pal.tree

Class ClockTree

java.lang.Object

pal.tree.ParameterizedTree.ParameterizedTreeBase

pal.tree.ClockTree

All Implemented Interfaces:

java.io.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:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.tree.ParameterizedTree

ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Nested classes/interfaces inherited from interface pal.tree.Tree

Tree.TreeBase

Field Summary

Fields

Modifier and Type	Field and Description
protected double[]	parameter

Fields inherited from interface pal.misc.Units

DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

Constructors

Constructor and Description
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

Methods

Modifier and Type	Method and Description
Tree	getCopy() The cheapy copy that just creates a SimpleTree
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
java.lang.String	getParameterizationInfo()
static ParameterizedTree.Factory	getParameterizedTreeFactory() Obtain a ParameterizedTree.Factory for generating Clock trees
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.ParameterizedTreeBase

createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getNodeCount, getOrthogonalHints, getRoot, getUnits, setAttribute, setBaseTree, setIdentifier, setRoot, toString, whichIdNumber

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pal.tree.ParameterizedTree

getOrthogonalHints

Methods inherited from interface pal.tree.Tree

createNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot

Methods inherited from interface pal.misc.IdGroup

getIdCount, getIdentifier, setIdentifier, whichIdNumber

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

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 java.lang.String getParameterizationInfo()

Specified by:

getParameterizationInfo in interface ParameterizedTree

getParameterizedTreeFactory

public static final ParameterizedTree.Factory getParameterizedTreeFactory()

Obtain a ParameterizedTree.Factory for generating Clock trees