Class ModificationLocalizationParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
- All Implemented Interfaces:
Serializable
public class ModificationLocalizationParameters extends ExperimentObject
This class contains the modification localization preferences.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description ModificationLocalizationParameters()
Constructor. -
Method Summary
Modifier and Type Method Description boolean
equals(ModificationLocalizationParameters otherParameters)
Returns true if the objects have identical settings.boolean
getAlignNonConfidentModifications()
Indicates whether the non confidently localized modifications should be aligned on the confident sites.double
getDScoreThreshold()
Returns the D-score threshold.double
getProbabilisticScoreThreshold()
Returns the probabilistic score threshold (inclusive).ModificationLocalizationScore
getSelectedProbabilisticScore()
Returns the selected probabilistic score.SequenceMatchingParameters
getSequenceMatchingParameters()
Returns the sequence matching preferences to use when mapping modifications on amino acid sequences.String
getShortDescription()
Returns a short description of the parameters.boolean
isProbabilisticScoreCalculation()
Indicates whether a probabilistic modification score is required.boolean
isProbabilisticScoreNeutralLosses()
Indicates whether the neutral losses shall be taken into account for spectrum annotation when calculating the probabilistic score.void
setAlignNonConfidentModifications(boolean alignNonConfidentModifications)
Sets whether the non confidently localized modifications should be aligned on the confident sites.void
setDScoreThreshold(double dScoreThreshold)
Sets the D-score threshold.void
setProbabilisticScoreCalculation(boolean probabilisticScoreCalculation)
Sets whether a probabilistic modification score is required.void
setProbabilisticScoreNeutralLosses(boolean probabilisticScoreNeutralLosses)
Sets whether the neutral losses shall be taken into account for spectrum annotation when calculating the probabilistic score.void
setProbabilisticScoreThreshold(double probabilisticScoreThreshold)
Sets the probabilistic score threshold (inclusive).void
setSelectedProbabilisticScore(ModificationLocalizationScore selectedProbabilisticScore)
Sets the selected probabilistic score.void
setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)
Sets the sequence matching preferences to use when mapping modifications on amino acid sequences.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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ModificationLocalizationParameters
public ModificationLocalizationParameters()Constructor.
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Method Details
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isProbabilisticScoreCalculation
public boolean isProbabilisticScoreCalculation()Indicates whether a probabilistic modification score is required.- Returns:
- a boolean indicating whether a probabilistic modification score is required
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setProbabilisticScoreCalculation
public void setProbabilisticScoreCalculation(boolean probabilisticScoreCalculation)Sets whether a probabilistic modification score is required.- Parameters:
probabilisticScoreCalculation
- a boolean indicating whether a probabilistic modification score is required
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getSelectedProbabilisticScore
Returns the selected probabilistic score.- Returns:
- the selected probabilistic score
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setSelectedProbabilisticScore
public void setSelectedProbabilisticScore(ModificationLocalizationScore selectedProbabilisticScore)Sets the selected probabilistic score.- Parameters:
selectedProbabilisticScore
- the selected probabilistic score
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getProbabilisticScoreThreshold
public double getProbabilisticScoreThreshold()Returns the probabilistic score threshold (inclusive).- Returns:
- The probabilistic score threshold (inclusive).
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setProbabilisticScoreThreshold
public void setProbabilisticScoreThreshold(double probabilisticScoreThreshold)Sets the probabilistic score threshold (inclusive).- Parameters:
probabilisticScoreThreshold
- The probabilistic score threshold (inclusive).
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getDScoreThreshold
public double getDScoreThreshold()Returns the D-score threshold.- Returns:
- the D-score threshold
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setDScoreThreshold
public void setDScoreThreshold(double dScoreThreshold)Sets the D-score threshold.- Parameters:
dScoreThreshold
- the D-score threshold
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isProbabilisticScoreNeutralLosses
public boolean isProbabilisticScoreNeutralLosses()Indicates whether the neutral losses shall be taken into account for spectrum annotation when calculating the probabilistic score.- Returns:
- a boolean indicating whether the neutral losses shall be taken into account for spectrum annotation when calculating the probabilistic score
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setProbabilisticScoreNeutralLosses
public void setProbabilisticScoreNeutralLosses(boolean probabilisticScoreNeutralLosses)Sets whether the neutral losses shall be taken into account for spectrum annotation when calculating the probabilistic score.- Parameters:
probabilisticScoreNeutralLosses
- indicates whether the neutral losses shall be taken into account for spectrum annotation when calculating the probabilistic score
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getSequenceMatchingParameters
Returns the sequence matching preferences to use when mapping modifications on amino acid sequences.- Returns:
- the sequence matching preferences to use when mapping modifications on amino acid sequences
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setSequenceMatchingParameters
Sets the sequence matching preferences to use when mapping modifications on amino acid sequences.- Parameters:
sequenceMatchingParameters
- the sequence matching preferences to use when mapping modifications on amino acid sequences
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getAlignNonConfidentModifications
public boolean getAlignNonConfidentModifications()Indicates whether the non confidently localized modifications should be aligned on the confident sites.- Returns:
- boolean indicating whether the non confidently localized modifications should be aligned on the confident sites
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setAlignNonConfidentModifications
public void setAlignNonConfidentModifications(boolean alignNonConfidentModifications)Sets whether the non confidently localized modifications should be aligned on the confident sites.- Parameters:
alignNonConfidentModifications
- a boolean indicating whether the non confidently localized modifications should be aligned on the confident sites
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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:
otherParameters
- the parameters to compare to- Returns:
- true if the objects have identical settings
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