Uses of Interface
jebl.evolution.trees.RootedTree
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Packages that use RootedTree Package Description jebl.evolution.align Provides classes and interfaces for pairwise alignment of two sequences.jebl.evolution.coalescent jebl.evolution.treemetrics jebl.evolution.trees jebl.evolution.treesimulation -
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Uses of RootedTree in jebl.evolution.align
Methods in jebl.evolution.align with parameters of type RootedTree Modifier and Type Method Description AlignmentBartonSternberg. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)AlignmentMultipleAligner. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress) -
Uses of RootedTree in jebl.evolution.coalescent
Constructors in jebl.evolution.coalescent with parameters of type RootedTree Constructor Description Coalescent(RootedTree tree, DemographicFunction demographicFunction)Intervals(RootedTree tree) -
Uses of RootedTree in jebl.evolution.treemetrics
Methods in jebl.evolution.treemetrics with parameters of type RootedTree Modifier and Type Method Description doubleBilleraMetric. getMetric(RootedTree tree1, RootedTree tree2)doubleCladeHeightMetric. getMetric(RootedTree tree1, RootedTree tree2)doubleRobinsonsFouldMetric. getMetric(RootedTree tree1, RootedTree tree2)doubleRootedTreeMetric. getMetric(RootedTree tree1, RootedTree tree2)calculates the metric between two rooted trees -
Uses of RootedTree in jebl.evolution.trees
Classes in jebl.evolution.trees that implement RootedTree Modifier and Type Class Description classAbstractRootedTreeclassCompactRootedTreeA memory efficient rooted tree.classFilteredRootedTreeclassMutableRootedTreeA simple rooted tree providing some ability to manipulate the tree.classReRootedTreeA rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree.classRootedFromUnrootedRoot an unrooted tree.classRootedSubtreeA simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..classSimpleRootedTreeA simple, and initially immutable rooted tree implementation.classSortedRootedTreeclassTransformedRootedTreeThis RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.Methods in jebl.evolution.trees that return RootedTree Modifier and Type Method Description static RootedTreeUtils. copyTree(RootedTree treeToCopy)This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.RootedTreeFilteredRootedTree. getSource()static RootedTreeUtils. rootTheTree(Tree tree)Return a rooted tree from any tree.static RootedTreeReRootedTree. rootTreeAtCenter(RootedTree tree)Root any tree by locating the "center" of tree and adding a new root node at that pointstatic RootedTreeUtils. rootTreeAtCenter(Tree tree)Root any tree by locating the "center" of tree and adding a new root node at that pointMethods in jebl.evolution.trees with parameters of type RootedTree Modifier and Type Method Description voidCladeSystem. add(RootedTree tree)adds all the clades in the treevoidCalculateSplitRates. addTreeToDensityMap(jebl.evolution.trees.CalculateSplitRates.DensityMap densityMap, RootedTree tree)static ConsensusTreeBuilderTreeBuilderFactory. buildRooted(RootedTree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)static RootedTreeUtils. copyTree(RootedTree treeToCopy)This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.static java.util.Comparator<Node>Utils. createNodeDensityComparator(RootedTree tree)static java.util.Comparator<Node>Utils. createNodeDensityMinNodeHeightComparator(RootedTree tree)NodeReRootedTree. createNodes(RootedTree tree, Node parent, Node child)Clones the entire tree structure from the given (unrooted) Tree.NodeSimpleRootedTree. createNodes(RootedTree tree, Node node)Clones the entire tree structure from the given RootedTree.static java.lang.StringUtils. DEBUGsubTreeRep(RootedTree tree, Node node)static booleanRootedTreeUtils. equal(RootedTree tree1, RootedTree tree2)Compares 2 trees and returns true if they have the same topology.static doubleRootedTreeUtils. getAverageTipDistance(RootedTree tree, Node node)returns the average distance from the given node to all the tips below itstatic NodeRootedTreeUtils. getCommonAncestorNode(RootedTree tree, java.util.Set<Node> tipNodes)Gets the most recent common ancestor (MRCA) node of a set of tip nodes.static java.util.Set<Node>RootedTreeUtils. getDescendantTips(RootedTree tree, Node node)Gets a set of tip nodes descended from the given node.static intUtils. getExternalNodeCount(RootedTree tree, Node node)Return the number of external nodes under this node.static doubleUtils. getLength(RootedTree tree)static doubleRootedTreeUtils. getMaxTipHeight(RootedTree tree, Node node)static doubleUtils. getMinNodeHeight(RootedTree tree, Node node)static doubleRootedTreeUtils. getMinTipHeight(RootedTree tree, Node node)static java.util.List<Node>Utils. getNodes(RootedTree tree, Node node)All nodes in subtree - parents before children (pre - order).static intRootedTreeUtils. getTipCount(RootedTree tree, Node node)Return the number of leaves under this node.static java.util.Set<Node>RootedTreeUtils. getTipsForTaxa(RootedTree tree, java.util.Collection<Taxon> taxa)Gets a set of external nodes that correspond to the given taxa.static booleanRootedTreeUtils. isBinary(RootedTree tree)static booleanUtils. isBinary(RootedTree rootedTree)static booleanRootedTreeUtils. isMonophyletic(RootedTree tree, java.util.Set<Node> tipNodes)Performs the a monophyly test on a set of tip nodes.static booleanRootedTreeUtils. isUltrametric(RootedTree tree, double tolerance)static booleanUtils. isUltrametric(RootedTree rootedTree)static NodeUtils. leftNb(RootedTree tree, Node node)Left Neighbour of a tip (taxon).static intUtils. maxLevels(RootedTree tree)static NodeUtils. rightNb(RootedTree tree, Node tipNode)Right Neighbour of a tip (taxon).static RootedTreeReRootedTree. rootTreeAtCenter(RootedTree tree)Root any tree by locating the "center" of tree and adding a new root node at that pointstatic doubleUtils. safeNodeHeight(RootedTree tree, Node node)static java.lang.StringUtils. toNewick(RootedTree tree)static java.lang.StringUtils. toUniqueNewick(RootedTree tree)Constructs a unique newick representation of a treestatic java.lang.StringUtils. toUniqueNewickByAttribute(RootedTree tree, java.lang.String attribute)Constructs a unique newick representation of a tree print only an attributestatic java.lang.StringRootedTreeUtils. uniqueNewick(RootedTree tree, Node node)Recursive function for constructing a newick tree representation in the given buffer.Constructors in jebl.evolution.trees with parameters of type RootedTree Constructor Description AttributedCladeSystem(java.lang.String name, RootedTree tree)CladeSystem(RootedTree tree)CompactRootedTree(RootedTree t)Do all the hard work.FilteredRootedTree(RootedTree source)MutableRootedTree(RootedTree tree)Construct a rooted tree from an immutable rooted tree.ReRootedTree(RootedTree source, Node ingroupNode, Node outgroupNode, double ingroupBranchLength)Make a copy of the given unrooted treeRootedSubtree(RootedTree tree, java.util.Set<Taxon> includedTaxa)Make a copy of the given rooted treeSimpleRootedTree(RootedTree tree)Make a copy of the given rooted treeSimpleRootedTree(RootedTree tree, java.util.Map<Node,Node> nodeMapping)Make a copy of the given rooted treeSortedRootedTree(RootedTree source, java.util.Comparator<Node> comparator)SortedRootedTree(RootedTree source, SortedRootedTree.BranchOrdering branchOrdering)TransformedRootedTree(RootedTree source, TransformedRootedTree.Transform transform)TreeBiPartitionInfo(RootedTree t, java.util.List<Taxon> taxa) -
Uses of RootedTree in jebl.evolution.treesimulation
Methods in jebl.evolution.treesimulation that return RootedTree Modifier and Type Method Description RootedTreeTreeSimulator. simulate(IntervalGenerator intervalGenerator)RootedTreeTreeSimulator. simulate(IntervalGenerator intervalGenerator, boolean medianHeights)
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