com.milaboratory.core.alignment.blast

Class AABlastAligner<P>

java.lang.Object

com.milaboratory.core.alignment.blast.BlastAlignerAbstract<AminoAcidSequence,P,AABlastHit<P>>

com.milaboratory.core.alignment.blast.AABlastAligner<P>

All Implemented Interfaces:

PipedBatchAligner<AminoAcidSequence,AABlastHit<P>>, PipedBatchAlignerWithBase<AminoAcidSequence,P,AABlastHit<P>>, WithBase<AminoAcidSequence,P>

public class AABlastAligner<P>
extends BlastAlignerAbstract<AminoAcidSequence,P,AABlastHit<P>>

Constructor Summary

Constructors

Constructor and Description
AABlastAligner()
AABlastAligner(BlastAlignerParameters parameters)

Method Summary

Methods

Modifier and Type	Method and Description
protected AABlastHit<P>	createHit(Alignment<AminoAcidSequence> alignment, P recordPayload, BlastHit<AminoAcidSequence,?> 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

AABlastAligner

public AABlastAligner()

AABlastAligner

public AABlastAligner(BlastAlignerParameters parameters)

Method Detail

createHit

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

Specified by:

createHit in class BlastAlignerAbstract<AminoAcidSequence,P,AABlastHit<P>>