jebl.evolution.trees
Class SplitUtils

java.lang.Object
  extended by 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
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


http://code.google.com/p/jebl2/