ReferencePoint (repseqio 1.3.5 API)

java.lang.Object
- io.repseq.core.ReferencePoint

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<ReferencePoint>
```
public final class ReferencePoint
extends java.lang.Object
implements java.lang.Comparable<ReferencePoint>, java.io.Serializable
```
Represents a BasicReferencePoint with offset.

See Also:

GeneFeature, Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`ReferencePoint.Deserializer`
`static class`	`ReferencePoint.JsonKeyDeserializer`
`static class`	`ReferencePoint.JsonKeySerializer`
`static class`	`ReferencePoint.Serializer`

Field Summary

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

Constructor Summary

Constructors
Constructor and Description

ReferencePoint(ReferencePoint referencePoint, int offset)
Creates generalized reference point that represents pure reference point.

Constructors
Constructor and Description
`ReferencePoint(ReferencePoint referencePoint, int offset)` Creates generalized reference point that represents pure reference point.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`compareTo(ReferencePoint o)`
`static java.lang.String`	`encode(ReferencePoint point, boolean begin)`
`boolean`	`equals(java.lang.Object o)`
`ReferencePoint`	`getActivationPoint()`
`GeneType`	`getGeneType()`
`static java.lang.String`	`getNameByPoint(ReferencePoint point)`
`int`	`getOffset()` Returns offset.
`int`	`getOffsetFrom(ReferencePoint other)`
`static ReferencePoint`	`getPointByName(java.lang.String pointName)`
`ReferencePoint`	`getWithoutOffset()`
`int`	`hashCode()`
`boolean`	`hasNoOffset()` Returns true if offset is equals to zero, so this object represents pure reference point.
`boolean`	`isAttachedToAlignmentBound()`
`boolean`	`isAttachedToLeftAlignmentBound()`
`boolean`	`isBasicPoint()`
`boolean`	`isCodingOnBothSides()` Returns isCodingSequenceOnTheLeft() && isCodingSequenceOnTheRight()
`boolean`	`isCodingSequenceBoundary()` Returns isCodingSequenceOnTheLeft() != isCodingSequenceOnTheRight()
`boolean`	`isCodingSequenceOnTheLeft()`
`boolean`	`isCodingSequenceOnTheRight()`
`boolean`	`isTrimmable()`
`boolean`	`isTripletBoundary()`
`ReferencePoint`	`move(int offset)`
`static ReferencePoint`	`parse(java.lang.String string)`
`boolean`	`sameOrigin(ReferencePoint referencePoint)`
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait