Class SimpleNode

Method Details

• reset

  public void reset()

• init

  protected void init(Node n)

• init

  protected void init(Node n, boolean keepId)

  Initialized node instance variables based on given Node. children are ignored.

• 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

• getParent

  public final Node getParent()

  Returns the parent node of this node.

  Specified by:

  getParent in interface Node

• setParent

  public void setParent(Node node)

  Set the parent node of this node.

  Specified by:

  setParent in interface Node

• removeParent

  public final void removeParent()

  removes parent.

• getSequenceString

  public String getSequenceString()

  Returns the sequence at this node, in the form of a String.

• getSequence

  public byte[] getSequence()

  Returns the sequence at this node, in the form of an array of bytes.

  Specified by:

  getSequence in interface Node

• setSequence

  public void setSequence(byte[] s)

  Sets the sequence at this node, in the form of an array of bytes.

  Specified by:

  setSequence in interface Node

• getBranchLength

  public final double getBranchLength()

  Get the length of the branch attaching this node to its parent.

  Specified by:

  getBranchLength in interface Node

• setBranchLength

  public final void setBranchLength(double value)

  Set the length of the branch attaching this node to its parent.

  Specified by:

  setBranchLength in interface Node

• getBranchLengthSE

  public final double getBranchLengthSE()

  Get the length SE of the branch attaching this node to its parent.

  Specified by:

  getBranchLengthSE in interface Node

• setBranchLengthSE

  public final void setBranchLengthSE(double value)

  Set the length SE of the branch attaching this node to its parent.

  Specified by:

  setBranchLengthSE in interface Node

• getNodeHeight

  public final double getNodeHeight()

  Get the height of this node relative to the most recent node.

  Specified by:

  getNodeHeight in interface Node

• setNodeHeight

  public final void setNodeHeight(double value)

  Set the height of this node relative to the most recent node.

  Specified by:

  setNodeHeight in interface Node

• 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 interface Node

  Parameters:

  adjustChildBranchLengths - if true

• getIdentifier

  public final Identifier getIdentifier()

  Returns the identifier for this node.

  Specified by:

  getIdentifier in interface Node

• setIdentifier

  public final void setIdentifier(Identifier id)

  Set identifier for this node.

  Specified by:

  setIdentifier in interface Node

• setNumber

  public void setNumber(int n)

  Description copied from interface: Node

  set the index of this node

  Specified by:

  setNumber in interface Node

• getNumber

  public int getNumber()

  Description copied from interface: Node

  return the index of this node

  Specified by:

  getNumber in interface Node

• getChild

  public Node getChild(int n)

  get child node

  Specified by:

  getChild in interface Node

  Parameters:

  n - number of child

  Returns:

  child node

• setChild

  public void setChild(int n, Node node)

  set child node

  Specified by:

  setChild in interface Node

  Parameters:

  n - number

• hasChildren

  public boolean hasChildren()

  check whether this node is an internal node

  Returns:

  result (true or false)

• isLeaf

  public boolean isLeaf()

  check whether this node is an external node

  Specified by:

  isLeaf in interface Node

  Returns:

  result (true or false)

• isRoot

  public boolean isRoot()

  check whether this node is a root node

  Specified by:

  isRoot in interface Node

  Returns:

  result (true or false)

• addChild

  public void addChild(Node n)

  add new child node

  Specified by:

  addChild in interface Node

  Parameters:

  n - new child node

• insertChild

  public void insertChild(Node n, int pos)

  add new child node (insertion at a specific position)

  Specified by:

  insertChild in interface Node

  Parameters:

  n - new child node + @param pos position

• removeChild

  public Node removeChild(int n)

  remove child

  Specified by:

  removeChild in interface Node

  Parameters:

  n - number of child to be removed

• lengths2HeightsContemp

  public void lengths2HeightsContemp()

  determines the height of this node and its descendants from branch lengths, assuming contemporaneous tips.

• setAttribute

  public final void setAttribute(String name, Object value)

  Sets a named attribute to the given value.

  Specified by:

  setAttribute in interface AttributeNode

  Parameters:

  name - the name of the attribute

  value - the value to set the attribute

• getAttribute

  public final Object getAttribute(String name)

  Specified by:

  getAttribute in interface AttributeNode

  Parameters:

  name - the name of the attribute.

  Returns:

  the attribute with the given name or null if it doesn't exist.

• getAttributeNames

  public final Enumeration getAttributeNames()

  Specified by:

  getAttributeNames in interface AttributeNode

  Returns:

  an enumeration of the attributes that this node has or null if the node has no attributes.

• getChildCount

  public final int getChildCount()

  Returns the number of children this node has.

  Specified by:

  getChildCount in interface Node

• toString

  public String toString()

  Overrides:

  toString in class Object