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

T

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

Flag turned on when user wants a snapshot of the current scene.

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

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

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

Only highlight group items for this tree, not all the others

title - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Title for this frame.

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

Title for the state frame (aka groups).

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

Title for the application.

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

The treejuxtaposer object for referencing the program instance that responds to user actions found in this class.

tj - Variable in class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch

The TJ for this set of found results, for calling updates to the drawers.

tj - Variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

Treejuxtaposer object for referencing state and all drawers.

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

Treejuxtaposer object, for referencing groups and other state.

tj - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeRemovalPanel

The TJ object used to get the tree names.

tj - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter

TreeJuxtaposer used to reset the differences and search dialog with TreeJuxtaposer.postDeleteTrees().

tj - Variable in class net.sourceforge.olduvai.treejuxtaposer.UI

TreeJuxtaposer object.

tmpParent - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree.TmpD

tmpPosorderNext - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree.TmpD

tmpScore - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree.TmpD

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

The drawing queue.

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

Toggle the value of AccordionDrawer.dimbrite

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

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

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

Toggle the value of AccordionDrawer.dimcolors

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

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

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

Toggles value of AccordionDrawer.drawGeoms

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

Toggle state of drawing tree nodes (geoms).

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

Toggles value of AccordionDrawer.drawGrid

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

Toggle state of drawing grid on all drawers.

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

Toggles value of AccordionDrawer.drawlabels

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

Toggle for the state of drawing split lines.

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

Toggle for drawing split lines (grid lines).

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

Toggles value of AccordionDrawer.dumpstats

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

Toggle debug state of sending rendering time information or other real-time information to a log file.

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

Toggles value of AccordionDrawer.labeldrawback

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

Toggle the drawing of the label background (for non-highlighted nodes).

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

Toggles value of AccordionDrawer.labelposright

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

Toggle for drawing labels on the right side of edges, or by the node junction between tree edges.

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

Toggles value of AccordionDrawer.linkednav

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

Toggle the state of linked navigation in all drawers.

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

Toggles value of AccordionDrawer.noflash

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

Toggle state of flash (mouse-over) drawing on all drawers.

toggleProgRenderString - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame

String for progressive rendering toggle

tokenize(long, String, JProgressBar) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser

Newick tokenizer: converts a string (tree as a string) into a tree object.

tokenizer - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeParser

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

Recursive descent print: For printing the split axis tree under this node (recursive).

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

Table of SplitTransition, which store information about SplitLine movements that are in progress.

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

Flags to indicate if menu options are active (true) or spaces (false).

toolkit - Variable in class net.sourceforge.olduvai.treejuxtaposer.UI

Toolkit used to get screen dimensions.

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

Index for Tools menu.

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

Strings for Tools menu section.

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

Return a coordinate (in screen space) for the top or right edge of this box.

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

Returns a string representation for objects of this class.

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

Return the string representation of this interaction box.

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

Display function for moving split lines.

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

String output routine for splitaxes, displays SplitLine.toLongString() for root of axis.

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

String representation of this split line.

toString() - Method in class net.sourceforge.olduvai.accordiondrawer.SplitTransition

Debugging output function.

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

debug output function, print the split line index for this line.

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

Convert tree into name used by screen shot writer.

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

Debug string for this range.

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

Debugging output function.

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

String value of this node, name + key + tree height information.

toString() - Method in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree.NodeScorePair

Debugging output.

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

An array of TreePairs objects: each TreePair contains the necessary data structures for the differences and node correspondences between nodes in a pair of trees.

tr - Variable in class net.sourceforge.olduvai.accordiondrawer.LabelBox

Top right coordinates, in pixels

tree - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer

Tree that is drawn in this drawer's canvas.

Tree - Class in net.sourceforge.olduvai.treejuxtaposer.drawer

A public class representing a (phylognenetic) tree.

Tree() - Constructor for class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree

Default tree constructor.

Tree(Tree) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree

Copy constructor used to create versions of trees that are identical to the supplied input tree.

Tree2Tree - Class in net.sourceforge.olduvai.treejuxtaposer

Tree2Tree does the precomputation for each pair of trees.

Tree2Tree(Tree, Tree, int) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Initialize the two vectors

Tree2Tree.NodeScorePair - Class in net.sourceforge.olduvai.treejuxtaposer

Container class for returning best corresponding node+score pair.

Tree2Tree.NodeScorePair(TreeNode, float) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree.NodeScorePair

Constructor for node+score pair.

Tree2Tree.TmpD - Class in net.sourceforge.olduvai.treejuxtaposer

Attachment to a node that is needed as temporary data structure when computing best corresponding nodes.

Tree2Tree.TmpD() - Constructor for class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree.TmpD

treeA - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Arbitrary tree A for this comparison.

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

Number of arguments passed to application.

treeB - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree

Arbitrary tree B for this comparison.

treeCount - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Number of tree objects.

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

Resizeable array of AccordionTreeDrawerFinal objects (not trees, which are TreeJuxtaposer.trees).

treeID - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeParser

Tree ID.

TreeJuxtaposer - Class in net.sourceforge.olduvai.treejuxtaposer

A class representing a tree juxtaposer.

TreeJuxtaposer() - Constructor for class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer

Main constructor for the TJ object, initializes states, and user interfaces.

treeList - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeRemovalPanel

List of trees from the TJ object.

TreeNode - Class in net.sourceforge.olduvai.treejuxtaposer.drawer

A class representing a node of a (phylognenetic) tree.

TreeNode() - Constructor for class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Default tree node constructor.

TreePairs - Class in net.sourceforge.olduvai.treejuxtaposer

TreePairs store all the pairwise data structures needed for structural comparison and visulization.

TreePairs() - Constructor for class net.sourceforge.olduvai.treejuxtaposer.TreePairs

Constructor for tree pairs.

TreeParser - Class in net.sourceforge.olduvai.treejuxtaposer

TreeParser(BufferedReader) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.TreeParser

Initializes parsing of a tree by creating a tokenizer and setting default properties (such as spacing, quoting characters).

TreeRemovalPanel - Class in net.sourceforge.olduvai.treejuxtaposer

Tree removal panel.

TreeRemovalPanel(TreeJuxtaposer) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.TreeRemovalPanel

Creates a tree removal panel from the current active trees drawn in the input TJ.

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

Resizeable array of Tree objects (not drawers, which are TreeJuxtaposer.treeDrawers).

trees - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreePairs

List of "raw" trees, these are used in the hashtable.

treeSectionTag - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeParser

Tree section.

treeTerminator - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter

End of tree character.

TreeWriter - Class in net.sourceforge.olduvai.treejuxtaposer

Static utility class to write a tree to a file.

TreeWriter(TreeNode, TreeJuxtaposer) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.TreeWriter

Start a tree writer dialog that allows a user to enter a new name for a node.