public class KAligner2<P> extends Object implements BatchAlignerWithBaseWithFilter<NucleotideSequence,P,KAlignmentHit2<P>>
| Constructor and Description |
|---|
KAligner2(KAlignerParameters2 parameters) |
KAligner2(KAlignerParameters2 parameters,
KAligner2Statistics stat) |
| Modifier and Type | Method and Description |
|---|---|
int |
addReference(NucleotideSequence sequence)
Adds new reference sequence to the base of this mapper and returns index assigned to it.
|
void |
addReference(NucleotideSequence sequence,
P payload)
Adds a record to the base of this aligner (a set of subject sequences that this instance aligns queries
with).
|
KAlignmentResult2<P> |
align(NucleotideSequence sequence) |
KAlignmentResult2<P> |
align(NucleotideSequence sequence,
int from,
int to) |
KAlignmentResult2<P> |
align(NucleotideSequence query,
int from,
int to,
BitArray filter) |
BitArray |
createFilter(cc.redberry.primitives.Filter<P> filter) |
NucleotideSequence |
getReference(int id)
Returns sequence by its id (order number) in a base.
|
public KAligner2(KAlignerParameters2 parameters)
public KAligner2(KAlignerParameters2 parameters, KAligner2Statistics stat)
public int addReference(NucleotideSequence sequence)
sequence - sequencepublic BitArray createFilter(cc.redberry.primitives.Filter<P> filter)
createFilter in interface BatchAlignerWithBaseWithFilter<NucleotideSequence,P,KAlignmentHit2<P>>public NucleotideSequence getReference(int id)
id - id of sequence to be returnedpublic void addReference(NucleotideSequence sequence, P payload)
WithBaseaddReference in interface WithBase<NucleotideSequence,P>sequence - sequencepayload - payload to store additional information with this record (can be retrieved from resulting AlignmentHit)public KAlignmentResult2<P> align(NucleotideSequence sequence)
align in interface BatchAligner<NucleotideSequence,KAlignmentHit2<P>>public KAlignmentResult2<P> align(NucleotideSequence sequence, int from, int to)
align in interface BatchAligner<NucleotideSequence,KAlignmentHit2<P>>public KAlignmentResult2<P> align(NucleotideSequence query, int from, int to, BitArray filter)
align in interface BatchAlignerWithBaseWithFilter<NucleotideSequence,P,KAlignmentHit2<P>>Copyright © 2018. All rights reserved.