com.milaboratory.core.alignment.batch

Class AbstractBatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>

java.lang.Object

com.milaboratory.core.alignment.batch.AbstractBatchAligner<S,H>

All Implemented Interfaces:

BatchAligner<S,H>, PipedBatchAligner<S,H>

Direct Known Subclasses:

SimpleBatchAligner

public abstract class AbstractBatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>
extends Object
implements BatchAligner<S,H>, PipedBatchAligner<S,H>

Field Summary

Fields

Modifier and Type	Field and Description
protected int	threads 0 -> Runtime.getRuntime().availableProcessors() 1 -> process in the same thread as take() method call 2...

Constructor Summary

Constructors

Constructor and Description
AbstractBatchAligner()

Method Summary

Methods

Modifier and Type	Method and Description
<Q extends HasSequence<S>> cc.redberry.pipe.OutputPort<PipedAlignmentResult<H,Q>>	align(cc.redberry.pipe.OutputPort<Q> input) Starts processing of input sequences and returns pipe of results.
<Q> cc.redberry.pipe.OutputPort<PipedAlignmentResult<H,Q>>	align(cc.redberry.pipe.OutputPort<Q> input, SequenceExtractor<Q,S> extractor) Starts processing of input sequences and returns pipe of results.
abstract AlignmentResult<H>	align(S sequence)

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.milaboratory.core.alignment.batch.BatchAligner

align

Field Detail

threads

protected volatile int threads

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

Constructor Detail

AbstractBatchAligner

public AbstractBatchAligner()

Method Detail

align

public abstract AlignmentResult<H> align(S sequence)

Specified by:

align in interface BatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>

align

public <Q> cc.redberry.pipe.OutputPort<PipedAlignmentResult<H,Q>> align(cc.redberry.pipe.OutputPort<Q> input,
                                                               SequenceExtractor<Q,S> extractor)

Description copied from interface: PipedBatchAligner

Starts processing of input sequences and returns pipe of results.

Specified by:

align in interface PipedBatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>

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<S>> cc.redberry.pipe.OutputPort<PipedAlignmentResult<H,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<S extends Sequence<S>,H extends AlignmentHit<S,?>>

Type Parameters:

Q - type of query objects

Parameters:

input - pipe of queries

Returns:

pipe of alignment results