pal.substmodel
Class InvariableSites

java.lang.Object
  pal.misc.PalObjectListener.EventGenerator
      pal.substmodel.RateDistribution
          pal.substmodel.InvariableSites

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

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary

Fields inherited from class pal.substmodel.RateDistribution

format, numRates, probability, rate

Constructor Summary

InvariableSites(double f)
construct discrete rate distribution with two rates (one invariable and one variable)

Method Summary

double	getDefaultValue(int n) get default value of parameter
double	getLowerLimit(int n) get lower parameter limit
int	getNumParameters() get number of parameters
double	getParameter(int n) get model parameter
double	getUpperLimit(int n) get upper parameter limit
boolean	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 parameter
void	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

Methods inherited from class pal.misc.PalObjectListener.EventGenerator

addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

InvariableSites

public InvariableSites(double f)

construct discrete rate distribution with two rates (one invariable and one variable)

Parameters:

f - fraction of invariable sites

Method Detail

report

public void report(java.io.PrintWriter out)

Description copied from interface: Report

print human readable report (e.g., on parameters and associated model)

Specified by:

report in interface Report

Parameters:

out - output stream

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Returns:

number of parameters

setParameter

public void setParameter(double param,
                         int n)

Description copied from interface: Parameterized

set model parameter

Specified by:

setParameter in interface Parameterized

Parameters:

param - parameter value

n - parameter number

getParameter

public double getParameter(int n)

Description copied from interface: Parameterized

get model parameter

Specified by:

getParameter in interface 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

Specified by:

setParameterSE in interface Parameterized

Parameters:

paramSE - standard error of parameter value

n - parameter number

getLowerLimit

public double getLowerLimit(int n)

Description copied from interface: Parameterized

get lower parameter limit

Specified by:

getLowerLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

lower bound

getUpperLimit

public double getUpperLimit(int n)

Description copied from interface: Parameterized

get upper parameter limit

Specified by:

getUpperLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

upper bound

getDefaultValue

public double getDefaultValue(int n)

Description copied from interface: Parameterized

get default value of parameter

Specified by:

getDefaultValue in interface Parameterized

Parameters:

n - parameter number

Returns:

default value

isDistributionIndependentlyMutable

public boolean isDistributionIndependentlyMutable()