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 Alignment
BartonSternberg. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment
MultipleAligner. doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
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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)
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Uses of RootedTree in jebl.evolution.treemetrics
Methods in jebl.evolution.treemetrics with parameters of type RootedTree Modifier and Type Method Description double
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 RootedTree Modifier and Type Class Description class
CompactRootedTree
A memory efficient rooted tree.class
FilteredRootedTree
class
MutableRootedTree
A simple rooted tree providing some ability to manipulate the tree.class
ReRootedTree
class
RootedFromUnrooted
Root an unrooted tree.class
RootedSubtree
A simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..class
SimpleRootedTree
A simple, and initially immutable rooted tree implementation.class
SortedRootedTree
class
TransformedRootedTree
This 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 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.RootedTree
FilteredRootedTree. getSource()
static RootedTree
Utils. rootTheTree(Tree tree)
Return a rooted tree from any tree.static 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 RootedTree Modifier and Type Method Description void
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 java.util.Comparator<Node>
Utils. createNodeDensityComparator(RootedTree tree)
static java.util.Comparator<Node>
Utils. createNodeDensityMinNodeHeightComparator(RootedTree tree)
Node
SimpleRootedTree. createNodes(RootedTree tree, Node node)
Clones the entire tree structure from the given RootedTree.static java.lang.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 Node
RootedTreeUtils. 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 int
Utils. getExternalNodeCount(RootedTree tree, Node node)
Return the number of external nodes under this node.static double
RootedTreeUtils. getMaxTipHeight(RootedTree tree, Node node)
static double
Utils. getMinNodeHeight(RootedTree tree, Node node)
static double
RootedTreeUtils. 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 int
RootedTreeUtils. 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 boolean
RootedTreeUtils. isBinary(RootedTree tree)
static boolean
Utils. isBinary(RootedTree rootedTree)
static boolean
RootedTreeUtils. isMonophyletic(RootedTree tree, java.util.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 double
Utils. safeNodeHeight(RootedTree tree, Node node)
static java.lang.String
Utils. toNewick(RootedTree tree)
static java.lang.String
Utils. toUniqueNewick(RootedTree tree)
Constructs a unique newick representation of a treestatic java.lang.String
Utils. toUniqueNewickByAttribute(RootedTree tree, java.lang.String attribute)
Constructs a unique newick representation of a tree print only an attributestatic java.lang.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 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, ReRootedTree.RootingType rootingType)
RootedSubtree(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)
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Uses of RootedTree in jebl.evolution.treesimulation
Methods in jebl.evolution.treesimulation that return RootedTree Modifier and Type Method Description RootedTree
TreeSimulator. simulate(IntervalGenerator intervalGenerator)
RootedTree
TreeSimulator. simulate(IntervalGenerator intervalGenerator, boolean medianHeights)
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