AccordionTreeDrawer
Class TreeNode

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

All Implemented Interfaces:

CellGeom, java.lang.Comparable

public class TreeNode

extends java.lang.Object

implements CellGeom, java.lang.Comparable

A class representing a node of a (phylognenetic) tree. The tree that this node belongs to is of type Tree. Nodes have fields that store a pre- and post-ordering. A TreeNode has a list of children, a unique key, a leftmostleaf and a rightmost leaf

Version:

Author:

Tamara Munzner, Li Zhang, Yunhong Zhou

See Also:

Tree, GridCell

Field Summary

(package private) java.lang.Double	bcnScore
java.awt.Color	cachedColor
int	cachedFrame
GridCell	cell The GridCell that this node is attached to
(package private) java.util.ArrayList	children
(package private) TreeEdge[]	edges
private int	fontSize
(package private) int	height
int	key key is unique for nodes in one tree
java.lang.String	label
TreeNode	leftmostLeaf
int	lindex leaf index
private int	max The index of the largest descendant node
private int	min The index of the smallest descendant node (Node in subtree rooted at this node).
(package private) java.lang.String	name node name with default "".
TreeNode	next next leaf added by Li
(package private) float[]	nodeOffset The offset of the point with respect to the cell.
int	numberLeaves
TreeNode	parent
TreeNode	posorderNext
TreeNode	preorderNext
TreeNode	rightmostLeaf
float	weight weight is actually edge length for the edge immediately above the node

Constructor Summary

TreeNode()
Children list initial capacity 2 as in most case binary.

TreeNode(java.lang.String s)

TreeNode(java.lang.String s, float w)
Allocate a new TreeNode object with node name and weight.

Method Summary

void	addChild(TreeNode n)
void	addEdge(TreeEdge edge, int xy) Add edge in either X/horizontal (xy==0) direction, or Y/vertical (xy==1)direction.
void	close() clean the node itself and the tree edge attached with it.
int	compareTo(java.lang.Object o) implement Comparable interface - sort on key field
void	drawInCell(java.awt.Color col, float plane, AccordionDrawer d) Draws this node inside cell, the GridCell that it is attached to, if cell is drawn large enough Prints the label of the node if the GridCell is drawn large enough
boolean	equals(TreeNode n)
protected void	finalize()
TreeNode	firstChild()
java.lang.Double	getBcnScore()
java.awt.Color	getCachedColor()
int	getCachedFrame()
GridCell	getCell()
TreeNode	getChild(int i)
AccordionTreeDrawer	getDrawer()
TreeEdge	getEdge(int xy)
int	getFontSize()
int	getKey()
int	getLeafCount()
TreeNode	getLeftmostLeaf()
int	getMax()
int	getMin()
java.lang.String	getName()
float	getPos(int xy) compute the real position of the node
TreeNode	getRightmostLeaf()
float	getWeight()
boolean	isAncestorOf(TreeNode that)
boolean	isInteriorNode()
boolean	isLeaf()
boolean	isRoot()
TreeNode	lastChild()
TreeNode	lca(TreeNode that) Compute the lowest common ancestor between this node and that.
TreeNode	leafLca(TreeNode that) Compute the lowest common ancestor between this leaf and "that" The two nodes must belong to the same tree and must be leaves
int	numberChildren()
TreeNode	parent()
boolean	pick(int x, int y)
void	print()
void	printSubtree()
void	setBcnScore(float n)
void	setCachedColor(java.awt.Color c)
void	setCachedFrame(int framenum)
void	setCell(GridCell c)
void	setFontSize(int fs)
void	setName(java.lang.String s)
void	setSubtreeExtremeLeaves()
(package private) void	setSubtreeMinMax()
(package private) void	setSubtreeNumberLeaves() set numberLeaves field for each subnode
void	setWeight(double w)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

children

java.util.ArrayList children

edges

TreeEdge[] edges

key

public int key

key is unique for nodes in one tree

cell

public GridCell cell

The GridCell that this node is attached to

min

private int min

The index of the smallest descendant node (Node in subtree rooted at this node).

max

private int max

The index of the largest descendant node

fontSize

private int fontSize

bcnScore

java.lang.Double bcnScore

nodeOffset

float[] nodeOffset

The offset of the point with respect to the cell. We only have this for the row offset as we assume that the vertical edges are all aligned. When computing the Y coordinate of a node, we add nodeOffsetR to the pointOffset[1], a fixed parameter set by AccordionDrawer.

cachedColor

public java.awt.Color cachedColor

cachedFrame

public int cachedFrame

parent

public TreeNode parent

name

java.lang.String name

node name with default "". Most internal nodes have no name and all leaf nodes have a name

label

public java.lang.String label

height

int height

weight

public float weight

weight is actually edge length for the edge immediately above the node

leftmostLeaf

public TreeNode leftmostLeaf

rightmostLeaf

public TreeNode rightmostLeaf

numberLeaves

public int numberLeaves

preorderNext

public TreeNode preorderNext

posorderNext

public TreeNode posorderNext

lindex

public int lindex

leaf index

next

public TreeNode next

next leaf added by Li

Constructor Detail

TreeNode

public TreeNode()

Children list initial capacity 2 as in most case binary.

TreeNode

public TreeNode(java.lang.String s,
                float w)

Allocate a new TreeNode object with node name and weight.

Parameters:

s - The name of the node given by a string

w - The weight of the edge immediately above the node

TreeNode

public TreeNode(java.lang.String s)

Method Detail

getMin

public int getMin()

Specified by:

getMin in interface CellGeom

Returns:

The index of the smallest descendant node

getMax

public int getMax()

Specified by:

getMax in interface CellGeom

Returns:

The index of the smallest descendant node

getKey

public int getKey()

Specified by:

getKey in interface CellGeom

getName

public java.lang.String getName()

Specified by:

getName in interface CellGeom

setCachedColor

public void setCachedColor(java.awt.Color c)

getCachedColor

public java.awt.Color getCachedColor()

setCachedFrame

public void setCachedFrame(int framenum)

getCachedFrame

public int getCachedFrame()

getDrawer

public AccordionTreeDrawer getDrawer()

pick

public boolean pick(int x,
                    int y)

Specified by:

pick in interface CellGeom

getPos

public float getPos(int xy)

compute the real position of the node

drawInCell

public void drawInCell(java.awt.Color col,
                       float plane,
                       AccordionDrawer d)

Draws this node inside cell, the GridCell that it is attached to, if cell is drawn large enough Prints the label of the node if the GridCell is drawn large enough

Specified by:

drawInCell in interface CellGeom

Parameters:

col - The color to draw this node in

plane - The plane to draw this node in

See Also:

GridCell

setCell

public void setCell(GridCell c)

Specified by:

setCell in interface CellGeom

getCell

public GridCell getCell()

Specified by:

getCell in interface CellGeom

addEdge

public void addEdge(TreeEdge edge,
                    int xy)

Add edge in either X/horizontal (xy==0) direction, or Y/vertical (xy==1)direction. Leaf nodes have no vertical edge.

getEdge

public TreeEdge getEdge(int xy)

compareTo

public int compareTo(java.lang.Object o)

implement Comparable interface - sort on key field

Specified by:

compareTo in interface java.lang.Comparable

close

public void close()

clean the node itself and the tree edge attached with it.

See Also:

TreeEdge.close, Tree.close

finalize

protected void finalize()
                 throws java.lang.Throwable

Overrides:

finalize in class java.lang.Object

java.lang.Throwable

setName

public void setName(java.lang.String s)

numberChildren

public int numberChildren()

getChild

public TreeNode getChild(int i)

getLeftmostLeaf

public TreeNode getLeftmostLeaf()

getRightmostLeaf

public TreeNode getRightmostLeaf()

isLeaf

public boolean isLeaf()

isRoot

public boolean isRoot()

getLeafCount

public int getLeafCount()

Returns:

the total number of leaves decedant to this node

equals

public boolean equals(TreeNode n)

addChild

public void addChild(TreeNode n)

parent

public TreeNode parent()

setWeight

public void setWeight(double w)

getWeight

public float getWeight()

firstChild

public TreeNode firstChild()

lastChild

public TreeNode lastChild()

isAncestorOf

public boolean isAncestorOf(TreeNode that)

Parameters:

that - Another TreeNode object

Returns:

true if this is an ancestor of that

lca

public TreeNode lca(TreeNode that)

Compute the lowest common ancestor between this node and that. The two nodes must belong to the same tree.

Parameters:

that - A TreeNode in the Tree that this TreeNode belongs to

Returns:

the lowest common ancestor between this node and "that"

leafLca

public TreeNode leafLca(TreeNode that)

Compute the lowest common ancestor between this leaf and "that" The two nodes must belong to the same tree and must be leaves

Parameters:

that - A TreeNode in the Tree that this TreeNode belongs to

Returns:

the lowest common ancestor between this leaf and that, null if one of the nodes is not a leaf

print

public void print()

printSubtree

public void printSubtree()

setSubtreeExtremeLeaves

public void setSubtreeExtremeLeaves()

setSubtreeMinMax

void setSubtreeMinMax()

setSubtreeNumberLeaves

void setSubtreeNumberLeaves()

set numberLeaves field for each subnode

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

setFontSize

public void setFontSize(int fs)

getFontSize

public int getFontSize()

isInteriorNode

public boolean isInteriorNode()

setBcnScore

public void setBcnScore(float n)

getBcnScore

public java.lang.Double getBcnScore()