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 Node
SimpleLikelihoodCalculator. 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 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
Classes in pal.gui that implement Node Modifier and Type Class Description class
PositionedNode
A 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 Node
PositionedNode. getPeer()
Methods in pal.gui with parameters of type Node Modifier and Type Method Description protected static double
TreePainter. getMaxLeafTime(Node node)
protected LabelDisplayer
TreePainter. getNodeDisplay(Node n, LabelDisplayer defaultDisplay)
protected java.lang.String
TreePainter. 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 interface
AttributeNode
interface 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 class
SimpleNode
data 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 Node
NodeFactory. createNode()
create a nodestatic Node
NodeFactory. createNode(Identifier id)
create a node, with a specified identifierstatic Node
NodeFactory. createNode(Identifier id, double height)
create a node, with a specified identifierstatic Node
NodeFactory. createNode(Node node)
constructor used to clone a node and all childrenstatic Node
NodeFactory. createNode(Node[] children)
static Node
NodeFactory. createNode(Node[] children, double height)
Create a node with the specified children, and the specified branch heightstatic Node
NodeFactory. createNodeBranchLength(double branchLength, Identifier id)
create a node, with a specified identifierstatic Node
NodeFactory. createNodeBranchLength(double branchLength, Node[] children)
Create a node with the specified children, and the specified branch lengthstatic Node
NodeUtils. 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 Node
NodeUtils. 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.Node
SimpleTree. findNode(int num)
return node with number num (as displayed in ASCII tree)Node
Tree.TreeBase. findNode(int num)
return node with number num (as displayed in ASCII tree)Node
TreeRestricter. generateNode()
Node[]
TreeManipulator. getAllRootedBy(java.lang.String[] outgroupNames)
Node
TreeManipulator. getAsInputRooting()
A method for recovering the input (construction) tree (with the EXPANSION/MIMIC/REDUCED differences)Node
Node. getChild(int n)
get child nodeNode
SimpleNode. getChild(int n)
get child nodestatic Node
RootedTreeUtils. getClade(Node root, Node clade)
Node
TreeManipulator. getDefaultRoot()
Node
ParameterizedTree.ParameterizedTreeBase. getExternalNode(int i)
returns the ith external node in the tree.Node
SimpleTree. getExternalNode(int i)
Returns the ith external node.Node
Tree. getExternalNode(int i)
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)Node
ParameterizedTree.ParameterizedTreeBase. getInternalNode(int i)
returns the ith internal node in the tree.Node
SimpleTree. getInternalNode(int i)
Returns the ith internal node.Node
Tree. getInternalNode(int i)
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 arrayNode
TreeManipulator. getMidPointRooted()
static Node
TreeUtils. getNodeByName(Node root, java.lang.String name)
static Node
TreeUtils. getNodeByName(Tree tree, java.lang.String name)
Node
TreeManipulator.PALNodeWrapper. getPALPeer()
Node
Node. getParent()
Returns the parent node of this node.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.Node
ParameterizedTree.ParameterizedTreeBase. getRoot()
Returns the root node of this tree.Node
SimpleTree. getRoot()
Returns the root node of this tree.Node
Tree. getRoot()
Node
Tree.TreeBase. getRoot()
Returns the root node of this tree.Node
TreeManipulator. getRootedAbove(Node base)
Node
TreeManipulator. getRootedBy(java.lang.String[] outgroupNames)
Node
TreeManipulator. getRootedBy(java.lang.String[] outgroupNames, double ingroupBranchLength)
static Node
RootedTreeUtils. getSubtree(Node root, Node 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
Node. removeChild(int n)
remove childNode
SimpleNode. removeChild(int n)
remove childMethods in pal.tree with parameters of type Node Modifier and Type Method Description void
Node. addChild(Node c)
add new child nodevoid
SimpleNode. addChild(Node n)
add new child nodeTreeManipulator
TreeManipulator.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, java.util.Vector trees)
static int
RootedTreeUtils. collectTaxa(Node root, java.util.Hashtable table)
Collects all of the names of the taxa in the tree into a hashtable.pal.tree.TreeRestricter.RNode
TreeRestricter. construct(Node peer, java.lang.String[] names, boolean inclusion, boolean isRoot)
static boolean
RootedTreeUtils. containsClade(Node root, Node clade)
static boolean
RootedTreeUtils. containsNovelTaxa(Node root, java.util.Hashtable taxa)
static boolean
RootedTreeUtils. containsSubtree(Node root, Node node)
static 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 Node
NodeFactory. createNode(Node node)
constructor used to clone a node and all childrenstatic Node
NodeFactory. createNode(Node[] children)
static Node
NodeFactory. createNode(Node[] children, double height)
Create a node with the specified children, and the specified branch heightstatic Node
NodeFactory. createNodeBranchLength(double branchLength, Node[] children)
Create a node with the specified children, and the specified branch lengthstatic boolean
RootedTreeUtils. equal(Node node1, Node node2)
static void
NodeUtils. exchangeInfo(Node node1, Node node2)
Exchange field info between two nodes.static Node
NodeUtils. 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 Node
NodeUtils. 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 double
NodeUtils. findLargestChild(Node node)
Finds the largest child (in terms of node height).java.lang.Object
ParameterizedTree.ParameterizedTreeBase. getAttribute(Node node, java.lang.String name)
java.lang.Object
SimpleTree. getAttribute(Node node, java.lang.String name)
java.lang.Object
Tree. getAttribute(Node node, java.lang.String name)
java.lang.Object
Tree.TreeBase. getAttribute(Node node, java.lang.String name)
static void
CladeSystem. getClade(IdGroup idGroup, Node internalNode, boolean[] clade)
get clade for internal nodestatic Node
RootedTreeUtils. getClade(Node root, Node clade)
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, java.util.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, java.util.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 double
NodeUtils. getMaximumPathLengthLengthToLeaf(Node root)
static int
NodeUtils. getMaxNodeDepth(Node root)
static double
RootedTreeUtils. getMeanCladeHeight(Node clade, java.util.Vector trees)
static double
RootedTreeUtils. getMeanSubtreeHeight(Node subtree, java.util.Vector trees)
static double
NodeUtils. getMinimumPathLengthLengthToLeaf(Node root)
static Node
TreeUtils. 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 lengthsNode
TreeManipulator. getRootedAbove(Node base)
static void
SplitUtils. getSplit(IdGroup idGroup, Node internalNode, boolean[] split)
get split for branch associated with internal nodestatic Node
RootedTreeUtils. getSubtree(Node root, Node node)
Tree
TreeManipulator. getTreeRootedAbove(Node n)
static 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
SimpleNode. init(Node n)
protected void
SimpleNode. init(Node n, boolean keepId)
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 void
RootedTreeInterface.Utils. instruct(Node palRoot, RootedTreeInterface treeInterface)
Build a tree display based on a normal pal node.static 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(java.io.PrintWriter out, Node node, boolean printLengths, boolean printInternalLabels)
prints node in New Hamshire format.static int
NodeUtils. printNH(java.io.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
SimpleTree. reroot(Node node)
make provided node the root nodevoid
Tree.TreeBase. reroot(Node node)
make provided node the root nodestatic void
TreeUtils. reroot(Tree tree, Node node)
static void
NodeUtils. restoreBranch(Node node)
restore internal branchstatic boolean
RootedTreeUtils. sameTaxa(Node node1, Node node2)
void
ParameterizedTree.ParameterizedTreeBase. setAttribute(Node node, java.lang.String name, java.lang.Object value)
void
SimpleTree. setAttribute(Node node, java.lang.String name, java.lang.Object value)
Sets an named attribute for a given node.void
Tree. setAttribute(Node node, java.lang.String name, java.lang.Object value)
Sets an named attribute for a given node.void
Tree.TreeBase. setAttribute(Node node, java.lang.String name, java.lang.Object value)
Sets an named attribute for a given node.void
Node. setChild(int n, Node node)
set child nodevoid
SimpleNode. setChild(int n, Node node)
set child nodevoid
Node. setParent(Node node)
Set the parent node of this node.void
SimpleNode. setParent(Node node)
Set the parent node of this node.void
ParameterizedTree.ParameterizedTreeBase. setRoot(Node root)
void
SimpleTree. setRoot(Node r)
Set a new node as root node.void
Tree. setRoot(Node root)
This method constructs a tree from the given root node.void
Tree.TreeBase. setRoot(Node theRoot)
Called by subclasses that can't give root at time of construction (of this class)static int
RootedTreeUtils. 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)
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Uses of Node in pal.treesearch
Methods in pal.treesearch that return Node Modifier and Type Method Description Node
AbstractParentableConstrainedNode. buildDescendentPALNodeBase()
Node
ConstrainedLeafNode. buildDescendentPALNodeBase()
Node
ConstrainedNode. buildDescendentPALNodeBase()
Build node model base units (eg years)Node
AbstractParentableConstrainedNode. buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager)
Node
ConstrainedLeafNode. buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager)
Node
ConstrainedNode. buildDescendentPALNodeES(ConstraintModel.GroupManager groupConstraints)
Build node with Expected Substitution Unitsprotected Node
AbstractParentableConstrainedNode. buildLeftDecendentPALNodeBase()
Node
FreeLeafNode. buildPALNode(double branchLength, FreeBranch caller)
Node
UnrootedMLSearcher. buildPALNode()
Node
FreeBranch. buildPALNodeBase()
Node
FreeBranch. buildPALNodeBase(FreeNode caller)
Node
FreeInternalNode. buildPALNodeBase(double branchLength, FreeBranch caller)
Node
FreeLeafNode. buildPALNodeBase(double branchLength, FreeBranch caller)
Node
FreeNode. buildPALNodeBase(double branchLength_, FreeBranch caller)
Node
GeneralLikelihoodSearcher. buildPALNodeBase()
Node
PivotNode. buildPALNodeBase()
Node
PivotNode. buildPALNodeBase(double branchLength_, FreeBranch caller)
Node
RootAccess. buildPALNodeBase()
Node
FreeBranch. buildPALNodeES()
Node
FreeBranch. buildPALNodeES(FreeNode caller)
Node
FreeInternalNode. buildPALNodeES(double branchLength, FreeBranch caller)
Node
FreeLeafNode. buildPALNodeES(double branchLength, FreeBranch caller)
Node
FreeNode. buildPALNodeES(double branchLength_, FreeBranch caller)
Node
GeneralLikelihoodSearcher. buildPALNodeES()
Node
PivotNode. buildPALNodeES()
Node
PivotNode. buildPALNodeES(double branchLength_, FreeBranch caller)
Node
RootAccess. buildPALNodeES()
protected Node
AbstractParentableConstrainedNode. buildRightDecendentPALNodeBase()
Methods in pal.treesearch with parameters of type Node Modifier and Type Method Description UnrootedMLSearcher
BranchAccess. attach(Node subTree, Alignment fullAlignment)
Create a new Tree Searcher with a new sub tree attachedUnrootedMLSearcher
BranchAccess. attach(Node subTree, Alignment fullAlignment, SubstitutionModel model)
Create a new Tree Searcher with a new sub tree attachedConstrainedNode
GeneralConstructionTool. createConstrainedNode(Node peer, ParentableConstrainedNode parent, GeneralConstraintGroupManager.Store store, GeneralConstraintGroupManager groupManager)
Create an appropriate constrained node given a peer, and it's parent nodeFreeNode
GeneralConstructionTool. createFreeNode(Node peer, FreeBranch parent, GeneralConstraintGroupManager.Store store)
Create an appropriate free node given a peer, and it's parent branchRootAccess
GeneralConstructionTool. createRootAccess(Node baseTree, GeneralConstraintGroupManager.Store store)
java.lang.String[]
GeneralConstructionTool. getLeafLabelSet(Node peer)
A horibly inefficient way of doing things.void
GeneralConstructionTool. 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 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
Methods in pal.xml that return Node Modifier and Type Method Description static Node
ElementParser. parseEdgeNodeElement(org.w3c.dom.Element e)
static Node
ElementParser. parseNodeElement(org.w3c.dom.Element e)
Methods in pal.xml with parameters of type Node Modifier and Type Method Description static org.w3c.dom.Element
ElementFactory. createEdgeNodeElement(Node node, org.w3c.dom.Document document)
static org.w3c.dom.Element
ElementFactory. createNodeElement(Node node, org.w3c.dom.Document document)
static org.w3c.dom.Element
ElementFactory. createNodeElement(Node node, org.w3c.dom.Document document, boolean includeEdges)
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