Uses of Interface
jebl.evolution.trees.RootedTree

Packages that use RootedTree
jebl.evolution.align Provides classes and interfaces for pairwise alignment of two sequences. 
jebl.evolution.coalescent   
jebl.evolution.treemetrics   
jebl.evolution.trees   
jebl.evolution.treesimulation   
 

Uses of RootedTree in jebl.evolution.align
 

Methods in jebl.evolution.align with parameters of type RootedTree
 Alignment BartonSternberg.doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
           
 Alignment MultipleAligner.doAlign(java.util.List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)
           
 

Uses of RootedTree in jebl.evolution.coalescent
 

Constructors in jebl.evolution.coalescent with parameters of type RootedTree
Coalescent(RootedTree tree, DemographicFunction demographicFunction)
           
Intervals(RootedTree tree)
           
 

Uses of RootedTree in jebl.evolution.treemetrics
 

Methods in jebl.evolution.treemetrics with parameters of type RootedTree
 double CladeHeightMetric.getMetric(RootedTree tree1, RootedTree tree2)
           
 double RootedTreeMetric.getMetric(RootedTree tree1, RootedTree tree2)
          calculates the metric between two rooted trees
 double RobinsonsFouldMetric.getMetric(RootedTree tree1, RootedTree tree2)
           
 double BilleraMetric.getMetric(RootedTree tree1, RootedTree tree2)
           
 

Uses of RootedTree in jebl.evolution.trees
 

Classes in jebl.evolution.trees that implement RootedTree
 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 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 RootedTree
static RootedTree Utils.copyTree(RootedTree treeToCopy)
          This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.
 RootedTree FilteredRootedTree.getSource()
           
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.

 

Methods in jebl.evolution.trees with parameters of type RootedTree
 void CladeSystem.add(RootedTree tree)
          adds all the clades in the tree
 void CalculateSplitRates.addTreeToDensityMap(jebl.evolution.trees.CalculateSplitRates.DensityMap densityMap, RootedTree tree)
           
static ConsensusTreeBuilder TreeBuilderFactory.buildRooted(RootedTree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)
           
static RootedTree Utils.copyTree(RootedTree treeToCopy)
          This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.
static java.util.Comparator<Node> Utils.createNodeDensityComparator(RootedTree tree)
           
static java.util.Comparator<Node> Utils.createNodeDensityMinNodeHeightComparator(RootedTree tree)
           
 Node SimpleRootedTree.createNodes(RootedTree tree, Node node)
          Clones the entire tree structure from the given RootedTree.
static java.lang.String Utils.DEBUGsubTreeRep(RootedTree tree, Node node)
           
static boolean RootedTreeUtils.equal(RootedTree tree1, RootedTree tree2)
          Compares 2 trees and returns true if they have the same topology.
static Node RootedTreeUtils.getCommonAncestorNode(RootedTree tree, java.util.Set<Node> tipNodes)
          Gets the most recent common ancestor (MRCA) node of a set of tip nodes.
static java.util.Set<Node> RootedTreeUtils.getDescendantTips(RootedTree tree, Node node)
          Gets a set of tip nodes descended from the given node.
static int Utils.getExternalNodeCount(RootedTree tree, Node node)
          Return the number of external nodes under this node.
static double RootedTreeUtils.getMaxTipHeight(RootedTree tree, Node node)
           
static double Utils.getMinNodeHeight(RootedTree tree, Node node)
           
static double RootedTreeUtils.getMinTipHeight(RootedTree tree, Node node)
           
static java.util.List<Node> Utils.getNodes(RootedTree tree, Node node)
          All nodes in subtree - parents before children (pre - order).
static int RootedTreeUtils.getTipCount(RootedTree tree, Node node)
          Return the number of leaves under this node.
static java.util.Set<Node> RootedTreeUtils.getTipsForTaxa(RootedTree tree, java.util.Collection<Taxon> taxa)
          Gets a set of external nodes that correspond to the given taxa.
static boolean Utils.isBinary(RootedTree rootedTree)
           
static boolean RootedTreeUtils.isBinary(RootedTree tree)
           
static boolean RootedTreeUtils.isMonophyletic(RootedTree tree, java.util.Set<Node> tipNodes)
          Performs the a monophyly test on a set of tip nodes.
static boolean Utils.isUltrametric(RootedTree rootedTree)
           
static boolean RootedTreeUtils.isUltrametric(RootedTree tree, double tolerance)
           
static Node Utils.leftNb(RootedTree tree, Node node)
          Left Neighbour of a tip (taxon).
static int Utils.maxLevels(RootedTree tree)
           
static Node Utils.rightNb(RootedTree tree, Node tipNode)
          Right Neighbour of a tip (taxon).
static double Utils.safeNodeHeight(RootedTree tree, Node node)
           
static java.lang.String Utils.toNewick(RootedTree tree)
           
static java.lang.String Utils.toUniqueNewick(RootedTree tree)
          Constructs a unique newick representation of a tree
static java.lang.String Utils.toUniqueNewickByAttribute(RootedTree tree, java.lang.String attribute)
          Constructs a unique newick representation of a tree print only an attribute
static java.lang.String RootedTreeUtils.uniqueNewick(RootedTree tree, Node node)
          Recursive function for constructing a newick tree representation in the given buffer.
 

Constructors in jebl.evolution.trees with parameters of type RootedTree
AttributedCladeSystem(java.lang.String name, RootedTree tree)
           
CladeSystem(RootedTree tree)
           
CompactRootedTree(RootedTree t)
          Do all the hard work.
FilteredRootedTree(RootedTree source)
           
ReRootedTree(RootedTree source, ReRootedTree.RootingType rootingType)
           
RootedSubtree(RootedTree tree, java.util.Set<Taxon> includedTaxa)
          Make a copy of the given rooted tree
SimpleRootedTree(RootedTree tree)
          Make a copy of the given rooted tree
SimpleRootedTree(RootedTree tree, java.util.Map<Node,Node> nodeMapping)
          Make a copy of the given rooted tree
SortedRootedTree(RootedTree source, java.util.Comparator<Node> comparator)
           
SortedRootedTree(RootedTree source, SortedRootedTree.BranchOrdering branchOrdering)
           
TransformedRootedTree(RootedTree source, TransformedRootedTree.Transform transform)
           
TreeBiPartitionInfo(RootedTree t, java.util.List<Taxon> taxa)
           
 

Uses of RootedTree in jebl.evolution.treesimulation
 

Methods in jebl.evolution.treesimulation that return RootedTree
 RootedTree TreeSimulator.simulate(IntervalGenerator intervalGenerator)
           
 RootedTree TreeSimulator.simulate(IntervalGenerator intervalGenerator, boolean medianHeights)
           
 



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