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Packages that use CannotBuildDistanceMatrixException | |
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jebl.evolution.align | Provides classes and interfaces for pairwise alignment of two sequences. |
jebl.evolution.distances |
Uses of CannotBuildDistanceMatrixException in jebl.evolution.align |
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Methods in jebl.evolution.align that throw CannotBuildDistanceMatrixException | |
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java.lang.String[] |
BartonSternberg.align(java.util.List<Sequence> sourceSequences,
ProgressListener progress,
boolean refineOnly,
boolean estimateMatchMismatchCosts)
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static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(Alignment alignment,
TreeBuilderFactory.Method method,
TreeBuilderFactory.DistanceModel model,
ProgressListener progressListener)
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static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(Alignment alignment,
TreeBuilderFactory.Method method,
TreeBuilderFactory.DistanceModel model,
ProgressListener progressListener,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs,
TreeBuilderFactory.Method method,
MultipleAligner aligner,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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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 acid |
static AlignmentTreeBuilderFactory.Result |
AlignmentTreeBuilderFactory.build(java.util.List<Sequence> seqs,
TreeBuilderFactory.Method method,
PairwiseAligner aligner,
ProgressListener progressListener,
TreeBuilderFactory.DistanceModel model)
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Constructors in jebl.evolution.align that throw CannotBuildDistanceMatrixException | |
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SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress)
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SequenceAlignmentsDistanceMatrix(java.util.List<Sequence> seqs,
PairwiseAligner aligner,
ProgressListener progress,
TreeBuilderFactory.DistanceModel model)
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Uses of CannotBuildDistanceMatrixException in jebl.evolution.distances |
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Constructors in jebl.evolution.distances that throw CannotBuildDistanceMatrixException | |
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HKYDistanceMatrix(Alignment alignment,
ProgressListener progress)
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HKYDistanceMatrix(Alignment alignment,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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JukesCantorDistanceMatrix(Alignment alignment,
ProgressListener progress)
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JukesCantorDistanceMatrix(Alignment alignment,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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TamuraNeiDistanceMatrix(Alignment alignment,
ProgressListener progress)
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TamuraNeiDistanceMatrix(Alignment alignment,
ProgressListener progress,
boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
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