Uses of Class
jebl.evolution.distances.CannotBuildDistanceMatrixException
Packages that use CannotBuildDistanceMatrixException
Package
Description
Provides classes and interfaces for pairwise alignment of two sequences.
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Uses of CannotBuildDistanceMatrixException in jebl.evolution.align
Methods in jebl.evolution.align that throw CannotBuildDistanceMatrixExceptionModifier and TypeMethodDescriptionfinal String[]BartonSternberg.align(List<Sequence> sourceSequences, ProgressListener progress, boolean refineOnly, boolean estimateMatchMismatchCosts) AlignmentTreeBuilderFactory.build(List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) AlignmentTreeBuilderFactory.build(List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener) Will use model F84 for nucleotides and Jukes-Cantor for amino acidAlignmentTreeBuilderFactory.build(List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model) AlignmentTreeBuilderFactory.build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener) AlignmentTreeBuilderFactory.build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) Constructors in jebl.evolution.align that throw CannotBuildDistanceMatrixExceptionModifierConstructorDescriptionSequenceAlignmentsDistanceMatrix(List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress) SequenceAlignmentsDistanceMatrix(List<Sequence> seqs, PairwiseAligner aligner, ProgressListener progress, TreeBuilderFactory.DistanceModel model) -
Uses of CannotBuildDistanceMatrixException in jebl.evolution.distances
Constructors in jebl.evolution.distances that throw CannotBuildDistanceMatrixExceptionModifierConstructorDescriptionHKYDistanceMatrix(Alignment alignment, ProgressListener progress) HKYDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress) JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable) TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress) TamuraNeiDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)