java.lang.Object
- pal.tree.SimpleNode

All Implemented Interfaces:

java.io.Serializable, AttributeNode, Node

Direct Known Subclasses:

PositionedNode
```
public class SimpleNode
extends java.lang.Object
implements AttributeNode
```
data structure for a node (includes branch) in a binary/non-binary rooted/unrooted tree

Version:

$Id: SimpleNode.java,v 1.27 2003/10/19 02:35:26 matt Exp $

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Field Summary
- Fields inherited from interface pal.tree.AttributeNode
  CLADE_PROBABILITY, MEAN_CLADE_HEIGHT, NODE_HEIGHT_SE, SUBTREE_PROBABILITY

Constructor Summary

Constructors
Modifier	Constructor	Description
	`SimpleNode()`	constructor default node
	`SimpleNode(java.lang.String name, double branchLength)`
	`SimpleNode(Node n)`	constructor used to clone a node and all children
`protected`	`SimpleNode(Node[] children)`
`protected`	`SimpleNode(Node[] children, double branchLength)`	Constructor
	`SimpleNode(Node n, boolean keepIds)`
	`SimpleNode(Node n, LabelMapping lm)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addChild(Node n)`	add new child node
`java.lang.Object`	`getAttribute(java.lang.String name)`
`java.util.Enumeration`	`getAttributeNames()`
`double`	`getBranchLength()`	Get the length of the branch attaching this node to its parent.
`double`	`getBranchLengthSE()`	Get the length SE of the branch attaching this node to its parent.
`Node`	`getChild(int n)`	get child node
`int`	`getChildCount()`	Returns the number of children this node has.
`Identifier`	`getIdentifier()`	Returns the identifier for this node.
`double`	`getNodeHeight()`	Get the height of this node relative to the most recent node.
`int`	`getNumber()`	return the index of this node
`Node`	`getParent()`	Returns the parent node of this node.
`byte[]`	`getSequence()`	Returns the sequence at this node, in the form of an array of bytes.
`java.lang.String`	`getSequenceString()`	Returns the sequence at this node, in the form of a String.
`boolean`	`hasChildren()`	check whether this node is an internal node
`protected void`	`init(Node n)`
`protected void`	`init(Node n, boolean keepId)`	Initialized node instance variables based on given Node.
`protected void`	`init(Node n, boolean keepId, LabelMapping lm)`	Initialized node instance variables based on given Node.
`void`	`insertChild(Node n, int pos)`	add new child node (insertion at a specific position)
`boolean`	`isLeaf()`	check whether this node is an external node
`boolean`	`isRoot()`	check whether this node is a root node
`void`	`lengths2HeightsContemp()`	determines the height of this node and its descendants from branch lengths, assuming contemporaneous tips.
`Node`	`removeChild(int n)`	remove child
`void`	`removeParent()`	removes parent.
`void`	`reset()`
`void`	`setAttribute(java.lang.String name, java.lang.Object value)`	Sets a named attribute to the given value.
`void`	`setBranchLength(double value)`	Set the length of the branch attaching this node to its parent.
`void`	`setBranchLengthSE(double value)`	Set the length SE of the branch attaching this node to its parent.
`void`	`setChild(int n, Node node)`	set child node
`void`	`setIdentifier(Identifier id)`	Set identifier for this node.
`void`	`setNodeHeight(double value)`	Set the height of this node relative to the most recent node.
`void`	`setNodeHeight(double value, boolean adjustChildBranchLengths)`	Set the height of this node relative to the most recent node.
`void`	`setNumber(int n)`	set the index of this node
`void`	`setParent(Node node)`	Set the parent node of this node.
`void`	`setSequence(byte[] s)`	Sets the sequence at this node, in the form of an array of bytes.
`java.lang.String`	`toString()`

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

- Constructor Detail
  - SimpleNode
```
public SimpleNode()
```
    constructor default node
  - SimpleNode
```
public SimpleNode(java.lang.String name,
                  double branchLength)
```
  - SimpleNode
```
protected SimpleNode(Node[] children,
                     double branchLength)
```
    Constructor
    
    Parameters:
    
    children -
    
    branchLength -
    
    Throws:
    
    java.lang.IllegalArgumentException - if only one child!
  - SimpleNode
```
protected SimpleNode(Node[] children)
```
  - SimpleNode
```
public SimpleNode(Node n)
```
    constructor used to clone a node and all children
  - SimpleNode
```
public SimpleNode(Node n,
                  boolean keepIds)
```
  - SimpleNode
```
public SimpleNode(Node n,
                  LabelMapping lm)
```
- Method Detail
  - reset
```
public void reset()
```
  - init
```
protected void init(Node n)
```
  - init
```
protected void init(Node n,
                    boolean keepId)
```
    Initialized node instance variables based on given Node. children are ignored.
  - init
```
protected void init(Node n,
                    boolean keepId,
                    LabelMapping lm)
```
    Initialized node instance variables based on given Node. children are ignored.
    
    Parameters:
    
    lm - - may be null
  - getParent
```
public final Node getParent()
```
    Returns the parent node of this node.
    
    Specified by:
    
    getParent in interface Node
  - setParent
```
public void setParent(Node node)
```
    Set the parent node of this node.
    
    Specified by:
    
    setParent in interface Node
  - removeParent
```
public final void removeParent()
```
    removes parent.
  - getSequenceString
```
public java.lang.String getSequenceString()
```
    Returns the sequence at this node, in the form of a String.
  - getSequence
```
public byte[] getSequence()
```
    Returns the sequence at this node, in the form of an array of bytes.
    
    Specified by:
    
    getSequence in interface Node
  - setSequence
```
public void setSequence(byte[] s)
```
    Sets the sequence at this node, in the form of an array of bytes.
    
    Specified by:
    
    setSequence in interface Node
  - getBranchLength
```
public final double getBranchLength()
```
    Get the length of the branch attaching this node to its parent.
    
    Specified by:
    
    getBranchLength in interface Node
  - setBranchLength
```
public final void setBranchLength(double value)
```
    Set the length of the branch attaching this node to its parent.
    
    Specified by:
    
    setBranchLength in interface Node
  - getBranchLengthSE
```
public final double getBranchLengthSE()
```
    Get the length SE of the branch attaching this node to its parent.
    
    Specified by:
    
    getBranchLengthSE in interface Node
  - setBranchLengthSE
```
public final void setBranchLengthSE(double value)
```
    Set the length SE of the branch attaching this node to its parent.
    
    Specified by:
    
    setBranchLengthSE in interface Node
  - getNodeHeight
```
public final double getNodeHeight()
```
    Get the height of this node relative to the most recent node.
    
    Specified by:
    
    getNodeHeight in interface Node
  - setNodeHeight
```
public final void setNodeHeight(double value)
```
    Set the height of this node relative to the most recent node.
    
    Specified by:
    
    setNodeHeight in interface Node
  - setNodeHeight
```
public final void setNodeHeight(double value,
                                boolean adjustChildBranchLengths)
```
    Set the height of this node relative to the most recent node.
    
    Specified by:
    
    setNodeHeight in interface Node
    
    Parameters:
    
    adjustChildBranchLengths - if true
  - getIdentifier
```
public final Identifier getIdentifier()
```
    Returns the identifier for this node.
    
    Specified by:
    
    getIdentifier in interface Node
  - setIdentifier
```
public final void setIdentifier(Identifier id)
```
    Set identifier for this node.
    
    Specified by:
    
    setIdentifier in interface Node
  - setNumber
```
public void setNumber(int n)
```
    Description copied from interface: Node
    
    set the index of this node
    
    Specified by:
    
    setNumber in interface Node
  - getNumber
```
public int getNumber()
```
    Description copied from interface: Node
    
    return the index of this node
    
    Specified by:
    
    getNumber in interface Node
  - getChild
```
public Node getChild(int n)
```
    get child node
    
    Specified by:
    
    getChild in interface Node
    
    Parameters:
    
    n - number of child
    
    Returns:
    
    child node
  - setChild
```
public void setChild(int n,
                     Node node)
```
    set child node
    
    Specified by:
    
    setChild in interface Node
    
    Parameters:
    
    n - number
  - hasChildren
```
public boolean hasChildren()
```
    check whether this node is an internal node
    
    Returns:
    
    result (true or false)
  - isLeaf
```
public boolean isLeaf()
```
    check whether this node is an external node
    
    Specified by:
    
    isLeaf in interface Node
    
    Returns:
    
    result (true or false)
  - isRoot
```
public boolean isRoot()
```
    check whether this node is a root node
    
    Specified by:
    
    isRoot in interface Node
    
    Returns:
    
    result (true or false)
  - addChild
```
public void addChild(Node n)
```
    add new child node
    
    Specified by:
    
    addChild in interface Node
    
    Parameters:
    
    n - new child node
  - insertChild
```
public void insertChild(Node n,
                        int pos)
```
    add new child node (insertion at a specific position)
    
    Specified by:
    
    insertChild in interface Node
    
    Parameters:
    
    n - new child node + @param pos position
  - removeChild
```
public Node removeChild(int n)
```
    remove child
    
    Specified by:
    
    removeChild in interface Node
    
    Parameters:
    
    n - number of child to be removed
  - lengths2HeightsContemp
```
public void lengths2HeightsContemp()
```
    determines the height of this node and its descendants from branch lengths, assuming contemporaneous tips.
  - setAttribute
```
public final void setAttribute(java.lang.String name,
                               java.lang.Object value)
```
    Sets a named attribute to the given value.
    
    Specified by:
    
    setAttribute in interface AttributeNode
    
    Parameters:
    
    name - the name of the attribute
    
    value - the value to set the attribute
  - getAttribute
```
public final java.lang.Object getAttribute(java.lang.String name)
```
    Specified by:
    
    getAttribute in interface AttributeNode
    
    Parameters:
    
    name - the name of the attribute.
    
    Returns:
    
    the attribute with the given name or null if it doesn't exist.
  - getAttributeNames
```
public final java.util.Enumeration getAttributeNames()
```
    Specified by:
    
    getAttributeNames in interface AttributeNode
    
    Returns:
    
    an enumeration of the attributes that this node has or null if the node has no attributes.
  - getChildCount
```
public final int getChildCount()
```
    Returns the number of children this node has.
    
    Specified by:
    
    getChildCount in interface Node
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object

Class SimpleNode

Field Summary

Fields inherited from interface pal.tree.AttributeNode

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SimpleNode

SimpleNode

SimpleNode

SimpleNode

SimpleNode

SimpleNode

SimpleNode

Method Detail

reset

init

init

init

getParent

setParent

removeParent

getSequenceString

getSequence

setSequence

getBranchLength

setBranchLength

getBranchLengthSE

setBranchLengthSE

getNodeHeight

setNodeHeight

setNodeHeight

getIdentifier

setIdentifier

setNumber

getNumber

getChild

setChild

hasChildren

isLeaf

isRoot

addChild

insertChild

removeChild

lengths2HeightsContemp

setAttribute

getAttribute

getAttributeNames

getChildCount

toString