Uses of Interface
jebl.evolution.trees.Tree

Packages that use Tree

jebl.evolution.align	Provides classes and interfaces for pairwise alignment of two sequences.
jebl.evolution.io
jebl.evolution.parsimony
jebl.evolution.trees
jebl.gui.trees.treeviewer
jebl.gui.trees.treeviewer_dev
jebl.gui.trees.treeviewer_dev.painters
jebl.gui.trees.treeviewer_dev.treelayouts
jebl.gui.trees.treeviewer.decorators
jebl.gui.trees.treeviewer.treelayouts

Uses of Tree in jebl.evolution.align

Fields in jebl.evolution.align declared as Tree

Tree	AlignmentTreeBuilderFactory.Result.tree

Uses of Tree in jebl.evolution.io

Methods in jebl.evolution.io that return Tree

Tree	NewickImporter.importNextTree()
Tree	NexusImporter.importNextTree() import the next tree.
Tree	TreeImporter.importNextTree() Import a single tree

Methods in jebl.evolution.io that return types with arguments of type Tree

List<Tree>	NewickImporter.importTrees()
List<Tree>	NexusImporter.importTrees()
List<Tree>	TreeImporter.importTrees() Import all the trees
Iterator<Tree>	NewickImporter.iterator() Returns an iterator over a set of elements of type T.
Iterator<Tree>	NexusImporter.iterator() Returns an iterator over a set of elements of type T.
List<Tree>	NexusImporter.parseTreesBlock(List<Taxon> taxonList) Parses a 'TREES' block.

Methods in jebl.evolution.io with parameters of type Tree

void	NewickExporter.exportTree(Tree tree) Export a single tree
void	NexusExporter.exportTree(Tree tree) Export a single tree
void	TreeExporter.exportTree(Tree tree) Export a single tree

Method parameters in jebl.evolution.io with type arguments of type Tree

void	NewickExporter.exportTrees(Collection<? extends Tree> trees) Export a collection of trees
void	NexusExporter.exportTrees(Collection<? extends Tree> trees) export trees
void	TreeExporter.exportTrees(Collection<? extends Tree> trees) Export a collection of trees
void	NexusExporter.exportTreesWithTranslation(Collection<? extends Tree> trees, Map<String,String> t)

Uses of Tree in jebl.evolution.parsimony

Methods in jebl.evolution.parsimony with parameters of type Tree

double	FitchParsimony.getScore(Tree tree)
double	ParsimonyCriterion.getScore(Tree tree) 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[]	FitchParsimony.getStates(Tree tree, Node node) Returns the reconstructed character states for a given node in the tree.
State[]	ParsimonyCriterion.getStates(Tree tree, Node node) 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 Tree

class	ClusteringTreeBuilder<T extends Tree> An abstract base class for clustering algorithms from pairwise distances
class	ConsensusTreeBuilder<T extends Tree> Build a consensus tree for a set of trees.
interface	TreeBuilder<T extends Tree>

Subinterfaces of Tree in jebl.evolution.trees

interface

RootedTree A tree with a root (node with maximum height).

Classes in jebl.evolution.trees that implement Tree

class	CompactRootedTree A memory efficient rooted tree.
class	FilteredRootedTree
class	MutableRootedTree A simple rooted tree providing some ability to manipulate the tree.
class	RootedFromUnrooted Root an unrooted tree.
class	SimpleRootedTree A simple, and initially immutable rooted tree implementation.
class	SimpleTree A basic implementation on an unrooted tree.
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 Tree

Tree	GreedyUnrootedConsensusTreeBuilder.build()
protected Tree	NeighborJoiningTreeBuilder.getTree()
Tree	TreeSimulator.simulate()
Tree	TreeSimulator.simulate(boolean medianHeights)

Methods in jebl.evolution.trees with parameters of type Tree

static String[]	Utils.asText(Tree tree, int widthGuide)
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)
Node	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	SplitUtils.getSplit(List<Taxon> taxa, Tree tree, Edge edge, boolean[] split) get split for branch associated with internal node
static SplitSystem	SplitUtils.getSplits(List<Taxon> taxa, Tree tree) creates a split system from a tree (using a pre-specified order of sequences)
static SplitSystem	SplitUtils.getSplits(Tree tree) 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)

Constructors in jebl.evolution.trees with parameters of type Tree

MRCACConsensusTreeBuilder(Tree[] trees, double supportThreshold)

MRCACConsensusTreeBuilder(Tree[] trees, double supportThreshold, String supportAttributeName, boolean asPercent)

MutableRootedTree(Tree tree, Node outGroup)
Construct a rooted tree from unrooted.

RootedFromUnrooted(Tree source, Node root, boolean intent)
Root tree source at root.

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 tree

Uses of Tree in jebl.gui.trees.treeviewer

Methods in jebl.gui.trees.treeviewer with parameters of type Tree

void	MultipleTreeViewer.setTree(Tree tree)
void	TreeViewer.setTree(Tree tree)
void	TreeViewer.setTree(Tree inTree, int defaultLabelSize)

Method parameters in jebl.gui.trees.treeviewer with type arguments of type Tree

void	MultipleTreeViewer.setTrees(Collection<? extends Tree> trees)
void	MultipleTreeViewer.setTrees(Collection<? extends Tree> trees, int defaultLabelSize)

Uses of Tree in jebl.gui.trees.treeviewer_dev

Methods in jebl.gui.trees.treeviewer_dev that return Tree

Tree	TreeViewer.getTree()

Methods in jebl.gui.trees.treeviewer_dev that return types with arguments of type Tree

List<Tree>

MultipleTreeViewer.getTrees()

Methods in jebl.gui.trees.treeviewer_dev with parameters of type Tree

protected void	MultipleTreeViewer.addTree(Tree tree)
void	MultipleTreeViewer.setTree(Tree tree)
void	TreeViewer.setTree(Tree tree)

Method parameters in jebl.gui.trees.treeviewer_dev with type arguments of type Tree

void	MultipleTreeViewer.addTrees(Collection<? extends Tree> trees)
void	MultipleTreeViewer.setTrees(Collection<? extends Tree> trees)

Uses of Tree in jebl.gui.trees.treeviewer_dev.painters

Methods in jebl.gui.trees.treeviewer_dev.painters with parameters of type Tree

protected String	BasicLabelPainter.getLabel(Tree tree, Node node)
void	BasicLabelPainter.setupAttributes(Tree tree)
abstract void	LabelPainter.setupAttributes(Tree tree)
void	NodeBarPainter.setupAttributes(Tree tree)
void	NodeShapePainter.setupAttributes(Tree tree)
void	ScaleBarPainter.setupAttributes(Tree tree)

Uses of Tree in jebl.gui.trees.treeviewer_dev.treelayouts

Methods in jebl.gui.trees.treeviewer_dev.treelayouts with parameters of type Tree

void	AbstractTreeLayout.setTree(Tree tree)
void	TreeLayout.setTree(Tree tree) Set the tree for the layout0

Uses of Tree in jebl.gui.trees.treeviewer.decorators

Methods in jebl.gui.trees.treeviewer.decorators with parameters of type Tree

Paint	AttributeBranchDecorator.getBranchPaint(Tree tree, Node node)
Paint	BranchDecorator.getBranchPaint(Tree tree, Node node)

Uses of Tree in jebl.gui.trees.treeviewer.treelayouts

Methods in jebl.gui.trees.treeviewer.treelayouts with parameters of type Tree

void	AbstractTreeLayout.setTree(Tree tree)
void	TreeLayout.setTree(Tree tree) Set the tree for the layout0