Package pal.substmodel
Class InvariableSites
- java.lang.Object
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- pal.misc.PalObjectListener.EventGenerator
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- pal.substmodel.RateDistribution
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- pal.substmodel.InvariableSites
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,Parameterized
,Report
public class InvariableSites extends RateDistribution implements java.io.Serializable
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:
- Serialized Form
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Nested Class Summary
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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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Field Summary
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Fields inherited from class pal.substmodel.RateDistribution
format, numRates, probability, rate
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Constructor Summary
Constructors Constructor Description InvariableSites(double f)
construct discrete rate distribution with two rates (one invariable and one variable)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
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 parameterdouble
getUpperLimit(int n)
get upper parameter limitboolean
isDistributionIndependentlyMutable()
void
report(java.io.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 parameter-
Methods inherited from class pal.substmodel.RateDistribution
clone, getCategoryProbabilities, getCategoryProbability, getNumberOfRates, getRate, getRates, printRates
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Methods inherited from class pal.misc.PalObjectListener.EventGenerator
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener
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Method Detail
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report
public void report(java.io.PrintWriter out)
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)
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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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isDistributionIndependentlyMutable
public boolean isDistributionIndependentlyMutable()
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