pal.substmodel

Class YangCodonModel

java.lang.Object

pal.substmodel.AbstractRateMatrix

pal.substmodel.CodonModel

pal.substmodel.YangCodonModel

All Implemented Interfaces:

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

public class YangCodonModel
extends CodonModel
implements java.io.Serializable, XMLConstants

Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models). They appear to be correct compare to PAML for the purposes of evaluating the likelihood. More models (eg M3 and others) will be added over time.

Version:

$Id: YangCodonModel.java,v 1.25 2004/10/18 01:45:40 matt Exp $

Author:

Andrew Rambaut, Alexei Drummond, Matthew Goode

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	YangCodonModel.SimpleNeutralSelection A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of trwo base YangCodon models where omega=0, omega=1 repectively [1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
static class	YangCodonModel.SimplePositiveSelection A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of a three base Codon model where omega=0, omega=1 and omega=free [1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
static class	YangCodonModel.Utils A Utility class

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

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_KAPPA
static double	DEFAULT_OMEGA
static int	KAPPA_PARAMETER
static double	MAXIMUM_KAPPA
static double	MAXIMUM_OMEGA
static double	MINIMUM_KAPPA
static double	MINIMUM_OMEGA
static int	OMEGA_PARAMETER

Fields inherited from class pal.substmodel.AbstractRateMatrix

format

Fields inherited from interface pal.util.XMLConstants

A_TO_C, A_TO_G, A_TO_T, ALIGNMENT, ALPHA, ANCESTRAL_MU_RATE, ANCESTRAL_POP_SIZE, ATTRIBUTE, BACKWARDS, BLOSUM62, C_TO_G, C_TO_T, COALESCENT, CONST_EXP_CONST, CONST_EXP_GROWTH, CONSTANT_MUTATION_RATE, CONSTANT_POPULATION, CPREV, CURRENT_POP_SIZE_DURATION, DATA_TYPE, DATA_TYPE_ID, DAYHOFF, DAYS, DEMOGRAPHIC_MODEL, DIRECTION, EDGE, EXPANDING_POPULATION, EXPONENTIAL_GROWTH, F81, F84, FREQUENCIES, G_TO_T, GAMMA_ALPHA, GAMMA_DISTRIBUTION, GENERATIONS, GROWTH_PHASE_DURATION, GROWTH_RATE, GTR, HEIGHT, HKY, ID, JC, JTT, KAPPA, LENGTH, MISSING, MODEL, MONTHS, MTREV24, MU_STEP_TIME, MUTATION_RATE, MUTATION_RATE_MODEL, MUTATIONS, NAME, NODE, NUMBER_CATEGORIES, OMEGA, ORIGIN, PARAMETER, POPULATION_SIZE, PYRIMIDINE_PURINE_RATIO, RATE_DISTRIBUTION, RATE_MATRIX, SEQUENCE, SPACES_PER_LEVEL, STEPPED_MUTATION_RATE, TIME, TIME_DATA, TN, TREE, TS_TV_RATIO, TWO_STATE, TYPE, UNIFORM, UNIFORM_RATE_DISTRIBUTION, UNITS, UNKNOWN, VALUE, VT, WAG, YANG_CODON_MODEL, YEARS

Constructor Summary

Constructors

Constructor and Description
YangCodonModel(double[] params, double[] freq) constructor 4 (universal codon table)
YangCodonModel(double[] params, double[] freq, CodonTable codonTable) constructor 3
YangCodonModel(double omega, double kappa, double[] freq) constructor 2 (universal codon table)
YangCodonModel(double omega, double kappa, double[] freq, CodonTable codonTable) constructor 1

Method Summary

Methods

Modifier and Type	Method and Description
static MutableDouble	createKappaStore(double initialValue)
static MutableDouble	createKappaStore(double initialValue, java.lang.String name)
static MutableDouble	createOmegaStore(double initialValue)
static MutableDouble	createOmegaStore(double initialValue, java.lang.String name)
double	getDefaultValue(int n) get default value of parameter
double	getKappa()
double	getKappaDefaultValue()
double	getKappaLowerLimit()
double	getKappaUpperLimit()
double	getLowerLimit(int n) get lower parameter limit
int	getModelID() get numerical code describing the model type
int	getNumParameters() get number of parameters
double	getOmega()
double	getOmegaDefaultValue()
double	getOmegaLowerLimit()
double	getOmegaUpperLimit()
java.lang.String	getParameterName(int i)
java.lang.String	getUniqueName()
double	getUpperLimit(int n) get upper parameter limit
protected void	rebuildRateMatrix(double[][] rate, double[] parameters)
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)
void	setKappa(double value)
void	setKappaSE(double value)
void	setOmega(double value)
void	setOmegaSE(double value)
void	setParameterSE(double paramSE, int n) set standard errors for model parameter
java.lang.String	toString()

Methods inherited from class pal.substmodel.CodonModel

getInstance, printFrequencies, printRatios

Methods inherited from class pal.substmodel.AbstractRateMatrix

addPalObjectListener, clone, fireParametersChangedEvent, fireParametersChangedEvent, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getFrequencies, getOrthogonalHints, getParameter, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, parameterChanged, rebuild, removePalObjectListener, scale, setDataType, setDistance, setDistanceTranspose, setFrequencies, setParameter, setParameters, setParametersNoScale, updateMatrixExp

Methods inherited from class java.lang.Object

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

Methods inherited from interface pal.substmodel.RateMatrix

addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale

Methods inherited from interface pal.misc.Parameterized

getParameter, setParameter

Field Detail

MAXIMUM_OMEGA

public static final double MAXIMUM_OMEGA

See Also:

Constant Field Values

MAXIMUM_KAPPA

public static final double MAXIMUM_KAPPA

See Also:

Constant Field Values

MINIMUM_OMEGA

public static final double MINIMUM_OMEGA

See Also:

Constant Field Values

MINIMUM_KAPPA

public static final double MINIMUM_KAPPA

See Also:

Constant Field Values

DEFAULT_KAPPA

public static final double DEFAULT_KAPPA

See Also:

Constant Field Values

DEFAULT_OMEGA

public static final double DEFAULT_OMEGA

See Also:

Constant Field Values

KAPPA_PARAMETER

public static final int KAPPA_PARAMETER

See Also:

Constant Field Values

OMEGA_PARAMETER

public static final int OMEGA_PARAMETER

See Also:

Constant Field Values

Constructor Detail

YangCodonModel

public YangCodonModel(double omega,
              double kappa,
              double[] freq,
              CodonTable codonTable)

constructor 1

Parameters:

omega - N/S rate ratio

kappa - transition/transversion rate ratio

freq - codon frequencies

codonTable - codon table

YangCodonModel

public YangCodonModel(double omega,
              double kappa,
              double[] freq)

constructor 2 (universal codon table)

Parameters:

omega - N/S rate ratio

kappa - transition/transversion rate ratio

freq - codon frequencies

YangCodonModel

public YangCodonModel(double[] params,
              double[] freq)

constructor 4 (universal codon table)

Parameters:

params - parameter list

freq - nucleotide frequencies

YangCodonModel

public YangCodonModel(double[] params,
              double[] freq,
              CodonTable codonTable)

constructor 3

Parameters:

params - parameter list

freq - nucleotide frequencies

codonTable - codon table

Method Detail

getModelID

public int getModelID()

Description copied from class: AbstractRateMatrix

get numerical code describing the model type

Specified by:

getModelID in interface RateMatrix

Specified by:

getModelID in class AbstractRateMatrix

Returns:

integer code identifying a substitution model

report

public void report(java.io.PrintWriter out)

Description copied from interface: Report

print human readable report (e.g., on parameters and associated model)

Specified by:

report in interface Report

Parameters:

out - output stream

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Returns:

number of parameters

setParameterSE

public void setParameterSE(double paramSE,
                  int n)

Description copied from interface: Parameterized

set standard errors for model parameter

Specified by:

setParameterSE in interface Parameterized

Parameters:

paramSE - standard error of parameter value

n - parameter number

getKappaLowerLimit

public final double getKappaLowerLimit()

getOmegaLowerLimit

public final double getOmegaLowerLimit()

getKappaUpperLimit

public final double getKappaUpperLimit()

getOmegaUpperLimit

public final double getOmegaUpperLimit()

getKappaDefaultValue

public final double getKappaDefaultValue()

getOmegaDefaultValue

public final double getOmegaDefaultValue()

getOmega

public final double getOmega()

getKappa

public final double getKappa()

setKappaSE

public final void setKappaSE(double value)

setOmegaSE

public final void setOmegaSE(double value)

setKappa

public final void setKappa(double value)

setOmega

public final void setOmega(double value)

getLowerLimit

public double getLowerLimit(int n)

Description copied from interface: Parameterized

get lower parameter limit

Specified by:

getLowerLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

lower bound

getUpperLimit

public double getUpperLimit(int n)

Description copied from interface: Parameterized

get upper parameter limit

Specified by:

getUpperLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

upper bound

getDefaultValue

public double getDefaultValue(int n)

Description copied from interface: Parameterized

get default value of parameter

Specified by:

getDefaultValue in interface Parameterized

Parameters:

n - parameter number

Returns:

default value

getParameterName

public java.lang.String getParameterName(int i)

Specified by:

getParameterName in interface NamedParameterized

Returns:

a short identifier for this parameter type. Should be the same for all instances of a given class!

getUniqueName

public java.lang.String getUniqueName()

Specified by:

getUniqueName in interface RateMatrix

Returns:

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

rebuildRateMatrix

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

Specified by:

rebuildRateMatrix in class AbstractRateMatrix

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

createKappaStore

public static final MutableDouble createKappaStore(double initialValue)

createKappaStore

public static final MutableDouble createKappaStore(double initialValue,
                             java.lang.String name)

createOmegaStore

public static final MutableDouble createOmegaStore(double initialValue)

createOmegaStore

public static final MutableDouble createOmegaStore(double initialValue,
                             java.lang.String name)