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

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