com.compomics.util.preferences

Class ProcessingPreferences

java.lang.Object

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

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.
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.
ArrayList<Integer>	getScores(int advocateIndex) Returns the scores used for a given advocate.
void	initializeAlgorithmScores() Sets the default score selection for the implemented advocates.
boolean	isAScoreCalculated() Deprecated. use the PTM scoring preferences instead
boolean	isScoringNeeded(ArrayList<Integer> advocates) Indicates whether a score computation is needed for the given advocates.
boolean	isScoringNeeded(int advocate) Indicates whether a score computation is needed for the given advocate.
boolean	isTargetDecoyNeededForPsmScoring(ArrayList<Integer> advocates) Indicates whether target decoy databases are needed for PSM scoring.
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.
void	setScoresForAlgorithm(int advocateIndex, ArrayList<Integer> scores) Sets the scores to use for a given advocate.

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

initializeAlgorithmScores

public void initializeAlgorithmScores()

Sets the default score selection for the implemented advocates. Note: this silently erases any previous selection.

setScoresForAlgorithm

public void setScoresForAlgorithm(int advocateIndex,
                         ArrayList<Integer> scores)

Sets the scores to use for a given advocate.

Parameters:

advocateIndex - the index of the advocate

scores - the scores

getScores

public ArrayList<Integer> getScores(int advocateIndex)

Returns the scores used for a given advocate.

Parameters:

advocateIndex - the index of the advocate

Returns:

the scores used for a given advocate

isScoringNeeded

public boolean isScoringNeeded(int advocate)

Indicates whether a score computation is needed for the given advocate.

Parameters:

advocate - the index of the advocate of interest

Returns:

a boolean indicating whether a score computation is needed

isScoringNeeded

public boolean isScoringNeeded(ArrayList<Integer> advocates)

Indicates whether a score computation is needed for the given advocates.

Parameters:

advocates - the advocates of interest

Returns:

a boolean indicating whether a score computation is needed

isTargetDecoyNeededForPsmScoring

public boolean isTargetDecoyNeededForPsmScoring(ArrayList<Integer> advocates)

Indicates whether target decoy databases are needed for PSM scoring.

Parameters:

advocates - the advocates of interest

Returns:

a boolean indicating whether a score computation is needed