Package pal.tree

Class ClockTree

java.lang.Object
pal.tree.ParameterizedTree.ParameterizedTreeBase
pal.tree.ClockTree
All Implemented Interfaces:
Serializable, IdGroup, Parameterized, Units, UnitsProvider, ParameterizedTree, Tree
Direct Known Subclasses:
DemographicClockTree
public class ClockTree extends ParameterizedTree.ParameterizedTreeBase implements ParameterizedTree
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
Version:
$Id: ClockTree.java,v 1.16 2003/06/04 03:17:52 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:

  • Field Details

    • parameter

      protected double[] parameter

  • Constructor Details

    • 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 Details

    • update

      public void update()
      make clocktree consistent with branch lengths

    • getNumParameters

      public int getNumParameters()
      Description copied from interface: Parameterized
      get number of parameters
      Specified by:
      getNumParameters in interface Parameterized
      Returns:
      number of parameters

    • setParameter

      public void setParameter(double param, int n)
      Description copied from interface: Parameterized
      set model parameter
      Specified by:
      setParameter in interface Parameterized
      Parameters:
      param - parameter value
      n - parameter number

    • getParameter

      public double getParameter(int n)
      Description copied from interface: Parameterized
      get model parameter
      Specified by:
      getParameter in interface 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
      Specified by:
      setParameterSE in interface 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
      Specified by:
      getLowerLimit in interface Parameterized
      Parameters:
      n - parameter number
      Returns:
      lower bound

    • getUpperLimit

      public double getUpperLimit(int n)
      Description copied from interface: Parameterized
      get upper parameter limit
      Specified by:
      getUpperLimit in interface Parameterized
      Parameters:
      n - parameter number
      Returns:
      upper bound

    • getDefaultValue

      public double getDefaultValue(int n)
      Description copied from interface: Parameterized
      get default value of parameter
      Specified by:
      getDefaultValue in interface Parameterized
      Parameters:
      n - parameter number
      Returns:
      default value

    • parameters2Heights

      protected void parameters2Heights()

    • heights2parameters

      protected void heights2parameters()

    • getCopy

      public Tree getCopy()
      Description copied from class: ParameterizedTree.ParameterizedTreeBase
      The cheapy copy that just creates a SimpleTree
      Specified by:
      getCopy in interface Tree
      Overrides:
      getCopy in class ParameterizedTree.ParameterizedTreeBase
      Returns:
      a clone of this tree

    • getParameterizationInfo

      public String getParameterizationInfo()
      Specified by:
      getParameterizationInfo in interface ParameterizedTree

    • getParameterizedTreeFactory

      public static final ParameterizedTree.Factory getParameterizedTreeFactory()
      Obtain a ParameterizedTree.Factory for generating Clock trees