Package pal.tree

Interface Node

All Superinterfaces:
Serializable
All Known Subinterfaces:
AttributeNode
All Known Implementing Classes:
PositionedNode, SimpleNode
public interface Node extends 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

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addChild(Node c)
    add new child node
    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 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 node
    boolean
    isRoot()
    check whether this node is a root node
    Node
    removeChild(int n)
    remove child
    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 number)
    set the index of this node
    void
    setParent(Node node)
    Set the parent node of this node.
    void
    setSequence(byte[] array)
    Sets the sequence using an array of bytes.

  • Method Details

    • getParent

      Node getParent()
      Returns the parent node of this node.

    • setParent

      void setParent(Node node)
      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

      void setIdentifier(Identifier id)
      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

      Node getChild(int n)
      get child node
      Parameters:
      n - number of child
      Returns:
      child node

    • setChild

      void setChild(int n, Node node)
      set child node
      Parameters:
      n - number

    • addChild

      void addChild(Node c)
      add new child node
      Parameters:
      c - new child node

    • insertChild

      void insertChild(Node c, int pos)
      add new child node (insertion at a specific position)
      Parameters:
      c - new child node + @param pos position

    • removeChild

      Node removeChild(int n)
      remove child
      Parameters:
      n - number of child to be removed