Package pal.tree
Class UnconstrainedTree
- java.lang.Object
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- pal.tree.ParameterizedTree.ParameterizedTreeBase
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- pal.tree.UnconstrainedTree
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Nested classes/interfaces inherited from interface pal.tree.ParameterizedTree
ParameterizedTree.Factory, ParameterizedTree.ParameterizedTreeBase
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Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
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Field Summary
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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
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)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description Tree
getCopy()
The cheapy copy that just creates a SimpleTreedouble
getDefaultValue(int n)
get default value of parameterdouble
getLowerLimit(int n)
get lower parameter limitint
getNumParameters()
get number of parametersdouble
getParameter(int n)
get model parameterjava.lang.String
getParameterizationInfo()
static ParameterizedTree.Factory
getParameterizedTreeFactory()
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 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
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Methods inherited from interface pal.tree.ParameterizedTree
getOrthogonalHints
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Methods inherited from interface pal.tree.Tree
createNodeList, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setRoot
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Constructor Detail
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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)
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UnconstrainedTree
protected UnconstrainedTree(UnconstrainedTree toCopy)
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Method Detail
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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
public java.lang.String 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
public Tree 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
public static final ParameterizedTree.Factory getParameterizedTreeFactory()
Obtain a ParameterizedTree.Factory for generating Unconstrained trees
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