Package pal.tree
Interface Node
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- All Superinterfaces:
java.io.Serializable
- All Known Subinterfaces:
AttributeNode
- All Known Implementing Classes:
PositionedNode
,SimpleNode
public interface Node extends java.io.Serializable
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree- Version:
- $Id: Node.java,v 1.23 2002/09/08 03:43:04 matt Exp $
- Author:
- Alexei Drummond, Korbinian Strimmer
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
addChild(Node c)
add new child nodedouble
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 an array of bytes.void
insertChild(Node c, 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 nodeNode
removeChild(int n)
remove childvoid
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 number)
set the index of this nodevoid
setParent(Node node)
Set the parent node of this node.void
setSequence(byte[] array)
Sets the sequence using an array of bytes.
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Method Detail
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getParent
Node getParent()
Returns the parent node of this node.
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setParent
void setParent(Node node)
Set the parent node of this node.
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getSequence
byte[] getSequence()
Returns the sequence at this node, in the form an array of bytes.
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setSequence
void setSequence(byte[] array)
Sets the sequence using an array of bytes.
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getNumber
int getNumber()
return the index of this node
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setNumber
void setNumber(int number)
set the index of this node
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getBranchLength
double getBranchLength()
Get the length of the branch attaching this node to its parent.
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setBranchLength
void setBranchLength(double value)
Set the length of the branch attaching this node to its parent.
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getBranchLengthSE
double getBranchLengthSE()
Get the length SE of the branch attaching this node to its parent.
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setBranchLengthSE
void setBranchLengthSE(double value)
Set the length SE of the branch attaching this node to its parent.
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getNodeHeight
double getNodeHeight()
Get the height of this node relative to the most recent node.
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setNodeHeight
void setNodeHeight(double value)
Set the height of this node relative to the most recent node.
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setNodeHeight
void setNodeHeight(double value, boolean adjustChildBranchLengths)
Set the height of this node relative to the most recent node.- Parameters:
adjustChildBranchLengths
- if true
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getIdentifier
Identifier getIdentifier()
Returns the identifier for this node.
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setIdentifier
void setIdentifier(Identifier id)
Set identifier for this node.
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getChildCount
int getChildCount()
Returns the number of children this node has.
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isLeaf
boolean isLeaf()
check whether this node is an external node- Returns:
- result (true or false)
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isRoot
boolean isRoot()
check whether this node is a root node- Returns:
- result (true or false)
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getChild
Node getChild(int n)
get child node- Parameters:
n
- number of child- Returns:
- child node
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setChild
void setChild(int n, Node node)
set child node- Parameters:
n
- number
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addChild
void addChild(Node c)
add new child node- Parameters:
c
- new child node
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insertChild
void insertChild(Node c, int pos)
add new child node (insertion at a specific position)- Parameters:
c
- new child node + @param pos position
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removeChild
Node removeChild(int n)
remove child- Parameters:
n
- number of child to be removed
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