public class TraceAlignmentWithGuideTreeInput
extends java.lang.Object
Constructor and Description |
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TraceAlignmentWithGuideTreeInput() |
public void setIsDeriveSubstitutionIndelScores(boolean isDeriveSubstitutionIndelScores)
public void setSubstitutionScoreFileName(java.lang.String substitutionScoreFileName)
public void setIndelScoreFileName(java.lang.String indelScoreFileName)
public boolean isDeriveSubstitutionIndelScores()
public void setScoringMatrix(ScoringMatrix scoringMatrix)
public void setAlignmentAlgorithm(AlignmentAlgorithm alignmentAlgorithm)
public void setIsIncrementLikeSubstitutionScores(boolean isIncrementLikeSubstitutionScores)
public void setIncrementLikeSubstitutionScoreValue(int incrementLikeSubstitutionScoreValue)
public void setIsGapPenalty(boolean isGapPenalty)
public java.lang.String getSubstitutionScoreFileName()
public java.lang.String getIndelScoreFileName()
public AlignmentAlgorithm getAlignmentAlgorithm()
public ScoringMatrix getScoringMatrix()
public boolean isIncrementLikeSubstitutionScores()
public boolean isScaleIndelScores()
public void setIsScaleIndelScores(boolean isScaleIndelScores)
public void setIndelScoreScaleValue(float indelScoreScaleValue)
public void setIsPerformRealignment(boolean isPerformRealignment)
public void setRealignmentStrategy(RealignmentStrategy realignmentStrategy)
public boolean isPerformRealignment()
public RealignmentStrategy getRealignmentStrategy()
public float getIndelScoreScaleValue()
public int getIncrementLikeSubstitutionScoreValue()
public boolean isGapPenalty()