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Packages that use Tree | |
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net.sourceforge.olduvai.treejuxtaposer | |
net.sourceforge.olduvai.treejuxtaposer.drawer |
Uses of Tree in net.sourceforge.olduvai.treejuxtaposer |
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Fields in net.sourceforge.olduvai.treejuxtaposer declared as Tree | |
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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 | |
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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 | |
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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 | |
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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. |
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Tree2Tree(Tree t1,
Tree t2,
int edgeweightLevels)
Initialize the two vectors |
Uses of Tree in net.sourceforge.olduvai.treejuxtaposer.drawer |
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Fields in net.sourceforge.olduvai.treejuxtaposer.drawer declared as Tree | |
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Tree |
AccordionTreeDrawer.tree
Tree that is drawn in this drawer's canvas. |
Methods in net.sourceforge.olduvai.treejuxtaposer.drawer that return Tree | |
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Tree |
AccordionTreeDrawer.getTree()
Get the tree that this drawer represents. |
Methods in net.sourceforge.olduvai.treejuxtaposer.drawer with parameters of type Tree | |
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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 | |
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AccordionTreeDrawer(Tree t,
int w,
int h,
javax.swing.JProgressBar jpb)
Class constructor for new tree drawers. |
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Tree(Tree treeToCopy)
Copy constructor used to create versions of trees that are identical to the supplied input tree. |
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