Uses of Class
io.repseq.core.Chains

Packages that use Chains

Package	Description
io.repseq.cli
io.repseq.core
io.repseq.dto

Uses of Chains in io.repseq.cli

Methods in io.repseq.cli that return Chains

Modifier and Type	Method and Description
Chains	ExportCloneSequencesAction.Params.getChains()

Uses of Chains in io.repseq.core

Fields in io.repseq.core declared as Chains

Modifier and Type	Field and Description
static Chains	Chains.ALL Special chains object represents all possible alleles.
static Chains	Chains.EMPTY
static Chains	Chains.IG
static Chains	Chains.IGH
static Chains	Chains.IGK
static Chains	Chains.IGL
static Chains	Chains.TCR
static Chains	Chains.TRA
static Chains	Chains.TRB
static Chains	Chains.TRD
static Chains	Chains.TRG

Methods in io.repseq.core that return Chains

Modifier and Type	Method and Description
Chains	VDJCGene.getChains() Returns set of chains (e.g.
Chains	Chains.intersection(Chains other)
Chains	Chains.merge(Chains other)
static Chains	Chains.parse(String value) Parse chains including TCR, TR, IG and ALL abbreviations, can parse coma-separated list.

Methods in io.repseq.core with parameters of type Chains

Modifier and Type	Method and Description
Collection<VDJCGene>	VDJCLibrary.getGenes(Chains chains) Returns collection of all genes in this library with specific chains
Collection<VDJCGene>	VDJCLibrary.getGenes(Chains chains, GeneType geneType) Returns collection of all genes in this library with specific geneType and chains
Chains	Chains.intersection(Chains other)
boolean	Chains.intersects(Chains other)
Chains	Chains.merge(Chains other)

Uses of Chains in io.repseq.dto

Methods in io.repseq.dto that return Chains

Modifier and Type	Method and Description
Chains	VDJCGeneData.getChains()

Constructors in io.repseq.dto with parameters of type Chains

Constructor and Description
VDJCGeneData(BaseSequence baseSequence, String name, GeneType geneType, boolean isFunctional, Chains chains, String note, Set<GeneTag> tags, SortedMap<ReferencePoint,Long> anchorPoints)