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