Uses of Interface
jebl.evolution.graphs.Node
Packages that use Node
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Uses of Node in jebl.evolution.graphs
Methods in jebl.evolution.graphs that return NodeModifier and TypeMethodDescriptionNode[]
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 NodeModifier and TypeMethodDescriptionGraph.getAdjacencies
(Node node) Returns a list of nodes connected to this node by an edgeGraph.getNodes()
Graph.getNodes
(int degree) Methods in jebl.evolution.graphs with parameters of type NodeModifier and TypeMethodDescriptionGraph.getAdjacencies
(Node node) Returns a list of nodes connected to this node by an edgestatic int
Returns the Edge that connects these two nodesdouble
Graph.getEdgeLength
(Node node1, Node node2) Returns the length of the edge that connects these two nodesReturns 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 -
Uses of Node in jebl.evolution.trees
Classes in jebl.evolution.trees that implement NodeModifier and TypeClassDescriptionclass
Common implementation of Attributable interface used by Nodes.Methods in jebl.evolution.trees that return NodeModifier and TypeMethodDescriptionAdds a new node at the midpoint of the given edgeAdds a new node at the midpoint of the edge connecting the given node to its parent.MutableRootedTree.createExternalNode
(Taxon taxon) Creates a new external node with the given taxon.SimpleRootedTree.createExternalNode
(Taxon taxon) Creates a new external node with the given taxon.SimpleTree.createExternalNode
(Taxon taxon) Creates a new external node with the given taxon.SimpleTree.createInternalNode
(List<Node> adjacencies) Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.ReRootedTree.createNodes
(RootedTree tree, Node parent, Node child) Clones the entire tree structure from the given (unrooted) Tree.SimpleRootedTree.createNodes
(RootedTree tree, Node node) Clones the entire tree structure from the given RootedTree.SimpleRootedTree.createNodes
(Tree tree, Node parent, Node child) Clones the entire tree structure from the given (unrooted) Tree.MutableRootedTree.detachChildren
(Node node, List<Integer> split) static Node
RootedTreeUtils.getCommonAncestorNode
(RootedTree tree, Set<Node> tipNodes) Gets the most recent common ancestor (MRCA) node of a set of tip nodes.Node[]
Node[]
Node[]
Returns an array of 2 nodes which are the nodes at either end of the edge.Node[]
Returns an array of 2 nodes which are the nodes at either end of the edge.Node[]
Node[]
Returns an array of 2 nodes which are the nodes at either end of the edge.Node[]
Returns an array of 2 nodes which are the nodes at either end of the edge.Node[]
Returns an array of 2 nodes which are the nodes at either end of the edge.CompactRootedTree.getRootNode()
FilteredRootedTree.getRootNode()
MutableRootedTree.getRootNode()
The root of the tree has the largest node height of all nodes in the tree.ReRootedTree.getRootNode()
The root of the tree has the largest node height of all nodes in the tree.RootedFromUnrooted.getRootNode()
RootedSubtree.getRootNode()
The root of the tree has the largest node height of all nodes in the tree.RootedTree.getRootNode()
The root of the tree has the largest node height of all nodes in the tree.SimpleRootedTree.getRootNode()
The root of the tree has the largest node height of all nodes in the tree.ReRootedTree.getSourceNode
(Node node) 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 NodeModifier and TypeMethodDescriptionstatic Comparator<Node>
Utils.createNodeDensityComparator
(RootedTree tree) static Comparator<Node>
Utils.createNodeDensityMinNodeHeightComparator
(RootedTree tree) CompactRootedTree.getAdjacencies
(Node node) FilteredRootedTree.getAdjacencies
(Node node) MutableRootedTree.getAdjacencies
(Node node) ReRootedTree.getAdjacencies
(Node node) RootedFromUnrooted.getAdjacencies
(Node node) RootedSubtree.getAdjacencies
(Node node) SimpleRootedTree.getAdjacencies
(Node node) SimpleTree.getAdjacencies
(Node node) CompactRootedTree.getChildren
(Node node) FilteredRootedTree.getChildren
(Node node) MutableRootedTree.getChildren
(Node node) ReRootedTree.getChildren
(Node node) RootedFromUnrooted.getChildren
(Node node) RootedSubtree.getChildren
(Node node) RootedTree.getChildren
(Node node) SimpleRootedTree.getChildren
(Node node) SortedRootedTree.getChildren
(Node node) RootedTreeUtils.getDescendantTips
(RootedTree tree, Node node) Gets a set of tip nodes descended from the given node.AbstractRootedTree.getExternalNodes
(Node node) CompactRootedTree.getExternalNodes()
CompactRootedTree.getExternalNodes
(Node node) FilteredRootedTree.getExternalNodes()
MutableRootedTree.getExternalNodes()
ReRootedTree.getExternalNodes()
RootedFromUnrooted.getExternalNodes()
RootedSubtree.getExternalNodes()
RootedTree.getExternalNodes
(Node node) SimpleRootedTree.getExternalNodes()
SimpleRootedTree.getExternalNodes
(Node node) SimpleTree.getExternalNodes()
Tree.getExternalNodes()
CompactRootedTree.getInternalNodes()
FilteredRootedTree.getInternalNodes()
MutableRootedTree.getInternalNodes()
ReRootedTree.getInternalNodes()
RootedFromUnrooted.getInternalNodes()
RootedSubtree.getInternalNodes()
SimpleRootedTree.getInternalNodes()
SimpleTree.getInternalNodes()
Tree.getInternalNodes()
CompactRootedTree.getNodes()
CompactRootedTree.getNodes
(int degree) FilteredRootedTree.getNodes()
FilteredRootedTree.getNodes
(int degree) MutableRootedTree.getNodes()
MutableRootedTree.getNodes
(int degree) ReRootedTree.getNodes()
ReRootedTree.getNodes
(int degree) RootedFromUnrooted.getNodes()
RootedFromUnrooted.getNodes
(int degree) RootedSubtree.getNodes()
RootedSubtree.getNodes
(int degree) SimpleRootedTree.getNodes()
SimpleRootedTree.getNodes
(int degree) SimpleTree.getNodes()
SimpleTree.getNodes
(int degree) Utils.getNodes
(RootedTree tree, Node node) All nodes in subtree - parents before children (pre - order).TreeSelectionChangeEvent.getSelectedNodes()
RootedTreeUtils.getTipsForTaxa
(RootedTree tree, Collection<Taxon> taxa) Gets a set of external nodes that correspond to the given taxa.Methods in jebl.evolution.trees with parameters of type NodeModifier and TypeMethodDescriptionvoid
Insert a child node.void
Add a new edge between two existing (non adjacent yet) nodes.Adds a new node at the midpoint of the edge connecting the given node to its parent.ReRootedTree.createNodes
(RootedTree tree, Node parent, Node child) Clones the entire tree structure from the given (unrooted) Tree.SimpleRootedTree.createNodes
(RootedTree tree, Node node) Clones the entire tree structure from the given RootedTree.SimpleRootedTree.createNodes
(Tree tree, Node parent, Node child) Clones the entire tree structure from the given (unrooted) Tree.static String
Utils.DEBUGsubTreeRep
(RootedTree tree, Node node) void
SimpleRootedTree.deleteInternalNode
(Node node) Removes an internal node in this tree.MutableRootedTree.detachChildren
(Node node, List<Integer> split) CompactRootedTree.getAdjacencies
(Node node) FilteredRootedTree.getAdjacencies
(Node node) MutableRootedTree.getAdjacencies
(Node node) ReRootedTree.getAdjacencies
(Node node) RootedFromUnrooted.getAdjacencies
(Node node) RootedSubtree.getAdjacencies
(Node node) SimpleRootedTree.getAdjacencies
(Node node) SimpleTree.getAdjacencies
(Node node) static double
RootedTreeUtils.getAverageTipDistance
(RootedTree tree, Node node) returns the average distance from the given node to all the tips below itCompactRootedTree.getChildren
(Node node) FilteredRootedTree.getChildren
(Node node) MutableRootedTree.getChildren
(Node node) ReRootedTree.getChildren
(Node node) RootedFromUnrooted.getChildren
(Node node) RootedSubtree.getChildren
(Node node) RootedTree.getChildren
(Node node) SimpleRootedTree.getChildren
(Node node) SortedRootedTree.getChildren
(Node node) RootedTreeUtils.getDescendantTips
(RootedTree tree, Node node) Gets a set of tip nodes descended from the given node.Returns the Edge that connects these two nodesReturns the Edge that connects these two nodesReturns the Edge that connects these two nodesReturns the Edge that connects these two nodesReturns the Edge that connects these two nodesdouble
CompactRootedTree.getEdgeLength
(Node node1, Node node2) double
FilteredRootedTree.getEdgeLength
(Node node1, Node node2) double
MutableRootedTree.getEdgeLength
(Node node1, Node node2) double
ReRootedTree.getEdgeLength
(Node node1, Node node2) double
RootedFromUnrooted.getEdgeLength
(Node node1, Node node2) double
RootedSubtree.getEdgeLength
(Node node1, Node node2) double
SimpleRootedTree.getEdgeLength
(Node node1, Node node2) double
SimpleTree.getEdgeLength
(Node node1, Node node2) Returns a list of edges connected to this nodeReturns a list of edges connected to this nodeReturns a list of edges connected to this nodeReturns a list of edges connected to this nodeReturns a list of edges connected to this nodeReturns a list of edges connected to this nodeint
AbstractRootedTree.getExternalNodeCount
(Node node) int
CompactRootedTree.getExternalNodeCount
(Node node) int
RootedTree.getExternalNodeCount
(Node node) int
SimpleRootedTree.getExternalNodeCount
(Node node) static int
Utils.getExternalNodeCount
(RootedTree tree, Node node) Return the number of external nodes under this node.AbstractRootedTree.getExternalNodes
(Node node) CompactRootedTree.getExternalNodes
(Node node) RootedTree.getExternalNodes
(Node node) SimpleRootedTree.getExternalNodes
(Node node) double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
double
static double
RootedTreeUtils.getMaxTipHeight
(RootedTree tree, Node node) static double
Utils.getMinNodeHeight
(RootedTree tree, Node node) static double
RootedTreeUtils.getMinTipHeight
(RootedTree tree, Node node) Utils.getNodes
(RootedTree tree, Node node) All nodes in subtree - parents before children (pre - order).CompactRootedTree.getParentEdge
(Node node) MutableRootedTree.getParentEdge
(Node node) ReRootedTree.getParentEdge
(Node node) RootedSubtree.getParentEdge
(Node node) SimpleRootedTree.getParentEdge
(Node node) static double
Utils.getPathLength
(Tree tree, Node node1, Node node2) ReRootedTree.getSourceNode
(Node node) static final int
RootedTreeUtils.getTipCount
(RootedTree tree, Node node) Return the number of leaves under this node.boolean
CompactRootedTree.isExternal
(Node node) boolean
FilteredRootedTree.isExternal
(Node node) boolean
MutableRootedTree.isExternal
(Node node) boolean
ReRootedTree.isExternal
(Node node) boolean
RootedFromUnrooted.isExternal
(Node node) boolean
RootedSubtree.isExternal
(Node node) boolean
SimpleRootedTree.isExternal
(Node node) boolean
SimpleTree.isExternal
(Node node) boolean
Tree.isExternal
(Node node) boolean
boolean
boolean
boolean
boolean
boolean
boolean
boolean
static Node
Utils.leftNb
(RootedTree tree, Node node) Left Neighbour of a tip (taxon).void
MutableRootedTree.refineNode
(Node node, int[] leftSet) void
MutableRootedTree.removeChild
(Node child, Node parent) Remove a child node.void
MutableRootedTree.removeInternalNode
(Node node) Remove internal node.void
MutableRootedTree.reRootWithOutgroup
(Node outGroup, Set<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
void
void
void
void
void
void
void
void
Set the root node.void
static 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 NodeModifier and TypeMethodDescriptionjebl.evolution.trees.MutableRootedTree.MutableRootedNode
MutableRootedTree.createInternalNode
(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
(List<? extends Node> children) Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.SimpleTree.createInternalNode
(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, Set<Node> tipNodes) Gets the most recent common ancestor (MRCA) node of a set of tip nodes.static boolean
RootedTreeUtils.isMonophyletic
(RootedTree tree, Set<Node> tipNodes) Performs the a monophyly test on a set of tip nodes.Constructors in jebl.evolution.trees with parameters of type NodeModifierConstructorDescriptionMutableRootedTree
(Tree tree, Node outGroup) Construct a rooted tree from unrooted.ReRootedTree
(RootedTree source, Node ingroupNode, Node outgroupNode, double ingroupBranchLength) Make a copy of the given unrooted treeRootedFromUnrooted
(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 treeConstructor parameters in jebl.evolution.trees with type arguments of type NodeModifierConstructorDescriptionSimpleRootedTree
(RootedTree tree, Map<Node, Node> nodeMapping) Make a copy of the given rooted treeSimpleRootedTree
(RootedTree tree, Map<Node, Node> nodeMapping) Make a copy of the given rooted treeSortedRootedTree
(RootedTree source, Comparator<Node> comparator) TreeSelectionChangeEvent
(Set<Node> selectedNodes)