public class ProcessingPreferences extends Object implements Serializable
Constructor and Description |
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ProcessingPreferences()
Constructor with default settings.
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Modifier and Type | Method and Description |
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void |
estimateAScore(boolean shouldEstimateAScore)
Deprecated.
use the PTM scoring preferences instead
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int |
getnThreads()
Returns the number of threads to use.
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double |
getPeptideFDR()
Deprecated.
use the IdValidationPreferences instead
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Double |
getProteinConfidenceMwPlots()
Deprecated.
use the IdValidationPreferences instead
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double |
getProteinFDR()
Deprecated.
use the IdValidationPreferences instead
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double |
getPsmFDR()
Deprecated.
use the IdValidationPreferences instead
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ArrayList<Integer> |
getScores(int advocateIndex)
Deprecated.
use the IdValidationPreferences instead
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void |
initializeAlgorithmScores()
Deprecated.
use the IdValidationPreferences instead
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boolean |
isAScoreCalculated()
Deprecated.
use the PTM scoring preferences instead
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boolean |
isScoringNeeded(ArrayList<Integer> advocates)
Deprecated.
use the IdValidationPreferences instead
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boolean |
isScoringNeeded(int advocate)
Deprecated.
use the IdValidationPreferences instead
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boolean |
isTargetDecoyNeededForPsmScoring(ArrayList<Integer> advocates)
Deprecated.
use the IdValidationPreferences instead
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void |
setnThreads(int nThreads)
Sets the number of threads to use.
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void |
setPeptideFDR(double peptideFDR)
Deprecated.
use the IdValidationPreferences instead
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void |
setProteinConfidenceMwPlots(Double proteinConfidenceMwPlots)
Deprecated.
use the IdValidationPreferences instead
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void |
setProteinFDR(double proteinFDR)
Deprecated.
use the IdValidationPreferences instead
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void |
setPsmFDR(double psmFDR)
Deprecated.
use the IdValidationPreferences instead
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void |
setScoresForAlgorithm(int advocateIndex,
ArrayList<Integer> scores)
Deprecated.
use the IdValidationPreferences instead
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public ProcessingPreferences()
public boolean isAScoreCalculated()
public void estimateAScore(boolean shouldEstimateAScore)
shouldEstimateAScore
- whether the A-score should be calculatedpublic double getPeptideFDR()
public void setPeptideFDR(double peptideFDR)
peptideFDR
- the initial peptide FDRpublic double getProteinFDR()
public void setProteinFDR(double proteinFDR)
proteinFDR
- the initial protein FDRpublic double getPsmFDR()
public void setPsmFDR(double psmFDR)
psmFDR
- the initial PSM FDRpublic Double getProteinConfidenceMwPlots()
public void setProteinConfidenceMwPlots(Double proteinConfidenceMwPlots)
proteinConfidenceMwPlots
- minimum confidencepublic void initializeAlgorithmScores()
public void setScoresForAlgorithm(int advocateIndex, ArrayList<Integer> scores)
advocateIndex
- the index of the advocatescores
- the scorespublic ArrayList<Integer> getScores(int advocateIndex)
advocateIndex
- the index of the advocatepublic boolean isScoringNeeded(int advocate)
advocate
- the index of the advocate of interestpublic boolean isScoringNeeded(ArrayList<Integer> advocates)
advocates
- the advocates of interestpublic boolean isTargetDecoyNeededForPsmScoring(ArrayList<Integer> advocates)
advocates
- the advocates of interestpublic int getnThreads()
public void setnThreads(int nThreads)
nThreads
- the number of threads to useCopyright © 2014. All rights reserved.