pal.tree

Class SimpleNode

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 and Description
	SimpleNode() constructor default node
	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)
	SimpleNode(java.lang.String name, double branchLength)

Method Summary

Methods

Modifier and Type	Method and 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