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U

ui - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Object for controlling user interface functions directed from the top menu (FILE, HELP, etc), to separate the menu functionality handling (string names, setup, etc) from the application.
UI - Class in net.sourceforge.olduvai.treejuxtaposer
User interface class that externalizes most of the menu setup for the top menu bar, and the main implementation of the dialog to add new trees.
UI(TreeJuxtaposer, String) - Constructor for class net.sourceforge.olduvai.treejuxtaposer.UI
Initializes the drawing surface and menu bar on the main frame.
uncoloredNode - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Index for uncolored node in AccordionTreeDrawer.getLeftMostNodes(TreeNode, TreeNode).
undraw() - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox
Similar to InteractionBox.draw(Color, float, float), but only draw the rubber band with InteractionBox.drawRubberband() and the same set parameters, to undraw the previous interaction box.
uniformSplits - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Flags to set initial distribution of split lines (AccordionDrawer.X, AccordionDrawer.Y).
unmarkAllGroups() - Method in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Clear all user marked groups, and LCA mark checkbox.
unmarkGroup(int) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Remove LCA marked objects from the given group, then clear the contents of the group, which will force the previously marked objects to not be marked by that group's color.
updateBoundLeftEchelon(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Repair left subtree following a delete
updateBoundRightEchelon(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Repair right subtree following a delete
updateDrag(int[]) - Method in class net.sourceforge.olduvai.accordiondrawer.InteractionBox
Updates InteractionBox.oldDragEnd with the previous value of InteractionBox.dragEnd, and InteractionBox.dragEnd with the new value passed in.
updateEchelonBounds(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Repairs tree structure around the given split line following a delete operation.
updateMinLineX(ArrayList, StaticSplitLine) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Helper function for AccordionTreeDrawer.buildCells(JProgressBar).
updateSubtreeSize(SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Recursively update the size of subtrees under the given current split line.
updateTitle() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Update the title bar for the application.
uSum - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree.TmpD
 
utreeID - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeParser
Tree ID (same or similar to TreeParser.treeID?).

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