pal.substmodel
Class AbstractRateMatrix

java.lang.Object
  pal.substmodel.AbstractRateMatrix

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix

Direct Known Subclasses:

AminoAcidModel, CodonModel, NucleotideModel, TwoStateModel

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

abstract base class for all rate matrices

Version:

$Id: AbstractRateMatrix.java,v 1.30 2004/04/05 05:14:39 matt Exp $

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary

protected FormattedOutput

format

Constructor Summary

protected

AbstractRateMatrix(int dim)

Method Summary

void	addPalObjectListener(PalObjectListener pol) Add a PalObjectListener to be notified of changes to the model.
java.lang.Object	clone()
protected void	fireParametersChangedEvent()
protected void	fireParametersChangedEvent(PalObjectEvent pe)
DataType	getDataType() Get the data type of this rate matrix
int	getDimension()
double[]	getEquilibriumFrequencies()
double	getEquilibriumFrequency(int i)
protected double[]	getFrequencies()
abstract int	getModelID() get numerical code describing the model type
OrthogonalHints	getOrthogonalHints()
double	getParameter(int parameter) get model parameter
double[][]	getRelativeRates()
void	getTransitionProbabilities(double[][] probabilityStore) A utility method for speed, transfers trans prob information quickly into store
double	getTransitionProbability(int fromState, int toState) Returns the probability of going from one state to another given the current distance
int	getTypeID() get numerical code describing the data type
void	parameterChanged(ParameterEvent pe) For the external parameter interface.
protected void	printFrequencies(java.io.PrintWriter out)
void	rebuild()
protected abstract void	rebuildRateMatrix(double[][] rate, double[] parameters)
void	removePalObjectListener(PalObjectListener pol)
void	scale(double scale)
protected void	setDataType(DataType dt)
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)
void	setParameter(double value, int parameter) set model parameter
void	setParameters(double[] parameters)
double	setParametersNoScale(double[] parameters)
protected void	updateMatrixExp()

Methods inherited from class java.lang.Object

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

Methods inherited from interface pal.substmodel.RateMatrix

getUniqueName

Methods inherited from interface pal.misc.NamedParameterized

getParameterName

Methods inherited from interface pal.misc.Parameterized

getDefaultValue, getLowerLimit, getNumParameters, getUpperLimit, setParameterSE

Methods inherited from interface pal.misc.Report

report

Field Detail

format

protected FormattedOutput format

Constructor Detail

AbstractRateMatrix

protected AbstractRateMatrix(int dim)

Method Detail

getTypeID

public int getTypeID()

get numerical code describing the data type

Specified by:

getTypeID in interface RateMatrix

Returns:

integer code identifying a data type

getModelID

public abstract int getModelID()

get numerical code describing the model type

Specified by:

getModelID in interface RateMatrix

Returns:

integer code identifying a substitution model

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

getDataType

public DataType getDataType()

Description copied from interface: RateMatrix

Get the data type of this rate matrix

Specified by:

getDataType in interface RateMatrix

setDataType

protected final void setDataType(DataType 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)

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

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.

Specified by:

setDistanceTranspose in interface RateMatrix

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)

Specified by:

scale in interface RateMatrix

printFrequencies

protected void printFrequencies(java.io.PrintWriter out)

setFrequencies

protected void setFrequencies(double[] f)

setParametersNoScale

public double setParametersNoScale(double[] parameters)

Specified by:

setParametersNoScale in interface RateMatrix

setParameters

public void setParameters(double[] parameters)

setParameter

public final void setParameter(double value,
                               int parameter)

Description copied from interface: Parameterized

set model parameter

Specified by:

setParameter in interface Parameterized

Parameters:

value - parameter value

parameter - parameter number

getParameter

public final double getParameter(int parameter)

Description copied from interface: Parameterized

get model parameter

Specified by:

getParameter in interface Parameterized

Parameters:

parameter - parameter number

Returns:

parameter value

rebuildRateMatrix

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

addPalObjectListener

public void addPalObjectListener(PalObjectListener pol)

Description copied from interface: RateMatrix

Add a PalObjectListener to be notified of changes to the model. Only the parametersChanged method will generally be called

Specified by:

addPalObjectListener in interface RateMatrix

removePalObjectListener

public void removePalObjectListener(PalObjectListener pol)

Specified by:

removePalObjectListener in interface RateMatrix

fireParametersChangedEvent

protected void fireParametersChangedEvent()

fireParametersChangedEvent

protected void fireParametersChangedEvent(PalObjectEvent pe)

updateMatrixExp

protected void updateMatrixExp()

parameterChanged

public void parameterChanged(ParameterEvent pe)

For the external parameter interface. This can be ignored unless you want to use this Rate Matrix as an external parameter listener This method does two things.First it sets a flag indicating that rebuild method should be called the next time a setDistance method is called, and then it notifies any PalObject listeners that a parameter has changed

Specified by:

parameterChanged in interface ExternalParameterListener

clone

public java.lang.Object clone()

Specified by:

clone in interface RateMatrix

Overrides:

clone in class java.lang.Object

getOrthogonalHints

public OrthogonalHints getOrthogonalHints()

Specified by:

getOrthogonalHints in interface RateMatrix

Returns:

null

getFrequencies

protected final double[] getFrequencies()