Uses of Interface
pal.tree.Node
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Packages that use Node Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.gui GUI components for some special objects (e.g., trees).pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).pal.treesearch pal.xml Utility classes for converting PAL objects to and from XML documents. -
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Uses of Node in pal.eval
Methods in pal.eval that return Node Modifier and Type Method Description protected NodeSimpleLikelihoodCalculator. getNextBranch(Node branch, Node center)get next branch around a center node (center may be root, but root is never returned)Methods in pal.eval with parameters of type Node Modifier and Type Method Description protected 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
Classes in pal.gui that implement Node Modifier and Type Class Description classPositionedNodeA tree node that has a scalar position for the purposes of drawing the tree.Methods in pal.gui that return Node Modifier and Type Method Description NodePositionedNode. getPeer()Methods in pal.gui with parameters of type Node Modifier and Type Method Description protected static doubleTreePainter. getMaxLeafTime(Node node)protected LabelDisplayerTreePainter. getNodeDisplay(Node n, LabelDisplayer defaultDisplay)protected java.lang.StringTreePainter. getNodeName(Node node)Constructors in pal.gui with parameters of type Node Constructor Description PositionedNode(Node node)PositionedNode(Node node, Node highlightNode)Builds a tree based on node, but highlights highlightNode -
Uses of Node in pal.tree
Subinterfaces of Node in pal.tree Modifier and Type Interface Description interfaceAttributeNodeinterface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.Classes in pal.tree that implement Node Modifier and Type Class Description classSimpleNodedata structure for a node (includes branch) in a binary/non-binary rooted/unrooted treeMethods in pal.tree that return Node Modifier and Type Method Description static NodeNodeFactory. createNode()create a nodestatic NodeNodeFactory. createNode(Identifier id)create a node, with a specified identifierstatic NodeNodeFactory. createNode(Identifier id, double height)create a node, with a specified identifierstatic NodeNodeFactory. createNode(Node node)constructor used to clone a node and all childrenstatic NodeNodeFactory. createNode(Node[] children)static NodeNodeFactory. createNode(Node[] children, double height)Create a node with the specified children, and the specified branch heightstatic NodeNodeFactory. createNodeBranchLength(double branchLength, Identifier id)create a node, with a specified identifierstatic NodeNodeFactory. createNodeBranchLength(double branchLength, Node[] children)Create a node with the specified children, and the specified branch lengthstatic NodeNodeUtils. findByIdentifier(Node node, java.lang.String identifierName)Returns the first node in this tree that has the required identifier.static Node[]NodeUtils. findByIdentifier(Node node, java.lang.String[] identifierNames)Returns the first nodes in this tree that has the required identifiers.static NodeNodeUtils. findByIdentifier(Node node, Identifier identifier)Returns the first node in this tree that has the required identifier.static Node[]NodeUtils. findByIdentifier(Node node, Identifier[] identifiers)Returns the first nodes in this tree that has the required identifiers.NodeSimpleTree. findNode(int num)return node with number num (as displayed in ASCII tree)NodeTree.TreeBase. findNode(int num)return node with number num (as displayed in ASCII tree)NodeTreeRestricter. generateNode()Node[]TreeManipulator. getAllRootedBy(java.lang.String[] outgroupNames)NodeTreeManipulator. getAsInputRooting()A method for recovering the input (construction) tree (with the EXPANSION/MIMIC/REDUCED differences)NodeNode. getChild(int n)get child nodeNodeSimpleNode. getChild(int n)get child nodestatic NodeRootedTreeUtils. getClade(Node root, Node clade)NodeTreeManipulator. getDefaultRoot()NodeParameterizedTree.ParameterizedTreeBase. getExternalNode(int i)returns the ith external node in the tree.NodeSimpleTree. getExternalNode(int i)Returns the ith external node.NodeTree. getExternalNode(int i)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)NodeParameterizedTree.ParameterizedTreeBase. getInternalNode(int i)returns the ith internal node in the tree.NodeSimpleTree. getInternalNode(int i)Returns the ith internal node.NodeTree. getInternalNode(int i)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 arrayNodeTreeManipulator. getMidPointRooted()static NodeTreeUtils. getNodeByName(Node root, java.lang.String name)static NodeTreeUtils. getNodeByName(Tree tree, java.lang.String name)NodeTreeManipulator.PALNodeWrapper. getPALPeer()NodeNode. getParent()Returns the parent node of this node.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.NodeParameterizedTree.ParameterizedTreeBase. getRoot()Returns the root node of this tree.NodeSimpleTree. getRoot()Returns the root node of this tree.NodeTree. getRoot()NodeTree.TreeBase. getRoot()Returns the root node of this tree.NodeTreeManipulator. getRootedAbove(Node base)NodeTreeManipulator. getRootedBy(java.lang.String[] outgroupNames)NodeTreeManipulator. getRootedBy(java.lang.String[] outgroupNames, double ingroupBranchLength)static NodeRootedTreeUtils. getSubtree(Node root, Node node)NodeTreeManipulator. getUnrooted()return unrooted nodestatic NodeNodeUtils. postorderSuccessor(Node node)determine postorder successor of a nodestatic NodeNodeUtils. preorderSuccessor(Node node)determine preorder successor of this nodeNodeNode. removeChild(int n)remove childNodeSimpleNode. removeChild(int n)remove childMethods in pal.tree with parameters of type Node Modifier and Type Method Description voidNode. addChild(Node c)add new child nodevoidSimpleNode. addChild(Node n)add new child nodeTreeManipulatorTreeManipulator.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, java.util.Vector trees)static intRootedTreeUtils. collectTaxa(Node root, java.util.Hashtable table)Collects all of the names of the taxa in the tree into a hashtable.pal.tree.TreeRestricter.RNodeTreeRestricter. construct(Node peer, java.lang.String[] names, boolean inclusion, boolean isRoot)static booleanRootedTreeUtils. containsClade(Node root, Node clade)static booleanRootedTreeUtils. containsNovelTaxa(Node root, java.util.Hashtable taxa)static booleanRootedTreeUtils. containsSubtree(Node root, Node node)static 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 NodeNodeFactory. createNode(Node node)constructor used to clone a node and all childrenstatic NodeNodeFactory. createNode(Node[] children)static NodeNodeFactory. createNode(Node[] children, double height)Create a node with the specified children, and the specified branch heightstatic NodeNodeFactory. createNodeBranchLength(double branchLength, Node[] children)Create a node with the specified children, and the specified branch lengthstatic booleanRootedTreeUtils. equal(Node node1, Node node2)static voidNodeUtils. exchangeInfo(Node node1, Node node2)Exchange field info between two nodes.static NodeNodeUtils. findByIdentifier(Node node, java.lang.String identifierName)Returns the first node in this tree that has the required identifier.static Node[]NodeUtils. findByIdentifier(Node node, java.lang.String[] identifierNames)Returns the first nodes in this tree that has the required identifiers.static NodeNodeUtils. findByIdentifier(Node node, Identifier identifier)Returns the first node in this tree that has the required identifier.static 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).java.lang.ObjectParameterizedTree.ParameterizedTreeBase. getAttribute(Node node, java.lang.String name)java.lang.ObjectSimpleTree. getAttribute(Node node, java.lang.String name)java.lang.ObjectTree. getAttribute(Node node, java.lang.String name)java.lang.ObjectTree.TreeBase. getAttribute(Node node, java.lang.String name)static voidCladeSystem. getClade(IdGroup idGroup, Node internalNode, boolean[] clade)get clade for internal nodestatic NodeRootedTreeUtils. getClade(Node root, Node clade)static 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, java.util.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, java.util.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 doubleNodeUtils. getMaximumPathLengthLengthToLeaf(Node root)static intNodeUtils. getMaxNodeDepth(Node root)static doubleRootedTreeUtils. getMeanCladeHeight(Node clade, java.util.Vector trees)static doubleRootedTreeUtils. getMeanSubtreeHeight(Node subtree, java.util.Vector trees)static doubleNodeUtils. getMinimumPathLengthLengthToLeaf(Node root)static NodeTreeUtils. getNodeByName(Node root, java.lang.String name)static double[]NodeUtils. getPathLengthInfo(Node root)Calculates max/min lengths of paths from root to leaf, taking into account branch lengthsNodeTreeManipulator. getRootedAbove(Node base)static voidSplitUtils. getSplit(IdGroup idGroup, Node internalNode, boolean[] split)get split for branch associated with internal nodestatic NodeRootedTreeUtils. getSubtree(Node root, Node node)TreeTreeManipulator. getTreeRootedAbove(Node n)static 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 voidSimpleNode. init(Node n)protected voidSimpleNode. init(Node n, boolean keepId)Initialized 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 voidRootedTreeInterface.Utils. instruct(Node palRoot, RootedTreeInterface treeInterface)Build a tree display based on a normal pal node.static 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(java.io.PrintWriter out, Node node, boolean printLengths, boolean printInternalLabels)prints node in New Hamshire format.static intNodeUtils. printNH(java.io.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 childvoidSimpleTree. reroot(Node node)make provided node the root nodevoidTree.TreeBase. reroot(Node node)make provided node the root nodestatic voidTreeUtils. reroot(Tree tree, Node node)static voidNodeUtils. restoreBranch(Node node)restore internal branchstatic booleanRootedTreeUtils. sameTaxa(Node node1, Node node2)voidParameterizedTree.ParameterizedTreeBase. setAttribute(Node node, java.lang.String name, java.lang.Object value)voidSimpleTree. setAttribute(Node node, java.lang.String name, java.lang.Object value)Sets an named attribute for a given node.voidTree. setAttribute(Node node, java.lang.String name, java.lang.Object value)Sets an named attribute for a given node.voidTree.TreeBase. setAttribute(Node node, java.lang.String name, java.lang.Object value)Sets an named attribute for a given node.voidNode. setChild(int n, Node node)set child nodevoidSimpleNode. setChild(int n, Node node)set child nodevoidNode. setParent(Node node)Set the parent node of this node.voidSimpleNode. setParent(Node node)Set the parent node of this node.voidParameterizedTree.ParameterizedTreeBase. setRoot(Node root)voidSimpleTree. setRoot(Node r)Set a new node as root node.voidTree. setRoot(Node root)This method constructs a tree from the given root node.voidTree.TreeBase. setRoot(Node theRoot)Called by subclasses that can't give root at time of construction (of this class)static intRootedTreeUtils. subtreeCount(Node subtree, java.util.Vector trees)Constructors in pal.tree with parameters of type Node Constructor Description PALNodeWrapper(Node peer)PALNodeWrapper(Node peer, TreeManipulator.PALNodeWrapper parent)SimpleNode(Node n)constructor used to clone a node and all childrenSimpleNode(Node[] children)SimpleNode(Node[] children, double branchLength)ConstructorSimpleNode(Node n, boolean keepIds)SimpleNode(Node n, LabelMapping lm)SimpleTree(Node r)constructor taking a root nodeTreeBase(Node theRoot)constructorTreeBase(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, java.lang.String[] names, boolean inclusion) -
Uses of Node in pal.treesearch
Methods in pal.treesearch that return Node Modifier and Type Method Description NodeAbstractParentableConstrainedNode. buildDescendentPALNodeBase()NodeConstrainedLeafNode. buildDescendentPALNodeBase()NodeConstrainedNode. buildDescendentPALNodeBase()Build node model base units (eg years)NodeAbstractParentableConstrainedNode. buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager)NodeConstrainedLeafNode. buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager)NodeConstrainedNode. buildDescendentPALNodeES(ConstraintModel.GroupManager groupConstraints)Build node with Expected Substitution Unitsprotected NodeAbstractParentableConstrainedNode. buildLeftDecendentPALNodeBase()NodeFreeLeafNode. buildPALNode(double branchLength, FreeBranch caller)NodeUnrootedMLSearcher. buildPALNode()NodeFreeBranch. buildPALNodeBase()NodeFreeBranch. buildPALNodeBase(FreeNode caller)NodeFreeInternalNode. buildPALNodeBase(double branchLength, FreeBranch caller)NodeFreeLeafNode. buildPALNodeBase(double branchLength, FreeBranch caller)NodeFreeNode. buildPALNodeBase(double branchLength_, FreeBranch caller)NodeGeneralLikelihoodSearcher. buildPALNodeBase()NodePivotNode. buildPALNodeBase()NodePivotNode. buildPALNodeBase(double branchLength_, FreeBranch caller)NodeRootAccess. buildPALNodeBase()NodeFreeBranch. buildPALNodeES()NodeFreeBranch. buildPALNodeES(FreeNode caller)NodeFreeInternalNode. buildPALNodeES(double branchLength, FreeBranch caller)NodeFreeLeafNode. buildPALNodeES(double branchLength, FreeBranch caller)NodeFreeNode. buildPALNodeES(double branchLength_, FreeBranch caller)NodeGeneralLikelihoodSearcher. buildPALNodeES()NodePivotNode. buildPALNodeES()NodePivotNode. buildPALNodeES(double branchLength_, FreeBranch caller)NodeRootAccess. buildPALNodeES()protected NodeAbstractParentableConstrainedNode. buildRightDecendentPALNodeBase()Methods in pal.treesearch with parameters of type Node Modifier and Type Method Description UnrootedMLSearcherBranchAccess. attach(Node subTree, Alignment fullAlignment)Create a new Tree Searcher with a new sub tree attachedUnrootedMLSearcherBranchAccess. attach(Node subTree, Alignment fullAlignment, SubstitutionModel model)Create a new Tree Searcher with a new sub tree attachedConstrainedNodeGeneralConstructionTool. createConstrainedNode(Node peer, ParentableConstrainedNode parent, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager)Create an appropriate constrained node given a peer, and it's parent nodeFreeNodeGeneralConstructionTool. createFreeNode(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store)Create an appropriate free node given a peer, and it's parent branchRootAccessGeneralConstructionTool. createRootAccess(Node baseTree, GeneralConstraintGroupManager.Store store)java.lang.String[]GeneralConstructionTool. getLeafLabelSet(Node peer)A horibly inefficient way of doing things.voidGeneralConstructionTool. getLeafLabelSet(Node peer, java.util.ArrayList al)Constructors in pal.treesearch with parameters of type Node Constructor Description 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 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Uses of Node in pal.xml
Methods in pal.xml that return Node Modifier and Type Method Description static NodeElementParser. parseEdgeNodeElement(org.w3c.dom.Element e)static NodeElementParser. parseNodeElement(org.w3c.dom.Element e)Methods in pal.xml with parameters of type Node Modifier and Type Method Description static org.w3c.dom.ElementElementFactory. createEdgeNodeElement(Node node, org.w3c.dom.Document document)static org.w3c.dom.ElementElementFactory. createNodeElement(Node node, org.w3c.dom.Document document)static org.w3c.dom.ElementElementFactory. createNodeElement(Node node, org.w3c.dom.Document document, boolean includeEdges)
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