Uses of Interface
jebl.evolution.trees.RootedTree
Packages that use RootedTree
Package
Description
Provides classes and interfaces for pairwise alignment of two sequences.
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Uses of RootedTree in jebl.evolution.align
Methods in jebl.evolution.align with parameters of type RootedTreeModifier and TypeMethodDescriptionBartonSternberg.doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress) MultipleAligner.doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress) -
Uses of RootedTree in jebl.evolution.coalescent
Constructors in jebl.evolution.coalescent with parameters of type RootedTreeModifierConstructorDescriptionCoalescent(RootedTree tree, DemographicFunction demographicFunction) Intervals(RootedTree tree) -
Uses of RootedTree in jebl.evolution.treemetrics
Methods in jebl.evolution.treemetrics with parameters of type RootedTreeModifier and TypeMethodDescriptiondoubleBilleraMetric.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 RootedTreeModifier and TypeClassDescriptionclassclassA memory efficient rooted tree.classclassA simple rooted tree providing some ability to manipulate the tree.final classA rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree.classRoot an unrooted tree.final classA simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..final classA simple, and initially immutable rooted tree implementation.classclassThis RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.Methods in jebl.evolution.trees that return RootedTreeModifier and TypeMethodDescriptionstatic 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.FilteredRootedTree.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 RootedTreeModifier and TypeMethodDescriptionvoidCladeSystem.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 Comparator<Node> Utils.createNodeDensityComparator(RootedTree tree) static Comparator<Node> Utils.createNodeDensityMinNodeHeightComparator(RootedTree tree) ReRootedTree.createNodes(RootedTree tree, Node parent, Node child) Clones the entire tree structure from the given (unrooted) Tree.SimpleRootedTree.createNodes(RootedTree tree, Node node) Clones the entire tree structure from the given RootedTree.static 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, Set<Node> tipNodes) Gets the most recent common ancestor (MRCA) node of a set of tip nodes.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) Utils.getNodes(RootedTree tree, Node node) All nodes in subtree - parents before children (pre - order).static final intRootedTreeUtils.getTipCount(RootedTree tree, Node node) Return the number of leaves under this node.RootedTreeUtils.getTipsForTaxa(RootedTree tree, 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, 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 StringUtils.toNewick(RootedTree tree) static StringUtils.toUniqueNewick(RootedTree tree) Constructs a unique newick representation of a treestatic StringUtils.toUniqueNewickByAttribute(RootedTree tree, String attribute) Constructs a unique newick representation of a tree print only an attributestatic 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 RootedTreeModifierConstructorDescriptionAttributedCladeSystem(String name, RootedTree tree) CladeSystem(RootedTree tree) 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, Set<Taxon> includedTaxa) Make a copy of the given rooted treeSimpleRootedTree(RootedTree tree) Make a copy of the given rooted treeSimpleRootedTree(RootedTree tree, Map<Node, Node> nodeMapping) Make a copy of the given rooted treeSortedRootedTree(RootedTree source, Comparator<Node> comparator) SortedRootedTree(RootedTree source, SortedRootedTree.BranchOrdering branchOrdering) TransformedRootedTree(RootedTree source, TransformedRootedTree.Transform transform) TreeBiPartitionInfo(RootedTree t, List<Taxon> taxa) -
Uses of RootedTree in jebl.evolution.treesimulation
Methods in jebl.evolution.treesimulation that return RootedTreeModifier and TypeMethodDescriptionTreeSimulator.simulate(IntervalGenerator intervalGenerator) TreeSimulator.simulate(IntervalGenerator intervalGenerator, boolean medianHeights)