Package com.compomics.util.parameters.identification.advanced

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:

  • Constructor Details

    • ModificationLocalizationParameters

      public ModificationLocalizationParameters()
      Constructor.

  • 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