jebl.evolution.trees

Class SplitUtils

java.lang.Object

jebl.evolution.trees.SplitUtils

public class SplitUtils
extends java.lang.Object

utilities for split systems

Version:

$Id: SplitUtils.java 849 2007-12-06 00:10:14Z twobeers $

Author:

Korbinian Strimmer

Method Summary

Methods

Modifier and Type	Method and Description
static void	getSplit(java.util.List<Taxon> taxa, Tree tree, Edge edge, boolean[] split) get split for branch associated with internal node
static SplitSystem	getSplits(java.util.List<Taxon> taxa, Tree tree) creates a split system from a tree (using a pre-specified order of sequences)
static SplitSystem	getSplits(Tree tree) creates a split system from a tree (using tree-induced order of sequences)
static boolean	isSame(boolean[] s1, boolean[] s2) Checks two splits for identity.

Methods inherited from class java.lang.Object

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

Method Detail

getSplits

public static SplitSystem getSplits(Tree tree)

creates a split system from a tree (using tree-induced order of sequences)

Parameters:

tree -

getSplits

public static SplitSystem getSplits(java.util.List<Taxon> taxa,
                    Tree tree)

creates a split system from a tree (using a pre-specified order of sequences)

Parameters:

taxa - the list of taxa (order is important)

tree -

getSplit

public static void getSplit(java.util.List<Taxon> taxa,
            Tree tree,
            Edge edge,
            boolean[] split)

get split for branch associated with internal node

Parameters:

taxa - order of labels

tree - Tree

edge - Edge

split -

isSame

public static boolean isSame(boolean[] s1,
             boolean[] s2)

Checks two splits for identity. This method assumes that the two splits are of the same length and use the same leaf order/

Parameters:

s1 - split 1

s2 - split 2

Returns:

true if the two splits are identical

Throws:

java.lang.IllegalArgumentException - if splits don't have the same length