pal.substmodel
Class MatrixExponential

java.lang.Object
  pal.substmodel.MatrixExponential

All Implemented Interfaces:

java.lang.Cloneable, java.io.Serializable

public class MatrixExponential

extends java.lang.Object

implements java.lang.Cloneable, java.io.Serializable

compute matrix exponential and, subsequently, transition probabilities for a given rate matrix

See Also:

Serialized Form

Constructor Summary

MatrixExponential(int dimension)
create module

MatrixExponential(RateMatrix r)
create module

Method Summary

int	getDimension()
void	getTransitionProbabilities(double[][] probabilityStore) A utility method for speed, transfers trans prob information quickly into store
double	getTransitionProbability(int from, int to)
void	setDistance(double arc) compute transition probabilities for a expected distance using the prespecified rate matrix
void	setDistanceTranspose(double arc) compute transition probabilities for a expected distance using the prespecified rate matrix
void	setMatrix(RateMatrix r) update rate matrix used in present module
void	updateByRelativeRates(double[][] relativeRates)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MatrixExponential

public MatrixExponential(int dimension)

create module

MatrixExponential

public MatrixExponential(RateMatrix r)

create module

Parameters:

r - rate matrix

Method Detail

getTransitionProbability

public final double getTransitionProbability(int from,
                                             int to)

getDimension

public int getDimension()

updateByRelativeRates

public void updateByRelativeRates(double[][] relativeRates)

setMatrix

public void setMatrix(RateMatrix r)

update rate matrix used in present module

Parameters:

r - rate matrix

getTransitionProbabilities

public final void getTransitionProbabilities(double[][] probabilityStore)

A utility method for speed, transfers trans prob information quickly into store

setDistance

public final void setDistance(double arc)

compute transition probabilities for a expected distance using the prespecified rate matrix

Parameters:

arc - expected distance

setDistanceTranspose

public final void setDistanceTranspose(double arc)

compute transition probabilities for a expected distance using the prespecified rate matrix

Parameters:

arc - expected distance