jebl.evolution.substmodel
Class AbstractRateMatrix

java.lang.Object
  jebl.evolution.substmodel.AbstractRateMatrix

All Implemented Interfaces:

Serializable, Cloneable, RateMatrix

Direct Known Subclasses:

AminoAcidModel

public abstract class AbstractRateMatrix
extends Object
implements RateMatrix

abstract base class for all rate matrices

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Constructor Summary

protected

AbstractRateMatrix(int dim)

Method Summary

int	getDimension()
double[]	getEquilibriumFrequencies()
double	getEquilibriumFrequency(int i)
protected double[]	getFrequencies()
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()
protected abstract void	rebuildRateMatrix(double[][] rate, double[] parameters)
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.
protected void	setFrequencies(double[] f)
double	setParametersNoScale(double[] parameters)
protected void	setSequenceType(SequenceType dt)
protected void	updateMatrixExp()

Methods inherited from class java.lang.Object

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

Methods inherited from interface jebl.evolution.substmodel.RateMatrix

getUniqueName

Constructor Detail

AbstractRateMatrix

protected AbstractRateMatrix(int dim)

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

setSequenceType

protected final void setSequenceType(SequenceType dt)

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)

setFrequencies

protected void setFrequencies(double[] f)

setParametersNoScale

public double setParametersNoScale(double[] parameters)

rebuildRateMatrix

protected abstract void rebuildRateMatrix(double[][] rate,
                                          double[] parameters)

updateMatrixExp

protected void updateMatrixExp()

getFrequencies

protected final double[] getFrequencies()