Uses of Class
io.repseq.core.VDJCGene

Packages that use VDJCGene

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

Uses of VDJCGene in io.repseq.core

Methods in io.repseq.core that return VDJCGene

Modifier and Type	Method and Description
static VDJCGene	VDJCLibrary.addGene(VDJCLibrary library, VDJCGeneData geneData) Creates full featured VDJCGene object from VDJCGene DTO object, and adds it to VDJCLibrary
VDJCGene	VDJCLibrary.get(String geneName) Get gene by name.
VDJCGene	VDJCLibraryRegistry.getGene(VDJCGeneId geneId) Return gene by it's global id.
VDJCGene	VDJCLibrary.getSafe(String geneName) Get gene by name.

Methods in io.repseq.core that return types with arguments of type VDJCGene

Modifier and Type	Method and Description
Collection<VDJCGene>	VDJCLibrary.getGenes() Returns collection of all genes in this library
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
Collection<VDJCGene>	VDJCLibrary.getGenes(GeneType geneType) Returns collection of all genes in this library with specific geneType

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

Modifier and Type	Method and Description
int	VDJCGene.compareTo(VDJCGene o)

Uses of VDJCGene in io.repseq.gen

Fields in io.repseq.gen declared as VDJCGene

Modifier and Type	Field and Description
VDJCGene	VDJCGenes.c null represents absence of certain gene
VDJCGene	VDJCGenes.d null represents absence of certain gene
VDJCGene	VDJCGenes.j null represents absence of certain gene
VDJCGene	VDJCGenes.v null represents absence of certain gene

Constructors in io.repseq.gen with parameters of type VDJCGene

Constructor and Description
GGene(GeneFeature definedIn, VDJCGene v, VDJCGene d, VDJCGene j, VDJCGene c, int vTrimming, int jTrimming, Integer d5Trimming, Integer d3Trimming, com.milaboratory.core.sequence.NucleotideSequence vInsert, com.milaboratory.core.sequence.NucleotideSequence djInsert)
VDJCGenes(VDJCGene v, VDJCGene d, VDJCGene j, VDJCGene c)

Uses of VDJCGene in io.repseq.gen.dist

Fields in io.repseq.gen.dist declared as VDJCGene

Modifier and Type	Field and Description
VDJCGene	DJDependentVDJCGenesModel.VDJCGene2.gene1
VDJCGene	DJCDependentVDJCGenesModel.VDJCGene3.gene1
VDJCGene	DJDependentVDJCGenesModel.VDJCGene2.gene2
VDJCGene	DJCDependentVDJCGenesModel.VDJCGene3.gene2
VDJCGene	DJCDependentVDJCGenesModel.VDJCGene3.gene3

Methods in io.repseq.gen.dist that return VDJCGene

Modifier and Type	Method and Description
static VDJCGene	IndependentVDJCGenesModel.geneOrNull(VDJCLibrary library, String name, GeneType expectedGeneType)
VDJCGene	DJDependentVDJCGenesModel.VDJCGene2.get(int index)
VDJCGene	DJCDependentVDJCGenesModel.VDJCGene3.get(int index)

Methods in io.repseq.gen.dist that return types with arguments of type VDJCGene

Modifier and Type	Method and Description
static List<VDJCGene>	DJCDependentVDJCGenesModel.genes(org.apache.commons.math3.distribution.EnumeratedDistribution<DJCDependentVDJCGenesModel.VDJCGene3> d, int index)
static List<VDJCGene>	DJDependentVDJCGenesModel.genes(org.apache.commons.math3.distribution.EnumeratedDistribution<DJDependentVDJCGenesModel.VDJCGene2> d, int index)
static List<VDJCGene>	IndependentVDJCGenesModel.genes(org.apache.commons.math3.distribution.EnumeratedDistribution<VDJCGene> d)
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)

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

Modifier and Type	Method and Description
GeneTrimmingGenerator	SeparateCategoricalGeneTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCGene gene)
DTrimmingGenerator	SeparateCategoricalDGeneTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCGene gene)
GeneTrimmingGenerator	GeneTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCGene gene)
DTrimmingGenerator	DTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCGene gene)
GeneTrimmingGenerator	CommonNormalGeneTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCGene gene)
DTrimmingGenerator	CommonNormalDTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCGene gene)
GeneTrimmingGenerator	CommonCategoricalGeneTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCGene gene)
DTrimmingGenerator	CommonCategoricalDGeneTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCGene gene)

Method parameters in io.repseq.gen.dist with type arguments of type VDJCGene

Modifier and Type	Method and Description
InsertGenerator	MarkovInsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
InsertGenerator	MarkovInsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
InsertGenerator	MarkovInsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
InsertGenerator	MarkovInsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
InsertGenerator	InsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes) Initialize insert generator
InsertGenerator	InsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes) Initialize insert generator
InsertGenerator	InsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes) Initialize insert generator
InsertGenerator	InsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes) Initialize insert generator
InsertGenerator	FixedInsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
InsertGenerator	FixedInsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
InsertGenerator	FixedInsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
InsertGenerator	FixedInsertModel.create(org.apache.commons.math3.random.RandomGenerator random, boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
VDJTrimmingGenerator	VDJTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
VDJTrimmingGenerator	VDJTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
VDJTrimmingGenerator	VDJTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
VDJTrimmingGenerator	VDJTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
VDJTrimmingGenerator	IndependentVDJTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
VDJTrimmingGenerator	IndependentVDJTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
VDJTrimmingGenerator	IndependentVDJTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
VDJTrimmingGenerator	IndependentVDJTrimmingModel.create(org.apache.commons.math3.random.RandomGenerator random, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes)
static List<VDJCGene>	IndependentVDJCGenesModel.genes(org.apache.commons.math3.distribution.EnumeratedDistribution<VDJCGene> d)

Constructors in io.repseq.gen.dist with parameters of type VDJCGene

Constructor and Description
DJCDependentVDJCGenesModel.VDJCGene3(VDJCGene gene1, VDJCGene gene2, VDJCGene gene3)
DJDependentVDJCGenesModel.VDJCGene2(VDJCGene gene1, VDJCGene gene2)