pal.substmodel
Class GeneralPoissonRateMatrix

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

GeneralPoissonRateMatrix(int dimension)

Method Summary

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