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