public abstract class BlastAlignerAbstract<S extends Sequence<S>,P,H extends BlastHit<S,P>> extends Object implements PipedBatchAlignerWithBase<S,P,H>
| Constructor and Description |
|---|
BlastAlignerAbstract() |
BlastAlignerAbstract(BlastAlignerParameters parameters) |
| 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>> |
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). |
public BlastAlignerAbstract()
public BlastAlignerAbstract(BlastAlignerParameters parameters)
public void setConcurrentBlastProcessCount(int processCount)
align(OutputPort) or align(OutputPort, SequenceExtractor method invocation).processCount - number of concurrent processespublic <Q> cc.redberry.pipe.OutputPort<? extends PipedAlignmentResult<H,Q>> align(cc.redberry.pipe.OutputPort<Q> input, SequenceExtractor<Q,S> extractor)
PipedBatchAlignerpublic <Q extends HasSequence<S>> cc.redberry.pipe.OutputPort<PipedAlignmentResult<H,Q>> align(cc.redberry.pipe.OutputPort<Q> input)
PipedBatchAlignerpublic void addReference(S sequence, P payload)
WithBaseaddReference in interface WithBase<S extends Sequence<S>,P>sequence - sequencepayload - payload to store additional information with this record (can be retrieved from resulting AlignmentHit)Copyright © 2018. All rights reserved.