jebl.evolution.trees

Interface RootedTree

All Superinterfaces:

Attributable, Graph, Tree

All Known Implementing Classes:

CompactRootedTree, FilteredRootedTree, MutableRootedTree, ReRootedTree, RootedFromUnrooted, RootedSubtree, SimpleRootedTree, SortedRootedTree, TransformedRootedTree

public interface RootedTree
extends Tree

A tree with a root (node with maximum height). This interface provides the concept of a direction of time that flows from the root to the tips. Each node in the tree has a node height that is less than its parent's height and greater than it children's heights.

Version:

$Id: RootedTree.java 936 2008-08-06 14:12:07Z rambaut $

Author:

rambaut, Alexei Drummond

Nested Class Summary

Nested classes/interfaces inherited from interface jebl.evolution.graphs.Graph

Graph.NoEdgeException, Graph.Utils

Method Summary

Methods

Modifier and Type	Method and Description
boolean	conceptuallyUnrooted() Due to current implementation limitations, trees store "branch" information in nodes.
java.util.List<Node>	getChildren(Node node)
double	getHeight(Node node)
double	getLength(Node node)
Node	getParent(Node node)
Node	getRootNode() The root of the tree has the largest node height of all nodes in the tree.
boolean	hasHeights()
boolean	hasLengths()
boolean	isRoot(Node node)

Methods inherited from interface jebl.evolution.trees.Tree

getExternalEdges, getExternalNodes, getInternalEdges, getInternalNodes, getNode, getTaxa, getTaxon, isExternal, renameTaxa

Methods inherited from interface jebl.evolution.graphs.Graph

getAdjacencies, getEdge, getEdgeLength, getEdges, getEdges, getNodes, getNodes, getNodes

Methods inherited from interface jebl.util.Attributable

getAttribute, getAttributeMap, getAttributeNames, removeAttribute, setAttribute

Method Detail

getChildren

java.util.List<Node> getChildren(Node node)

Parameters:

node - the node whose children are being requested.

Returns:

the list of nodes that are the children of the given node. The set may be empty for a terminal node (a tip).

hasHeights

boolean hasHeights()

Returns:

Whether this tree has node heights available

getHeight

double getHeight(Node node)

Parameters:

node - the node whose height is being requested.

Returns:

the height of the given node. The height will be less than the parent's height and greater than it children's heights.

hasLengths

boolean hasLengths()

Returns:

Whether this tree has branch lengths available

getLength

double getLength(Node node)

Parameters:

node - the node whose branch length (to its parent) is being requested.

Returns:

the length of the branch to the parent node (0.0 if the node is the root).

getParent

Node getParent(Node node)

Parameters:

node - the node whose parent is requested

Returns:

the parent node of the given node, or null if the node is the root node.

getRootNode

Node getRootNode()

The root of the tree has the largest node height of all nodes in the tree.

Returns:

the root of the tree.

conceptuallyUnrooted

boolean conceptuallyUnrooted()

Due to current implementation limitations, trees store "branch" information in nodes. So, internally rooted trees are genetrated when un-rooted would be more natural. This should be removed. If this is a rooted tree then it is rooted. This can really only confuse things. Trees are unrooted, RootedTrees are rooted. This is not an implementation limitation. It may be that a RootedTree has an arbitrary root but it is still rooted. With a rooted tree, it is convenient to store branch information at the node (i.e., for the branch above the node) because there is no "branch" object. Andrew. This function will probably become deprecated once the "development" tree viewer becomes in sync with the main tree viewer branch and some method of handling this concept has been introduced. Until then, this method remains.

Returns:

true if tree(s) are to be viewed as unrooted

isRoot

boolean isRoot(Node node)

Parameters:

node - the node

Returns:

true if the node is the root of this tree.