io.repseq.core

Class ReferencePoints

java.lang.Object

io.repseq.core.SequencePartitioning

io.repseq.core.AbstractReferencePoints<ReferencePoints>

io.repseq.core.ReferencePoints

All Implemented Interfaces:

java.io.Serializable

public final class ReferencePoints
extends AbstractReferencePoints<ReferencePoints>
implements java.io.Serializable

Basic reference points, excluding extended points (alignment-attached points like VEndTrimmed).

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ReferencePoints.JDeserializer
static class	ReferencePoints.JSerializer

Field Summary

Fields

Modifier and Type	Field and Description
static boolean[]	BASIC_REFERENCE_POINTS_TO_CHECK

Constructor Summary

Constructors

Constructor and Description
ReferencePoints(int[] points)
ReferencePoints(int start, int[] points)

Method Summary

Modifier and Type	Method and Description
protected ReferencePoints	create(int[] points)
protected int	indexFromReferencePoint(ReferencePoint point)

Methods inherited from class io.repseq.core.AbstractReferencePoints

equals, getContainingRegion, getFirstAvailablePosition, getLastAvailablePosition, getLengthBetweenBoundaryPoints, getPosition, hashCode, isReversed, move, numberOfDefinedPoints, relative, toString, without

Methods inherited from class io.repseq.core.SequencePartitioning

floorDiv, floorMod, getAbsolutePosition, getLength, getLength, getRange, getRange, getRanges, getRelativePosition, getRelativeRange, getTranslationParameters, getTranslationParameters, isAvailable, isAvailable, isAvailable

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

BASIC_REFERENCE_POINTS_TO_CHECK

public static final boolean[] BASIC_REFERENCE_POINTS_TO_CHECK

Constructor Detail

ReferencePoints

public ReferencePoints(int[] points)

ReferencePoints

public ReferencePoints(int start,
                       int[] points)

Method Detail

indexFromReferencePoint

protected int indexFromReferencePoint(ReferencePoint point)

Specified by:

indexFromReferencePoint in class AbstractReferencePoints<ReferencePoints>

create

protected ReferencePoints create(int[] points)

Specified by:

create in class AbstractReferencePoints<ReferencePoints>