pal.tree
Class ParameterizedTree

java.lang.Object
  |
  +--pal.tree.ParameterizedTree
All Implemented Interfaces:
Parameterized, java.io.Serializable, Tree, Units
Direct Known Subclasses:
ClockTree, DatedTipsClockTree, LogParameterizedTree, MutationRateModelTree, UnconstrainedTree

public abstract class ParameterizedTree
extends java.lang.Object
implements Parameterized, Tree

abstract base class for a tree with an Parameterized interface

See Also:
Serialized Form

Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, YEARS
 
Constructor Summary
ParameterizedTree()
           
 
Method Summary
 void createNodeList()
          This method is called to ensure that the calls to other methods in this interface are valid.
 java.lang.Object getAttribute(Node node, java.lang.String name)
           
 Tree getBaseTree()
           
 Node getExternalNode(int i)
          returns the ith external node in the tree.
 int getExternalNodeCount()
          returns a count of the number of external nodes (tips) in this tree.
 Node getInternalNode(int i)
          returns the ith internal node in the tree.
 int getInternalNodeCount()
          returns a count of the number of internal nodes (and hence clades) in this tree.
 Node getRoot()
          Returns the root node of this tree.
 int getUnits()
          Gets the units that this tree's branch lengths and node heights are expressed in.
 void setAttribute(Node node, java.lang.String name, java.lang.Object value)
          Sets an named attribute for a given node.
 void setBaseTree(Tree tree)
           
 void setRoot(Node root)
          This method constructs a tree from the given root node.
 void setUnits(int units)
          Sets the units that this tree's branch lengths and node heights are expressed in.
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
 

Constructor Detail

ParameterizedTree

public ParameterizedTree()
Method Detail

setBaseTree

public void setBaseTree(Tree tree)

getBaseTree

public Tree getBaseTree()

getRoot

public final Node getRoot()
Returns the root node of this tree.
Specified by:
getRoot in interface Tree
Following copied from interface: pal.tree.Tree
Returns:
the root node of this tree.

setRoot

public final void setRoot(Node root)
Description copied from interface: Tree
This method constructs a tree from the given root node.
Specified by:
setRoot in interface Tree
Following copied from interface: pal.tree.Tree
Parameters:
root - the root node of the tree to construct.

getExternalNodeCount

public final int getExternalNodeCount()
returns a count of the number of external nodes (tips) in this tree.
Specified by:
getExternalNodeCount in interface Tree
Following copied from interface: pal.tree.Tree
Returns:
a count of the number of external nodes (tips) in this tree.

getInternalNodeCount

public final int getInternalNodeCount()
returns a count of the number of internal nodes (and hence clades) in this tree.
Specified by:
getInternalNodeCount in interface Tree
Following copied from interface: pal.tree.Tree
Returns:
a count of the number of internal nodes (and hence clades) in this tree.

getExternalNode

public final Node getExternalNode(int i)
returns the ith external node in the tree.
Specified by:
getExternalNode in interface Tree
Following copied from interface: pal.tree.Tree
Returns:
the ith external node in the tree.

getInternalNode

public final Node getInternalNode(int i)
returns the ith internal node in the tree.
Specified by:
getInternalNode in interface Tree
Following copied from interface: pal.tree.Tree
Returns:
the ith internal node in the tree.

createNodeList

public final void createNodeList()
This method is called to ensure that the calls to other methods in this interface are valid.
Specified by:
createNodeList in interface Tree

getUnits

public final int getUnits()
Description copied from interface: Tree
Gets the units that this tree's branch lengths and node heights are expressed in.
Specified by:
getUnits in interface Tree

setUnits

public final void setUnits(int units)
Description copied from interface: Tree
Sets the units that this tree's branch lengths and node heights are expressed in.
Specified by:
setUnits in interface Tree

setAttribute

public final void setAttribute(Node node,
                               java.lang.String name,
                               java.lang.Object value)
Description copied from interface: Tree
Sets an named attribute for a given node.
Specified by:
setAttribute in interface Tree
Following copied from interface: pal.tree.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 final java.lang.Object getAttribute(Node node,
                                           java.lang.String name)
Specified by:
getAttribute in interface Tree
Following copied from interface: pal.tree.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.

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object