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	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 Description

RateDistribution(int n)
construct discrete distribution

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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