- GClone - Class in io.repseq.gen
-
Represents single clonotype
- GClone(double, Map<String, GGene>) - Constructor for class io.repseq.gen.GClone
-
- GCloneGenerator - Interface in io.repseq.gen.dist
-
- GCloneModel - Interface in io.repseq.gen.dist
-
- gene1 - Variable in class io.repseq.gen.dist.DJCDependentVDJCGenesModel.VDJCGene3
-
- gene1 - Variable in class io.repseq.gen.dist.DJDependentVDJCGenesModel.VDJCGene2
-
- gene2 - Variable in class io.repseq.gen.dist.DJCDependentVDJCGenesModel.VDJCGene3
-
- gene2 - Variable in class io.repseq.gen.dist.DJDependentVDJCGenesModel.VDJCGene2
-
- gene3 - Variable in class io.repseq.gen.dist.DJCDependentVDJCGenesModel.VDJCGene3
-
- GeneFeature - Class in io.repseq.core
-
- GeneFeature(GeneFeature...) - Constructor for class io.repseq.core.GeneFeature
-
- GeneFeature(ReferencePoint, ReferencePoint) - Constructor for class io.repseq.core.GeneFeature
-
- GeneFeature(GeneFeature, int, int) - Constructor for class io.repseq.core.GeneFeature
-
- GeneFeature(ReferencePoint, int, int) - Constructor for class io.repseq.core.GeneFeature
-
- GeneFeature.Deserializer - Class in io.repseq.core
-
- GeneFeature.Deserializer() - Constructor for class io.repseq.core.GeneFeature.Deserializer
-
- GeneFeature.ReferenceRange - Class in io.repseq.core
-
- GeneFeature.Serializer - Class in io.repseq.core
-
- GeneFeature.Serializer() - Constructor for class io.repseq.core.GeneFeature.Serializer
-
- GeneFeatureSerializer - Class in io.repseq.core
-
- GeneFeatureSerializer() - Constructor for class io.repseq.core.GeneFeatureSerializer
-
- GeneFeatureSerializer(boolean) - Constructor for class io.repseq.core.GeneFeatureSerializer
-
Constructor for custom serialization
- geneModels - Variable in class io.repseq.gen.dist.BasicGCloneModel
-
- GeneNotFoundException - Exception in io.repseq.core
-
- GeneNotFoundException(String, VDJCLibrary) - Constructor for exception io.repseq.core.GeneNotFoundException
-
- geneOrNull(VDJCLibrary, String, GeneType) - Static method in class io.repseq.gen.dist.IndependentVDJCGenesModel
-
- generate() - Method in interface io.repseq.gen.dist.GGeneGenerator
-
- generate() - Method in interface io.repseq.gen.dist.IndependentRealGenerator
-
- generate(GGene) - Method in interface io.repseq.gen.dist.InsertGenerator
-
Generates insert, using information from GGene with empty sequence V and DJ insertions.
- generate(RandomGenerator) - Method in interface io.repseq.gen.VDJCUsageDistributionInstance
-
- GenerateClonesAction - Class in io.repseq.cli
-
- GenerateClonesAction() - Constructor for class io.repseq.cli.GenerateClonesAction
-
- GenerateClonesAction.Params - Class in io.repseq.cli
-
- GenerateClonesAction.Params() - Constructor for class io.repseq.cli.GenerateClonesAction.Params
-
- genes(EnumeratedDistribution<DJCDependentVDJCGenesModel.VDJCGene3>, int) - Static method in class io.repseq.gen.dist.DJCDependentVDJCGenesModel
-
- genes(EnumeratedDistribution<DJDependentVDJCGenesModel.VDJCGene2>, int) - Static method in class io.repseq.gen.dist.DJDependentVDJCGenesModel
-
- genes(EnumeratedDistribution<VDJCGene>) - Static method in class io.repseq.gen.dist.IndependentVDJCGenesModel
-
- genes(GeneType) - Method in interface io.repseq.gen.dist.VDJCGenesGenerator
-
- genes - Variable in class io.repseq.gen.GClone
-
Map from immunological chain to gene
- GeneTag - Enum in io.repseq.dto
-
Manually or automatically attached gene annotation tag.
- GeneTrimmingGenerator - Interface in io.repseq.gen.dist
-
- GeneTrimmingGeneratorEnumerated - Class in io.repseq.gen.dist
-
- GeneTrimmingGeneratorEnumerated(EnumeratedIntegerDistribution) - Constructor for class io.repseq.gen.dist.GeneTrimmingGeneratorEnumerated
-
- GeneTrimmingModel - Interface in io.repseq.gen.dist
-
- geneType - Variable in class io.repseq.cli.FromPaddedFastaAction.Params
-
- GeneType - Enum in io.repseq.core
-
Group type of a segment.
- GeneType.Deserializer - Class in io.repseq.core
-
- GeneType.Deserializer() - Constructor for class io.repseq.core.GeneType.Deserializer
-
- GeneType.Serializer - Class in io.repseq.core
-
- GeneType.Serializer() - Constructor for class io.repseq.core.GeneType.Serializer
-
- GermlineDPSegment - Static variable in class io.repseq.core.GeneFeature
-
- GermlineJCDR3Part - Static variable in class io.repseq.core.GeneFeature
-
- GermlineJPSegment - Static variable in class io.repseq.core.GeneFeature
-
- GermlinePRegionSize - Static variable in class io.repseq.core.GeneFeature
-
- GermlineVCDR3Part - Static variable in class io.repseq.core.GeneFeature
-
- GermlineVPSegment - Static variable in class io.repseq.core.GeneFeature
-
- get(int) - Static method in enum io.repseq.core.GeneType
-
Gets a segment by id
- get(String) - Method in class io.repseq.core.VDJCLibrary
-
Get gene by name.
- get(int) - Method in class io.repseq.gen.dist.DJCDependentVDJCGenesModel.VDJCGene3
-
- get(int) - Method in class io.repseq.gen.dist.DJDependentVDJCGenesModel.VDJCGene2
-
- get(int...) - Method in class io.repseq.gen.dist.DoubleTensor
-
- get(String, Range) - Method in class io.repseq.util.SequenceBase
-
- getAbsoluteMinScore() - Method in class io.repseq.cli.InferAnchorPointsAction.Params
-
- getAbsolutePosition(GeneFeature, int) - Method in class io.repseq.core.SequencePartitioning
-
Returns absolute position in reference sequence for the specified local position in specified feature
or -1 if this position can't be projected.
- getActivationPoint() - Method in class io.repseq.core.ReferencePoint
-
- getAnchorPoints() - Method in class io.repseq.dto.VDJCGeneData
-
- getAvailableParameterNames() - Static method in class io.repseq.gen.dist.GModels
-
- getAvailableRange(String, Range) - Method in class io.repseq.util.SequenceBase
-
- getBaseSequence() - Method in class io.repseq.dto.VDJCGeneData
-
- getCacheDir() - Method in class io.repseq.seqbase.HTTPFastaSequenceResolver
-
- getCacheDir() - Method in class io.repseq.seqbase.HTTPRedirectSequenceResolver
-
- getCacheDir() - Method in class io.repseq.seqbase.HTTPResolversContext
-
- getChains() - Method in class io.repseq.cli.ExportCloneSequencesAction.Params
-
- getChains() - Method in class io.repseq.core.VDJCGene
-
Returns set of chains (e.g.
- getChains() - Method in class io.repseq.dto.VDJCGeneData
-
- getCheckAll() - Method in class io.repseq.cli.DebugAction.Params
-
- getChecksum() - Method in class io.repseq.core.VDJCLibrary
-
Return checksum for this library.
- getChecksum() - Method in class io.repseq.core.VDJCLibraryId
-
Return checksum
- getClassLoader() - Method in class io.repseq.core.VDJCLibraryRegistry.ClasspathLibraryResolver
-
- getCodingGeneFeature(GeneFeature) - Static method in class io.repseq.core.GeneFeature
-
Returns coding gene feature contained in input gene feature
- getComments() - Method in class io.repseq.core.VDJCLibrary
-
All comment blocks associated with the library
- getComments(VDJCLibraryNoteType) - Method in class io.repseq.core.VDJCLibrary
-
Return comments of a particular type
- getComments(VDJCLibraryNoteType) - Method in class io.repseq.dto.VDJCLibraryData
-
Return notes of a particular type
- getCompact() - Method in class io.repseq.cli.FormatAction.Params
-
- getCompleteNumberOfReferencePoints() - Method in enum io.repseq.core.GeneType
-
- getContainingRegion() - Method in class io.repseq.core.AbstractReferencePoints
-
- getContext() - Method in class io.repseq.core.VDJCLibrary
-
Returns library context folder
- getContext(String) - Method in class io.repseq.core.VDJCLibraryRegistry.ClasspathLibraryResolver
-
- getContext(String) - Method in class io.repseq.core.VDJCLibraryRegistry.FolderLibraryResolver
-
- getContext(String) - Method in interface io.repseq.core.VDJCLibraryRegistry.LibraryResolver
-
- getContext() - Method in class io.repseq.seqbase.SequenceAddress
-
- getData() - Method in class io.repseq.core.VDJCGene
-
Returns serializable gene data
- getData() - Method in class io.repseq.core.VDJCLibrary
-
Returns serializable library data
- getDefault() - Static method in class io.repseq.core.VDJCLibraryRegistry
-
Returns default VDJCLibraryRegistry.
- getDefault() - Static method in class io.repseq.seqbase.SequenceResolvers
-
- getDefaultLibrary(String) - Static method in class io.repseq.core.VDJCLibraryRegistry
-
- getDefaultLibrary(long) - Static method in class io.repseq.core.VDJCLibraryRegistry
-
- getDimension(int) - Method in class io.repseq.gen.dist.DoubleTensor
-
- getExtractors(VDJCLibrary) - Method in class io.repseq.cli.ExportCloneSequencesAction.Params
-
- getFamilyName() - Method in class io.repseq.core.VDJCGene
-
Gene family name (e.g.
- getFamilyName() - Method in class io.repseq.dto.VDJCGeneData
-
Gene family name (e.g.
- getFASTAFile(SequenceAddress) - Method in class io.repseq.seqbase.AbstractRAFastaResolver
-
Resolves uri to existing fasta file.
- getFASTAFile(SequenceAddress) - Method in class io.repseq.seqbase.HTTPFastaSequenceResolver
-
- getFASTAFile(SequenceAddress) - Method in class io.repseq.seqbase.LocalFileResolver
-
- getFeature(GeneFeature) - Method in class io.repseq.core.PartitionedSequence
-
- getFeature(GeneFeature) - Method in class io.repseq.core.PartitionedSequenceCached
-
- getFeatureByName(String) - Static method in class io.repseq.core.GeneFeature
-
- getFeaturesByName() - Static method in class io.repseq.core.GeneFeature
-
- getFirstAvailablePosition() - Method in class io.repseq.core.AbstractReferencePoints
-
- getFirstPoint() - Method in class io.repseq.core.GeneFeature
-
- getFragments() - Method in class io.repseq.dto.VDJCDataUtils.FragmentsBuilder
-
- getFrameReference(GeneFeature) - Static method in class io.repseq.core.GeneFeature
-
Returns reference point that is triplet boundary (so defines reading frame) inside provided gene feature or
returns null.
- getFullName() - Method in class io.repseq.core.VDJCGene
-
Return full gene name, including library id (e.g.
- getFullName() - Method in class io.repseq.core.VDJCGeneId
-
Return full gene name.
- getFunctionalityRegexp() - Method in class io.repseq.cli.FromPaddedFastaAction.Params
-
- getGCloneModelByName(String) - Static method in class io.repseq.gen.dist.GModels
-
- getGene(VDJCGeneId) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Return gene by it's global id.
- getGeneFeature() - Method in class io.repseq.cli.ExportCloneSequencesAction.Params
-
- getGeneFeature() - Method in class io.repseq.cli.FastaAction.Params
-
- getGeneFeature() - Method in class io.repseq.cli.InferAnchorPointsAction.Params
-
- getGeneName() - Method in class io.repseq.core.VDJCGene
-
Name without allele index (e.g.
- getGeneName() - Method in class io.repseq.dto.VDJCGeneData
-
Name without allele index (e.g.
- getGenes() - Method in class io.repseq.core.VDJCLibrary
-
Returns collection of all genes in this library
- getGenes(Chains) - Method in class io.repseq.core.VDJCLibrary
-
Returns collection of all genes in this library with specific chains
- getGenes(GeneType) - Method in class io.repseq.core.VDJCLibrary
-
Returns collection of all genes in this library with specific geneType
- getGenes(Chains, GeneType) - Method in class io.repseq.core.VDJCLibrary
-
Returns collection of all genes in this library with specific geneType and chains
- getGenes() - Method in class io.repseq.dto.VDJCLibraryData
-
- getGeneType() - Method in class io.repseq.cli.FromPaddedFastaAction.Params
-
- getGeneType() - Method in class io.repseq.core.GeneFeature
-
- getGeneType() - Method in class io.repseq.core.GeneFeature.ReferenceRange
-
- getGeneType() - Method in class io.repseq.core.ReferencePoint
-
- getGeneType() - Method in class io.repseq.core.VDJCGene
-
Returns gene type
- getGeneType() - Method in class io.repseq.dto.VDJCGeneData
-
- getHttpClient() - Method in class io.repseq.seqbase.HTTPResolversContext
-
- getId() - Method in class io.repseq.core.VDJCGene
-
Returns global gene identifier including library id
- getIgnoreDuplicates() - Method in class io.repseq.cli.FromPaddedFastaAction.Params
-
- getIndexOfFirstReferencePoint() - Method in enum io.repseq.core.GeneType
-
- getInput() - Method in class io.repseq.cli.CompileAction.Params
-
- getInput() - Method in class io.repseq.cli.DebugAction.Params
-
- getInput() - Method in class io.repseq.cli.ExportCloneSequencesAction.Params
-
- getInput() - Method in class io.repseq.cli.FastaAction.Params
-
- getInput() - Method in class io.repseq.cli.FilterAction.Params
-
- getInput() - Method in class io.repseq.cli.FormatAction.Params
-
- getInput() - Method in class io.repseq.cli.FromPaddedFastaAction.Params
-
- getInput() - Method in class io.repseq.cli.InferAnchorPointsAction.Params
-
- getInput() - Method in class io.repseq.cli.ListAction.Params
-
- getInput() - Method in class io.repseq.cli.MergeAction.Params
-
- getInput() - Method in class io.repseq.cli.NormalizeCloneAbundancesAction.Params
-
- getInput() - Method in class io.repseq.cli.StatAction.Params
-
- getInput() - Method in class io.repseq.cli.TsvAction.Params
-
- getIntermediatePoints() - Method in class io.repseq.core.GeneFeature.ReferenceRange
-
- getLastAvailablePosition() - Method in class io.repseq.core.AbstractReferencePoints
-
- getLastPoint() - Method in class io.repseq.core.GeneFeature
-
- getLeftBoundary() - Method in class io.repseq.core.GeneFeature.ReferenceRange
-
- getLength(GeneFeature) - Method in class io.repseq.core.SequencePartitioning
-
- getLength(GeneFeature.ReferenceRange) - Method in class io.repseq.core.SequencePartitioning
-
- getLengthBetweenBoundaryPoints() - Method in class io.repseq.core.AbstractReferencePoints
-
- getLetter() - Method in enum io.repseq.core.GeneType
-
Gets the associated letter, e.g.
- getLibrary(String, String) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Returns library with specified name and specified species.
- getLibrary(String, long) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Returns library with specified name and specified species.
- getLibrary(VDJCLibraryId) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Returns library with specified name and specified species.
- getLibrary() - Method in class io.repseq.gen.GRepertoireReader
-
- getLibraryId() - Method in class io.repseq.core.VDJCGeneId
-
- getLibraryId() - Method in class io.repseq.core.VDJCLibrary
-
Returns identifier of this library
- getLibraryName() - Method in class io.repseq.core.VDJCLibraryId
-
Library name
- getLibraryNameList() - Method in class io.repseq.core.VDJCLibraryRegistry.ClasspathLibraryResolver
-
- getLibraryNameList() - Method in class io.repseq.core.VDJCLibraryRegistry.FolderLibraryResolver
-
- getLibraryNameList() - Method in interface io.repseq.core.VDJCLibraryRegistry.LibraryNameListProvider
-
- getLibraryResolvers() - Method in class io.repseq.core.VDJCLibraryRegistry
-
Return the list of library resolvers used by this registry
- getLoadedLibraries() - Method in class io.repseq.core.VDJCLibraryRegistry
-
Returns collection of libraries that are currently loaded by this registry.
- getLoadedLibrariesByName(String) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Returns list of libraries that are currently loaded by this registry and has specified name.
- getLoadedLibrariesByNamePattern(Pattern) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Returns list of libraries that are currently loaded by this registry and has specified name pattern.
- getModelName() - Method in class io.repseq.cli.GenerateClonesAction.Params
-
- getModifiedString() - Method in class io.repseq.util.StringWithMapping
-
- getMutations() - Method in class io.repseq.core.BaseSequence
-
- getName() - Method in class io.repseq.core.VDJCGene
-
Returns gene name (e.g.
- getName() - Method in class io.repseq.core.VDJCGeneId
-
Return gene name.
- getName() - Method in class io.repseq.core.VDJCLibrary
-
Library name
- getName() - Method in class io.repseq.dto.VDJCGeneData
-
Full gene name
- getNameByFeature(GeneFeature) - Static method in class io.repseq.core.GeneFeature
-
- getNameByFeature() - Static method in class io.repseq.core.GeneFeature
-
- getNameByPoint(ReferencePoint) - Static method in class io.repseq.core.ReferencePoint
-
- getNotes() - Method in class io.repseq.dto.VDJCLibraryData
-
- getOffset() - Method in class io.repseq.core.ReferencePoint
-
Returns offset.
- getOffsetFrom(ReferencePoint) - Method in class io.repseq.core.ReferencePoint
-
- getOrder() - Method in enum io.repseq.core.GeneType
-
- getOrigin() - Method in class io.repseq.core.BaseSequence
-
- getOutput() - Method in class io.repseq.cli.CompileAction.Params
-
- getOutput() - Method in class io.repseq.cli.ExportCloneSequencesAction.Params
-
- getOutput() - Method in class io.repseq.cli.FastaAction.Params
-
- getOutput() - Method in class io.repseq.cli.FilterAction.Params
-
- getOutput() - Method in class io.repseq.cli.GenerateClonesAction.Params
-
- getOutput() - Method in class io.repseq.cli.InferAnchorPointsAction.Params
-
- getOutput() - Method in class io.repseq.cli.MergeAction.Params
-
- getOutput() - Method in class io.repseq.cli.NormalizeCloneAbundancesAction.Params
-
- getOutputFasta() - Method in class io.repseq.cli.FromPaddedFastaAction.Params
-
- getOutputFiles() - Method in class io.repseq.cli.CompileAction.Params
-
- getOutputFiles() - Method in class io.repseq.cli.ExportCloneSequencesAction.Params
-
- getOutputFiles() - Method in class io.repseq.cli.FastaAction.Params
-
- getOutputFiles() - Method in class io.repseq.cli.FilterAction.Params
-
- getOutputFiles() - Method in class io.repseq.cli.FromPaddedFastaAction.Params
-
- getOutputFiles() - Method in class io.repseq.cli.GenerateClonesAction.Params
-
- getOutputFiles() - Method in class io.repseq.cli.InferAnchorPointsAction.Params
-
- getOutputFiles() - Method in class io.repseq.cli.MergeAction.Params
-
- getOutputFiles() - Method in class io.repseq.cli.NormalizeCloneAbundancesAction.Params
-
- getOutputFiles() - Method in class io.repseq.cli.TsvAction.Params
-
- getOutputJSON() - Method in class io.repseq.cli.FromPaddedFastaAction.Params
-
- getOutputStream() - Method in class io.repseq.cli.TsvAction.Params
-
- getParent() - Method in class io.repseq.core.VDJCLibrary
-
Returns parent registry
- getParent() - Method in class io.repseq.seqbase.HTTPRedirectSequenceResolver
-
- getParentLibrary() - Method in class io.repseq.core.VDJCGene
-
Returns parent VDJCLibrary
- getPartitioning() - Method in class io.repseq.core.PartitionedSequence
-
- getPartitioning() - Method in class io.repseq.core.SequenceProviderAndReferencePoints
-
- getPartitioning() - Method in class io.repseq.core.VDJCGene
-
Returns reference point object for this gene
- getPartitioning() - Method in class io.repseq.gen.GGene
-
- getPath() - Method in class io.repseq.core.VDJCLibraryRegistry.ClasspathLibraryResolver
-
- getPath() - Method in class io.repseq.core.VDJCLibraryRegistry.FolderLibraryResolver
-
- getPointByName(String) - Static method in class io.repseq.core.ReferencePoint
-
- getPosition(ReferencePoint) - Method in class io.repseq.core.AbstractReferencePoints
-
- getPosition(ReferencePoint) - Method in class io.repseq.core.SequencePartitioning
-
Return position of specific anchor point
- getProblemOnly() - Method in class io.repseq.cli.DebugAction.Params
-
- getRange(GeneFeature) - Method in class io.repseq.core.SequencePartitioning
-
Return sequence range for non-composite gene features
- getRange(GeneFeature.ReferenceRange) - Method in class io.repseq.core.SequencePartitioning
-
- getRange() - Method in class io.repseq.dto.KnownSequenceFragmentData
-
- getRanges(GeneFeature) - Method in class io.repseq.core.SequencePartitioning
-
- getReference() - Method in class io.repseq.cli.InferAnchorPointsAction.Params
-
- getReferencePointIndex(ReferencePoint) - Static method in class io.repseq.core.ReferenceUtil
-
Returns underlying reference point id.
- getReferenceRange(int) - Method in class io.repseq.core.GeneFeature
-
- getRegion(GeneType) - Static method in class io.repseq.core.GeneFeature
-
- getRegion(Range) - Method in class io.repseq.gen.ConcatenatedLazySequence
-
- getRegions() - Method in class io.repseq.core.BaseSequence
-
- getRelativePosition(GeneFeature, ReferencePoint) - Method in class io.repseq.core.SequencePartitioning
-
Returns a relative position of specified referencePoint in specified feature or -1 if this
position is not available.
- getRelativeRange(GeneFeature, GeneFeature) - Method in class io.repseq.core.SequencePartitioning
-
Returns a relative range of specified subFeature in specified feature or null if this is not
available.
- getReporter() - Method in class io.repseq.seqbase.AbstractRAFastaResolver
-
Returns instance specific reporter
- getReporter() - Method in class io.repseq.seqbase.HTTPFastaSequenceResolver
-
- getReporter(Class<?>) - Method in class io.repseq.seqbase.HTTPResolversContext
-
- getReporter() - Method in class io.repseq.seqbase.LocalFileResolver
-
- getRightBoundary() - Method in class io.repseq.core.GeneFeature.ReferenceRange
-
- getSafe(String) - Method in class io.repseq.core.VDJCLibrary
-
Get gene by name.
- getSeed() - Method in class io.repseq.cli.GenerateClonesAction.Params
-
- getSequence(Range) - Method in class io.repseq.core.PartitionedSequence
-
- getSequence(Range) - Method in class io.repseq.core.SequenceProviderAndReferencePoints
-
- getSequence(Range) - Method in class io.repseq.core.VDJCGene
-
- getSequence() - Method in class io.repseq.dto.KnownSequenceFragmentData
-
- getSequence(Range) - Method in class io.repseq.gen.GGene
-
- getSequenceFragments() - Method in class io.repseq.dto.VDJCLibraryData
-
- getSequenceProvider() - Method in class io.repseq.core.VDJCGene
-
Returns sequence provider associated with this gene
- getSequenceResolver() - Method in class io.repseq.core.VDJCLibraryRegistry
-
Return sequence resolver used by this registry
- getSPAndRPs() - Method in class io.repseq.core.VDJCGene
-
- getSpeciesNames(long) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Returns list of known species names for a given taxon id.
- getSpeciesNames() - Method in class io.repseq.dto.VDJCLibraryData
-
- getTags() - Method in class io.repseq.dto.VDJCGeneData
-
- getTaxonId() - Method in class io.repseq.core.VDJCLibrary
-
Return species (taxon id)
- getTaxonId() - Method in class io.repseq.core.VDJCLibraryId
-
Taxon id
- getTaxonId() - Method in class io.repseq.dto.VDJCLibraryData
-
- getText() - Method in class io.repseq.dto.VDJCLibraryNote
-
- getTranslationParameters(GeneFeature) - Method in class io.repseq.core.SequencePartitioning
-
Calculates translation parameters ( ~ translation frame ) for given gene feature using current sequence
partitioning.
- getType() - Method in class io.repseq.dto.VDJCLibraryNote
-
- getUri() - Method in class io.repseq.dto.KnownSequenceFragmentData
-
- getUri() - Method in class io.repseq.seqbase.SequenceAddress
-
- getWithoutOffset() - Method in class io.repseq.core.GeneFeature.ReferenceRange
-
- getWithoutOffset() - Method in class io.repseq.core.ReferencePoint
-
- GGene - Class in io.repseq.gen
-
Represents rearranged TCR/IG gene / sequence.
- GGene(GeneFeature, VDJCGenes, VDJTrimming, NucleotideSequence, NucleotideSequence) - Constructor for class io.repseq.gen.GGene
-
- GGene(GeneFeature, VDJCGene, VDJCGene, VDJCGene, VDJCGene, int, int, Integer, Integer, NucleotideSequence, NucleotideSequence) - Constructor for class io.repseq.gen.GGene
-
- GGeneGenerator - Interface in io.repseq.gen.dist
-
- GGeneModel - Interface in io.repseq.gen.dist
-
- GModels - Class in io.repseq.gen.dist
-
- go(ActionHelper) - Method in class io.repseq.cli.CheckAction
-
- go(ActionHelper) - Method in class io.repseq.cli.CompileAction
-
- go(ActionHelper) - Method in class io.repseq.cli.DebugAction
-
- go(ActionHelper) - Method in class io.repseq.cli.ExportCloneSequencesAction
-
- go(ActionHelper) - Method in class io.repseq.cli.FastaAction
-
- go(ActionHelper) - Method in class io.repseq.cli.FilterAction
-
- go(ActionHelper) - Method in class io.repseq.cli.FormatAction
-
- go(ActionHelper) - Method in class io.repseq.cli.FromPaddedFastaAction
-
- go(ActionHelper) - Method in class io.repseq.cli.GenerateClonesAction
-
- go(ActionHelper) - Method in class io.repseq.cli.InferAnchorPointsAction
-
- go(ActionHelper) - Method in class io.repseq.cli.ListAction
-
- go(ActionHelper) - Method in class io.repseq.cli.MergeAction
-
- go(ActionHelper) - Method in class io.repseq.cli.NormalizeCloneAbundancesAction
-
- go(ActionHelper) - Method in class io.repseq.cli.StatAction
-
- go(ActionHelper) - Method in class io.repseq.cli.TsvAction
-
- GRepertoire - Class in io.repseq.gen
-
Represents immunological clone repertoire
- GRepertoire(List<GClone>) - Constructor for class io.repseq.gen.GRepertoire
-
- GRepertoireReader - Class in io.repseq.gen
-
- GRepertoireReader(BufferedReader) - Constructor for class io.repseq.gen.GRepertoireReader
-
- GRepertoireWriter - Class in io.repseq.gen
-
- GRepertoireWriter(OutputStream, VDJCLibrary) - Constructor for class io.repseq.gen.GRepertoireWriter
-
- randomizedRound(double, RandomGenerator) - Static method in class io.repseq.cli.ExportCloneSequencesAction
-
- read(PrimitivI) - Method in class io.repseq.core.GeneFeatureSerializer
-
- readArrayFromFile(String) - Static method in class io.repseq.dto.VDJCDataUtils
-
- readArrayFromFile(Path) - Static method in class io.repseq.dto.VDJCDataUtils
-
- readeFully() - Method in class io.repseq.gen.GRepertoireReader
-
- ReferencePoint - Class in io.repseq.core
-
Represents a BasicReferencePoint with offset.
- ReferencePoint(ReferencePoint, int) - Constructor for class io.repseq.core.ReferencePoint
-
Creates generalized reference point that represents pure reference point.
- ReferencePoint.Deserializer - Class in io.repseq.core
-
- ReferencePoint.Deserializer() - Constructor for class io.repseq.core.ReferencePoint.Deserializer
-
- ReferencePoint.JsonKeyDeserializer - Class in io.repseq.core
-
- ReferencePoint.JsonKeyDeserializer() - Constructor for class io.repseq.core.ReferencePoint.JsonKeyDeserializer
-
- ReferencePoint.JsonKeySerializer - Class in io.repseq.core
-
- ReferencePoint.JsonKeySerializer() - Constructor for class io.repseq.core.ReferencePoint.JsonKeySerializer
-
- ReferencePoint.Serializer - Class in io.repseq.core
-
- ReferencePoint.Serializer() - Constructor for class io.repseq.core.ReferencePoint.Serializer
-
- ReferencePoints - Class in io.repseq.core
-
- ReferencePoints(int[]) - Constructor for class io.repseq.core.ReferencePoints
-
- ReferencePoints(int, int[]) - Constructor for class io.repseq.core.ReferencePoints
-
- referencePoints - Variable in class io.repseq.core.SequenceProviderAndReferencePoints
-
- ReferencePoints.JDeserializer - Class in io.repseq.core
-
- ReferencePoints.JDeserializer() - Constructor for class io.repseq.core.ReferencePoints.JDeserializer
-
- ReferencePoints.JSerializer - Class in io.repseq.core
-
- ReferencePoints.JSerializer() - Constructor for class io.repseq.core.ReferencePoints.JSerializer
-
- ReferencePointsBuilder - Class in io.repseq.core
-
- ReferencePointsBuilder() - Constructor for class io.repseq.core.ReferencePointsBuilder
-
- ReferenceUtil - Class in io.repseq.core
-
- registerLibraries(String) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Register libraries from specific file
- registerLibraries(String, String) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Register libraries from specific file with specified name
- registerLibraries(Path) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Register libraries from specific file
- registerLibraries(Path, String) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Register libraries from specific file with specified name
- registerLibrary(Path, String, VDJCLibraryData) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Creates and registers single library from VDJCLibraryData
- registerParent(SequenceResolver) - Method in class io.repseq.seqbase.HTTPRedirectSequenceResolver
-
- registerParent(SequenceResolver) - Method in interface io.repseq.seqbase.ParentAwareResolver
-
Parent resolver invokes this method to provide link to itself for child
- relative(Range) - Method in class io.repseq.core.AbstractReferencePoints
-
- removeSymbol(String, char) - Static method in class io.repseq.util.StringWithMapping
-
- requireChecksumCheck() - Method in class io.repseq.core.VDJCLibraryId
-
Returns whether this id also contain checksum information
- resetDefaultRegistry() - Static method in class io.repseq.core.VDJCLibraryRegistry
-
Resets default VDJLibrary registry
- resetDefaultRegistry(SequenceResolver) - Static method in class io.repseq.core.VDJCLibraryRegistry
-
Resets default VDJLibrary registry and sets specific sequence resolver
- resolve(Path, SequenceResolver) - Method in class io.repseq.core.BaseSequence
-
Returns SequenceProvider to access underlying sequence
- resolve(String) - Method in class io.repseq.core.VDJCLibraryRegistry.ClasspathLibraryResolver
-
- resolve(String) - Method in class io.repseq.core.VDJCLibraryRegistry.FolderLibraryResolver
-
- resolve(String) - Method in interface io.repseq.core.VDJCLibraryRegistry.LibraryResolver
-
- resolve(SequenceAddress) - Method in class io.repseq.seqbase.AbstractRAFastaResolver
-
- resolve(SequenceAddress) - Method in class io.repseq.seqbase.AnySequenceResolver
-
- resolve(SequenceAddress) - Method in class io.repseq.seqbase.HTTPRedirectSequenceResolver
-
- resolve(SequenceAddress) - Method in class io.repseq.seqbase.MultiSequenceResolver
-
- resolve(SequenceAddress) - Method in interface io.repseq.seqbase.SequenceResolver
-
Resolves address and returns corresponding
- resolveAlias(String) - Method in interface io.repseq.core.VDJCLibraryRegistry.AliasResolver
-
- resolveAlias(String) - Method in class io.repseq.core.VDJCLibraryRegistry.ClasspathLibraryResolver
-
- resolveAlias(String) - Method in class io.repseq.core.VDJCLibraryRegistry.FolderLibraryResolver
-
- resolveCacheFileName(URI) - Method in class io.repseq.seqbase.HTTPFastaSequenceResolver
-
Resolves HTTP address to file name
- resolveCacheFileName(URI) - Method in class io.repseq.seqbase.HTTPRedirectSequenceResolver
-
Resolves HTTP address to file name
- resolveCacheFileName(URI) - Method in class io.repseq.seqbase.HTTPSequenceResolvers.NucCoreResolver
-
- resolveHTTPAddress(URI) - Method in class io.repseq.seqbase.HTTPFastaSequenceResolver
-
Resolves address to http/https link
- resolveHTTPAddress(URI) - Method in class io.repseq.seqbase.HTTPRedirectSequenceResolver
-
Resolves address to http/https link
- resolveHTTPAddress(URI) - Method in class io.repseq.seqbase.HTTPSequenceResolvers.NucCoreResolver
-
- resolveReader(SequenceAddress) - Method in class io.repseq.seqbase.AbstractRAFastaResolver
-
- resolveReaderId(SequenceAddress) - Method in class io.repseq.seqbase.AbstractRAFastaResolver
-
Extracts id to be used as key for reader from original address
- resolveReaderId(SequenceAddress) - Method in class io.repseq.seqbase.HTTPFastaSequenceResolver
-
- resolveReaderId(SequenceAddress) - Method in class io.repseq.seqbase.LocalFileResolver
-
- resolveRecordId(URI) - Method in class io.repseq.seqbase.AbstractRAFastaResolver
-
Extracts record name from original address
- resolveRecordId(URI) - Method in class io.repseq.seqbase.HTTPSequenceResolvers.NucCoreResolver
-
- resolveRecordId(URI) - Method in class io.repseq.seqbase.LocalFileResolver
-
- resolveSpecies(String) - Method in class io.repseq.core.VDJCLibraryRegistry
-
Resolves species name to taxon id
- reverse() - Method in class io.repseq.core.GeneFeature.ReferenceRange
-
- reverse() - Method in class io.repseq.core.GeneFeature
-
- reverse() - Method in class io.repseq.core.SequenceProviderAndReferencePoints
-
- v - Variable in class io.repseq.gen.dist.IndependentVDJCGenesModel
-
- v - Variable in class io.repseq.gen.dist.IndependentVDJTrimmingModel
-
- v - Variable in class io.repseq.gen.VDJCGenes
-
null represents absence of certain gene
- V5UTR - Static variable in class io.repseq.core.GeneFeature
-
- V5UTRBeginTrimmed - Static variable in class io.repseq.core.ReferencePoint
-
Beginning of IG/TCR transcript
- V5UTREnd - Static variable in class io.repseq.core.ReferencePoint
-
Beginning of IG/TCR transcript
- V5UTRGermline - Static variable in class io.repseq.core.GeneFeature
-
- validate(String, String) - Method in class io.repseq.cli.CLIUtils.GeneFeatureValidator
-
- validate() - Method in class io.repseq.cli.ExportCloneSequencesAction.Params
-
- validate() - Method in class io.repseq.cli.FromPaddedFastaAction.Params
-
- validate() - Method in class io.repseq.cli.GenerateClonesAction.Params
-
- validate() - Method in class io.repseq.cli.NormalizeCloneAbundancesAction.Params
-
- value - Variable in class io.repseq.gen.dist.FixedRealModel
-
- valueOf(String) - Static method in enum io.repseq.core.GeneType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.repseq.dto.GeneTag
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.repseq.dto.VDJCLibraryNoteType
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum io.repseq.core.GeneType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.repseq.dto.GeneTag
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.repseq.dto.VDJCLibraryNoteType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- VCDR3Part - Static variable in class io.repseq.core.GeneFeature
-
- VDJC_REFERENCE - Static variable in enum io.repseq.core.GeneType
-
- VDJCDataUtils - Class in io.repseq.dto
-
- VDJCDataUtils.FragmentsBuilder - Class in io.repseq.dto
-
- VDJCDataUtils.FragmentsBuilder() - Constructor for class io.repseq.dto.VDJCDataUtils.FragmentsBuilder
-
- VDJCGene - Class in io.repseq.core
-
This class represents the same entity as Allele class in previous abstraction version.
- VDJCGene(VDJCLibrary, VDJCGeneData, SequenceProvider<NucleotideSequence>, ReferencePoints) - Constructor for class io.repseq.core.VDJCGene
-
- VDJCGeneData - Class in io.repseq.dto
-
DTO for VDJC Gene
- VDJCGeneData(BaseSequence, String, GeneType, boolean, Chains, String, Set<GeneTag>, SortedMap<ReferencePoint, Long>) - Constructor for class io.repseq.dto.VDJCGeneData
-
- VDJCGeneId - Class in io.repseq.core
-
- VDJCGeneId(VDJCLibraryId, String) - Constructor for class io.repseq.core.VDJCGeneId
-
- vdjcGenes - Variable in class io.repseq.gen.GGene
-
V, D, J, C genes.
- VDJCGenes - Class in io.repseq.gen
-
Tuple of VDJC genes.
- VDJCGenes(VDJCGene, VDJCGene, VDJCGene, VDJCGene) - Constructor for class io.repseq.gen.VDJCGenes
-
- VDJCGenesGenerator - Interface in io.repseq.gen.dist
-
- vdjcGenesModel - Variable in class io.repseq.gen.dist.BasicGGeneModel
-
- VDJCGenesModel - Interface in io.repseq.gen.dist
-
- VDJCLibrary - Class in io.repseq.core
-
Class represent a single library of V, D, J, C genes from a single species.
- VDJCLibrary(VDJCLibraryData, String, VDJCLibraryRegistry, Path) - Constructor for class io.repseq.core.VDJCLibrary
-
- vdjcLibrary - Variable in class io.repseq.gen.dist.BasicGCloneModel
-
- VDJCLibraryData - Class in io.repseq.dto
-
- VDJCLibraryData(VDJCLibraryData, List<VDJCGeneData>) - Constructor for class io.repseq.dto.VDJCLibraryData
-
Creates VDJCLibraryData object from other VDJCLibraryData given new sed of genes
- VDJCLibraryData(long, List<String>, List<VDJCGeneData>, List<VDJCLibraryNote>, List<KnownSequenceFragmentData>) - Constructor for class io.repseq.dto.VDJCLibraryData
-
- VDJCLibraryId - Class in io.repseq.core
-
Taxon id and library name and optional library checksum
- VDJCLibraryId(String, long) - Constructor for class io.repseq.core.VDJCLibraryId
-
Creates VDJCLibraryId from taxonId and library name
- VDJCLibraryId(String, long, byte[]) - Constructor for class io.repseq.core.VDJCLibraryId
-
Creates VDJCLibraryId from taxonId, library name and checksum
- VDJCLibraryNote - Class in io.repseq.dto
-
Represents note block
- VDJCLibraryNote(VDJCLibraryNoteType, String) - Constructor for class io.repseq.dto.VDJCLibraryNote
-
- VDJCLibraryNoteType - Enum in io.repseq.dto
-
- VDJCLibraryRegistry - Class in io.repseq.core
-
Registry of VDJCLibraries.
- VDJCLibraryRegistry() - Constructor for class io.repseq.core.VDJCLibraryRegistry
-
Creates new VDJCLibraryRegistry with default sequence resolver
- VDJCLibraryRegistry(SequenceResolver) - Constructor for class io.repseq.core.VDJCLibraryRegistry
-
Creates new VDJCLibraryRegistry with specific sequence resolver.
- VDJCLibraryRegistry.AliasResolver - Interface in io.repseq.core
-
- VDJCLibraryRegistry.ClasspathLibraryResolver - Class in io.repseq.core
-
Load library data from {libraryName}.json files in specified folder.
- VDJCLibraryRegistry.ClasspathLibraryResolver(String, ClassLoader) - Constructor for class io.repseq.core.VDJCLibraryRegistry.ClasspathLibraryResolver
-
- VDJCLibraryRegistry.FolderLibraryResolver - Class in io.repseq.core
-
Load library data from {libraryName}.json files in specified folder.
- VDJCLibraryRegistry.FolderLibraryResolver(Path, boolean) - Constructor for class io.repseq.core.VDJCLibraryRegistry.FolderLibraryResolver
-
- VDJCLibraryRegistry.LibraryNameListProvider - Interface in io.repseq.core
-
- VDJCLibraryRegistry.LibraryResolver - Interface in io.repseq.core
-
Tries to resolve library name to array of VDJCLibraryData[] objects
E.g.
- VDJCUsageDistribution - Interface in io.repseq.gen
-
Represents "abstract" distribution of V, D, J, C genes.
- VDJCUsageDistributionInstance - Interface in io.repseq.gen
-
Represents actual distribution of V, D, J, C genes.
- VDJRegion - Static variable in class io.repseq.core.GeneFeature
-
- VDJTranscript - Static variable in class io.repseq.core.GeneFeature
-
- VDJTranscriptWithout5UTR - Static variable in class io.repseq.core.GeneFeature
-
- vdjTrimming - Variable in class io.repseq.gen.GGene
-
V, D, J genes trimming.
- VDJTrimming - Class in io.repseq.gen
-
Represents information on number of nucleotides deleted from 3' V, 5' J and both sides of D gene, if present;
or sizes of corresponding P-segments.
- VDJTrimming(int, int, DTrimming) - Constructor for class io.repseq.gen.VDJTrimming
-
- VDJTrimming(int, int) - Constructor for class io.repseq.gen.VDJTrimming
-
- VDJTrimming(int, int, int, int) - Constructor for class io.repseq.gen.VDJTrimming
-
- VDJTrimming(int, int, Integer, Integer) - Constructor for class io.repseq.gen.VDJTrimming
-
- VDJTrimmingGenerator - Interface in io.repseq.gen.dist
-
- VDJTrimmingModel - Interface in io.repseq.gen.dist
-
Trimming model, that depends on selected v, d, j, c genes.
- VDJunction - Static variable in class io.repseq.core.GeneFeature
-
- VEnd - Static variable in class io.repseq.core.ReferencePoint
-
Beginning of IG/TCR transcript
- VEndTrimmed - Static variable in class io.repseq.core.ReferencePoint
-
Beginning of IG/TCR transcript
- VExon2 - Static variable in class io.repseq.core.GeneFeature
-
- VExon2Trimmed - Static variable in class io.repseq.core.GeneFeature
-
- VGene - Static variable in class io.repseq.core.GeneFeature
-
- VGeneWithP - Static variable in class io.repseq.core.GeneFeature
-
- vInsert - Variable in class io.repseq.gen.GGene
-
Insert between V and D (if present) or J (if D gene is not present) genes
- vInsertModel - Variable in class io.repseq.gen.dist.BasicGGeneModel
-
- VIntron - Static variable in class io.repseq.core.GeneFeature
-
- VIntronBegin - Static variable in class io.repseq.core.ReferencePoint
-
Beginning of IG/TCR transcript
- VIntronEnd - Static variable in class io.repseq.core.ReferencePoint
-
Beginning of IG/TCR transcript
- VJC_REFERENCE - Static variable in enum io.repseq.core.GeneType
-
- VJJunction - Static variable in class io.repseq.core.GeneFeature
-
- VLIntronL - Static variable in class io.repseq.core.GeneFeature
-
- VPSegment - Static variable in class io.repseq.core.GeneFeature
-
- VRegion - Static variable in class io.repseq.core.GeneFeature
-
- VRegionTrimmed - Static variable in class io.repseq.core.GeneFeature
-
- VRegionWithP - Static variable in class io.repseq.core.GeneFeature
-
- VTranscript - Static variable in class io.repseq.core.GeneFeature
-
- VTranscriptWithout5UTR - Static variable in class io.repseq.core.GeneFeature
-
- VTranscriptWithout5UTRWithP - Static variable in class io.repseq.core.GeneFeature
-
- VTranscriptWithP - Static variable in class io.repseq.core.GeneFeature
-
- vTrimming - Variable in class io.repseq.gen.VDJTrimming
-