Package pal.substmodel
Class InvariableSites
java.lang.Object
pal.misc.PalObjectListener.EventGenerator
pal.substmodel.RateDistribution
pal.substmodel.InvariableSites
- All Implemented Interfaces:
Serializable
,Cloneable
,Parameterized
,Report
invariable sites model (two-rate model with mean rate = 1.0)
- Version:
- $Id: InvariableSites.java,v 1.4 2003/06/11 05:26:46 matt Exp $
- Author:
- Korbinian Strimmer
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Field Summary
Fields inherited from class pal.substmodel.RateDistribution
format, numRates, probability, rate
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Constructor Summary
ConstructorsConstructorDescriptionInvariableSites
(double f) construct discrete rate distribution with two rates (one invariable and one variable) -
Method Summary
Modifier and TypeMethodDescriptiondouble
getDefaultValue
(int n) get default value of parameterdouble
getLowerLimit
(int n) get lower parameter limitint
get number of parametersdouble
getParameter
(int n) get model parameterdouble
getUpperLimit
(int n) get upper parameter limitboolean
void
report
(PrintWriter out) print human readable report (e.g., on parameters and associated model)void
setParameter
(double param, int n) set model parametervoid
setParameterSE
(double paramSE, int n) set standard errors for model parameterMethods inherited from class pal.substmodel.RateDistribution
clone, getCategoryProbabilities, getCategoryProbability, getNumberOfRates, getRate, getRates, printRates
Methods inherited from class pal.misc.PalObjectListener.EventGenerator
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener
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Constructor Details
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InvariableSites
public InvariableSites(double f) construct discrete rate distribution with two rates (one invariable and one variable)- Parameters:
f
- fraction of invariable sites
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Method Details
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report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model) -
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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isDistributionIndependentlyMutable
public boolean isDistributionIndependentlyMutable()
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