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

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:

  • Constructor Details

    • PsmScoringParameters

      public PsmScoringParameters()
      Constructor.

  • Method Details

    • addScore

      public void addScore(Integer advocateId, Integer scoreId)
      Adds a score for a given algorithm to the scoring preferences.
      Parameters:
      advocateId - the index of the algorithm
      scoreId - the index of the score

    • clearScores

      public void clearScores(Integer advocateId)
      Clears the score for the given algorithm.
      Parameters:
      advocateId - the score for the given algorithm

    • clearAllScores

      public void clearAllScores()
      Clears all scores.

    • getScoreForAlgorithm

      public HashSet<Integer> getScoreForAlgorithm(int advocateId)
      Returns the scores set for a given algorithm.
      Parameters:
      advocateId - the index of the algorithm
      Returns:
      the index of the score

    • 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

    • getAdvocates

      public Set<Integer> getAdvocates()
      Returns the advocates with a specific scoring.
      Returns:
      the advocates with a specific scoring

    • isScoringNeeded

      public boolean isScoringNeeded(ArrayList<Integer> advocates)
      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

    • isTargetDecoyNeededForPsmScoring

      public boolean isTargetDecoyNeededForPsmScoring(ArrayList<Integer> advocates)
      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

    • getShortDescription

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

    • equals

      public boolean equals(PsmScoringParameters otherPsmScoringPreferences)
      Returns true if the objects have identical settings.
      Parameters:
      otherPsmScoringPreferences - the PsmScoringPreferences to compare to
      Returns:
      true if the objects have identical settings

    • getDefaultScores

      public HashSet<Integer> getDefaultScores()
      Returns the default scores.
      Returns:
      the default scores

    • 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

    • setDecoysInFirstBin

      public void setDecoysInFirstBin(Integer decoysInFirstBin)
      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