com.milaboratory.core.alignment.blast

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

java.lang.Object

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

com.milaboratory.core.alignment.blast.BlastAligner<S,P>

All Implemented Interfaces:

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

public class BlastAligner<S extends Sequence<S>,P>
extends BlastAlignerAbstract<S,P,BlastHit<S,P>>

Constructor Summary

Constructors

Constructor and Description
BlastAligner()
BlastAligner(BlastAlignerParameters parameters)

Method Summary

Methods

Modifier and Type	Method and Description
protected BlastHit<S,P>	createHit(Alignment<S> alignment, P recordPayload, BlastHit<S,?> hit)

Methods inherited from class com.milaboratory.core.alignment.blast.BlastAlignerAbstract

addReference, align, align, setConcurrentBlastProcessCount

Methods inherited from class java.lang.Object

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

Constructor Detail

BlastAligner

public BlastAligner()

BlastAligner

public BlastAligner(BlastAlignerParameters parameters)

Method Detail

createHit

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

Specified by:

createHit in class BlastAlignerAbstract<S extends Sequence<S>,P,BlastHit<S extends Sequence<S>,P>>