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.

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