io.repseq.core

Enum GeneType

java.lang.Object

java.lang.Enum<GeneType>

io.repseq.core.GeneType

All Implemented Interfaces:

Serializable, Comparable<GeneType>

public enum GeneType
extends Enum<GeneType>
implements Serializable

Group type of a segment.

Author:

Bolotin Dmitriy (bolotin.dmitriy@gmail.com), Shugay Mikhail (mikhail.shugay@gmail.com)

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GeneType.Deserializer
static class	GeneType.Serializer

Enum Constant Summary

Enum Constants

Enum Constant and Description
Constant
Diversity
Joining
Variable

Field Summary

Fields

Modifier and Type	Field and Description
static int	NUMBER_OF_TYPES
static GeneType[]	VDJC_REFERENCE
static GeneType[]	VJC_REFERENCE

Method Summary

Methods

Modifier and Type	Method and Description
int	cdr3Site() Gets an integer indicating position of segment of this type relative to CDR3
static GeneType	fromChar(char letter)
static GeneType	get(int id) Gets a segment by id
int	getCompleteNumberOfReferencePoints()
int	getIndexOfFirstReferencePoint()
char	getLetter() Gets the associated letter, e.g.
byte	getOrder()
byte	id() Id of segment
static GeneType	valueOf(String name) Returns the enum constant of this type with the specified name.
static GeneType[]	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

Variable

public static final GeneType Variable

Diversity

public static final GeneType Diversity

Joining

public static final GeneType Joining

Constant

public static final GeneType Constant

Field Detail

VJC_REFERENCE

public static final GeneType[] VJC_REFERENCE

VDJC_REFERENCE

public static final GeneType[] VDJC_REFERENCE

NUMBER_OF_TYPES

public static final int NUMBER_OF_TYPES

Method Detail

values

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

Returns:

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

valueOf

public static GeneType 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

getOrder

public byte getOrder()

getIndexOfFirstReferencePoint

public int getIndexOfFirstReferencePoint()

fromChar

public static GeneType fromChar(char letter)

get

public static GeneType get(int id)

Gets a segment by id

Parameters:

id -

getLetter

public char getLetter()

Gets the associated letter, e.g. V for TRBV

id

public byte id()

Id of segment

cdr3Site

public int cdr3Site()

Gets an integer indicating position of segment of this type relative to CDR3

Returns:

+1 (upstream of CDR3, V gene), 0 (inside CDR3, D gene), -1 (downstream of CDR3, J gene) and -2 (downstream of CDR3, C segment)

getCompleteNumberOfReferencePoints

public int getCompleteNumberOfReferencePoints()