phylosort
Class TreeNode

java.lang.Object
  phylosort.TreeNode

public class TreeNode
extends java.lang.Object

A generic tree node that can be root, internal or leaf (operational taxonomic unit "OTU") node.

Version:

$Revision: 1.5 $

Author:

Ahmed Moustafa

Field Summary

static float	DEFAULT_BRANCH_LENGTH Default branch length
static int	DEFAULT_ROOT_ID Default root node id
static int	DEFAULT_ROOT_LEVEL Default root node level
static int	INVALID_NODE_ID Invalid node id (for example, node not found)

Constructor Summary

TreeNode()
Default constructor

Method Summary

void	addChild(TreeNode child) Adds a child to the tree
java.lang.String	depthFirstSearch() Performs a depth-first search (DFS) starting at the current node
static TreeNode	find(TreeNode tree, java.lang.String label) Finds a node with a specific label
java.lang.Iterable<TreeNode>	getChildren() Returns an iterator to the children
int	getChildrenCount() Returns the number of children
int	getId() Returns the node id
java.lang.String	getLabel() Returns the label of the node
java.util.List<TreeNode>	getLeaves() Returns all leaves under this node
float	getLength() Returns the length of the node branch
int	getLevel() Returns the node level
int	getMaximumId() Returns the maximum node id under this node
TreeNode	getNode(int id) Retrieve a node using its id
TreeNode	getParent() Returns the parent of the node
Path	getPathFromRoot() Returns an ordered list representing the path from the root to this node.
TreeNode	getRoot() Returns the root of the tree of a node
java.lang.Iterable<TreeNode>	getSortedChildren() Returns an iterorator to the sorted children
java.lang.String	getTaxon() Extracts a taxon string from the node label
java.lang.String	getTaxon(boolean labelOnNoMatch) Extracts a taxon string from the node label
boolean	isLeaf() Returns true if the nodes does not have any children
boolean	isRoot() Returns true if this the root node of the tree (i.e.
java.lang.Iterable<TreeNode>	iterator() Returns depth first search Iterable
void	preprocess() Processes the tree and sets the id and level for each in the tree
int	preprocess(int id, int level) Processes the tree and sets the id and level for each in the tree
void	removeChild(int child) Removes a child
void	removeChild(TreeNode child) Removes a child
void	setId(int id) Sets the node id
void	setLabel(java.lang.String label) Sets the label of the node
void	setLength(float length) Sets the length of the node branch
void	setLevel(int level) Sets the node level
void	setParent(TreeNode parent) Sets the parent of the node
int	size() Returns the number of terminal nodes in a tree
java.lang.String	toString() Returns a string representation of the tree

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_ROOT_ID

public static final int DEFAULT_ROOT_ID

Default root node id

See Also:

Constant Field Values

DEFAULT_ROOT_LEVEL

public static final int DEFAULT_ROOT_LEVEL

Default root node level

See Also:

Constant Field Values

DEFAULT_BRANCH_LENGTH

public static final float DEFAULT_BRANCH_LENGTH

Default branch length

See Also:

Constant Field Values

INVALID_NODE_ID

public static final int INVALID_NODE_ID

Invalid node id (for example, node not found)

See Also:

Constant Field Values

Constructor Detail

TreeNode

public TreeNode()

Default constructor

Method Detail

addChild

public void addChild(TreeNode child)

Adds a child to the tree

Parameters:

child - A child to be added

getChildren

public java.lang.Iterable<TreeNode> getChildren()

Returns an iterator to the children

Returns:

an iterator to the children

getSortedChildren

public java.lang.Iterable<TreeNode> getSortedChildren()

Returns an iterorator to the sorted children

Returns:

an iterorator to the sorted children

getChildrenCount

public int getChildrenCount()

Returns the number of children

Returns:

the number of children

getLabel

public java.lang.String getLabel()

Returns the label of the node

Returns:

the label of the node

setLabel

public void setLabel(java.lang.String label)

Sets the label of the node

Parameters:

label - The label to set

getLength

public float getLength()

Returns the length of the node branch

Returns:

the length of the node branch

setLength

public void setLength(float length)

Sets the length of the node branch

Parameters:

length - The length to set

getId

public int getId()

Returns the node id

Returns:

int The node id

setId

public void setId(int id)

Sets the node id

Parameters:

id - The node id to set

getLevel

public int getLevel()

Returns the node level

Returns:

int The node level

setLevel

public void setLevel(int level)

Sets the node level

Parameters:

level - The node level to set

isLeaf

public boolean isLeaf()

Returns true if the nodes does not have any children

Returns:

true if the nodes does not have any children otherwise false

getParent

public TreeNode getParent()

Returns the parent of the node

Returns:

TreeNode The parent of the node

setParent

public void setParent(TreeNode parent)

Sets the parent of the node

Parameters:

parent - The parent to set

isRoot

public boolean isRoot()

Returns true if this the root node of the tree (i.e. it does not have a parent node)

Returns:

true if this the root node of the tree

depthFirstSearch

public java.lang.String depthFirstSearch()

Performs a depth-first search (DFS) starting at the current node

Returns:

String A string representation of the tree

toString

public java.lang.String toString()

Returns a string representation of the tree

Overrides:

toString in class java.lang.Object

Returns:

String A string representation of the tree

preprocess

public void preprocess()

Processes the tree and sets the id and level for each in the tree

preprocess

public int preprocess(int id,
                      int level)

Processes the tree and sets the id and level for each in the tree

Parameters:

id - The node id to set

level - The node level to set

Returns:

int The node id

getNode

public TreeNode getNode(int id)

Retrieve a node using its id

Parameters:

id - The node id

Returns:

TreeNode that has the specified id

getMaximumId

public int getMaximumId()

Returns the maximum node id under this node

Returns:

int The maximum node id under this node

getPathFromRoot

public Path getPathFromRoot()

Returns an ordered list representing the path from the root to this node. Each node in the path is represented by its id integer value.

Returns:

An ordered list representing the path from the root to this node

removeChild

public void removeChild(TreeNode child)

Removes a child

Parameters:

child - Child to be removed

removeChild

public void removeChild(int child)

Removes a child

Parameters:

child - Child to be removed

size

public int size()

Returns the number of terminal nodes in a tree

Returns:

the number of terminal nodes in a tree

getLeaves

public java.util.List<TreeNode> getLeaves()

Returns all leaves under this node

Returns:

all leaves under this node

getTaxon

public java.lang.String getTaxon()

Extracts a taxon string from the node label

Returns:

String taxon

getTaxon

public java.lang.String getTaxon(boolean labelOnNoMatch)

Extracts a taxon string from the node label

Parameters:

labelOnNoMatch - Flag to return the node label if no match

Returns:

String taxon

find

public static TreeNode find(TreeNode tree,
                            java.lang.String label)

Finds a node with a specific label

Parameters:

tree - TreeNode root of tree

label - String query label

Returns:

TreeNode with query label

getRoot

public TreeNode getRoot()

Returns the root of the tree of a node

Returns:

Root TreeNode

iterator

public java.lang.Iterable<TreeNode> iterator()

Returns depth first search Iterable

Returns:

Depth first search Iterable