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.

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