io.repseq.core

Class SequenceProviderAndReferencePoints

java.lang.Object

io.repseq.core.PartitionedSequence<S>

io.repseq.core.PartitionedSequenceCached<com.milaboratory.core.sequence.NucleotideSequence>

io.repseq.core.SequenceProviderAndReferencePoints

public final class SequenceProviderAndReferencePoints
extends PartitionedSequenceCached<com.milaboratory.core.sequence.NucleotideSequence>

Tuple of SequenceProvider and ReferencePoints with useful methods.

Field Summary

Fields

Modifier and Type	Field and Description
ReferencePoints	referencePoints
com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence>	sequenceProvider

Constructor Summary

Constructors

Constructor and Description
SequenceProviderAndReferencePoints(com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> sequenceProvider, ReferencePoints referencePoints)

Method Summary

Modifier and Type	Method and Description
protected SequencePartitioning	getPartitioning()
protected com.milaboratory.core.sequence.NucleotideSequence	getSequence(com.milaboratory.core.Range range)
SequenceProviderAndReferencePoints	nonReversedView()
SequenceProviderAndReferencePoints	reverse()

Methods inherited from class io.repseq.core.PartitionedSequenceCached

getFeature

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

sequenceProvider

public final com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> sequenceProvider

referencePoints

public final ReferencePoints referencePoints

Constructor Detail

SequenceProviderAndReferencePoints

public SequenceProviderAndReferencePoints(com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> sequenceProvider,
                                          ReferencePoints referencePoints)

Method Detail

getSequence

protected com.milaboratory.core.sequence.NucleotideSequence getSequence(com.milaboratory.core.Range range)

Specified by:

getSequence in class PartitionedSequence<com.milaboratory.core.sequence.NucleotideSequence>

getPartitioning

protected SequencePartitioning getPartitioning()

Specified by:

getPartitioning in class PartitionedSequence<com.milaboratory.core.sequence.NucleotideSequence>

reverse

public SequenceProviderAndReferencePoints reverse()

nonReversedView

public SequenceProviderAndReferencePoints nonReversedView()