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 TypeMethodDescriptiondouble
BilleraMetric.getMetric
(RootedTree tree1, RootedTree tree2) double
CladeHeightMetric.getMetric
(RootedTree tree1, RootedTree tree2) double
RobinsonsFouldMetric.getMetric
(RootedTree tree1, RootedTree tree2) double
RootedTreeMetric.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 TypeClassDescriptionclass
class
A memory efficient rooted tree.class
class
A simple rooted tree providing some ability to manipulate the tree.final class
A rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree.class
Root an unrooted tree.final class
A simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..final class
A simple, and initially immutable rooted tree implementation.class
class
This 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 RootedTree
Utils.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 RootedTree
Utils.rootTheTree
(Tree tree) Return a rooted tree from any tree.static RootedTree
ReRootedTree.rootTreeAtCenter
(RootedTree tree) Root any tree by locating the "center" of tree and adding a new root node at that pointstatic RootedTree
Utils.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 TypeMethodDescriptionvoid
CladeSystem.add
(RootedTree tree) adds all the clades in the treevoid
CalculateSplitRates.addTreeToDensityMap
(jebl.evolution.trees.CalculateSplitRates.DensityMap densityMap, RootedTree tree) static ConsensusTreeBuilder
TreeBuilderFactory.buildRooted
(RootedTree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method) static RootedTree
Utils.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 String
Utils.DEBUGsubTreeRep
(RootedTree tree, Node node) static boolean
RootedTreeUtils.equal
(RootedTree tree1, RootedTree tree2) Compares 2 trees and returns true if they have the same topology.static double
RootedTreeUtils.getAverageTipDistance
(RootedTree tree, Node node) returns the average distance from the given node to all the tips below itstatic Node
RootedTreeUtils.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 int
Utils.getExternalNodeCount
(RootedTree tree, Node node) Return the number of external nodes under this node.static double
Utils.getLength
(RootedTree tree) static double
RootedTreeUtils.getMaxTipHeight
(RootedTree tree, Node node) static double
Utils.getMinNodeHeight
(RootedTree tree, Node node) static double
RootedTreeUtils.getMinTipHeight
(RootedTree tree, Node node) Utils.getNodes
(RootedTree tree, Node node) All nodes in subtree - parents before children (pre - order).static final int
RootedTreeUtils.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 boolean
RootedTreeUtils.isBinary
(RootedTree tree) static boolean
Utils.isBinary
(RootedTree rootedTree) static boolean
RootedTreeUtils.isMonophyletic
(RootedTree tree, Set<Node> tipNodes) Performs the a monophyly test on a set of tip nodes.static boolean
RootedTreeUtils.isUltrametric
(RootedTree tree, double tolerance) static boolean
Utils.isUltrametric
(RootedTree rootedTree) static Node
Utils.leftNb
(RootedTree tree, Node node) Left Neighbour of a tip (taxon).static int
Utils.maxLevels
(RootedTree tree) static Node
Utils.rightNb
(RootedTree tree, Node tipNode) Right Neighbour of a tip (taxon).static RootedTree
ReRootedTree.rootTreeAtCenter
(RootedTree tree) Root any tree by locating the "center" of tree and adding a new root node at that pointstatic double
Utils.safeNodeHeight
(RootedTree tree, Node node) static String
Utils.toNewick
(RootedTree tree) static String
Utils.toUniqueNewick
(RootedTree tree) Constructs a unique newick representation of a treestatic String
Utils.toUniqueNewickByAttribute
(RootedTree tree, String attribute) Constructs a unique newick representation of a tree print only an attributestatic String
RootedTreeUtils.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)