Uses of Package
io.repseq.core

Packages that use io.repseq.core

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

Classes in io.repseq.core used by io.repseq.cli

Class and Description
Chains Immutable set of strings
GeneFeature
GeneType Group type of a segment.
VDJCLibrary Class represent a single library of V, D, J, C genes from a single species.

Classes in io.repseq.core used by io.repseq.core

Class and Description
AbstractReferencePoints
AbstractReferencePointsBuilder
BaseSequence DTO for BaseSequence Represents base sequence where V/D/J/C gene is located.
Chains Immutable set of strings
ExtendedReferencePoints
GeneFeature
GeneFeature.ReferenceRange
GeneType Group type of a segment.
PartitionedSequence
PartitionedSequenceCached
ReferencePoint Represents a BasicReferencePoint with offset.
ReferencePoints
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.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.

Classes in io.repseq.core used by io.repseq.dto

Class and Description
BaseSequence DTO for BaseSequence Represents base sequence where V/D/J/C gene is located.
Chains Immutable set of strings
GeneType Group type of a segment.
ReferencePoint Represents a BasicReferencePoint with offset.

Classes in io.repseq.core used by io.repseq.gen

Class and Description
GeneFeature
PartitionedSequence
PartitionedSequenceCached
SequencePartitioning Object stores information about sequence partitioning (positions of specific anchor points)
VDJCGene This class represents the same entity as Allele class in previous abstraction version.
VDJCLibrary Class represent a single library of V, D, J, C genes from a single species.

Classes in io.repseq.core used by io.repseq.gen.dist

Class and Description
GeneFeature
GeneType Group type of a segment.
VDJCGene This class represents the same entity as Allele class in previous abstraction version.
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.