Uses of Interface
jebl.evolution.trees.Tree

Packages that use Tree
jebl.evolution.align Provides classes and interfaces for pairwise alignment of two sequences. 
jebl.evolution.io   
jebl.evolution.parsimony   
jebl.evolution.trees   
 

Uses of Tree in jebl.evolution.align
 

Fields in jebl.evolution.align declared as Tree
 Tree AlignmentTreeBuilderFactory.Result.tree
           
 

Uses of Tree in jebl.evolution.io
 

Methods in jebl.evolution.io that return Tree
 Tree NexusImporter.importNextTree()
          If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks in the process if necessary.
 Tree TreeImporter.importNextTree()
          Import a single tree
 Tree NewickImporter.importNextTree()
           
 

Methods in jebl.evolution.io that return types with arguments of type Tree
 java.util.List<Tree> NexusImporter.importTrees()
          Import all trees in the file from the current position.
 java.util.List<Tree> TreeImporter.importTrees()
          Import all the trees
 java.util.List<Tree> NewickImporter.importTrees()
           
 java.util.Iterator<Tree> NexusImporter.iterator()
           
 java.util.Iterator<Tree> NewickImporter.iterator()
          Returns an iterator over a set of elements of type T.
 java.util.List<Tree> NexusImporter.parseTreesBlock(java.util.List<Taxon> taxonList)
          Parse the next 'TREES' block encountered in the input.
 

Methods in jebl.evolution.io with parameters of type Tree
 void NewickExporter.exportTree(Tree tree)
          Export a single tree
 void NexusExporter.exportTree(Tree tree)
          Export a single tree
 void PHYLIPExporter.exportTree(Tree tree)
           
 void TreeExporter.exportTree(Tree tree)
          Export a single tree
 

Method parameters in jebl.evolution.io with type arguments of type Tree
 void NewickExporter.exportTrees(java.util.Collection<? extends Tree> trees)
          Export a collection of trees
 void NexusExporter.exportTrees(java.util.Collection<? extends Tree> trees)
           
 void PHYLIPExporter.exportTrees(java.util.Collection<? extends Tree> trees)
           
 void TreeExporter.exportTrees(java.util.Collection<? extends Tree> trees)
          Export a collection of trees
 void NexusExporter.exportTreesWithTranslation(java.util.Collection<? extends Tree> trees, java.util.Map<java.lang.String,java.lang.String> t)
           
 

Uses of Tree in jebl.evolution.parsimony
 

Methods in jebl.evolution.parsimony with parameters of type Tree
 double FitchParsimony.getScore(Tree tree)
           
 double ParsimonyCriterion.getScore(Tree tree)
          Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
 double[] FitchParsimony.getSiteScores(Tree tree)
          Calculates the minimum number of siteScores for the parsimony reconstruction of a a set of character patterns on a tree.
 double[] ParsimonyCriterion.getSiteScores(Tree tree)
          Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
 State[] FitchParsimony.getStates(Tree tree, Node node)
          Returns the reconstructed character states for a given node in the tree.
 State[] ParsimonyCriterion.getStates(Tree tree, Node node)
          Returns the reconstructed character states for a given node in the tree.
 

Uses of Tree in jebl.evolution.trees
 

Classes in jebl.evolution.trees with type parameters of type Tree
 class ClusteringTreeBuilder<T extends Tree>
          An abstract base class for clustering algorithms from pairwise distances
 class ConsensusTreeBuilder<T extends Tree>
          A TreeBuilder that builds a consensus tree for a set of trees on identical leaf sets.
 interface TreeBuilder<T extends Tree>
           
 

Subinterfaces of Tree in jebl.evolution.trees
 interface RootedTree
          A tree with a root (node with maximum height).
 

Classes in jebl.evolution.trees that implement Tree
 class CompactRootedTree
          A memory efficient rooted tree.
 class FilteredRootedTree
           
 class MutableRootedTree
          A simple rooted tree providing some ability to manipulate the tree.
 class ReRootedTree
           
 class RootedFromUnrooted
          Root an unrooted tree.
 class RootedSubtree
          A simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..
 class SimpleRootedTree
          A simple, and initially immutable rooted tree implementation.
 class SimpleTree
          A basic implementation on an unrooted tree.
 class SortedRootedTree
           
 class TransformedRootedTree
          This RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.
 

Methods in jebl.evolution.trees that return Tree
 Tree TreeChangeEvent.getTree()
           
 

Methods in jebl.evolution.trees that return types with arguments of type Tree
 java.util.List<Tree> MostProbableTopology.get(int max, double threshold)
          Get the most probable tree(s)
 

Methods in jebl.evolution.trees with parameters of type Tree
static java.lang.String Utils.asText(Tree tree)
           
static java.lang.String[] Utils.asText(Tree tree, int widthGuide)
           
static ConsensusTreeBuilder TreeBuilderFactory.buildRooted(Tree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
          convenience method.
static ConsensusTreeBuilder TreeBuilderFactory.buildUnRooted(Tree[] trees, Taxon outGroup, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
           
 Node SimpleRootedTree.createNodes(Tree tree, Node parent, Node child)
          Clones the entire tree structure from the given (unrooted) Tree.
static double Utils.getPathLength(Tree tree, Node node1, Node node2)
           
static void SplitUtils.getSplit(java.util.List<Taxon> taxa, Tree tree, Edge edge, boolean[] split)
          get split for branch associated with internal node
static SplitSystem SplitUtils.getSplits(java.util.List<Taxon> taxa, Tree tree)
          creates a split system from a tree (using a pre-specified order of sequences)
static SplitSystem SplitUtils.getSplits(Tree tree)
          creates a split system from a tree (using tree-induced order of sequences)
static RootedTree Utils.rootTheTree(Tree tree)
          Return a rooted tree from any tree.
static RootedTree Utils.rootTreeAtCenter(Tree tree)
          Root any tree by locating the "center" of tree and adding a new root node at that point

for any point on the tree x let D(x) = Max{distance between x and t : for all tips t} The "center" c is the point with the smallest distance, i.e.

 

Method parameters in jebl.evolution.trees with type arguments of type Tree
static void Utils.assertAllTreesHaveTheSameTaxa(java.util.List<? extends Tree> trees)
          Checks whether all of the trees passed in have the same taxa sets (ignoring order of taxa), and throws an IllegalArgumentException if this is not the case.
 

Constructors in jebl.evolution.trees with parameters of type Tree
MutableRootedTree(Tree tree, Node outGroup)
          Construct a rooted tree from unrooted.
RootedFromUnrooted(Tree source, Node root, boolean intentUnrooted)
          Root tree at some internal node.
RootedFromUnrooted(Tree source, Node left, Node right, double fromLeft)
          Root source by creating a new internal node whose children are (the adjacent) left and right.
SimpleRootedTree(Tree tree, Node ingroupNode, Node outgroupNode, double ingroupBranchLength)
          Make a copy of the given unrooted tree
SimpleTree(Tree tree)
          Duplicate a tree.
TreeChangeEvent(Tree tree)
           
 

Constructor parameters in jebl.evolution.trees with type arguments of type Tree
MostProbableTopology(java.util.Collection<? extends Tree> trees)
           
 



http://code.google.com/p/jebl2/