pal.substmodel
Class YangCodonModel.SimpleNeutralSelection

java.lang.Object
  pal.misc.PalObjectListener.EventGenerator
      pal.substmodel.YangCodonModel.SimpleNeutralSelection

All Implemented Interfaces:

java.io.Serializable, Parameterized, Report, SubstitutionModel

Enclosing class:

YangCodonModel

public static class YangCodonModel.SimpleNeutralSelection
extends PalObjectListener.EventGenerator
implements SubstitutionModel

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. Genetics 148: 929-936.

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel

SubstitutionModel.Utils

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

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser

Field Summary

static double	P_DEFAULT_VALUE
static double	P_LOWER_LIMIT
static double	P_UPPER_LIMIT

Constructor Summary

YangCodonModel.SimpleNeutralSelection(CodonTable translator, double[] codonProbabilities, double startingKappa)

YangCodonModel.SimpleNeutralSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double proportionZero)

Method Summary

java.lang.Object	clone()
SubstitutionModel	getCopy()
DataType	getDataType()
double	getDefaultValue(int n) get default value of parameter
double[]	getEquilibriumFrequencies() Should return a double[] array of the related equilibrium frequencies.
double[]	getEquilibriumProbabilities()
double	getLowerLimit(int n) get lower parameter limit
int	getNumberOfTransitionCategories()
int	getNumParameters() Two parameters, kappa, p,
OrthogonalHints	getOrthogonalHints() May return null
double	getParameter(int n) get model parameter
double[]	getTransitionCategoryProbabilities()
double	getTransitionCategoryProbability(int category)
void	getTransitionProbabilities(double branchLength, double[][][] tableStore) Table is organized as [tree_group][from][to]
void	getTransitionProbabilities(double branchLength, int category, double[][] tableStore) Table is organized as [transition_group][from][to]
void	getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore) Table is organized as [transition_group][to][from]
void	getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore) Table is organized as [transition_group][to][from]
double	getUpperLimit(int n) get upper parameter limit
void	report(java.io.PrintWriter pw) print human readable report (e.g., on parameters and associated model)
void	setParameter(double param, int n) set model parameter
void	setParameterSE(double paramSE, int n) set standard errors for model parameter
java.lang.String	toString()

Methods inherited from class pal.misc.PalObjectListener.EventGenerator

addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface pal.substmodel.SubstitutionModel

addPalObjectListener, removePalObjectListener

Field Detail

P_UPPER_LIMIT

public static final double P_UPPER_LIMIT

See Also:

Constant Field Values

P_LOWER_LIMIT

public static final double P_LOWER_LIMIT

See Also:

Constant Field Values

P_DEFAULT_VALUE

public static final double P_DEFAULT_VALUE

See Also:

Constant Field Values

Constructor Detail

YangCodonModel.SimpleNeutralSelection

public YangCodonModel.SimpleNeutralSelection(CodonTable translator,
                                             double[] codonProbabilities,
                                             double startingKappa)

YangCodonModel.SimpleNeutralSelection

public YangCodonModel.SimpleNeutralSelection(CodonTable translator,
                                             double[] codonProbabilities,
                                             double startingKappa,
                                             double proportionZero)

Method Detail

clone

public java.lang.Object clone()

Specified by:

clone in interface SubstitutionModel

Overrides:

clone in class java.lang.Object

getEquilibriumFrequencies

public double[] getEquilibriumFrequencies()

Description copied from interface: SubstitutionModel

Should return a double[] array of the related equilibrium frequencies. As a rule, callers should not alter the returned array (it may be used internally)

Specified by:

getEquilibriumFrequencies in interface SubstitutionModel

getCopy

public SubstitutionModel getCopy()

getEquilibriumProbabilities

public double[] getEquilibriumProbabilities()

getDataType

public DataType getDataType()

Specified by:

getDataType in interface SubstitutionModel

getNumberOfTransitionCategories

public int getNumberOfTransitionCategories()

Specified by:

getNumberOfTransitionCategories in interface SubstitutionModel

getTransitionCategoryProbability

public double getTransitionCategoryProbability(int category)

Specified by:

getTransitionCategoryProbability in interface SubstitutionModel

getTransitionCategoryProbabilities

public double[] getTransitionCategoryProbabilities()

Specified by:

getTransitionCategoryProbabilities in interface SubstitutionModel

Returns:

all the category probabilites for each category respectively.

getTransitionProbabilities

public void getTransitionProbabilities(double branchLength,
                                       double[][][] tableStore)

Table is organized as [tree_group][from][to]

Specified by:

getTransitionProbabilities in interface SubstitutionModel

getTransitionProbabilities

public void getTransitionProbabilities(double branchLength,
                                       int category,
                                       double[][] tableStore)

Description copied from interface: SubstitutionModel

Table is organized as [transition_group][from][to]

Specified by:

getTransitionProbabilities in interface SubstitutionModel

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double branchLength,
                                                double[][][] tableStore)

Description copied from interface: SubstitutionModel

Table is organized as [transition_group][to][from]

Specified by:

getTransitionProbabilitiesTranspose in interface SubstitutionModel

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double branchLength,
                                                int category,
                                                double[][] tableStore)

Description copied from interface: SubstitutionModel

Table is organized as [transition_group][to][from]

Specified by:

getTransitionProbabilitiesTranspose in interface SubstitutionModel

getNumParameters

public int getNumParameters()

Two parameters, kappa, p,

Specified by:

getNumParameters in interface Parameterized

Returns:

number of parameters

setParameter

public void setParameter(double param,
                         int n)

Description copied from interface: Parameterized

set model parameter

Specified by:

setParameter in interface Parameterized

Parameters:

param - parameter value

n - parameter number

getParameter

public double getParameter(int n)

Description copied from interface: Parameterized

get model parameter

Specified by:

getParameter in interface Parameterized

Parameters:

n - parameter number

Returns:

parameter value

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

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

getOrthogonalHints

public OrthogonalHints getOrthogonalHints()

Description copied from interface: SubstitutionModel

May return null

Specified by:

getOrthogonalHints in interface SubstitutionModel

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

report

public void report(java.io.PrintWriter pw)

Description copied from interface: Report

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

Specified by:

report in interface Report

Parameters:

pw - output stream