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 intGraph.Utils. getDegree(Graph graph, Node node)EdgeGraph. getEdge(Node node1, Node node2)Returns the Edge that connects these two nodesdoubleGraph. 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 classBaseNodeCommon implementation of Attributable interface used by Nodes.Methods in jebl.evolution.trees that return Node Modifier and Type Method Description NodeSimpleRootedTree. addNode(Edge edge)Adds a new node at the midpoint of the given edgeNodeSimpleRootedTree. addNode(Node node)Adds a new node at the midpoint of the edge connecting the given node to its parent.NodeMutableRootedTree. createExternalNode(Taxon taxon)Creates a new external node with the given taxon.NodeSimpleRootedTree. createExternalNode(Taxon taxon)Creates a new external node with the given taxon.NodeSimpleTree. createExternalNode(Taxon taxon)Creates a new external node with the given taxon.NodeSimpleTree. createInternalNode(java.util.List<Node> adjacencies)Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.NodeSimpleRootedTree. createNodes(RootedTree tree, Node node)Clones the entire tree structure from the given RootedTree.NodeSimpleRootedTree. createNodes(Tree tree, Node parent, Node child)Clones the entire tree structure from the given (unrooted) Tree.NodeMutableRootedTree. detachChildren(Node node, java.util.List<java.lang.Integer> split)static NodeRootedTreeUtils. getCommonAncestorNode(RootedTree tree, java.util.Set<Node> tipNodes)Gets the most recent common ancestor (MRCA) node of a set of tip nodes.NodeCompactRootedTree. getNode(Taxon taxon)NodeFilteredRootedTree. getNode(Taxon taxon)NodeMutableRootedTree. getNode(Taxon taxon)NodeRootedFromUnrooted. getNode(Taxon taxon)NodeRootedSubtree. getNode(Taxon taxon)NodeSimpleRootedTree. getNode(Taxon taxon)NodeSimpleTree. getNode(Taxon taxon)NodeTree. 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[]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.NodeCompactRootedTree. getParent(Node node)NodeFilteredRootedTree. getParent(Node node)NodeMutableRootedTree. getParent(Node node)NodeRootedFromUnrooted. getParent(Node node)NodeRootedSubtree. getParent(Node node)NodeRootedTree. getParent(Node node)NodeSimpleRootedTree. getParent(Node node)NodeCompactRootedTree. getRootNode()NodeFilteredRootedTree. getRootNode()NodeMutableRootedTree. getRootNode()The root of the tree has the largest node height of all nodes in the tree.NodeRootedFromUnrooted. getRootNode()NodeRootedSubtree. getRootNode()The root of the tree has the largest node height of all nodes in the tree.NodeRootedTree. getRootNode()The root of the tree has the largest node height of all nodes in the tree.NodeSimpleRootedTree. getRootNode()The root of the tree has the largest node height of all nodes in the tree.static NodeUtils. leftNb(RootedTree tree, Node node)Left Neighbour of a tip (taxon).static NodeUtils. 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>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>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.Set<Node>CompactRootedTree. getExternalNodes()java.util.Set<Node>FilteredRootedTree. getExternalNodes()java.util.Set<Node>MutableRootedTree. getExternalNodes()java.util.Set<Node>RootedFromUnrooted. getExternalNodes()java.util.Set<Node>RootedSubtree. getExternalNodes()java.util.Set<Node>SimpleRootedTree. getExternalNodes()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>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>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 voidMutableRootedTree. addChild(Node child, Node parent)Insert a child node.voidSimpleTree. addEdge(Node node1, Node node2, double length)Add a new edge between two existing (non adjacent yet) nodes.NodeSimpleRootedTree. addNode(Node node)Adds a new node at the midpoint of the edge connecting the given node to its parent.NodeSimpleRootedTree. createNodes(RootedTree tree, Node node)Clones the entire tree structure from the given RootedTree.NodeSimpleRootedTree. createNodes(Tree tree, Node parent, Node child)Clones the entire tree structure from the given (unrooted) Tree.static java.lang.StringUtils. DEBUGsubTreeRep(RootedTree tree, Node node)voidSimpleRootedTree. deleteInternalNode(Node node)Removes an internal node in this tree.NodeMutableRootedTree. 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>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>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.EdgeCompactRootedTree. getEdge(Node node1, Node node2)EdgeFilteredRootedTree. getEdge(Node node1, Node node2)EdgeMutableRootedTree. getEdge(Node node1, Node node2)Returns the Edge that connects these two nodesEdgeRootedFromUnrooted. getEdge(Node node1, Node node2)EdgeRootedSubtree. getEdge(Node node1, Node node2)Returns the Edge that connects these two nodesEdgeSimpleRootedTree. getEdge(Node node1, Node node2)Returns the Edge that connects these two nodesEdgeSimpleTree. getEdge(Node node1, Node node2)Returns the Edge that connects these two nodesdoubleCompactRootedTree. getEdgeLength(Node node1, Node node2)doubleFilteredRootedTree. getEdgeLength(Node node1, Node node2)doubleMutableRootedTree. getEdgeLength(Node node1, Node node2)doubleRootedFromUnrooted. getEdgeLength(Node node1, Node node2)doubleRootedSubtree. getEdgeLength(Node node1, Node node2)doubleSimpleRootedTree. getEdgeLength(Node node1, Node node2)doubleSimpleTree. 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>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 nodestatic intUtils. getExternalNodeCount(RootedTree tree, Node node)Return the number of external nodes under this node.doubleCompactRootedTree. getHeight(Node node)doubleFilteredRootedTree. getHeight(Node node)doubleMutableRootedTree. getHeight(Node node)doubleRootedFromUnrooted. getHeight(Node node)doubleRootedSubtree. getHeight(Node node)doubleRootedTree. getHeight(Node node)doubleSimpleRootedTree. getHeight(Node node)doubleTransformedRootedTree. getHeight(Node node)doubleCompactRootedTree. getLength(Node node)doubleFilteredRootedTree. getLength(Node node)doubleMutableRootedTree. getLength(Node node)doubleRootedFromUnrooted. getLength(Node node)doubleRootedSubtree. getLength(Node node)doubleRootedTree. getLength(Node node)doubleSimpleRootedTree. getLength(Node node)doubleTransformedRootedTree. getLength(Node node)static doubleRootedTreeUtils. getMaxTipHeight(RootedTree tree, Node node)static doubleUtils. getMinNodeHeight(RootedTree tree, Node node)static doubleRootedTreeUtils. 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).NodeCompactRootedTree. getParent(Node node)NodeFilteredRootedTree. getParent(Node node)NodeMutableRootedTree. getParent(Node node)NodeRootedFromUnrooted. getParent(Node node)NodeRootedSubtree. getParent(Node node)NodeRootedTree. getParent(Node node)NodeSimpleRootedTree. getParent(Node node)EdgeCompactRootedTree. getParentEdge(Node node)EdgeMutableRootedTree. getParentEdge(Node node)EdgeRootedSubtree. getParentEdge(Node node)EdgeSimpleRootedTree. getParentEdge(Node node)static doubleUtils. getPathLength(Tree tree, Node node1, Node node2)TaxonCompactRootedTree. getTaxon(Node node)TaxonFilteredRootedTree. getTaxon(Node node)TaxonMutableRootedTree. getTaxon(Node node)TaxonRootedFromUnrooted. getTaxon(Node node)TaxonRootedSubtree. getTaxon(Node node)TaxonSimpleRootedTree. getTaxon(Node node)TaxonSimpleTree. getTaxon(Node node)TaxonTree. getTaxon(Node node)static intRootedTreeUtils. getTipCount(RootedTree tree, Node node)Return the number of leaves under this node.booleanCompactRootedTree. isExternal(Node node)booleanFilteredRootedTree. isExternal(Node node)booleanMutableRootedTree. isExternal(Node node)booleanRootedFromUnrooted. isExternal(Node node)booleanRootedSubtree. isExternal(Node node)booleanSimpleRootedTree. isExternal(Node node)booleanSimpleTree. isExternal(Node node)booleanTree. isExternal(Node node)booleanCompactRootedTree. isRoot(Node node)booleanFilteredRootedTree. isRoot(Node node)booleanMutableRootedTree. isRoot(Node node)booleanRootedFromUnrooted. isRoot(Node node)booleanRootedSubtree. isRoot(Node node)booleanRootedTree. isRoot(Node node)booleanSimpleRootedTree. isRoot(Node node)static NodeUtils. leftNb(RootedTree tree, Node node)Left Neighbour of a tip (taxon).voidMutableRootedTree. refineNode(Node node, int[] leftSet)voidMutableRootedTree. removeChild(Node child, Node parent)Remove a child node.voidMutableRootedTree. removeInternalNode(Node node)Remove internal node.voidMutableRootedTree. reRootWithOutgroup(Node outGroup, java.util.Set<java.lang.String> attributeNames)Re-root tree using an outgroup.static NodeUtils. rightNb(RootedTree tree, Node tipNode)Right Neighbour of a tip (taxon).static doubleUtils. safeNodeHeight(RootedTree tree, Node node)voidSimpleTree. setEdgeLength(Node node1, Node node2, double length)Set edge distance between two adjacent nodes.voidMutableRootedTree. setHeight(Node node, double height)voidRootedSubtree. setHeight(Node node, double height)voidSimpleRootedTree. setHeight(Node node, double height)voidMutableRootedTree. setLength(Node node, double length)voidRootedSubtree. setLength(Node node, double length)voidSimpleRootedTree. setLength(Node node, double length)voidMutableRootedTree. setRoot(Node root)Set the root node.voidSimpleRootedTree. swapNodes(Node n, int i0, int i1)static java.lang.StringRootedTreeUtils. 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.MutableRootedNodeMutableRootedTree. 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.SimpleRootedNodeSimpleRootedTree. createInternalNode(java.util.List<? extends Node> children)Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.NodeSimpleTree. createInternalNode(java.util.List<Node> adjacencies)Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.static NodeRootedTreeUtils. getCommonAncestorNode(RootedTree tree, java.util.Set<Node> tipNodes)Gets the most recent common ancestor (MRCA) node of a set of tip nodes.static booleanRootedTreeUtils. 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.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 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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