Enum Phase
- java.lang.Object
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- java.lang.Enum<Phase>
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- beagleutil.Phase
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- 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 (
For the case of two sets of phased genotypes for the same markers, the two sets havea1
,a2
) and (b1
,b2
), then
1) the genotypes have IDENTICAL phase if a) allelesa1
andb1
are equivalent, b) allelesa2
andb2
are equivalent, and c) either allelesa1
andb2
are not equivalent or allelesa2
andb1
are not equivalent.
2) the genotypes have OPPOSITE phase if a) allelesa1
andb2
are equivalent, b) allelesa2
andb1
are equivalent, and c) either allelesa1
andb1
are not equivalent or allelesa2
andb2
are not equivalent.
3) the genotypes have UNKOWN phase if a) allelesa1
andb1
are equivalent, b) allelesa2
andb2
are equivalent, c) allelesa1
andb2
are equivalent, and d) allelesa2
andb1
are equivalent.
4) the genotypes have INCONSISTENT phase if a) either allelesa1
andb1
are not equivalent or allelesa2
andb2
are not equivalent, and b) either allelesa1
andb2
are not equivalent or allelesa2
andb1
are not equivalent.
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.
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Enum Constant Summary
Enum Constants Enum Constant Description IDENTICAL
INCONSISTENT
OPPOSITE
UNKNOWN
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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.
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Method Detail
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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
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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 namejava.lang.NullPointerException
- if the argument is null
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