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.Result
AlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, MultipleAligner aligner, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
static AlignmentTreeBuilderFactory.Result
AlignmentTreeBuilderFactory. 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.Result
AlignmentTreeBuilderFactory. build(java.util.List<Sequence> seqs, TreeBuilderFactory.Method method, PairwiseAligner aligner, ProgressListener progressListener, TreeBuilderFactory.DistanceModel model)
static AlignmentTreeBuilderFactory.Result
AlignmentTreeBuilderFactory. build(Alignment alignment, TreeBuilderFactory.Method method, TreeBuilderFactory.DistanceModel model, ProgressListener progressListener)
static AlignmentTreeBuilderFactory.Result
AlignmentTreeBuilderFactory. 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)
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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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