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.
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Uses of Node in pal.eval
Modifier and TypeMethodDescriptionprotected NodeSimpleLikelihoodCalculator.getNextBranch(Node branch, Node center) get next branch around a center node (center may be root, but root is never returned)Modifier and TypeMethodDescriptionprotected NodeSimpleLikelihoodCalculator.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 voidSimpleLikelihoodCalculator.partialsExternal(Node branch) compute partials for external branchprotected voidSimpleLikelihoodCalculator.partialsInternal(Node center) compute partials for branch around center node (it is assumed that multiplied partials are available in the neighbor branch)protected voidSimpleLikelihoodCalculator.productPartials(Node center) multiply partials into the neighbour of branch -
Uses of Node in pal.gui
Modifier and TypeClassDescriptionclassA tree node that has a scalar position for the purposes of drawing the tree.Modifier and TypeMethodDescriptionprotected static final doubleTreePainter.getMaxLeafTime(Node node) protected final LabelDisplayerTreePainter.getNodeDisplay(Node n, LabelDisplayer defaultDisplay) protected final StringTreePainter.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 TypeInterfaceDescriptioninterfaceinterface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.Modifier and TypeClassDescriptionclassdata structure for a node (includes branch) in a binary/non-binary rooted/unrooted treeModifier and TypeMethodDescriptionstatic final NodeNodeFactory.createNode()create a nodestatic final NodeNodeFactory.createNode(Identifier id) create a node, with a specified identifierstatic final NodeNodeFactory.createNode(Identifier id, double height) create a node, with a specified identifierstatic final NodeNodeFactory.createNode(Node node) constructor used to clone a node and all childrenstatic final NodeNodeFactory.createNode(Node[] children) static final NodeNodeFactory.createNode(Node[] children, double height) Create a node with the specified children, and the specified branch heightstatic final NodeNodeFactory.createNodeBranchLength(double branchLength, Identifier id) create a node, with a specified identifierstatic final NodeNodeFactory.createNodeBranchLength(double branchLength, Node[] children) Create a node with the specified children, and the specified branch lengthstatic final NodeNodeUtils.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 NodeNodeUtils.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 NodeTreeRestricter.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 NodeTreeManipulator.getDefaultRoot()final NodeParameterizedTree.ParameterizedTreeBase.getExternalNode(int i) returns the ith external node in the tree.final NodeSimpleTree.getExternalNode(int i) Returns the ith external node.Tree.getExternalNode(int i) final NodeTree.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 NodeNodeUtils.getFirstCommonAncestor(Node[] nodes) For a set of nodes in the tree returns the common ancestor closest to all nodes (most recent common ancestor)static NodeNodeUtils.getFirstCommonAncestor(Node nodeOne, Node nodeTwo) For two nodes in the tree returns the common ancestor closest to both nodes (most recent common ancestor)final NodeParameterizedTree.ParameterizedTreeBase.getInternalNode(int i) returns the ith internal node in the tree.final NodeSimpleTree.getInternalNode(int i) Returns the ith internal node.Tree.getInternalNode(int i) final NodeTree.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 NodeTreeUtils.getNodeByName(Node root, String name) static final NodeTreeUtils.getNodeByName(Tree tree, String name) TreeManipulator.PALNodeWrapper.getPALPeer()Node.getParent()Returns the parent node of this node.final NodeSimpleNode.getParent()Returns the parent node of this node.static NodeTreeUtils.getRandomNode(Tree tree) Returns a uniformly distributed random node from the tree, including both internal and external nodes.final NodeParameterizedTree.ParameterizedTreeBase.getRoot()Returns the root node of this tree.final NodeSimpleTree.getRoot()Returns the root node of this tree.Tree.getRoot()final NodeTree.TreeBase.getRoot()Returns the root node of this tree.TreeManipulator.getRootedAbove(Node base) TreeManipulator.getRootedBy(String[] outgroupNames) TreeManipulator.getRootedBy(String[] outgroupNames, double ingroupBranchLength) static NodeRootedTreeUtils.getSubtree(Node root, Node node) TreeManipulator.getUnrooted()return unrooted nodestatic NodeNodeUtils.postorderSuccessor(Node node) determine postorder successor of a nodestatic NodeNodeUtils.preorderSuccessor(Node node) determine preorder successor of this nodeNode.removeChild(int n) remove childSimpleNode.removeChild(int n) remove childModifier and TypeMethodDescriptionvoidadd new child nodevoidadd 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 intRootedTreeUtils.cladeCount(Node subtree, Vector trees) static intRootedTreeUtils.collectTaxa(Node root, Hashtable table) Collects all of the names of the taxa in the tree into a hashtable.final pal.tree.TreeRestricter.RNodestatic booleanRootedTreeUtils.containsClade(Node root, Node clade) static booleanRootedTreeUtils.containsNovelTaxa(Node root, Hashtable taxa) static booleanRootedTreeUtils.containsSubtree(Node root, Node node) static final voidNodeUtils.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 NodeNodeFactory.createNode(Node node) constructor used to clone a node and all childrenstatic final NodeNodeFactory.createNode(Node[] children) static final NodeNodeFactory.createNode(Node[] children, double height) Create a node with the specified children, and the specified branch heightstatic final NodeNodeFactory.createNodeBranchLength(double branchLength, Node[] children) Create a node with the specified children, and the specified branch lengthstatic booleanstatic voidNodeUtils.exchangeInfo(Node node1, Node node2) Exchange field info between two nodes.static final NodeNodeUtils.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 NodeNodeUtils.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 doubleNodeUtils.findLargestChild(Node node) Finds the largest child (in terms of node height).final ObjectParameterizedTree.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 voidget clade for internal nodestatic Nodestatic doubleNodeUtils.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 voidNodeUtils.getExternalNodes(Node root, Vector store) Appends all external nodes from tree defined by root to Vector storestatic NodeNodeUtils.getFirstCommonAncestor(Node[] nodes) For a set of nodes in the tree returns the common ancestor closest to all nodes (most recent common ancestor)static NodeNodeUtils.getFirstCommonAncestor(Node nodeOne, Node nodeTwo) For two nodes in the tree returns the common ancestor closest to both nodes (most recent common ancestor)static intNodeUtils.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 voidNodeUtils.getInternalNodes(Node root, Vector store) Appends all internal nodes from tree defined by root to Vector storestatic intNodeUtils.getLeafCount(Node node) Return the number of terminal leaves below this node or 1 if this is a terminal leaf.static final doubleNodeUtils.getMaximumPathLengthLengthToLeaf(Node root) static intNodeUtils.getMaxNodeDepth(Node root) static doubleRootedTreeUtils.getMeanCladeHeight(Node clade, Vector trees) static doubleRootedTreeUtils.getMeanSubtreeHeight(Node subtree, Vector trees) static final doubleNodeUtils.getMinimumPathLengthLengthToLeaf(Node root) static final NodeTreeUtils.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 voidget split for branch associated with internal nodestatic NodeRootedTreeUtils.getSubtree(Node root, Node node) TreeManipulator.getTreeRootedAbove(Node n) static final intNodeUtils.getUnrootedBranchCount(Node center) returns number of branches centered around an internal node in an unrooted treestatic voidNodeUtils.heights2Lengths(Node node) determines branch lengths of this and all descendent nodes from heightsstatic voidNodeUtils.heights2Lengths(Node node, boolean respectMinimum) determines branch lengths of this and all descendent nodes from heightsprotected voidprotected voidInitialized node instance variables based on given Node.protected voidSimpleNode.init(Node n, boolean keepId, LabelMapping lm) Initialized node instance variables based on given Node.voidNode.insertChild(Node c, int pos) add new child node (insertion at a specific position)voidSimpleNode.insertChild(Node n, int pos) add new child node (insertion at a specific position)static final voidRootedTreeInterface.Utils.instruct(Node palRoot, RootedTreeInterface treeInterface) Build a tree display based on a normal pal node.static final voidUnrootedTreeInterface.Utils.instruct(Node root, UnrootedTreeInterface treeInterface) Build a tree display based on a normal pal node.static booleanNodeUtils.isAncestor(Node possibleAncestor, Node node) For two nodes in the tree true if the first node is the ancestor of the secondstatic voidNodeUtils.joinChilds(Node node, int n1, int n2) join two childs, introducing a new node/branch in the tree that replaces the first childstatic voidNodeUtils.lengths2Heights(Node root) Converts lengths to heights, *without* assuming contemporaneous tips.static voidNodeUtils.lengths2HeightsKeepTips(Node node, boolean useMax) Converts lengths to heights, but maintains tip heights.static voidNodeUtils.localHeights2Lengths(Node node, boolean respectMinimum) determines branch lengths of this node and its immediate descendent nodes from heights.static NodeNodeUtils.postorderSuccessor(Node node) determine postorder successor of a nodestatic NodeNodeUtils.preorderSuccessor(Node node) determine preorder successor of this nodestatic voidNodeUtils.printNH(PrintWriter out, Node node, boolean printLengths, boolean printInternalLabels) prints node in New Hamshire format.static intNodeUtils.printNH(PrintWriter out, Node node, boolean printLengths, boolean printInternalLabels, int column, boolean breakLines) static voidNodeUtils.removeBranch(Node node) remove internal branch (collapse node with its parent)static voidNodeUtils.removeChild(Node parent, Node child) remove childvoidmake provided node the root nodevoidmake provided node the root nodestatic voidstatic voidNodeUtils.restoreBranch(Node node) restore internal branchstatic booleanfinal voidParameterizedTree.ParameterizedTreeBase.setAttribute(Node node, String name, Object value) voidSimpleTree.setAttribute(Node node, String name, Object value) Sets an named attribute for a given node.voidTree.setAttribute(Node node, String name, Object value) Sets an named attribute for a given node.voidTree.TreeBase.setAttribute(Node node, String name, Object value) Sets an named attribute for a given node.voidset child nodevoidset child nodevoidSet the parent node of this node.voidSet the parent node of this node.final voidfinal voidSet a new node as root node.voidThis method constructs a tree from the given root node.voidCalled by subclasses that can't give root at time of construction (of this class)static intRootedTreeUtils.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 childrenprotectedSimpleNode(Node[] children) protectedSimpleNode(Node[] children, double branchLength) ConstructorSimpleNode(Node n, boolean keepIds) SimpleNode(Node n, LabelMapping lm) SimpleTree(Node r) constructor taking a root nodeprotectedconstructorprotectedTreeBase(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 NodeAbstractParentableConstrainedNode.buildDescendentPALNodeBase()ConstrainedLeafNode.buildDescendentPALNodeBase()ConstrainedNode.buildDescendentPALNodeBase()Build node model base units (eg years)final NodeAbstractParentableConstrainedNode.buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager) final NodeConstrainedLeafNode.buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager) ConstrainedNode.buildDescendentPALNodeES(ConstraintModel.GroupManager groupConstraints) Build node with Expected Substitution Unitsprotected final NodeAbstractParentableConstrainedNode.buildLeftDecendentPALNodeBase()final NodeFreeLeafNode.buildPALNode(double branchLength, FreeBranch caller) UnrootedMLSearcher.buildPALNode()FreeBranch.buildPALNodeBase()FreeBranch.buildPALNodeBase(FreeNode caller) FreeInternalNode.buildPALNodeBase(double branchLength, FreeBranch caller) final NodeFreeLeafNode.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 NodeFreeLeafNode.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 NodeAbstractParentableConstrainedNode.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.voidGeneralConstructionTool.getLeafLabelSet(Node peer, ArrayList al) Constructors in pal.treesearch with parameters of type NodeModifierConstructorDescriptionprotectedAbstractParentableConstrainedNode(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 NodeElementParser.parseEdgeNodeElement(Element e) static NodeElementParser.parseNodeElement(Element e) Modifier and TypeMethodDescriptionstatic ElementElementFactory.createEdgeNodeElement(Node node, Document document) static ElementElementFactory.createNodeElement(Node node, Document document) static ElementElementFactory.createNodeElement(Node node, Document document, boolean includeEdges)