|
||||||||||
PREV LETTER NEXT LETTER | FRAMES NO FRAMES |
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
SettingsFrame.labelDensitySlider
.
AccordionDrawer.labelbgplane
, below AccordionDrawer.interactionplane
, for drawing actual label text
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
-
|
||||||||||
PREV LETTER NEXT LETTER | FRAMES NO FRAMES |