Uses of Interface
jebl.evolution.graphs.Node
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Packages that use Node Package Description jebl.evolution.graphs jebl.evolution.parsimony jebl.evolution.trees -
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Uses of Node in jebl.evolution.graphs
Methods in jebl.evolution.graphs that return Node Modifier and Type Method Description 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 Modifier and Type Method Description java.util.List<Node>
Graph. getAdjacencies(Node node)
Returns a list of nodes connected to this node by an edgejava.util.Set<Node>
Graph. getNodes()
java.util.Set<Node>
Graph. getNodes(int degree)
Methods in jebl.evolution.graphs with parameters of type Node Modifier and Type Method Description java.util.List<Node>
Graph. getAdjacencies(Node node)
Returns a list of nodes connected to this node by an edgestatic int
Graph.Utils. getDegree(Graph graph, Node node)
Edge
Graph. getEdge(Node node1, Node node2)
Returns the Edge that connects these two nodesdouble
Graph. getEdgeLength(Node node1, Node node2)
Returns the length of the edge that connects these two nodesjava.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 Modifier and Type Method Description 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 Modifier and Type Class Description class
BaseNode
Common implementation of Attributable interface used by Nodes.Methods in jebl.evolution.trees that return Node Modifier and Type Method Description Node
SimpleRootedTree. addNode(Edge edge)
Adds a new node at the midpoint of the given edgeNode
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
SimpleRootedTree. 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
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
ReRootedTree. createNodes(RootedTree tree, Node parent, Node child)
Clones the entire tree structure from the given (unrooted) Tree.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
CompactRootedTree. getNode(Taxon taxon)
Node
FilteredRootedTree. getNode(Taxon taxon)
Node
MutableRootedTree. getNode(Taxon taxon)
Node
ReRootedTree. getNode(Taxon taxon)
Node
RootedFromUnrooted. getNode(Taxon taxon)
Node
RootedSubtree. getNode(Taxon taxon)
Node
SimpleRootedTree. getNode(Taxon taxon)
Node
SimpleTree. getNode(Taxon taxon)
Node
Tree. getNode(Taxon taxon)
Node[]
CompactRootedTree. getNodes(Edge edge)
Node[]
FilteredRootedTree. getNodes(Edge edge)
Node[]
MutableRootedTree. getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.Node[]
ReRootedTree. getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the 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[]
SimpleRootedTree. getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.Node[]
SimpleTree. getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge.Node
CompactRootedTree. getParent(Node node)
Node
FilteredRootedTree. getParent(Node node)
Node
MutableRootedTree. getParent(Node node)
Node
ReRootedTree. getParent(Node node)
Node
RootedFromUnrooted. getParent(Node node)
Node
RootedSubtree. getParent(Node node)
Node
RootedTree. getParent(Node node)
Node
SimpleRootedTree. getParent(Node node)
Node
CompactRootedTree. getRootNode()
Node
FilteredRootedTree. getRootNode()
Node
MutableRootedTree. getRootNode()
The root of the tree has the largest node height of all nodes in the tree.Node
ReRootedTree. getRootNode()
The root of the tree has the largest node height of all nodes in the tree.Node
RootedFromUnrooted. getRootNode()
Node
RootedSubtree. getRootNode()
The root of the tree has the largest node height of all nodes in the tree.Node
RootedTree. getRootNode()
The root of the tree has the largest node height of all nodes in the tree.Node
SimpleRootedTree. getRootNode()
The root of the tree has the largest node height of all nodes in the tree.Node
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 Node Modifier and Type Method Description static java.util.Comparator<Node>
Utils. createNodeDensityComparator(RootedTree tree)
static java.util.Comparator<Node>
Utils. createNodeDensityMinNodeHeightComparator(RootedTree tree)
java.util.List<Node>
CompactRootedTree. getAdjacencies(Node node)
java.util.List<Node>
FilteredRootedTree. getAdjacencies(Node node)
java.util.List<Node>
MutableRootedTree. getAdjacencies(Node node)
java.util.List<Node>
ReRootedTree. getAdjacencies(Node node)
java.util.List<Node>
RootedFromUnrooted. getAdjacencies(Node node)
java.util.List<Node>
RootedSubtree. getAdjacencies(Node node)
java.util.List<Node>
SimpleRootedTree. getAdjacencies(Node node)
java.util.List<Node>
SimpleTree. getAdjacencies(Node node)
java.util.List<Node>
CompactRootedTree. getChildren(Node node)
java.util.List<Node>
FilteredRootedTree. getChildren(Node node)
java.util.List<Node>
MutableRootedTree. getChildren(Node node)
java.util.List<Node>
ReRootedTree. getChildren(Node node)
java.util.List<Node>
RootedFromUnrooted. getChildren(Node node)
java.util.List<Node>
RootedSubtree. getChildren(Node node)
java.util.List<Node>
RootedTree. getChildren(Node node)
java.util.List<Node>
SimpleRootedTree. getChildren(Node node)
java.util.List<Node>
SortedRootedTree. 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.List<Node>
AbstractRootedTree. getExternalNodes(Node node)
java.util.Set<Node>
CompactRootedTree. getExternalNodes()
java.util.List<Node>
CompactRootedTree. getExternalNodes(Node node)
java.util.Set<Node>
FilteredRootedTree. getExternalNodes()
java.util.Set<Node>
MutableRootedTree. getExternalNodes()
java.util.Set<Node>
ReRootedTree. getExternalNodes()
java.util.Set<Node>
RootedFromUnrooted. getExternalNodes()
java.util.Set<Node>
RootedSubtree. getExternalNodes()
java.util.List<Node>
RootedTree. getExternalNodes(Node node)
java.util.Set<Node>
SimpleRootedTree. getExternalNodes()
java.util.List<Node>
SimpleRootedTree. getExternalNodes(Node node)
java.util.Set<Node>
SimpleTree. getExternalNodes()
java.util.Set<Node>
Tree. getExternalNodes()
java.util.Set<Node>
CompactRootedTree. getInternalNodes()
java.util.Set<Node>
FilteredRootedTree. getInternalNodes()
java.util.Set<Node>
MutableRootedTree. getInternalNodes()
java.util.Set<Node>
ReRootedTree. getInternalNodes()
java.util.Set<Node>
RootedFromUnrooted. getInternalNodes()
java.util.Set<Node>
RootedSubtree. getInternalNodes()
java.util.Set<Node>
SimpleRootedTree. getInternalNodes()
java.util.Set<Node>
SimpleTree. getInternalNodes()
java.util.Set<Node>
Tree. getInternalNodes()
java.util.Set<Node>
CompactRootedTree. getNodes()
java.util.Set<Node>
CompactRootedTree. getNodes(int degree)
java.util.Set<Node>
FilteredRootedTree. getNodes()
java.util.Set<Node>
FilteredRootedTree. getNodes(int degree)
java.util.Set<Node>
MutableRootedTree. getNodes()
java.util.Set<Node>
MutableRootedTree. getNodes(int degree)
java.util.Set<Node>
ReRootedTree. getNodes()
java.util.Set<Node>
ReRootedTree. getNodes(int degree)
java.util.Set<Node>
RootedFromUnrooted. getNodes()
java.util.Set<Node>
RootedFromUnrooted. getNodes(int degree)
java.util.Set<Node>
RootedSubtree. getNodes()
java.util.Set<Node>
RootedSubtree. getNodes(int degree)
java.util.Set<Node>
SimpleRootedTree. getNodes()
java.util.Set<Node>
SimpleRootedTree. getNodes(int degree)
java.util.Set<Node>
SimpleTree. getNodes()
java.util.Set<Node>
SimpleTree. 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 Modifier and Type Method Description void
MutableRootedTree. addChild(Node child, Node parent)
Insert a child 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
ReRootedTree. createNodes(RootedTree tree, Node parent, Node child)
Clones the entire tree structure from the given (unrooted) Tree.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>
CompactRootedTree. getAdjacencies(Node node)
java.util.List<Node>
FilteredRootedTree. getAdjacencies(Node node)
java.util.List<Node>
MutableRootedTree. getAdjacencies(Node node)
java.util.List<Node>
ReRootedTree. getAdjacencies(Node node)
java.util.List<Node>
RootedFromUnrooted. getAdjacencies(Node node)
java.util.List<Node>
RootedSubtree. getAdjacencies(Node node)
java.util.List<Node>
SimpleRootedTree. getAdjacencies(Node node)
java.util.List<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 itjava.util.List<Node>
CompactRootedTree. getChildren(Node node)
java.util.List<Node>
FilteredRootedTree. getChildren(Node node)
java.util.List<Node>
MutableRootedTree. getChildren(Node node)
java.util.List<Node>
ReRootedTree. getChildren(Node node)
java.util.List<Node>
RootedFromUnrooted. getChildren(Node node)
java.util.List<Node>
RootedSubtree. getChildren(Node node)
java.util.List<Node>
RootedTree. getChildren(Node node)
java.util.List<Node>
SimpleRootedTree. getChildren(Node node)
java.util.List<Node>
SortedRootedTree. 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
CompactRootedTree. getEdge(Node node1, Node node2)
Edge
FilteredRootedTree. getEdge(Node node1, Node node2)
Edge
MutableRootedTree. getEdge(Node node1, Node node2)
Returns the Edge that connects these two nodesEdge
ReRootedTree. getEdge(Node node1, Node node2)
Returns the Edge that connects these two nodesEdge
RootedFromUnrooted. getEdge(Node node1, Node node2)
Edge
RootedSubtree. getEdge(Node node1, Node node2)
Returns the Edge that connects these two nodesEdge
SimpleRootedTree. getEdge(Node node1, Node node2)
Returns the Edge that connects these two nodesEdge
SimpleTree. getEdge(Node node1, Node node2)
Returns 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)
java.util.List<Edge>
CompactRootedTree. getEdges(Node node)
java.util.List<Edge>
FilteredRootedTree. getEdges(Node node)
java.util.List<Edge>
MutableRootedTree. getEdges(Node node)
Returns a list of edges connected to this nodejava.util.List<Edge>
ReRootedTree. getEdges(Node node)
Returns a list of edges connected to this nodejava.util.List<Edge>
RootedFromUnrooted. getEdges(Node node)
Returns a list of edges connected to this nodejava.util.List<Edge>
RootedSubtree. getEdges(Node node)
Returns a list of edges connected to this nodejava.util.List<Edge>
SimpleRootedTree. getEdges(Node node)
Returns a list of edges connected to this nodejava.util.List<Edge>
SimpleTree. getEdges(Node node)
Returns 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.java.util.List<Node>
AbstractRootedTree. getExternalNodes(Node node)
java.util.List<Node>
CompactRootedTree. getExternalNodes(Node node)
java.util.List<Node>
RootedTree. getExternalNodes(Node node)
java.util.List<Node>
SimpleRootedTree. getExternalNodes(Node node)
double
CompactRootedTree. getHeight(Node node)
double
FilteredRootedTree. getHeight(Node node)
double
MutableRootedTree. getHeight(Node node)
double
ReRootedTree. getHeight(Node node)
double
RootedFromUnrooted. getHeight(Node node)
double
RootedSubtree. getHeight(Node node)
double
RootedTree. getHeight(Node node)
double
SimpleRootedTree. getHeight(Node node)
double
TransformedRootedTree. getHeight(Node node)
double
CompactRootedTree. getLength(Node node)
double
FilteredRootedTree. getLength(Node node)
double
MutableRootedTree. getLength(Node node)
double
ReRootedTree. getLength(Node node)
double
RootedFromUnrooted. getLength(Node node)
double
RootedSubtree. getLength(Node node)
double
RootedTree. getLength(Node node)
double
SimpleRootedTree. getLength(Node node)
double
TransformedRootedTree. 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
CompactRootedTree. getParent(Node node)
Node
FilteredRootedTree. getParent(Node node)
Node
MutableRootedTree. getParent(Node node)
Node
ReRootedTree. getParent(Node node)
Node
RootedFromUnrooted. getParent(Node node)
Node
RootedSubtree. getParent(Node node)
Node
RootedTree. getParent(Node node)
Node
SimpleRootedTree. getParent(Node node)
Edge
CompactRootedTree. getParentEdge(Node node)
Edge
MutableRootedTree. getParentEdge(Node node)
Edge
ReRootedTree. getParentEdge(Node node)
Edge
RootedSubtree. getParentEdge(Node node)
Edge
SimpleRootedTree. getParentEdge(Node node)
static double
Utils. getPathLength(Tree tree, Node node1, Node node2)
Node
ReRootedTree. getSourceNode(Node node)
Taxon
CompactRootedTree. getTaxon(Node node)
Taxon
FilteredRootedTree. getTaxon(Node node)
Taxon
MutableRootedTree. getTaxon(Node node)
Taxon
ReRootedTree. getTaxon(Node node)
Taxon
RootedFromUnrooted. getTaxon(Node node)
Taxon
RootedSubtree. getTaxon(Node node)
Taxon
SimpleRootedTree. getTaxon(Node node)
Taxon
SimpleTree. getTaxon(Node node)
Taxon
Tree. getTaxon(Node node)
static 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
CompactRootedTree. isRoot(Node node)
boolean
FilteredRootedTree. isRoot(Node node)
boolean
MutableRootedTree. isRoot(Node node)
boolean
ReRootedTree. isRoot(Node node)
boolean
RootedFromUnrooted. isRoot(Node node)
boolean
RootedSubtree. isRoot(Node node)
boolean
RootedTree. 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. removeChild(Node child, Node parent)
Remove a child node.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
ReRootedTree. 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
ReRootedTree. setLength(Node node, double length)
void
RootedSubtree. setLength(Node node, double length)
void
SimpleRootedTree. setLength(Node node, double length)
void
MutableRootedTree. setRoot(Node root)
Set the root node.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 Modifier and Type Method Description 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 Constructor Description MutableRootedTree(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 Node Constructor Description SimpleRootedTree(RootedTree tree, java.util.Map<Node,Node> nodeMapping)
Make a copy of the given rooted treeSimpleRootedTree(RootedTree tree, java.util.Map<Node,Node> nodeMapping)
Make a copy of the given rooted treeSortedRootedTree(RootedTree source, java.util.Comparator<Node> comparator)
TreeSelectionChangeEvent(java.util.Set<Node> selectedNodes)
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