Package pal.tree
Interface Node
- All Superinterfaces:
Serializable
- All Known Subinterfaces:
AttributeNode
- All Known Implementing Classes:
PositionedNode
,SimpleNode
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
-
Method Summary
Modifier and TypeMethodDescriptionvoid
add new child nodedouble
Get the length of the branch attaching this node to its parent.double
Get the length SE of the branch attaching this node to its parent.getChild
(int n) get child nodeint
Returns the number of children this node has.Returns the identifier for this node.double
Get the height of this node relative to the most recent node.int
return the index of this nodeReturns the parent node of this node.byte[]
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 noderemoveChild
(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
set child nodevoid
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
Set the parent node of this node.void
setSequence
(byte[] array) Sets the sequence using an array of bytes.
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Method Details
-
getParent
Node getParent()Returns the parent node of this node. -
setParent
Set the parent node of this node. -
getSequence
byte[] getSequence()Returns the sequence at this node, in the form an array of bytes. -
setSequence
void setSequence(byte[] array) Sets the sequence using an array of bytes. -
getNumber
int getNumber()return the index of this node -
setNumber
void setNumber(int number) set the index of this node -
getBranchLength
double getBranchLength()Get the length of the branch attaching this node to its parent. -
setBranchLength
void setBranchLength(double value) Set the length of the branch attaching this node to its parent. -
getBranchLengthSE
double getBranchLengthSE()Get the length SE of the branch attaching this node to its parent. -
setBranchLengthSE
void setBranchLengthSE(double value) Set the length SE of the branch attaching this node to its parent. -
getNodeHeight
double getNodeHeight()Get the height of this node relative to the most recent node. -
setNodeHeight
void setNodeHeight(double value) Set the height of this node relative to the most recent node. -
setNodeHeight
void setNodeHeight(double value, boolean adjustChildBranchLengths) Set the height of this node relative to the most recent node.- Parameters:
adjustChildBranchLengths
- if true
-
getIdentifier
Identifier getIdentifier()Returns the identifier for this node. -
setIdentifier
Set identifier for this node. -
getChildCount
int getChildCount()Returns the number of children this node has. -
isLeaf
boolean isLeaf()check whether this node is an external node- Returns:
- result (true or false)
-
isRoot
boolean isRoot()check whether this node is a root node- Returns:
- result (true or false)
-
getChild
get child node- Parameters:
n
- number of child- Returns:
- child node
-
setChild
set child node- Parameters:
n
- number
-
addChild
add new child node- Parameters:
c
- new child node
-
insertChild
add new child node (insertion at a specific position)- Parameters:
c
- new child node + @param pos position
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removeChild
remove child- Parameters:
n
- number of child to be removed
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