io.repseq.core

Class AbstractReferencePoints<T extends AbstractReferencePoints<T>>

java.lang.Object

io.repseq.core.SequencePartitioning

io.repseq.core.AbstractReferencePoints<T>

Direct Known Subclasses:

ExtendedReferencePoints, ReferencePoints

public abstract class AbstractReferencePoints<T extends AbstractReferencePoints<T>>
extends SequencePartitioning

Method Summary

Modifier and Type	Method and Description
protected abstract T	create(int[] points)
boolean	equals(java.lang.Object o)
com.milaboratory.core.Range	getContainingRegion()
int	getFirstAvailablePosition()
int	getLastAvailablePosition()
int	getLengthBetweenBoundaryPoints()
int	getPosition(ReferencePoint referencePoint) Return position of specific anchor point
int	hashCode()
protected abstract int	indexFromReferencePoint(ReferencePoint point)
boolean	isReversed() Return true if sequence partitioning is defined on the reverse-complement strand of the sequence, false if on forward strand.
T	move(int offset)
int	numberOfDefinedPoints()
T	relative(com.milaboratory.core.Range range)
java.lang.String	toString()
T	without(ReferencePoint referencePoint)

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

Method Detail

create

protected abstract T create(int[] points)

indexFromReferencePoint

protected abstract int indexFromReferencePoint(ReferencePoint point)

isReversed

public boolean isReversed()

Description copied from class: SequencePartitioning

Return true if sequence partitioning is defined on the reverse-complement strand of the sequence, false if on forward strand.

Specified by:

isReversed in class SequencePartitioning

Returns:

true if partitioning is defined on the reverse-complement strand

numberOfDefinedPoints

public int numberOfDefinedPoints()

without

public T without(ReferencePoint referencePoint)

move

public T move(int offset)

relative

public T relative(com.milaboratory.core.Range range)

getFirstAvailablePosition

public int getFirstAvailablePosition()

getLastAvailablePosition

public int getLastAvailablePosition()

getContainingRegion

public com.milaboratory.core.Range getContainingRegion()

getLengthBetweenBoundaryPoints

public int getLengthBetweenBoundaryPoints()

getPosition

public int getPosition(ReferencePoint referencePoint)

Description copied from class: SequencePartitioning

Return position of specific anchor point

Specified by:

getPosition in class SequencePartitioning

Parameters:

referencePoint - anchor point

Returns:

position of anchor point

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object