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.misc.IdGroup
  IdGroup.Utils
- 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.ParameterizedTree
  ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase
- 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	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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber

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

- 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

Class UnconstrainedTree

Nested Class Summary

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

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

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

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

Field Summary

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class pal.tree.ParameterizedTree.ParameterizedTreeBase

Methods inherited from class java.lang.Object

Methods inherited from interface pal.misc.IdGroup

Methods inherited from interface pal.tree.ParameterizedTree

Methods inherited from interface pal.tree.Tree

Constructor Detail

UnconstrainedTree

UnconstrainedTree

Method Detail

getNumParameters

setParameter

getParameterizationInfo

getParameter

setParameterSE

getLowerLimit

getUpperLimit

getDefaultValue

getCopy

getParameterizedTreeFactory