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
  • Constructor Details

  • Method Details

    • isProbabilisticScoreCalculation

      public boolean isProbabilisticScoreCalculation()
      Indicates whether a probabilistic modification score is required.
      Returns:
      a boolean indicating whether a probabilistic modification score is required
    • 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
    • getSelectedProbabilisticScore

      public ModificationLocalizationScore getSelectedProbabilisticScore()
      Returns the selected probabilistic score.
      Returns:
      the selected probabilistic score
    • setSelectedProbabilisticScore

      public void setSelectedProbabilisticScore​(ModificationLocalizationScore selectedProbabilisticScore)
      Sets the selected probabilistic score.
      Parameters:
      selectedProbabilisticScore - the selected probabilistic score
    • getProbabilisticScoreThreshold

      public double getProbabilisticScoreThreshold()
      Returns the probabilistic score threshold (inclusive).
      Returns:
      The probabilistic score threshold (inclusive).
    • setProbabilisticScoreThreshold

      public void setProbabilisticScoreThreshold​(double probabilisticScoreThreshold)
      Sets the probabilistic score threshold (inclusive).
      Parameters:
      probabilisticScoreThreshold - The probabilistic score threshold (inclusive).
    • getDScoreThreshold

      public double getDScoreThreshold()
      Returns the D-score threshold.
      Returns:
      the D-score threshold
    • setDScoreThreshold

      public void setDScoreThreshold​(double dScoreThreshold)
      Sets the D-score threshold.
      Parameters:
      dScoreThreshold - the D-score threshold
    • 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
    • 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
    • getSequenceMatchingParameters

      public SequenceMatchingParameters 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
    • setSequenceMatchingParameters

      public void setSequenceMatchingParameters​(SequenceMatchingParameters sequenceMatchingParameters)
      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
    • 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
    • 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
    • getShortDescription

      public String getShortDescription()
      Returns a short description of the parameters.
      Returns:
      a short description of the parameters
    • equals

      public boolean equals​(ModificationLocalizationParameters otherParameters)
      Returns true if the objects have identical settings.
      Parameters:
      otherParameters - the parameters to compare to
      Returns:
      true if the objects have identical settings