com.milaboratory.core.alignment.batch

Class SimpleBatchAligner<S extends Sequence<S>,P>

java.lang.Object

com.milaboratory.core.alignment.batch.AbstractBatchAligner<S,AlignmentHit<S,P>>

com.milaboratory.core.alignment.batch.SimpleBatchAligner<S,P>

Type Parameters:

S - type of sequence

P - type of record payload, used to store additional information along with sequence to simplify it's subsequent identification in result (e.g. Integer to just index sequences.

All Implemented Interfaces:

BatchAligner<S,AlignmentHit<S,P>>, BatchAlignerWithBase<S,P,AlignmentHit<S,P>>, PipedBatchAligner<S,AlignmentHit<S,P>>, WithBase<S,P>

public class SimpleBatchAligner<S extends Sequence<S>,P>
extends AbstractBatchAligner<S,AlignmentHit<S,P>>
implements BatchAlignerWithBase<S,P,AlignmentHit<S,P>>

Simplest implementation of BatchAligner, which aligns target sequence with all subjects using classical (low performance) alignment algorithms.

Field Summary

Fields inherited from class com.milaboratory.core.alignment.batch.AbstractBatchAligner

threads

Constructor Summary

Constructors

Constructor and Description
SimpleBatchAligner(SimpleBatchAlignerParameters<S> parameters)

Method Summary

Methods

Modifier and Type	Method and Description
void	addReference(S sequence, P payload) Adds a record to the base of this aligner (a set of subject sequences that this instance aligns queries with).
AlignmentResult<AlignmentHit<S,P>>	align(S sequence)
AlignmentResult<AlignmentHit<S,P>>	align(S sequence, int from, int to)

Methods inherited from class com.milaboratory.core.alignment.batch.AbstractBatchAligner

align, align

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleBatchAligner

public SimpleBatchAligner(SimpleBatchAlignerParameters<S> parameters)

Method Detail

addReference

public void addReference(S 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<S extends Sequence<S>,P>

Parameters:

sequence - sequence

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

align

public AlignmentResult<AlignmentHit<S,P>> align(S sequence,
                                       int from,
                                       int to)

Specified by:

align in interface BatchAligner<S extends Sequence<S>,AlignmentHit<S extends Sequence<S>,P>>

align

public AlignmentResult<AlignmentHit<S,P>> align(S sequence)

Specified by:

align in interface BatchAligner<S extends Sequence<S>,AlignmentHit<S extends Sequence<S>,P>>

Specified by:

align in class AbstractBatchAligner<S extends Sequence<S>,AlignmentHit<S extends Sequence<S>,P>>