com.milaboratory.core.alignment.blast

Class BlastAlignerAbstract<S extends Sequence<S>,P,H extends BlastHit<S,P>>

java.lang.Object

com.milaboratory.core.alignment.blast.BlastAlignerAbstract<S,P,H>

All Implemented Interfaces:

PipedBatchAligner<S,H>, PipedBatchAlignerWithBase<S,P,H>, WithBase<S,P>

Direct Known Subclasses:

AABlastAligner, BlastAligner, NBlastAligner

public abstract class BlastAlignerAbstract<S extends Sequence<S>,P,H extends BlastHit<S,P>>
extends Object
implements PipedBatchAlignerWithBase<S,P,H>

Constructor Summary

Constructors

Constructor and Description
BlastAlignerAbstract()
BlastAlignerAbstract(BlastAlignerParameters 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).
<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<? extends PipedAlignmentResult<H,Q>>	align(cc.redberry.pipe.OutputPort<Q> input, SequenceExtractor<Q,S> extractor) Starts processing of input sequences and returns pipe of results.
protected abstract H	createHit(Alignment<S> alignment, P recordPayload, BlastHit<S,?> hit)
void	setConcurrentBlastProcessCount(int processCount) Sets the number of concurrent BLAST processes to serve a single alignment session (single align(OutputPort) or align(OutputPort, SequenceExtractor method invocation).

Methods inherited from class java.lang.Object

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

Constructor Detail

BlastAlignerAbstract

public BlastAlignerAbstract()

BlastAlignerAbstract

public BlastAlignerAbstract(BlastAlignerParameters parameters)

Method Detail

setConcurrentBlastProcessCount

public void setConcurrentBlastProcessCount(int processCount)

Sets the number of concurrent BLAST processes to serve a single alignment session (single align(OutputPort) or align(OutputPort, SequenceExtractor method invocation).

Parameters:

processCount - number of concurrent processes

align

public <Q> cc.redberry.pipe.OutputPort<? extends 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 BlastHit<S,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<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 BlastHit<S,P>>

Type Parameters:

Q - type of query objects

Parameters:

input - pipe of queries

Returns:

pipe of alignment results

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)

createHit

protected abstract H createHit(Alignment<S> alignment,
          P recordPayload,
          BlastHit<S,?> hit)