Uses of Class
io.repseq.core.VDJCLibrary

Packages that use VDJCLibrary

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

Uses of VDJCLibrary in io.repseq.cli

Methods in io.repseq.cli with parameters of type VDJCLibrary

Modifier and Type	Method and Description
List<io.repseq.cli.ExportCloneSequencesAction.DescriptionExtractor>	ExportCloneSequencesAction.Params.getExtractors(VDJCLibrary library)
static io.repseq.cli.ExportCloneSequencesAction.DescriptionExtractor	ExportCloneSequencesAction.parseExtractor(String str, VDJCLibrary library)

Uses of VDJCLibrary in io.repseq.core

Methods in io.repseq.core that return VDJCLibrary

Modifier and Type	Method and Description
static VDJCLibrary	VDJCLibraryRegistry.getDefaultLibrary(long taxonId) Retrieves default library (see description for VDJCLibraryRegistry.DEFAULT_LIBRARY_NAME) from default registry for the specified species.
static VDJCLibrary	VDJCLibraryRegistry.getDefaultLibrary(String species) Retrieves default library (see description for VDJCLibraryRegistry.DEFAULT_LIBRARY_NAME) from default registry for the specified species name.
VDJCLibrary	VDJCLibraryRegistry.getLibrary(String libraryName, long taxonId) Returns library with specified name and specified species.
VDJCLibrary	VDJCLibraryRegistry.getLibrary(String libraryName, String species) Returns library with specified name and specified species.
VDJCLibrary	VDJCLibraryRegistry.getLibrary(VDJCLibraryId libraryId) Returns library with specified name and specified species.
VDJCLibrary	VDJCGene.getParentLibrary() Returns parent VDJCLibrary
VDJCLibrary	VDJCLibraryRegistry.registerLibrary(Path context, String name, VDJCLibraryData data) Creates and registers single library from VDJCLibraryData

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

Modifier and Type	Method and Description
Collection<VDJCLibrary>	VDJCLibraryRegistry.getLoadedLibraries() Returns collection of libraries that are currently loaded by this registry.
List<VDJCLibrary>	VDJCLibraryRegistry.getLoadedLibrariesByName(String libraryName) Returns list of libraries that are currently loaded by this registry and has specified name.
List<VDJCLibrary>	VDJCLibraryRegistry.getLoadedLibrariesByNamePattern(Pattern libraryNamePattern) Returns list of libraries that are currently loaded by this registry and has specified name pattern.

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

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
int	VDJCLibrary.compareTo(VDJCLibrary o)

Constructors in io.repseq.core with parameters of type VDJCLibrary

Constructor and Description
GeneNotFoundException(String geneName, VDJCLibrary library)
VDJCGene(VDJCLibrary parentLibrary, VDJCGeneData data, com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> sequenceProvider, ReferencePoints referencePoints) Use addGene(VDJCLibrary, VDJCGeneData) to create instances of this object.

Uses of VDJCLibrary in io.repseq.gen

Methods in io.repseq.gen that return VDJCLibrary

Modifier and Type	Method and Description
VDJCLibrary	GRepertoireReader.getLibrary()

Methods in io.repseq.gen with parameters of type VDJCLibrary

Modifier and Type	Method and Description
VDJCUsageDistributionInstance	VDJCUsageDistribution.create(VDJCLibrary library)

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

Constructor and Description
GRepertoireWriter(OutputStream os, VDJCLibrary library)

Uses of VDJCLibrary in io.repseq.gen.dist

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

Modifier and Type	Method and Description
VDJCGenesGenerator	VDJCGenesModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCLibrary library)
VDJCGenesGenerator	IndependentVDJCGenesModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCLibrary library)
GGeneGenerator	GGeneModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCLibrary library)
VDJCGenesGenerator	DJDependentVDJCGenesModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCLibrary library)
VDJCGenesGenerator	DJCDependentVDJCGenesModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCLibrary library)
GGeneGenerator	BasicGGeneModel.create(org.apache.commons.math3.random.RandomGenerator random, VDJCLibrary library)
static VDJCGene	IndependentVDJCGenesModel.geneOrNull(VDJCLibrary library, String name, GeneType expectedGeneType)
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)