io.repseq.gen

Class GGene

java.lang.Object

io.repseq.core.PartitionedSequence<S>

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

io.repseq.gen.GGene

public final class GGene
extends PartitionedSequenceCached<com.milaboratory.core.sequence.NucleotideSequence>

Represents rearranged TCR/IG gene / sequence.

Field Summary

Fields

Modifier and Type	Field and Description
GeneFeature	definedIn Gene region where this gene is defined.
com.milaboratory.core.sequence.NucleotideSequence	djInsert Insert between D or J genes.
VDJCGenes	vdjcGenes V, D, J, C genes.
VDJTrimming	vdjTrimming V, D, J genes trimming.
com.milaboratory.core.sequence.NucleotideSequence	vInsert Insert between V and D (if present) or J (if D gene is not present) genes

Constructor Summary

Constructors

Constructor and Description
GGene(GeneFeature definedIn, VDJCGenes vdjcGenes, VDJTrimming vdjTrimming, com.milaboratory.core.sequence.NucleotideSequence vInsert, com.milaboratory.core.sequence.NucleotideSequence djInsert)
GGene(GeneFeature definedIn, VDJCGene v, VDJCGene d, VDJCGene j, VDJCGene c, int vTrimming, int jTrimming, java.lang.Integer d5Trimming, java.lang.Integer d3Trimming, com.milaboratory.core.sequence.NucleotideSequence vInsert, com.milaboratory.core.sequence.NucleotideSequence djInsert)

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
SequencePartitioning	getPartitioning()
com.milaboratory.core.sequence.NucleotideSequence	getSequence(com.milaboratory.core.Range range)
int	hashCode()

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

definedIn

public final GeneFeature definedIn

Gene region where this gene is defined. Access to sequences outside this region is forbidden.

vdjcGenes

public final VDJCGenes vdjcGenes

V, D, J, C genes.

vdjTrimming

public final VDJTrimming vdjTrimming

V, D, J genes trimming.

vInsert

public final com.milaboratory.core.sequence.NucleotideSequence vInsert

Insert between V and D (if present) or J (if D gene is not present) genes

djInsert

public final com.milaboratory.core.sequence.NucleotideSequence djInsert

Insert between D or J genes. Only if D gene is present.

Constructor Detail

GGene

public GGene(GeneFeature definedIn,
             VDJCGenes vdjcGenes,
             VDJTrimming vdjTrimming,
             com.milaboratory.core.sequence.NucleotideSequence vInsert,
             com.milaboratory.core.sequence.NucleotideSequence djInsert)

GGene

public GGene(GeneFeature definedIn,
             VDJCGene v,
             VDJCGene d,
             VDJCGene j,
             VDJCGene c,
             int vTrimming,
             int jTrimming,
             java.lang.Integer d5Trimming,
             java.lang.Integer d3Trimming,
             com.milaboratory.core.sequence.NucleotideSequence vInsert,
             com.milaboratory.core.sequence.NucleotideSequence djInsert)

Method Detail

getSequence

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

Specified by:

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

getPartitioning

public SequencePartitioning getPartitioning()

Specified by:

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

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