TreeJuxtaposer
Class TreeJuxtaposer

java.lang.Object
  |
  +--TreeJuxtaposer.TreeJuxtaposer

public class TreeJuxtaposer

extends java.lang.Object

A class representing a tree juxtaposer. A TreeJuxtaposer takes a set of trees and build the data structures for each pair for best corresponding nodes lookup and range intersection queries. The TreePairs class encapsulates all the Tree2Tree classes required to relate pairs of trees in the list "trees".

Version:

Author:

Tamara Munzner, Serdar Tasiran, Li Zhang, Yunhong Zhou

See Also:

AccordionDrawer.Tree, AccordionDrawer.TreeNode, CellGeom, TreePairs, AccordionDrawer.AccordionTreeDrawer, AccordionTreeDrawerFinal

Field Summary

(package private) java.util.ArrayList	ATDMatrix
(package private) java.awt.Color	backgroundColor
(package private) float	bcnScore
(package private) ButterflyFrame	butterflyFrame
(package private) javax.swing.JPanel	controlPanel
(package private) DebugFrame	debugFrame
(package private) static int	diffGroup
static boolean	drawButterFly
(package private) java.awt.GridLayout	drawLayout
(package private) javax.swing.JPanel	drawPanel
(package private) int	edgeweightLevels
(package private) int	edgeweightLevelUsed
(package private) boolean	firstTime
(package private) CellGeom	flashGeomOld
(package private) static int	flashGroup these numbers are permanent, but the ordering of the groups changes to reflect user interactions for which color wins out in a tie
(package private) static int	foundGroup
(package private) java.util.LinkedList	groups Rearrangable list of RangeLists (groups)
(package private) java.util.Vector	groupsByIndex
(package private) java.awt.Color	labelBackColor
(package private) java.awt.Color	labelBackHiColor
(package private) java.awt.Color	labelColor
(package private) java.awt.Color	labelHiColor
(package private) static int	lcaGroup
java.util.ArrayList	lcaNode
(package private) int	leftRight
(package private) float	linethickness
(package private) java.awt.Frame	mainFrame
(package private) static int[]	markGroup
(package private) boolean	matrix
(package private) java.awt.Color	objectColor
(package private) static Parser.status.Status	parser_status
(package private) boolean	quasimode
(package private) IncrementalSearch	searchFrame
(package private) static TreeJuxtaposer	self
(package private) SettingsFrame	settingsFrame
(package private) boolean	showStructDiffs
(package private) StateFrame	stateFrame
(package private) java.lang.String	title
(package private) TreePairs	TPs an array of TreePairs objects each TreePair contains the necessary data structure for each pair
private int	treeArgs
(package private) static int	treeCount
(package private) java.util.ArrayList	treeDrawers Resizeable array of AccordionTreeDrawerFinal objects
(package private) java.util.ArrayList	trees Resizeable array of Tree objects
(package private) UI	ui
(package private) int	viewDirection
(package private) AccordionTreeDrawer	wantsFocusATD
(package private) int[]	winSize

Constructor Summary

TreeJuxtaposer()

Method Summary

protected void	addAction()
private AccordionTreeDrawerFinal	addATD(Tree newTree, int width, int height) Utility function to make new AccordionTreeDrawer, set initial parameters and do treeDrawer list bookkeeping.
int	addGroup(boolean thisTreeOnly)
void	addLeaves()
void	addNodesToGroup(int min, int max, int group, AccordionTreeDrawer atd)
void	addTree(Tree newTree) Adds a new tree to "trees", performs all the pairwise tree comparisons and stores results.
void	changedMarks()
void	clearGroup(int group)
void	clearObserve()
void	decreaseLabelBuffer()
void	decreaseLabelBuffer(int xy)
void	decreaseLineThickness()
void	decreaseMaxFontHeight()
void	decreaseMinFontHeight()
void	deleteTree(java.lang.String fileName) Delete a tree from "trees", clean up all the data structures constructed for tree comparisons.
(package private) void	doFlashGeom(CellGeom flashGeom, int group, AccordionTreeDrawerFinal thisTree, int x, int y, boolean all) Acts as a toggle on group members: turn off old ones, turn on new ones, do lightweight frontbuffer drawing per item not whole screen redraw
(package private) void	doLCAGeom(int group, AccordionTreeDrawer thisTree)
(package private) void	doSelectGeom(CellGeom g, boolean selectSubtree, int group, AccordionTreeDrawer thisTree)
(package private) void	doSelectGeoms(java.util.ArrayList attachedGeoms, boolean selectSubtree, int group, AccordionTreeDrawer thisTree)
(package private) void	doStructuralDiff(AccordionTreeDrawer atd1, AccordionTreeDrawer atd2, int group) Compute perfectly matched nodes between two trees A node X is perfectly matched by a node Y if they have exactly the same leaf set.
void	drawDD()
void	drawLL()
void	drawRL()
void	drawRR()
void	drawUU()
void	drawWithViewDirection()
float	getBcnScore()
(package private) java.util.ArrayList	getColorsForRange(int objMin, int objMax, AccordionTreeDrawer callingTreeDrawer)
boolean	getDimBrite()
boolean	getDimColors()
boolean	getDrawLabels()
(package private) RangeList	getGroup(int group)
java.awt.Color	getGroupColor(int group)
java.util.ArrayList	getGroupForest(int groupindex, AccordionTreeDrawer atd) Return one TreeNode per group range item.
java.lang.String	getLabelByFQName(java.lang.String FQName)
boolean	getLCAGroup()
boolean	getLCAMark()
int	getLeftRight()
boolean	getLinkedNav()
(package private) boolean	getQuasimode()
boolean	getShowDiffs()
Tree	getTreeByName(java.lang.String name) Fetch a tree by its name.
void	increaseLabelBuffer()
void	increaseLabelBuffer(int xy)
void	increaseLineThickness()
void	increaseMaxFontHeight()
void	increaseMinFontHeight()
protected void	loadNewickTree(java.lang.String fname)
protected void	loadNexusTree(java.lang.String fname, java.util.Vector numbers)
static void	main(java.lang.String[] args)
void	observe()
void	observeActionGroup()
void	observeActionMode() a more compact version of implementation for observing functions
void	observeActionTarget()
void	observeMarkGroup()
protected void	quitAction()
void	removeNodesFromGroup(int min, int max, int group, AccordionTreeDrawer atd)
void	requestRedrawAll()
void	reset()
void	resizeGroup(int groupindex, boolean grow, int numSteps, boolean horizontal, boolean vertical)
void	resizeGroup(int groupindex, boolean grow, int numSteps, boolean horizontal, boolean vertical, AccordionTreeDrawer atd)
void	resizeRectOthers(TreeNode tn, float[] minChangeRatio, float[] maxChangeRatio, int numAnimSteps, AccordionTreeDrawer thisatd)
(package private) void	seedQueue(AccordionTreeDrawer atd)
void	setBcnScore(float score)
void	setBigGrid(boolean on)
void	setCacheRange(boolean on)
void	setCheckTime(boolean on)
void	setColorGrid(boolean on)
void	setDimBrite(boolean on)
void	setDimColors(boolean on)
void	setDrawLabels(boolean on)
void	setDrawOrder(int order)
void	setDrawSplits(boolean on)
void	setDumpStats(boolean on)
void	setExpandLeaves(int expand)
(package private) void	setFocus(CellGeom g, AccordionTreeDrawer atd)
void	setGroupColor(int group, java.awt.Color c)
void	setGroupEnable(int group, boolean on)
void	setGroupPriority(int group)
void	setGuarVis(boolean on)
void	setHorizontalDirection()
void	setLabelBuffer(int buffer)
void	setLabelBuffer(int buffer, int xy)
void	setLabelDrawBack(boolean on)
void	setLabelPopup(boolean on)
void	setLabelPosRight(boolean on)
void	setLabelTransp(boolean on)
void	setLCAGroup(boolean on)
void	setLCAMark(boolean on)
void	setLeftRight(int i)
void	setLineThickness(float thickness)
void	setLinkedNav(boolean on)
void	setMaxFontHeight(int fontsize)
void	setMinFontHeight(int fontsize)
void	setNoFlash(boolean on)
void	setNoGeoms(boolean on)
void	setNoGrid(boolean on)
(package private) void	setQuasimode(boolean on)
void	setShowAlg(boolean on)
void	setShowDiffs(boolean on)
void	setTitle(java.lang.String t)
void	setVerticalDirection()
void	toggleBigGrid()
void	toggleCacheRange()
void	toggleCheckTime()
void	toggleColorGrid()
void	toggleDimBrite()
void	toggleDimColors()
void	toggleDrawLabels()
void	toggleDrawOrder()
void	toggleDrawSplits()
void	toggleDumpStats()
void	toggleExpandLeaves()
void	toggleGuarVis()
void	toggleLabelDrawBack()
void	toggleLabelPopup()
void	toggleLabelPosRight()
void	toggleLabelTransp()
void	toggleLinkedNav()
void	toggleNoFlash()
void	toggleNoGeoms()
void	toggleNoGrid()
void	toggleShowAlg()
void	toggleShowDiffs()
void	unmarkGroup(int group)
(package private) void	wantsFocusInQuasi(AccordionTreeDrawer atd)

Methods inherited from class java.lang.Object

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

Field Detail

mainFrame

java.awt.Frame mainFrame

title

java.lang.String title

stateFrame

StateFrame stateFrame

settingsFrame

SettingsFrame settingsFrame

searchFrame

IncrementalSearch searchFrame

debugFrame

DebugFrame debugFrame

butterflyFrame

ButterflyFrame butterflyFrame

controlPanel

javax.swing.JPanel controlPanel

drawPanel

javax.swing.JPanel drawPanel

drawLayout

java.awt.GridLayout drawLayout

treeDrawers

java.util.ArrayList treeDrawers

Resizeable array of AccordionTreeDrawerFinal objects

ATDMatrix

java.util.ArrayList ATDMatrix

trees

java.util.ArrayList trees

Resizeable array of Tree objects

groups

java.util.LinkedList groups

Rearrangable list of RangeLists (groups)

groupsByIndex

java.util.Vector groupsByIndex

TPs

TreePairs TPs

an array of TreePairs objects each TreePair contains the necessary data structure for each pair

backgroundColor

java.awt.Color backgroundColor

objectColor

java.awt.Color objectColor

labelColor

java.awt.Color labelColor

labelBackColor

java.awt.Color labelBackColor

labelHiColor

java.awt.Color labelHiColor

labelBackHiColor

java.awt.Color labelBackHiColor

flashGroup

static int flashGroup

these numbers are permanent, but the ordering of the groups changes to reflect user interactions for which color wins out in a tie

diffGroup

static int diffGroup

lcaGroup

static int lcaGroup

markGroup

static int[] markGroup

foundGroup

static int foundGroup

treeCount

static int treeCount

flashGeomOld

CellGeom flashGeomOld

showStructDiffs

boolean showStructDiffs

matrix

boolean matrix

linethickness

float linethickness

parser_status

static Parser.status.Status parser_status

firstTime

boolean firstTime

treeArgs

private int treeArgs

quasimode

boolean quasimode

wantsFocusATD

AccordionTreeDrawer wantsFocusATD

edgeweightLevels

int edgeweightLevels

edgeweightLevelUsed

int edgeweightLevelUsed

self

static TreeJuxtaposer self

ui

UI ui

bcnScore

float bcnScore

viewDirection

int viewDirection

leftRight

int leftRight

drawButterFly

public static boolean drawButterFly

winSize

int[] winSize

lcaNode

public java.util.ArrayList lcaNode

Constructor Detail

TreeJuxtaposer

public TreeJuxtaposer()

Method Detail

wantsFocusInQuasi

void wantsFocusInQuasi(AccordionTreeDrawer atd)

setQuasimode

void setQuasimode(boolean on)

getQuasimode

boolean getQuasimode()

setTitle

public void setTitle(java.lang.String t)

addTree

public void addTree(Tree newTree)

Adds a new tree to "trees", performs all the pairwise tree comparisons and stores results.

See Also:

AccordionDrawer.Tree, TreePairs.addTree

setHorizontalDirection

public void setHorizontalDirection()

setVerticalDirection

public void setVerticalDirection()

drawWithViewDirection

public void drawWithViewDirection()

drawRL

public void drawRL()

drawRR

public void drawRR()

drawUU

public void drawUU()

drawDD

public void drawDD()

drawLL

public void drawLL()

addATD

private AccordionTreeDrawerFinal addATD(Tree newTree,
                                        int width,
                                        int height)

Utility function to make new AccordionTreeDrawer, set initial parameters and do treeDrawer list bookkeeping.

deleteTree

public void deleteTree(java.lang.String fileName)

Delete a tree from "trees", clean up all the data structures constructed for tree comparisons.

See Also:

AccordionDrawer.AccordionDrawer.close, AccordionDrawer.AccordionTreeDrawer.close, AccordionDrawer.GridCell.close, AccordionDrawer.Tree.close, AccordionDrawer.TreeEdge.close, AccordionDrawer.TreeNode.close, Parse.Newick.close, Tree2Tree.close, TreePairs.removeTree

getTreeByName

public Tree getTreeByName(java.lang.String name)

Fetch a tree by its name. This is done by linear search as we do not expect to have many trees in memory.

addAction

protected void addAction()

quitAction

protected void quitAction()

changedMarks

public void changedMarks()

requestRedrawAll

public void requestRedrawAll()

addLeaves

public void addLeaves()

addGroup

public int addGroup(boolean thisTreeOnly)

setGroupPriority

public void setGroupPriority(int group)

setGroupColor

public void setGroupColor(int group,
                          java.awt.Color c)

setGroupEnable

public void setGroupEnable(int group,
                           boolean on)

addNodesToGroup

public void addNodesToGroup(int min,
                            int max,
                            int group,
                            AccordionTreeDrawer atd)

removeNodesFromGroup

public void removeNodesFromGroup(int min,
                                 int max,
                                 int group,
                                 AccordionTreeDrawer atd)

getGroupColor

public java.awt.Color getGroupColor(int group)

clearGroup

public void clearGroup(int group)

unmarkGroup

public void unmarkGroup(int group)

getGroup

RangeList getGroup(int group)

seedQueue

void seedQueue(AccordionTreeDrawer atd)

getColorsForRange

java.util.ArrayList getColorsForRange(int objMin,
                                      int objMax,
                                      AccordionTreeDrawer callingTreeDrawer)

doFlashGeom

void doFlashGeom(CellGeom flashGeom,
                 int group,
                 AccordionTreeDrawerFinal thisTree,
                 int x,
                 int y,
                 boolean all)

Acts as a toggle on group members: turn off old ones, turn on new ones, do lightweight frontbuffer drawing per item not whole screen redraw

See Also:

AccordionDrawer.Tree, AccordionDrawer.TreeNode, TreeJuxtaposer.RangeList

doSelectGeoms

void doSelectGeoms(java.util.ArrayList attachedGeoms,
                   boolean selectSubtree,
                   int group,
                   AccordionTreeDrawer thisTree)

doSelectGeom

void doSelectGeom(CellGeom g,
                  boolean selectSubtree,
                  int group,
                  AccordionTreeDrawer thisTree)

doLCAGeom

void doLCAGeom(int group,
               AccordionTreeDrawer thisTree)

doStructuralDiff

void doStructuralDiff(AccordionTreeDrawer atd1,
                      AccordionTreeDrawer atd2,
                      int group)

Compute perfectly matched nodes between two trees A node X is perfectly matched by a node Y if they have exactly the same leaf set.

See Also:

AccordionDrawer.Tree, AccordionDrawer.TreeNode, TreePairs

setFocus

void setFocus(CellGeom g,
              AccordionTreeDrawer atd)

getLabelByFQName

public java.lang.String getLabelByFQName(java.lang.String FQName)

setBigGrid

public void setBigGrid(boolean on)

toggleBigGrid

public void toggleBigGrid()

setCacheRange

public void setCacheRange(boolean on)

toggleCacheRange

public void toggleCacheRange()

setCheckTime

public void setCheckTime(boolean on)

toggleCheckTime

public void toggleCheckTime()

setColorGrid

public void setColorGrid(boolean on)

toggleColorGrid

public void toggleColorGrid()

setDimBrite

public void setDimBrite(boolean on)

toggleDimBrite

public void toggleDimBrite()

getDimBrite

public boolean getDimBrite()

setDimColors

public void setDimColors(boolean on)

toggleDimColors

public void toggleDimColors()

getDimColors

public boolean getDimColors()

setDrawLabels

public void setDrawLabels(boolean on)

toggleDrawLabels

public void toggleDrawLabels()

getDrawLabels

public boolean getDrawLabels()

setDrawOrder

public void setDrawOrder(int order)

toggleDrawOrder

public void toggleDrawOrder()

setDumpStats

public void setDumpStats(boolean on)

toggleDumpStats

public void toggleDumpStats()

setGuarVis

public void setGuarVis(boolean on)

toggleGuarVis

public void toggleGuarVis()

setExpandLeaves

public void setExpandLeaves(int expand)

toggleExpandLeaves

public void toggleExpandLeaves()

setLabelBuffer

public void setLabelBuffer(int buffer)

increaseLabelBuffer

public void increaseLabelBuffer()

decreaseLabelBuffer

public void decreaseLabelBuffer()

setLabelBuffer

public void setLabelBuffer(int buffer,
                           int xy)

increaseLabelBuffer

public void increaseLabelBuffer(int xy)

decreaseLabelBuffer

public void decreaseLabelBuffer(int xy)

setLabelDrawBack

public void setLabelDrawBack(boolean on)

toggleLabelDrawBack

public void toggleLabelDrawBack()

setLabelPopup

public void setLabelPopup(boolean on)

toggleLabelPopup

public void toggleLabelPopup()

setLabelPosRight

public void setLabelPosRight(boolean on)

toggleLabelPosRight

public void toggleLabelPosRight()

setLabelTransp

public void setLabelTransp(boolean on)

toggleLabelTransp

public void toggleLabelTransp()

setDrawSplits

public void setDrawSplits(boolean on)

toggleDrawSplits

public void toggleDrawSplits()

setLineThickness

public void setLineThickness(float thickness)

increaseLineThickness

public void increaseLineThickness()

decreaseLineThickness

public void decreaseLineThickness()

setLinkedNav

public void setLinkedNav(boolean on)

toggleLinkedNav

public void toggleLinkedNav()

getLinkedNav

public boolean getLinkedNav()

setMaxFontHeight

public void setMaxFontHeight(int fontsize)

increaseMaxFontHeight

public void increaseMaxFontHeight()

decreaseMaxFontHeight

public void decreaseMaxFontHeight()

setMinFontHeight

public void setMinFontHeight(int fontsize)

increaseMinFontHeight

public void increaseMinFontHeight()

decreaseMinFontHeight

public void decreaseMinFontHeight()

setNoFlash

public void setNoFlash(boolean on)

toggleNoFlash

public void toggleNoFlash()

setNoGeoms

public void setNoGeoms(boolean on)

toggleNoGeoms

public void toggleNoGeoms()

setNoGrid

public void setNoGrid(boolean on)

toggleNoGrid

public void toggleNoGrid()

setShowAlg

public void setShowAlg(boolean on)

toggleShowAlg

public void toggleShowAlg()

setShowDiffs

public void setShowDiffs(boolean on)

toggleShowDiffs

public void toggleShowDiffs()

getShowDiffs

public boolean getShowDiffs()

setLCAGroup

public void setLCAGroup(boolean on)

getLCAGroup

public boolean getLCAGroup()

setLCAMark

public void setLCAMark(boolean on)

getLCAMark

public boolean getLCAMark()

reset

public void reset()

getGroupForest

public java.util.ArrayList getGroupForest(int groupindex,
                                          AccordionTreeDrawer atd)

Return one TreeNode per group range item.

resizeGroup

public void resizeGroup(int groupindex,
                        boolean grow,
                        int numSteps,
                        boolean horizontal,
                        boolean vertical,
                        AccordionTreeDrawer atd)

resizeGroup

public void resizeGroup(int groupindex,
                        boolean grow,
                        int numSteps,
                        boolean horizontal,
                        boolean vertical)

resizeRectOthers

public void resizeRectOthers(TreeNode tn,
                             float[] minChangeRatio,
                             float[] maxChangeRatio,
                             int numAnimSteps,
                             AccordionTreeDrawer thisatd)

loadNewickTree

protected void loadNewickTree(java.lang.String fname)

loadNexusTree

protected void loadNexusTree(java.lang.String fname,
                             java.util.Vector numbers)

main

public static void main(java.lang.String[] args)

observe

public void observe()

observeActionMode

public void observeActionMode()

a more compact version of implementation for observing functions

clearObserve

public void clearObserve()

observeActionGroup

public void observeActionGroup()

observeActionTarget

public void observeActionTarget()

observeMarkGroup

public void observeMarkGroup()

setBcnScore

public void setBcnScore(float score)

getBcnScore

public float getBcnScore()

setLeftRight

public void setLeftRight(int i)

getLeftRight

public int getLeftRight()