Package pal.tree

Interface Node

  • 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

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      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 Detail

      • 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