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

C

cancelButton - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeRemovalPanel

The cancel button.

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

Cancel button that does not change the node and does not reset differences.

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

The drawing surface object, a 1-to-1 relationship between AccordionDrawer.canvas and this AccordionDrawer

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

Edge length of squares used to show the color for each marking group.

cell - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

The GridCell that this node is attached to.

CellGeom - Interface in net.sourceforge.olduvai.accordiondrawer

This interface represents an object that goes inside of a single cell defined by four split Lines (left, right, top, bottom) which are available in the GridCell for this object.

center - Variable in class net.sourceforge.olduvai.accordiondrawer.LabelBox

Center of the label box, between LabelBox.bl and LabelBox.tr

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

Verify that the split axis structure is valid.

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

Recursive part of SplitAxis.Debug.checkAllBounds().

checkCreateFont(Font) - Method in class net.sourceforge.olduvai.accordiondrawer.FontWrapper

Create a font renderer.

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

Check the size of the subtrees, recursively.

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

Recursive part of SplitAxis.Debug.checkSubTreeSizes().

children - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Array of child nodes that are attached below this internal node.

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

Place between children of a subtree root.

chooseNames(ArrayList) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser

Pops a dialog to select the trees to load from a nexus file.

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

Clears the canvas.

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

Removes all mappings from this TreeMap.

clear() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeList

Reset rangeList

clearButton - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

Buttons for clearing, indexed by group clear StateFrame.G_CLEAR and clear all StateFrame.A_CLEAR.

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

The number of times clear is called by any drawer.

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

Clear state in all accordion drawers.

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

Force clear the contents of the given group without unmarking the LCA group.

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

Labels for clearing user group buttons StateFrame.clearButton.

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

Clears the drawing queue, AccordionDrawer.ToDrawQ.

close() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree

Clean up method, called when the tree is deleted.

close() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Clean this node of children.

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

Close bracket to wrap children of a subtree root.

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

Helper function to determine if the cursor is close to a stuck line, within pickFuzz.

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

Outline color of interaction box

color - Variable in class net.sourceforge.olduvai.accordiondrawer.AbstractRangeList

The drawing color for this range list, if appropriate.

color - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitLine

State for red-black tree.

color - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

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

Index for colored node in AccordionTreeDrawer.getLeftMostNodes(TreeNode, TreeNode).

colorOf(SplitLine) - Static method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Returns the color of a given node (split line)

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

Titles for color manipulation dialogs (window title), which pop up after selecting a group color swatch (canvas StateFrame.markCanvas or StateFrame.activeCanvas).

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

Nexus comment close.

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

Nexus comment open.

compare(Object, Object) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.LeafComparator

Subtract o2.leafindex from o1.leafindex to get comparator value that is negative (o1 < o2), positive (o2 < o1) or zero (equal)

compare(Object, Object) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.NameComparator

String comparator, uses Collator comparator.

compareTo(Object) - Method in class net.sourceforge.olduvai.accordiondrawer.LabelBox

Compare label boxes with another for vertical overlap (0 = overlap).

compareTo(Object) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis.MovingSplitLine

Use the split line comparison function to compare two moving split lines for similarity.

compareTo(Object) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitLine

Compares absolute values of two SplitLines.

compareTo(Object) - Method in class net.sourceforge.olduvai.accordiondrawer.StaticSplitLine

Natural order comparator that uses indices to determine which object (this or the input) precedes the other, or if they are the same.

compareTo(Object) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeInTree

Special comparator: overlaps are equal, even adjacent non-overlaps if RangeInTree.doAdj is true.

compareTo(Object) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Implements Comparable interface - sorts on key field.

computeAllSL(SplitLine, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

For debugging: compute positions of all split lines.

computeBestMatch(TreeNode, Tree, Tree, float, Tree2Tree.TmpD[]) - Method in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Compute the best match for sourceNode from sourceTree in the targetTree.

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

Gets the indices for the bounds of the given split line

computedFrame - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitLine

Current frame for rendering, monotonically increasing, for determining validity of SplitLine.absoluteValue (caching).

computedFrame - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

The last frame that had a computed TreeNode.midYPosition, for caching.

computeFinalAbsolute(double, double, double, double, double) - Static method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Helper function for moveSplitLineSet.

computeFinalRelative(double, double, double) - Static method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Helper function for moveSplitLineSet.

computeForest(Hashtable, Tree, Tree, AccordionTreeDrawer, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Compute the forest of marked nodes in treeY, for subtrees under every node in treeX.

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

Computes and returns line's first left bound.

computePlaceThisFrame(SplitLine, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Computes a position for the given splitline for the frame number given.

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

Computes and Returns line's first right bound.

computeSplitLineIndex(int) - Method in class net.sourceforge.olduvai.accordiondrawer.StaticSplitLine

Recursively descend and assign split line index values to all split lines.

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

True when the current drawing continues a previously unfinished frame, set in AccordionDrawer.continueFrame()

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

Continues a scene by drawing an additional frame related to what is already visible.

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

Start time for first drawing frame, set in AccordionDrawer.startNewFrame()

countDrawnFrame - Static variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Count of number of objects drawn for the current frame, benchmark.

countDrawnScene - Static variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Count of number of objects drawn for the current scene, benchmark.

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

Creates an interaction box with a given stuck line, if one has been chosen.

createBoxFromCells(int[], int[]) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Creates an interaction box from the drag motion input.

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

Helper function for resizeForest.

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

Used for SplitAxis.resizeForest(AbstractRangeList, int, Hashtable, double) true when the last range was to the left of the max stuck position

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

Used for SplitAxis.resizeForest(AbstractRangeList, int, Hashtable, double) true when the first range was to the right of the min stuck position

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

Make an InteractionBox from the GridCells nearest to the box of the mousedrag.

createSplitLineArray(int) - Method in class net.sourceforge.olduvai.accordiondrawer.StaticSplitAxis

Create the StaticSplitAxis.staticSplitLineArray.

cullingObject - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitLine

An object to assist with aggregation when multiple splitcells are hidden under a single pixel.

cumFrameTime - Static variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Cumulative time for a frame, benchmark.

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

Current directory used for file loaders (saving and opening trees).

currLine - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitAxis.AxisIterator

Iterator state, the current pointed to split line.

curStep - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitTransition

Current step of transition, between 0 and SplitTransition.maxStep - 1.

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

This is called from the init method of AccordionDrawer.

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

Stub function.