Uses of Class
io.repseq.core.GeneFeature

Packages that use GeneFeature

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

Uses of GeneFeature in io.repseq.cli

Fields in io.repseq.cli declared as GeneFeature

Modifier and Type	Field and Description
GeneFeature	CLIUtils.GeneFeatureWithOriginalName.feature

Methods in io.repseq.cli that return GeneFeature

Modifier and Type	Method and Description
GeneFeature	InferAnchorPointsAction.Params.getGeneFeature()
GeneFeature	FastaAction.Params.getGeneFeature()
GeneFeature	ExportCloneSequencesAction.Params.getGeneFeature()

Constructors in io.repseq.cli with parameters of type GeneFeature

Constructor and Description
CLIUtils.GeneFeatureWithOriginalName(GeneFeature feature, String originalName)
TsvAction.NameAndGeneFeature(String name, GeneFeature feature)

Uses of GeneFeature in io.repseq.core

Fields in io.repseq.core declared as GeneFeature

Modifier and Type	Field and Description
static GeneFeature	GeneFeature.CDR1
static GeneFeature	GeneFeature.CDR2
static GeneFeature	GeneFeature.CDR3
static GeneFeature	GeneFeature.CExon1
static GeneFeature	GeneFeature.CRegion
static GeneFeature	GeneFeature.DCDR3Part
static GeneFeature	GeneFeature.DJJunction
static GeneFeature	GeneFeature.DLeftPSegment
static GeneFeature	GeneFeature.DRegion
static GeneFeature	GeneFeature.DRegionTrimmed
static GeneFeature	GeneFeature.DRegionWithP
static GeneFeature	GeneFeature.DRightPSegment
static GeneFeature	GeneFeature.Exon1
static GeneFeature	GeneFeature.Exon2
static GeneFeature	GeneFeature.FR1
static GeneFeature	GeneFeature.FR2
static GeneFeature	GeneFeature.FR3
static GeneFeature	GeneFeature.FR4
static GeneFeature	GeneFeature.GermlineDPSegment
static GeneFeature	GeneFeature.GermlineJCDR3Part
static GeneFeature	GeneFeature.GermlineJPSegment
static GeneFeature	GeneFeature.GermlineVCDR3Part
static GeneFeature	GeneFeature.GermlineVPSegment
static GeneFeature	GeneFeature.JCDR3Part
static GeneFeature	GeneFeature.JPSegment
static GeneFeature	GeneFeature.JRegion
static GeneFeature	GeneFeature.JRegionTrimmed
static GeneFeature	GeneFeature.JRegionWithP
static GeneFeature	GeneFeature.L
static GeneFeature	GeneFeature.L1
static GeneFeature	GeneFeature.L2
static GeneFeature	GeneFeature.ShortCDR3
static GeneFeature	GeneFeature.V5UTR
static GeneFeature	GeneFeature.V5UTRGermline
static GeneFeature	GeneFeature.VCDR3Part
static GeneFeature	GeneFeature.VDJRegion
static GeneFeature	GeneFeature.VDJTranscript
static GeneFeature	GeneFeature.VDJTranscriptWithout5UTR
static GeneFeature	GeneFeature.VDJunction
static GeneFeature	GeneFeature.VExon2
static GeneFeature	GeneFeature.VExon2Trimmed
static GeneFeature	GeneFeature.VGene
static GeneFeature	GeneFeature.VGeneWithP
static GeneFeature	GeneFeature.VIntron
static GeneFeature	GeneFeature.VJJunction
static GeneFeature	GeneFeature.VLIntronL
static GeneFeature	GeneFeature.VPSegment
static GeneFeature	GeneFeature.VRegion
static GeneFeature	GeneFeature.VRegionTrimmed
static GeneFeature	GeneFeature.VRegionWithP
static GeneFeature	GeneFeature.VTranscript
static GeneFeature	GeneFeature.VTranscriptWithout5UTR
static GeneFeature	GeneFeature.VTranscriptWithout5UTRWithP
static GeneFeature	GeneFeature.VTranscriptWithP

Methods in io.repseq.core that return GeneFeature

Modifier and Type	Method and Description
GeneFeature	GeneFeature.append(GeneFeature gf)
GeneFeature	GeneFeature.Deserializer.deserialize(com.fasterxml.jackson.core.JsonParser jp, com.fasterxml.jackson.databind.DeserializationContext ctxt)
static GeneFeature	GeneFeature.getCodingGeneFeature(GeneFeature feature) Returns coding gene feature contained in input gene feature
static GeneFeature	GeneFeature.getFeatureByName(String pointName)
static GeneFeature	GeneFeature.getRegion(GeneType type)
static GeneFeature	GeneFeature.intersection(GeneFeature gf1, GeneFeature gf2)
static GeneFeature	GeneFeature.intersection(GeneFeature gf1, GeneFeature gf2, boolean strict)
static GeneFeature	GeneFeature.intersectionStrict(GeneFeature gf1, GeneFeature gf2)
static GeneFeature	GeneFeature.parse(String string)
GeneFeature	GeneFeatureSerializer.read(com.milaboratory.primitivio.PrimitivI input)
GeneFeature	GeneFeature.reverse()

Methods in io.repseq.core that return types with arguments of type GeneFeature

Modifier and Type	Method and Description
static Map<String,GeneFeature>	GeneFeature.getFeaturesByName()
static Map<GeneFeature,String>	GeneFeature.getNameByFeature()

Methods in io.repseq.core with parameters of type GeneFeature

Modifier and Type	Method and Description
GeneFeature	GeneFeature.append(GeneFeature gf)
int	GeneFeature.compareTo(GeneFeature o)
boolean	GeneFeature.contains(GeneFeature geneFeature)
static String	GeneFeature.encode(GeneFeature feature)
int	SequencePartitioning.getAbsolutePosition(GeneFeature feature, int positionInFeature) Returns absolute position in reference sequence for the specified local position in specified feature or -1 if this position can't be projected.
static GeneFeature	GeneFeature.getCodingGeneFeature(GeneFeature feature) Returns coding gene feature contained in input gene feature
S	PartitionedSequenceCached.getFeature(GeneFeature feature)
S	PartitionedSequence.getFeature(GeneFeature feature)
static ReferencePoint	GeneFeature.getFrameReference(GeneFeature feature) Returns reference point that is triplet boundary (so defines reading frame) inside provided gene feature or returns null.
int	SequencePartitioning.getLength(GeneFeature feature)
static String	GeneFeature.getNameByFeature(GeneFeature point)
com.milaboratory.core.Range	SequencePartitioning.getRange(GeneFeature feature) Return sequence range for non-composite gene features
com.milaboratory.core.Range[]	SequencePartitioning.getRanges(GeneFeature feature)
int	SequencePartitioning.getRelativePosition(GeneFeature feature, ReferencePoint referencePoint) Returns a relative position of specified referencePoint in specified feature or -1 if this position is not available.
com.milaboratory.core.Range	SequencePartitioning.getRelativeRange(GeneFeature feature, GeneFeature subFeature) Returns a relative range of specified subFeature in specified feature or null if this is not available.
com.milaboratory.core.sequence.TranslationParameters	SequencePartitioning.getTranslationParameters(GeneFeature feature) Calculates translation parameters ( ~ translation frame ) for given gene feature using current sequence partitioning.
static GeneFeature	GeneFeature.intersection(GeneFeature gf1, GeneFeature gf2)
static GeneFeature	GeneFeature.intersection(GeneFeature gf1, GeneFeature gf2, boolean strict)
static GeneFeature	GeneFeature.intersectionStrict(GeneFeature gf1, GeneFeature gf2)
boolean	SequencePartitioning.isAvailable(GeneFeature feature) Checks if position of gene feature can be obtained using this partitioning
static boolean	GeneFeature.match(GeneFeature.ReferenceRange a, GeneFeature b)
void	GeneFeature.Serializer.serialize(GeneFeature value, com.fasterxml.jackson.core.JsonGenerator jgen, com.fasterxml.jackson.databind.SerializerProvider provider)
void	GeneFeatureSerializer.write(com.milaboratory.primitivio.PrimitivO output, GeneFeature object)

Constructors in io.repseq.core with parameters of type GeneFeature

Constructor and Description
GeneFeature(GeneFeature... features)
GeneFeature(GeneFeature feature, int leftOffset, int rightOffset)

Uses of GeneFeature in io.repseq.gen

Fields in io.repseq.gen declared as GeneFeature

Modifier and Type	Field and Description
GeneFeature	GGene.definedIn Gene region where this gene is defined.

Constructors in io.repseq.gen with parameters of type GeneFeature

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, Integer d5Trimming, Integer d3Trimming, com.milaboratory.core.sequence.NucleotideSequence vInsert, com.milaboratory.core.sequence.NucleotideSequence djInsert)

Uses of GeneFeature in io.repseq.gen.dist

Methods in io.repseq.gen.dist that return GeneFeature

Modifier and Type	Method and Description
static GeneFeature	CommonNormalGeneTrimmingModel.cdr3Part(GeneType geneType)