Package beagleutil

Enum Phase

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<Phase>

    public enum Phase
    extends java.lang.Enum<Phase>

    Class Phase represents the equivalence of two phased genotypes for a marker or for a set of markers. Genotype equivalence is defined in terms of allele equivalence. Two alleles are equivalent if either allele is missing or if both alleles are non-missing and equal.

    For the case of a single marker with phased (i.e. ordered) genotypes (a1, a2) and (b1, b2), then
    1) the genotypes have IDENTICAL phase if a) alleles a1 and b1 are equivalent, b) alleles a2 and b2 are equivalent, and c) either alleles a1 and b2 are not equivalent or alleles a2 and b1 are not equivalent.
    2) the genotypes have OPPOSITE phase if a) alleles a1 and b2 are equivalent, b) alleles a2 and b1 are equivalent, and c) either alleles a1 and b1 are not equivalent or alleles a2 and b2 are not equivalent.
    3) the genotypes have UNKOWN phase if a) alleles a1 and b1 are equivalent, b) alleles a2 and b2 are equivalent, c) alleles a1 and b2 are equivalent, and d) alleles a2 and b1 are equivalent.
    4) the genotypes have INCONSISTENT phase if a) either alleles a1 and b1 are not equivalent or alleles a2 and b2 are not equivalent, and b) either alleles a1 and b2 are not equivalent or alleles a2 and b1 are not equivalent.

    For the case of two sets of phased genotypes for the same markers, the two sets have
    1) IDENTICAL phase if the phase is IDENTICAL for at least one marker and is either IDENTICAL or UNKNOWN for all markers.
    2) OPPOSITE phase if the if the phase is OPPOSITE for at lease one marker and is either OPPOSITE or UNKNOWN for all markers.
    3) UNKNOWN phase if the phase is UNKNOWN for all markers.
    4) INCONSISTENT phase if a) the phase is INCONSISTENT for at least one marker or if b) the relative phase is IDENTICAL for at least one marker and OPPOSITE for at least one marker.
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static Phase valueOf​(java.lang.String name)
      Returns the enum constant of this type with the specified name.
      static Phase[] values()
      Returns an array containing the constants of this enum type, in the order they are declared.
      • Methods inherited from class java.lang.Enum

        clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
      • Methods inherited from class java.lang.Object

        getClass, notify, notifyAll, wait, wait, wait
    • Enum Constant Detail

      • IDENTICAL

        public static final Phase IDENTICAL
      • OPPOSITE

        public static final Phase OPPOSITE
      • UNKNOWN

        public static final Phase UNKNOWN
      • INCONSISTENT

        public static final Phase INCONSISTENT
    • Method Detail

      • values

        public static Phase[] values()
        Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
        for (Phase c : Phase.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static Phase valueOf​(java.lang.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:
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        java.lang.NullPointerException - if the argument is null