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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.

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