io.repseq.core

Class Chains

java.lang.Object

io.repseq.core.Chains

All Implemented Interfaces:

java.lang.Iterable<java.lang.String>

public final class Chains
extends java.lang.Object
implements java.lang.Iterable<java.lang.String>

Immutable set of strings

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Chains.NamedChains

Field Summary

Fields

Modifier and Type	Field and Description
static Chains	ALL Special chains object represents all possible alleles.
static Chains.NamedChains	ALL_NAMED
static Chains	EMPTY
static Chains.NamedChains	EMPTY_NAMED
static Chains	IG
static Chains.NamedChains	IG_NAMED
static Chains	IGH
static Chains.NamedChains	IGH_NAMED
static Chains	IGK
static Chains.NamedChains	IGK_NAMED
static Chains	IGKL
static Chains.NamedChains	IGKL_NAMED
static Chains	IGL
static Chains.NamedChains	IGL_NAMED
static Chains	TCR
static Chains.NamedChains	TCR_NAMED
static Chains	TRA
static Chains.NamedChains	TRA_NAMED
static Chains	TRAD
static Chains.NamedChains	TRAD_NAMED
static Chains	TRB
static Chains.NamedChains	TRB_NAMED
static Chains	TRD
static Chains.NamedChains	TRD_NAMED
static Chains	TRG
static Chains.NamedChains	TRG_NAMED
static java.util.List<Chains.NamedChains>	WELL_KNOWN_CHAINS
static java.util.Map<java.lang.String,Chains>	WELL_KNOWN_CHAINS_MAP

Constructor Summary

Constructors

Constructor and Description
Chains(java.util.Set<java.lang.String> chains)
Chains(java.lang.String... chains)

Method Summary

Modifier and Type	Method and Description
boolean	contains(Chains other)
boolean	contains(java.lang.String chain)
boolean	equals(java.lang.Object o)
int	hashCode()
Chains	intersection(Chains other)
boolean	intersects(Chains other)
boolean	isEmpty()
java.util.Iterator<java.lang.String>	iterator()
Chains	merge(Chains other)
static Chains	parse(java.lang.String value) Parse chains including TCR, TR, IG and ALL abbreviations, can parse coma-separated list.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

ALL

public static final Chains ALL

Special chains object represents all possible alleles.

ALL_NAMED

public static final Chains.NamedChains ALL_NAMED

EMPTY

public static final Chains EMPTY

EMPTY_NAMED

public static final Chains.NamedChains EMPTY_NAMED

TRA

public static final Chains TRA

TRA_NAMED

public static final Chains.NamedChains TRA_NAMED

TRB

public static final Chains TRB

TRB_NAMED

public static final Chains.NamedChains TRB_NAMED

TRG

public static final Chains TRG

TRG_NAMED

public static final Chains.NamedChains TRG_NAMED

TRD

public static final Chains TRD

TRD_NAMED

public static final Chains.NamedChains TRD_NAMED

TRAD

public static final Chains TRAD

TRAD_NAMED

public static final Chains.NamedChains TRAD_NAMED

TCR

public static final Chains TCR

TCR_NAMED

public static final Chains.NamedChains TCR_NAMED

IGH

public static final Chains IGH

IGH_NAMED

public static final Chains.NamedChains IGH_NAMED

IGK

public static final Chains IGK

IGK_NAMED

public static final Chains.NamedChains IGK_NAMED

IGL

public static final Chains IGL

IGL_NAMED

public static final Chains.NamedChains IGL_NAMED

IGKL

public static final Chains IGKL

IGKL_NAMED

public static final Chains.NamedChains IGKL_NAMED

IG

public static final Chains IG

IG_NAMED

public static final Chains.NamedChains IG_NAMED

WELL_KNOWN_CHAINS

public static final java.util.List<Chains.NamedChains> WELL_KNOWN_CHAINS

WELL_KNOWN_CHAINS_MAP

public static final java.util.Map<java.lang.String,Chains> WELL_KNOWN_CHAINS_MAP

Constructor Detail

Chains

public Chains(java.lang.String... chains)

Chains

public Chains(java.util.Set<java.lang.String> chains)

Method Detail

iterator

public java.util.Iterator<java.lang.String> iterator()

Specified by:

iterator in interface java.lang.Iterable<java.lang.String>

merge

public Chains merge(Chains other)

intersection

public Chains intersection(Chains other)

contains

public boolean contains(Chains other)

isEmpty

public boolean isEmpty()

contains

public boolean contains(java.lang.String chain)

intersects

public boolean intersects(Chains other)

parse

public static Chains parse(java.lang.String value)

Parse chains including TCR, TR, IG and ALL abbreviations, can parse coma-separated list. Example: "TR", "TCR,IGH"

Parameters:

value - string representation

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object