pro.parseq.vcf.fields.types

Enum Genotype

java.lang.Object

java.lang.Enum<Genotype>

pro.parseq.vcf.fields.types.Genotype

All Implemented Interfaces:

Serializable, Comparable<Genotype>

public enum Genotype
extends Enum<Genotype>

Enumeration for possible zygosity values

Author:

aafanasyev

Enum Constant Summary

Enum Constants

Enum Constant and Description
HEMIZYGOUS_REFERENCE
HEMIZYGOUS_VARIANT
HETEROZYGOUS_WITH_REFERENCE
HETEROZYGOUS_WITH_VARIANT
HOMOZYGOUS_REFERENCE
HOMOZYGOUS_VARIANT
UNDEFINED

Method Summary

Modifier and Type	Method and Description
static Genotype	extractFor(int alleleNumber, String genotype) Allows to extract zygosity value from genotype format field (see VCFv4.2 specification for more details)
static Genotype	valueOf(String name) Returns the enum constant of this type with the specified name.
static Genotype[]	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

UNDEFINED

public static final Genotype UNDEFINED

HOMOZYGOUS_REFERENCE

public static final Genotype HOMOZYGOUS_REFERENCE

HETEROZYGOUS_WITH_REFERENCE

public static final Genotype HETEROZYGOUS_WITH_REFERENCE

HETEROZYGOUS_WITH_VARIANT

public static final Genotype HETEROZYGOUS_WITH_VARIANT

HOMOZYGOUS_VARIANT

public static final Genotype HOMOZYGOUS_VARIANT

HEMIZYGOUS_VARIANT

public static final Genotype HEMIZYGOUS_VARIANT

HEMIZYGOUS_REFERENCE

public static final Genotype HEMIZYGOUS_REFERENCE

Method Detail

values

public static Genotype[] 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 (Genotype c : Genotype.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static Genotype 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

extractFor

public static final Genotype extractFor(int alleleNumber,
                                        String genotype)

Allows to extract zygosity value from genotype format field (see VCFv4.2 specification for more details)

Parameters:

alleleNumber - Allele number to extract zygosity information for (0 is for reference allele, 1,2.. are for alternate specified in ALT column)

genotype - Genotype format field value to extract zygosity information from

Returns:

Genotype for specified allele number