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N

N_RES - Static variable in class net.sourceforge.olduvai.treejuxtaposer.StateFrame
Node marking mode.
name - Variable in class net.sourceforge.olduvai.accordiondrawer.LabelBox
The string to draw as the label
name - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Node name with default "".
NameComparator - Class in net.sourceforge.olduvai.treejuxtaposer.drawer
Comparator class for Strings
NameComparator() - Constructor for class net.sourceforge.olduvai.treejuxtaposer.drawer.NameComparator
 
net.sourceforge.olduvai.accordiondrawer - package net.sourceforge.olduvai.accordiondrawer
 
net.sourceforge.olduvai.treejuxtaposer.drawer - package net.sourceforge.olduvai.treejuxtaposer.drawer
 
newLabel - Variable in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter
Text area to read new label name.
newMouseOver(TreeNode, TreeNode) - Method in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal
Called by any of the arrow action functions, to update the drawer with a flash draw.
newPixelDiv(double, int) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Sets the size of a block, in pixels.
newSnapshotName(String, File) - Method in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Assembles a snapshot name to write a postscript figure that looks like the current scene.
next() - Method in class net.sourceforge.olduvai.accordiondrawer.SplitAxis.AxisIterator
Get the next split line in the axis from the current value of SplitAxis.AxisIterator.currLine.
nexusCharacterTokenize() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser
Tokenize the character section of a nexus file only.
nexusFileID - Static variable in class net.sourceforge.olduvai.treejuxtaposer.TreeParser
Nexus file identifier.
nexusFileTreeNames(String) - Static method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser
Parses names of trees in nexus file.
nexusIndex - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree
Index of tree in nexus file, if this tree is from a nexus file.
nexusTaxaTokenize() - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser
Nexus taxa tokenizer, does nothing for now, but can be used later.
nexusTokenize(Vector, JProgressBar) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser
Tokenize a nexus file, uses newick tokenizer after identifying the region with the tree information.
nexusTreeTokenize(Vector) - Method in class net.sourceforge.olduvai.treejuxtaposer.TreeParser
Tokenize the tree section of a nexus file only, uses newick tokenizer.
NODE - Static variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal
Mark mode: single node
node - Variable in class net.sourceforge.olduvai.treejuxtaposer.Tree2Tree.NodeScorePair
Tree node reference.
nodeKeyToSplitLine(int, boolean) - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.RangeList
Return a list of ranges of split line indices.
nodes - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree
The list of nodes of the tree indexed by their keys, indexed by key
nodesByName - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree
Most internal nodes don't have names.
nodeWriter(TreeNode, BufferedWriter) - Static method in class net.sourceforge.olduvai.treejuxtaposer.TreeWriter
Write a single node to the writer object, after calling the subtree writer on each child.
noflash - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Flag to turn flash drawing on (default, true), or off (false).
NONE - Static variable in class net.sourceforge.olduvai.treejuxtaposer.AccordionTreeDrawerFinal
value of NONE for AccordionTreeDrawerFinal.keytarget and AccordionTreeDrawerFinal.actionmode
now - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Refreshed during a rendering pass in AccordionDrawer.drawFrame(), used to check time spent rendering.
numAnimSteps - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
The number of animations steps for navigation transitions.
numberChildren() - Method in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
Get the number of children under this node.
numberLeaves - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode
The number of leaves under this internal node (or 1 for leaves).
numCellsDrawnThisFrame - Variable in class net.sourceforge.olduvai.accordiondrawer.AccordionDrawer
Debugging value used to compute efficiency of drawing algorithm, incremented once per geometric object, reset to 0 at start of each frame.
numFound - Variable in class net.sourceforge.olduvai.treejuxtaposer.IncrementalSearch
The number of items in the list of results IncrementalSearch.results.
numLeaves - Variable in class net.sourceforge.olduvai.treejuxtaposer.drawer.Tree
Leaf counter, for determining grid size, making arrays for tree comparisons

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