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

I

ignoreProgressive - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
State of progressive rendering.
incr() - Method in class net.sourceforge.olduvai.accordiondrawer.SplitTransition
Update the SplitTransition.curStep by one, used before SplitTransition.move().
increaseLabelBuffer(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Increment the size for the label buffer in the given axis by 1.
increaseLabelBuffer(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Increment the label buffer (the minimum distance between two labels) in the given direction.
increaseLineThickness() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Increases the line thickness used in drawing by 1 (AccordionDrawer.linethickness, TJ only)
increaseLineThickness() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Increment the width of tree edge lines in each drawer.
increaseMaxFontHeight() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Increment maximum font height by 1.
increaseMaxFontHeight() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Increment the maximum font height in each drawer.
increaseMinFontHeight() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Increment minimum font height by 1.
increaseMinFontHeight() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Increment the minimum font height in each drawer.
IncrementalSearch - Class in net.sourceforge.olduvai.treejuxtaposer
Incremental search functionality and GUI class.
IncrementalSearch(TreeJuxtaposer) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch
Initialize the search box with default values.
IncrementalSearch(TreeJuxtaposer, ArrayList) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch
Initialize the search box with a list of names.
incrementFrameNumber() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Adds 1 to the frame number.
incrementSize() - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Increments counters SplitAxis.modCount and SplitAxis.size.
incrementTreeRecursive(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Ascend recursively incrementing subtree counters as we go.
index - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitTransition
Pointer to split line that is moving.
indices - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeRemovalPanel
Indices that have been selected for deleting.
inflateIncr - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Percentage to add for an inflate (stretch), or subtract for deflate (squish); used to determine how much to grow each region, this value is split between resizing regions depending on their initial relative sizes.
infoSeparator - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter
UNUSED separator for placing more information after the node name.
init(GLAutoDrawable) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
JOGL-called initialization function that sets up fonts and the main GUI window.
initCells(JProgressBar) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Initialize the split line hierarchies, including the axes and set the initial sizes.
initCells(JProgressBar) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Initializes split lines, and builds cells for each tree node.
initComponents() - Method in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Initialize components and set up GUI.
initComponents() - Method in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Initialize GUI and set up listeners.
initGUI() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter
Initialize the GUI for changing the label of a node.
initialColor - Static variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Initial colors for groups.
initializeFont() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Initialize variable font family wrapper.
initializeList(ArrayList) - Method in class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch
Initialize nodes in the search list if the input is not null.
initialText - Static variable in class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch
Initial text in comment box IncrementalSearch.searchStatus.
initNexusChooser() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser
Layout and listeners for the nexus chooser.
initSplitLines(boolean, boolean, int, int) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Initialize the split lines for a two dimensional accordion drawing object.
initSplitValues(int, boolean) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
This initializes a split line tree (empty) of size 'size'.
initStaticSplitSubtree(StaticSplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Recursively initialize binary tree structure.
InteractionBox - Class in net.sourceforge.olduvai.accordiondrawer
Draw and cache information about an onscreen rubberband box.
InteractionBox(SplitLine[], SplitLine[], CellGeom, AccordionDrawer) - Constructor for class net.sourceforge.olduvai.accordiondrawer.InteractionBox
Creates an interaction box with the given split lines, data object, and drawer
interactionplane - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Highest plane for drawing, above AccordionDrawer.labelplane, for performing interactions and mouse-over label drawing
internalDrawCount - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Debugging value, for information of drawing efficiency.
intersectLabelBox(LabelBox, ArrayList) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Occlusion check of LabelBox against array of all drawn labels.
isAncestorOf(TreeNode) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Test function for determining if one node is an ancestor of another.
isDiffOn() - Method in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Flag check for testing if diffs are on.
isDoingFlash() - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
State accessor for determining if flash drawing is active.
isEnabled() - Method in class net.sourceforge.olduvai.accordiondrawer.AbstractRangeList
Accessor for the value of enabled
isFakeLine - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitLine
State for fake lines or real lines.
isHorizontal() - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Determines if this is a horizontal SplitAxis
isLeaf() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Tests to determine if this node is a leaf.
isLeftChild() - Method in class net.sourceforge.olduvai.accordiondrawer.SplitLine
Test function for internal nodes, true if this line is a left child of its immediate parent.
isLoaded() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Detect loading status of tree files, initially set to false, sets to true after all trees have been loaded and first drawing cycles can start.
isMinLineMoving(int, int) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox
Determines if dragPosition (the starting drag value) is closer to min or max.
isNexusFile(String) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser
Guess the type of treeFile based on the presence of nexus identifiers.
isNodePicked(double, double, double, double) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Test function to determine if this tree node is picked.
isReal(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Some split lines are 'fake' leaf lines that are created to be loaded into the partitioned set.
isRoot(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Checks whether param is the root of this split axis.
isRoot() - Method in class net.sourceforge.olduvai.accordiondrawer.SplitLine
Root test.
isRoot() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Tests to determine if this node is the root of its tree.
isSplitLeftChild(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Checks whether parameter is a left child of its parent.
isThisRangeInList(int, int, AccordionTreeDrawer) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeList
Determines if the given range of min,max is overlapping with this rangelist
isThisTreeOnly() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeList
Flag access to RangeList.thisTreeOnly.
item - Variable in class net.sourceforge.olduvai.accordiondrawer.InteractionBox
The item that is contained in the interaction box, if applicable
iterator() - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Returns an iterator over the axis.

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