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.

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