public class PTMScoringPreferences extends Object implements Serializable
Constructor and Description |
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PTMScoringPreferences()
Constructor.
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Modifier and Type | Method and Description |
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boolean |
aScoreCalculation()
Deprecated.
use isProbabilitsticScoreCalculation instead
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double |
getFlrThreshold()
Returns the FLR threshold.
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double |
getProbabilisticScoreThreshold()
Returns the probabilistic score threshold.
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PtmScore |
getSelectedProbabilisticScore()
Returns the selected probabilistic score.
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SequenceMatchingPreferences |
getSequenceMatchingPreferences()
Returns the sequence matching preferences to use when mapping PTMs on
amino acid sequences.
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boolean |
isaScoreNeutralLosses()
Deprecated.
use isProbabilisticScoreNeutralLosses instead
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boolean |
isEstimateFlr()
Indicates whether the threshold is FLR based.
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Boolean |
isProbabilisticScoreNeutralLosses()
Indicates whether the neutral losses shall be taken into account for
spectrum annotation when calculating the probabilistic score.
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Boolean |
isProbabilitsticScoreCalculation()
Indicates whether a probabilistic PTM score is required.
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void |
setaScoreCalculation(boolean aScoreCalculation)
Deprecated.
use setProbabilitsticScoreCalculation instead
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void |
setaScoreNeutralLosses(boolean aScoreNeutralLosses)
Deprecated.
use setProbabilisticScoreNeutralLosses instead
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void |
setEstimateFlr(boolean estimateFlr)
Sets whether the threshold is FLR based.
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void |
setFlrThreshold(double flr)
Sets the FLR threshold.
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void |
setProbabilisticScoreNeutralLosses(boolean probabilisticScoreNeutralLosses)
Sets whether the neutral losses shall be taken into account for spectrum
annotation when calculating the probabilistic score.
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void |
setProbabilisticScoreThreshold(double probabilisticScoreThreshold)
Sets the probabilistic score threshold.
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void |
setProbabilitsticScoreCalculation(boolean probabilitsticScoreCalculation)
Sets whether a probabilistic PTM score is required.
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void |
setSelectedProbabilisticScore(PtmScore selectedProbabilisticScore)
Sets the selected probabilistic score.
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void |
setSequenceMatchingPreferences(SequenceMatchingPreferences sequenceMatchingPreferences)
Sets the sequence matching preferences to use when mapping PTMs on amino
acid sequences.
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public Boolean isProbabilitsticScoreCalculation()
public void setProbabilitsticScoreCalculation(boolean probabilitsticScoreCalculation)
probabilitsticScoreCalculation
- a boolean indicating whether a
probabilistic PTM score is requiredpublic PtmScore getSelectedProbabilisticScore()
public void setSelectedProbabilisticScore(PtmScore selectedProbabilisticScore)
selectedProbabilisticScore
- the selected probabilistic scorepublic boolean isEstimateFlr()
public void setEstimateFlr(boolean estimateFlr)
estimateFlr
- indicates whether the threshold is FLR basedpublic double getProbabilisticScoreThreshold()
public void setProbabilisticScoreThreshold(double probabilisticScoreThreshold)
probabilisticScoreThreshold
- the probabilistic score thresholdpublic Boolean isProbabilisticScoreNeutralLosses()
public void setProbabilisticScoreNeutralLosses(boolean probabilisticScoreNeutralLosses)
probabilisticScoreNeutralLosses
- indicates whether the neutral
losses shall be taken into account for spectrum annotation when
calculating the probabilistic scorepublic SequenceMatchingPreferences getSequenceMatchingPreferences()
public void setSequenceMatchingPreferences(SequenceMatchingPreferences sequenceMatchingPreferences)
sequenceMatchingPreferences
- the sequence matching preferences to
use when mapping PTMs on amino acid sequencespublic boolean aScoreCalculation()
public void setaScoreCalculation(boolean aScoreCalculation)
aScoreCalculation
- a boolean indicating whether the A-score should
be calculatedpublic boolean isaScoreNeutralLosses()
public void setaScoreNeutralLosses(boolean aScoreNeutralLosses)
aScoreNeutralLosses
- a boolean indicating whether the A-score
calculation should take neutral losses into accountpublic double getFlrThreshold()
public void setFlrThreshold(double flr)
flr
- the FLR thresholdCopyright © 2015. All rights reserved.