jebl.evolution.substmodel

Class AbstractRateMatrix

java.lang.Object

jebl.evolution.substmodel.AbstractRateMatrix

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, RateMatrix

Direct Known Subclasses:

AminoAcidModel

public abstract class AbstractRateMatrix
extends java.lang.Object
implements RateMatrix

abstract base class for all rate matrices

Version:

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

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Method Summary

Methods

Modifier and Type	Method and Description
int	getDimension()
double[]	getEquilibriumFrequencies()
double	getEquilibriumFrequency(int i)
double[][]	getRelativeRates()
SequenceType	getSequenceType() Get the data type of this rate matrix
void	getTransitionProbabilities(double[][] probabilityStore) A utility method for speed, transfers trans prob information quickly into store
double	getTransitionProbability(int fromState, int toState)
void	rebuild()
void	scale(double scale)
void	setDistance(double distance) Sets the distance (such as time/branch length) used when calculating the probabilities.
void	setDistanceTranspose(double distance) Sets the distance (such as time/branch length) used when calculating the probabilities.
double	setParametersNoScale(double[] parameters)

Methods inherited from class java.lang.Object

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

Methods inherited from interface jebl.evolution.substmodel.RateMatrix

getUniqueName

Method Detail

getDimension

public int getDimension()

Specified by:

getDimension in interface RateMatrix

Returns:

the dimension of this rate matrix.

getEquilibriumFrequencies

public double[] getEquilibriumFrequencies()

Specified by:

getEquilibriumFrequencies in interface RateMatrix

Returns:

stationary frequencies (sum = 1.0)

getEquilibriumFrequency

public double getEquilibriumFrequency(int i)

Specified by:

getEquilibriumFrequency in interface RateMatrix

Returns:

stationary frequencie (sum = 1.0) for ith state

getSequenceType

public SequenceType getSequenceType()

Description copied from interface: RateMatrix

Get the data type of this rate matrix

Specified by:

getSequenceType in interface RateMatrix

getRelativeRates

public double[][] getRelativeRates()

Specified by:

getRelativeRates in interface RateMatrix

Returns:

rate matrix (transition: from 1st index to 2nd index)

getTransitionProbability

public double getTransitionProbability(int fromState,
                              int toState)

Specified by:

getTransitionProbability in interface RateMatrix

Parameters:

fromState - The state from which we are starting

toState - The resulting state

Returns:

the probability of going from one state to another given the current distance

rebuild

public final void rebuild()

setDistance

public final void setDistance(double distance)

Sets the distance (such as time/branch length) used when calculating the probabilities.

Specified by:

setDistance in interface RateMatrix

setDistanceTranspose

public final void setDistanceTranspose(double distance)

Sets the distance (such as time/branch length) used when calculating the probabilities. The resulting transition probabilities will be in reverse (that is in the matrix instead of [from][to] it's [to][from])

getTransitionProbabilities

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

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

Specified by:

getTransitionProbabilities in interface RateMatrix

scale

public void scale(double scale)

setParametersNoScale

public double setParametersNoScale(double[] parameters)