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

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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.