jebl.evolution.trees
Class RootedTreeUtils

java.lang.Object
  jebl.evolution.trees.RootedTreeUtils

public class RootedTreeUtils
extends Object

Static utility functions for rooted trees.

Author:

Andrew Rambaut, Alexei Drummond

Constructor Summary

RootedTreeUtils()

Method Summary

static boolean	equal(RootedTree tree1, RootedTree tree2) Compares 2 trees and returns true if they have the same topology.
static Node	getCommonAncestorNode(RootedTree tree, Set<Node> tipNodes) Gets the most recent common ancestor (MRCA) node of a set of tip nodes.
static Set<Node>	getDescendantTips(RootedTree tree, Node node) Gets a set of tip nodes descended from the given node.
static double	getMaxTipHeight(RootedTree tree, Node node)
static double	getMinTipHeight(RootedTree tree, Node node)
static int	getTipCount(RootedTree tree, Node node) Return the number of leaves under this node.
static Set<Node>	getTipsForTaxa(RootedTree tree, Collection<Taxon> taxa) Gets a set of external nodes that correspond to the given taxa.
static boolean	isBinary(RootedTree tree)
static boolean	isMonophyletic(RootedTree tree, Set<Node> tipNodes) Performs the a monophyly test on a set of tip nodes.
static boolean	isUltrametric(RootedTree tree, double tolerance)
static String	uniqueNewick(RootedTree tree, Node node) Recursive function for constructing a newick tree representation in the given buffer.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RootedTreeUtils

public RootedTreeUtils()

Method Detail

getTipCount

public static final int getTipCount(RootedTree tree,
                                    Node node)

Return the number of leaves under this node.

Parameters:

tree -

node -

Returns:

the number of leaves under this node.

getMinTipHeight

public static double getMinTipHeight(RootedTree tree,
                                     Node node)

getMaxTipHeight

public static double getMaxTipHeight(RootedTree tree,
                                     Node node)

isUltrametric

public static boolean isUltrametric(RootedTree tree,
                                    double tolerance)

Returns:

true only if all tips have height 0.0

isBinary

public static boolean isBinary(RootedTree tree)

Returns:

true only if internal nodes have 2 children

getTipsForTaxa

public static Set<Node> getTipsForTaxa(RootedTree tree,
                                       Collection<Taxon> taxa)
                                throws MissingTaxonException

Gets a set of external nodes that correspond to the given taxa.

Throws:

MissingTaxonException

getDescendantTips

public static Set<Node> getDescendantTips(RootedTree tree,
                                          Node node)

Gets a set of tip nodes descended from the given node.

getCommonAncestorNode

public static Node getCommonAncestorNode(RootedTree tree,
                                         Set<Node> tipNodes)

Gets the most recent common ancestor (MRCA) node of a set of tip nodes.

Parameters:

tree - the Tree

tipNodes - a set of tip nodes

Returns:

the Node of the MRCA

isMonophyletic

public static boolean isMonophyletic(RootedTree tree,
                                     Set<Node> tipNodes)

Performs the a monophyly test on a set of tip nodes. The nodes are monophyletic if there is a node in the tree which subtends all the tips in the set (and only those tips).

Parameters:

tree - a tree object to perform test on

tipNodes - a set containing the tip node.

Returns:

boolean is monophyletic?

uniqueNewick

public static String uniqueNewick(RootedTree tree,
                                  Node node)

Recursive function for constructing a newick tree representation in the given buffer.

equal

public static boolean equal(RootedTree tree1,
                            RootedTree tree2)

Compares 2 trees and returns true if they have the same topology.