Uses of Class
jebl.evolution.trees.TreeBuilderFactory.Method
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Packages that use TreeBuilderFactory.Method Package Description jebl.evolution.align Provides classes and interfaces for pairwise alignment of two sequences.jebl.evolution.trees -
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Uses of TreeBuilderFactory.Method in jebl.evolution.align
Methods in jebl.evolution.align with parameters of type TreeBuilderFactory.Method Modifier and Type Method Description 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)
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Uses of TreeBuilderFactory.Method in jebl.evolution.trees
Methods in jebl.evolution.trees that return TreeBuilderFactory.Method Modifier and Type Method Description static TreeBuilderFactory.Method
TreeBuilderFactory.Method. valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.static TreeBuilderFactory.Method[]
TreeBuilderFactory.Method. values()
Returns an array containing the constants of this enum type, in the order they are declared.Methods in jebl.evolution.trees with parameters of type TreeBuilderFactory.Method Modifier and Type Method Description static ClusteringTreeBuilder
ClusteringTreeBuilder. getBuilder(TreeBuilderFactory.Method method, DistanceMatrix distances)
A factory method to create a ClusteringTreeBuilderstatic ClusteringTreeBuilder
TreeBuilderFactory. getBuilder(TreeBuilderFactory.Method method, DistanceMatrix distances)
static boolean
TreeBuilderFactory. isRootedMethod(TreeBuilderFactory.Method method)
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