io.repseq.core

Class ExtendedReferencePoints

java.lang.Object

io.repseq.core.SequencePartitioning

io.repseq.core.AbstractReferencePoints<ExtendedReferencePoints>

io.repseq.core.ExtendedReferencePoints

public final class ExtendedReferencePoints
extends AbstractReferencePoints<ExtendedReferencePoints>

All reference points, including alignment-attached reference points (e.g. VEndTrimmed).

Field Summary

Fields

Modifier and Type	Field and Description
static boolean[]	EXTENDED_REFERENCE_POINTS_TO_CHECK

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
protected ExtendedReferencePoints	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

EXTENDED_REFERENCE_POINTS_TO_CHECK

public static final boolean[] EXTENDED_REFERENCE_POINTS_TO_CHECK

Constructor Detail

ExtendedReferencePoints

public ExtendedReferencePoints(int[] points)

ExtendedReferencePoints

public ExtendedReferencePoints(int start,
                               int[] points)

Method Detail

indexFromReferencePoint

protected int indexFromReferencePoint(ReferencePoint point)

Specified by:

indexFromReferencePoint in class AbstractReferencePoints<ExtendedReferencePoints>

create

protected ExtendedReferencePoints create(int[] points)

Specified by:

create in class AbstractReferencePoints<ExtendedReferencePoints>