Uses of Class
AccordionTreeDrawer.Tree

Packages that use Tree

AccordionTreeDrawer
Parser
TreeJuxtaposer

Uses of Tree in AccordionTreeDrawer

Fields in AccordionTreeDrawer declared as Tree

Tree	AccordionTreeDrawer.tree

Methods in AccordionTreeDrawer that return Tree

Tree	AccordionTreeDrawer.getTree()

Methods in AccordionTreeDrawer with parameters of type Tree

int	AccordionTreeDrawer.computeBottomSizeOne(Tree tree) We now create a certain number of empty (NOT null) cells between adjacent leaves for better separation of subtrees.
void	AccordionTreeDrawer.resizeForest(Tree inTree, java.util.ArrayList _forestRoots, boolean grow, int numSteps, boolean horizontal, boolean vertical) Resize (grow=true ==> expand, shrink otherwise) the subtree rooted at node contained in Geoms.
void	AccordionTreeDrawer.resizeSubtree(Tree thisTree, TreeNode tn, boolean grow, int numSteps, boolean horizontal, boolean vertical)

Constructors in AccordionTreeDrawer with parameters of type Tree

Tree(Tree t)

AccordionTreeDrawer(Tree t, int w, int h)

Uses of Tree in Parser

Fields in Parser declared as Tree

private static Tree

Newick.tree the tree to be generated from this parser

Methods in Parser with parameters of type Tree

void	Newick.parseTree(Tree t) function parseTree initiates field tree, call function Input to parse the input.

Uses of Tree in TreeJuxtaposer

Fields in TreeJuxtaposer declared as Tree

(package private) Tree	Tree2Tree.treeA
(package private) Tree	Tree2Tree.treeB

Methods in TreeJuxtaposer that return Tree

Tree	TreeJuxtaposer.getTreeByName(java.lang.String name) Fetch a tree by its name.

Methods in TreeJuxtaposer with parameters of type Tree

(package private) void	TreePairs.addTree(Tree newTree, int eL) Add a new tree Create the data structure between the tree and all the previously added trees.
(package private) Tree2Tree	TreePairs.getPair(Tree t1, Tree t2)
(package private) Tree2Tree	TreePairs.getPair(Tree t1, Tree t2)
(package private) void	TreePairs.removeTree(Tree deletedTree) remove a tree and the relevant tree pairs
(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	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) 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.
(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.
(package private) float	TreePairs.computeDistance(Tree source, Tree other, float a, int m) Computes the dissimilarity distance between source and other The distance is computed by summing up getBestCorrNode scores between each tree node in source and the best matching node in other
(package private) float	TreePairs.computeDistance(Tree source, Tree other, float a, int m) Computes the dissimilarity distance between source and other The distance is computed by summing up getBestCorrNode scores between each tree node in source and the best matching node in other
int	TreePairs.isRangeInRange(Tree treeA, int AMin, int AMax, Tree treeB, int BMin, int BMax) given a node range in one tree, say whether there's an overlap with the node range in the other tree.
int	TreePairs.isRangeInRange(Tree treeA, int AMin, int AMax, Tree treeB, int BMin, int BMax) given a node range in one tree, say whether there's an overlap with the node range in the other tree.
void	TreeJuxtaposer.addTree(Tree newTree) Adds a new tree to "trees", performs all the pairwise tree comparisons and stores results.
private AccordionTreeDrawerFinal	TreeJuxtaposer.addATD(Tree newTree, int width, int height) Utility function to make new AccordionTreeDrawer, set initial parameters and do treeDrawer list bookkeeping.
private void	Tree2Tree.computeForest(java.util.Hashtable X2Y, Tree treeX, Tree treeY, AccordionTreeDrawer atdY, int cutoff)
private void	Tree2Tree.computeForest(java.util.Hashtable X2Y, Tree treeX, Tree treeY, AccordionTreeDrawer atdY, int cutoff)
(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) 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) 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) java.util.ArrayList	Tree2Tree.getCorrRange(Tree source, TreeNode n, Tree other, int el)
(package private) int	Tree2Tree.isRangeInRange(Tree source, int AMin, int AMax, Tree other, int BMin, int BMax) Given a node range in one tree, say whether there's an overlap with the node range in the other tree.
(package private) int	Tree2Tree.isRangeInRange(Tree source, int AMin, int AMax, Tree other, int BMin, int BMax) Given a node range in one tree, say whether there's an overlap with the node range in the other tree.
(package private) void	Tree2Tree.computeBestMatch(Tree t1, Tree t2, java.util.Vector v12, int eL) For each node om Tree t1, computes the best matching node in Tree t2 and stores it in HashMap h12
(package private) void	Tree2Tree.computeBestMatch(Tree t1, Tree t2, java.util.Vector v12, int eL) For each node om Tree t1, computes the best matching node in Tree t2 and stores it in HashMap h12
(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)

Constructors in TreeJuxtaposer with parameters of type Tree

Tree2Tree(Tree t1, Tree t2, int eL)

Tree2Tree(Tree t1, Tree t2, int eL)

RangeTree(Tree treeA, Tree treeB, Tree2Tree t2t)
constructor: builds a 2D RangeTree data structure.

RangeTree(Tree treeA, Tree treeB, Tree2Tree t2t)
constructor: builds a 2D RangeTree data structure.

AccordionTreeDrawerFinal(Tree t, int w, int h, TreeJuxtaposer thetj)