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

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.