pal.tree

Class UnconstrainedTree

java.lang.Object

pal.tree.ParameterizedTree.ParameterizedTreeBase

pal.tree.UnconstrainedTree

All Implemented Interfaces:

java.io.Serializable, IdGroup, Parameterized, Units, UnitsProvider, ParameterizedTree, Tree

public class UnconstrainedTree
extends ParameterizedTree.ParameterizedTreeBase
implements ParameterizedTree

provides parameter interface to an unconstrained tree (parameters are all available branch lengths)

Version:

$Id: UnconstrainedTree.java,v 1.13 2004/04/25 22:53:14 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 inherited from interface pal.misc.Units

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

Constructor Summary

Constructors

Modifier	Constructor and Description
	UnconstrainedTree(Tree t) take any tree and afford it with an interface suitable for an unconstrained tree (parameters are all available branch lengths)
protected	UnconstrainedTree(UnconstrainedTree toCopy)

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 Unconstrained trees
double	getUpperLimit(int n) get upper parameter limit
void	setParameter(double param, int n) set model parameter
void	setParameterSE(double paramSE, int n) set standard errors for model parameter

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

Constructor Detail

UnconstrainedTree

public UnconstrainedTree(Tree t)

take any tree and afford it with an interface suitable for an unconstrained tree (parameters are all available branch lengths)

UnconstrainedTree

protected UnconstrainedTree(UnconstrainedTree toCopy)

Method Detail

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

getParameterizationInfo

public java.lang.String getParameterizationInfo()

Specified by:

getParameterizationInfo in interface ParameterizedTree

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

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

getParameterizedTreeFactory

public static final ParameterizedTree.Factory getParameterizedTreeFactory()

Obtain a ParameterizedTree.Factory for generating Unconstrained trees