pal.substmodel
Interface RateMatrix

All Superinterfaces:

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

All Known Implementing Classes:

AbstractRateMatrix, AminoAcidModel, CachedRateMatrix, CodonModel, NucleotideModel, TwoStateModel

public interface RateMatrix

extends NamedParameterized, Report, java.lang.Cloneable, java.io.Serializable

abstract base class for all rate matrices

Nested Class Summary

Nested classes inherited from class pal.misc.Parameterized

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

Method Summary

void	addPalObjectListener(PalObjectListener pol) Add a PalObjectListener to be notified of changes to the model.
java.lang.Object	clone()
DataType	getDataType() Get the data type of this rate matrix
int	getDimension()
double[]	getEquilibriumFrequencies()
double	getEquilibriumFrequency(int i)
int	getModelID() get numerical code describing the model type
OrthogonalHints	getOrthogonalHints()
double[][]	getRelativeRates() Deprecated. try not to use.
void	getTransitionProbabilities(double[][] probabilityStore) A utility method for speed, transfers trans prob information quickly into store
double	getTransitionProbability(int fromState, int toState)
int	getTypeID() get numerical code describing the data type
java.lang.String	getUniqueName()
void	removePalObjectListener(PalObjectListener pol)
void	scale(double scaleValue)
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 interface pal.misc.NamedParameterized

getParameterName

Methods inherited from interface pal.misc.Parameterized

getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE

Methods inherited from interface pal.misc.Report

report

Method Detail

getTypeID

public int getTypeID()

get numerical code describing the data type

Returns:

integer code identifying a data type

getModelID

public int getModelID()

get numerical code describing the model type

Returns:

integer code identifying a substitution model

getUniqueName

public java.lang.String getUniqueName()

Returns:

a short unique human-readable identifier for this rate matrix.

getDimension

public int getDimension()

Returns:

the dimension of this rate matrix.

getEquilibriumFrequencies

public double[] getEquilibriumFrequencies()

Returns:

stationary frequencies (sum = 1.0)

getEquilibriumFrequency

public double getEquilibriumFrequency(int i)

Returns:

stationary frequency (sum = 1.0) for ith state Preferred method for infrequent use.

getDataType

public DataType getDataType()

Get the data type of this rate matrix

getRelativeRates

public double[][] getRelativeRates()

Deprecated. try not to use.

Returns:

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

getTransitionProbability

public double getTransitionProbability(int fromState,
                                       int toState)

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

getTransitionProbabilities

public void getTransitionProbabilities(double[][] probabilityStore)

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

setDistance

public void setDistance(double distance)

Sets the distance (such as time/branch length) used when calculating the probabilities. This method may well take the most time!

setDistanceTranspose

public void setDistanceTranspose(double distance)

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

addPalObjectListener

public void addPalObjectListener(PalObjectListener pol)

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

removePalObjectListener

public void removePalObjectListener(PalObjectListener pol)

getOrthogonalHints

public OrthogonalHints getOrthogonalHints()

Returns:

an orthogonal hints object for orthogonal optimisation (may return null for no hints)

clone

public java.lang.Object clone()

setParametersNoScale

public double setParametersNoScale(double[] parameters)

scale

public void scale(double scaleValue)