pal.tree
Class ClockTree

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

public class ClockTree
extends ParameterizedTree

provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)

See Also:
Serialized Form

Field Summary
protected  double[] parameter
           
 
Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, YEARS
 
Constructor Summary
ClockTree()
           
ClockTree(Tree t)
          take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).
 
Method Summary
 double getDefaultValue(int n)
          get default value of parameter
 double getLowerLimit(int n)
          get lower parameter limit
 int getNumParameters()
          get number of parameters
 double getParameter(int n)
          get model parameter
 double getUpperLimit(int n)
          get upper parameter limit
protected  void heights2parameters()
           
protected  void parameters2Heights()
           
 void setParameter(double param, int n)
          set model parameter
 void setParameterSE(double paramSE, int n)
          set standard errors for model parameter
 void update()
          make clocktree consistent with branch lengths
 
Methods inherited from class pal.tree.ParameterizedTree
createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setBaseTree, setRoot, setUnits, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

parameter

protected double[] parameter
Constructor Detail

ClockTree

public ClockTree()

ClockTree

public ClockTree(Tree t)
take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).

This parameterisation of a clock-tree, ensuring that all parameters are independent of each other is due to Andrew Rambaut (personal communication).

Method Detail

update

public void update()
make clocktree consistent with branch lengths

getNumParameters

public int getNumParameters()
Description copied from interface: Parameterized
get number of parameters
Following copied from interface: pal.misc.Parameterized
Returns:
number of parameters

setParameter

public void setParameter(double param,
                         int n)
Description copied from interface: Parameterized
set model parameter
Following copied from interface: pal.misc.Parameterized
Parameters:
param - parameter value
n - parameter number

getParameter

public double getParameter(int n)
Description copied from interface: Parameterized
get model parameter
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
parameter value

setParameterSE

public void setParameterSE(double paramSE,
                           int n)
Description copied from interface: Parameterized
set standard errors for model parameter
Following copied from interface: pal.misc.Parameterized
Parameters:
paramSE - standard error of parameter value
n - parameter number

getLowerLimit

public double getLowerLimit(int n)
Description copied from interface: Parameterized
get lower parameter limit
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
lower bound

getUpperLimit

public double getUpperLimit(int n)
Description copied from interface: Parameterized
get upper parameter limit
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
upper bound

getDefaultValue

public double getDefaultValue(int n)
Description copied from interface: Parameterized
get default value of parameter
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
default value

parameters2Heights

protected void parameters2Heights()

heights2parameters

protected void heights2parameters()