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.
|
Modifier and Type | Method and 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)
|
Modifier and Type | Method and 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 branch
|
protected void |
SimpleLikelihoodCalculator.partialsExternal(Node branch)
compute partials for external branch
|
protected 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
|
Modifier and Type | Class and Description |
---|---|
class |
PositionedNode
A tree node that has a scalar position for the purposes of drawing the tree.
|
Modifier and Type | Method and Description |
---|---|
Node |
PositionedNode.getPeer() |
Modifier and Type | Method and Description |
---|---|
protected static double |
TreePainter.getMaxLeafTime(Node node) |
protected LabelDisplayer |
TreePainter.getNodeDisplay(Node n,
LabelDisplayer defaultDisplay) |
protected java.lang.String |
TreePainter.getNodeName(Node node) |
Constructor and Description |
---|
PositionedNode(Node node) |
PositionedNode(Node node,
Node highlightNode)
Builds a tree based on node, but highlights highlightNode
|
Modifier and Type | Interface and Description |
---|---|
interface |
AttributeNode
interface for a node (includes branch) in a binary/non-binary
rooted/unrooted tree.
|
Modifier and Type | Class and Description |
---|---|
class |
SimpleNode
data structure for a node (includes branch) in a binary/non-binary
rooted/unrooted tree
|
Modifier and Type | Method and Description |
---|---|
static Node |
NodeFactory.createNode()
create a node
|
static Node |
NodeFactory.createNode(Identifier id)
create a node, with a specified identifier
|
static Node |
NodeFactory.createNode(Identifier id,
double height)
create a node, with a specified identifier
|
static Node |
NodeFactory.createNode(Node node)
constructor used to clone a node and all children
|
static Node |
NodeFactory.createNode(Node[] children) |
static Node |
NodeFactory.createNode(Node[] children,
double height)
Create a node with the specified children, and the specified branch height
|
static Node |
NodeFactory.createNodeBranchLength(double branchLength,
Identifier id)
create a node, with a specified identifier
|
static Node |
NodeFactory.createNodeBranchLength(double branchLength,
Node[] children)
Create a node with the specified children, and the specified branch length
|
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 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.
|
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 |
SimpleNode.getChild(int n)
get child node
|
Node |
Node.getChild(int n)
get child node
|
static Node |
RootedTreeUtils.getClade(Node root,
Node clade) |
Node |
TreeManipulator.getDefaultRoot() |
Node |
SimpleTree.getExternalNode(int i)
Returns the ith external node.
|
Node |
ParameterizedTree.ParameterizedTreeBase.getExternalNode(int i)
returns the ith external node in the tree.
|
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 array
|
static 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 |
SimpleTree.getInternalNode(int i)
Returns the ith internal node.
|
Node |
ParameterizedTree.ParameterizedTreeBase.getInternalNode(int i)
returns the ith internal node in the tree.
|
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 array
|
Node |
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 |
SimpleNode.getParent()
Returns the parent node of this node.
|
Node |
Node.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 |
SimpleTree.getRoot()
Returns the root node of this tree.
|
Node |
ParameterizedTree.ParameterizedTreeBase.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 node
|
static Node |
NodeUtils.postorderSuccessor(Node node)
determine postorder successor of a node
|
static Node |
NodeUtils.preorderSuccessor(Node node)
determine preorder successor of this node
|
Node |
SimpleNode.removeChild(int n)
remove child
|
Node |
Node.removeChild(int n)
remove child
|
Modifier and Type | Method and Description |
---|---|
void |
SimpleNode.addChild(Node n)
add new child node
|
void |
Node.addChild(Node c)
add new child node
|
TreeManipulator |
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 children
|
static Node |
NodeFactory.createNode(Node[] children) |
static Node |
NodeFactory.createNode(Node[] children,
double height)
Create a node with the specified children, and the specified branch height
|
static Node |
NodeFactory.createNodeBranchLength(double branchLength,
Node[] children)
Create a node with the specified children, and the specified branch length
|
static 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,
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 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 double |
NodeUtils.findLargestChild(Node node)
Finds the largest child (in terms of node height).
|
java.lang.Object |
SimpleTree.getAttribute(Node node,
java.lang.String name) |
java.lang.Object |
ParameterizedTree.ParameterizedTreeBase.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 node
|
static Node |
RootedTreeUtils.getClade(Node root,
Node clade) |
static double |
NodeUtils.getDistanceToRoot(Node node)
determine distance to root
|
static Node[] |
NodeUtils.getExternalNodes(Node root)
Obtains all external nodes from tree defined by root and returns as an array
|
static void |
NodeUtils.getExternalNodes(Node root,
java.util.Vector store)
Appends all external nodes from tree defined by root to Vector store
|
static 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 array
|
static void |
NodeUtils.getInternalNodes(Node root,
java.util.Vector store)
Appends all internal nodes from tree defined by root to Vector store
|
static 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 lengths
|
Node |
TreeManipulator.getRootedAbove(Node base) |
static void |
SplitUtils.getSplit(IdGroup idGroup,
Node internalNode,
boolean[] split)
get split for branch associated with internal node
|
static 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 tree
|
static void |
NodeUtils.heights2Lengths(Node node)
determines branch lengths of this and all descendent nodes
from heights
|
static void |
NodeUtils.heights2Lengths(Node node,
boolean respectMinimum)
determines branch lengths of this and all descendent nodes
from heights
|
protected 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 |
SimpleNode.insertChild(Node n,
int pos)
add new child node (insertion at a specific position)
|
void |
Node.insertChild(Node c,
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 second
|
static void |
NodeUtils.joinChilds(Node node,
int n1,
int n2)
join two childs, introducing a new node/branch in the tree
that replaces the first child
|
static 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 node
|
static Node |
NodeUtils.preorderSuccessor(Node node)
determine preorder successor of this node
|
static 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 child
|
void |
SimpleTree.reroot(Node node)
make provided node the root node
|
void |
Tree.TreeBase.reroot(Node node)
make provided node the root node
|
static void |
TreeUtils.reroot(Tree tree,
Node node) |
static void |
NodeUtils.restoreBranch(Node node)
restore internal branch
|
static boolean |
RootedTreeUtils.sameTaxa(Node node1,
Node node2) |
void |
SimpleTree.setAttribute(Node node,
java.lang.String name,
java.lang.Object value)
Sets an named attribute for a given node.
|
void |
ParameterizedTree.ParameterizedTreeBase.setAttribute(Node node,
java.lang.String name,
java.lang.Object value) |
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 |
SimpleNode.setChild(int n,
Node node)
set child node
|
void |
Node.setChild(int n,
Node node)
set child node
|
void |
SimpleNode.setParent(Node node)
Set the parent node of this node.
|
void |
Node.setParent(Node node)
Set the parent node of this node.
|
void |
SimpleTree.setRoot(Node r)
Set a new node as root node.
|
void |
ParameterizedTree.ParameterizedTreeBase.setRoot(Node root) |
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) |
Constructor and Description |
---|
SimpleNode(Node n)
constructor used to clone a node and all children
|
SimpleNode(Node[] children) |
SimpleNode(Node[] children,
double branchLength)
Constructor
|
SimpleNode(Node n,
boolean keepIds) |
SimpleNode(Node n,
LabelMapping lm) |
SimpleTree(Node r)
constructor taking a root node
|
Tree.TreeBase(Node theRoot)
constructor
|
Tree.TreeBase(Tree.TreeBase tree,
Node newRoot)
clone constructor
|
TreeManipulator.PALNodeWrapper(Node peer) |
TreeManipulator.PALNodeWrapper(Node peer,
TreeManipulator.PALNodeWrapper parent) |
TreeManipulator(Node base)
Units will be Units.UNKNOWN
|
TreeManipulator(Node base,
int units)
Construct a TreeManipulator based around a normal tree
|
TreeManipulator(Node base,
int units,
int constructionMode)
Construct a TreeManipulator based around a normal tree
|
TreeRestricter(Node root,
int units,
java.lang.String[] names,
boolean inclusion) |
Modifier and Type | Method and Description |
---|---|
Node |
ConstrainedNode.buildDescendentPALNodeBase()
Build node model base units (eg years)
|
Node |
AbstractParentableConstrainedNode.buildDescendentPALNodeBase() |
Node |
ConstrainedLeafNode.buildDescendentPALNodeBase() |
Node |
ConstrainedNode.buildDescendentPALNodeES(ConstraintModel.GroupManager groupConstraints)
Build node with Expected Substitution Units
|
Node |
AbstractParentableConstrainedNode.buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager) |
Node |
ConstrainedLeafNode.buildDescendentPALNodeES(ConstraintModel.GroupManager groupManager) |
protected Node |
AbstractParentableConstrainedNode.buildLeftDecendentPALNodeBase() |
Node |
UnrootedMLSearcher.buildPALNode() |
Node |
FreeLeafNode.buildPALNode(double branchLength,
FreeBranch caller) |
Node |
PivotNode.buildPALNodeBase() |
Node |
RootAccess.buildPALNodeBase() |
Node |
GeneralLikelihoodSearcher.buildPALNodeBase() |
Node |
FreeBranch.buildPALNodeBase() |
Node |
FreeInternalNode.buildPALNodeBase(double branchLength,
FreeBranch caller) |
Node |
PivotNode.buildPALNodeBase(double branchLength_,
FreeBranch caller) |
Node |
FreeNode.buildPALNodeBase(double branchLength_,
FreeBranch caller) |
Node |
FreeLeafNode.buildPALNodeBase(double branchLength,
FreeBranch caller) |
Node |
FreeBranch.buildPALNodeBase(FreeNode caller) |
Node |
PivotNode.buildPALNodeES() |
Node |
RootAccess.buildPALNodeES() |
Node |
GeneralLikelihoodSearcher.buildPALNodeES() |
Node |
FreeBranch.buildPALNodeES() |
Node |
FreeInternalNode.buildPALNodeES(double branchLength,
FreeBranch caller) |
Node |
PivotNode.buildPALNodeES(double branchLength_,
FreeBranch caller) |
Node |
FreeNode.buildPALNodeES(double branchLength_,
FreeBranch caller) |
Node |
FreeLeafNode.buildPALNodeES(double branchLength,
FreeBranch caller) |
Node |
FreeBranch.buildPALNodeES(FreeNode caller) |
protected Node |
AbstractParentableConstrainedNode.buildRightDecendentPALNodeBase() |
Modifier and Type | Method and Description |
---|---|
UnrootedMLSearcher |
BranchAccess.attach(Node subTree,
Alignment fullAlignment)
Create a new Tree Searcher with a new sub tree attached
|
UnrootedMLSearcher |
BranchAccess.attach(Node subTree,
Alignment fullAlignment,
SubstitutionModel model)
Create a new Tree Searcher with a new sub tree attached
|
ConstrainedNode |
GeneralConstructionTool.createConstrainedNode(Node peer,
ParentableConstrainedNode parent,
GeneralConstraintGroupManager.Store store,
GeneralConstraintGroupManager groupManager)
Create an appropriate constrained node given a peer, and it's parent node
|
FreeNode |
GeneralConstructionTool.createFreeNode(Node peer,
FreeBranch parent,
GeneralConstraintGroupManager.Store store)
Create an appropriate free node given a peer, and it's parent branch
|
RootAccess |
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) |
Modifier and Type | Method and Description |
---|---|
static Node |
ElementParser.parseEdgeNodeElement(org.w3c.dom.Element e) |
static Node |
ElementParser.parseNodeElement(org.w3c.dom.Element e) |
Modifier and Type | Method and 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) |