public interface TraceAlignmentWithGuideTreeSettingsListener
Modifier and Type | Method and Description |
---|---|
void |
setAlignmentAlgorithm(AlignmentAlgorithm alignmentAlgorithm) |
void |
setIncrementLikeSubstitutionScoreValue(int incrementLikeSubstitutionScoreValue) |
void |
setIndelScoreFileName(java.lang.String indelScoreFileName) |
void |
setIndelScoreScaleValue(float indelScoreScaleValue) |
void |
setIsDeriveSubstitutionIndelScores(boolean isDeriveSubstitutionIndelScores) |
void |
setIsGapPenalty(boolean isGapPenalty) |
void |
setIsIncrementLikeSubstitutionScores(boolean isIncrementLikeSubstitutionScores) |
void |
setIsPerformRealignment(boolean isPerformRealignment) |
void |
setIsScaleIndelScores(boolean isScaleIndelScores) |
void |
setRealignmentStrategy(RealignmentStrategy realignmentStrategy) |
void |
setScoringMatrix(ScoringMatrix scoringMatrix) |
void |
setSubstitutionScoreFileName(java.lang.String substitutionScoreFileName) |
void setIsDeriveSubstitutionIndelScores(boolean isDeriveSubstitutionIndelScores)
void setSubstitutionScoreFileName(java.lang.String substitutionScoreFileName)
void setIndelScoreFileName(java.lang.String indelScoreFileName)
void setAlignmentAlgorithm(AlignmentAlgorithm alignmentAlgorithm)
void setScoringMatrix(ScoringMatrix scoringMatrix)
void setIsIncrementLikeSubstitutionScores(boolean isIncrementLikeSubstitutionScores)
void setIsScaleIndelScores(boolean isScaleIndelScores)
void setIncrementLikeSubstitutionScoreValue(int incrementLikeSubstitutionScoreValue)
void setIndelScoreScaleValue(float indelScoreScaleValue)
void setIsGapPenalty(boolean isGapPenalty)
void setIsPerformRealignment(boolean isPerformRealignment)
void setRealignmentStrategy(RealignmentStrategy realignmentStrategy)