io.repseq.core

Class VDJCLibrary

java.lang.Object

io.repseq.core.VDJCLibrary

All Implemented Interfaces:

java.lang.Comparable<VDJCLibrary>

public class VDJCLibrary
extends java.lang.Object
implements java.lang.Comparable<VDJCLibrary>

Class represent a single library of V, D, J, C genes from a single species. This class may represent a full set of genes in organism e.g. TRA,B,G,D/IGH,L,K or just a set of segments for a single immune receptor chain. VDJCLibrary can be loaded using VDJCLibraryRegistry.

Constructor Summary

Constructors

Constructor and Description
VDJCLibrary(VDJCLibraryData libraryData, java.lang.String name, VDJCLibraryRegistry registry, java.nio.file.Path context)

Method Summary

Modifier and Type	Method and Description
static VDJCGene	addGene(VDJCLibrary library, VDJCGeneData geneData) Creates full featured VDJCGene object from VDJCGene DTO object, and adds it to VDJCLibrary
int	compareTo(VDJCLibrary o)
VDJCGene	get(java.lang.String geneName) Get gene by name.
byte[]	getChecksum() Return checksum for this library.
java.util.SortedSet<java.lang.String>	getCitations() Set of citations specified for this library.
java.util.SortedSet<java.lang.String>	getComments() All comment blocks associated with the library
java.nio.file.Path	getContext() Returns library context folder
VDJCLibraryData	getData() Returns serializable library data
java.util.Collection<VDJCGene>	getGenes() Returns collection of all genes in this library
java.util.Collection<VDJCGene>	getGenes(Chains chains) Returns collection of all genes in this library with specific chains
java.util.Collection<VDJCGene>	getGenes(Chains chains, GeneType geneType) Returns collection of all genes in this library with specific geneType and chains
java.util.Collection<VDJCGene>	getGenes(GeneType geneType) Returns collection of all genes in this library with specific geneType
VDJCLibraryId	getLibraryId() Returns identifier of this library
java.lang.String	getName() Library name
VDJCLibraryRegistry	getParent() Returns parent registry
VDJCGene	getSafe(java.lang.String geneName) Get gene by name.
long	getTaxonId() Return species (taxon id)
java.util.SortedSet<java.lang.String>	getWarnings() Warnings, associated with the library.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

VDJCLibrary

public VDJCLibrary(VDJCLibraryData libraryData,
                   java.lang.String name,
                   VDJCLibraryRegistry registry,
                   java.nio.file.Path context)

Method Detail

getChecksum

public byte[] getChecksum()

Return checksum for this library.

Returns:

checksum for this library

getData

public VDJCLibraryData getData()

Returns serializable library data

Returns:

serializable library data

getParent

public VDJCLibraryRegistry getParent()

Returns parent registry

Returns:

parent registry

getContext

public java.nio.file.Path getContext()

Returns library context folder

Returns:

library context folder

getGenes

public java.util.Collection<VDJCGene> getGenes()

Returns collection of all genes in this library

Returns:

collection of all genes in this library

getGenes

public java.util.Collection<VDJCGene> getGenes(Chains chains)

Returns collection of all genes in this library with specific chains

Returns:

collection of all genes in this library with specific chains

getGenes

public java.util.Collection<VDJCGene> getGenes(GeneType geneType)

Returns collection of all genes in this library with specific geneType

Returns:

collection of all genes in this library with specific geneType

getGenes

public java.util.Collection<VDJCGene> getGenes(Chains chains,
                                               GeneType geneType)

Returns collection of all genes in this library with specific geneType and chains

Returns:

collection of all genes in this library with specific geneType and chains

get

public VDJCGene get(java.lang.String geneName)

Get gene by name. Returns VDJCGene or null if gene with provided name is not found

Returns:

VDJCGene or null if gene with provided name is not found

getSafe

public VDJCGene getSafe(java.lang.String geneName)

Get gene by name. Returns VDJCGene or throws GeneNotFoundException if gene not found.

Returns:

gene

Throws:

GeneNotFoundException

getLibraryId

public VDJCLibraryId getLibraryId()

Returns identifier of this library

Returns:

identifier of this library

getTaxonId

public long getTaxonId()

Return species (taxon id)

Returns:

species (taxon id)

getName

public java.lang.String getName()

Library name

Returns:

library name

getCitations

public java.util.SortedSet<java.lang.String> getCitations()

Set of citations specified for this library. E.g. can be used to remind academic users to cite specific paper, that this library was published with.

getWarnings

public java.util.SortedSet<java.lang.String> getWarnings()

Warnings, associated with the library. E.g. it is not finished yet (beta release).

getComments

public java.util.SortedSet<java.lang.String> getComments()

All comment blocks associated with the library

addGene

public static VDJCGene addGene(VDJCLibrary library,
                               VDJCGeneData geneData)

Creates full featured VDJCGene object from VDJCGene DTO object, and adds it to VDJCLibrary

Parameters:

library - library

geneData - gene DTO

Returns:

full featured VDJCGene object

compareTo

public int compareTo(VDJCLibrary o)

Specified by:

compareTo in interface java.lang.Comparable<VDJCLibrary>