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Packages that use Node | |
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jebl.evolution.graphs | |
jebl.evolution.parsimony | |
jebl.evolution.trees |
Uses of Node in jebl.evolution.graphs |
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Methods in jebl.evolution.graphs that return Node | |
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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 | |
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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 | |
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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 |
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Methods in jebl.evolution.parsimony with parameters of type Node | |
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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 |
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Classes in jebl.evolution.trees that implement Node | |
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class |
BaseNode
Common implementation of Attributable interface used by Nodes. |
Methods in jebl.evolution.trees that return Node | |
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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 |
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 |
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 |
RootedFromUnrooted.getNode(Taxon taxon)
|
Node |
MutableRootedTree.getNode(Taxon taxon)
|
Node |
CompactRootedTree.getNode(Taxon taxon)
|
Node |
SimpleRootedTree.getNode(Taxon taxon)
|
Node |
Tree.getNode(Taxon taxon)
|
Node |
FilteredRootedTree.getNode(Taxon taxon)
|
Node |
SimpleTree.getNode(Taxon taxon)
|
Node |
RootedSubtree.getNode(Taxon taxon)
|
Node[] |
RootedFromUnrooted.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[] |
CompactRootedTree.getNodes(Edge edge)
|
Node[] |
SimpleRootedTree.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[] |
RootedSubtree.getNodes(Edge edge)
Returns an array of 2 nodes which are the nodes at either end of the edge. |
Node |
RootedTree.getParent(Node node)
|
Node |
RootedFromUnrooted.getParent(Node node)
|
Node |
MutableRootedTree.getParent(Node node)
|
Node |
CompactRootedTree.getParent(Node node)
|
Node |
SimpleRootedTree.getParent(Node node)
|
Node |
FilteredRootedTree.getParent(Node node)
|
Node |
RootedSubtree.getParent(Node node)
|
Node |
RootedTree.getRootNode()
The root of the tree has the largest node height of all nodes in the tree. |
Node |
RootedFromUnrooted.getRootNode()
|
Node |
MutableRootedTree.getRootNode()
The root of the tree has the largest node height of all nodes in the tree. |
Node |
CompactRootedTree.getRootNode()
|
Node |
SimpleRootedTree.getRootNode()
The root of the tree has the largest node height of all nodes in the tree. |
Node |
FilteredRootedTree.getRootNode()
|
Node |
RootedSubtree.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 | |
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static java.util.Comparator<Node> |
Utils.createNodeDensityComparator(RootedTree tree)
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static java.util.Comparator<Node> |
Utils.createNodeDensityMinNodeHeightComparator(RootedTree tree)
|
java.util.List<Node> |
RootedFromUnrooted.getAdjacencies(Node node)
|
java.util.List<Node> |
MutableRootedTree.getAdjacencies(Node node)
|
java.util.List<Node> |
CompactRootedTree.getAdjacencies(Node node)
|
java.util.List<Node> |
SimpleRootedTree.getAdjacencies(Node node)
|
java.util.List<Node> |
FilteredRootedTree.getAdjacencies(Node node)
|
java.util.List<Node> |
SimpleTree.getAdjacencies(Node node)
|
java.util.List<Node> |
RootedSubtree.getAdjacencies(Node node)
|
java.util.List<Node> |
RootedTree.getChildren(Node node)
|
java.util.List<Node> |
RootedFromUnrooted.getChildren(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> |
SimpleRootedTree.getChildren(Node node)
|
java.util.List<Node> |
FilteredRootedTree.getChildren(Node node)
|
java.util.List<Node> |
RootedSubtree.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> |
RootedFromUnrooted.getExternalNodes()
|
java.util.Set<Node> |
MutableRootedTree.getExternalNodes()
|
java.util.Set<Node> |
CompactRootedTree.getExternalNodes()
|
java.util.Set<Node> |
SimpleRootedTree.getExternalNodes()
|
java.util.Set<Node> |
Tree.getExternalNodes()
|
java.util.Set<Node> |
FilteredRootedTree.getExternalNodes()
|
java.util.Set<Node> |
SimpleTree.getExternalNodes()
|
java.util.Set<Node> |
RootedSubtree.getExternalNodes()
|
java.util.Set<Node> |
RootedFromUnrooted.getInternalNodes()
|
java.util.Set<Node> |
MutableRootedTree.getInternalNodes()
|
java.util.Set<Node> |
CompactRootedTree.getInternalNodes()
|
java.util.Set<Node> |
SimpleRootedTree.getInternalNodes()
|
java.util.Set<Node> |
Tree.getInternalNodes()
|
java.util.Set<Node> |
FilteredRootedTree.getInternalNodes()
|
java.util.Set<Node> |
SimpleTree.getInternalNodes()
|
java.util.Set<Node> |
RootedSubtree.getInternalNodes()
|
java.util.Set<Node> |
RootedFromUnrooted.getNodes()
|
java.util.Set<Node> |
MutableRootedTree.getNodes()
|
java.util.Set<Node> |
CompactRootedTree.getNodes()
|
java.util.Set<Node> |
SimpleRootedTree.getNodes()
|
java.util.Set<Node> |
FilteredRootedTree.getNodes()
|
java.util.Set<Node> |
SimpleTree.getNodes()
|
java.util.Set<Node> |
RootedSubtree.getNodes()
|
java.util.Set<Node> |
RootedFromUnrooted.getNodes(int degree)
|
java.util.Set<Node> |
MutableRootedTree.getNodes(int degree)
|
java.util.Set<Node> |
CompactRootedTree.getNodes(int degree)
|
java.util.Set<Node> |
SimpleRootedTree.getNodes(int degree)
|
java.util.Set<Node> |
FilteredRootedTree.getNodes(int degree)
|
java.util.Set<Node> |
SimpleTree.getNodes(int degree)
|
java.util.Set<Node> |
RootedSubtree.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 | |
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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> |
RootedFromUnrooted.getAdjacencies(Node node)
|
java.util.List<Node> |
MutableRootedTree.getAdjacencies(Node node)
|
java.util.List<Node> |
CompactRootedTree.getAdjacencies(Node node)
|
java.util.List<Node> |
SimpleRootedTree.getAdjacencies(Node node)
|
java.util.List<Node> |
FilteredRootedTree.getAdjacencies(Node node)
|
java.util.List<Node> |
SimpleTree.getAdjacencies(Node node)
|
java.util.List<Node> |
RootedSubtree.getAdjacencies(Node node)
|
java.util.List<Node> |
RootedTree.getChildren(Node node)
|
java.util.List<Node> |
RootedFromUnrooted.getChildren(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> |
SimpleRootedTree.getChildren(Node node)
|
java.util.List<Node> |
FilteredRootedTree.getChildren(Node node)
|
java.util.List<Node> |
RootedSubtree.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 |
RootedFromUnrooted.getEdge(Node node1,
Node node2)
|
Edge |
MutableRootedTree.getEdge(Node node1,
Node node2)
Returns the Edge that connects these two nodes |
Edge |
CompactRootedTree.getEdge(Node node1,
Node node2)
|
Edge |
SimpleRootedTree.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 |
RootedSubtree.getEdge(Node node1,
Node node2)
Returns the Edge that connects these two nodes |
double |
RootedFromUnrooted.getEdgeLength(Node node1,
Node node2)
|
double |
MutableRootedTree.getEdgeLength(Node node1,
Node node2)
|
double |
CompactRootedTree.getEdgeLength(Node node1,
Node node2)
|
double |
SimpleRootedTree.getEdgeLength(Node node1,
Node node2)
|
double |
FilteredRootedTree.getEdgeLength(Node node1,
Node node2)
|
double |
SimpleTree.getEdgeLength(Node node1,
Node node2)
|
double |
RootedSubtree.getEdgeLength(Node node1,
Node node2)
|
java.util.List<Edge> |
RootedFromUnrooted.getEdges(Node node)
Returns a list of edges connected to this node |
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> |
SimpleRootedTree.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> |
RootedSubtree.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 |
RootedTree.getHeight(Node node)
|
double |
TransformedRootedTree.getHeight(Node node)
|
double |
RootedFromUnrooted.getHeight(Node node)
|
double |
MutableRootedTree.getHeight(Node node)
|
double |
CompactRootedTree.getHeight(Node node)
|
double |
SimpleRootedTree.getHeight(Node node)
|
double |
FilteredRootedTree.getHeight(Node node)
|
double |
RootedSubtree.getHeight(Node node)
|
double |
RootedTree.getLength(Node node)
|
double |
TransformedRootedTree.getLength(Node node)
|
double |
RootedFromUnrooted.getLength(Node node)
|
double |
MutableRootedTree.getLength(Node node)
|
double |
CompactRootedTree.getLength(Node node)
|
double |
SimpleRootedTree.getLength(Node node)
|
double |
FilteredRootedTree.getLength(Node node)
|
double |
RootedSubtree.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 |
RootedTree.getParent(Node node)
|
Node |
RootedFromUnrooted.getParent(Node node)
|
Node |
MutableRootedTree.getParent(Node node)
|
Node |
CompactRootedTree.getParent(Node node)
|
Node |
SimpleRootedTree.getParent(Node node)
|
Node |
FilteredRootedTree.getParent(Node node)
|
Node |
RootedSubtree.getParent(Node node)
|
Edge |
MutableRootedTree.getParentEdge(Node node)
|
Edge |
CompactRootedTree.getParentEdge(Node node)
|
Edge |
SimpleRootedTree.getParentEdge(Node node)
|
Edge |
RootedSubtree.getParentEdge(Node node)
|
static double |
Utils.getPathLength(Tree tree,
Node node1,
Node node2)
|
Taxon |
RootedFromUnrooted.getTaxon(Node node)
|
Taxon |
MutableRootedTree.getTaxon(Node node)
|
Taxon |
CompactRootedTree.getTaxon(Node node)
|
Taxon |
SimpleRootedTree.getTaxon(Node node)
|
Taxon |
Tree.getTaxon(Node node)
|
Taxon |
FilteredRootedTree.getTaxon(Node node)
|
Taxon |
SimpleTree.getTaxon(Node node)
|
Taxon |
RootedSubtree.getTaxon(Node node)
|
static int |
RootedTreeUtils.getTipCount(RootedTree tree,
Node node)
Return the number of leaves under this node. |
boolean |
RootedFromUnrooted.isExternal(Node node)
|
boolean |
MutableRootedTree.isExternal(Node node)
|
boolean |
CompactRootedTree.isExternal(Node node)
|
boolean |
SimpleRootedTree.isExternal(Node node)
|
boolean |
Tree.isExternal(Node node)
|
boolean |
FilteredRootedTree.isExternal(Node node)
|
boolean |
SimpleTree.isExternal(Node node)
|
boolean |
RootedSubtree.isExternal(Node node)
|
boolean |
RootedTree.isRoot(Node node)
|
boolean |
RootedFromUnrooted.isRoot(Node node)
|
boolean |
MutableRootedTree.isRoot(Node node)
|
boolean |
CompactRootedTree.isRoot(Node node)
|
boolean |
SimpleRootedTree.isRoot(Node node)
|
boolean |
FilteredRootedTree.isRoot(Node node)
|
boolean |
RootedSubtree.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 |
SimpleRootedTree.setHeight(Node node,
double height)
|
void |
RootedSubtree.setHeight(Node node,
double height)
|
void |
MutableRootedTree.setLength(Node node,
double length)
|
void |
SimpleRootedTree.setLength(Node node,
double length)
|
void |
RootedSubtree.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 | |
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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)
|
|
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