Uses of Class
AccordionTreeDrawer.TreeNode

Packages that use TreeNode

AccordionTreeDrawer
Parser
TreeJuxtaposer

Uses of TreeNode in AccordionTreeDrawer

Fields in AccordionTreeDrawer declared as TreeNode

TreeNode	TreeNode.parent
TreeNode	TreeNode.leftmostLeaf
TreeNode	TreeNode.rightmostLeaf
TreeNode	TreeNode.preorderNext
TreeNode	TreeNode.posorderNext
TreeNode	TreeNode.next next leaf added by Li
TreeNode	TreeEdge.node
(package private) TreeNode	Tree.root
(package private) TreeNode	Tree.leftmostLeaf
TreeNode	Tree.preorderStartNode the start node for preorder list of all the nodes
TreeNode	Tree.posorderStartNode the start node for postorder list of all the nodes
protected TreeNode	AccordionTreeDrawer.rootNode

Methods in AccordionTreeDrawer that return TreeNode

TreeNode	TreeNode.getChild(int i)
TreeNode	TreeNode.getLeftmostLeaf()
TreeNode	TreeNode.getRightmostLeaf()
TreeNode	TreeNode.parent()
TreeNode	TreeNode.firstChild()
TreeNode	TreeNode.lastChild()
TreeNode	TreeNode.lca(TreeNode that) Compute the lowest common ancestor between this node and that.
TreeNode	TreeNode.leafLca(TreeNode that) Compute the lowest common ancestor between this leaf and "that" The two nodes must belong to the same tree and must be leaves
TreeNode	Tree.getNodeByKey(int key)
TreeNode	Tree.getNodeByName(java.lang.String s)
TreeNode	Tree.getLeftmostLeaf()
TreeNode	Tree.getRightmostLeaf()
TreeNode	Tree.getRoot()
TreeNode	AccordionTreeDrawer.getNodeByKey(int key)
TreeNode	AccordionTreeDrawer.getNodeByName(java.lang.String name)

Methods in AccordionTreeDrawer with parameters of type TreeNode

boolean	TreeNode.equals(TreeNode n)
void	TreeNode.addChild(TreeNode n)
boolean	TreeNode.isAncestorOf(TreeNode that)
TreeNode	TreeNode.lca(TreeNode that) Compute the lowest common ancestor between this node and that.
TreeNode	TreeNode.leafLca(TreeNode that) Compute the lowest common ancestor between this leaf and "that" The two nodes must belong to the same tree and must be leaves
(package private) int	Tree.getGapDistanceFromLeaves(TreeNode n1, TreeNode n2)
(package private) int	Tree.getGapDistanceFromLeaves(TreeNode n1, TreeNode n2)
(package private) int	Tree.getLCADistanceFromLeaves(TreeNode n1, TreeNode n2)
(package private) int	Tree.getLCADistanceFromLeaves(TreeNode n1, TreeNode n2)
(package private) void	Tree.setRoot(TreeNode rn)
private void	Tree.linkSubtreeNodesInPreorder(TreeNode n) Traverses the subtree rooted at TreeNode n in pre-order, stores the ordering in the preorderNext field of TreeNodes.
private void	Tree.linkSubtreeNodesInPosorder(TreeNode n) Traverses the subtree rooted at TreeNode n in post-order, stores the ordering in the posorderNext field of TreeNodes.
private void	AccordionTreeDrawer.drawBruteForceRecurse(TreeNode n) Draw a tree edge, recurse to draw its children.
void	AccordionTreeDrawer.resizeSubtree(Tree thisTree, TreeNode tn, boolean grow, int numSteps, boolean horizontal, boolean vertical)

Constructors in AccordionTreeDrawer with parameters of type TreeNode

TreeEdge(TreeNode n, GridCell startCell, GridCell endCell)

Tree(TreeNode rn)

Uses of TreeNode in Parser

Fields in Parser declared as TreeNode

private static TreeNode	Newick.current_node the current TreeNode that the parser is visiting and initiating
private static TreeNode	Newick.tn a helper TreeNode field

Uses of TreeNode in TreeJuxtaposer

Fields in TreeJuxtaposer declared as TreeNode

(package private) TreeNode	Tree2Tree.NodeScorePair.node
(package private) TreeNode	Tree2Tree.TmpD.tmpParent
(package private) TreeNode	Tree2Tree.TmpD.tmpPosorderNext
(package private) TreeNode	AccordionTreeDrawerFinal.mouseOverNode

Methods in TreeJuxtaposer that return TreeNode

(package private) TreeNode	TreePairs.getBestCorrNode(Tree source, TreeNode n, Tree other, int el) Computes the node in Tree "other" whose set of descendant leaves best matches that of TreeNode n in Tree "source" The best match is the node n' maximizing the following score | S(n) Intersection S(n') | / | S(n) Union S(n') | where S(n) is the set of leaves that are descendants of node n.
(package private) TreeNode	Tree2Tree.getBestCorrNode(Tree source, TreeNode n, Tree other, int el) Computes the node in Tree "other" whose set of descendant leaves best matches that of TreeNode n in Tree "source" The best match is the node n' maximizing the following score | S(n) Intersection S(n') | / | S(n) Union S(n') | where S(n) is the set of leaves that are descendants of node n.
private TreeNode	AccordionTreeDrawerFinal.rightAlignFind(TreeNode parentNode, TreeNode originalNode, int originalNodeChildNumber, boolean goingDown)

Methods in TreeJuxtaposer with parameters of type TreeNode

(package private) TreeNode	TreePairs.getBestCorrNode(Tree source, TreeNode n, Tree other, int el) Computes the node in Tree "other" whose set of descendant leaves best matches that of TreeNode n in Tree "source" The best match is the node n' maximizing the following score | S(n) Intersection S(n') | / | S(n) Union S(n') | where S(n) is the set of leaves that are descendants of node n.
(package private) java.util.ArrayList	TreePairs.getBestNodeList(Tree source, TreeNode n, Tree other, int el)
(package private) float	TreePairs.getBestCorrNodeScore(Tree source, TreeNode n, Tree other, int el) Computes the matching score for the node in Tree "other" whose set of descendant leaves best matches that of TreeNode n in Tree "source" The matching score between nodes n and n' is computed as follows: | S(n) Intersection S(n') | / | S(n) Union S(n') | where S(n) is the set of leaves that are descendants of node n.
void	TreeJuxtaposer.resizeRectOthers(TreeNode tn, float[] minChangeRatio, float[] maxChangeRatio, int numAnimSteps, AccordionTreeDrawer thisatd)
private void	Tree2Tree.addNodeToForest(TreeNode node, java.util.ArrayList array, java.util.Hashtable hash)
private void	Tree2Tree.removeNodeFromForest(TreeNode node, java.util.ArrayList array, java.util.Hashtable hash)
(package private) TreeNode	Tree2Tree.getBestCorrNode(Tree source, TreeNode n, Tree other, int el) Computes the node in Tree "other" whose set of descendant leaves best matches that of TreeNode n in Tree "source" The best match is the node n' maximizing the following score | S(n) Intersection S(n') | / | S(n) Union S(n') | where S(n) is the set of leaves that are descendants of node n.
(package private) float	Tree2Tree.getBestCorrNodeScore(Tree source, TreeNode n, Tree other, int el)
(package private) java.util.ArrayList	Tree2Tree.getCorrRange(Tree source, TreeNode n, Tree other, int el)
(package private) Tree2Tree.NodeScorePair	Tree2Tree.computeBestMatch(TreeNode an, Tree t, java.lang.Object[] tmpData) compute the best corresponding node for each node node B is the best corresponding node of node A if it maximizes | L(A) U L(B)| ---------------- | L(A) n L(B)| where L(A),L(B) represent the set of leaves underneath the node A and node B respectively.
(package private) Tree2Tree.NodeScorePair	Tree2Tree.computeBestMatch(TreeNode an, Tree t, float alpha, java.lang.Object[] tmpData)
private void	AccordionTreeDrawerFinal.newMouseOver(TreeNode originalNode, TreeNode newNode)
private void	AccordionTreeDrawerFinal.newMouseOver(TreeNode originalNode, TreeNode newNode)
private boolean	AccordionTreeDrawerFinal.inHorizRange(TreeNode a, TreeNode b)
private boolean	AccordionTreeDrawerFinal.inHorizRange(TreeNode a, TreeNode b)
private int	AccordionTreeDrawerFinal.findChildNumber(TreeNode parentNode, TreeNode originalNode)
private int	AccordionTreeDrawerFinal.findChildNumber(TreeNode parentNode, TreeNode originalNode)
private TreeNode	AccordionTreeDrawerFinal.rightAlignFind(TreeNode parentNode, TreeNode originalNode, int originalNodeChildNumber, boolean goingDown)
private TreeNode	AccordionTreeDrawerFinal.rightAlignFind(TreeNode parentNode, TreeNode originalNode, int originalNodeChildNumber, boolean goingDown)

Constructors in TreeJuxtaposer with parameters of type TreeNode

Tree2Tree.NodeScorePair(TreeNode n, float s)