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.
Enum Constant and Description |
---|
IDENTICAL |
INCONSISTENT |
OPPOSITE |
UNKNOWN |
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.
|
public static final Phase IDENTICAL
public static final Phase OPPOSITE
public static final Phase UNKNOWN
public static final Phase INCONSISTENT
public static Phase[] values()
for (Phase c : Phase.values()) System.out.println(c);
public static Phase valueOf(java.lang.String name)
name
- the name of the enum constant to be returned.java.lang.IllegalArgumentException
- if this enum type has no constant with the specified namejava.lang.NullPointerException
- if the argument is null