com.compomics.util.preferences

Class ProcessingPreferences

java.lang.Object

com.compomics.util.preferences.ProcessingPreferences

All Implemented Interfaces:

java.io.Serializable

public class ProcessingPreferences
extends java.lang.Object
implements java.io.Serializable

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

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ProcessingPreferences() Constructor with default settings.

Method Summary

Methods

Modifier and Type	Method and Description
void	estimateAScore(boolean shouldEstimateAScore) Deprecated. use the PTM scoring preferences instead
double	getPeptideFDR() Returns the initial peptide FDR.
java.lang.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(java.lang.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 java.lang.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(java.lang.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