Uses of Interface
pal.tree.Node
Packages that use Node
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
GUI components for some special objects (e.g., trees).
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
Utility classes for converting PAL objects to and from XML documents.
-
Uses of Node in pal.eval
Modifier and TypeMethodDescriptionprotected Node
SimpleLikelihoodCalculator.getNextBranch
(Node branch, Node center) get next branch around a center node (center may be root, but root is never returned)Modifier and TypeMethodDescriptionprotected Node
SimpleLikelihoodCalculator.getNextBranch
(Node branch, Node center) get next branch around a center node (center may be root, but root is never returned)protected double[][]
SimpleLikelihoodCalculator.getPartial
(Node branch) get partial likelihood of a branchprotected void
SimpleLikelihoodCalculator.partialsExternal
(Node branch) compute partials for external branchprotected void
SimpleLikelihoodCalculator.partialsInternal
(Node center) compute partials for branch around center node (it is assumed that multiplied partials are available in the neighbor branch)protected void
SimpleLikelihoodCalculator.productPartials
(Node center) multiply partials into the neighbour of branch -
Uses of Node in pal.gui
Modifier and TypeClassDescriptionclass
A tree node that has a scalar position for the purposes of drawing the tree.Modifier and TypeMethodDescriptionprotected static final double
TreePainter.getMaxLeafTime
(Node node) protected final LabelDisplayer
TreePainter.getNodeDisplay
(Node n, LabelDisplayer defaultDisplay) protected final String
TreePainter.getNodeName
(Node node) ModifierConstructorDescriptionPositionedNode
(Node node) PositionedNode
(Node node, Node highlightNode) Builds a tree based on node, but highlights highlightNode -
Uses of Node in pal.tree
Modifier and TypeInterfaceDescriptioninterface
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.Modifier and TypeClassDescriptionclass
data structure for a node (includes branch) in a binary/non-binary rooted/unrooted treeModifier and TypeMethodDescriptionstatic final Node
NodeFactory.createNode()
create a nodestatic final Node
NodeFactory.createNode
(Identifier id) create a node, with a specified identifierstatic final Node
NodeFactory.createNode
(Identifier id, double height) create a node, with a specified identifierstatic final Node
NodeFactory.createNode
(Node node) constructor used to clone a node and all childrenstatic final Node
NodeFactory.createNode
(Node[] children) static final Node
NodeFactory.createNode
(Node[] children, double height) Create a node with the specified children, and the specified branch heightstatic final Node
NodeFactory.createNodeBranchLength
(double branchLength, Identifier id) create a node, with a specified identifierstatic final Node
NodeFactory.createNodeBranchLength
(double branchLength, Node[] children) Create a node with the specified children, and the specified branch lengthstatic final Node
NodeUtils.findByIdentifier
(Node node, String identifierName) Returns the first node in this tree that has the required identifier.static final Node[]
NodeUtils.findByIdentifier
(Node node, String[] identifierNames) Returns the first nodes in this tree that has the required identifiers.static final Node
NodeUtils.findByIdentifier
(Node node, Identifier identifier) Returns the first node in this tree that has the required identifier.static final Node[]
NodeUtils.findByIdentifier
(Node node, Identifier[] identifiers) Returns the first nodes in this tree that has the required identifiers.SimpleTree.findNode
(int num) return node with number num (as displayed in ASCII tree)Tree.TreeBase.findNode
(int num) return node with number num (as displayed in ASCII tree)final Node
TreeRestricter.generateNode()
Node[]
TreeManipulator.getAllRootedBy
(String[] outgroupNames) TreeManipulator.getAsInputRooting()
A method for recovering the input (construction) tree (with the EXPANSION/MIMIC/REDUCED differences)Node.getChild
(int n) get child nodeSimpleNode.getChild
(int n) get child nodestatic Node
TreeManipulator.getDefaultRoot()
final Node
ParameterizedTree.ParameterizedTreeBase.getExternalNode
(int i) returns the ith external node in the tree.final Node
SimpleTree.getExternalNode
(int i) Returns the ith external node.Tree.getExternalNode
(int i) final Node
Tree.TreeBase.getExternalNode
(int i) Returns the ith external node.static Node[]
NodeUtils.getExternalNodes
(Node root) Obtains all external nodes from tree defined by root and returns as an arraystatic Node
NodeUtils.getFirstCommonAncestor
(Node[] nodes) For a set of nodes in the tree returns the common ancestor closest to all nodes (most recent common ancestor)static Node
NodeUtils.getFirstCommonAncestor
(Node nodeOne, Node nodeTwo) For two nodes in the tree returns the common ancestor closest to both nodes (most recent common ancestor)final Node
ParameterizedTree.ParameterizedTreeBase.getInternalNode
(int i) returns the ith internal node in the tree.final Node
SimpleTree.getInternalNode
(int i) Returns the ith internal node.Tree.getInternalNode
(int i) final Node
Tree.TreeBase.getInternalNode
(int i) Returns the ith internal node.static Node[]
NodeUtils.getInternalNodes
(Node root, boolean includeRoot) Obtains all internal nodes from tree defined by root and returns as an arrayTreeManipulator.getMidPointRooted()
static final Node
TreeUtils.getNodeByName
(Node root, String name) static final Node
TreeUtils.getNodeByName
(Tree tree, String name) TreeManipulator.PALNodeWrapper.getPALPeer()
Node.getParent()
Returns the parent node of this node.final Node
SimpleNode.getParent()
Returns the parent node of this node.static Node
TreeUtils.getRandomNode
(Tree tree) Returns a uniformly distributed random node from the tree, including both internal and external nodes.final Node
ParameterizedTree.ParameterizedTreeBase.getRoot()
Returns the root node of this tree.final Node
SimpleTree.getRoot()
Returns the root node of this tree.Tree.getRoot()
final Node
Tree.TreeBase.getRoot()
Returns the root node of this tree.TreeManipulator.getRootedAbove
(Node base) TreeManipulator.getRootedBy
(String[] outgroupNames) TreeManipulator.getRootedBy
(String[] outgroupNames, double ingroupBranchLength) static Node
RootedTreeUtils.getSubtree
(Node root, Node node) TreeManipulator.getUnrooted()
return unrooted nodestatic Node
NodeUtils.postorderSuccessor
(Node node) determine postorder successor of a nodestatic Node
NodeUtils.preorderSuccessor
(Node node) determine preorder successor of this nodeNode.removeChild
(int n) remove childSimpleNode.removeChild
(int n) remove childModifier and TypeMethodDescriptionvoid
add new child nodevoid
add new child nodeTreeManipulator.BranchAccess.attachSubTree
(Node subTree, int constructionMode) Create a new TreeManipulator object that has sub grafted on (half way across this branch)static int
RootedTreeUtils.cladeCount
(Node subtree, Vector trees) static int
RootedTreeUtils.collectTaxa
(Node root, Hashtable table) Collects all of the names of the taxa in the tree into a hashtable.final pal.tree.TreeRestricter.RNode
static boolean
RootedTreeUtils.containsClade
(Node root, Node clade) static boolean
RootedTreeUtils.containsNovelTaxa
(Node root, Hashtable taxa) static boolean
RootedTreeUtils.containsSubtree
(Node root, Node node) static final void
NodeUtils.convertNegativeBranchLengthsToZeroLength
(Node node) If the given node or the sub tree defined by that node have negative branch lengths, they'll have zeron branch lengths after a call to this function!static final Node
NodeFactory.createNode
(Node node) constructor used to clone a node and all childrenstatic final Node
NodeFactory.createNode
(Node[] children) static final Node
NodeFactory.createNode
(Node[] children, double height) Create a node with the specified children, and the specified branch heightstatic final Node
NodeFactory.createNodeBranchLength
(double branchLength, Node[] children) Create a node with the specified children, and the specified branch lengthstatic boolean
static void
NodeUtils.exchangeInfo
(Node node1, Node node2) Exchange field info between two nodes.static final Node
NodeUtils.findByIdentifier
(Node node, String identifierName) Returns the first node in this tree that has the required identifier.static final Node[]
NodeUtils.findByIdentifier
(Node node, String[] identifierNames) Returns the first nodes in this tree that has the required identifiers.static final Node
NodeUtils.findByIdentifier
(Node node, Identifier identifier) Returns the first node in this tree that has the required identifier.static final Node[]
NodeUtils.findByIdentifier
(Node node, Identifier[] identifiers) Returns the first nodes in this tree that has the required identifiers.static double
NodeUtils.findLargestChild
(Node node) Finds the largest child (in terms of node height).final Object
ParameterizedTree.ParameterizedTreeBase.getAttribute
(Node node, String name) SimpleTree.getAttribute
(Node node, String name) Tree.getAttribute
(Node node, String name) Tree.TreeBase.getAttribute
(Node node, String name) static void
get clade for internal nodestatic Node
static double
NodeUtils.getDistanceToRoot
(Node node) determine distance to rootstatic Node[]
NodeUtils.getExternalNodes
(Node root) Obtains all external nodes from tree defined by root and returns as an arraystatic void
NodeUtils.getExternalNodes
(Node root, Vector store) Appends all external nodes from tree defined by root to Vector storestatic Node
NodeUtils.getFirstCommonAncestor
(Node[] nodes) For a set of nodes in the tree returns the common ancestor closest to all nodes (most recent common ancestor)static Node
NodeUtils.getFirstCommonAncestor
(Node nodeOne, Node nodeTwo) For two nodes in the tree returns the common ancestor closest to both nodes (most recent common ancestor)static int
NodeUtils.getInternalNodeCount
(Node root) static Node[]
NodeUtils.getInternalNodes
(Node root, boolean includeRoot) Obtains all internal nodes from tree defined by root and returns as an arraystatic void
NodeUtils.getInternalNodes
(Node root, Vector store) Appends all internal nodes from tree defined by root to Vector storestatic int
NodeUtils.getLeafCount
(Node node) Return the number of terminal leaves below this node or 1 if this is a terminal leaf.static final double
NodeUtils.getMaximumPathLengthLengthToLeaf
(Node root) static int
NodeUtils.getMaxNodeDepth
(Node root) static double
RootedTreeUtils.getMeanCladeHeight
(Node clade, Vector trees) static double
RootedTreeUtils.getMeanSubtreeHeight
(Node subtree, Vector trees) static final double
NodeUtils.getMinimumPathLengthLengthToLeaf
(Node root) static final Node
TreeUtils.getNodeByName
(Node root, String name) static final double[]
NodeUtils.getPathLengthInfo
(Node root) Calculates max/min lengths of paths from root to leaf, taking into account branch lengthsTreeManipulator.getRootedAbove
(Node base) static void
get split for branch associated with internal nodestatic Node
RootedTreeUtils.getSubtree
(Node root, Node node) TreeManipulator.getTreeRootedAbove
(Node n) static final int
NodeUtils.getUnrootedBranchCount
(Node center) returns number of branches centered around an internal node in an unrooted treestatic void
NodeUtils.heights2Lengths
(Node node) determines branch lengths of this and all descendent nodes from heightsstatic void
NodeUtils.heights2Lengths
(Node node, boolean respectMinimum) determines branch lengths of this and all descendent nodes from heightsprotected void
protected void
Initialized node instance variables based on given Node.protected void
SimpleNode.init
(Node n, boolean keepId, LabelMapping lm) Initialized node instance variables based on given Node.void
Node.insertChild
(Node c, int pos) add new child node (insertion at a specific position)void
SimpleNode.insertChild
(Node n, int pos) add new child node (insertion at a specific position)static final void
RootedTreeInterface.Utils.instruct
(Node palRoot, RootedTreeInterface treeInterface) Build a tree display based on a normal pal node.static final void
UnrootedTreeInterface.Utils.instruct
(Node root, UnrootedTreeInterface treeInterface) Build a tree display based on a normal pal node.static boolean
NodeUtils.isAncestor
(Node possibleAncestor, Node node) For two nodes in the tree true if the first node is the ancestor of the secondstatic void
NodeUtils.joinChilds
(Node node, int n1, int n2) join two childs, introducing a new node/branch in the tree that replaces the first childstatic void
NodeUtils.lengths2Heights
(Node root) Converts lengths to heights, *without* assuming contemporaneous tips.static void
NodeUtils.lengths2HeightsKeepTips
(Node node, boolean useMax) Converts lengths to heights, but maintains tip heights.static void
NodeUtils.localHeights2Lengths
(Node node, boolean respectMinimum) determines branch lengths of this node and its immediate descendent nodes from heights.static Node
NodeUtils.postorderSuccessor
(Node node) determine postorder successor of a nodestatic Node
NodeUtils.preorderSuccessor
(Node node) determine preorder successor of this nodestatic void
NodeUtils.printNH
(PrintWriter out, Node node, boolean printLengths, boolean printInternalLabels) prints node in New Hamshire format.static int
NodeUtils.printNH
(PrintWriter out, Node node, boolean printLengths, boolean printInternalLabels, int column, boolean breakLines) static void
NodeUtils.removeBranch
(Node node) remove internal branch (collapse node with its parent)static void
NodeUtils.removeChild
(Node parent, Node child) remove childvoid
make provided node the root nodevoid
make provided node the root nodestatic void
static void
NodeUtils.restoreBranch
(Node node) restore internal branchstatic boolean
final void
ParameterizedTree.ParameterizedTreeBase.setAttribute
(Node node, String name, Object value) void
SimpleTree.setAttribute
(Node node, String name, Object value) Sets an named attribute for a given node.void
Tree.setAttribute
(Node node, String name, Object value) Sets an named attribute for a given node.void
Tree.TreeBase.setAttribute
(Node node, String name, Object value) Sets an named attribute for a given node.void
set child nodevoid
set child nodevoid
Set the parent node of this node.void
Set the parent node of this node.final void
final void
Set a new node as root node.void
This method constructs a tree from the given root node.void
Called by subclasses that can't give root at time of construction (of this class)static int
RootedTreeUtils.subtreeCount
(Node subtree, Vector trees) ModifierConstructorDescriptionPALNodeWrapper
(Node peer) PALNodeWrapper
(Node peer, TreeManipulator.PALNodeWrapper parent) SimpleNode
(Node n) constructor used to clone a node and all childrenprotected
SimpleNode
(Node[] children) protected
SimpleNode
(Node[] children, double branchLength) ConstructorSimpleNode
(Node n, boolean keepIds) SimpleNode
(Node n, LabelMapping lm) SimpleTree
(Node r) constructor taking a root nodeprotected
constructorprotected
TreeBase
(Tree.TreeBase tree, Node newRoot) clone constructorTreeManipulator
(Node base) Units will be Units.UNKNOWNTreeManipulator
(Node base, int units) Construct a TreeManipulator based around a normal treeTreeManipulator
(Node base, int units, int constructionMode) Construct a TreeManipulator based around a normal treeTreeRestricter
(Node root, int units, String[] names, boolean inclusion) -
Uses of Node in pal.treesearch
Methods in pal.treesearch that return NodeModifier and TypeMethodDescriptionfinal Node
AbstractParentableConstrainedNode.buildDescendentPALNodeBase()
ConstrainedLeafNode.buildDescendentPALNodeBase()
ConstrainedNode.buildDescendentPALNodeBase()
Build node model base units (eg years)final Node
AbstractParentableConstrainedNode.buildDescendentPALNodeES
(ConstraintModel.GroupManager groupManager) final Node
ConstrainedLeafNode.buildDescendentPALNodeES
(ConstraintModel.GroupManager groupManager) ConstrainedNode.buildDescendentPALNodeES
(ConstraintModel.GroupManager groupConstraints) Build node with Expected Substitution Unitsprotected final Node
AbstractParentableConstrainedNode.buildLeftDecendentPALNodeBase()
final Node
FreeLeafNode.buildPALNode
(double branchLength, FreeBranch caller) UnrootedMLSearcher.buildPALNode()
FreeBranch.buildPALNodeBase()
FreeBranch.buildPALNodeBase
(FreeNode caller) FreeInternalNode.buildPALNodeBase
(double branchLength, FreeBranch caller) final Node
FreeLeafNode.buildPALNodeBase
(double branchLength, FreeBranch caller) FreeNode.buildPALNodeBase
(double branchLength_, FreeBranch caller) GeneralLikelihoodSearcher.buildPALNodeBase()
PivotNode.buildPALNodeBase()
PivotNode.buildPALNodeBase
(double branchLength_, FreeBranch caller) RootAccess.buildPALNodeBase()
FreeBranch.buildPALNodeES()
FreeBranch.buildPALNodeES
(FreeNode caller) FreeInternalNode.buildPALNodeES
(double branchLength, FreeBranch caller) final Node
FreeLeafNode.buildPALNodeES
(double branchLength, FreeBranch caller) FreeNode.buildPALNodeES
(double branchLength_, FreeBranch caller) GeneralLikelihoodSearcher.buildPALNodeES()
PivotNode.buildPALNodeES()
PivotNode.buildPALNodeES
(double branchLength_, FreeBranch caller) RootAccess.buildPALNodeES()
protected final Node
AbstractParentableConstrainedNode.buildRightDecendentPALNodeBase()
Methods in pal.treesearch with parameters of type NodeModifier and TypeMethodDescriptionCreate a new Tree Searcher with a new sub tree attachedBranchAccess.attach
(Node subTree, Alignment fullAlignment, SubstitutionModel model) Create a new Tree Searcher with a new sub tree attachedGeneralConstructionTool.createConstrainedNode
(Node peer, ParentableConstrainedNode parent, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager) Create an appropriate constrained node given a peer, and it's parent nodeGeneralConstructionTool.createFreeNode
(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store) Create an appropriate free node given a peer, and it's parent branchGeneralConstructionTool.createRootAccess
(Node baseTree, GeneralConstraintGroupManager.Store store) String[]
GeneralConstructionTool.getLeafLabelSet
(Node peer) A horibly inefficient way of doing things.void
GeneralConstructionTool.getLeafLabelSet
(Node peer, ArrayList al) Constructors in pal.treesearch with parameters of type NodeModifierConstructorDescriptionprotected
AbstractParentableConstrainedNode
(Node peer, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager) ConstrainedInternalNode
(Node peer, ParentableConstrainedNode parentNode, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager) ConstrainedLeafNode
(ParentableConstrainedNode parentNode, Node peer, double height, GeneralConstructionTool tool, ConstraintModel.GroupManager parentGroup) FreeBranch
(Node n, FreeNode parent, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store) Continuing recurison constructor for a given treeFreeBranch
(Node n, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store) The starting constructor for building from a given treeFreeInternalNode
(Node i, FreeBranch parentFreeBranch, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store) GeneralLikelihoodSearcher
(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel) PivotNode
(Node tree, FreeBranch parentConnection, GeneralConstructionTool tool, GeneralConstraintGroupManager constraintGroupManager, GeneralConstraintGroupManager.Store store) The subtree constructor with a connection to the rest of the treePivotNode
(Node subTree, GeneralConstructionTool tool, GeneralConstraintGroupManager groupManager, GeneralConstraintGroupManager.Store store) The root constructor, only used when the whole tree is constrainedUnrootedMLSearcher
(Node root) Create a searcher based on a given tree, that has no alignment , or model, specified (useful as backbone tree for attaching new nodes)UnrootedMLSearcher
(Node root, Alignment alignment, SubstitutionModel model) UnrootedMLSearcher
(Node root, Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory) UnrootedMLSearcher
(Node root, SubstitutionModel model) Create a searcher based on a given tree, that has no alignment specified (useful as backbone tree for attaching new nodes) -
Uses of Node in pal.xml
Modifier and TypeMethodDescriptionstatic Node
ElementParser.parseEdgeNodeElement
(Element e) static Node
ElementParser.parseNodeElement
(Element e) Modifier and TypeMethodDescriptionstatic Element
ElementFactory.createEdgeNodeElement
(Node node, Document document) static Element
ElementFactory.createNodeElement
(Node node, Document document) static Element
ElementFactory.createNodeElement
(Node node, Document document, boolean includeEdges)