AccordionTreeDrawer
Class Tree

java.lang.Object
  |
  +--AccordionTreeDrawer.Tree

public class Tree

extends java.lang.Object

A public class representing a (phylognenetic) tree. Nodes of the tree are of type TreeNode. Nodes are traversed in pre- and post-orders.

Version:

Author:

Yunhong Zhou, Li Zhang

See Also:

TreeNode, Newick, Nexus, Status

Field Summary

private int	height
private int	key key should be unique for each tree, set by object that creates trees
private int	leafCount the number of leave nodes
(package private) float	leafSpace
(package private) TreeNode	leftmostLeaf
(package private) java.lang.String	name
private int	nodeCount total number of nodes for the tree
java.util.ArrayList	nodes The list of nodes of the tree indexed by their keys, indexed by key
(package private) java.util.HashMap	nodesByName Most internal nodes don't have names.
(package private) static Newick	parser the parser responsible for parsing Newick format file, normally with a suffix nh
(package private) static Parser.nexus.Nexus	parser_nexus the parser responsible for parsing Nexus format file, normally with a suffix nexus or nxs
TreeNode	posorderStartNode the start node for postorder list of all the nodes
TreeNode	preorderStartNode the start node for preorder list of all the nodes
(package private) TreeNode	root

Constructor Summary

Tree()

Tree(java.lang.String tn)

Tree(Tree t)

Tree(TreeNode rn)

Method Summary

void	close() clean up method, called when the tree is deleted
int	computeBin(int fontRange)
protected void	finalize()
(package private) int	getGapDistanceFromLeaves(TreeNode n1, TreeNode n2)
(package private) int	getHeight()
(package private) int	getInteriorCount()
int	getKey()
(package private) int	getLCADistanceFromLeaves(TreeNode n1, TreeNode n2)
int	getLeafCount()
TreeNode	getLeftmostLeaf()
java.lang.String	getName()
TreeNode	getNodeByKey(int key)
TreeNode	getNodeByName(java.lang.String s)
TreeNode	getRightmostLeaf()
TreeNode	getRoot()
int	getSize()
(package private) int	getTotalNodeCount()
private void	linkLeaves() Links leaves of the tree in pre-order check to see whether leaves have distinct names if leaves have the same name, add a suffix index separated by ":"
private void	linkNodesInPosorder() Traverses the tree in pos-order, stores the ordering in the posorderNext field of TreeNodes
private void	linkNodesInPreorder() Traverses the tree in pre-order, stores the ordering in the preorderNext field of TreeNodes Sets nodecount for the tree
private void	linkSubtreeNodesInPosorder(TreeNode n) Traverses the subtree rooted at TreeNode n in post-order, stores the ordering in the posorderNext field of TreeNodes.
private void	linkSubtreeNodesInPreorder(TreeNode n) Traverses the subtree rooted at TreeNode n in pre-order, stores the ordering in the preorderNext field of TreeNodes.
void	load_nexus(java.lang.String fname, int index) Reads a tree with giving index in a file fname with Nexus format and initiates the Tree object.
void	load(java.lang.String fname) Reads a tree in file fname described in Newick format and initiate the tree object.
void	postProcess() Post processing includes computing size of each node, linking nodes in different order, etc.
void	printLeaves()
(package private) void	printName()
void	setKey(int i)
(package private) void	setName(java.lang.String tn)
void	setNodeFontSize(int maxFontSize, int minFontSize)
(package private) void	setRoot(TreeNode rn)

Methods inherited from class java.lang.Object

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

Field Detail

parser

static Newick parser

the parser responsible for parsing Newick format file, normally with a suffix nh

parser_nexus

static Parser.nexus.Nexus parser_nexus

the parser responsible for parsing Nexus format file, normally with a suffix nexus or nxs

nodes

public java.util.ArrayList nodes

The list of nodes of the tree indexed by their keys, indexed by key

nodesByName

java.util.HashMap nodesByName

Most internal nodes don't have names. Do we assign a unique name to each of them? No! each node has a key and the key is unique for nodes.

nodeCount

private int nodeCount

total number of nodes for the tree

key

private int key

key should be unique for each tree, set by object that creates trees

height

private int height

name

java.lang.String name

root

TreeNode root

leftmostLeaf

TreeNode leftmostLeaf

leafSpace

float leafSpace

leafCount

private int leafCount

the number of leave nodes

preorderStartNode

public TreeNode preorderStartNode

the start node for preorder list of all the nodes

posorderStartNode

public TreeNode posorderStartNode

the start node for postorder list of all the nodes

Constructor Detail

Tree

public Tree()

Tree

public Tree(java.lang.String tn)

Tree

public Tree(TreeNode rn)

Tree

public Tree(Tree t)

Method Detail

close

public void close()

clean up method, called when the tree is deleted

See Also:

TreeJuxtaposer.TreeJuxtaposer.deleteTree, TreeNode.close

finalize

protected void finalize()
                 throws java.lang.Throwable

Overrides:

finalize in class java.lang.Object

java.lang.Throwable

load

public void load(java.lang.String fname)

Reads a tree in file fname described in Newick format and initiate the tree object. Function load reads in the file, call the newick parser to parse it, and do some post processing afterwards. The tree object is originally empty. After calling the parser, it generates all the nodes decedant to the root. For each node of the tree, its name and edge weight will be set after parsing is complete. If the node has no name (internal nodes) or weight (some trees have no edge weight), then these fields will take the default value.

Parameters:

fname - The file name

See Also:

Newick

load_nexus

public void load_nexus(java.lang.String fname,
                       int index)

Reads a tree with giving index in a file fname with Nexus format and initiates the Tree object. Function load_nexus reads in the file, call the nexus parser to parse it, and do some post processing afterwards. The tree object is originally empty. After calling the parser, it generates all the nodes decedant to the root. For each node of the tree, its name and edge weight will be set after parsing is complete. If the node has no name (internal nodes) or weight (some trees have no edge weight), then these fields will take the default value.

Parameters:

fname - The file name

index - Index of the tree in the nexus file

See Also:

Nexus

getGapDistanceFromLeaves

int getGapDistanceFromLeaves(TreeNode n1,
                             TreeNode n2)

getLCADistanceFromLeaves

int getLCADistanceFromLeaves(TreeNode n1,
                             TreeNode n2)

getInteriorCount

int getInteriorCount()

getTotalNodeCount

int getTotalNodeCount()

getNodeByKey

public TreeNode getNodeByKey(int key)

getNodeByName

public TreeNode getNodeByName(java.lang.String s)

getHeight

int getHeight()

setKey

public void setKey(int i)

getKey

public int getKey()

getName

public java.lang.String getName()

getSize

public int getSize()

getLeftmostLeaf

public TreeNode getLeftmostLeaf()

getRightmostLeaf

public TreeNode getRightmostLeaf()

getRoot

public TreeNode getRoot()

setRoot

void setRoot(TreeNode rn)

setName

void setName(java.lang.String tn)

printName

void printName()

getLeafCount

public int getLeafCount()

postProcess

public void postProcess()

Post processing includes computing size of each node, linking nodes in different order, etc. Sets left and right-most leaves of the tree Computes and stores pre- and post-orders for leaves can't do minmax until after linkNodesInPreorder is called to set index values!

See Also:

TreeNode

linkNodesInPreorder

private void linkNodesInPreorder()

Traverses the tree in pre-order, stores the ordering in the preorderNext field of TreeNodes Sets nodecount for the tree

See Also:

TreeNode

linkSubtreeNodesInPreorder

private void linkSubtreeNodesInPreorder(TreeNode n)

Traverses the subtree rooted at TreeNode n in pre-order, stores the ordering in the preorderNext field of TreeNodes.

Parameters:

n - the root of the subtree

See Also:

TreeNode

linkNodesInPosorder

private void linkNodesInPosorder()

Traverses the tree in pos-order, stores the ordering in the posorderNext field of TreeNodes

See Also:

TreeNode

linkSubtreeNodesInPosorder

private void linkSubtreeNodesInPosorder(TreeNode n)

Traverses the subtree rooted at TreeNode n in post-order, stores the ordering in the posorderNext field of TreeNodes.

Parameters:

n - the root of the subtree

See Also:

TreeNode

linkLeaves

private void linkLeaves()

Links leaves of the tree in pre-order check to see whether leaves have distinct names if leaves have the same name, add a suffix index separated by ":"

See Also:

linkNodesInPreorder(), TreeNode, NameComparator

printLeaves

public void printLeaves()

computeBin

public int computeBin(int fontRange)

setNodeFontSize

public void setNodeFontSize(int maxFontSize,
                            int minFontSize)