jebl.evolution.trees
Class Utils

java.lang.Object
  jebl.evolution.trees.Utils

public final class Utils
extends Object

A collection of utility functions for trees.

Author:

rambaut, Alexei Drummond

Constructor Summary

Utils()

Method Summary

static String[]	asText(Tree tree, int widthGuide)
static Comparator<Node>	createNodeDensityComparator(RootedTree tree)
static Comparator<Node>	createNodeDensityMinNodeHeightComparator(RootedTree tree)
static String	DEBUGsubTreeRep(RootedTree t, Node n)
static int	getExternalNodeCount(RootedTree tree, Node node) Return the number of external nodes under this node.
static double	getMinNodeHeight(RootedTree tree, Node node)
static double	getPathLength(Tree tree, Node node1, Node node2)
static boolean	isBinary(RootedTree rootedTree)
static boolean	isUltrametric(RootedTree rootedTree)
static int	maxLevels(RootedTree tree)
static RootedTree	rootTheTree(Tree tree) Return a rooted tree from any tree.
static RootedTree	rootTreeAtCenter(Tree tree)
static double	safeNodeHeight(RootedTree tree, Node node)
static String	toNewick(RootedTree tree)

Methods inherited from class java.lang.Object

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

Constructor Detail

Utils

public Utils()

Method Detail

toNewick

public static String toNewick(RootedTree tree)

Parameters:

tree -

Returns:

the rooted tree as a newick format string

safeNodeHeight

public static double safeNodeHeight(RootedTree tree,
                                    Node node)

maxLevels

public static int maxLevels(RootedTree tree)

asText

public static String[] asText(Tree tree,
                              int widthGuide)

rootTheTree

public static RootedTree rootTheTree(Tree tree)

Return a rooted tree from any tree. If tree already rooted, return it. Otherwise if there is a "natuarl root" (i.e. a node of degree 2) use it as root. Otherwise use an internal node close to the center of the tree as a root.

Parameters:

tree - to root

Returns:

rooted representation

rootTreeAtCenter

public static RootedTree rootTreeAtCenter(Tree tree)

getPathLength

public static double getPathLength(Tree tree,
                                   Node node1,
                                   Node node2)

Parameters:

tree - the tree

node1 -

node2 -

Returns:

the path length between the two nodes

isBinary

public static boolean isBinary(RootedTree rootedTree)

Parameters:

rootedTree - the rooted tree

Returns:

true if all internal nodes in the given tree are of degree 3, except the root which must have a degree of 2.

isUltrametric

public static boolean isUltrametric(RootedTree rootedTree)

Parameters:

rootedTree - the rooted tree

Returns:

true if all the external nodes in the tree have a height of 0.0

getExternalNodeCount

public static int getExternalNodeCount(RootedTree tree,
                                       Node node)

Return the number of external nodes under this node.

Parameters:

tree -

node -

Returns:

the number of external nodes under this node.

getMinNodeHeight

public static double getMinNodeHeight(RootedTree tree,
                                      Node node)

Parameters:

tree -

node -

Returns:

the minimum node height

createNodeDensityComparator

public static Comparator<Node> createNodeDensityComparator(RootedTree tree)

createNodeDensityMinNodeHeightComparator

public static Comparator<Node> createNodeDensityMinNodeHeightComparator(RootedTree tree)

DEBUGsubTreeRep

public static String DEBUGsubTreeRep(RootedTree t,
                                     Node n)