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

S

s2w(int, int) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Converts pixel (screen) coordinates into relative (world) fractional coordinates [0,1].

s2w(double, int) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Converts pixel (screen) coordinates into relative (world) fractional coordinates [0,1].

s2w(int[]) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Converts pixel (screen) coordinates into relative (world) fractional coordinates [0,1].

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

Index for shrinking, for StateFrame.growButton.

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

Subtree marking mode.

saveAction() - Method in class net.sourceforge.olduvai.treejuxtaposer.UI

Performs a save operation with the current trees.

SAVEOPT - Static variable in class net.sourceforge.olduvai.treejuxtaposer.UI

Index for File->Save option.

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

Saves a screen shot of current GL frame to the specified file.

score - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree.NodeScorePair

Score for the tree node, with respect to a second node (known by the calling function).

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

Read actual screen dimensions.

searchFrame - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Incremental search frame, for doing text searches.

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

Incremental search frame.

searchResults - Variable in class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch

List of results that can be picked that is put into the text field IncrementalSearch.results.

searchStatus - Variable in class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch

Comment box that displays the number of things that match a user selection.

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

Seed the marked groups for the given accordion drawer.

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

Seed the drawing queue, application specific

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

Wrapper function for TreeJuxtaposer.seedQueue(AccordionTreeDrawerFinal).

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

Seed the queue for the given drawer.

selection - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeParser

For listing the selected results from the list of Nexus tree names.

selectionFrame - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeParser

Frame for selecting Nexus trees from the full set.

selectionResolutionDefault - Variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal

Mark mode default: 1

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

ID for serialization purposes.

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

Depending on whether line is a left or right child node, set the opBound value of line to be the left or right bound.

setBackgroundColor(Color) - Static method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Modifier for background color.

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

Set the TreeNode.bcnScore for this node.

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

Sets bcn filtering score, shows differences if nodeBCNScore < TreeJuxtaposer.bcnScore.

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

Depending on whether line is a left or right child node, set the opBound value of line to be the left or right bound.

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

Sets the grid cell for this node to the given value.

setCellHighlight(GridCell, boolean) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Turn on the highlight flag for the given cell

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

Set the background color (the neutral "clear" color) for this drawer.

setColor(Color) - Method in class net.sourceforge.olduvai.accordiondrawer.AbstractRangeList

Sets the color of the marked ranges.

setColor(SplitLine, boolean) - Static method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Sets the value of SplitLine.color for a given split line.

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

Set the color to be used for the next GL drawing primitive.

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

Set the color to be used for the next GL drawing primitive.

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

Modifier for SplitLine.cullingObject.

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

Sets the value of dimmed/bright viewing state (TJ only).

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

Set state of the non-colored node rendering, either dimmed edges according to a node's tree depth (true) or all black (false).

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

Sets the value of dimmed/bright viewing state for marked nodes (TJ only).

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

Set state of the color rendering, either dimmed colors according to a node's tree depth (true) or equal saturation (false).

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

Sets the state of double buffering in this drawer, and sets the drawing buffer depending on the current drawing state (different for flash drawing than starting or continuing a frame).

setDragPoints(int[], int[]) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Sets the start and end drag point variables.

setDrawBackground(boolean) - Method in class net.sourceforge.olduvai.accordiondrawer.GridCell

Sets the value of AccordionDrawer.drawBackground to the parameter value.

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

Sets the state of drawing geometric objects to represent a dataset (AccordionDrawer.drawGeoms).

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

Turn on/off tree nodes.

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

Sets the state of drawing the background grid (splitlines, AccordionDrawer.drawGrid).

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

Turn on/off grid drawing.

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

Sets the state of label drawing (AccordionDrawer.drawlabels), then redraws.

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

Turn on/off tree labels.

setDrawnFrame(int) - Method in class net.sourceforge.olduvai.accordiondrawer.GridCell

Updates the drawn frame GridCell.drawnFrame to the given value.

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

Set the state of split drawing, the drawing of all split lines with no culling.

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

Sets the state of stats output (AccordionDrawer.dumpstats)

setEnabled(boolean) - Method in class net.sourceforge.olduvai.accordiondrawer.AbstractRangeList

Sets the value of enabled, turning on (true) or off (false) the rendering of the group defined by this abstract range list.

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

Set the extreme leaves for this node.

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

Sets the file name.

setFlash(CellGeom, Color, int, int, boolean) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Sets the flash state and calls the flash drawing function, AccordionDrawer.doFlash().

setFocus(CellGeom, AccordionTreeDrawer) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Set the focus, for each drawer, to the given tree node in the given drawer.

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

Sets the focus cell to the given grid cell

setGLColor(AccordionTreeDrawer, Color) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Draws this TreeEdge inside the GridCell to which it is attached, and its label if appropriate.

setGroup(AbstractRangeList) - Method in class net.sourceforge.olduvai.accordiondrawer.DrawableRange

Mutator for DrawableRange.group, the group for this range.

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

Change the priority of user mark groups, to layer the most important (latest) changed marks over previously changed groups.

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

Sets the height of the highlight plane.

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

Modifier for the inflation increment for each automated stretching action.

setKey(int) - Method in class net.sourceforge.olduvai.accordiondrawer.AbstractRangeList

Sets the key to the given value.

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

Sets the unique integer identifier for this drawer.

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

Mutator for key

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

Modifier for label background color.

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

Modifier for highlighted label background color.

setLabelBuffer(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Set the size for the label buffer in both axes.

setLabelBuffer(int, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Set the size for the label buffer in the given axis.

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

Modifier for label font color.

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

Sets the state of drawing the label background (AccordionDrawer.labeldrawback).

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

Modifier for highlighted label font color.

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

Sets the state of where TJ draws labels relative to mouse cursor (AccordionDrawer.labelposright)

setLabelsOn(boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Activate/deactivate state of drawing labels.

setLCAGroup(boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

Set state of LCA group checkbox StateFrame.LCAGroup.

setLCAMark(boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

Set state of LCA marking checkbox StateFrame.LCAMark.

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

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

Modifier for left child.

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

Sets the line thickness used in drawing (AccordionDrawer.linethickness, TJ only)

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

Sets the state of linked navigation (AccordionDrawer.linkednav, TJ only).

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

Set the state of linked navigation to the given value.

setLinkedNavigation(boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Activate/deactivate state of linked navigation.

setMax(int) - Method in class net.sourceforge.olduvai.accordiondrawer.DrawableRange

Maximum split line mutator.

setMaxFontHeight(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Set the maximum font height to the given value.

setMaxLine(SplitLine, int) - Method in class net.sourceforge.olduvai.accordiondrawer.GridCell

Sets the maximum split line in the given dimension.

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

The max stuck value is a world space double value from 0 ..

setMin(int) - Method in class net.sourceforge.olduvai.accordiondrawer.DrawableRange

Minimum split line mutator.

setMinCellDims(int, double) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Sets the minimum cell dimensions in screen coordinates to the given block size.

setMinFontHeight(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Set the minimum font height to the given value.

setMinLine(SplitLine, int) - Method in class net.sourceforge.olduvai.accordiondrawer.GridCell

Sets the minimum split line in the given dimension.

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

The min stuck value is a world space double value from 0 ..

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

Modifier for number of animated transitions for mouse movements.

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

Set the name for this node, the name is usually the label drawn with this node.

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

Sets the state of mouse-over flash drawing (AccordionDrawer.noflash).

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

Modifier for number of animated transition steps.

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

Sets the number of leaves, must be run on leaves first (pre-order)

setObjectColor(Color) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Set the AccordionTreeDrawer.objectColor.

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

Sets the height of the object plane.

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

Modifier for SplitLine.opBound.

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

Modifier for parent object.

setPositions(float[], float[], boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Sets positions for a tree edge, starting and ending points for the lines that make a single edge.

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

Toggles progressive rendering.

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

Turns the quasimode to the value of "on".

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

Modifier for right child.

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

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

Modifier for SplitLine.rowObject.

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

Modifier for rubber band color.

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

Set the split line index for this line.

setStructDiff(boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Activate/deactivate state of drawing diffs.

setSubTreeSize(int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitLine

Modifier for SplitLine.subTreeSize.

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

SETTINGOPT - Static variable in class net.sourceforge.olduvai.treejuxtaposer.UI

Index for Tools->Settings option.

SettingsFrame - Class in net.sourceforge.olduvai.treejuxtaposer

GUI for settings.

SettingsFrame(TreeJuxtaposer) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Constructor.

settingsFrame - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Settings frame object, for changing font size, progressive rendering, and other options.

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

Settings frame for options such as line width and font size.

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

Traverse the tree and initialize the Tree.nodesByName and Tree.nodes data structures.

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

Set the weight of this treenode, which encodes the length of the horizontal edge.

SHOW_DIFF - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Index for diffs in SettingsFrame.showString

SHOW_LABEL - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Index for labels string in SettingsFrame.showString.

showAboutFrame() - Static method in class net.sourceforge.olduvai.treejuxtaposer.Help

Show the help file in a frame.

showCheck - Variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Toggle boxes for diffs and labels.

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

Flag to turn automated difference marking on (default, true), or off (false).

showLabel - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Title for toggle boxes in SettingsFrame.showCheck.

showString - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Strings for checkbox SettingsFrame.showCheck.

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

Clear all the data structures initiated in AD, called when tree(s) get deleted from AD.

shutdown() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Clear the objects initiated in ATD.

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

Accessor for the number of ranges in the set of ranges ranges.

size(int) - Method in class net.sourceforge.olduvai.accordiondrawer.LabelBox

Returns the size of the label box, in the given dimension.

size - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

The number of entries in the tree.

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

Small number used to avoid division by 0 in SplitAxis.computeFinalRelative(double, double, double).

snapshotButton - Variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Button for taking snapshots

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

Extension used for postscipt output figures.

snapshotLabel - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

String for snapshot label

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

Global snapshot name that is derived from one AD object.

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

Snapshot writer object, one for each AD, created when snapshot function (AccordionDrawer.doSnapshot(ArrayList)) is run.

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

The split axis objects in the AccordionDrawer.X and AccordionDrawer.Y directions.

SplitAxis - Class in net.sourceforge.olduvai.accordiondrawer

A SplitAxis object represents either the X or Y axis of accordionDrawer (set using the horizontal boolean).

SplitAxis(AccordionDrawer, boolean, double, double, int, boolean, boolean) - Constructor for class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Constructor for initializing split axes with pre-determined values.

SplitAxis() - Constructor for class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Test constructor.

SplitAxis.AxisIterator - Class in net.sourceforge.olduvai.accordiondrawer

Iterator for the SplitAxis class of objects.

SplitAxis.AxisIterator() - Constructor for class net.sourceforge.olduvai.accordiondrawer.SplitAxis.AxisIterator

Creates iterator object, initializes state values.

SplitAxis.Debug - Class in net.sourceforge.olduvai.accordiondrawer

Internal class for debugging the split axis class.

SplitAxis.Debug() - Constructor for class net.sourceforge.olduvai.accordiondrawer.SplitAxis.Debug

SplitAxis.MovingSplitLine - Class in net.sourceforge.olduvai.accordiondrawer

Wrapper class for storing end position and Split line state for a moving split line.

SplitAxis.MovingSplitLine(SplitLine, double) - Constructor for class net.sourceforge.olduvai.accordiondrawer.SplitAxis.MovingSplitLine

Constructor for moving split lines.

SplitAxisTest - Class in net.sourceforge.olduvai.accordiondrawer

Test class for Split Axis debugging.

SplitAxisTest() - Constructor for class net.sourceforge.olduvai.accordiondrawer.SplitAxisTest

Test function.

SplitLine - Class in net.sourceforge.olduvai.accordiondrawer

An instance of a SplitLine.

SplitLine() - Constructor for class net.sourceforge.olduvai.accordiondrawer.SplitLine

Default split line constructor.

SplitLine(double, SplitLine, SplitLine, boolean) - Constructor for class net.sourceforge.olduvai.accordiondrawer.SplitLine

Make a new splitline with given key, value, and parent, and with null child links, and BLACK color.

splitLineFound - Static variable in class net.sourceforge.olduvai.accordiondrawer.SplitLine

Global static variable for storing a found split line from the split axis.

splitLineIndex - Variable in class net.sourceforge.olduvai.accordiondrawer.StaticSplitLine

Position of split line in array.

SplitTransition - Class in net.sourceforge.olduvai.accordiondrawer

A class that helps compute coordinates for smooth animated transitions.

SplitTransition(SplitLine, double, int) - Constructor for class net.sourceforge.olduvai.accordiondrawer.SplitTransition

Create a split transition.

ST_FREEMOVE - Static variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal

ActionMode: Free move state with shift pressed

ST_FREEMOVEAGAIN - Static variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal

ActionMode: Free move state with shift pressed following a reshape

ST_RESHAPE - Static variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal

ActionMode: Free move state with shift pressed during a mouse drag event

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

True when drawing a frame for the first time, set when in AccordionDrawer.startNewFrame()

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

Starts a new scene, performs a transition, seeds the drawing queue, and starts drawing the next frame.

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

Starting relative position of this split line, between SplitLine.getOpBound() and SplitLine.getParent().

stateChanged(ChangeEvent) - Method in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Other state changes not detectable by SettingsFrame.actionPerformed(ActionEvent), such as slider movement.

StateFrame - Class in net.sourceforge.olduvai.treejuxtaposer

GUI for marking and current stretching/squishing group.

StateFrame(TreeJuxtaposer) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.StateFrame

Constructor for StateFrame.

stateFrame - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

State frame object, for manipulating which marking group is active for resizing or coloring.

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

State frame for marking and active group manipulation.

staticLines - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Hook flag for TJ: true when we use static split lines.

StaticSplitAxis - Class in net.sourceforge.olduvai.accordiondrawer

Static hook class for static split lines, as those used by TreeJuxtaposer are not dynamic for optimal performance.

StaticSplitAxis(AccordionDrawer, boolean, double, double, int, boolean, boolean) - Constructor for class net.sourceforge.olduvai.accordiondrawer.StaticSplitAxis

Wrapper constructor for Static Split Axes.

StaticSplitLine - Class in net.sourceforge.olduvai.accordiondrawer

StaticSplitLine(double, SplitLine, SplitLine, boolean) - Constructor for class net.sourceforge.olduvai.accordiondrawer.StaticSplitLine

Create a static split line, with the constructor of SplitLine.

staticSplitLineArray - Variable in class net.sourceforge.olduvai.accordiondrawer.StaticSplitAxis

Array of all split lines.

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

Statistics (rendering time for different setups) buffered writer, currently not enabled as most original (pre 2.0) techniques for drawing are deprecated.

statusPane - Variable in class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch

Pane for the search status IncrementalSearch.searchStatus.

stringHeight(String, Font) - Method in class net.sourceforge.olduvai.accordiondrawer.FontWrapper

Get the height of the string in pixels.

stringWidth(String, Font) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer

Get the width of a string in pixels.

stringWidth(String, Font) - Method in class net.sourceforge.olduvai.accordiondrawer.FontWrapper

Get the width of the string in pixels.

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

Stuck split lines when starting drag

SUBTREE - Static variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal

Mark mode: subtree

subtree2Forest(AccordionTreeDrawer, AccordionTreeDrawer, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Preprocessing: calculate and store forests that correspond to subtrees.

SubtreeLeafCutoff - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Restriction on the maximum number of nodes to store for any subtree's forest of best corresponding nodes.

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

How many nodes are below me, including me (1 for leaves).

subtreeWriter(TreeNode, BufferedWriter) - Static method in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter

Wrap a series of nodes in brackets, then call the node writer on each child of the input subtree root.

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

Returns the successor (next) of the specified Entry, or null if no such.