Package pal.tree
Class UnconstrainedTree
java.lang.Object
pal.tree.ParameterizedTree.ParameterizedTreeBase
pal.tree.UnconstrainedTree
- All Implemented Interfaces:
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:
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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
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Field Summary
Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
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Constructor Summary
ConstructorsModifierConstructorDescriptiontake 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
Modifier and TypeMethodDescriptiongetCopy()
The cheapy copy that just creates a SimpleTreedouble
getDefaultValue
(int n) get default value of parameterdouble
getLowerLimit
(int n) get lower parameter limitint
get number of parametersdouble
getParameter
(int n) get model parameterstatic final ParameterizedTree.Factory
Obtain a ParameterizedTree.Factory for generating Unconstrained treesdouble
getUpperLimit
(int n) get upper parameter limitvoid
setParameter
(double param, int n) set model parametervoid
setParameterSE
(double paramSE, int n) set standard errors for model parameterMethods 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
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Constructor Details
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UnconstrainedTree
take any tree and afford it with an interface suitable for an unconstrained tree (parameters are all available branch lengths) -
UnconstrainedTree
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Method Details
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getNumParameters
public int getNumParameters()Description copied from interface:Parameterized
get number of parameters- Specified by:
getNumParameters
in interfaceParameterized
- Returns:
- number of parameters
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setParameter
public void setParameter(double param, int n) Description copied from interface:Parameterized
set model parameter- Specified by:
setParameter
in interfaceParameterized
- Parameters:
param
- parameter valuen
- parameter number
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getParameterizationInfo
- Specified by:
getParameterizationInfo
in interfaceParameterizedTree
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getParameter
public double getParameter(int n) Description copied from interface:Parameterized
get model parameter- Specified by:
getParameter
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- parameter value
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setParameterSE
public void setParameterSE(double paramSE, int n) Description copied from interface:Parameterized
set standard errors for model parameter- Specified by:
setParameterSE
in interfaceParameterized
- Parameters:
paramSE
- standard error of parameter valuen
- parameter number
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getLowerLimit
public double getLowerLimit(int n) Description copied from interface:Parameterized
get lower parameter limit- Specified by:
getLowerLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- lower bound
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getUpperLimit
public double getUpperLimit(int n) Description copied from interface:Parameterized
get upper parameter limit- Specified by:
getUpperLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- upper bound
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getDefaultValue
public double getDefaultValue(int n) Description copied from interface:Parameterized
get default value of parameter- Specified by:
getDefaultValue
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- default value
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getCopy
Description copied from class:ParameterizedTree.ParameterizedTreeBase
The cheapy copy that just creates a SimpleTree- Specified by:
getCopy
in interfaceTree
- Overrides:
getCopy
in classParameterizedTree.ParameterizedTreeBase
- Returns:
- a clone of this tree
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getParameterizedTreeFactory
Obtain a ParameterizedTree.Factory for generating Unconstrained trees
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