

Constructor Summary
ProcessingPreferences()
          Constructor with default settings.
 
Method Summary
 void estimateAScore(boolean shouldEstimateAScore)
          Deprecated. use the PTM scoring preferences instead
 double getPeptideFDR()
          Returns the initial peptide FDR.
 Double getProteinConfidenceMwPlots()
          Returns the minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab.
 double getProteinFDR()
          Returns the initial protein FDR.
 double getPsmFDR()
          Returns the initial PSM FDR.
 boolean isAScoreCalculated()
          Deprecated. use the PTM scoring preferences instead
 void setPeptideFDR(double peptideFDR)
          Sets the initial peptide FDR.
 void setProteinConfidenceMwPlots(Double proteinConfidenceMwPlots)
          Sets the minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab.
 void setProteinFDR(double proteinFDR)
          Sets the initial protein FDR.
 void setPsmFDR(double psmFDR)
          Sets the initial PSM FDR.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ProcessingPreferences

public ProcessingPreferences()
Constructor with default settings.

Method Detail

isAScoreCalculated

public boolean isAScoreCalculated()
Deprecated. use the PTM scoring preferences instead

Indicates whether the A-score should be calculated.

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

estimateAScore

public void estimateAScore(boolean shouldEstimateAScore)
Deprecated. use the PTM scoring preferences instead

Sets whether the A-score should be calculated.

Parameters:
shouldEstimateAScore - whether the A-score should be calculated

getPeptideFDR

public double getPeptideFDR()
Returns the initial peptide FDR.

Returns:
the initial peptide FDR

setPeptideFDR

public void setPeptideFDR(double peptideFDR)
Sets the initial peptide FDR.

Parameters:
peptideFDR - the initial peptide FDR

getProteinFDR

public double getProteinFDR()
Returns the initial protein FDR.

Returns:
the initial protein FDR

setProteinFDR

public void setProteinFDR(double proteinFDR)
Sets the initial protein FDR.

Parameters:
proteinFDR - the initial protein FDR

getPsmFDR

public double getPsmFDR()
Returns the initial PSM FDR.

Returns:
the initial PSM FDR

setPsmFDR

public void setPsmFDR(double psmFDR)
Sets the initial PSM FDR.

Parameters:
psmFDR - the initial PSM FDR

getProteinConfidenceMwPlots

public Double getProteinConfidenceMwPlots()
Returns the minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab.

Returns:
the minimum confidence

setProteinConfidenceMwPlots

public void setProteinConfidenceMwPlots(Double proteinConfidenceMwPlots)
Sets the minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab.

Parameters:
proteinConfidenceMwPlots - minimum confidence


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