pal.tree
Class ClockTree
java.lang.Object
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+--pal.tree.ParameterizedTree
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+--pal.tree.ClockTree
- All Implemented Interfaces:
- Parameterized, java.io.Serializable, Tree, Units
- Direct Known Subclasses:
- DemographicClockTree
- public class ClockTree
- extends ParameterizedTree
provides parameter interface to a clock tree
(parameters are the minimal node height differences
at each internal node)
- See Also:
- Serialized Form
Constructor Summary |
ClockTree()
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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).
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Methods inherited from class pal.tree.ParameterizedTree |
createNodeList, getAttribute, getBaseTree, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, setAttribute, setBaseTree, setRoot, setUnits, toString |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
parameter
protected double[] parameter
ClockTree
public ClockTree()
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).
update
public void update()
- make clocktree consistent with branch lengths
getNumParameters
public int getNumParameters()
- Description copied from interface:
Parameterized
- get number of parameters
- Following copied from interface:
pal.misc.Parameterized
- Returns:
- number of parameters
setParameter
public void setParameter(double param,
int n)
- Description copied from interface:
Parameterized
- set model parameter
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
param
- parameter valuen
- parameter number
getParameter
public double getParameter(int n)
- Description copied from interface:
Parameterized
- get model parameter
- Following copied from interface:
pal.misc.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
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
paramSE
- standard error of parameter valuen
- parameter number
getLowerLimit
public double getLowerLimit(int n)
- Description copied from interface:
Parameterized
- get lower parameter limit
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
n
- parameter number- Returns:
- lower bound
getUpperLimit
public double getUpperLimit(int n)
- Description copied from interface:
Parameterized
- get upper parameter limit
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
n
- parameter number- Returns:
- upper bound
getDefaultValue
public double getDefaultValue(int n)
- Description copied from interface:
Parameterized
- get default value of parameter
- Following copied from interface:
pal.misc.Parameterized
- Parameters:
n
- parameter number- Returns:
- default value
parameters2Heights
protected void parameters2Heights()
heights2parameters
protected void heights2parameters()