Uses of Interface
jebl.evolution.graphs.Node

Packages that use Node
jebl.evolution.graphs   
jebl.evolution.parsimony   
jebl.evolution.trees   
 

Uses of Node in jebl.evolution.graphs
 

Methods in jebl.evolution.graphs that return Node
 Node[] Graph.getNodes(Edge edge)
          Returns an array of 2 nodes which are the nodes at either end of the edge.
 

Methods in jebl.evolution.graphs that return types with arguments of type Node
 java.util.List<Node> Graph.getAdjacencies(Node node)
          Returns a list of nodes connected to this node by an edge
 java.util.Set<Node> Graph.getNodes()
           
 java.util.Set<Node> Graph.getNodes(int degree)
           
 

Methods in jebl.evolution.graphs with parameters of type Node
 java.util.List<Node> Graph.getAdjacencies(Node node)
          Returns a list of nodes connected to this node by an edge
static int Graph.Utils.getDegree(Graph graph, Node node)
           
 Edge Graph.getEdge(Node node1, Node node2)
          Returns the Edge that connects these two nodes
 double Graph.getEdgeLength(Node node1, Node node2)
          Returns the length of the edge that connects these two nodes
 java.util.List<Edge> Graph.getEdges(Node node)
          Returns a list of edges connected to this node
 

Uses of Node in jebl.evolution.parsimony
 

Methods in jebl.evolution.parsimony with parameters of type Node
 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 Node in jebl.evolution.trees
 

Classes in jebl.evolution.trees that implement Node
 class BaseNode
          Common implementation of Attributable interface used by Nodes.
 

Methods in jebl.evolution.trees that return Node
 Node SimpleRootedTree.addNode(Edge edge)
          Adds a new node at the midpoint of the given edge
 Node SimpleRootedTree.addNode(Node node)
          Adds a new node at the midpoint of the edge connecting the given node to its parent.
 Node MutableRootedTree.createExternalNode(Taxon taxon)
          Creates a new external node with the given taxon.
 Node SimpleTree.createExternalNode(Taxon taxon)
          Creates a new external node with the given taxon.
 Node SimpleRootedTree.createExternalNode(Taxon taxon)
          Creates a new external node with the given taxon.
 Node SimpleTree.createInternalNode(java.util.List<Node> adjacencies)
          Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
 Node SimpleRootedTree.createNodes(RootedTree tree, Node node)
          Clones the entire tree structure from the given RootedTree.
 Node SimpleRootedTree.createNodes(Tree tree, Node parent, Node child)
          Clones the entire tree structure from the given (unrooted) Tree.
 Node MutableRootedTree.detachChildren(Node node, java.util.List<java.lang.Integer> split)
           
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.
 Node MutableRootedTree.getNode(Taxon taxon)
           
 Node Tree.getNode(Taxon taxon)
           
 Node CompactRootedTree.getNode(Taxon taxon)
           
 Node RootedFromUnrooted.getNode(Taxon taxon)
           
 Node RootedSubtree.getNode(Taxon taxon)
           
 Node FilteredRootedTree.getNode(Taxon taxon)
           
 Node SimpleTree.getNode(Taxon taxon)
           
 Node SimpleRootedTree.getNode(Taxon taxon)
           
 Node[] MutableRootedTree.getNodes(Edge edge)
          Returns an array of 2 nodes which are the nodes at either end of the edge.
 Node[] CompactRootedTree.getNodes(Edge edge)
           
 Node[] RootedFromUnrooted.getNodes(Edge edge)
           
 Node[] RootedSubtree.getNodes(Edge edge)
          Returns an array of 2 nodes which are the nodes at either end of the edge.
 Node[] FilteredRootedTree.getNodes(Edge edge)
           
 Node[] SimpleTree.getNodes(Edge edge)
          Returns an array of 2 nodes which are the nodes at either end of the edge.
 Node[] SimpleRootedTree.getNodes(Edge edge)
          Returns an array of 2 nodes which are the nodes at either end of the edge.
 Node MutableRootedTree.getParent(Node node)
           
 Node CompactRootedTree.getParent(Node node)
           
 Node RootedFromUnrooted.getParent(Node node)
           
 Node RootedTree.getParent(Node node)
           
 Node RootedSubtree.getParent(Node node)
           
 Node FilteredRootedTree.getParent(Node node)
           
 Node SimpleRootedTree.getParent(Node node)
           
 Node MutableRootedTree.getRootNode()
          The root of the tree has the largest node height of all nodes in the tree.
 Node CompactRootedTree.getRootNode()
           
 Node RootedFromUnrooted.getRootNode()
           
 Node RootedTree.getRootNode()
          The root of the tree has the largest node height of all nodes in the tree.
 Node RootedSubtree.getRootNode()
          The root of the tree has the largest node height of all nodes in the tree.
 Node FilteredRootedTree.getRootNode()
           
 Node SimpleRootedTree.getRootNode()
          The root of the tree has the largest node height of all nodes in the tree.
static Node Utils.leftNb(RootedTree tree, Node node)
          Left Neighbour of a tip (taxon).
static Node Utils.rightNb(RootedTree tree, Node tipNode)
          Right Neighbour of a tip (taxon).
 

Methods in jebl.evolution.trees that return types with arguments of type Node
static java.util.Comparator<Node> Utils.createNodeDensityComparator(RootedTree tree)
           
static java.util.Comparator<Node> Utils.createNodeDensityMinNodeHeightComparator(RootedTree tree)
           
 java.util.List<Node> MutableRootedTree.getAdjacencies(Node node)
           
 java.util.List<Node> CompactRootedTree.getAdjacencies(Node node)
           
 java.util.List<Node> RootedFromUnrooted.getAdjacencies(Node node)
           
 java.util.List<Node> RootedSubtree.getAdjacencies(Node node)
           
 java.util.List<Node> FilteredRootedTree.getAdjacencies(Node node)
           
 java.util.List<Node> SimpleTree.getAdjacencies(Node node)
           
 java.util.List<Node> SimpleRootedTree.getAdjacencies(Node node)
           
 java.util.List<Node> SortedRootedTree.getChildren(Node node)
           
 java.util.List<Node> MutableRootedTree.getChildren(Node node)
           
 java.util.List<Node> CompactRootedTree.getChildren(Node node)
           
 java.util.List<Node> RootedFromUnrooted.getChildren(Node node)
           
 java.util.List<Node> RootedTree.getChildren(Node node)
           
 java.util.List<Node> RootedSubtree.getChildren(Node node)
           
 java.util.List<Node> FilteredRootedTree.getChildren(Node node)
           
 java.util.List<Node> SimpleRootedTree.getChildren(Node node)
           
static java.util.Set<Node> RootedTreeUtils.getDescendantTips(RootedTree tree, Node node)
          Gets a set of tip nodes descended from the given node.
 java.util.Set<Node> MutableRootedTree.getExternalNodes()
           
 java.util.Set<Node> Tree.getExternalNodes()
           
 java.util.Set<Node> CompactRootedTree.getExternalNodes()
           
 java.util.Set<Node> RootedFromUnrooted.getExternalNodes()
           
 java.util.Set<Node> RootedSubtree.getExternalNodes()
           
 java.util.Set<Node> FilteredRootedTree.getExternalNodes()
           
 java.util.Set<Node> SimpleTree.getExternalNodes()
           
 java.util.Set<Node> SimpleRootedTree.getExternalNodes()
           
 java.util.Set<Node> MutableRootedTree.getInternalNodes()
           
 java.util.Set<Node> Tree.getInternalNodes()
           
 java.util.Set<Node> CompactRootedTree.getInternalNodes()
           
 java.util.Set<Node> RootedFromUnrooted.getInternalNodes()
           
 java.util.Set<Node> RootedSubtree.getInternalNodes()
           
 java.util.Set<Node> FilteredRootedTree.getInternalNodes()
           
 java.util.Set<Node> SimpleTree.getInternalNodes()
           
 java.util.Set<Node> SimpleRootedTree.getInternalNodes()
           
 java.util.Set<Node> MutableRootedTree.getNodes()
           
 java.util.Set<Node> CompactRootedTree.getNodes()
           
 java.util.Set<Node> RootedFromUnrooted.getNodes()
           
 java.util.Set<Node> RootedSubtree.getNodes()
           
 java.util.Set<Node> FilteredRootedTree.getNodes()
           
 java.util.Set<Node> SimpleTree.getNodes()
           
 java.util.Set<Node> SimpleRootedTree.getNodes()
           
 java.util.Set<Node> MutableRootedTree.getNodes(int degree)
           
 java.util.Set<Node> CompactRootedTree.getNodes(int degree)
           
 java.util.Set<Node> RootedFromUnrooted.getNodes(int degree)
           
 java.util.Set<Node> RootedSubtree.getNodes(int degree)
           
 java.util.Set<Node> FilteredRootedTree.getNodes(int degree)
           
 java.util.Set<Node> SimpleTree.getNodes(int degree)
           
 java.util.Set<Node> SimpleRootedTree.getNodes(int degree)
           
static java.util.List<Node> Utils.getNodes(RootedTree tree, Node node)
          All nodes in subtree - parents before children (pre - order).
 java.util.Set<Node> TreeSelectionChangeEvent.getSelectedNodes()
           
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.
 

Methods in jebl.evolution.trees with parameters of type Node
 void SimpleTree.addEdge(Node node1, Node node2, double length)
          Add a new edge between two existing (non adjacent yet) nodes.
 Node SimpleRootedTree.addNode(Node node)
          Adds a new node at the midpoint of the edge connecting the given node to its parent.
 Node SimpleRootedTree.createNodes(RootedTree tree, Node node)
          Clones the entire tree structure from the given RootedTree.
 Node SimpleRootedTree.createNodes(Tree tree, Node parent, Node child)
          Clones the entire tree structure from the given (unrooted) Tree.
static java.lang.String Utils.DEBUGsubTreeRep(RootedTree tree, Node node)
           
 void SimpleRootedTree.deleteInternalNode(Node node)
          Removes an internal node in this tree.
 Node MutableRootedTree.detachChildren(Node node, java.util.List<java.lang.Integer> split)
           
 java.util.List<Node> MutableRootedTree.getAdjacencies(Node node)
           
 java.util.List<Node> CompactRootedTree.getAdjacencies(Node node)
           
 java.util.List<Node> RootedFromUnrooted.getAdjacencies(Node node)
           
 java.util.List<Node> RootedSubtree.getAdjacencies(Node node)
           
 java.util.List<Node> FilteredRootedTree.getAdjacencies(Node node)
           
 java.util.List<Node> SimpleTree.getAdjacencies(Node node)
           
 java.util.List<Node> SimpleRootedTree.getAdjacencies(Node node)
           
 java.util.List<Node> SortedRootedTree.getChildren(Node node)
           
 java.util.List<Node> MutableRootedTree.getChildren(Node node)
           
 java.util.List<Node> CompactRootedTree.getChildren(Node node)
           
 java.util.List<Node> RootedFromUnrooted.getChildren(Node node)
           
 java.util.List<Node> RootedTree.getChildren(Node node)
           
 java.util.List<Node> RootedSubtree.getChildren(Node node)
           
 java.util.List<Node> FilteredRootedTree.getChildren(Node node)
           
 java.util.List<Node> SimpleRootedTree.getChildren(Node node)
           
static java.util.Set<Node> RootedTreeUtils.getDescendantTips(RootedTree tree, Node node)
          Gets a set of tip nodes descended from the given node.
 Edge MutableRootedTree.getEdge(Node node1, Node node2)
          Returns the Edge that connects these two nodes
 Edge CompactRootedTree.getEdge(Node node1, Node node2)
           
 Edge RootedFromUnrooted.getEdge(Node node1, Node node2)
           
 Edge RootedSubtree.getEdge(Node node1, Node node2)
          Returns the Edge that connects these two nodes
 Edge FilteredRootedTree.getEdge(Node node1, Node node2)
           
 Edge SimpleTree.getEdge(Node node1, Node node2)
          Returns the Edge that connects these two nodes
 Edge SimpleRootedTree.getEdge(Node node1, Node node2)
          Returns the Edge that connects these two nodes
 double MutableRootedTree.getEdgeLength(Node node1, Node node2)
           
 double CompactRootedTree.getEdgeLength(Node node1, Node node2)
           
 double RootedFromUnrooted.getEdgeLength(Node node1, Node node2)
           
 double RootedSubtree.getEdgeLength(Node node1, Node node2)
           
 double FilteredRootedTree.getEdgeLength(Node node1, Node node2)
           
 double SimpleTree.getEdgeLength(Node node1, Node node2)
           
 double SimpleRootedTree.getEdgeLength(Node node1, Node node2)
           
 java.util.List<Edge> MutableRootedTree.getEdges(Node node)
          Returns a list of edges connected to this node
 java.util.List<Edge> CompactRootedTree.getEdges(Node node)
           
 java.util.List<Edge> RootedFromUnrooted.getEdges(Node node)
          Returns a list of edges connected to this node
 java.util.List<Edge> RootedSubtree.getEdges(Node node)
          Returns a list of edges connected to this node
 java.util.List<Edge> FilteredRootedTree.getEdges(Node node)
           
 java.util.List<Edge> SimpleTree.getEdges(Node node)
          Returns a list of edges connected to this node
 java.util.List<Edge> SimpleRootedTree.getEdges(Node node)
          Returns a list of edges connected to this node
static int Utils.getExternalNodeCount(RootedTree tree, Node node)
          Return the number of external nodes under this node.
 double MutableRootedTree.getHeight(Node node)
           
 double CompactRootedTree.getHeight(Node node)
           
 double RootedFromUnrooted.getHeight(Node node)
           
 double RootedTree.getHeight(Node node)
           
 double RootedSubtree.getHeight(Node node)
           
 double FilteredRootedTree.getHeight(Node node)
           
 double TransformedRootedTree.getHeight(Node node)
           
 double SimpleRootedTree.getHeight(Node node)
           
 double MutableRootedTree.getLength(Node node)
           
 double CompactRootedTree.getLength(Node node)
           
 double RootedFromUnrooted.getLength(Node node)
           
 double RootedTree.getLength(Node node)
           
 double RootedSubtree.getLength(Node node)
           
 double FilteredRootedTree.getLength(Node node)
           
 double TransformedRootedTree.getLength(Node node)
           
 double SimpleRootedTree.getLength(Node 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).
 Node MutableRootedTree.getParent(Node node)
           
 Node CompactRootedTree.getParent(Node node)
           
 Node RootedFromUnrooted.getParent(Node node)
           
 Node RootedTree.getParent(Node node)
           
 Node RootedSubtree.getParent(Node node)
           
 Node FilteredRootedTree.getParent(Node node)
           
 Node SimpleRootedTree.getParent(Node node)
           
 Edge MutableRootedTree.getParentEdge(Node node)
           
 Edge CompactRootedTree.getParentEdge(Node node)
           
 Edge RootedSubtree.getParentEdge(Node node)
           
 Edge SimpleRootedTree.getParentEdge(Node node)
           
static double Utils.getPathLength(Tree tree, Node node1, Node node2)
           
 Taxon MutableRootedTree.getTaxon(Node node)
           
 Taxon Tree.getTaxon(Node node)
           
 Taxon CompactRootedTree.getTaxon(Node node)
           
 Taxon RootedFromUnrooted.getTaxon(Node node)
           
 Taxon RootedSubtree.getTaxon(Node node)
           
 Taxon FilteredRootedTree.getTaxon(Node node)
           
 Taxon SimpleTree.getTaxon(Node node)
           
 Taxon SimpleRootedTree.getTaxon(Node node)
           
static int RootedTreeUtils.getTipCount(RootedTree tree, Node node)
          Return the number of leaves under this node.
 boolean MutableRootedTree.isExternal(Node node)
           
 boolean Tree.isExternal(Node node)
           
 boolean CompactRootedTree.isExternal(Node node)
           
 boolean RootedFromUnrooted.isExternal(Node node)
           
 boolean RootedSubtree.isExternal(Node node)
           
 boolean FilteredRootedTree.isExternal(Node node)
           
 boolean SimpleTree.isExternal(Node node)
           
 boolean SimpleRootedTree.isExternal(Node node)
           
 boolean MutableRootedTree.isRoot(Node node)
           
 boolean CompactRootedTree.isRoot(Node node)
           
 boolean RootedFromUnrooted.isRoot(Node node)
           
 boolean RootedTree.isRoot(Node node)
           
 boolean RootedSubtree.isRoot(Node node)
           
 boolean FilteredRootedTree.isRoot(Node node)
           
 boolean SimpleRootedTree.isRoot(Node node)
           
static Node Utils.leftNb(RootedTree tree, Node node)
          Left Neighbour of a tip (taxon).
 void MutableRootedTree.refineNode(Node node, int[] leftSet)
           
 void MutableRootedTree.removeInternalNode(Node node)
          Remove internal node.
 void MutableRootedTree.reRootWithOutgroup(Node outGroup, java.util.Set<java.lang.String> attributeNames)
          Re-root tree using an outgroup.
static Node Utils.rightNb(RootedTree tree, Node tipNode)
          Right Neighbour of a tip (taxon).
static double Utils.safeNodeHeight(RootedTree tree, Node node)
           
 void SimpleTree.setEdgeLength(Node node1, Node node2, double length)
          Set edge distance between two adjacent nodes.
 void MutableRootedTree.setHeight(Node node, double height)
           
 void RootedSubtree.setHeight(Node node, double height)
           
 void SimpleRootedTree.setHeight(Node node, double height)
           
 void MutableRootedTree.setLength(Node node, double length)
           
 void RootedSubtree.setLength(Node node, double length)
           
 void SimpleRootedTree.setLength(Node node, double length)
           
 void SimpleRootedTree.swapNodes(Node n, int i0, int i1)
           
static java.lang.String RootedTreeUtils.uniqueNewick(RootedTree tree, Node node)
          Recursive function for constructing a newick tree representation in the given buffer.
 

Method parameters in jebl.evolution.trees with type arguments of type Node
 jebl.evolution.trees.MutableRootedTree.MutableRootedNode MutableRootedTree.createInternalNode(java.util.List<? extends Node> children)
          Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
 jebl.evolution.trees.SimpleRootedTree.SimpleRootedNode SimpleRootedTree.createInternalNode(java.util.List<? extends Node> children)
          Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
 Node SimpleTree.createInternalNode(java.util.List<Node> adjacencies)
          Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
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 boolean RootedTreeUtils.isMonophyletic(RootedTree tree, java.util.Set<Node> tipNodes)
          Performs the a monophyly test on a set of tip nodes.
 

Constructors in jebl.evolution.trees with parameters of type Node
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
 

Constructor parameters in jebl.evolution.trees with type arguments of type Node
SimpleRootedTree(RootedTree tree, java.util.Map<Node,Node> nodeMapping)
          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)
           
TreeSelectionChangeEvent(java.util.Set<Node> selectedNodes)
           
 



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