Uses of Interface
jebl.evolution.trees.RootedTree

Packages that use RootedTree

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

Uses of RootedTree in jebl.evolution.align

Methods in jebl.evolution.align with parameters of type RootedTree

Alignment	BartonSternberg.doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
Alignment	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 RootedTree

Coalescent(RootedTree tree, DemographicFunction demographicFunction)

Intervals(RootedTree tree)

Uses of RootedTree in jebl.evolution.trees

Classes in jebl.evolution.trees that implement RootedTree

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	SortedRootedTree
class	TransformedRootedTree This RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.

Fields in jebl.evolution.trees declared as RootedTree

protected RootedTree

FilteredRootedTree.source

Methods in jebl.evolution.trees that return RootedTree

RootedTree	GreedyRootedConsensusTreeBuilder.build()
RootedTree	MRCACConsensusTreeBuilder.build()
RootedTree	FilteredRootedTree.getSource()
static RootedTree	Utils.rootTheTree(Tree tree) Return a rooted tree from any tree.
static RootedTree	Utils.rootTreeAtCenter(Tree tree)

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

void	CladeSystem.add(RootedTree tree) adds all the clades in the tree
static ConsensusTreeBuilder	TreeBuilderFactory.buildRooted(RootedTree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
static Comparator<Node>	Utils.createNodeDensityComparator(RootedTree tree)
static Comparator<Node>	Utils.createNodeDensityMinNodeHeightComparator(RootedTree tree)
Node	SimpleRootedTree.createNodes(RootedTree tree, Node node) Clones the entire tree structure from the given RootedTree.
static String	Utils.DEBUGsubTreeRep(RootedTree t, Node n)
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, Set<Node> tipNodes) Gets the most recent common ancestor (MRCA) node of a set of tip nodes.
static 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 int	RootedTreeUtils.getTipCount(RootedTree tree, Node node) Return the number of leaves under this node.
static Set<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	Utils.isUltrametric(RootedTree rootedTree)
static boolean	RootedTreeUtils.isUltrametric(RootedTree tree, double tolerance)
static int	Utils.maxLevels(RootedTree tree)
static double	Utils.safeNodeHeight(RootedTree tree, Node node)
static String	Utils.toNewick(RootedTree tree)
static 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

CladeSystem(RootedTree tree)

CompactRootedTree(RootedTree t)
Do all the hard work.

FilteredRootedTree(RootedTree source)

GreedyRootedConsensusTreeBuilder(RootedTree[] trees, double supportThreshold)

GreedyRootedConsensusTreeBuilder(RootedTree[] trees, double supportThreshold, String supportAttributeName, boolean asPercent)

SimpleRootedTree(RootedTree tree)
Make a copy of the given rooted tree

SimpleTree(RootedTree tree)
Make a copy of the given rooted tree.

SortedRootedTree(RootedTree source, Comparator<Node> comparator)

SortedRootedTree(RootedTree source, SortedRootedTree.BranchOrdering branchOrdering)

TransformedRootedTree(RootedTree source, TransformedRootedTree.Transform transform)

Uses of RootedTree in jebl.gui.trees.treecomponent

Fields in jebl.gui.trees.treecomponent declared as RootedTree

protected RootedTree

RootedTreeComponent.tree the tree

Methods in jebl.gui.trees.treecomponent with parameters of type RootedTree

void	RootedTreeComponent.Listener.nodeClicked(RootedTree tree, Node node)
void	RootedTreeComponent.Adaptor.nodeClicked(RootedTree tree, Node node)
void	RootedTreePainter.paintTree(Graphics2D g, Dimension size, RootedTree tree) Do the actual painting.
void	SquareTreePainter.paintTree(Graphics2D g2, Dimension size, RootedTree tree) Do the actual painting.
void	RootedTreeComponent.setTree(RootedTree tree) Set the tree.

Constructors in jebl.gui.trees.treecomponent with parameters of type RootedTree

RootedTreeComponent(RootedTreePainter treePainter, RootedTree tree)

Uses of RootedTree in jebl.gui.trees.treeviewer

Fields in jebl.gui.trees.treeviewer declared as RootedTree

protected RootedTree

TreeViewer.tree

Methods in jebl.gui.trees.treeviewer that return RootedTree

RootedTree

TreePane.getTree()

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

void	TreePane.setTree(RootedTree tree)

Uses of RootedTree in jebl.gui.trees.treeviewer_dev

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

RootedTree	TreePane.getOriginalTree()
RootedTree	TreePane.getTree()

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

void	TreePane.setTree(RootedTree tree)

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

Fields in jebl.gui.trees.treeviewer_dev.treelayouts declared as RootedTree

protected RootedTree

AbstractTreeLayout.tree

Uses of RootedTree in jebl.gui.trees.treeviewer.painters

Constructors in jebl.gui.trees.treeviewer.painters with parameters of type RootedTree

BasicLabelPainter(String title, RootedTree tree, BasicLabelPainter.PainterIntent intent)

BasicLabelPainter(String title, RootedTree tree, BasicLabelPainter.PainterIntent intent, int defaultSize)

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

Fields in jebl.gui.trees.treeviewer.treelayouts declared as RootedTree

protected RootedTree

AbstractTreeLayout.tree