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.

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