Package pal.tree
Class ClockTree
- java.lang.Object
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- pal.tree.ParameterizedTree.ParameterizedTreeBase
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- pal.tree.ClockTree
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- 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
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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
Fields Modifier and Type Field Description protected double[]
parameter
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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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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 Clock treesdouble
getUpperLimit(int n)
get upper parameter limitprotected void
heights2parameters()
protected void
parameters2Heights()
void
setParameter(double param, int n)
set model parametervoid
setParameterSE(double paramSE, int n)
set standard errors for model parametervoid
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
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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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ClockTree
public ClockTree()
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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).
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Method Detail
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update
public void update()
make clocktree consistent with branch lengths
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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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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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parameters2Heights
protected void parameters2Heights()
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heights2parameters
protected void heights2parameters()
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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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getParameterizationInfo
public java.lang.String getParameterizationInfo()
- Specified by:
getParameterizationInfo
in interfaceParameterizedTree
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getParameterizedTreeFactory
public static final ParameterizedTree.Factory getParameterizedTreeFactory()
Obtain a ParameterizedTree.Factory for generating Clock trees
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