Package io.repseq.core

Interface Summary

Interface	Description
VDJCLibraryRegistry.AliasResolver	Interface implemented by VDJCLibraryRegistry.LibraryResolver if it can also resolve library name aliases
VDJCLibraryRegistry.LibraryNameListProvider	Interface implemented by VDJCLibraryRegistry.LibraryResolver if it can provide list of all base library names it can resolve
VDJCLibraryRegistry.LibraryResolver	Tries to resolve library name to array of VDJCLibraryData[] objects E.g.

Class Summary

Class	Description
AbstractReferencePoints<T extends AbstractReferencePoints<T>>
AbstractReferencePointsBuilder<T extends AbstractReferencePoints<T>>
BaseSequence	DTO for BaseSequence Represents base sequence where V/D/J/C gene is located.
BaseSequence.Deserializer
BaseSequence.Serializer
Chains	Immutable set of strings
ExtendedReferencePoints
ExtendedReferencePointsBuilder
GeneFeature
GeneFeature.Deserializer
GeneFeature.ReferenceRange
GeneFeature.Serializer
GeneFeatureSerializer
GeneType.Deserializer
GeneType.Serializer
PartitionedSequence<S extends com.milaboratory.core.sequence.Seq<S>>
PartitionedSequenceCached<S extends com.milaboratory.core.sequence.Seq<S>>
ReferencePoint	Represents a BasicReferencePoint with offset.
ReferencePoint.Deserializer
ReferencePoint.JsonKeyDeserializer
ReferencePoint.JsonKeySerializer
ReferencePoint.Serializer
ReferencePoints
ReferencePoints.JDeserializer
ReferencePoints.JSerializer
ReferencePointsBuilder
ReferenceUtil
SequencePartitioning	Object stores information about sequence partitioning (positions of specific anchor points)
SequenceProviderAndReferencePoints	Tuple of SequenceProvider and ReferencePoints with useful methods.
VDJCGene	This class represents the same entity as Allele class in previous abstraction version.
VDJCGeneId
VDJCLibrary	Class represent a single library of V, D, J, C genes from a single species.
VDJCLibraryId	Taxon id and library name and optional library checksum
VDJCLibraryRegistry	Registry of VDJCLibraries.
VDJCLibraryRegistry.ClasspathLibraryResolver	Load library data from {libraryName}.json files in specified folder.
VDJCLibraryRegistry.FolderLibraryResolver	Load library data from {libraryName}.json files in specified folder.

Enum Summary

Enum	Description
GeneType	Group type of a segment.

Exception Summary

Exception	Description
GeneNotFoundException