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A

A2B - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree
Subtree hashtable for A->B.
A_CLEAR - Static variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
"Clear all" label and button index in StateFrame.clearButton.
aboutFrame - Static variable in class net.sourceforge.olduvai.treejuxtaposer.Help
Class state needed by the internal declaration of ActionListener for the help window: The JFrame.
ABOUTOPT - Static variable in class net.sourceforge.olduvai.treejuxtaposer.UI
Index for Help->Readme option.
absoluteValue - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitLine
Absolute value, between 0 and 1, between SplitAxis.minStuckLine and SplitAxis.maxStuckLine.
AbstractRangeList - Class in net.sourceforge.olduvai.accordiondrawer
This class represents a list of ranges along ONE axis.
AbstractRangeList() - Constructor for class net.sourceforge.olduvai.accordiondrawer.AbstractRangeList
 
AccordionDrawer - Class in net.sourceforge.olduvai.accordiondrawer
An abstract class representing a two dimensional rectangular grid on which any geometric shape can be drawn.
AccordionDrawer(int, int) - Constructor for class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Main constructor for Accordion Drawer objects.
AccordionTreeDrawer - Class in net.sourceforge.olduvai.treejuxtaposer.drawer
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, JProgressBar) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Class constructor for new tree drawers.
AccordionTreeDrawerFinal - Class in net.sourceforge.olduvai.treejuxtaposer
A class that implements the abstract methods left in AccordionTreeDrawer, mainly user interface and application-specific hooks for TreeJuxtaposer.
AccordionTreeDrawerFinal(Tree, int, int, TreeJuxtaposer, JProgressBar) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal
Constructor for a drawer with defined key and mouse interaction methods, and bindings from the drawer to the TreeJuxtaposer application.
actionmode - Variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal
state of interaction: 0, 1, 2, 3, 4, 5, 6, 7, 11
actionmodeDefault - Static variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal
ActionMode: default to mouseover action
actionmodeReset() - Method in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal
Initialize or reset the state of all object state.
actionPerformed(ActionEvent) - Method in class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch
Action Listener for the reset button.
actionPerformed(ActionEvent) - Method in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Update state of UI after a user event.
actionPerformed(ActionEvent) - Method in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Button press action listener.
actionPerformed(ActionEvent) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeRemovalPanel
Action listener callback.
actionPerformed(ActionEvent) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter
Capture button press for newly renamed node.
actionPerformed(ActionEvent) - Method in class net.sourceforge.olduvai.treejuxtaposer.UI
Menu listener.
activeCanvas - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Active color swatches for currently growing group color selection.
activeGroupPanel - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Active group panel.
activeGrow - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
The current group that will be grown on an automated action, such as grow/shrink.
activeLabel - Static variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Active group labels for user groups and automated marking.
activeMark - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
The current group that will be marked on user-directed marking actions.
activeMarkAction(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Sets the current marking group (local state StateFrame.activeMark) to mark when user selects 'm' to highlight nodes or subtrees.
activeMode - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Buttons to select current active growing group, see StateFrame.activeLabel for their names.
activeModeAction(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Sets the current active group (local state StateFrame.activeGrow) to automatically grow/shrink or perform other actions on.
activePanel - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Active Panel Includes the following panels: grow direction, grow action, active group.
activePanelLabel - Static variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Label for StateFrame.activePanel.
activeResolution - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
The current mark mode for internal nodes: either StateFrame.N_RES or StateFrame.S_RES (node, subtree)
activeResolutionAction(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Set the user group marking resolution to the given mode.
activeSelect - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Group of buttons (one active at a time) for StateFrame.activeMode set of buttons.
ad - Variable in class net.sourceforge.olduvai.accordiondrawer.FontWrapper
Accordion drawer that uses this font wrapper.
ad - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Link to the accordion drawer using this SplitAxis object
addAction() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Wrapper for calling the add tree option in the UI object.
addAction() - Method in class net.sourceforge.olduvai.treejuxtaposer.UI
Add a new tree action.
addATD(Tree, int, int, JProgressBar) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Utility function to make new AccordionTreeDrawer, set initial parameters and do treeDrawer list bookkeeping.
addCell(GridCell, SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Set the cell's boundaries given a known left (or top) split line for the cell.
addCell(GridCell, SplitLine, SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Set the cell's boundaries given a known left (or top) split line for the cell.
addChild(TreeNode) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Add a child to the end of the list of children.
addGroup(int, boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Add a group to the set of all markable groups TreeJuxtaposer.groups.
addMenuBar() - Method in class net.sourceforge.olduvai.treejuxtaposer.UI
Set up the menu bar, with all the items that are defined with the string externalization.
addNamesToSearchList() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Initialize the searching dialog with the set of tree node labels.
addNodesToGroup(int, int, int, AccordionTreeDrawer) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Add nodes indirectly marked in each tree.
addNodeToForest(TreeNode, ArrayList, Hashtable) - Method in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree
Adds the node to the hashtable, indexed by its key (as an Integer).
addOneTreeStructuralDiffs() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Helper to process the last tree as a special case, do diffs for tree n-1 wrt each of the others.
addRange(int, int, AccordionTreeDrawer) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeList
Add a range to the list of ranges.
addSplitLine(int, SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.StaticSplitAxis
Puts a split line at the given position in StaticSplitAxis.staticSplitLineArray.
addToDrawQueue(Object) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Add an object (RangeInTree, or TreeNode) to the drawing queue AccordionDrawer#toDrawQ
addTree(Tree, JProgressBar) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Adds a new tree to "trees", performs all the pairwise tree comparisons and stores results.
addTree(Tree, int, boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreePairs
Add a new tree.
ALL - Static variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal
BOTH X and Y directions
ALL_GROUPS - Static variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal
After a user selects 'a' for all groups, keytarget will be set to this value.
allActive - Static variable in class net.sourceforge.olduvai.treejuxtaposer.UI
Collection of sets of flags that define if a string is selectable or a space.
allMenu - Static variable in class net.sourceforge.olduvai.treejuxtaposer.UI
Collection of all menu strings.
animatedReset(int) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
 
animatedReset(Hashtable, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Enqueue SplitTransitions to reset the entire display back to its default position.
areLabelsOn() - Method in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Flag check for testing if labels are on.
ascendTreeMark(AccordionTreeDrawer, AccordionTreeDrawer, TreeNode, RangeList) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Ascend from the given node and add nodes to the marking group if the BCN of ancestors have been marked before.
atd - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeInTree
Drawer for this range.
ATDMatrix - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
List of lists of tree drawers, each list is a row of drawers in the matrix layout.
attachedObject - Variable in class net.sourceforge.olduvai.accordiondrawer.LabelBox
Attached object for this label, if applicable.

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