java.lang.Object
- pal.substmodel.GeneralPoissonRateMatrix

All Implemented Interfaces:

java.io.Serializable, NeoRateMatrix
```
public class GeneralPoissonRateMatrix
extends java.lang.Object
implements NeoRateMatrix
```
A general rate matrix class for JC69/F81 style rate matrices (but for all data types)
Version:

$Id: GeneralPoissonRateMatrix.java,v 1.3 2004/08/15 03:00:37 matt Exp $

Author:
Matthew Goode
- 11 May 2004 - Created file
See Also:

Serialized Form

Constructor Summary

Constructors
Constructor Description

GeneralPoissonRateMatrix(int dimension)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`createRelativeRates(double[][] rateStore, double[] rateParameters, int startIndex)`	Create the relative rates array
`void`	`getDefaultRateParameters(double[] store, int startIndex)`
`int`	`getDimension()`
`int`	`getNumberOfRateParameters()`
`double`	`getRateParameterLowerBound(int parameter)`
`double`	`getRateParameterUpperBound(int parameter)`
`java.lang.String`	`getUniqueName()`
`boolean`	`isDataTypeCompatible(DataType dt)`	Check the compatibility of a data type to be used with the rate matrix
`boolean`	`isReversible()`	Is the relative rate matrix described by this rate matrix meant to represent a reversible process? If true only the upper part of the rate matrix needs to be filled in (eg in matrix[i][j], for all where j > i );

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

- Constructor Detail
  - GeneralPoissonRateMatrix
```
public GeneralPoissonRateMatrix(int dimension)
```
- Method Detail
  - getUniqueName
```
public java.lang.String getUniqueName()
```
    Specified by:
    
    getUniqueName in interface NeoRateMatrix
    
    Returns:
    
    a short unique human-readable identifier for this rate matrix.
  - isReversible
```
public boolean isReversible()
```
    Description copied from interface: NeoRateMatrix
    
    Is the relative rate matrix described by this rate matrix meant to represent a reversible process? If true only the upper part of the rate matrix needs to be filled in (eg in matrix[i][j], for all where j > i );
    
    Specified by:
    
    isReversible in interface NeoRateMatrix
    
    Returns:
    
    true (doesn't really matter)
  - getDimension
```
public int getDimension()
```
    Specified by:
    
    getDimension in interface NeoRateMatrix
    
    Returns:
    
    the dimension of this rate matrix. (as for construction)
  - isDataTypeCompatible
```
public boolean isDataTypeCompatible(DataType dt)
```
    Check the compatibility of a data type to be used with the rate matrix
    
    Specified by:
    
    isDataTypeCompatible in interface NeoRateMatrix
    
    Parameters:
    
    dt - the data type to test
    
    Returns:
    
    true if data type state count is equal to dimension
  - createRelativeRates
```
public void createRelativeRates(double[][] rateStore,
                                double[] rateParameters,
                                int startIndex)
```
    Description copied from interface: NeoRateMatrix
    
    Create the relative rates array
    
    Specified by:
    
    createRelativeRates in interface NeoRateMatrix
    
    Parameters:
    
    rateStore - The place where the relative rates are stored (should be assumed to be large enough - based on dimension)
    
    rateParameters - The parameters to be used to construct the rate store
    
    startIndex - The index into the rateParameters to start reading parameters
  - getNumberOfRateParameters
```
public int getNumberOfRateParameters()
```
    Specified by:
    
    getNumberOfRateParameters in interface NeoRateMatrix
  - getRateParameterLowerBound
```
public double getRateParameterLowerBound(int parameter)
```
    Specified by:
    
    getRateParameterLowerBound in interface NeoRateMatrix
  - getRateParameterUpperBound
```
public double getRateParameterUpperBound(int parameter)
```
    Specified by:
    
    getRateParameterUpperBound in interface NeoRateMatrix
  - getDefaultRateParameters
```
public void getDefaultRateParameters(double[] store,
                                     int startIndex)
```
    Specified by:
    
    getDefaultRateParameters in interface NeoRateMatrix

Class GeneralPoissonRateMatrix

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

GeneralPoissonRateMatrix

Method Detail

getUniqueName

isReversible

getDimension

isDataTypeCompatible

createRelativeRates

getNumberOfRateParameters

getRateParameterLowerBound

getRateParameterUpperBound

getDefaultRateParameters