WAG (JEBL2 lib API)

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java.lang.Object
- jebl.evolution.substmodel.AbstractRateMatrix
- - jebl.evolution.substmodel.AminoAcidModel
  - - jebl.evolution.substmodel.WAG

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, RateMatrix
```
public class WAG
extends AminoAcidModel
```
WAG model of amino acid evolution (S. Whelan and N. Goldman 2000)

Version:

$Id: WAG.java 185 2006-01-23 23:03:18Z rambaut $

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor Description

WAG(double[] f)
constructor

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static double[]`	`getOriginalFrequencies()`
`static void`	`getOriginalFrequencies(double[] f)`	get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
`java.lang.String`	`getUniqueName()`

Methods inherited from class jebl.evolution.substmodel.AbstractRateMatrix
getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getRelativeRates, getSequenceType, getTransitionProbabilities, getTransitionProbability, rebuild, scale, setDistance, setDistanceTranspose, setParametersNoScale

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - WAG
```
public WAG(double[] f)
```
    constructor
    
    Parameters:
    
    f - amino acid frequencies
- Method Detail
  - getOriginalFrequencies
```
public static void getOriginalFrequencies(double[] f)
```
    get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
    
    Parameters:
    
    f - array where amino acid frequencies will be stored
  - getOriginalFrequencies
```
public static double[] getOriginalFrequencies()
```
    Returns:
    
    the frequencies of the original data set that formed the basis for the estimation of the rate matrix
  - getUniqueName
```
public java.lang.String getUniqueName()
```
    Returns:
    
    a short unique human-readable identifier for this rate matrix.

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http://code.google.com/p/jebl2/