Uses of Interface
jebl.evolution.trees.Tree
Packages that use Tree
Package
Description
Provides classes and interfaces for pairwise alignment of two sequences.
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Uses of Tree in jebl.evolution.align
Fields in jebl.evolution.align declared as Tree -
Uses of Tree in jebl.evolution.io
Methods in jebl.evolution.io that return TreeModifier and TypeMethodDescriptionNewickImporter.importNextTree()
NexusImporter.importNextTree()
If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks in the process if necessary.TreeImporter.importNextTree()
Import a single treeMethods in jebl.evolution.io that return types with arguments of type TreeModifier and TypeMethodDescriptionNewickImporter.importTrees()
NexusImporter.importTrees()
Import all trees in the file from the current position.TreeImporter.importTrees()
Import all the treesNewickImporter.iterator()
Returns an iterator over a set of elements of type T.NexusImporter.iterator()
NexusImporter.parseTreesBlock
(List<Taxon> taxonList) Parse the next 'TREES' block encountered in the input.Methods in jebl.evolution.io with parameters of type TreeModifier and TypeMethodDescriptionvoid
NewickExporter.exportTree
(Tree tree) Export a single treevoid
NexusExporter.exportTree
(Tree tree) Export a single treevoid
PHYLIPExporter.exportTree
(Tree tree) void
TreeExporter.exportTree
(Tree tree) Export a single treeMethod parameters in jebl.evolution.io with type arguments of type TreeModifier and TypeMethodDescriptionvoid
NewickExporter.exportTrees
(Collection<? extends Tree> trees) Export a collection of treesvoid
NexusExporter.exportTrees
(Collection<? extends Tree> trees) void
NexusExporter.exportTrees
(Collection<? extends Tree> trees, boolean writeTaxa) void
PHYLIPExporter.exportTrees
(Collection<? extends Tree> trees) void
TreeExporter.exportTrees
(Collection<? extends Tree> trees) Export a collection of treesvoid
NexusExporter.exportTreesWithTranslation
(Collection<? extends Tree> trees, Map<String, String> translationMap) -
Uses of Tree in jebl.evolution.parsimony
Methods in jebl.evolution.parsimony with parameters of type TreeModifier and TypeMethodDescriptiondouble
double
Calculates the minimum number of steps for the parsimony reconstruction for the given tree.double[]
FitchParsimony.getSiteScores
(Tree tree) Calculates the minimum number of siteScores for the parsimony reconstruction of a a set of character patterns on a tree.double[]
ParsimonyCriterion.getSiteScores
(Tree tree) Calculates the minimum number of steps for the parsimony reconstruction for the given tree.State[]
Returns the reconstructed character states for a given node in the tree.State[]
Returns the reconstructed character states for a given node in the tree. -
Uses of Tree in jebl.evolution.trees
Classes in jebl.evolution.trees with type parameters of type TreeModifier and TypeClassDescriptionclass
ClusteringTreeBuilder<T extends Tree>
An abstract base class for clustering algorithms from pairwise distancesclass
ConsensusTreeBuilder<T extends Tree>
ATreeBuilder
that builds a consensus tree for a set of trees on identical leaf sets.interface
TreeBuilder<T extends Tree>
Subinterfaces of Tree in jebl.evolution.treesModifier and TypeInterfaceDescriptioninterface
A tree with a root (node with maximum height).Classes in jebl.evolution.trees that implement TreeModifier and TypeClassDescriptionclass
A memory efficient rooted tree.class
class
A simple rooted tree providing some ability to manipulate the tree.class
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.final class
A basic implementation on an unrooted tree.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 TreeMethods in jebl.evolution.trees that return types with arguments of type TreeModifier and TypeMethodDescriptionMostProbableTopology.get
(int max, double threshold) Get the most probable tree(s)Methods in jebl.evolution.trees with parameters of type TreeModifier and TypeMethodDescriptionstatic String
static String[]
static ConsensusTreeBuilder
TreeBuilderFactory.buildRooted
(Tree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method) convenience method.static ConsensusTreeBuilder
TreeBuilderFactory.buildUnRooted
(Tree[] trees, Taxon outGroup, double supportThreshold, TreeBuilderFactory.ConsensusMethod method) SimpleRootedTree.createNodes
(Tree tree, Node parent, Node child) Clones the entire tree structure from the given (unrooted) Tree.static double
Utils.getPathLength
(Tree tree, Node node1, Node node2) static void
get split for branch associated with internal nodestatic SplitSystem
creates a split system from a tree (using a pre-specified order of sequences)static SplitSystem
creates a split system from a tree (using tree-induced order of sequences)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 pointMethod parameters in jebl.evolution.trees with type arguments of type TreeModifier and TypeMethodDescriptionstatic void
Utils.assertAllTreesHaveTheSameTaxa
(List<? extends Tree> trees) Checks whether all of the trees passed in have the same taxa sets (ignoring order of taxa), and throws an IllegalArgumentException if this is not the case.Constructors in jebl.evolution.trees with parameters of type TreeModifierConstructorDescriptionMutableRootedTree
(Tree tree, Node outGroup) Construct a rooted tree from unrooted.RootedFromUnrooted
(Tree source, Node root, boolean intentUnrooted) Root tree at some internal node.RootedFromUnrooted
(Tree source, Node left, Node right, double fromLeft) Root source by creating a new internal node whose children are (the adjacent) left and right.SimpleRootedTree
(Tree tree, Node ingroupNode, Node outgroupNode, double ingroupBranchLength) Make a copy of the given unrooted treeSimpleTree
(Tree tree) Duplicate a tree.TreeChangeEvent
(Tree tree) Constructor parameters in jebl.evolution.trees with type arguments of type Tree