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Packages that use TreeNode | |
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net.sourceforge.olduvai.treejuxtaposer | |
net.sourceforge.olduvai.treejuxtaposer.drawer |
Uses of TreeNode in net.sourceforge.olduvai.treejuxtaposer |
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Fields in net.sourceforge.olduvai.treejuxtaposer declared as TreeNode | |
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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
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private TreeNode |
Tree2Tree.TmpD.tmpPosorderNext
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Methods in net.sourceforge.olduvai.treejuxtaposer that return TreeNode | |
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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 | |
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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 | |
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Tree2Tree.NodeScorePair(TreeNode n,
float s)
Constructor for node+score pair. |
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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 |
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Fields in net.sourceforge.olduvai.treejuxtaposer.drawer declared as TreeNode | |
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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 | |
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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 | |
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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)
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