pal.tree

Class CladeSystem

java.lang.Object

pal.tree.CladeSystem

public class CladeSystem
extends java.lang.Object

data structure for a set of splits

Version:

$Id: CladeSystem.java,v 1.1 2002/06/03 09:17:52 alexi Exp $

Author:

Alexei Drummond

Constructor Summary

Constructors

Constructor and Description
CladeSystem(IdGroup idGroup, int size)

Method Summary

Methods

Modifier and Type	Method and Description
static void	calculateCladeProbabilities(Tree tree, CladeSystem[] cladeSystems)
static void	getClade(IdGroup idGroup, Node internalNode, boolean[] clade) get clade for internal node
boolean[]	getClade(int i) get clade
boolean[][]	getCladeArray() get clade array
int	getCladeCount() get number of clades
static CladeSystem	getClades(IdGroup idGroup, Tree tree) creates a clade system from a tree (using a pre-specified order of sequences)
static CladeSystem	getClades(Tree tree) creates a clade system from a tree (using tree-induced order of sequences)
static CladeSystem[]	getCladeSystems(Tree[] trees)
IdGroup	getIdGroup() get idGroup
int	getLabelCount() get number of labels
boolean	hasClade(boolean[] clade) + test whether a clade is contained in this clade system (assuming the same leaf order)
static boolean	isSame(boolean[] s1, boolean[] s2) checks whether two clades are identical (assuming they are of the same length and use the same leaf order)
java.lang.String	toString() print clade system

Methods inherited from class java.lang.Object

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

Constructor Detail

CladeSystem

public CladeSystem(IdGroup idGroup,
           int size)

Parameters:

idGroup - sequence labels

size - number of clades

Method Detail

getCladeCount

public int getCladeCount()

get number of clades

getLabelCount

public int getLabelCount()

get number of labels

getCladeArray

public boolean[][] getCladeArray()

get clade array

getClade

public boolean[] getClade(int i)

get clade

getIdGroup

public IdGroup getIdGroup()

get idGroup

hasClade

public boolean hasClade(boolean[] clade)

+ test whether a clade is contained in this clade system (assuming the same leaf order)

Parameters:

clade - clade

toString

public java.lang.String toString()

print clade system

Overrides:

toString in class java.lang.Object

getCladeSystems

public static CladeSystem[] getCladeSystems(Tree[] trees)

Returns:

all clade systems for a group of trees.

calculateCladeProbabilities

public static void calculateCladeProbabilities(Tree tree,
                               CladeSystem[] cladeSystems)

getClades

public static CladeSystem getClades(IdGroup idGroup,
                    Tree tree)

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

Parameters:

idGroup - sequence order for the matrix

tree -

getClades

public static CladeSystem getClades(Tree tree)

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

Parameters:

tree -

getClade

public static void getClade(IdGroup idGroup,
            Node internalNode,
            boolean[] clade)

get clade for internal node

Parameters:

idGroup - order of labels

internalNode - Node

boolean[] - clade

isSame

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

checks whether two clades are identical (assuming they are of the same length and use the same leaf order)

Parameters:

s1 - clade 1

s2 - clade 2