com.milaboratory.core.alignment.kaligner1

Class KAligner<P>

java.lang.Object

com.milaboratory.core.alignment.kaligner1.KAligner<P>

All Implemented Interfaces:

BatchAligner<NucleotideSequence,KAlignmentHit<P>>, BatchAlignerWithBase<NucleotideSequence,P,KAlignmentHit<P>>, BatchAlignerWithBaseWithFilter<NucleotideSequence,P,KAlignmentHit<P>>, PipedBatchAligner<NucleotideSequence,KAlignmentHit<P>>, PipedBatchAlignerWithBase<NucleotideSequence,P,KAlignmentHit<P>>, WithBase<NucleotideSequence,P>, Serializable

public class KAligner<P>
extends Object
implements PipedBatchAlignerWithBase<NucleotideSequence,P,KAlignmentHit<P>>, BatchAlignerWithBaseWithFilter<NucleotideSequence,P,KAlignmentHit<P>>, Serializable

KAligner is a comprehensive aligner for nucleotide sequences.

Complete alignment of sequence performed using KMapper.addReference(com.milaboratory.core.sequence.NucleotideSequence, int, int) method from which preliminary hits are obtained and used by align(com.milaboratory.core.sequence.NucleotideSequence), align(com.milaboratory.core.sequence.NucleotideSequence, int, int), align(com.milaboratory.core.sequence.NucleotideSequence, int, int, boolean, BitArray) methods.

All settings are stored in parameters property.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
KAligner(KAlignerParameters parameters) Creates new KAligner.
KAligner(KAlignerParameters parameters, boolean lazyResults) Creates new KAligner.

Method Summary

Methods

Modifier and Type	Method and Description
int	addReference(NucleotideSequence sequence) Adds new reference sequence to the base of this aligner and returns index assigned to it.
int	addReference(NucleotideSequence sequence, int offset, int length) 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).
KAlignmentResult<P>	align(NucleotideSequence sequence) Performs a comprehensive alignment of a sequence.
KAlignmentResult<P>	align(NucleotideSequence sequence, int from, int to) Performs a comprehensive alignment of a sequence.
AlignmentResult<KAlignmentHit<P>>	align(NucleotideSequence sequence, int from, int to, BitArray filter)
KAlignmentResult<P>	align(NucleotideSequence sequence, int from, int to, boolean restrictToRange, BitArray filter) Performs a comprehensive alignment of a sequence.
<Q extends HasSequence<NucleotideSequence>> cc.redberry.pipe.OutputPort<KAlignmentResultP<P,Q>>	align(cc.redberry.pipe.OutputPort<Q> input) Starts processing of input sequences and returns pipe of results.
<Q> cc.redberry.pipe.OutputPort<KAlignmentResultP<P,Q>>	align(cc.redberry.pipe.OutputPort<Q> input, SequenceExtractor<Q,NucleotideSequence> extractor) Starts processing of input sequences and returns pipe of results.
BitArray	createFilter(cc.redberry.primitives.Filter<P> filter)
NucleotideSequence	getReference(int id) Returns sequence by its id (order number) in a base.
void	setThreadCount(int threads) Sets number of threads to be used in piped processing. 0 -> Runtime.getRuntime().availableProcessors() 1 -> process in the same thread as take() method call 2...

Methods inherited from class java.lang.Object

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

Constructor Detail

KAligner

public KAligner(KAlignerParameters parameters)

Creates new KAligner.

Sets lazyResults flag to false, which means that all alignments inside KAlignmentResult obtained by align(com.milaboratory.core.sequence.NucleotideSequence, int, int, boolean, BitArray) method will be loaded immediately.

Parameters:

parameters - parameters from which new KAligner needs to be created

KAligner

public KAligner(KAlignerParameters parameters,
        boolean lazyResults)

Creates new KAligner.

Parameters:

parameters - parameters from which new KAligner needs to be created

lazyResults - true if all alignments inside KAlignmentResult obtained by align(com.milaboratory.core.sequence.NucleotideSequence, int, int, boolean, BitArray) method need to be loaded at first request

Method Detail

setThreadCount

public void setThreadCount(int threads)

Sets number of threads to be used in piped processing.

0 -> Runtime.getRuntime().availableProcessors()
1 -> process in the same thread as take() method call
2... -> parallel processor

addReference

public int addReference(NucleotideSequence sequence)

Adds new reference sequence to the base of this aligner 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,KAlignmentHit<P>>

addReference

public int addReference(NucleotideSequence sequence,
               int offset,
               int length)

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

User can specify a part of a sequence to be indexed by KMapper, but KAligner stores whole adding sequences.

Parameters:

sequence - sequence

offset - offset of subsequence to be indexed by KMapper

length - length of subsequence to be indexed by KMapper

Returns:

index assigned to the sequence

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

align

public KAlignmentResult<P> align(NucleotideSequence sequence)

Performs a comprehensive alignment of a sequence.

The procedure consists of 2 steps:

• 1. Obtaining KMappingResult from KMapper using KMapper.align(com.milaboratory.core.sequence.NucleotideSequence) which contains preliminary hits
• 2. Using KMappingResult from step 1, obtaining KAlignmentResult by align(com.milaboratory.core.sequence.NucleotideSequence, int, int, boolean, BitArray) method, where all hit alignments may be loaded lazily (at first request) or immediately (depends on lazyResults flag value)

Specified by:

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

Parameters:

sequence - sequence to be aligned

Returns:

a list of hits found in target sequence

align

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

Performs a comprehensive alignment of a sequence.

The procedure consists of 2 steps:

• 1. Obtaining KMappingResult from KMapper using KMapper.align(com.milaboratory.core.sequence.NucleotideSequence) which contains preliminary hits
• 2. Using KMappingResult from step 1, obtaining KAlignmentResult by align(com.milaboratory.core.sequence.NucleotideSequence, int, int, boolean, BitArray) method, where all hit alignments may be loaded lazily (at first request) or immediately (depends on lazyResults flag value)

Specified by:

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

Parameters:

sequence - sequence to be aligned

from - first nucleotide to be aligned (inclusive)

to - last nucleotide to be aligned (exclusive)

Returns:

a list of hits found in target sequence

align

public KAlignmentResult<P> align(NucleotideSequence sequence,
                        int from,
                        int to,
                        boolean restrictToRange,
                        BitArray filter)

Performs a comprehensive alignment of a sequence.

The procedure consists of 2 steps:

• 1. Obtaining KMappingResult from KMapper using KMapper.align(com.milaboratory.core.sequence.NucleotideSequence) which contains preliminary hits
• 2. Using KMappingResult from step 1, obtaining KAlignmentResult by align(com.milaboratory.core.sequence.NucleotideSequence, int, int, boolean, BitArray) method, where all hit alignments may be loaded lazily (at first request) or immediately (depends on lazyResults flag value)

Parameters:

sequence - sequence to be aligned

from - first nucleotide to be aligned by KMapper (inclusive)

to - last nucleotide to be aligned by KMapper (exclusive)

restrictToRange - true if hits alignments from obtained KAlignmentResult should be restricted by the same range (from - to)

Returns:

a list of hits found in target sequence

align

public AlignmentResult<KAlignmentHit<P>> align(NucleotideSequence sequence,
                                      int from,
                                      int to,
                                      BitArray filter)

Specified by:

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

align

public <Q> cc.redberry.pipe.OutputPort<KAlignmentResultP<P,Q>> align(cc.redberry.pipe.OutputPort<Q> input,
                                                            SequenceExtractor<Q,NucleotideSequence> extractor)

Description copied from interface: PipedBatchAligner

Starts processing of input sequences and returns pipe of results.

Specified by:

align in interface PipedBatchAligner<NucleotideSequence,KAlignmentHit<P>>

Type Parameters:

Q - type of query object

Parameters:

input - pipe of queries

extractor - extractor of sequences from query object

Returns:

pipe of alignment results

align

public <Q extends HasSequence<NucleotideSequence>> cc.redberry.pipe.OutputPort<KAlignmentResultP<P,Q>> align(cc.redberry.pipe.OutputPort<Q> input)

Description copied from interface: PipedBatchAligner

Starts processing of input sequences and returns pipe of results.

Specified by:

align in interface PipedBatchAligner<NucleotideSequence,KAlignmentHit<P>>

Type Parameters:

Q - type of query objects

Parameters:

input - pipe of queries

Returns:

pipe of alignment results

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)