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

D

d - Variable in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

The drawer for this interaction box.

D_ACT - Static variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

Automated difference group number

debug - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Object for debugging.

debugFrame - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Debugging frame, for reporting information that is meant to be hidden on releases.

debugFrame - Variable in class net.sourceforge.olduvai.treejuxtaposer.UI

Debug frame.

DEBUGOPT - Static variable in class net.sourceforge.olduvai.treejuxtaposer.UI

Index for Tools->Debug option.

debugOutput - Static variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Set flag to true to display debug output, false for interactive performance or releases.

debugOutput - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeParser

True: show debug output.

debugOutput(String) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser

Debug printout function.

decreaseLabelBuffer(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Decrement the size for the label buffer in the given axis by 1.

decreaseLabelBuffer(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Decrement the label buffer (the minimum distance between two labels) in the given direction.

decreaseLineThickness() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Decreases the line thickness used in drawing by 1 (AccordionDrawer.linethickness, TJ only)

decreaseLineThickness() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Decrement the width of tree edge lines in each drawer.

decreaseMaxFontHeight() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Decrement maximum font height by 1.

decreaseMaxFontHeight() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Decrement the maximum font height in each drawer.

decreaseMinFontHeight() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Decrement minimum font height by 1.

decreaseMinFontHeight() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Decrement the minimum font height by one in each drawer.

decrementSize() - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Decrements counters SplitAxis.modCount and SplitAxis.size.

decrementTreeRecursive(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Ascend recursively decrementing subtree counters as we go.

defaultFocusCell - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

DEFAULTFONTFAMILY - Static variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Default font family (concatenate string with other font properties) to use for all labels.

DEFAULTLABELFONT - Static variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Default title font type, using normal fonts in the default label size.

DEFAULTLABELFONTSIZE - Static variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Default label font size, in points.

defaultMaxStuckValue - Static variable in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Default value of maximum stuck line in X and Y directions.

defaultMinStuckValue - Static variable in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Default value of minimum stuck line in X and Y directions.

defaultSplitValue - Static variable in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Default value of split line value for all bounded split lines.

DEFAULTTITLEFONT - Static variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Default title font type, using bolded fonts in the default title size.

DEFAULTTITLEFONTSIZE - Static variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Default title font size, in points.

deleteEntry(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Delete node p, and then rebalance the tree.

deleteTrees(int[]) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

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

dequeueChunkPerTimeCheck - Static variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

The number of enqueued objects to draw per inner drawing loop before checking the timer.

descendTreeMark(AccordionTreeDrawer, AccordionTreeDrawer, TreeNode, RangeList) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Recursively descend subtree and mark descendants, including BCN for each node marked in each drawer.

DEVELOPER - Static variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal

Developer mode for keytarget

dialogLabel - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter

Label for the text field.

DIM_MARK - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Index of Marked dimming option for dimming strings in SettingsFrame.dimString.

DIM_UNMARK - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Index of Unmarked dimming option for dimming strings in SettingsFrame.dimString.

dimbrite - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

(currently only TJ) Flag to draw unmarked nodes dimmer (less saturated for visual depth cues).

dimCheck - Variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Dimming check boxes.

dimcolors - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

(currently only TJ) Flag to draw marked colors dimmer (less saturated).

dimLabel - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Dimming label title for both check boxes.

dimString - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Dimming strings for SettingsFrame.dimCheck checkbox.

display(GLAutoDrawable) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Display function that is called ONLY by JOGL (via canvas.display()), NEVER call this directly.

displayChanged(GLAutoDrawable, boolean, boolean) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

JOGL canvas function for updating the display.

displayFrame() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Function that contains the logic to either continue an existing frame (we have started a frame already, or there's more to draw and a user hasn't performed a stretch operation) or start a new frame from a blank canvas.

doAdj - Static variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeInTree

if true, adjacent ranges are equal, and will be combined.

doBox - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Flag to request drawing the interaction box (AccordionDrawer.flashBox) in the drawer.

doDoubleBuffer - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

True: double buffering is active, draw on back buffer and swap to front.

doFlash() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Perform application-specific flash drawing.

doFlash() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Flash drawing wrapper, must be called for flash requests; AccordionTreeDrawer.flashDraw() is later called back within a drawing cycle.

doFlashGeom(CellGeom, int, AccordionTreeDrawerFinal, int, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Callback function from cursor movement highlighting.

doFrameMove() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Transition function to perform a single animation step.

doingFlash - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

State flag to indicate that we are currently requesting a flash draw, not a full redraw (used by AccordionDrawer.requestRedraw() to avoid extra AccordionDrawer.drawFrame()).

doLCAGeom(int, AccordionTreeDrawer) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Find the LCA skeleton (minimal paths) for the nodes marked while the LCA box is active.

done() - Method in class net.sourceforge.olduvai.accordiondrawer.SplitTransition

Test to see if the transitions are done for SplitTransition.index.

doOneDiff(int, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

A single diff process.

doSelectGeom(TreeNode, boolean, int, AccordionTreeDrawer) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Wrapper for adding nodes to a group when user selects a subtree or node for user-directed marking.

doSnapshot(ArrayList) - Static method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Wrapper for starting a snapshot (postscript) output.

doStructuralDiff(AccordionTreeDrawer, AccordionTreeDrawer, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

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

doublebuffer - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

State of the double buffer state of GL, which is turned off during some mouse-over flash actions.

doubleQuote - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter

Quote object to wrap node names.

doUI() - Method in class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch

Set up the user interface.

dragEnd - Variable in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Store where the interaction box drag ends in the interaction box

dragEnd - Variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal

The X/Y pixel location of a mouse dragging action at it's current position.

dragStart - Variable in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Store where the interaction box drag starts in the interaction box

dragStart - Variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal

The X/Y pixel location of a mouse dragging action at the start.

draw(Color, float, float) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Set the color, plane height and line width, then draw the rubber band (interaction box outer ring) with those properties.

DrawableRange - Class in net.sourceforge.olduvai.accordiondrawer

A drawable range represents a range of objects on a given axis.

DrawableRange() - Constructor for class net.sourceforge.olduvai.accordiondrawer.DrawableRange

drawActiveSubtreeBox() - Method in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal

Make an InteractionBox from the GridCells nearest to the box of the cursor position, and update the view with a flash draw.

drawAscend(int, float) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Don't draw self, just call this on parents after calling drawDescend ascend drawing until the root is drawn or the node drew in the frame already.

drawBackground - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Flag for background drawing

drawDescend(int, float, int, int, Tree) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Descend from this node and draw children down to leaves.

drawEnd(boolean) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Drawing wrapper function called after drawing ends.

drawer - Variable in class net.sourceforge.olduvai.accordiondrawer.DrawableRange

The drawer for this range.

drawer - Variable in class net.sourceforge.olduvai.accordiondrawer.GridCell

The accordoin drawer for this grid cell.

drawFrame() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Main drawing loop: draws the objects in the ToDrawQ.

drawGeom(CellGeom, DrawableRange) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Draws a single geom.

drawGeom(CellGeom, DrawableRange) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Draws a geometric object (treenode here) within a containing cell A node is drawn when it's larger than some ratio of block value, as determined from the drawRange function, or when a node is marked individually, such as mouse over highlighting or single node marking

drawGeoms - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Flag to draw the geometries, which is default true (do draw geometries for data objects).

drawGrid - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Flag to draw a background grid, with one line from min SplitAxis to max SplitAxis.

drawInCell(Color, double) - Method in interface net.sourceforge.olduvai.accordiondrawer.CellGeom

Draws the object contained in its cell object, in the given color and depth.

drawInCell(Color, double) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Draws this node inside cell, the GridCell that it is attached to.

drawInCell(ArrayList, double) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

The color and drawing depth determining function that calls down to TreeNode.drawInCell(Color, double), for edge splitting (horizontal and vertical)

drawInCell(Color, double, boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Main drawing function for tree nodes, draws one edge.

drawLabelBig(int, boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

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

drawLabelBox(LabelBox, int, boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Draw a LabelBox.

drawlabels - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Flag to turn label drawing on (default, true), or off (false).

drawLayout - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Layout manager for the drawing panel.

drawLayout - Variable in class net.sourceforge.olduvai.treejuxtaposer.UI

Layout for drawing panel.

drawnFrame - Variable in class net.sourceforge.olduvai.accordiondrawer.GridCell

Cache the last drawn frame for detecting determining when this cell was last drawn in.

drawnLabels - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

The set of labels that we have drawn, checked by drawing functions to prevent overlaps.

drawnlabelsize - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

width and height of last mouseover label drawn

drawPanel - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Drawing panel (canvas panel) for the main frame.

drawPanel - Variable in class net.sourceforge.olduvai.treejuxtaposer.UI

Drawing panel that hold canvas objects.

drawPostFrame() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Perform application-specific drawing after each frame

drawPostFrame() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Function that runs following a frame.

drawPostScene() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Perform application-specific drawing after each a complete scene

drawPostScene() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Function that runs following a scene's completion.

drawPreContFrame() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Perform application-specific pre-drawing before a continuing frame

drawPreContFrame() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Function that runs before a frame that is being drawn for a continued scene.

drawPreNewFrame() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Perform application-specific pre-drawing before a scene starting frame

drawPreNewFrame() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Function that runs prior to a new scene.

drawRange(DrawableRange) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Draws a range of geoms by a DrawableRange object (see DrawableRange): - TJ draws a range of leaf nodes, and ascends to the root - SJ draws a range of marked nodes, or a column range of site nodes

drawRange(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Draws a range of geoms by a splitline object (objects between split line boundaries of the input split line): - TJ determines which leaf node to draw, and ascends to the root - SJ determines which column of nucleotides to draw, and renders the color column.

drawRange(DrawableRange) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Draw a given range.

drawRange(SplitLine) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Stub function.

drawRubberband() - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Rendering function for interaction boxes.

drawSplits(SplitAxis, double, double) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Draw the split lines for an axis that are in the partitioned list.

drawStart(boolean) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Drawing wrapper function called before drawing starts.

drawString(GL, Point2D, double, String, Font, Color) - Method in class net.sourceforge.olduvai.accordiondrawer.FontWrapper

Draw the text string at the given location.

drawText(double, double, String, Font, Color, double, Color) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Draw text on jogl canvas, or write text layer to postscript file.

dumpstats - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Flag to indicate that we are currently dumping stats (i.e.

dynamicStart - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Start time for any new rendering pass, refreshed in AccordionDrawer.startNewFrame() and AccordionDrawer.continueFrame()

dynamicTime - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Dynamic time frame that specifies minimum time spent (in ms) for a rendering pass, set to 30 milliseconds for most applications.