jebl.evolution.substmodel
Class MatrixExponential

java.lang.Object
  jebl.evolution.substmodel.MatrixExponential

All Implemented Interfaces:

Serializable, Cloneable

public class MatrixExponential
extends Object
implements Cloneable, Serializable

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

Author:

Korbinian Strimmer

See Also:

Serialized Form

Constructor Summary

MatrixExponential(int dimension)

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)

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. The resulting matrix works [to][from] as opposed to [from][to]

Parameters:

arc - expected distance