beagleutil

Enum Phase

java.lang.Object

java.lang.Enum<Phase>

beagleutil.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.

Enum Constant Summary

Enum Constants

Enum Constant and Description
IDENTICAL
INCONSISTENT
OPPOSITE
UNKNOWN

Method Summary

Modifier and Type	Method and 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