public class PsmScoringPreferences extends Object implements Serializable
Constructor and Description |
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PsmScoringPreferences()
Constructor.
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Modifier and Type | Method and Description |
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void |
addScore(Integer advocateId,
Integer scoreId)
Adds a score for a given algorithm to the scoring preferences.
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void |
clearAllScores()
Clears all scores.
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void |
clearScores(Integer advocateId)
Clears the score for the given algorithm.
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boolean |
equals(PsmScoringPreferences otherPsmScoringPreferences)
Returns true if the objects have identical settings.
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Set<Integer> |
getAdvocates()
Returns the advocates with a specific scoring.
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Integer |
getDecoysInFirstBin()
Returns the minimal number of decoys to include in a bin to set the bin
size of the score histogram.
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HashSet<Integer> |
getDefaultScores()
Returns the default scores.
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HashSet<Integer> |
getScoreForAlgorithm(Integer advocateId)
Returns the scores set for a given algorithm.
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String |
getShortDescription()
Returns a short description of the parameters.
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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 |
setDecoysInFirstBin(Integer decoysInFirstBin)
Sets the minimal number of decoys to include in a bin to set the bin size
of the score histogram.
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public void addScore(Integer advocateId, Integer scoreId)
advocateId
- the index of the algorithmscoreId
- the index of the scorepublic void clearScores(Integer advocateId)
advocateId
- the score for the given algorithmpublic void clearAllScores()
public HashSet<Integer> getScoreForAlgorithm(Integer advocateId)
advocateId
- the index of the algorithmpublic boolean isScoringNeeded(int advocate)
advocate
- the index of the advocate of interestpublic Set<Integer> getAdvocates()
public boolean isScoringNeeded(ArrayList<Integer> advocates)
advocates
- the advocates of interestpublic boolean isTargetDecoyNeededForPsmScoring(ArrayList<Integer> advocates)
advocates
- the advocates of interestpublic String getShortDescription()
public boolean equals(PsmScoringPreferences otherPsmScoringPreferences)
otherPsmScoringPreferences
- the PsmScoringPreferences to compare topublic HashSet<Integer> getDefaultScores()
public Integer getDecoysInFirstBin()
public void setDecoysInFirstBin(Integer decoysInFirstBin)
decoysInFirstBin
- the minimal number of decoys to include in a bin
to set the bin size of the score histogramCopyright © 2019. All rights reserved.