Package pal.substmodel
Class RateDistribution
java.lang.Object
pal.misc.PalObjectListener.EventGenerator
pal.substmodel.RateDistribution
- All Implemented Interfaces:
Serializable
,Cloneable
,Parameterized
,Report
- Direct Known Subclasses:
GammaRates
,InvariableSites
,UniformRate
public abstract class RateDistribution
extends PalObjectListener.EventGenerator
implements Parameterized, Report, Cloneable, 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:
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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
FieldsModifier and TypeFieldDescriptionprotected FormattedOutput
int
number of rate categoriesdouble[]
probability of each ratedouble[]
rates of each rate category -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionclone()
final double[]
The non direct access methodfinal double
getCategoryProbability
(int category) final int
final double
getRate
(int category) final double[]
getRates()
protected void
printRates
(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
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Field Details
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numRates
public int numRatesnumber of rate categories -
rate
public double[] raterates of each rate category -
probability
public double[] probabilityprobability of each rate -
format
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Constructor Details
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RateDistribution
public RateDistribution(int n) construct discrete distribution- Parameters:
n
- number of rate categories
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Method Details
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getNumberOfRates
public final int getNumberOfRates() -
getRates
public final double[] getRates() -
getRate
public final double getRate(int category) -
printRates
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getCategoryProbabilities
public final double[] getCategoryProbabilities()The non direct access method -
getCategoryProbability
public final double getCategoryProbability(int category) -
clone
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