Package com.compomics.util.experiment.identification.psm_scoring

Enum PsmScore

java.lang.Object
java.lang.Enum<PsmScore>
com.compomics.util.experiment.identification.psm_scoring.PsmScore
All Implemented Interfaces:
Serializable, Comparable<PsmScore>, java.lang.constant.Constable
public enum PsmScore extends Enum<PsmScore>
Enum listing the PSM scores implemented in compomics utilities.
Author:
Marc Vaudel

  • Enum Constant Details

    • native_score

      public static final PsmScore native_score
      The native score of the search engine.

    • precursor_accuracy

      public static final PsmScore precursor_accuracy
      The precursor accuracy.

    • hyperScore

      public static final PsmScore hyperScore
      Hyperscore as variation of the score implemented in X!Tandem www.thegpm.org/tandem. See com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore for details.

    • snrScore

      public static final PsmScore snrScore
      Signal to noise ratio score.

  • Field Details

    • index

      public final Integer index
      The index of the score of interest.

    • name

      public final String name
      The name of the score.

    • increasing

      public final boolean increasing
      Indicates whether the score increases with the quality of the match.

    • description

      public final String description
      Short description of the score.

  • Method Details

    • values

      public static PsmScore[] values()
      Returns an array containing the constants of this enum type, in the order they are declared.
      Returns:
      an array containing the constants of this enum type, in the order they are declared

    • valueOf

      public static PsmScore valueOf(String name)
      Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
      Parameters:
      name - the name of the enum constant to be returned.
      Returns:
      the enum constant with the specified name
      Throws:
      IllegalArgumentException - if this enum type has no constant with the specified name
      NullPointerException - if the argument is null

    • getScore

      public static PsmScore getScore(int scoreIndex)
      Returns the PSM score of the given index. Null if not found.
      Parameters:
      scoreIndex - the index of the desired score
      Returns:
      the score of given index

    • getScore

      public static PsmScore getScore(String scoreName)
      Returns the PSM score of the given name. Null if not found.
      Parameters:
      scoreName - the name of the desired score
      Returns:
      the score of given name