Constructor Detail

• TreeBase

  protected TreeBase​(Node theRoot)

  constructor

  Parameters:

  theRoot - the node to base tree on

• TreeBase

  protected TreeBase()

  constructor

• TreeBase

  protected TreeBase​(Tree.TreeBase tree,
                     Node newRoot)

  clone constructor

Method Detail

• setRoot

  public void setRoot​(Node theRoot)

  Called by subclasses that can't give root at time of construction (of this class)

  Specified by:

  setRoot in interface Tree

  Parameters:

  theRoot - the root node of the tree to construct.

• getUnits

  public final int getUnits()

  Return the units that this tree is expressed in.

  Specified by:

  getUnits in interface Tree

  Specified by:

  getUnits in interface UnitsProvider

  Returns:

  the units relating to this object.

• setUnits

  public final void setUnits​(int units)

  Sets the units that this tree is expressed in.

• getExternalNodeCount

  public final int getExternalNodeCount()

  Returns the number of external nodes.

  Specified by:

  getExternalNodeCount in interface Tree

  Returns:

  a count of the number of external nodes (tips) in this tree.

• getExternalNode

  public final Node getExternalNode​(int i)

  Returns the ith external node.

  Specified by:

  getExternalNode in interface Tree

  Returns:

  the ith external node in the tree.

• getInternalNodeCount

  public final int getInternalNodeCount()

  Returns the number of internal nodes.

  Specified by:

  getInternalNodeCount in interface Tree

  Returns:

  a count of the number of internal nodes (and hence clades) in this tree.

• getInternalNode

  public final Node getInternalNode​(int i)

  Returns the ith internal node.

  Specified by:

  getInternalNode in interface Tree

  Returns:

  the ith internal node in the tree.

• getRoot

  public final Node getRoot()

  Returns the root node of this tree.

  Specified by:

  getRoot in interface Tree

  Returns:

  the root node of this tree.

• findNode

  public Node findNode​(int num)

  return node with number num (as displayed in ASCII tree)

  Parameters:

  num - number of node

  Returns:

  node

• createNodeList

  public void createNodeList()

  count and list external and internal nodes and compute heights of each node

  Specified by:

  createNodeList in interface Tree

• setSetupLengthsAndHeights

  protected void setSetupLengthsAndHeights​(boolean value)

  Set whether or not this class should call methods to adjust either heights or lengths automatically

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object

• setAttribute

  public void setAttribute​(Node node,
                           java.lang.String name,
                           java.lang.Object value)

  Sets an named attribute for a given node.

  Specified by:

  setAttribute in interface Tree

  Parameters:

  node - the node whose attribute is being set.

  name - the name of the attribute.

  value - the new value of the attribute.

• getAttribute

  public java.lang.Object getAttribute​(Node node,
                                       java.lang.String name)

  Specified by:

  getAttribute in interface Tree

  Parameters:

  node - the node being interrogated.

  name - the name of the attribute of interest.

  Returns:

  an object representing the named attributed for the numbered node.

• reroot

  public void reroot​(int num)

  make node with number num to root node

  Parameters:

  num - number of node

• reroot

  public void reroot​(Node node)

  make provided node the root node

  Parameters:

  node - the node to make the root.

• getIdCount

  public int getIdCount()

  Description copied from interface: IdGroup
  Returns the number of identifiers in this group

  Specified by:

  getIdCount in interface IdGroup

• getIdentifier

  public Identifier getIdentifier​(int i)

  Description copied from interface: IdGroup
  Returns the ith identifier.

  Specified by:

  getIdentifier in interface IdGroup

• setIdentifier

  public void setIdentifier​(int i,
                            Identifier id)

  Description copied from interface: IdGroup
  Sets the ith identifier.

  Specified by:

  setIdentifier in interface IdGroup

• whichIdNumber

  public int whichIdNumber​(java.lang.String s)

  Description copied from interface: IdGroup
  returns the index of the identifier with the given name.

  Specified by:

  whichIdNumber in interface IdGroup

• report

  public void report​(java.io.PrintWriter out)

  Description copied from interface: Report
  print human readable report (e.g., on parameters and associated model)

  Specified by:

  report in interface Report

  Parameters:

  out - output stream