A B C D E F G H I J K L M N O P Q R S T U V W X Y

A

a - Variable in class AccordionDrawer.SplitTransition

aboutFrame - Static variable in class TreeJuxtaposer.Help

accept(File) - Method in class TreeJuxtaposer.NexusFilter

accept(File) - Method in class TreeJuxtaposer.NewickFilter

AccordionDrawer - package AccordionDrawer

AccordionDrawer - class AccordionDrawer.AccordionDrawer.

An abstract class representing a multi-scale rectangular grid on which shapes consisting of horizontal and vertical line segments (such as trees and graphs) can be drawn

AccordionDrawer(int, int) - Constructor for class AccordionDrawer.AccordionDrawer

AccordionTreeDrawer - package AccordionTreeDrawer

AccordionTreeDrawer - class AccordionTreeDrawer.AccordionTreeDrawer.

An abstract class representing a multi-scale rectangular grid on which a tree consisting of horizontal and vertical line segments is drawn Fills in the fields of the abstract class AccordionDrawer based on information from the Tree class.

AccordionTreeDrawer(Tree, int, int) - Constructor for class AccordionTreeDrawer.AccordionTreeDrawer

AccordionTreeDrawerFinal - class TreeJuxtaposer.AccordionTreeDrawerFinal.

A class that fleshes out the abstract methods left in AccordionTreeDrawer.

ACT_GROWDIR - Static variable in class TreeJuxtaposer.DebugFrame

ACT_MODE - Static variable in class TreeJuxtaposer.DebugFrame

ACT_SELECTION - Static variable in class TreeJuxtaposer.DebugFrame

ACT_TYPE - Static variable in class TreeJuxtaposer.DebugFrame

actionModeLabel - Static variable in class TreeJuxtaposer.DebugFrame

actionPerformed(ActionEvent) - Method in class TreeJuxtaposer.TreeRemovalPanel

actionPerformed(ActionEvent) - Method in class TreeJuxtaposer.StateFrame

actionPerformed(ActionEvent) - Method in class TreeJuxtaposer.SettingsFrame

actionTargetLabel - Static variable in class TreeJuxtaposer.DebugFrame

activeLabel - Static variable in class TreeJuxtaposer.StateFrame

activeMarkAction(int) - Method in class TreeJuxtaposer.StateFrame

activeModeAction(int) - Method in class TreeJuxtaposer.StateFrame

activeResolutionAction(int) - Method in class TreeJuxtaposer.StateFrame

aCurValue - Variable in class AccordionDrawer.SplitTransition

addCellToQueue(GridCell) - Method in class AccordionDrawer.AccordionDrawer

addChild(TreeNode) - Method in class AccordionTreeDrawer.TreeNode

addEdge(TreeEdge, int) - Method in class AccordionTreeDrawer.TreeNode

Add edge in either X/horizontal (xy==0) direction, or Y/vertical (xy==1)direction.

addGeom(CellGeom) - Method in class AccordionDrawer.GridCell

addGeom(CellGeom) - Method in class AccordionTreeDrawer.TreeQuadGridCell

addGeom(CellGeom) - Method in class AccordionTreeDrawer.TreeLeafGridCell

addGroup(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

addLeaves() - Method in class TreeJuxtaposer.TreeJuxtaposer

addNodesToGroup(int, int, int, AccordionTreeDrawer) - Method in class TreeJuxtaposer.TreeJuxtaposer

addRange(int, int, AccordionTreeDrawer) - Method in class AccordionTreeDrawer.RangeList

addTree(Tree) - Method in class TreeJuxtaposer.TreeJuxtaposer

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

adjustBeginLineColumn(int, int) - Method in class Parser.SimpleCharStream

Method to adjust line and column numbers for the start of a token.

alpha - Static variable in interface Parser.NewickConstants

aMinBoundary - Variable in class AccordionDrawer.SplitTransition

aNewValue - Variable in class AccordionDrawer.SplitTransition

aOldValue - Variable in class AccordionDrawer.SplitTransition

area - Variable in class AccordionDrawer.GridCell

attachEdges() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

Creates TreeEdges, attaches them to enclosing GridCells.

B

b - Variable in class AccordionDrawer.SplitTransition

backup(int) - Method in class Parser.SimpleCharStream

BCN_SCORE - Static variable in class TreeJuxtaposer.DebugFrame

bCurValue - Variable in class AccordionDrawer.SplitTransition

beginColumn - Variable in class Parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

beginLine - Variable in class Parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

BeginToken() - Method in class Parser.SimpleCharStream

bigEnough() - Method in class AccordionDrawer.GridCell

bigEnough() - Method in class AccordionTreeDrawer.TreeQuadGridCell

bigEnough() - Method in class AccordionTreeDrawer.TreeLeafGridCell

biggrid - Variable in class AccordionDrawer.AccordionDrawer

BinaryGridCell - class AccordionDrawer.BinaryGridCell.

BinaryGridCell(AccordionDrawer, int, int, int, boolean) - Constructor for class AccordionDrawer.BinaryGridCell

BinaryTree - class AccordionDrawer.BinaryTree.

A class which implements a quadtree This class is a tree of GridCells; each GridCell has up to 4 children.

BinaryTree(AccordionDrawer) - Constructor for class AccordionDrawer.BinaryTree

Constructor.

BitmapFont - package BitmapFont

BitmapFont - class BitmapFont.BitmapFont.

BitmapFont() - Constructor for class BitmapFont.BitmapFont

BitmapFont(char) - Constructor for class BitmapFont.BitmapFont

BitmapFonts - class BitmapFont.BitmapFonts.

BitmapFonts() - Constructor for class BitmapFont.BitmapFonts

BitmapFontsFamily - class BitmapFont.BitmapFontsFamily.

Class used to generate, read, and render bitmap fonts.

BitmapFontsFamily(String) - Constructor for class BitmapFont.BitmapFontsFamily

bMinBoundary - Variable in class AccordionDrawer.SplitTransition

bNewValue - Variable in class AccordionDrawer.SplitTransition

bOldValue - Variable in class AccordionDrawer.SplitTransition

both_char - Static variable in interface Parser.NewickConstants

bottomBiggerThanTop(LabelBox) - Method in class AccordionDrawer.LabelBox

branch_length() - Static method in class Parser.Newick

BRUTEFORCE - Static variable in class AccordionDrawer.AccordionDrawer

bufpos - Variable in class Parser.SimpleCharStream

build2D(Point[], int, int) - Method in class TreeJuxtaposer.RangeTree

builds a 2D range tree using points from A[start] to A[end].

ButterflyFrame - class TreeJuxtaposer.ButterflyFrame.

ButterflyFrame(TreeJuxtaposer) - Constructor for class TreeJuxtaposer.ButterflyFrame

C

cachedColor - Variable in class AccordionTreeDrawer.TreeNode

cachedFrame - Variable in class AccordionTreeDrawer.TreeNode

cacherange - Variable in class AccordionDrawer.AccordionDrawer

cell - Variable in class AccordionTreeDrawer.TreeNode

The GridCell that this node is attached to

CellGeom - interface AccordionDrawer.CellGeom.

center - Variable in class AccordionDrawer.Lens

center point, in pixel coordinates

center - Variable in class AccordionDrawer.InteractionBox

center point, in pixel coordinates

changedMarks() - Method in class AccordionDrawer.AccordionDrawer

changedMarks() - Method in class TreeJuxtaposer.TreeJuxtaposer

changedMarksFrame - Variable in class AccordionDrawer.AccordionDrawer

charWidth(char) - Method in class BitmapFont.BitmapFonts

charWidth(String, int, int) - Method in class BitmapFont.BitmapFontsFamily

checktime - Variable in class AccordionDrawer.AccordionDrawer

childless() - Method in class AccordionTreeDrawer.ColorNode

childless() - Method in class TreeJuxtaposer.RangeNode

clear() - Method in class AccordionTreeDrawer.RangeList

clearGroup(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

clearLens() - Method in class AccordionDrawer.AccordionDrawer

clearObserve() - Method in class TreeJuxtaposer.TreeJuxtaposer

clearQueue() - Method in class AccordionDrawer.AccordionDrawer

close() - Method in class AccordionDrawer.AccordionDrawer

clear all the data structures initiated in AD, called when tree(s) get deleted from AD

close() - Method in class AccordionTreeDrawer.TreeNode

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

close() - Method in class AccordionTreeDrawer.TreeEdge

clean the tree edge

close() - Method in class AccordionTreeDrawer.Tree

clean up method, called when the tree is deleted

close() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

clear the objects initiated in ATD

close() - Method in class Parser.Newick

colorgrid - Variable in class AccordionDrawer.AccordionDrawer

ColorNode - class AccordionTreeDrawer.ColorNode.

A class representing a RangeList in a RangeTree.

ColorNode() - Constructor for class AccordionTreeDrawer.ColorNode

empty constructor

ColorNode(RangeInTree, ColorNode, ColorNode) - Constructor for class AccordionTreeDrawer.ColorNode

constructor with Data initiated

ColorTree - class AccordionTreeDrawer.ColorTree.

A class representing a two-dimensional orthogonal range tree.

ColorTree(RangeList) - Constructor for class AccordionTreeDrawer.ColorTree

Constructor: calls RangeTreeBuild to build the tree

comment - Static variable in interface Parser.NewickConstants

compare(Object, Object) - Method in class AccordionTreeDrawer.TreeNodeCompareToY

implement Comparable interface - sort on key field

compare(Object, Object) - Method in class AccordionTreeDrawer.LeafComparator

compareBtoT(LabelBox, int, int) - Method in class AccordionDrawer.LabelBox

compareTo(Object) - Method in class AccordionDrawer.LabelBox

implement Comparable interface - sort on y values

compareTo(Object) - Method in class AccordionDrawer.GridCell

compareTo(Object) - Method in class AccordionTreeDrawer.TreeQuadGridCell

compareTo(Object) - Method in class AccordionTreeDrawer.TreeNode

implement Comparable interface - sort on key field

compareTo(Object) - Method in class AccordionTreeDrawer.TreeLeafGridCell

compareTo(Object) - Method in class AccordionTreeDrawer.RangeInTree

computeBin(int) - Method in class AccordionTreeDrawer.Tree

computeBottomSizeOne(Tree) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

We now create a certain number of empty (NOT null) cells between adjacent leaves for better separation of subtrees.

computePlaceThisFrame() - Method in class AccordionDrawer.GridCell

Computes min[], max[], and splitPos, the minimum, maximum and split point coordinates for this GridCell in absolute window coordinates.

contentFrame - Static variable in class TreeJuxtaposer.Help

countDrawnFrame - Static variable in class AccordionTreeDrawer.AccordionTreeDrawer

countDrawnScene - Static variable in class AccordionTreeDrawer.AccordionTreeDrawer

counter - Variable in class AccordionDrawer.AccordionDrawer

createCell(int, int, int, boolean) - Method in class AccordionDrawer.GridCell

createCell(int, int, int, boolean) - Method in class AccordionTreeDrawer.TreeQuadGridCell

createCell(int, int, int, boolean) - Method in class AccordionTreeDrawer.TreeLeafGridCell

cumFrameTime - Static variable in class AccordionTreeDrawer.AccordionTreeDrawer

currentToken - Variable in class Parser.ParseException

This is the last token that has been consumed successfully.

curStep - Variable in class AccordionDrawer.SplitTransition

D

D_ACT - Static variable in class TreeJuxtaposer.StateFrame

DebugFrame - class TreeJuxtaposer.DebugFrame.

DebugFrame(TreeJuxtaposer) - Constructor for class TreeJuxtaposer.DebugFrame

DebugFrame(TreeJuxtaposer, GraphicsConfiguration) - Constructor for class TreeJuxtaposer.DebugFrame

DebugFrame(TreeJuxtaposer, String) - Constructor for class TreeJuxtaposer.DebugFrame

DebugFrame(TreeJuxtaposer, String, GraphicsConfiguration) - Constructor for class TreeJuxtaposer.DebugFrame

debugStream - Static variable in class Parser.NewickTokenManager

decreaseLabelBuffer() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

decreaseLabelBuffer() - Method in class TreeJuxtaposer.TreeJuxtaposer

decreaseLabelBuffer(int) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

decreaseLabelBuffer(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

decreaseLineThickness() - Method in class AccordionDrawer.AccordionDrawer

decreaseLineThickness() - Method in class TreeJuxtaposer.TreeJuxtaposer

decreaseMaxFontHeight() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

decreaseMaxFontHeight() - Method in class TreeJuxtaposer.TreeJuxtaposer

decreaseMinFontHeight() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

decreaseMinFontHeight() - Method in class TreeJuxtaposer.TreeJuxtaposer

DEFAULT - Static variable in interface Parser.NewickConstants

defaultFocusCell - Variable in class AccordionDrawer.AccordionDrawer

deleteTree(String) - Method in class TreeJuxtaposer.TreeJuxtaposer

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

depthAdd - Static variable in class AccordionDrawer.BinaryTree

descendant_list() - Static method in class Parser.Newick

digit - Static variable in interface Parser.NewickConstants

dimbrite - Variable in class AccordionDrawer.AccordionDrawer

dimcolors - Variable in class AccordionDrawer.AccordionDrawer

disable_tracing() - Static method in class Parser.Newick

display() - Method in class AccordionDrawer.AccordionDrawer

doCleanup() - Method in class AccordionDrawer.AccordionDrawer

doFlash() - Method in class AccordionDrawer.AccordionDrawer

doFlash() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

On mouseover, flash the object under the mouse and draw its label at maximum size.

doLens() - Method in class AccordionDrawer.AccordionDrawer

render lens in a special mode readPixels form the front buffer in x and y direction to avoid flickering and overwrite only diffPos in x and y to render the lens do a twolinesmove with picked cells render the solution in a small viewport in the back buffer read pixels of this viewport switch back in the original viewport draw stored pixels TODO: x-distortion, check boundaries, flowmenu like zooming

Done() - Method in class Parser.SimpleCharStream

double_number - Static variable in interface Parser.NewickConstants

DOWN - Variable in class AccordionDrawer.AccordionDrawer

draw() - Method in class AccordionDrawer.GridCell

Draws this GridCell.

draw() - Method in class AccordionTreeDrawer.TreeQuadGridCell

draw() - Method in class AccordionTreeDrawer.TreeLeafGridCell

draw(Color, float, double) - Method in class AccordionDrawer.InteractionBox

draw(Color, float, float) - Method in class AccordionDrawer.Lens

drawAttachedObjects() - Method in class AccordionDrawer.GridCell

drawButterFly - Static variable in class TreeJuxtaposer.TreeJuxtaposer

drawDD() - Method in class TreeJuxtaposer.TreeJuxtaposer

drawDescend() - Method in class AccordionDrawer.QuadGridCell

drawDescend() - Method in class AccordionDrawer.LeafGridCell

drawDescend() - Method in class AccordionDrawer.GridCell

drawDescend() - Method in class AccordionDrawer.BinaryGridCell

drawEnd() - Method in class AccordionDrawer.AccordionDrawer

drawer - Variable in class AccordionDrawer.GridCell

drawFlowMenu() - Method in class AccordionDrawer.Lens

drawInCell(Color, float, AccordionDrawer) - Method in interface AccordionDrawer.CellGeom

drawInCell(Color, float, AccordionDrawer) - Method in class AccordionTreeDrawer.TreeNode

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

drawInCell(Color, float, AccordionDrawer) - Method in class AccordionTreeDrawer.TreeEdge

Draws this TreeEdge inside the GridCell to which it is attached, and its label if appropriate.

drawLabelBig(int, int) - Method in class AccordionTreeDrawer.TreeEdge

Draw label of this TreeEdge at maximum size (intended for mouseover highlighting).

drawlabels - Variable in class AccordionDrawer.AccordionDrawer

drawLens() - Method in class AccordionDrawer.Lens

drawLL() - Method in class TreeJuxtaposer.TreeJuxtaposer

drawNextFancy(CellGeom) - Method in class AccordionDrawer.AccordionDrawer

drawNextFancy(CellGeom) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

Decide what GridCells to enqueue for drawing based on tree topology.

draworder - Variable in class AccordionDrawer.AccordionDrawer

Order to draw elements in scene.

drawRL() - Method in class TreeJuxtaposer.TreeJuxtaposer

drawRR() - Method in class TreeJuxtaposer.TreeJuxtaposer

drawRubberband() - Method in class AccordionDrawer.InteractionBox

drawsplits - Variable in class AccordionDrawer.AccordionDrawer

drawStart() - Method in class AccordionDrawer.AccordionDrawer

drawString(GLFunc, String, int) - Method in class BitmapFont.BitmapFontsFamily

drawUU() - Method in class TreeJuxtaposer.TreeJuxtaposer

drawWithViewDirection() - Method in class TreeJuxtaposer.TreeJuxtaposer

drewMarkedAttachedFrame - Variable in class AccordionDrawer.GridCell

dumpstats - Variable in class AccordionDrawer.AccordionDrawer

E

enable_tracing() - Static method in class Parser.Newick

encloses - Variable in class AccordionTreeDrawer.TreeEdge

The GridCell that this TreeEdge is attached to

end - Variable in class AccordionTreeDrawer.TreeEdge

The GridCell the other endpoint (the "end" node) of the TreeEdge is attached to

endColumn - Variable in class Parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

endLine - Variable in class Parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

EOF - Static variable in interface Parser.NewickConstants

equals(Object) - Method in class AccordionDrawer.GridCell

equals(Object) - Method in class AccordionTreeDrawer.TreeQuadGridCell

equals(Object) - Method in class AccordionTreeDrawer.TreeLeafGridCell

equals(Object) - Method in class AccordionTreeDrawer.RangeInTree

equals(TreeNode) - Method in class AccordionTreeDrawer.TreeNode

expandleaves - Variable in class AccordionDrawer.AccordionDrawer

expandLeaves(int) - Method in class AccordionDrawer.AccordionDrawer

expectedTokenSequences - Variable in class Parser.ParseException

Each entry in this array is an array of integers.

exponent - Static variable in interface Parser.NewickConstants

F

F_ACT - Static variable in class TreeJuxtaposer.StateFrame

findEnclosingCell(int, int, int, int) - Method in class AccordionDrawer.AccordionDrawer

findSplitRangeNode(ColorNode, RangeInTree) - Method in class AccordionTreeDrawer.ColorTree

Find a RangeInSequence

firstChild() - Method in class AccordionTreeDrawer.TreeNode

flashDown() - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

flashLeft() - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

flashRight() - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

flashUp() - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

fname - Variable in class BitmapFont.BitmapFontsFamily

focusCell - Variable in class AccordionDrawer.AccordionDrawer

fontPixelHeight(int) - Method in class BitmapFont.BitmapFontsFamily

FROMFOCUSCELL - Static variable in class AccordionDrawer.AccordionDrawer

fullyQualified - Static variable in class AccordionTreeDrawer.AccordionTreeDrawer

G

GA_ACT - Static variable in class TreeJuxtaposer.StateFrame

GB_ACT - Static variable in class TreeJuxtaposer.StateFrame

GC_ACT - Static variable in class TreeJuxtaposer.StateFrame

GD_ACT - Static variable in class TreeJuxtaposer.StateFrame

generate(BufferedImage, int[], FontMetrics) - Method in class BitmapFont.BitmapFont

generate(int, int, int) - Method in class BitmapFont.BitmapFontsFamily

generate(String, int) - Method in class BitmapFont.BitmapFonts

generateParseException() - Static method in class Parser.Newick

getActionGroup() - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

getActionMode() - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

getArea(boolean) - Method in class AccordionDrawer.GridCell

getAreaPix(boolean) - Method in class AccordionDrawer.GridCell

getAscent(int) - Method in class BitmapFont.BitmapFontsFamily

getBackgroundColor() - Method in class AccordionDrawer.AccordionDrawer

getBcnScore() - Method in class AccordionTreeDrawer.TreeNode

getBcnScore() - Method in class TreeJuxtaposer.TreeJuxtaposer

getBeginColumn() - Method in class Parser.SimpleCharStream

getBeginLine() - Method in class Parser.SimpleCharStream

getBigGrid() - Method in class AccordionDrawer.AccordionDrawer

getButtons() - Method in class TreeJuxtaposer.ButterflyFrame

getCachedColor() - Method in class AccordionTreeDrawer.TreeNode

getCachedFrame() - Method in class AccordionTreeDrawer.TreeNode

getCacheRange() - Method in class AccordionDrawer.AccordionDrawer

getCanvas() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

getCell() - Method in interface AccordionDrawer.CellGeom

getCell() - Method in class AccordionTreeDrawer.TreeNode

getCell() - Method in class AccordionTreeDrawer.TreeEdge

getCellGeomDummy() - Method in class AccordionDrawer.GridCell

getCenter() - Method in class AccordionDrawer.Lens

getCheckTime() - Method in class AccordionDrawer.AccordionDrawer

getChild(int) - Method in class AccordionTreeDrawer.TreeNode

getChildAt(BinaryGridCell, int, int, int) - Method in class AccordionDrawer.BinaryTree

Gets a child at a specified x, y, depth location.

getChildAt(QuadGridCell, int, int, int) - Method in class AccordionDrawer.QuadTree

Gets a child at a specified x, y, depth location.

getColor() - Method in class AccordionTreeDrawer.RangeList

getColorGrid() - Method in class AccordionDrawer.AccordionDrawer

getColorsForGridCell(GridCell, int) - Method in class AccordionDrawer.AccordionDrawer

getColorsForGridCell(GridCell, int) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

getColorsForRange(int, int) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

getColorTree() - Method in class AccordionTreeDrawer.RangeList

getColumn() - Method in class Parser.SimpleCharStream

Deprecated.

getDescent() - Method in class BitmapFont.BitmapFonts

getDescent(int) - Method in class BitmapFont.BitmapFontsFamily

getDescription() - Method in class TreeJuxtaposer.NexusFilter

getDescription() - Method in class TreeJuxtaposer.NewickFilter

getDimBrite() - Method in class AccordionDrawer.AccordionDrawer

getDimBrite() - Method in class TreeJuxtaposer.TreeJuxtaposer

getDimColors() - Method in class AccordionDrawer.AccordionDrawer

getDimColors() - Method in class TreeJuxtaposer.TreeJuxtaposer

getDoubleBuffer() - Method in class AccordionDrawer.AccordionDrawer

getDrawAngle() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

getDrawer() - Method in class AccordionTreeDrawer.TreeNode

getDrawer() - Method in class AccordionTreeDrawer.TreeEdge

getDrawLabels() - Method in class AccordionDrawer.AccordionDrawer

getDrawLabels() - Method in class TreeJuxtaposer.TreeJuxtaposer

getDrawnLabels() - Method in class AccordionDrawer.AccordionDrawer

getDrawOrder() - Method in class AccordionDrawer.AccordionDrawer

getDrewMarkedAttachedFrame() - Method in class AccordionDrawer.GridCell

getDumpStats() - Method in class AccordionDrawer.AccordionDrawer

getEdge(int) - Method in class AccordionTreeDrawer.TreeNode

getElement() - Method in class TreeJuxtaposer.RangeTree

getElement() - Method in class TreeJuxtaposer.RangeNode

getEnabled() - Method in class AccordionTreeDrawer.RangeList

getEndColumn() - Method in class Parser.SimpleCharStream

getEndLine() - Method in class Parser.SimpleCharStream

getExpandLeaves() - Method in class AccordionDrawer.AccordionDrawer

getExtension(File) - Static method in class TreeJuxtaposer.Utils

getFirst() - Method in class AccordionTreeDrawer.RangeList

getFontSize() - Method in class AccordionTreeDrawer.TreeNode

getFrameNum() - Method in class AccordionDrawer.AccordionDrawer

getGeoms() - Method in class AccordionDrawer.GridCell

getGeomsSize() - Method in class AccordionDrawer.GridCell

getGraphicsStuff() - Method in class AccordionDrawer.AccordionDrawer

getGridCell(int, int, int) - Method in class AccordionDrawer.QuadTree

Returns the GridCell at the specified row, column and level.

getGridCell(int, int, int) - Method in class AccordionDrawer.BinaryTree

Returns the GridCell at the specified row, column and level.

getGridSize(int, int) - Static method in class AccordionDrawer.BinaryTree

getGroupColor(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

getGroupForest(int, AccordionTreeDrawer) - Method in class TreeJuxtaposer.TreeJuxtaposer

Return one TreeNode per group range item.

getGrowDirection() - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

getGuarVis() - Method in class AccordionDrawer.AccordionDrawer

GetImage() - Method in class Parser.SimpleCharStream

getInflateIncr() - Method in class AccordionDrawer.AccordionDrawer

getKey() - Method in interface AccordionDrawer.CellGeom

getKey() - Method in class AccordionDrawer.AccordionDrawer

getKey() - Method in class AccordionTreeDrawer.TreeNode

getKey() - Method in class AccordionTreeDrawer.TreeEdge

getKey() - Method in class AccordionTreeDrawer.Tree

getKey() - Method in class AccordionTreeDrawer.RangeList

getLabelBackColor() - Method in class AccordionDrawer.AccordionDrawer

getLabelBackHiColor() - Method in class AccordionDrawer.AccordionDrawer

getLabelBuffer(int) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

getLabelByFQName(String) - Method in class TreeJuxtaposer.TreeJuxtaposer

getLabelColor() - Method in class AccordionDrawer.AccordionDrawer

getLabelDrawBack() - Method in class AccordionDrawer.AccordionDrawer

getLabelHiColor() - Method in class AccordionDrawer.AccordionDrawer

getLabelplane() - Method in class AccordionDrawer.AccordionDrawer

getLabelPopup() - Method in class AccordionDrawer.AccordionDrawer

getLabelPosRight() - Method in class AccordionDrawer.AccordionDrawer

getLabelTransp() - Method in class AccordionDrawer.AccordionDrawer

getLargest(int) - Method in class AccordionTreeDrawer.RangeInTree

getLast() - Method in class AccordionTreeDrawer.RangeList

getLCAGroup() - Method in class TreeJuxtaposer.TreeJuxtaposer

getLCAGroup() - Method in class TreeJuxtaposer.StateFrame

getLCAMark() - Method in class TreeJuxtaposer.TreeJuxtaposer

getLCAMark() - Method in class TreeJuxtaposer.StateFrame

getLeafCount() - Method in class AccordionTreeDrawer.TreeNode

getLeafCount() - Method in class AccordionTreeDrawer.Tree

getLeftmostLeaf() - Method in class AccordionTreeDrawer.TreeNode

getLeftmostLeaf() - Method in class AccordionTreeDrawer.Tree

getLeftRight() - Method in class TreeJuxtaposer.TreeJuxtaposer

getLevel() - Method in class AccordionDrawer.GridCell

getLine() - Method in class Parser.SimpleCharStream

Deprecated.

getLineThickness() - Method in class AccordionDrawer.AccordionDrawer

getLinkedNav() - Method in class AccordionDrawer.AccordionDrawer

getLinkedNav() - Method in class TreeJuxtaposer.TreeJuxtaposer

getMarkGroup() - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

getMax() - Method in class AccordionDrawer.Lens

getMax() - Method in interface AccordionDrawer.CellGeom

getMax() - Method in class AccordionTreeDrawer.TreeNode

getMax() - Method in class AccordionTreeDrawer.TreeEdge

getMax() - Method in class AccordionTreeDrawer.RangeInTree

getMax(int, boolean) - Method in class AccordionDrawer.GridCell

getMaxFontHeight() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

getMaxLine(int) - Method in class AccordionDrawer.GridCell

getMaxPix(int, boolean) - Method in class AccordionDrawer.GridCell

getMessage() - Method in class Parser.TokenMgrError

You can also modify the body of this method to customize your error messages.

getMessage() - Method in class Parser.ParseException

This method has the standard behavior when this object has been created using the standard constructors.

getMin() - Method in class AccordionDrawer.Lens

getMin() - Method in interface AccordionDrawer.CellGeom

getMin() - Method in class AccordionTreeDrawer.TreeNode

getMin() - Method in class AccordionTreeDrawer.TreeEdge

getMin() - Method in class AccordionTreeDrawer.RangeInTree

getMin(int, boolean) - Method in class AccordionDrawer.GridCell

getMinCellDims(int) - Method in class AccordionDrawer.AccordionDrawer

getMinCellSize(int) - Method in class AccordionDrawer.AccordionDrawer

getMinFontHeight() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

getMinLine(int) - Method in class AccordionDrawer.GridCell

getMinPix(int, boolean) - Method in class AccordionDrawer.GridCell

getName() - Method in class AccordionDrawer.LabelBox

getName() - Method in interface AccordionDrawer.CellGeom

getName() - Method in class AccordionTreeDrawer.TreeNode

getName() - Method in class AccordionTreeDrawer.TreeEdge

getName() - Method in class AccordionTreeDrawer.Tree

getNextToken() - Static method in class Parser.NewickTokenManager

getNextToken() - Static method in class Parser.Newick

getNodeByKey(int) - Method in class AccordionTreeDrawer.Tree

getNodeByKey(int) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

getNodeByName(String) - Method in class AccordionTreeDrawer.Tree

getNodeByName(String) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

getNoFlash() - Method in class AccordionDrawer.AccordionDrawer

getNoGeoms() - Method in class AccordionDrawer.AccordionDrawer

getNoGrid() - Method in class AccordionDrawer.AccordionDrawer

getNumAnimSteps() - Method in class AccordionDrawer.AccordionDrawer

getNumRanges() - Method in class AccordionTreeDrawer.RangeList

getObjectColor() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

getObjMax() - Method in class AccordionDrawer.GridCell

getObjMin() - Method in class AccordionDrawer.GridCell

getObjplane() - Method in class AccordionDrawer.AccordionDrawer

getOwner() - Method in class AccordionDrawer.BinaryTree

getParent() - Method in class AccordionDrawer.QuadGridCell

getParent() - Method in class AccordionDrawer.LeafGridCell

getParent() - Method in class AccordionDrawer.GridCell

getParent() - Method in class AccordionDrawer.BinaryGridCell

getPos(int) - Method in class AccordionTreeDrawer.TreeNode

compute the real position of the node

getRanges() - Method in class AccordionTreeDrawer.RangeList

getRightmostLeaf() - Method in class AccordionTreeDrawer.TreeNode

getRightmostLeaf() - Method in class AccordionTreeDrawer.Tree

getRoot() - Method in class AccordionTreeDrawer.Tree

getRoot() - Method in class AccordionTreeDrawer.ColorTree

getRoot() - Method in class TreeJuxtaposer.RangeTree

getRubberbandColor() - Method in class AccordionDrawer.AccordionDrawer

getSelectionResolution() - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

getShowAlg() - Method in class AccordionDrawer.AccordionDrawer

getShowDiffs() - Method in class TreeJuxtaposer.TreeJuxtaposer

getSize() - Method in class AccordionDrawer.Lens

getSize() - Method in class AccordionTreeDrawer.Tree

getSize(int, boolean) - Method in class AccordionDrawer.GridCell

getSizeInPix(int, boolean) - Method in class AccordionDrawer.GridCell

getSmallest(int) - Method in class AccordionTreeDrawer.RangeInTree

getSplitPix(int, boolean) - Method in class AccordionDrawer.GridCell

getSplitPos(int, boolean) - Method in class AccordionDrawer.GridCell

GetSuffix(int) - Method in class Parser.SimpleCharStream

getToken(int) - Static method in class Parser.Newick

getTree() - Method in class AccordionTreeDrawer.RangeInTree

getTree() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

getTreeByName(String) - Method in class TreeJuxtaposer.TreeJuxtaposer

Fetch a tree by its name.

getWeight() - Method in class AccordionTreeDrawer.TreeNode

getWinMax(int) - Method in class AccordionDrawer.AccordionDrawer

getWinMaxX() - Method in class AccordionDrawer.AccordionDrawer

getWinMaxY() - Method in class AccordionDrawer.AccordionDrawer

getWinsize(int) - Method in class AccordionDrawer.AccordionDrawer

getXInterval() - Method in class AccordionTreeDrawer.TreeEdge

getYInterval() - Method in class AccordionTreeDrawer.TreeEdge

glc - Variable in class AccordionDrawer.AccordionDrawer

GridCell - class AccordionDrawer.GridCell.

A class representing a cell in the quad tree data structure A GridCell can have up to four (4) kid cells and may have a parent cell

GridCell(AccordionDrawer, int, int, int, boolean) - Constructor for class AccordionDrawer.GridCell

gridSize - Variable in class AccordionDrawer.QuadTree

gridSize - Static variable in class AccordionDrawer.BinaryTree

growModeAction(int) - Method in class TreeJuxtaposer.StateFrame

guarvis - Variable in class AccordionDrawer.AccordionDrawer

Whether to guarantee visibility.

H

Help - class TreeJuxtaposer.Help.

horiz - Variable in class AccordionDrawer.AccordionDrawer

horiz - Variable in class AccordionTreeDrawer.TreeEdge

Whether this TreeEdge is horizontal

I

image - Variable in class Parser.Token

The string image of the token.

incr() - Method in class AccordionDrawer.SplitTransition

increaseLabelBuffer() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

increaseLabelBuffer() - Method in class TreeJuxtaposer.TreeJuxtaposer

increaseLabelBuffer(int) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

increaseLabelBuffer(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

increaseLineThickness() - Method in class AccordionDrawer.AccordionDrawer

increaseLineThickness() - Method in class TreeJuxtaposer.TreeJuxtaposer

increaseMaxFontHeight() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

increaseMaxFontHeight() - Method in class TreeJuxtaposer.TreeJuxtaposer

increaseMinFontHeight() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

increaseMinFontHeight() - Method in class TreeJuxtaposer.TreeJuxtaposer

IncrementalSearch - class TreeJuxtaposer.IncrementalSearch.

incrementCountBBoxDraw() - Static method in class AccordionDrawer.GridCell

indexByHeight - Variable in class BitmapFont.BitmapFontsFamily

init() - Method in class AccordionDrawer.Lens

init() - Method in class AccordionDrawer.AccordionDrawer

init() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

Initialization done after graphics context has been established.

init(int) - Method in class AccordionDrawer.QuadTree

Initializes a few variables.

init(int, int, int) - Method in class AccordionDrawer.BinaryTree

Initializes a few variables.

initCells() - Method in class AccordionDrawer.AccordionDrawer

initCells() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

Initializes level 0 GridCells based on Tree tree, assign tree nodes to them.

initComponents() - Method in class TreeJuxtaposer.ButterflyFrame

initializeList(ArrayList) - Method in class TreeJuxtaposer.IncrementalSearch

Input() - Static method in class Parser.Newick

insideFixedStrip - Variable in class AccordionDrawer.SplitTransition

InteractionBox - class AccordionDrawer.InteractionBox.

Draw and cache information about an onscreen rubberband box.

InteractionBox(GridCell[], GridCell[], CellGeom, AccordionDrawer) - Constructor for class AccordionDrawer.InteractionBox

InteractionBox(int[], int[], AccordionDrawer) - Constructor for class AccordionDrawer.InteractionBox

interactionplane - Variable in class AccordionDrawer.AccordionDrawer

intersectBoxes(LabelBox) - Method in class AccordionDrawer.LabelBox

intersects(RangeInTree) - Method in class AccordionTreeDrawer.RangeInTree

isAncestorOf(TreeNode) - Method in class AccordionTreeDrawer.TreeNode

isDoingFlash() - Method in class AccordionDrawer.AccordionDrawer

isEmpty() - Method in class AccordionTreeDrawer.ColorTree

isEmpty() - Method in class TreeJuxtaposer.RangeTree

isInteriorNode() - Method in class AccordionTreeDrawer.TreeNode

isLeaf() - Method in class AccordionTreeDrawer.TreeNode

isQuadTree() - Method in class AccordionDrawer.GridCell

isRangeInRange(Tree, int, int, Tree, int, int) - Method in class TreeJuxtaposer.TreePairs

given a node range in one tree, say whether there's an overlap with the node range in the other tree.

isRoot() - Method in class AccordionTreeDrawer.TreeNode

isThisTreeOnly() - Method in class AccordionTreeDrawer.RangeList

item - Variable in class AccordionDrawer.Lens

item - Variable in class AccordionDrawer.InteractionBox

J

jj_nt - Static variable in class Parser.Newick

jjstrLiteralImages - Static variable in class Parser.NewickTokenManager

K

keepDrawing - Variable in class AccordionDrawer.AccordionDrawer

keepMoving - Variable in class AccordionDrawer.AccordionDrawer

key - Variable in class AccordionTreeDrawer.TreeNode

key is unique for nodes in one tree

keyPressed(KeyEvent) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

keyReleased(KeyEvent) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

keyTyped(KeyEvent) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

Used when hitting a key should trigger an atomic action.

kind - Variable in class Parser.Token

An integer that describes the kind of this token.

L

label - Variable in class AccordionTreeDrawer.TreeNode

label() - Static method in class Parser.Newick

LabelBox - class AccordionDrawer.LabelBox.

Axis-aligned bounding box class for label drawing.

LabelBox(int[], int[], int[], int[], int[], int, String, int, double, int) - Constructor for class AccordionDrawer.LabelBox

LabelBox(int[], int[], int[], int, String) - Constructor for class AccordionDrawer.LabelBox

labeldrawback - Variable in class AccordionDrawer.AccordionDrawer

labelpopup - Variable in class AccordionDrawer.AccordionDrawer

labelposright - Variable in class AccordionDrawer.AccordionDrawer

labeltransp - Variable in class AccordionDrawer.AccordionDrawer

lastChild() - Method in class AccordionTreeDrawer.TreeNode

LCA_ACT - Static variable in class TreeJuxtaposer.StateFrame

lca(TreeNode) - Method in class AccordionTreeDrawer.TreeNode

Compute the lowest common ancestor between this node and that.

LCAMark - Variable in class TreeJuxtaposer.StateFrame

lcaNode - Variable in class TreeJuxtaposer.TreeJuxtaposer

LeafComparator - class AccordionTreeDrawer.LeafComparator.

LeafComparator() - Constructor for class AccordionTreeDrawer.LeafComparator

LeafGridCell - class AccordionDrawer.LeafGridCell.

LeafGridCell(AccordionDrawer, int, int, int, boolean) - Constructor for class AccordionDrawer.LeafGridCell

leafLca(TreeNode) - Method in class AccordionTreeDrawer.TreeNode

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

LEFT - Variable in class AccordionDrawer.AccordionDrawer

leftmostLeaf - Variable in class AccordionTreeDrawer.TreeNode

leftRight - Variable in class AccordionDrawer.AccordionDrawer

lens - Variable in class AccordionDrawer.AccordionDrawer

Lens - class AccordionDrawer.Lens.

Lens(GridCell[], GridCell[], int[], int[], CellGeom, AccordionDrawer) - Constructor for class AccordionDrawer.Lens

Lens(int[], int[], int[], int[], int[], AccordionDrawer) - Constructor for class AccordionDrawer.Lens

level - Variable in class AccordionDrawer.QuadGridCell

level - Variable in class AccordionDrawer.BinaryGridCell

lexStateNames - Static variable in class Parser.NewickTokenManager

lindex - Variable in class AccordionTreeDrawer.TreeNode

leaf index

lineMove(int, GridCell, float, boolean) - Method in class AccordionDrawer.AccordionDrawer

Moves the splitPos of GridCell a to absolute position value in window coordinates.

linethickness - Variable in class AccordionDrawer.AccordionDrawer

linkednav - Variable in class AccordionDrawer.AccordionDrawer

load_nexus(String, int) - Method in class AccordionTreeDrawer.Tree

Reads a tree with giving index in a file fname with Nexus format and initiates the Tree object.

load(String) - Method in class AccordionTreeDrawer.Tree

Reads a tree in file fname described in Newick format and initiate the tree object.

loadImages() - Method in class TreeJuxtaposer.ButterflyFrame

lookingAhead - Static variable in class Parser.Newick

M

M_ACT - Static variable in class TreeJuxtaposer.StateFrame

M_GROUP - Static variable in class TreeJuxtaposer.DebugFrame

main(String[]) - Static method in class BitmapFont.TestRead

main(String[]) - Static method in class BitmapFont.BitmapFontsFamily

main(String[]) - Static method in class TreeJuxtaposer.TreeJuxtaposer

main(String[]) - Static method in class TreeJuxtaposer.IncrementalSearch

makeBox(CellGeom) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

Create box enclosing the subtree beneath input node/edge.

makeChildAt(BinaryGridCell, int, int, int) - Method in class AccordionDrawer.BinaryTree

Like getChildAt, but makes new cells whenever necessary.

makeChildAt(QuadGridCell, int, int, int) - Method in class AccordionDrawer.QuadTree

Like getChildAt, but makes new cells whenever necessary.

max - Variable in class AccordionDrawer.Lens

top right corner, in pixel coordinates

max - Variable in class AccordionDrawer.InteractionBox

top right corner, in pixel coordinates

maxBoundCell - Variable in class AccordionDrawer.SplitTransition

maxc - Variable in class AccordionDrawer.Lens

maxc - Variable in class AccordionDrawer.InteractionBox

maxFontHeight - Variable in class AccordionTreeDrawer.AccordionTreeDrawer

maxHeight - Variable in class BitmapFont.BitmapFontsFamily

maxStep - Variable in class AccordionDrawer.SplitTransition

mergeSort(Point[], int) - Static method in class TreeJuxtaposer.RangeTree

This implements a regular merge sort algorithm.

min - Variable in class AccordionDrawer.Lens

bottom left corner, in pixel coordinates

min - Variable in class AccordionDrawer.InteractionBox

bottom left corner, in pixel coordinates

minBoundCell - Variable in class AccordionDrawer.SplitTransition

minc - Variable in class AccordionDrawer.Lens

minc - Variable in class AccordionDrawer.InteractionBox

minFontHeight - Variable in class AccordionTreeDrawer.AccordionTreeDrawer

mouseClicked(MouseEvent) - Method in class TreeJuxtaposer.StateFrame

mouseClicked(MouseEvent) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

mouseDragged(MouseEvent) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

mouseEntered(MouseEvent) - Method in class TreeJuxtaposer.StateFrame

mouseEntered(MouseEvent) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

mouseExited(MouseEvent) - Method in class TreeJuxtaposer.StateFrame

mouseExited(MouseEvent) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

mouseMoved(MouseEvent) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

mousePressed(MouseEvent) - Method in class TreeJuxtaposer.StateFrame

mousePressed(MouseEvent) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

mouseReleased(MouseEvent) - Method in class TreeJuxtaposer.StateFrame

mouseReleased(MouseEvent) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

N

NAV_TYPE - Static variable in class TreeJuxtaposer.DebugFrame

newick - Static variable in class TreeJuxtaposer.Utils

Newick - class Parser.Newick.

A static class used for parsing a Newick format file containing just one tree

newick_file_description - Static variable in class TreeJuxtaposer.Utils

Newick(InputStream) - Constructor for class Parser.Newick

Newick(NewickTokenManager) - Constructor for class Parser.Newick

Newick(Reader) - Constructor for class Parser.Newick

NewickConstants - interface Parser.NewickConstants.

NewickFilter - class TreeJuxtaposer.NewickFilter.

NewickFilter() - Constructor for class TreeJuxtaposer.NewickFilter

NewickTokenManager - class Parser.NewickTokenManager.

NewickTokenManager(SimpleCharStream) - Constructor for class Parser.NewickTokenManager

NewickTokenManager(SimpleCharStream, int) - Constructor for class Parser.NewickTokenManager

newToken(int) - Static method in class Parser.Token

Returns a new Token object, by default.

next - Variable in class AccordionTreeDrawer.TreeNode

next leaf added by Li

next - Variable in class Parser.Token

A reference to the next regular (non-special) token from the input stream.

nexus - Static variable in class TreeJuxtaposer.Utils

nexus_file_description - Static variable in class TreeJuxtaposer.Utils

NexusFilter - class TreeJuxtaposer.NexusFilter.

NexusFilter() - Constructor for class TreeJuxtaposer.NexusFilter

node - Variable in class AccordionTreeDrawer.TreeEdge

nodes - Variable in class AccordionTreeDrawer.Tree

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

noflash - Variable in class AccordionDrawer.AccordionDrawer

nofonts - Variable in class BitmapFont.BitmapFontsFamily

nogeoms - Variable in class AccordionDrawer.AccordionDrawer

nogrid - Variable in class AccordionDrawer.AccordionDrawer

number - Static variable in interface Parser.NewickConstants

numberChildren() - Method in class AccordionTreeDrawer.TreeNode

numberLeaves - Variable in class AccordionTreeDrawer.TreeNode

O

objmax - Variable in class AccordionDrawer.GridCell

objmin - Variable in class AccordionDrawer.GridCell

observe() - Method in class TreeJuxtaposer.TreeJuxtaposer

observe() - Method in class TreeJuxtaposer.StateFrame

observe() - Method in class TreeJuxtaposer.SettingsFrame

observeActionGroup() - Method in class TreeJuxtaposer.TreeJuxtaposer

observeActionMode() - Method in class TreeJuxtaposer.TreeJuxtaposer

a more compact version of implementation for observing functions

observeActionTarget() - Method in class TreeJuxtaposer.TreeJuxtaposer

observeMarkGroup() - Method in class TreeJuxtaposer.TreeJuxtaposer

oldLens - Variable in class AccordionDrawer.AccordionDrawer

oldPos - Variable in class AccordionDrawer.Lens

only_quote_char - Static variable in interface Parser.NewickConstants

P

parent - Variable in class AccordionTreeDrawer.TreeNode

parent() - Method in class AccordionTreeDrawer.TreeNode

ParseException - exception Parser.ParseException.

This exception is thrown when parse errors are encountered.

ParseException() - Constructor for class Parser.ParseException

The following constructors are for use by you for whatever purpose you can think of.

ParseException(String) - Constructor for class Parser.ParseException

ParseException(Token, int[][], String[]) - Constructor for class Parser.ParseException

This constructor is used by the method "generateParseException" in the generated parser.

Parser - package Parser

parseTree(Tree) - Method in class Parser.Newick

function parseTree initiates field tree, call function Input to parse the input.

pick(int, int) - Method in interface AccordionDrawer.CellGeom

pick(int, int) - Method in class AccordionTreeDrawer.TreeNode

pick(int, int) - Method in class AccordionTreeDrawer.TreeEdge

Determines whether the window coordinates (x,y) fall on this TreeEdge There is a "snap" factor, determined by the pickFuzz field of the enclosing cell.

pickAttached(int, int) - Method in class AccordionDrawer.GridCell

Computes an ArrayList of features (CellGeom's, like TreeNode or TreeEdge) that are "picked", i.e., are around (x,y) in screen coordinates and are attached to this GridCell Recurses down the quadtree hierarchy, starting at this GridCell, until at least one picked object is found or the bottom of the hierarchy is reached.

pickAttached(int, int) - Method in class AccordionDrawer.AccordionDrawer

pickAttached(int, int) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

pickCell(int, int) - Method in class AccordionDrawer.GridCell

Computes the lowest level visible GridCell picked (selected) by a click at (x,y)

pickCell(int, int) - Method in class AccordionDrawer.AccordionDrawer

pickCellClosestTo(int, int, boolean) - Method in class AccordionDrawer.AccordionDrawer

Pick closest cell in either horizontal *or* vertical direction.

pickDescend(int, int) - Method in class AccordionDrawer.QuadGridCell

Computes the kid cell that contains the click at (x,y)

pickDescend(int, int) - Method in class AccordionDrawer.LeafGridCell

pickDescend(int, int) - Method in class AccordionDrawer.GridCell

pickDescend(int, int) - Method in class AccordionDrawer.BinaryGridCell

pixels - Variable in class AccordionDrawer.Lens

framebuffer pixels from last mouseover label drawn

popupFontHeight - Variable in class AccordionTreeDrawer.AccordionTreeDrawer

pos - Variable in class AccordionDrawer.Lens

pos(int) - Method in class AccordionDrawer.LabelBox

posorderNext - Variable in class AccordionTreeDrawer.TreeNode

posorderStartNode - Variable in class AccordionTreeDrawer.Tree

the start node for postorder list of all the nodes

possiblyEnqueue() - Method in class AccordionDrawer.GridCell

possiblyEnqueue() - Method in class AccordionTreeDrawer.TreeQuadGridCell

possiblyEnqueue() - Method in class AccordionTreeDrawer.TreeLeafGridCell

postProcess() - Method in class AccordionTreeDrawer.Tree

Post processing includes computing size of each node, linking nodes in different order, etc.

preorderNext - Variable in class AccordionTreeDrawer.TreeNode

preorderStartNode - Variable in class AccordionTreeDrawer.Tree

the start node for preorder list of all the nodes

prepareToShow() - Method in class TreeJuxtaposer.StateFrame

prepareToShow() - Method in class TreeJuxtaposer.SettingsFrame

print() - Method in class AccordionTreeDrawer.TreeNode

print(boolean) - Method in class BitmapFont.BitmapFontsFamily

print(boolean) - Method in class BitmapFont.BitmapFonts

print(boolean) - Method in class BitmapFont.BitmapFont

print(int) - Method in class AccordionDrawer.GridCell

printLeaves() - Method in class AccordionTreeDrawer.Tree

printSubtree() - Method in class AccordionTreeDrawer.TreeNode

putChildAt(BinaryGridCell, int, int, int, GridCell) - Method in class AccordionDrawer.BinaryTree

Like makeChildAt, but the instead of creating a new cell at the specified location, puts the specified cell there.

putChildAt(QuadGridCell, int, int, int, QuadGridCell) - Method in class AccordionDrawer.QuadTree

Like makeChildAt, but the instead of creating a new cell at the specified location, puts the specified cell there.

Q

QuadGridCell - class AccordionDrawer.QuadGridCell.

QuadGridCell(AccordionDrawer, int, int, int, boolean) - Constructor for class AccordionDrawer.QuadGridCell

QuadTree - class AccordionDrawer.QuadTree.

A class which implements a quadtree This class is a tree of GridCells; each GridCell has up to 4 children.

QuadTree(AccordionDrawer) - Constructor for class AccordionDrawer.QuadTree

Constructor.

query2D(int, int, int, int) - Method in class TreeJuxtaposer.RangeTree

Query2D returns the total number of points contained in the window [xlow, xhigh] X [ylow, yhigh].

quoted_char - Static variable in interface Parser.NewickConstants

quoted_label() - Static method in class Parser.Newick

for each quoted label, we remove double quotes from the string

quoted_string - Static variable in interface Parser.NewickConstants

R

RangeInTree - class AccordionTreeDrawer.RangeInTree.

A class representing a range (ordered pair (min,max)) of TreeNode indices in a Tree.

RangeInTree(int, int, AccordionTreeDrawer) - Constructor for class AccordionTreeDrawer.RangeInTree

RangeList - class AccordionTreeDrawer.RangeList.

A class representing a list of RangeInTrees.

RangeList(int) - Constructor for class AccordionTreeDrawer.RangeList

RangeList(int, Color, boolean, boolean) - Constructor for class AccordionTreeDrawer.RangeList

RangeNode - class TreeJuxtaposer.RangeNode.

A class representing a node in a RangeTree.

RangeNode() - Constructor for class TreeJuxtaposer.RangeNode

empty constructor

RangeNode(Object) - Constructor for class TreeJuxtaposer.RangeNode

constructor with Data initiated

RangeTree - class TreeJuxtaposer.RangeTree.

A class representing a two-dimensional orthogonal range tree.

RangeTree(Point[], int) - Constructor for class TreeJuxtaposer.RangeTree

Constructor: calls RangeTreeBuild to build the tree

RangeTree(Tree, Tree, Tree2Tree) - Constructor for class TreeJuxtaposer.RangeTree

constructor: builds a 2D RangeTree data structure.

read() - Method in class BitmapFont.BitmapFontsFamily

read(DataInputStream) - Method in class BitmapFont.BitmapFonts

read(DataInputStream) - Method in class BitmapFont.BitmapFont

readChar() - Method in class Parser.SimpleCharStream

ReInit(InputStream) - Method in class Parser.SimpleCharStream

ReInit(InputStream) - Static method in class Parser.Newick

ReInit(InputStream, int, int) - Method in class Parser.SimpleCharStream

ReInit(InputStream, int, int, int) - Method in class Parser.SimpleCharStream

ReInit(NewickTokenManager) - Method in class Parser.Newick

ReInit(Reader) - Method in class Parser.SimpleCharStream

ReInit(Reader) - Static method in class Parser.Newick

ReInit(Reader, int, int) - Method in class Parser.SimpleCharStream

ReInit(Reader, int, int, int) - Method in class Parser.SimpleCharStream

ReInit(SimpleCharStream) - Static method in class Parser.NewickTokenManager

ReInit(SimpleCharStream, int) - Static method in class Parser.NewickTokenManager

removeGeom(CellGeom) - Method in class AccordionDrawer.GridCell

removeNodesFromGroup(int, int, int, AccordionTreeDrawer) - Method in class TreeJuxtaposer.TreeJuxtaposer

removeRange(int, int, AccordionTreeDrawer) - Method in class AccordionTreeDrawer.RangeList

rendermode - Variable in class AccordionDrawer.AccordionDrawer

requestRedraw() - Method in class AccordionDrawer.AccordionDrawer

Redraw immediately, do not continue filling in details.

requestRedrawAll() - Method in class TreeJuxtaposer.TreeJuxtaposer

requestRedrawEventually() - Method in class AccordionDrawer.AccordionDrawer

Enqueue a redraw request, but don't stop what we're in the middle of doing.

reset() - Method in class AccordionDrawer.AccordionDrawer

reset() - Method in class TreeJuxtaposer.TreeJuxtaposer

resetGridUniform() - Method in class AccordionDrawer.AccordionDrawer

resetSearch() - Method in class TreeJuxtaposer.IncrementalSearch

reshape(int, int) - Method in class AccordionDrawer.AccordionDrawer

Reshapes the drawing area to new width w and height h in pixels

resizeArea(int, int, int, int, boolean, int) - Method in class AccordionDrawer.AccordionDrawer

Resizes the area delineated by areaStartX, areaStartY, areaEndX, areaEndY, by the relative increment inflateIncr.

resizeForest(Tree, ArrayList, boolean, int, boolean, boolean) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

Resize (grow=true ==> expand, shrink otherwise) the subtree rooted at node contained in Geoms.

resizeFromCellToCell(GridCell, GridCell, boolean, int, int) - Method in class AccordionDrawer.AccordionDrawer

Resizes the area delineated by GridCells a and b by the relative increment inflateIncr.

resizeGroup(int, boolean, int, boolean, boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

resizeGroup(int, boolean, int, boolean, boolean, AccordionTreeDrawer) - Method in class TreeJuxtaposer.TreeJuxtaposer

resizeRectangle(int, GridCell[], GridCell[], float[], float[]) - Method in class AccordionDrawer.AccordionDrawer

Creates smooth transitions for resizing an area determined by the splitPos's of minCell[] and maxCell[] to a rectanble determined by minBoundaryW[] and maxBoundaryW[].

resizeRectOthers(TreeNode, float[], float[], int, AccordionTreeDrawer) - Method in class TreeJuxtaposer.TreeJuxtaposer

resizeSubtree(ArrayList, boolean, int, boolean, boolean) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

Resize (grow=true ==> expand, shrink otherwise) the subtree rooted at node contained in Geoms.

resizeSubtree(Tree, TreeNode, boolean, int, boolean, boolean) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

result - Variable in class TreeJuxtaposer.DebugFrame

RIGHT - Variable in class AccordionDrawer.AccordionDrawer

rightmostLeaf - Variable in class AccordionTreeDrawer.TreeNode

rootCell - Variable in class AccordionDrawer.QuadTree

rootCell - Variable in class AccordionDrawer.BinaryTree

rootCell - Variable in class AccordionDrawer.AccordionDrawer

The root GridCell that contains all others.

rowcol - Variable in class AccordionDrawer.GridCell

rowcol[0] = column, rowcol[1] = row.

S

s2w(float, int) - Method in class AccordionDrawer.AccordionDrawer

s2w(int, int) - Method in class AccordionDrawer.AccordionDrawer

Converts pixel coordinates into relative "fractional" coordinates in [0,1]

seedQueue() - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setActionGroup(int) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setActionGroupWrapper(int, boolean) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setActionMode(int) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setActionModeWrapper(int, boolean) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setBackgroundColor(Color) - Method in class AccordionDrawer.AccordionDrawer

setBcnScore(float) - Method in class AccordionTreeDrawer.TreeNode

setBcnScore(float) - Method in class TreeJuxtaposer.TreeJuxtaposer

setBigGrid(boolean) - Method in class AccordionDrawer.AccordionDrawer

setBigGrid(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setButtonStatus(int) - Method in class TreeJuxtaposer.ButterflyFrame

setCachedColor(Color) - Method in class AccordionTreeDrawer.TreeNode

setCachedFrame(int) - Method in class AccordionTreeDrawer.TreeNode

setCacheRange(boolean) - Method in class AccordionDrawer.AccordionDrawer

setCacheRange(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setCell(GridCell) - Method in interface AccordionDrawer.CellGeom

setCell(GridCell) - Method in class AccordionTreeDrawer.TreeNode

setCell(GridCell) - Method in class AccordionTreeDrawer.TreeEdge

setCellGeomDummy(CellGeom) - Method in class AccordionDrawer.GridCell

setCellHighlight(GridCell, boolean) - Method in class AccordionDrawer.AccordionDrawer

setCenter(int[]) - Method in class AccordionDrawer.Lens

setCheckTime(boolean) - Method in class AccordionDrawer.AccordionDrawer

setCheckTime(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setChild(GridCell, int, int) - Method in class AccordionDrawer.QuadGridCell

setChild(GridCell, int, int) - Method in class AccordionDrawer.LeafGridCell

setChild(GridCell, int, int) - Method in class AccordionDrawer.GridCell

setChild(GridCell, int, int) - Method in class AccordionDrawer.BinaryGridCell

setColor(Color) - Method in class AccordionTreeDrawer.RangeList

setColorGL(Color) - Method in class AccordionDrawer.AccordionDrawer

setColorGrid(boolean) - Method in class AccordionDrawer.AccordionDrawer

setColorGrid(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setColorTree(ColorTree) - Method in class AccordionTreeDrawer.RangeList

setDebugStream(PrintStream) - Static method in class Parser.NewickTokenManager

setDimBrite(boolean) - Method in class AccordionDrawer.AccordionDrawer

setDimBrite(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setDimColors(boolean) - Method in class AccordionDrawer.AccordionDrawer

setDimColors(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setDoubleBuffer(boolean) - Method in class AccordionDrawer.AccordionDrawer

setDrawAngle(float) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

setDrawBackground(boolean) - Method in class AccordionDrawer.GridCell

setDrawLabels(boolean) - Method in class AccordionDrawer.AccordionDrawer

setDrawLabels(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setDrawOrder(int) - Method in class AccordionDrawer.AccordionDrawer

setDrawOrder(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

setDrawSplits(boolean) - Method in class AccordionDrawer.AccordionDrawer

setDrawSplits(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setDrewMarkedAttachedFrame(int) - Method in class AccordionDrawer.GridCell

setDumpStats(boolean) - Method in class AccordionDrawer.AccordionDrawer

setDumpStats(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setDynamicFrameTime(long) - Method in class AccordionDrawer.AccordionDrawer

setElement(int) - Method in class TreeJuxtaposer.RangeNode

set appropriate coordinate depending on the tree type.

setEnabled(boolean) - Method in class AccordionTreeDrawer.RangeList

setExpandLeaves(int) - Method in class AccordionDrawer.AccordionDrawer

setExpandLeaves(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

setFlash(CellGeom, Color, int, int, boolean) - Method in class AccordionDrawer.AccordionDrawer

setFocusCell(GridCell) - Method in class AccordionDrawer.AccordionDrawer

setFontSize(int) - Method in class AccordionTreeDrawer.TreeNode

setGridSize(int, int, int) - Static method in class AccordionDrawer.BinaryTree

setGroupColor(int, Color) - Method in class TreeJuxtaposer.TreeJuxtaposer

setGroupEnable(int, boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setGroupPriority(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

setGrowDirection(int) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setGrowDirectionWrapper(int, boolean) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setGuarVis(boolean) - Method in class AccordionDrawer.AccordionDrawer

setGuarVis(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setHorizontalDirection() - Method in class TreeJuxtaposer.TreeJuxtaposer

setInflateIncr(float) - Method in class AccordionDrawer.AccordionDrawer

setKey(int) - Method in class AccordionDrawer.AccordionDrawer

setKey(int) - Method in class AccordionTreeDrawer.Tree

setKey(int) - Method in class AccordionTreeDrawer.RangeList

setLabel(String) - Method in class AccordionTreeDrawer.TreeEdge

setLabelBackColor(Color) - Method in class AccordionDrawer.AccordionDrawer

setLabelBackHiColor(Color) - Method in class AccordionDrawer.AccordionDrawer

setLabelBuffer(int) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

setLabelBuffer(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

setLabelBuffer(int, int) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

setLabelBuffer(int, int) - Method in class TreeJuxtaposer.TreeJuxtaposer

setLabelColor(Color) - Method in class AccordionDrawer.AccordionDrawer

setLabelDrawBack(boolean) - Method in class AccordionDrawer.AccordionDrawer

setLabelDrawBack(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setLabelHiColor(Color) - Method in class AccordionDrawer.AccordionDrawer

setLabelPopup(boolean) - Method in class AccordionDrawer.AccordionDrawer

setLabelPopup(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setLabelPosRight(boolean) - Method in class AccordionDrawer.AccordionDrawer

setLabelPosRight(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setLabelTransp(boolean) - Method in class AccordionDrawer.AccordionDrawer

setLabelTransp(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setLCAGroup(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setLCAGroup(boolean) - Method in class TreeJuxtaposer.StateFrame

setLCAMark(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setLCAMark(boolean) - Method in class TreeJuxtaposer.StateFrame

setLeftRight(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

setLineThickness(float) - Method in class AccordionDrawer.AccordionDrawer

setLineThickness(float) - Method in class TreeJuxtaposer.TreeJuxtaposer

setLinkedNav(boolean) - Method in class AccordionDrawer.AccordionDrawer

setLinkedNav(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setMarkGroup(int) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setMarkGroupWrapper(int, boolean) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setMax(int[]) - Method in class AccordionDrawer.Lens

setMaxFontHeight(int) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

setMaxFontHeight(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

setMin(int[]) - Method in class AccordionDrawer.Lens

setMinCellDims(int, int) - Method in class AccordionDrawer.AccordionDrawer

setMinCellSize(int, int) - Method in class AccordionDrawer.AccordionDrawer

setMinFontHeight(int) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

setMinFontHeight(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

setName(String) - Method in class AccordionTreeDrawer.TreeNode

setNodeFontSize(int, int) - Method in class AccordionTreeDrawer.Tree

setNoFlash(boolean) - Method in class AccordionDrawer.AccordionDrawer

setNoFlash(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setNoGeoms(boolean) - Method in class AccordionDrawer.AccordionDrawer

setNoGeoms(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setNoGrid(boolean) - Method in class AccordionDrawer.AccordionDrawer

setNoGrid(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setNumAnimSteps(int) - Method in class AccordionDrawer.AccordionDrawer

setObjectColor(Color) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

setObjMax(int) - Method in class AccordionDrawer.GridCell

setObjMin(int) - Method in class AccordionDrawer.GridCell

setParent(GridCell) - Method in class AccordionDrawer.QuadGridCell

setParent(GridCell) - Method in class AccordionDrawer.LeafGridCell

setParent(GridCell) - Method in class AccordionDrawer.GridCell

setParent(GridCell) - Method in class AccordionDrawer.BinaryGridCell

setRootCell(BinaryGridCell) - Method in class AccordionDrawer.BinaryTree

setRootCell(QuadGridCell) - Method in class AccordionDrawer.QuadTree

setRubberbandColor(Color) - Method in class AccordionDrawer.AccordionDrawer

setSelectionResolution(int) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setSelectionResolutionWrapper(int, boolean) - Method in class TreeJuxtaposer.AccordionTreeDrawerFinal

setShowAlg(boolean) - Method in class AccordionDrawer.AccordionDrawer

setShowAlg(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setShowDiffs(boolean) - Method in class TreeJuxtaposer.TreeJuxtaposer

setSize(int[]) - Method in class AccordionDrawer.Lens

setSplit(GridCell, float, int) - Method in class AccordionDrawer.AccordionDrawer

setSubtreeExtremeLeaves() - Method in class AccordionTreeDrawer.TreeNode

setThisTreeOnly(boolean) - Method in class AccordionTreeDrawer.RangeList

SettingsFrame - class TreeJuxtaposer.SettingsFrame.

SettingsFrame(TreeJuxtaposer) - Constructor for class TreeJuxtaposer.SettingsFrame

SettingsFrame(TreeJuxtaposer, GraphicsConfiguration) - Constructor for class TreeJuxtaposer.SettingsFrame

SettingsFrame(TreeJuxtaposer, String) - Constructor for class TreeJuxtaposer.SettingsFrame

SettingsFrame(TreeJuxtaposer, String, GraphicsConfiguration) - Constructor for class TreeJuxtaposer.SettingsFrame

setTitle(String) - Method in class TreeJuxtaposer.TreeJuxtaposer

setupGL(GLFunc) - Method in class BitmapFont.BitmapFontsFamily

setupGL(GLFunc, int) - Method in class BitmapFont.BitmapFonts

setVerticalDirection() - Method in class TreeJuxtaposer.TreeJuxtaposer

setWeight(double) - Method in class AccordionTreeDrawer.TreeNode

showAboutFrame() - Method in class TreeJuxtaposer.Help

showalg - Variable in class AccordionDrawer.AccordionDrawer

showContentFrame() - Method in class TreeJuxtaposer.Help

showdiffs - Variable in class AccordionDrawer.AccordionDrawer

SimpleCharStream - class Parser.SimpleCharStream.

An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).

SimpleCharStream(InputStream) - Constructor for class Parser.SimpleCharStream

SimpleCharStream(InputStream, int, int) - Constructor for class Parser.SimpleCharStream

SimpleCharStream(InputStream, int, int, int) - Constructor for class Parser.SimpleCharStream

SimpleCharStream(Reader) - Constructor for class Parser.SimpleCharStream

SimpleCharStream(Reader, int, int) - Constructor for class Parser.SimpleCharStream

SimpleCharStream(Reader, int, int, int) - Constructor for class Parser.SimpleCharStream

single_quote - Static variable in interface Parser.NewickConstants

size - Variable in class AccordionDrawer.Lens

size() - Method in class AccordionTreeDrawer.RangeList

size(int) - Method in class AccordionDrawer.LabelBox

specialToken - Variable in class Parser.Token

This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.

SplitTransition - class AccordionDrawer.SplitTransition.

A class that helps compute coordinates for smooth animated transitions

SplitTransition(int, int, GridCell, float, float, GridCell, float, float) - Constructor for class AccordionDrawer.SplitTransition

SplitTransition(int, int, GridCell, float, float, GridCell, float, float, boolean, GridCell, GridCell) - Constructor for class AccordionDrawer.SplitTransition

start - Variable in class AccordionTreeDrawer.TreeEdge

The GridCell that one endpoint (the "start" node) of the TreeEdge is attached to

startNewFrameAccordionXDrawer() - Method in class AccordionTreeDrawer.AccordionTreeDrawer

stateChanged(ChangeEvent) - Method in class TreeJuxtaposer.SettingsFrame

StateFrame - class TreeJuxtaposer.StateFrame.

StateFrame(TreeJuxtaposer) - Constructor for class TreeJuxtaposer.StateFrame

Constructor for StateFrame.

StateFrame(TreeJuxtaposer, GraphicsConfiguration) - Constructor for class TreeJuxtaposer.StateFrame

Constructor for StateFrame.

StateFrame(TreeJuxtaposer, String) - Constructor for class TreeJuxtaposer.StateFrame

Constructor for StateFrame.

StateFrame(TreeJuxtaposer, String, GraphicsConfiguration) - Constructor for class TreeJuxtaposer.StateFrame

Constructor for StateFrame.

staticFlag - Static variable in class Parser.SimpleCharStream

stoprendering - Variable in class AccordionDrawer.AccordionDrawer

stringWidth(String, int) - Method in class BitmapFont.BitmapFontsFamily

subpixelDraw(GridCell) - Method in class AccordionDrawer.AccordionDrawer

subpixelDraw(GridCell) - Method in class AccordionTreeDrawer.AccordionTreeDrawer

subtree() - Static method in class Parser.Newick

function subtree will set name, length and weight for each tree node

SwitchTo(int) - Static method in class Parser.NewickTokenManager

T

temp_max - Variable in class AccordionDrawer.Lens

temp_min - Variable in class AccordionDrawer.Lens

temp_size - Variable in class AccordionDrawer.Lens

TestRead - class BitmapFont.TestRead.

TestRead() - Constructor for class BitmapFont.TestRead

toggleBigGrid() - Method in class AccordionDrawer.AccordionDrawer

toggleBigGrid() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleCacheRange() - Method in class AccordionDrawer.AccordionDrawer

toggleCacheRange() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleCheckTime() - Method in class AccordionDrawer.AccordionDrawer

toggleCheckTime() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleColorGrid() - Method in class AccordionDrawer.AccordionDrawer

toggleColorGrid() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleDimBrite() - Method in class AccordionDrawer.AccordionDrawer

toggleDimBrite() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleDimColors() - Method in class AccordionDrawer.AccordionDrawer

toggleDimColors() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleDrawLabels() - Method in class AccordionDrawer.AccordionDrawer

toggleDrawLabels() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleDrawOrder() - Method in class AccordionDrawer.AccordionDrawer

toggleDrawOrder() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleDrawSplits() - Method in class AccordionDrawer.AccordionDrawer

toggleDrawSplits() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleDumpStats() - Method in class AccordionDrawer.AccordionDrawer

toggleDumpStats() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleExpandLeaves() - Method in class AccordionDrawer.AccordionDrawer

toggleExpandLeaves() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleGuarVis() - Method in class AccordionDrawer.AccordionDrawer

toggleGuarVis() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleLabelDrawBack() - Method in class AccordionDrawer.AccordionDrawer

toggleLabelDrawBack() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleLabelPopup() - Method in class AccordionDrawer.AccordionDrawer

toggleLabelPopup() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleLabelPosRight() - Method in class AccordionDrawer.AccordionDrawer

toggleLabelPosRight() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleLabelTransp() - Method in class AccordionDrawer.AccordionDrawer

toggleLabelTransp() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleLinkedNav() - Method in class AccordionDrawer.AccordionDrawer

toggleLinkedNav() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleNoFlash() - Method in class AccordionDrawer.AccordionDrawer

toggleNoFlash() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleNoGeoms() - Method in class AccordionDrawer.AccordionDrawer

toggleNoGeoms() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleNoGrid() - Method in class AccordionDrawer.AccordionDrawer

toggleNoGrid() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleShowAlg() - Method in class AccordionDrawer.AccordionDrawer

toggleShowAlg() - Method in class TreeJuxtaposer.TreeJuxtaposer

toggleShowDiffs() - Method in class TreeJuxtaposer.TreeJuxtaposer

token - Static variable in class Parser.Newick

Token - class Parser.Token.

Describes the input token stream.

token_source - Static variable in class Parser.Newick

Token() - Constructor for class Parser.Token

tokenImage - Variable in class Parser.ParseException

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.

tokenImage - Static variable in interface Parser.NewickConstants

TokenMgrError - error Parser.TokenMgrError.

TokenMgrError() - Constructor for class Parser.TokenMgrError

TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for class Parser.TokenMgrError

TokenMgrError(String, int) - Constructor for class Parser.TokenMgrError

toMove - Variable in class AccordionDrawer.AccordionDrawer

topRightPos(int) - Method in class AccordionDrawer.LabelBox

toString() - Method in class AccordionDrawer.SplitTransition

toString() - Method in class AccordionTreeDrawer.TreeQuadGridCell

toString() - Method in class AccordionTreeDrawer.TreeNode

toString() - Method in class AccordionTreeDrawer.TreeLeafGridCell

toString() - Method in class AccordionTreeDrawer.RangeList

toString() - Method in class AccordionTreeDrawer.RangeInTree

toString() - Method in class AccordionTreeDrawer.ColorTree

toString() - Method in class AccordionTreeDrawer.ColorNode

toString() - Method in class Parser.Token

Returns the image.

totalDepth - Variable in class AccordionDrawer.QuadTree

totalDepth - Static variable in class AccordionDrawer.BinaryTree

tree - Variable in class AccordionTreeDrawer.AccordionTreeDrawer

Tree - class AccordionTreeDrawer.Tree.

A public class representing a (phylognenetic) tree.

Tree() - Constructor for class AccordionTreeDrawer.Tree

Tree(String) - Constructor for class AccordionTreeDrawer.Tree

Tree(Tree) - Constructor for class AccordionTreeDrawer.Tree

Tree(TreeNode) - Constructor for class AccordionTreeDrawer.Tree

TreeEdge - class AccordionTreeDrawer.TreeEdge.

A class representing an edge of a (phylognenetic) tree A TreeEdge represents a horizontal or vertical line segment used in drawing a tree.

TreeEdge(TreeNode, GridCell, GridCell) - Constructor for class AccordionTreeDrawer.TreeEdge

TreeJuxtaposer - package TreeJuxtaposer

TreeJuxtaposer - class TreeJuxtaposer.TreeJuxtaposer.

A class representing a tree juxtaposer.

TreeJuxtaposer() - Constructor for class TreeJuxtaposer.TreeJuxtaposer

TreeLeafGridCell - class AccordionTreeDrawer.TreeLeafGridCell.

TreeLeafGridCell(AccordionDrawer, int, int, int, boolean) - Constructor for class AccordionTreeDrawer.TreeLeafGridCell

TreeNode - class AccordionTreeDrawer.TreeNode.

A class representing a node of a (phylognenetic) tree.

TreeNode() - Constructor for class AccordionTreeDrawer.TreeNode

Children list initial capacity 2 as in most case binary.

TreeNode(String) - Constructor for class AccordionTreeDrawer.TreeNode

TreeNode(String, float) - Constructor for class AccordionTreeDrawer.TreeNode

Allocate a new TreeNode object with node name and weight.

TreeNodeCompareToY - class AccordionTreeDrawer.TreeNodeCompareToY.

TreeNodeCompareToY() - Constructor for class AccordionTreeDrawer.TreeNodeCompareToY

TreePairs - class TreeJuxtaposer.TreePairs.

TreePairs store all the pairwise data structures needed for structural comparison and visulization.

TreeQuadGridCell - class AccordionTreeDrawer.TreeQuadGridCell.

TreeQuadGridCell(AccordionDrawer, int, int, int, boolean) - Constructor for class AccordionTreeDrawer.TreeQuadGridCell

TreeRemovalPanel - class TreeJuxtaposer.TreeRemovalPanel.

TreeRemovalPanel(TreeJuxtaposer) - Constructor for class TreeJuxtaposer.TreeRemovalPanel

twoLinesMove(int, GridCell, float, GridCell, float) - Method in class AccordionDrawer.AccordionDrawer

Moves the splitPos of GridCells a and b to absolute position aValue and bValue, respectively.

twoLinesMoveInsideFixedStrip(int, GridCell, float, GridCell, float, GridCell, GridCell) - Method in class AccordionDrawer.AccordionDrawer

Moves the splitPos of GridCells a and b to absolute position aValue and bValue, respectively.

U

UI - class TreeJuxtaposer.UI.

UI(TreeJuxtaposer, String) - Constructor for class TreeJuxtaposer.UI

undraw() - Method in class AccordionDrawer.InteractionBox

undrawLens() - Method in class AccordionDrawer.Lens

unmarkAllGroups() - Method in class TreeJuxtaposer.StateFrame

unmarkGroup(int) - Method in class TreeJuxtaposer.TreeJuxtaposer

unquoted_char - Static variable in interface Parser.NewickConstants

unquoted_label() - Static method in class Parser.Newick

for each unquoted label, we need to replace '_' by ' '

unquoted_string - Static variable in interface Parser.NewickConstants

UP - Variable in class AccordionDrawer.AccordionDrawer

upDown - Variable in class AccordionDrawer.AccordionDrawer

Utils - class TreeJuxtaposer.Utils.

Utils() - Constructor for class TreeJuxtaposer.Utils

V

valueChanged(ListSelectionEvent) - Method in class TreeJuxtaposer.TreeRemovalPanel

W

w2s(float, int) - Method in class AccordionDrawer.AccordionDrawer

Converts "fractional" coordinates in [0,1] into pixel coordinates

weight - Variable in class AccordionTreeDrawer.TreeNode

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

whitespace - Static variable in interface Parser.NewickConstants

write() - Method in class BitmapFont.BitmapFontsFamily

write(DataOutputStream) - Method in class BitmapFont.BitmapFonts

write(DataOutputStream) - Method in class BitmapFont.BitmapFont

X

X - Static variable in class AccordionDrawer.AccordionDrawer

xInterval - Variable in class AccordionDrawer.AccordionDrawer

xy - Variable in class AccordionDrawer.SplitTransition

Y

Y - Static variable in class AccordionDrawer.AccordionDrawer

yInterval - Variable in class AccordionDrawer.AccordionDrawer

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