| Package | Description |
|---|---|
| io.repseq.core | |
| io.repseq.dto |
| 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
|
| 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) |
| Modifier and Type | Method and Description |
|---|---|
List<ReferencePoint> |
GeneFeature.ReferenceRange.getIntermediatePoints() |
| 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) |
| 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.
|
| Modifier and Type | Method and Description |
|---|---|
Map<ReferencePoint,Long> |
VDJCGeneData.getAnchorPoints() |
| Constructor and Description |
|---|
VDJCGeneData(BaseSequence baseSequence,
String name,
GeneType geneType,
boolean isFunctional,
Chains chains,
String note,
Set<GeneTag> tags,
SortedMap<ReferencePoint,Long> anchorPoints) |
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