io.repseq.core

Class VDJCGene

java.lang.Object

io.repseq.core.PartitionedSequence<S>

io.repseq.core.PartitionedSequenceCached<com.milaboratory.core.sequence.NucleotideSequence>

io.repseq.core.VDJCGene

All Implemented Interfaces:

java.lang.Comparable<VDJCGene>

public final class VDJCGene
extends PartitionedSequenceCached<com.milaboratory.core.sequence.NucleotideSequence>
implements java.lang.Comparable<VDJCGene>

This class represents the same entity as Allele class in previous abstraction version.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	JSON_CURRENT_LIBRARY_ATTRIBUTE_KEY Attribute key used to set current VDJCLibrary during serialization / deserialization.

Constructor Summary

Constructors

Constructor and Description
VDJCGene(VDJCLibrary parentLibrary, VDJCGeneData data, com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> sequenceProvider, ReferencePoints referencePoints) Use VDJCLibrary.addGene(VDJCLibrary, VDJCGeneData) to create instances of this object.

Method Summary

Modifier and Type	Method and Description
int	compareTo(VDJCGene o)
boolean	equals(java.lang.Object o)
Chains	getChains() Returns set of chains (e.g.
VDJCGeneData	getData() Returns serializable gene data
java.lang.String	getFamilyName() Gene family name (e.g.
java.lang.String	getFullName() Return full gene name, including library id (e.g.
java.lang.String	getGeneName() Name without allele index (e.g.
GeneType	getGeneType() Returns gene type
VDJCGeneId	getId() Returns global gene identifier including library id
java.lang.String	getName() Returns gene name (e.g.
VDJCLibrary	getParentLibrary() Returns parent VDJCLibrary
ReferencePoints	getPartitioning() Returns reference point object for this gene
protected com.milaboratory.core.sequence.NucleotideSequence	getSequence(com.milaboratory.core.Range range)
com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence>	getSequenceProvider() Returns sequence provider associated with this gene
SequenceProviderAndReferencePoints	getSPAndRPs() Returns tuple of SequenceProvider and ReferencePoints with useful methods
int	hashCode()
boolean	isComplete() Returns whether all reference points for this gene are defined
boolean	isFunctional() Returns true if this gene marked as functional

Methods inherited from class io.repseq.core.PartitionedSequenceCached

getFeature

Methods inherited from class java.lang.Object

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

Field Detail

JSON_CURRENT_LIBRARY_ATTRIBUTE_KEY

public static final java.lang.String JSON_CURRENT_LIBRARY_ATTRIBUTE_KEY

Attribute key used to set current VDJCLibrary during serialization / deserialization. If not set full gene names will be written to the output file, and global VDJCLibraryRegistry will be used for gene lookup.

See Also:

Constant Field Values

Constructor Detail

VDJCGene

public VDJCGene(VDJCLibrary parentLibrary,
                VDJCGeneData data,
                com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> sequenceProvider,
                ReferencePoints referencePoints)

Use VDJCLibrary.addGene(VDJCLibrary, VDJCGeneData) to create instances of this object.

Method Detail

getSequenceProvider

public com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> getSequenceProvider()

Returns sequence provider associated with this gene

Returns:

sequence provider associated with this gene

getData

public VDJCGeneData getData()

Returns serializable gene data

Returns:

serializable gene data

getParentLibrary

public VDJCLibrary getParentLibrary()

Returns parent VDJCLibrary

Returns:

parent VDJCLibrary

getId

public VDJCGeneId getId()

Returns global gene identifier including library id

Returns:

global gene identifier including library id

getFullName

public java.lang.String getFullName()

Return full gene name, including library id (e.g. repseqio.v.1.2:9060:6dc0513f4400b2abd19487474154a77e/TRBV12-3*00)

Returns:

full gene name, including library id (e.g. repseqio.v.1.2:9060:6dc0513f4400b2abd19487474154a77e/TRBV12-3*00)

getName

public java.lang.String getName()

Returns gene name (e.g. TRBV12-2*01)

Returns:

gene name (e.g. TRBV12-2*01)

getGeneName

public java.lang.String getGeneName()

Name without allele index (e.g. TRBV12-3 for TRBV12-3*01).

Returns:

without allele index (e.g. TRBV12-3 for TRBV12-3*01)

getFamilyName

public java.lang.String getFamilyName()

Gene family name (e.g. TRBV12 for TRBV12-3*01).

Returns:

gene family name (e.g. TRBV12 for TRBV12-3*01)

getGeneType

public GeneType getGeneType()

Returns gene type

Returns:

gene type

isFunctional

public boolean isFunctional()

Returns true if this gene marked as functional

Returns:

true if this gene marked as functional

getChains

public Chains getChains()

Returns set of chains (e.g. TRB, IGH, IGL, etc...) in which this gene can be used. For some genes set can contain several entries (e.g. TRA and TRD for TRAV23DV6)

Returns:

set of chains (e.g. TRA, TRD) in which this gene can be used.

getSPAndRPs

public SequenceProviderAndReferencePoints getSPAndRPs()

Returns tuple of SequenceProvider and ReferencePoints with useful methods

Returns:

tuple of SequenceProvider and ReferencePoints with useful methods

getSequence

protected com.milaboratory.core.sequence.NucleotideSequence getSequence(com.milaboratory.core.Range range)

Specified by:

getSequence in class PartitionedSequence<com.milaboratory.core.sequence.NucleotideSequence>

isComplete

public boolean isComplete()

Returns whether all reference points for this gene are defined

Returns:

whether all reference points for this gene are defined

getPartitioning

public ReferencePoints getPartitioning()

Returns reference point object for this gene

Specified by:

getPartitioning in class PartitionedSequence<com.milaboratory.core.sequence.NucleotideSequence>

Returns:

reference point object for this gene

compareTo

public int compareTo(VDJCGene o)

Specified by:

compareTo in interface java.lang.Comparable<VDJCGene>

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object