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

G

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

"Clear group" label and button index in StateFrame.clearButton.

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

1st group (A)

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

2nd group (B)

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

3rd group (C)

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

4th group (D)

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

5th group (E)

getAbsoluteValue(SplitLine, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Returns the absolute position of the specified split line.

getAbsoluteValue(int, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Returns the absolute position of the split line at the specified offset from the left of the tree, in world coordinates.

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

Returns the group number that is supposed to grow when grow option (bigger/smaller) is pressed.

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

Drawer accessor.

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

Get the object that is attached to this label box.

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

Accessor for background color.

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

Get the BCN score for this treenode.

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

Access the bcn filtering score for this tree.

getBestCorrNode(Tree, TreeNode, Tree, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Computes the node in Tree "other" whose set of descendant leaves best matches that of TreeNode n in Tree "source" The best match is the node n' maximizing the following score | S(n) Intersection S(n') | / | S(n) Union S(n') | where S(n) is the set of leaves that are descendants of node n.

getBestCorrNode(Tree, TreeNode, Tree, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreePairs

Computes the node in Tree "other" whose set of descendant leaves best matches that of TreeNode n in Tree "source" The best match is the node n' maximizing the following score | S(n) Intersection S(n') | / | S(n) Union S(n') | where S(n) is the set of leaves that are descendants of node n.

getBestCorrNodeScore(Tree, TreeNode, Tree, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Identify input trees as Tree2Tree.treeA or Tree2Tree.treeB and look up the best score from the BCN of the input node from A to tree B.

getBestCorrNodeScore(Tree, TreeNode, Tree, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreePairs

Retrieves the matching score for the node in Tree "other" whose set of descendant leaves best matches that of TreeNode n in Tree "source".

getBestNodeList(Tree, TreeNode, Tree, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreePairs

Get the list of nodes for the given node that will be highlighted if the node is selected.

getBestNodeScorePair(TreeNode, Tree, Tree, Tree2Tree.TmpD[]) - Method in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Find the best corresponding node for a given node sourceNode:sourceTree, in the target tree targetTree.

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

Retrieve the font family wrapper object to render text.

getBounds(SplitLine, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Retrieve left and right first bounds into an array.

getBounds(SplitAxis) - Method in class net.sourceforge.olduvai.accordiondrawer.StaticSplitLine

Get the bounds of this split line in the given axis, which are the parent and offparent.

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

Returns the cached value of the line without checking if it is up to date.

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

Accessor for the jogl canvas object.

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

Canvas accessor.

getCell() - Method in interface net.sourceforge.olduvai.accordiondrawer.CellGeom

Accessor for the cell that this object is contained in.

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

Gets the grid cell that surrounds this node.

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

Get a given child for this node, with range checking and casting.

getChildren(SplitLine, List<SplitLine>) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Recursively retrieves an pre-ordered list of the child splitlines of the specified line (min -> max)

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

Accessor for the range color, color

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

(TJ only) Get the list of possible colors for the given cell geometry

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

Wrapper for TreeJuxtaposer call to TreeJuxtaposer.getColorsForRange(int, int, AccordionTreeDrawer).

getColorsForRange(int, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal

Wrapper function for TreeJuxtaposer.getColorsForRange(int, int, AccordionTreeDrawer)

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

Get the list of colors for the given split line index range

getColorsForRange(int, int, AccordionTreeDrawer) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Get the list of colors for a range of tree nodes.

getCorrRange(Tree, TreeNode, Tree, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Identify input trees as Tree2Tree.treeA or Tree2Tree.treeB and look up the best matching nodes of the input node from A in tree B.

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

Accessor for SplitLine.cullingObject.

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

Get the debug frame DebugFrame.

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

Get the maximum descent for the family of fonts for the given height.

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

Get the descent (number of pixels below the baseline) of the string in pixels.

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

Returns true if we're drawing a dimmed view of objects, used in TJ to show the depth of nodes.

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

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

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

Returns true if we're drawing a dimmed view of marked objects, used in TJ to show the depth of nodes.

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

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

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

Gets the current state of double buffering.

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

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

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

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

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

Returns state of label drawing (AccordionDrawer.drawlabels)

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

Get the drawing layout manager.

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

Accessor for the last drawn frame for this cell.

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

Return the list of drawn labels, stored in an array list.

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

Return the drawing panel, which holds all the canvas objects that are the drawers.

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

Returns state of stats output (AccordionDrawer.dumpstats)

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

Tests to see if this node has a vertical or horizontal edge component.

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

Get the first range in the set.

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

Gets the flash box, the box that currently surrounds the highlighted node/region.

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

Gets the current flash color.

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

Accessor for font height value for this label box.

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

Accessor for current frame number.

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

Retrieves the GL context for this accordion drawer.

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

Group accessor for the range.

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

Get the marked group (a rangelist) by the given id tag.

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

Get the color for the chosen group.

getGroupForest(int, AccordionTreeDrawer) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Return an array of tree nodes to resize per group range item.

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

Accessor for height of tree.

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

Accessor for the highlight plane.

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

Accessor for inflate increment.

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

Returns the number of interior nodes in this tree.

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

Accessor for the key value, key

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

Returns the unique integer identifier for this drawer.

getKey() - Method in interface net.sourceforge.olduvai.accordiondrawer.CellGeom

Accessor for the key value of an object.

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

Accessor for key.

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

Returns the key for this node.

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

Accessor for label background color.

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

Accessor for highlighted label background color.

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

Get the size for the label buffer in the given axis by 1.

getLabelByFQName(String) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Return the label for a node, given its full name.

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

Accessor for label font color.

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

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

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

Accessor for highlighted label font color.

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

Accessor for the label plane, the depth in drawing for object labels.

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

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

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

Test to see if LCA group checkbox StateFrame.LCAGroup is selected.

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

Test to see if LCA group resize is active.

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

Test to see if LCA mark checkbox StateFrame.LCAMark is selected.

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

Get state of LCA marking from the TreeJuxtaposer.stateFrame.

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

Get the leaf indexed by the input value.

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

Get the leaf associated with the given leaf index.

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

Returns the number of leaves in this tree.

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

Get the leaves under this node.

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

Accessor for left child.

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

Left most leaf accessor.

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

Get the "left most nodes".

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

Assuming this is a leaf, return the leaf index (the split position in Y direction, actually)

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

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

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

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

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

Get the state of the linked navigation flag, which is stored in the first tree drawer, AccordionDrawer.linkednav.

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

Get the list of leaves, as determined by the visible (drawing) set from the partition list of split axis Y.

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

Return the main frame object for holding the drawing panel.

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

Return the number corresponding to the active mark group.

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

Maximum split line accessor.

getMax(int) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Returns the pixel-position of the maximum split line in the given dimension.

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

Returns the maximum key value of nodes in the subtree rooted but this node.

getMaxAbs(int) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Get the screen space position of the maximum split line for a given dimension.

getMaxBound(SplitLine, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Retrieve the given line's right (max) Split Line bound.

getMaxBoundI(SplitLine, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Get the index of the max bound split line for the given line.

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

Get the current maximum font height.

getMaxIndex(int) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Return the index of the maximum split line for a given dimension.

getMaxLine(int) - Method in interface net.sourceforge.olduvai.accordiondrawer.CellGeom

Returns the maximum split line in the given direction for this object.

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

Return the minimum split line in the given dimension.

getMaxLine(int) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Get the actual maximum split line for a given dimension.

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

Get the line in the maximum position in the tree.

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

Stub function.

getMaxLineForPixelValue(int, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Returns the next line over (successor).

getMaxLineForPixelValue(double, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Returns the next line greater than the specified world space coordinate for this axis.

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

Helper function for AccordionTreeDrawer.buildCells(JProgressBar).

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

Stub function

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

Gets the world-space position of the maximum split line for this cell, in X or Y.

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

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

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

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

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

Get the vertical endpoint (world-space) for the vertical tree edge for this node.

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

Get the position of the vertical world-space position of the horizontal tree edge for this node.

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

Minimum split line accessor.

getMin(int) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Returns the pixel-position of the minimum split line in the given dimension.

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

Returns the minimum key value of nodes in the subtree rooted by this node.

getMinAbs(int) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Get the screen space position of the minimum split line for a given dimension.

getMinBound(SplitLine, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Retrieve the given line's left (min) Split Line bound.

getMinBoundI(SplitLine, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Get the index of the min bound split line for the given line.

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

Accesses the minimum cell dimensions in screen coordinates for the current block size.

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

Get the current minimum font height.

getMinIndex(int) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Return the index of the minimum split line for a given dimension.

getMinLine(int) - Method in interface net.sourceforge.olduvai.accordiondrawer.CellGeom

Returns the minimum split line in the given direction for this object.

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

Return the minimum split line in the given dimension.

getMinLine(int) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox

Get the actual minimum split line for a given dimension.

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

Get the line in the minimum position in the tree.

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

Stub function.

getMinLineForPixelValue(int, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

This does the same thing as getSplitFromAbsolute and returns a minimum split line given an absolute position.

getMinLineForPixelValue(double, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

This does the same thing as getSplitFromAbsolute and returns a minimum split line given an absolute position.

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

Stub function

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

Gets the world-space position of the minimum split line for this cell, in X or Y.

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

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

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

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

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

Get the vertical starting point (world-space) for the vertical tree edge for this node.

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

Accessory for number of animated transitions for mouse movements.

getName() - Method in interface net.sourceforge.olduvai.accordiondrawer.CellGeom

Accessor for the name of this object.

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

Accessor for the name (label) contained in this label box.

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

File name accessor.

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

Returns the label for this node, which is TreeNode.name.

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

Returns the next splitline greater than the parameter.

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

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

Node access by node key.

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

Returns the node indexed by the given key.

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

Node access by node name.

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

Returns the node given by the string.

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

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

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

Accessor for number of animated transition steps.

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

Get the number of ranges in this list.

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

Get the AccordionTreeDrawer.objectColor.

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

Accessor for the object plane, the depth in drawing for geometric objects.

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

Get the off-parent object, as a StaticSplitLine.

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

Accessor for SplitLine.opBound.

getOverlapSplitCell(TreeSet, SplitLine) - Static method in class net.sourceforge.olduvai.accordiondrawer.SplitLine

Returns a SplitLine whose absoluteValue is either equal to the input SplitLine's absoluteValue, or is the closest SplitLine less than the input SplitLine's absoluteValue.

getOverlapStaticSplitCell(TreeSet, StaticSplitLine, SplitAxis) - Static method in class net.sourceforge.olduvai.accordiondrawer.StaticSplitLine

Returns a SplitLine whose absoluteValue is either equal to the input SplitLine's absoluteValue, or is the closest SplitLine less than the input SplitLine's absoluteValue.

getPair(Tree, Tree) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreePairs

Get the Tree2Tree table for t1 and t2 differences.

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

Accessor for parent object.

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

Get the partitioned list, the list created prior to rendering to determine the visible objects and culling limit.

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

Returns the size of a block in world ([0,1], fractional) space size.

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

Get the previous line, with the SplitAxis.previous(SplitLine) function supplied by the parent class.

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

Returns the splitLine previous to the parameter.

getProgressBar() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser

Get the progress bar object.

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

Returns state of the quasi-mode flag.

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

Get the range list (marked group) by the given key

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

Get a range list by the given key.

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

Get the whole Set of ranges

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

Load a resource (readme file) and return its contents as a string

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

Helper function used by Help.getReadme(), to load the text file resource.

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

Accessor for right child.

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

Gets the root split line for this axis.

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

Root accessor.

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

Returns ths index of the root split line.

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

Accessor for SplitLine.rowObject.

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

Accessor for rubber band color.

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

Get the search panel frame IncrementalSearch.

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

Get the settings frame SettingsFrame.

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

Returns the world-space size in X or Y for this cell.

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

Get the number of split lines on the axis, not including min and max stuck lines.

getSize(SplitAxis, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeInTree

Get the world-space size for this range.

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

Gets the cell world-space size (max - min) for this node's cell in the given direction.

getSizesOfAllRanges(SplitAxis, int) - Method in class net.sourceforge.olduvai.accordiondrawer.AbstractRangeList

For each range in ranges, store the size in world coordinates

getSizesOfAllRanges(SplitAxis, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeList

Collate range sizes into an array of doubles.

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

Accessor for split axes, X AccordionDrawer.X or Y AccordionDrawer.Y.

getSplitFromAbsolute(double, double, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Find a split line using absolute values to return the minimum bounding split line at the screen position.

getSplitFromIndex(int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Returns the split line at the specified offset in the tree.

getSplitFromIndexRecursive(int, int, SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Recursive helper function for 'getSplitFromIndex()'.

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

Calculate the index number of any splitline from the left side of the tree.

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

Get the split line index for this line.

getSplitIndexFromAbsolute(double, double, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Wrapper for getSplitFromAbsolute for places where we want the index number instead of a pointer to the SplitLine object.

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

Application-specific accessor for split line indices that surround this range.

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

Collate split line indices into an array of integers.

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

Global static variable for retrieving a split line from the split axis.

getSplitLineRange(int, boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeInTree

Convert the RangeInTree of leaf indices into a RangeInTree of split line indices.

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

Analagous to getSplitIndices(boolean) but returns the list of lines instead.

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

Get the state frame StateFrame.

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

Get the parent object, as a StaticSplitLine.

getStaticSeedBounds(StaticSplitLine, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Get the split line boundaries for the given split line, properly ordered in the return value [min, max].

getStaticSplitLineObject(int) - Method in class net.sourceforge.olduvai.accordiondrawer.StaticSplitAxis

Return the object at the given position, as a proper cell geom (TreeNode in TJ)

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

Accessor for SplitLine.subTreeSize.

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

Get the next line, with the SplitAxis.successor(SplitLine) function supplied by the parent class.

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

Accessor for the drawing queue.

getTotalExtent(double[]) - Static method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis

Helper function for resizeForest.

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

Returns the node count, for internal and leaf nodes.

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

Get the tree that this drawer represents.

getTree() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeInTree

Get the drawer for this range

getTreeByName(String) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Fetch a tree by its name.

getUnshrinkableTotal(AccordionDrawer, SplitAxis, int) - Method in class net.sourceforge.olduvai.accordiondrawer.AbstractRangeList

Return the quantity of world space that may not be shrunk by a stretching operation.

getUnshrinkableTotal(AccordionDrawer, SplitAxis, int) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeList

Accumulate the unshrinkable total for this set of ranges.

getValue(SplitAxis, int) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitLine

Returns the absolute value of this splitLine.

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

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

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

Return the size of the window, in AccordionDrawer.X or AccordionDrawer.Y direction

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

Accessor for the size of the drawing canvas, in pixels, in the given direction.

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

6th group (F)

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

7th group (G)

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

8th group (H)

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

Returns true if baseLine is a successor to comparator O(2 log n)

GridCell - Class in net.sourceforge.olduvai.accordiondrawer

A class representing a cell, which is a rectangular region between 2 pairs of split lines in an Accordion Drawer.

GridCell(AccordionDrawer) - Constructor for class net.sourceforge.olduvai.accordiondrawer.GridCell

Default constructor for grid cells, sets the min and max lines to null and initializes drawer.

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

Same as AccordionDrawer.backplane, the plane on which the deformable grid is drawn (default not drawn)

group - Variable in class net.sourceforge.olduvai.accordiondrawer.DrawableRange

The group that this range is within, if applicable.

groupID - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeList

group ID: key refers to priority, this is for reference to groups by well known static assigned integers to constants.

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

Group ID accessor.

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

Index for Tools->Groups option.

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

Flag to indicate a group pass for saving the current scene as a postscript figure.

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

Rearrangable list of RangeLists (groups).

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

List of marking groups by index.

growButton - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

Grow/shrink buttons.

growDirection - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

The current mode for growing, either vertical, horizontal, or both directions simultaneously.

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

Growing direction, default to 1

growDirectionPanel - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

Grow direction panel (horizontal, vertical, or both).

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

Label for StateFrame.growDirectionPanel.

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

Return true if growing horizontal, or in both directions.

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

Grow labels for StateFrame.growMode.

growMode - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

Radio buttons for stretching directions: horizontal, vertical, or both.

growModeAction(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

Handler for user-modifying grow direction not through the GUI.

growSelect - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame

Button group for StateFrame.growMode.

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

Return true if growing vertical, or in both directions.