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

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

Uses of Tree in net.sourceforge.olduvai.treejuxtaposer
 

Fields in net.sourceforge.olduvai.treejuxtaposer declared as Tree
private  Tree Tree2Tree.treeA
          Arbitrary tree A for this comparison.
private  Tree Tree2Tree.treeB
          Arbitrary tree B for this comparison.
 

Methods in net.sourceforge.olduvai.treejuxtaposer that return Tree
 Tree TreeJuxtaposer.getTreeByName(java.lang.String name)
          Fetch a tree by its name.
 Tree TreeParser.tokenize(long fileLength, java.lang.String streamName, javax.swing.JProgressBar progressBar)
          Newick tokenizer: converts a string (tree as a string) into a tree object.
 

Methods in net.sourceforge.olduvai.treejuxtaposer with parameters of type Tree
private  AccordionTreeDrawerFinal TreeJuxtaposer.addATD(Tree newTree, int width, int height, javax.swing.JProgressBar jpb)
          Utility function to make new AccordionTreeDrawer, set initial parameters and do treeDrawer list bookkeeping.
 void TreePairs.addTree(Tree newTree, int edgeweightLevels, boolean pruneNewLeaves)
          Add a new tree.
 void TreeJuxtaposer.addTree(Tree newTree, javax.swing.JProgressBar jpb)
          Adds a new tree to "trees", performs all the pairwise tree comparisons and stores results.
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 Tree2Tree.computeForest(java.util.Hashtable X2Y, Tree treeX, Tree treeY, AccordionTreeDrawer atdY, int cutoff)
          Compute the forest of marked nodes in treeY, for subtrees under every node in treeX.
 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.
 Tree2Tree TreePairs.getPair(Tree t1, Tree t2)
          Get the Tree2Tree table for t1 and t2 differences.
private  void Tree2Tree.onewayTreeCompare(Tree t1, Tree t2, java.util.Vector v12, int edgeweightLevels)
          For each node on Tree t1, computes the best matching node in Tree t2 and stores it in Vector v12.
 void TreePairs.removeTree(Tree deletedTree)
          Remove a tree from the list of trees.
static void TreeWriter.writeTree(Tree t, java.lang.String fileName)
          Writes Tree to file by name of fileName.
 

Constructors in net.sourceforge.olduvai.treejuxtaposer with parameters of type Tree
AccordionTreeDrawerFinal(Tree t, int w, int h, TreeJuxtaposer thetj, javax.swing.JProgressBar jpb)
          Constructor for a drawer with defined key and mouse interaction methods, and bindings from the drawer to the TreeJuxtaposer application.
Tree2Tree(Tree t1, Tree t2, int edgeweightLevels)
          Initialize the two vectors
 

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

Fields in net.sourceforge.olduvai.treejuxtaposer.drawer declared as Tree
 Tree AccordionTreeDrawer.tree
          Tree that is drawn in this drawer's canvas.
 

Methods in net.sourceforge.olduvai.treejuxtaposer.drawer that return Tree
 Tree AccordionTreeDrawer.getTree()
          Get the tree that this drawer represents.
 

Methods in net.sourceforge.olduvai.treejuxtaposer.drawer with parameters of type Tree
 void TreeNode.drawDescend(int frameNum, float plane, int min, int max, Tree tree)
          Descend from this node and draw children down to leaves.
 

Constructors in net.sourceforge.olduvai.treejuxtaposer.drawer with parameters of type Tree
AccordionTreeDrawer(Tree t, int w, int h, javax.swing.JProgressBar jpb)
          Class constructor for new tree drawers.
Tree(Tree treeToCopy)
          Copy constructor used to create versions of trees that are identical to the supplied input tree.