Index (Tree Juxtaposer Application)

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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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