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L

label - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
The text that appears when the node is highlighted or has a name displayed.
labelAtLeaves - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
set to true when we want to draw labels only at the leaf level.
labelBackColor - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Background color of label text.
labelBackColor - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Color for label background of normal (not highlighted) nodes.
labelBackHiColor - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Background color of highlighted label text.
labelBackHiColor - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Color for the label background for highlighted nodes.
labelbgplane - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Above AccordionDrawer.hiliteplane, below AccordionDrawer.labelplane, for drawing label backgrounds, where the label text is drawn 4 times (offset vertically and horizontally by a small number of pixels) in the label background color
LabelBox - Class in net.sourceforge.olduvai.accordiondrawer
Axis-aligned bounding box class for label drawing.
LabelBox(int[], int[], int[], int, String, CellGeom, int) - Constructor for class net.sourceforge.olduvai.accordiondrawer.LabelBox
Label box constructor.
labelbuffer - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Amount of space in X and Y (in pixels) that labels must be separated by.
labelColor - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Foreground color of label text.
labelColor - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Color for labels of normal (not highlighted) nodes.
labelDensityLabel - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Label for SettingsFrame.labelDensitySlider.
labelDensityMax - Variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Maximum value for label density.
labelDensitySlider - Variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Slider for label density.
labeldrawback - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Flag set to draw the background (filled bounding box) for non-mouseover labels.
labelHiColor - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Foreground color of highlighted label text.
labelHiColor - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Color for labels for highlighted nodes.
labeloffset - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Label offset for leaf nodes.
labelPixels - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
framebuffer pixels from last mouseover label drawn
labelplane - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Above AccordionDrawer.labelbgplane, below AccordionDrawer.interactionplane, for drawing actual label text
labelposright - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
(currently only TJ) Flag to set position of labels (non-mouseover).
lastChild() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Get the last child of this node.
lca(TreeNode) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Compute the lowest common ancestor between this node and that.
LCA - Static variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Label for least common ancestor checkboxes.
LCA_ACT - Static variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Lowest common ancestor group number
LCAGroup - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
For growing by LCA when checked.
LCAMark - Variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
For marking by LCA (ascend tree from marks to their LCA while this is checked)
lcaNode - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
List of TreeNodes that are marked with the LCA group color.
LeafComparator - Class in net.sourceforge.olduvai.treejuxtaposer.drawer
Leaf comparator, compares pair of leaves by leaf index values.
LeafComparator() - Constructor for class net.sourceforge.olduvai.treejuxtaposer.drawer.LeafComparator
 
leafDrawCount - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Debugging value, for information of drawing efficiency.
leafLca(TreeNode) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Compute the lowest common ancestor between this leaf and "that" The two nodes must belong to the same tree and must be leaves
leafSplitAxis - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree
Split axis reference for leaf recovery (leaves are attached to split line culling objects)
LEFT - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
array index for left bounds
LEFT_MASK - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Mask to OR by to access left side labels for fonts.
leftChild - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitLine
Left child of this split line, null if the child is null (possible leaf is right is also null).
leftmostLeaf - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Leftmost (minimum) leaf node under this internal node (or this node for leaves).
leftOf(SplitLine) - Static method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Gets the left child of a given split line.
leftPanel - Variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Objects on the left side of the GUI.
lessThan(SplitLine, SplitLine) - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis
Returns true if baseLine is previous to comparator O(2 log n)
line - Variable in class net.sourceforge.olduvai.accordiondrawer.SplitAxis.MovingSplitLine
Split line state variable.
lineLength - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Length of nodes for horizontal and vertical edges.
linePixel - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Drawing buffer for mouse-over drawing/undrawing.
linePos - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.AccordionTreeDrawer
Location of tree edges (for flash drawing) that we are storing in AccordionTreeDrawer.linePixel
lineTerminator - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeParser
Line (and tree information) termination.
lineTerminator - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter
End of tree character.
linethickness - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Thickness of lines used in geometric object drawing, currently only used in TJ, where marked nodes are (width+2).
linethickness - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Thickness of tree edge lines for default non-marked nodes.
linewidth - Variable in class net.sourceforge.olduvai.accordiondrawer.InteractionBox
Width of lines used to draw an interaction box
linewidthLabel - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Label for SettingsFrame.linewidthSlider.
linewidthSlider - Variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Slider for line width.
linkCheck - Variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
Checkbox for linked navigation.
linkednav - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
(currently only TJ) Linked navigation flag, defaults to true, where certain navigations (subtree stretching) are linked between drawers.
linkLeaves(JProgressBar) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree
Links leaves of the tree in pre-order, check to see whether leaves have distinct names.
linkNodesInPostorder() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Leaf->root traversal, starting at leftmost leaf of tree.
linkNodesInPreorder() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree
Wrapper for initiating Tree.linkSubtreeNodesInPreorder(TreeNode) with the root node.
linkNodesInPreorder() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
root->leaf traversal, depth first in direction of leftmost leaf.
linkString - Static variable in class net.sourceforge.olduvai.treejuxtaposer.SettingsFrame
String for SettingsFrame.linkCheck checkbox.
linkSubtreeNodesInPreorder(TreeNode) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree
Traverses the subtree rooted at TreeNode n in pre-order, stores the ordering in the preorderNext field of TreeNodes.
loaded - Static variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Set initially to false, true when data is done loading and AccordionDrawer.canvas is ready to draw.
loadNewickTree(String) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Load a newick tree.
loadTree(String, Vector) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
For loading specific nexus trees from the command line (or all trees if vector is null).
loadTree(String) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeJuxtaposer
Wrapper for loading all type of supported trees.
lSum - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree.TmpD
 

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