Uses of Class
io.repseq.core.GeneType

Packages that use GeneType

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

Uses of GeneType in io.repseq.cli

Methods in io.repseq.cli that return GeneType

Modifier and Type	Method and Description
GeneType	FromPaddedFastaAction.Params.getGeneType()

Uses of GeneType in io.repseq.core

Fields in io.repseq.core declared as GeneType

Modifier and Type	Field and Description
static GeneType[]	GeneType.VDJC_REFERENCE
static GeneType[]	GeneType.VJC_REFERENCE

Methods in io.repseq.core that return GeneType

Modifier and Type	Method and Description
GeneType	GeneType.Deserializer.deserialize(com.fasterxml.jackson.core.JsonParser jp, com.fasterxml.jackson.databind.DeserializationContext ctxt)
static GeneType	GeneType.fromChar(char letter)
static GeneType	GeneType.get(int id) Gets a segment by id
GeneType	VDJCGene.getGeneType() Returns gene type
GeneType	ReferencePoint.getGeneType()
GeneType	GeneFeature.getGeneType()
GeneType	GeneFeature.ReferenceRange.getGeneType()
static GeneType	GeneType.valueOf(String name) Returns the enum constant of this type with the specified name.
static GeneType[]	GeneType.values() Returns an array containing the constants of this enum type, in the order they are declared.

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

Modifier and Type	Method and Description
Collection<VDJCGene>	VDJCLibrary.getGenes(Chains chains, GeneType geneType) Returns collection of all genes in this library with specific geneType and chains
Collection<VDJCGene>	VDJCLibrary.getGenes(GeneType geneType) Returns collection of all genes in this library with specific geneType
static GeneFeature	GeneFeature.getRegion(GeneType type)
void	GeneType.Serializer.serialize(GeneType value, com.fasterxml.jackson.core.JsonGenerator jgen, com.fasterxml.jackson.databind.SerializerProvider provider)

Uses of GeneType in io.repseq.dto

Methods in io.repseq.dto that return GeneType

Modifier and Type	Method and Description
GeneType	VDJCGeneData.getGeneType()

Methods in io.repseq.dto with parameters of type GeneType

Modifier and Type	Method and Description
boolean	GeneTag.isSupportedGeneType(GeneType geneType)

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

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

Uses of GeneType in io.repseq.gen.dist

Methods in io.repseq.gen.dist with parameters of type GeneType

Modifier and Type	Method and Description
static GeneFeature	CommonNormalGeneTrimmingModel.cdr3Part(GeneType geneType)
static VDJCGene	IndependentVDJCGenesModel.geneOrNull(VDJCLibrary library, String name, GeneType expectedGeneType)
List<VDJCGene>	VDJCGenesGenerator.genes(GeneType gt)
static org.apache.commons.math3.distribution.EnumeratedDistribution<VDJCGene>	IndependentVDJCGenesModel.toDistribution(org.apache.commons.math3.random.RandomGenerator random, VDJCLibrary library, Map<String,Double> distMap, GeneType geneType)
static org.apache.commons.math3.distribution.EnumeratedDistribution<DJDependentVDJCGenesModel.VDJCGene2>	DJDependentVDJCGenesModel.toDistribution2(org.apache.commons.math3.random.RandomGenerator random, VDJCLibrary library, Map<String,Double> distMap, GeneType geneType1, GeneType geneType2)
static org.apache.commons.math3.distribution.EnumeratedDistribution<DJCDependentVDJCGenesModel.VDJCGene3>	DJCDependentVDJCGenesModel.toDistribution3(org.apache.commons.math3.random.RandomGenerator random, VDJCLibrary library, Map<String,Double> distMap, GeneType geneType1, GeneType geneType2, GeneType geneType3)