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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double |
getPeptideFDR()
Returns the initial peptide FDR.
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Double |
getProteinConfidenceMwPlots()
Returns the minimum confidence required for a protein to be included in
the average molecular weight analysis in the Fractions tab.
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double |
getProteinFDR()
Returns the initial protein FDR.
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double |
getPsmFDR()
Returns the initial PSM FDR.
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ArrayList<Integer> |
getScores(int advocateIndex)
Returns the scores used for a given advocate.
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void |
initializeAlgorithmScores()
Sets the default score selection for the implemented advocates.
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boolean |
isAScoreCalculated()
Deprecated.
use the PTM scoring preferences instead
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boolean |
isScoringNeeded(ArrayList<Integer> advocates)
Indicates whether a score computation is needed for the given advocates.
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boolean |
isScoringNeeded(int advocate)
Indicates whether a score computation is needed for the given advocate.
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boolean |
isTargetDecoyNeededForPsmScoring(ArrayList<Integer> advocates)
Indicates whether target decoy databases are needed for PSM scoring.
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void |
setPeptideFDR(double peptideFDR)
Sets the initial peptide FDR.
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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.
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void |
setProteinFDR(double proteinFDR)
Sets the initial protein FDR.
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void |
setPsmFDR(double psmFDR)
Sets the initial PSM FDR.
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void |
setScoresForAlgorithm(int advocateIndex,
ArrayList<Integer> scores)
Sets the scores to use for a given advocate.
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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 interestCopyright © 2014. All rights reserved.