Uses of Class
io.repseq.core.ReferencePoint

Packages that use ReferencePoint

Package	Description
io.repseq.core
io.repseq.dto

Uses of ReferencePoint in io.repseq.core

Fields in io.repseq.core declared as ReferencePoint

Modifier and Type	Field and Description
ReferencePoint	GeneFeature.ReferenceRange.begin
static ReferencePoint	ReferencePoint.CBegin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.CDR1Begin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.CDR1End Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.CDR2Begin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.CDR2End Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.CDR3Begin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.CDR3End Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.CEnd Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.CExon1End Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.DBegin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.DBeginTrimmed Beginning of IG/TCR transcript
static ReferencePoint[]	ReferencePoint.DefaultReferencePoints Default set of reference points.
static ReferencePoint	ReferencePoint.DEnd Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.DEndTrimmed Beginning of IG/TCR transcript
ReferencePoint	GeneFeature.ReferenceRange.end
static ReferencePoint	ReferencePoint.FR1Begin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.FR1End Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.FR2Begin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.FR2End Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.FR3Begin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.FR3End Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.FR4Begin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.FR4End Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.JBegin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.JBeginTrimmed Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.L1Begin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.L1End Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.L2Begin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.L2End Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.UTR5Begin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.V5UTRBeginTrimmed Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.V5UTREnd Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.VEnd Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.VEndTrimmed Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.VIntronBegin Beginning of IG/TCR transcript
static ReferencePoint	ReferencePoint.VIntronEnd Beginning of IG/TCR transcript

Methods in io.repseq.core that return ReferencePoint

Modifier and Type	Method and Description
ReferencePoint	ReferencePoint.Deserializer.deserialize(com.fasterxml.jackson.core.JsonParser jp, com.fasterxml.jackson.databind.DeserializationContext ctxt)
ReferencePoint	ReferencePoint.getActivationPoint()
ReferencePoint	GeneFeature.getFirstPoint()
static ReferencePoint	GeneFeature.getFrameReference(GeneFeature feature) Returns reference point that is triplet boundary (so defines reading frame) inside provided gene feature or returns null.
ReferencePoint	GeneFeature.getLastPoint()
ReferencePoint	GeneFeature.ReferenceRange.getLeftBoundary()
static ReferencePoint	ReferencePoint.getPointByName(String pointName)
ReferencePoint	GeneFeature.ReferenceRange.getRightBoundary()
ReferencePoint	ReferencePoint.getWithoutOffset()
ReferencePoint	ReferencePoint.move(int offset)
static ReferencePoint	ReferencePoint.parse(String string)

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

Modifier and Type	Method and Description
List<ReferencePoint>	GeneFeature.ReferenceRange.getIntermediatePoints()

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

Modifier and Type	Method and Description
int	ReferencePoint.compareTo(ReferencePoint o)
static String	ReferencePoint.encode(ReferencePoint point, boolean begin)
static String	ReferencePoint.getNameByPoint(ReferencePoint point)
int	ReferencePoint.getOffsetFrom(ReferencePoint other)
abstract int	SequencePartitioning.getPosition(ReferencePoint referencePoint) Return position of specific anchor point
int	AbstractReferencePoints.getPosition(ReferencePoint referencePoint)
static int	ReferenceUtil.getReferencePointIndex(ReferencePoint referencePoint) Returns underlying reference point id.
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.
protected int	ReferencePoints.indexFromReferencePoint(ReferencePoint point)
protected int	ExtendedReferencePoints.indexFromReferencePoint(ReferencePoint point)
protected abstract int	AbstractReferencePoints.indexFromReferencePoint(ReferencePoint point)
boolean	SequencePartitioning.isAvailable(ReferencePoint referencePoint) Checks if position of anchor point can be obtained using this partitioning
boolean	ReferencePoint.sameOrigin(ReferencePoint referencePoint)
void	ReferencePoint.Serializer.serialize(ReferencePoint value, com.fasterxml.jackson.core.JsonGenerator jgen, com.fasterxml.jackson.databind.SerializerProvider provider)
void	ReferencePoint.JsonKeySerializer.serialize(ReferencePoint value, com.fasterxml.jackson.core.JsonGenerator jgen, com.fasterxml.jackson.databind.SerializerProvider provider)
void	AbstractReferencePointsBuilder.setPosition(ReferencePoint referencePoint, int position)
T	AbstractReferencePoints.without(ReferencePoint referencePoint)

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

Constructor and Description
GeneFeature(ReferencePoint referencePoint, int leftOffset, int rightOffset)
GeneFeature(ReferencePoint begin, ReferencePoint end)
ReferencePoint(ReferencePoint referencePoint, int offset) Creates generalized reference point that represents pure reference point.

Uses of ReferencePoint in io.repseq.dto

Methods in io.repseq.dto that return types with arguments of type ReferencePoint

Modifier and Type	Method and Description
Map<ReferencePoint,Long>	VDJCGeneData.getAnchorPoints()

Constructor parameters in io.repseq.dto with type arguments of type ReferencePoint

Constructor and Description
VDJCGeneData(BaseSequence baseSequence, String name, GeneType geneType, boolean isFunctional, Chains chains, String note, Set<GeneTag> tags, SortedMap<ReferencePoint,Long> anchorPoints)