NodeUtils (net.maizegenetics:tassel 5.2.46 API)

java.lang.Object
- net.maizegenetics.taxa.tree.NodeUtils

```
public class NodeUtils
extends Object
```
Helper routines for dealing with nodes.

Version:

$Id: NodeUtils.java,v 1.1 2007/01/12 03:26:17 tcasstevens Exp $

Author:

Alexei Drummond, Korbinian Strimmer, Matthew Goode

Constructor Summary

Constructors
Constructor and Description

NodeUtils()

Constructors
Constructor and Description
`NodeUtils()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`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 void`	`exchangeInfo(Node node1, Node node2)` Exchange field info between two nodes.
`static Node`	`findByIdentifier(Node node, String identifierName)` Returns the first node in this tree that has the required identifier.
`static Node[]`	`findByIdentifier(Node node, String[] identifierNames)` Returns the first nodes in this tree that has the required identifiers.
`static Node`	`findByIdentifier(Node node, Taxon identifier)` Returns the first node in this tree that has the required identifier.
`static Node[]`	`findByIdentifier(Node node, Taxon[] identifiers)` Returns the first nodes in this tree that has the required identifiers.
`static double`	`findLargestChild(Node node)` Finds the largest child (in terms of node height).
`static double`	`getDistanceToRoot(Node node)` determine distance to root
`static Node[]`	`getExternalNodes(Node root)` Obtains all external nodes from tree defined by root and returns as an array
`static void`	`getExternalNodes(Node root, Vector store)` Appends all external nodes from tree defined by root to Vector store
`static Node`	`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`	`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`	`getInternalNodeCount(Node root)`
`static Node[]`	`getInternalNodes(Node root, boolean includeRoot)` Obtains all internal nodes from tree defined by root and returns as an array
`static void`	`getInternalNodes(Node root, Vector store)` Appends all internal nodes from tree defined by root to Vector store
`static int`	`getLeafCount(Node node)` Return the number of terminal leaves below this node or 1 if this is a terminal leaf.
`static double`	`getMaximumPathLengthLengthToLeaf(Node root)`
`static int`	`getMaxNodeDepth(Node root)`
`static double`	`getMinimumPathLengthLengthToLeaf(Node root)`
`static double[]`	`getPathLengthInfo(Node root)` Calculates max/min lengths of paths from root to leaf, taking into account branch lengths
`static int`	`getUnrootedBranchCount(Node center)` returns number of branches centered around an internal node in an unrooted tree
`static void`	`heights2Lengths(Node node)` determines branch lengths of this and all descendent nodes from heights
`static void`	`heights2Lengths(Node node, boolean respectMinimum)` determines branch lengths of this and all descendent nodes from heights
`static boolean`	`isAncestor(Node possibleAncestor, Node node)` For two nodes in the tree true if the first node is the ancestor of the second
`static void`	`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`	`lengths2Heights(Node root)` Converts lengths to heights, without assuming contemporaneous tips.
`static void`	`lengths2HeightsKeepTips(Node node, boolean useMax)` Converts lengths to heights, but maintains tip heights.
`static void`	`localHeights2Lengths(Node node, boolean respectMinimum)` determines branch lengths of this node and its immediate descendent nodes from heights.
`static Node`	`postorderSuccessor(Node node)` determine postorder successor of a node
`static Node`	`preorderSuccessor(Node node)` determine preorder successor of this node
`static void`	`printNH(PrintWriter out, Node node, boolean printLengths, boolean printInternalLabels)` prints node in New Hamshire format.
`static int`	`printNH(PrintWriter out, Node node, boolean printLengths, boolean printInternalLabels, int column, boolean breakLines)`
`static void`	`removeBranch(Node node)` remove internal branch (collapse node with its parent)
`static void`	`removeChild(Node parent, Node child)` remove child
`static void`	`restoreBranch(Node node)` restore internal branch

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - NodeUtils
```
public NodeUtils()
```
- Method Detail
  - getExternalNodes
```
public static void getExternalNodes(Node root,
                                    Vector store)
```
    Appends all external nodes from tree defined by root to Vector store
    
    Parameters:
    
    root - The root node defining tree
    
    store - Where leaf nodes are stored (original contents is not touched)
  - getExternalNodes
```
public static Node[] getExternalNodes(Node root)
```
    Obtains all external nodes from tree defined by root and returns as an array
    
    Parameters:
    
    root - The root node defining tree
    
    Returns:
    
    an array of nodes where each node is a leaf node, and is a member of the tree defined by root
  - getInternalNodes
```
public static void getInternalNodes(Node root,
                                    Vector store)
```
    Appends all internal nodes from tree defined by root to Vector store
    
    Parameters:
    
    root - The root node defining tree
    
    store - Where internal nodes are stored (original contents is not touched)
  - getInternalNodes
```
public static Node[] getInternalNodes(Node root,
                                      boolean includeRoot)
```
    Obtains all internal nodes from tree defined by root and returns as an array
    
    Parameters:
    
    root - The root node defining tree
    
    Returns:
    
    an array of nodes where each node is a internal node, and is a member of the tree defined by root
  - getMaxNodeDepth
```
public static int getMaxNodeDepth(Node root)
```
    Returns:
    
    the maxium distance in nodes from root to a leaf
  - getPathLengthInfo
```
public static final double[] getPathLengthInfo(Node root)
```
    Calculates max/min lengths of paths from root to leaf, taking into account branch lengths
    Returns:
    a double array where
    
    The first element is the minimum length path from root to leaf.
    
    The second element is the second most minimum length path from root to leaf.
    
    The third element is the second most maximum length path from root to leaf.
    
    The forth element is the maximum length path from root to leaf.
    See Also:
    
    getMaxNodeDepth()
  - getMaximumPathLengthLengthToLeaf
```
public static final double getMaximumPathLengthLengthToLeaf(Node root)
```
    Returns:
    
    the maximum length of a path from root to a leaf
  - getMinimumPathLengthLengthToLeaf
```
public static final double getMinimumPathLengthLengthToLeaf(Node root)
```
    Returns:
    
    the minimum length of a path from root to a leaf
  - lengths2Heights
```
public static void lengths2Heights(Node root)
```
    Converts lengths to heights, *without* assuming contemporaneous tips.
  - getInternalNodeCount
```
public static int getInternalNodeCount(Node root)
```
    Returns:
    
    the number of internal nodes from a root node
  - lengths2HeightsKeepTips
```
public static void lengths2HeightsKeepTips(Node node,
                                           boolean useMax)
```
    Converts lengths to heights, but maintains tip heights.
  - exchangeInfo
```
public static void exchangeInfo(Node node1,
                                Node node2)
```
    Exchange field info between two nodes. Specifically identifiers, branch lengths, node heights and branch length SEs.
  - heights2Lengths
```
public static void heights2Lengths(Node node)
```
    determines branch lengths of this and all descendent nodes from heights
  - heights2Lengths
```
public static void heights2Lengths(Node node,
                                   boolean respectMinimum)
```
    determines branch lengths of this and all descendent nodes from heights
  - localHeights2Lengths
```
public static void localHeights2Lengths(Node node,
                                        boolean respectMinimum)
```
    determines branch lengths of this node and its immediate descendent nodes from heights.
  - findLargestChild
```
public static double findLargestChild(Node node)
```
    Finds the largest child (in terms of node height).
  - removeChild
```
public static void removeChild(Node parent,
                               Node child)
```
    remove child
    
    Parameters:
    
    node - child node to be removed
  - removeBranch
```
public static void removeBranch(Node node)
```
    remove internal branch (collapse node with its parent)
    
    Parameters:
    
    node - node associated with internal branch
  - restoreBranch
```
public static void restoreBranch(Node node)
```
    restore internal branch
    
    Parameters:
    
    node - node associated with internal branch
  - joinChilds
```
public static void joinChilds(Node node,
                              int n1,
                              int n2)
```
    join two childs, introducing a new node/branch in the tree that replaces the first child
    
    Parameters:
    
    n1 - number of first child
    
    n2 - number of second child
  - preorderSuccessor
```
public static Node preorderSuccessor(Node node)
```
    determine preorder successor of this node
    
    Returns:
    
    next node
  - postorderSuccessor
```
public static Node postorderSuccessor(Node node)
```
    determine postorder successor of a node
    
    Returns:
    
    next node
  - printNH
```
public static void printNH(PrintWriter out,
                           Node node,
                           boolean printLengths,
                           boolean printInternalLabels)
                    throws IOException
```
    prints node in New Hamshire format.
    
    Throws:
    
    IOException
  - printNH
```
public static int printNH(PrintWriter out,
                          Node node,
                          boolean printLengths,
                          boolean printInternalLabels,
                          int column,
                          boolean breakLines)
                   throws IOException
```
    Throws:
    
    IOException
  - findByIdentifier
```
public static final Node[] findByIdentifier(Node node,
                                            String[] identifierNames)
```
    Returns the first nodes in this tree that has the required identifiers.
    
    Returns:
    
    null if none of the identifiers names match nodes in tree, else return array which may have null "blanks" for corresponding identifiers that do not match any node in the tree
  - findByIdentifier
```
public static final Node[] findByIdentifier(Node node,
                                            Taxon[] identifiers)
```
    Returns the first nodes in this tree that has the required identifiers.
  - findByIdentifier
```
public static final Node findByIdentifier(Node node,
                                          Taxon identifier)
```
    Returns the first node in this tree that has the required identifier.
  - findByIdentifier
```
public static final Node findByIdentifier(Node node,
                                          String identifierName)
```
    Returns the first node in this tree that has the required identifier.
  - getDistanceToRoot
```
public static double getDistanceToRoot(Node node)
```
    determine distance to root
    
    Returns:
    
    distance to root
  - getLeafCount
```
public static int getLeafCount(Node node)
```
    Return the number of terminal leaves below this node or 1 if this is a terminal leaf.
  - isAncestor
```
public static boolean isAncestor(Node possibleAncestor,
                                 Node node)
```
    For two nodes in the tree true if the first node is the ancestor of the second
    
    Parameters:
    
    possibleAncestor - the node that may be the ancestor of the other node
    
    node - the node that may have the other node as it's ancestor
  - getFirstCommonAncestor
```
public static Node getFirstCommonAncestor(Node[] nodes)
```
    For a set of nodes in the tree returns the common ancestor closest to all nodes (most recent common ancestor)
    
    Parameters:
    
    nodes - the nodes to check, is okay if array elements are null!
  - getFirstCommonAncestor
```
public static Node getFirstCommonAncestor(Node nodeOne,
                                          Node nodeTwo)
```
    For two nodes in the tree returns the common ancestor closest to both nodes (most recent common ancestor)
    
    Parameters:
    
    nodeOne -
    
    nodeTwo -
  - getUnrootedBranchCount
```
public static final int getUnrootedBranchCount(Node center)
```
    returns number of branches centered around an internal node in an unrooted tree
  - convertNegativeBranchLengthsToZeroLength
```
public static final void 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!

Class NodeUtils

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

NodeUtils

Method Detail

getExternalNodes

getExternalNodes

getInternalNodes

getInternalNodes

getMaxNodeDepth

getPathLengthInfo

getMaximumPathLengthLengthToLeaf

getMinimumPathLengthLengthToLeaf

lengths2Heights

getInternalNodeCount

lengths2HeightsKeepTips

exchangeInfo

heights2Lengths

heights2Lengths

localHeights2Lengths

findLargestChild

removeChild

removeBranch

restoreBranch

joinChilds

preorderSuccessor

postorderSuccessor

printNH

printNH

findByIdentifier

findByIdentifier

findByIdentifier

findByIdentifier

getDistanceToRoot

getLeafCount

isAncestor

getFirstCommonAncestor

getFirstCommonAncestor

getUnrootedBranchCount

convertNegativeBranchLengthsToZeroLength