com.milaboratory.core.alignment.kaligner2

Class KAligner2<P>

java.lang.Object

com.milaboratory.core.alignment.kaligner2.KAligner2<P>

All Implemented Interfaces:

BatchAligner<NucleotideSequence,KAlignmentHit2<P>>, BatchAlignerWithBase<NucleotideSequence,P,KAlignmentHit2<P>>, BatchAlignerWithBaseWithFilter<NucleotideSequence,P,KAlignmentHit2<P>>, WithBase<NucleotideSequence,P>

public class KAligner2<P>
extends Object
implements BatchAlignerWithBaseWithFilter<NucleotideSequence,P,KAlignmentHit2<P>>

Author:

Dmitry Bolotin, Stanislav Poslavsky

Constructor Summary

Constructors

Constructor and Description
KAligner2(KAlignerParameters2 parameters)
KAligner2(KAlignerParameters2 parameters, KAligner2Statistics stat)

Method Summary

Methods

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.

Methods inherited from class java.lang.Object

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

Constructor Detail

KAligner2

public KAligner2(KAlignerParameters2 parameters)

KAligner2

public KAligner2(KAlignerParameters2 parameters,
         KAligner2Statistics stat)

Method Detail

addReference

public int addReference(NucleotideSequence sequence)

Adds new reference sequence to the base of this mapper and returns index assigned to it.

Parameters:

sequence - sequence

Returns:

index assigned to the sequence

createFilter

public BitArray createFilter(cc.redberry.primitives.Filter<P> filter)

Specified by:

createFilter in interface BatchAlignerWithBaseWithFilter<NucleotideSequence,P,KAlignmentHit2<P>>

getReference

public NucleotideSequence getReference(int id)

Returns sequence by its id (order number) in a base.

Parameters:

id - id of sequence to be returned

Returns:

sequence

addReference

public void addReference(NucleotideSequence sequence,
                P payload)

Description copied from interface: WithBase

Adds a record to the base of this aligner (a set of subject sequences that this instance aligns queries with).

Specified by:

addReference in interface WithBase<NucleotideSequence,P>

Parameters:

sequence - sequence

payload - payload to store additional information with this record (can be retrieved from resulting AlignmentHit)

align

public KAlignmentResult2<P> align(NucleotideSequence sequence)

Specified by:

align in interface BatchAligner<NucleotideSequence,KAlignmentHit2<P>>

align

public KAlignmentResult2<P> align(NucleotideSequence sequence,
                         int from,
                         int to)

Specified by:

align in interface BatchAligner<NucleotideSequence,KAlignmentHit2<P>>

align

public KAlignmentResult2<P> align(NucleotideSequence query,
                         int from,
                         int to,
                         BitArray filter)

Specified by:

align in interface BatchAlignerWithBaseWithFilter<NucleotideSequence,P,KAlignmentHit2<P>>