Class PsmScoringParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.PsmScoringParameters
- All Implemented Interfaces:
Serializable
public class PsmScoringParameters extends ExperimentObject
Generic class for peptide spectrum match scoring.
- Author:
- Marc Vaudel
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description PsmScoringParameters()
Constructor. -
Method Summary
Modifier and Type Method Description void
addScore(Integer advocateId, Integer scoreId)
Adds a score for a given algorithm to the scoring preferences.void
clearAllScores()
Clears all scores.void
clearScores(Integer advocateId)
Clears the score for the given algorithm.boolean
equals(PsmScoringParameters otherPsmScoringPreferences)
Returns true if the objects have identical settings.Set<Integer>
getAdvocates()
Returns the advocates with a specific scoring.int
getDecoysInFirstBin()
Returns the minimal number of decoys to include in a bin to set the bin size of the score histogram.HashSet<Integer>
getDefaultScores()
Returns the default scores.HashSet<Integer>
getScoreForAlgorithm(int advocateId)
Returns the scores set for a given algorithm.String
getShortDescription()
Returns a short description of the parameters.boolean
isScoringNeeded(int advocate)
Indicates whether a score computation is needed for the given advocate.boolean
isScoringNeeded(ArrayList<Integer> advocates)
Indicates whether a score computation is needed for the given advocates.boolean
isTargetDecoyNeededForPsmScoring(ArrayList<Integer> advocates)
Indicates whether target decoy databases are needed for PSM scoring.void
setDecoysInFirstBin(Integer decoysInFirstBin)
Sets the minimal number of decoys to include in a bin to set the bin size of the score histogram.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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PsmScoringParameters
public PsmScoringParameters()Constructor.
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Method Details
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addScore
Adds a score for a given algorithm to the scoring preferences.- Parameters:
advocateId
- the index of the algorithmscoreId
- the index of the score
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clearScores
Clears the score for the given algorithm.- Parameters:
advocateId
- the score for the given algorithm
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clearAllScores
public void clearAllScores()Clears all scores. -
getScoreForAlgorithm
Returns the scores set for a given algorithm.- Parameters:
advocateId
- the index of the algorithm- Returns:
- the index of the score
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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
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getAdvocates
Returns the advocates with a specific scoring.- Returns:
- the advocates with a specific scoring
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isScoringNeeded
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
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isTargetDecoyNeededForPsmScoring
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
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getShortDescription
Returns a short description of the parameters.- Returns:
- a short description of the parameters
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equals
Returns true if the objects have identical settings.- Parameters:
otherPsmScoringPreferences
- the PsmScoringPreferences to compare to- Returns:
- true if the objects have identical settings
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getDefaultScores
Returns the default scores.- Returns:
- the default scores
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getDecoysInFirstBin
public int getDecoysInFirstBin()Returns the minimal number of decoys to include in a bin to set the bin size of the score histogram.- Returns:
- the minimal number of decoys to include in a bin to set the bin size of the score histogram
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setDecoysInFirstBin
Sets the minimal number of decoys to include in a bin to set the bin size of the score histogram.- Parameters:
decoysInFirstBin
- the minimal number of decoys to include in a bin to set the bin size of the score histogram
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