| 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 | 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
|
| Chains.NamedChains | |
| ExtendedReferencePoints |
All reference points, including alignment-attached reference points (e.g.
|
| 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>> | |
| RangeTranslationParameters | |
| ReferencePoint |
Represents a
BasicReferencePoint with offset. |
| ReferencePoint.Deserializer | |
| ReferencePoint.JsonKeyDeserializer | |
| ReferencePoint.JsonKeySerializer | |
| ReferencePoint.Serializer | |
| ReferencePoints |
Basic reference points, excluding extended points (alignment-attached points like VEndTrimmed).
|
| 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 | Description |
|---|---|
| GeneType |
Group type of a segment.
|
| Exception | Description |
|---|---|
| GeneNotFoundException |