com.milaboratory.core.alignment.blast

Class BlastAlignerExtAbstract<S extends Sequence<S>,H extends BlastHitExt<S>>

java.lang.Object

com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract<S,H>

All Implemented Interfaces:

PipedBatchAligner<S,H>

Direct Known Subclasses:

AABlastAlignerExt, BlastAlignerExt, NBlastAlignerExt

public abstract class BlastAlignerExtAbstract<S extends Sequence<S>,H extends BlastHitExt<S>>
extends Object
implements PipedBatchAligner<S,H>

Blast aligner of query sequences with external (non-milib-managed) database of sequences.

Constructor Summary

Constructors

Constructor and Description
BlastAlignerExtAbstract(BlastDB database)
BlastAlignerExtAbstract(BlastDB database, BlastAlignerParameters parameters)

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.
protected abstract H	createHit(Alignment<S> alignment, double score, double bitScore, double eValue, Range subjectRange, String subjectId, String subjectTitle)
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

BlastAlignerExtAbstract

public BlastAlignerExtAbstract(BlastDB database)

BlastAlignerExtAbstract

public BlastAlignerExtAbstract(BlastDB database,
                       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<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 BlastHitExt<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 BlastHitExt<S>>

Type Parameters:

Q - type of query objects

Parameters:

input - pipe of queries

Returns:

pipe of alignment results

createHit

protected abstract H createHit(Alignment<S> alignment,
          double score,
          double bitScore,
          double eValue,
          Range subjectRange,
          String subjectId,
          String subjectTitle)