pal.substmodel

Class RateDistribution

java.lang.Object

pal.misc.PalObjectListener.EventGenerator

pal.substmodel.RateDistribution

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, Parameterized, Report

Direct Known Subclasses:

GammaRates, InvariableSites, UniformRate

public abstract class RateDistribution
extends PalObjectListener.EventGenerator
implements Parameterized, Report, java.lang.Cloneable, java.io.Serializable

abstract base class for models of rate variation over sites employing a discrete rate distribution

Version:

$Id: RateDistribution.java,v 1.12 2004/05/19 04:05:21 matt Exp $

Author:

Korbinian Strimmer, Alexei Drummond

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

Modifier and Type	Field and Description
protected FormattedOutput	format
int	numRates number of rate categories
double[]	probability probability of each rate
double[]	rate rates of each rate category

Constructor Summary

Constructors

Constructor and Description
RateDistribution(int n) construct discrete distribution

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.Object	clone()
double[]	getCategoryProbabilities() The non direct access method
double	getCategoryProbability(int category)
int	getNumberOfRates()
double	getRate(int category)
double[]	getRates()
protected void	printRates(java.io.PrintWriter out)

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

Methods inherited from interface pal.misc.Parameterized

getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE

Methods inherited from interface pal.misc.Report

report

Field Detail

numRates

public int numRates

number of rate categories

rate

public double[] rate

rates of each rate category

probability

public double[] probability

probability of each rate

format

protected FormattedOutput format

Constructor Detail

RateDistribution

public RateDistribution(int n)

construct discrete distribution

Parameters:

n - number of rate categories

Method Detail

getNumberOfRates

public final int getNumberOfRates()

getRates

public final double[] getRates()

getRate

public final double getRate(int category)

printRates

protected void printRates(java.io.PrintWriter out)

getCategoryProbabilities

public final double[] getCategoryProbabilities()

The non direct access method

getCategoryProbability

public final double getCategoryProbability(int category)

clone

public java.lang.Object clone()

Overrides:

clone in class java.lang.Object