Enum ModificationLocalizationScore

java.lang.Object
java.lang.Enum<ModificationLocalizationScore>
com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
All Implemented Interfaces:
Serializable, Comparable<ModificationLocalizationScore>, java.lang.constant.Constable

public enum ModificationLocalizationScore
extends Enum<ModificationLocalizationScore>
An enum of the modification localization scores.
Author:
Marc Vaudel
  • Enum Constant Details

  • Method Details

    • values

      public static ModificationLocalizationScore[] 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 ModificationLocalizationScore 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
    • toString

      public String toString()
      Overrides:
      toString in class Enum<ModificationLocalizationScore>
    • getId

      public int getId()
      Returns the id number of the score.
      Returns:
      the id number of the score
    • getName

      public String getName()
      Returns the name of the score.
      Returns:
      the name of the score
    • getScore

      public static ModificationLocalizationScore getScore​(int id)
      Returns the PTM score indexed by the given id.
      Parameters:
      id - the id number of the PTM score
      Returns:
      the desired PTM score
    • getScore

      public static ModificationLocalizationScore getScore​(String name)
      Returns the PTM score of the given name.
      Parameters:
      name - the name of the score
      Returns:
      the desired PTM score
    • getCommandLineOptions

      public static String getCommandLineOptions()
      Returns the different implemented scores as list of command line option.
      Returns:
      the different implemented scores as list of command line option
    • getRandomThreshold

      public double getRandomThreshold​(int nModifications, int nSites)
      Returns the threshold (inclusive) to use to consider an assignment random. E.g. PhosphoRS with one modifications in two sites, a score of 50% is considered random. Returns Double.NaN if the number of modifications equals zero or the number of sites.
      Parameters:
      nModifications - The number of modifications.
      nSites - The number of sites.
      Returns:
      the threshold to use to consider an assignment random