Uses of Class
net.sourceforge.olduvai.treejuxtaposer.drawer.TreeNode

Packages that use TreeNode
net.sourceforge.olduvai.treejuxtaposer   
net.sourceforge.olduvai.treejuxtaposer.drawer   
 

Uses of TreeNode in net.sourceforge.olduvai.treejuxtaposer
 

Fields in net.sourceforge.olduvai.treejuxtaposer declared as TreeNode
private  TreeNode AccordionTreeDrawerFinal.mouseOverNode
          The current 'focus' object under the cursor, a TreeNode.
private  TreeNode Tree2Tree.NodeScorePair.node
          Tree node reference.
private  TreeNode AccordionTreeDrawerFinal.pickedNode
          The currently picked node (flash drawing).
private  TreeNode AccordionTreeDrawerFinal.pickedNodeOld
          The previously picked node (flash drawing).
private  TreeNode TreeWriter.renameNode
          Node that is being renamed.
private  TreeNode TreeParser.rootNode
          Root node of the tree being parsed.
private  TreeNode Tree2Tree.TmpD.tmpParent
           
private  TreeNode Tree2Tree.TmpD.tmpPosorderNext
           
 

Methods in net.sourceforge.olduvai.treejuxtaposer that return TreeNode
 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.
protected  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 TreeParser.popAndName(java.lang.String name, java.util.Stack nodeStack)
          Adds node at the top of the stack to the tree.
private  TreeNode AccordionTreeDrawerFinal.rightAlignFind(TreeNode parentNode, TreeNode originalNode, int originalNodeChildNumber, boolean goingDown)
          Find the right aligned cell that is below (above) the original node, using the parent node as reference.
 

Methods in net.sourceforge.olduvai.treejuxtaposer with parameters of type TreeNode
private  void Tree2Tree.addNodeToForest(TreeNode node, java.util.ArrayList array, java.util.Hashtable hash)
          Adds the node to the hashtable, indexed by its key (as an Integer).
private  void TreeJuxtaposer.ascendTreeMark(AccordionTreeDrawer atd, AccordionTreeDrawer currTree, TreeNode n, RangeList addToGroup)
          Ascend from the given node and add nodes to the marking group if the BCN of ancestors have been marked before.
private  Tree2Tree.NodeScorePair Tree2Tree.computeBestMatch(TreeNode sourceNode, Tree sourceTree, Tree targetTree, float edgeCoefficient, Tree2Tree.TmpD[] tmpData)
          Compute the best match for sourceNode from sourceTree in the targetTree.
private  void TreeJuxtaposer.descendTreeMark(AccordionTreeDrawer atd, AccordionTreeDrawer currTree, TreeNode n, RangeList addToGroup)
          Recursively descend subtree and mark descendants, including BCN for each node marked in each drawer.
protected  void TreeJuxtaposer.doSelectGeom(TreeNode g, boolean selectSubtree, int group, AccordionTreeDrawer thisTree)
          Wrapper for adding nodes to a group when user selects a subtree or node for user-directed marking.
private  int AccordionTreeDrawerFinal.findChildNumber(TreeNode parentNode, TreeNode originalNode)
          Find the child index of the originalNode as a child of the parent node
 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.
protected  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.
 float TreePairs.getBestCorrNodeScore(Tree source, TreeNode n, Tree other, int edgeweightLevel)
          Retrieves the matching score for the node in Tree "other" whose set of descendant leaves best matches that of TreeNode n in Tree "source".
protected  float Tree2Tree.getBestCorrNodeScore(Tree source, TreeNode n, Tree other, int el)
          Identify input trees as Tree2Tree.treeA or Tree2Tree.treeB and look up the best score from the BCN of the input node from A to tree B.
 java.util.ArrayList TreePairs.getBestNodeList(Tree source, TreeNode n, Tree other, int edgeweightLevel)
          Get the list of nodes for the given node that will be highlighted if the node is selected.
private  Tree2Tree.NodeScorePair Tree2Tree.getBestNodeScorePair(TreeNode sourceNode, Tree sourceTree, Tree targetTree, Tree2Tree.TmpD[] tmpData)
          Find the best corresponding node for a given node sourceNode:sourceTree, in the target tree targetTree.
protected  java.util.ArrayList Tree2Tree.getCorrRange(Tree source, TreeNode n, Tree other, int el)
          Identify input trees as Tree2Tree.treeA or Tree2Tree.treeB and look up the best matching nodes of the input node from A in tree B.
private  void AccordionTreeDrawerFinal.newMouseOver(TreeNode originalNode, TreeNode newNode)
          Called by any of the arrow action functions, to update the drawer with a flash draw.
private static void TreeWriter.nodeWriter(TreeNode currNode, java.io.BufferedWriter writer)
          Write a single node to the writer object, after calling the subtree writer on each child.
private  void Tree2Tree.removeNodeFromForest(TreeNode node, java.util.ArrayList array, java.util.Hashtable hash)
          Removes the node from the hashtable, indexed by its key (as an Integer).
 void TreeJuxtaposer.resizeRectOthers(TreeNode tn, double[] changeRatio, int numAnimSteps, AccordionTreeDrawer thisatd)
          Linked navigation function to iterate changes over all drawers.
private  TreeNode AccordionTreeDrawerFinal.rightAlignFind(TreeNode parentNode, TreeNode originalNode, int originalNodeChildNumber, boolean goingDown)
          Find the right aligned cell that is below (above) the original node, using the parent node as reference.
private static void TreeWriter.subtreeWriter(TreeNode subtreeRoot, java.io.BufferedWriter writer)
          Wrap a series of nodes in brackets, then call the node writer on each child of the input subtree root.
 

Constructors in net.sourceforge.olduvai.treejuxtaposer with parameters of type TreeNode
Tree2Tree.NodeScorePair(TreeNode n, float s)
          Constructor for node+score pair.
TreeWriter(TreeNode renameNode, TreeJuxtaposer tj)
          Start a tree writer dialog that allows a user to enter a new name for a node.
 

Uses of TreeNode in net.sourceforge.olduvai.treejuxtaposer.drawer
 

Fields in net.sourceforge.olduvai.treejuxtaposer.drawer declared as TreeNode
 TreeNode TreeNode.leftmostLeaf
          Leftmost (minimum) leaf node under this internal node (or this node for leaves).
 TreeNode TreeNode.parent
          The parent of this node.
 TreeNode TreeNode.posorderNext
          The next postorder node.
 TreeNode TreeNode.preorderNext
          The next preorder node.
 TreeNode TreeNode.rightmostLeaf
          Rightmost (maximum) leaf node under this internal node (or this node for leaves).
protected  TreeNode Tree.root
          Root node of this tree
protected  TreeNode AccordionTreeDrawer.rootNode
          Root of the AccordionTreeDrawer.tree.
 

Methods in net.sourceforge.olduvai.treejuxtaposer.drawer that return TreeNode
protected  TreeNode TreeNode.firstChild()
          Get the first child of this node.
 TreeNode TreeNode.getChild(int i)
          Get a given child for this node, with range checking and casting.
 TreeNode Tree.getLeaf(int index)
          Get the leaf associated with the given leaf index.
 TreeNode AccordionTreeDrawer.getLeaf(int leafNum)
          Get the leaf indexed by the input value.
 TreeNode Tree.getLeftmostLeaf()
          Left most leaf accessor.
private  TreeNode[] AccordionTreeDrawer.getLeftMostNodes(TreeNode minChild, TreeNode maxChild)
          Get the "left most nodes".
 TreeNode Tree.getNodeByKey(int key)
          Returns the node indexed by the given key.
 TreeNode AccordionTreeDrawer.getNodeByKey(int key)
          Node access by node key.
 TreeNode Tree.getNodeByName(java.lang.String s)
          Returns the node given by the string.
 TreeNode AccordionTreeDrawer.getNodeByName(java.lang.String name)
          Node access by node name.
 TreeNode Tree.getRoot()
          Root accessor.
 TreeNode TreeNode.lastChild()
          Get the last child of this node.
 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 TreeNode.parent()
          Get the parent for this node.
 TreeNode TreeNode.pickDescend(double x, double y, double xFuzz, double yFuzz)
          Non-recursion method used to descend the tree structure, finding the node close enough to the given cursor position.
 

Methods in net.sourceforge.olduvai.treejuxtaposer.drawer with parameters of type TreeNode
 void TreeNode.addChild(TreeNode n)
          Add a child to the end of the list of children.
 boolean TreeNode.equals(TreeNode n)
          Tests nodes for equality, based on the name of the node.
 java.util.LinkedList Tree.getLeaves(TreeNode node)
          Get the leaves under this node.
private  TreeNode[] AccordionTreeDrawer.getLeftMostNodes(TreeNode minChild, TreeNode maxChild)
          Get the "left most nodes".
 boolean TreeNode.isAncestorOf(TreeNode that)
          Test function for determining if one node is an ancestor of another.
 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
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.
 void Tree.setRootNode(TreeNode newRoot)