com.milaboratory.core.alignment.blast

Class AABlastAlignerExt

java.lang.Object

com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract<AminoAcidSequence,AABlastHitExt>

com.milaboratory.core.alignment.blast.AABlastAlignerExt

All Implemented Interfaces:

PipedBatchAligner<AminoAcidSequence,AABlastHitExt>

public class AABlastAlignerExt
extends BlastAlignerExtAbstract<AminoAcidSequence,AABlastHitExt>

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
protected AABlastHitExt	createHit(Alignment<AminoAcidSequence> alignment, double score, double bitScore, double eValue, Range subjectRange, String subjectId, String subjectTitle)

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

align, align, setConcurrentBlastProcessCount

Methods inherited from class java.lang.Object

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

Constructor Detail

AABlastAlignerExt

public AABlastAlignerExt(BlastDB database)

AABlastAlignerExt

public AABlastAlignerExt(BlastDB database,
                 BlastAlignerParameters parameters)

Method Detail

createHit

protected AABlastHitExt createHit(Alignment<AminoAcidSequence> alignment,
                      double score,
                      double bitScore,
                      double eValue,
                      Range subjectRange,
                      String subjectId,
                      String subjectTitle)

Specified by:

createHit in class BlastAlignerExtAbstract<AminoAcidSequence,AABlastHitExt>