pal.substmodel
Class YangCodonModel.SimplePositiveSelection

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

All Implemented Interfaces:

java.io.Serializable, Parameterized, Report, SubstitutionModel

Enclosing class:

YangCodonModel

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

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. 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

Constructor Summary

	YangCodonModel.SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega)
	YangCodonModel.SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1)
	YangCodonModel.SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1, double p2)
protected	YangCodonModel.SimplePositiveSelection(YangCodonModel.SimplePositiveSelection toCopy)

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	getLowerLimit(int n) get lower parameter limit
int	getNumberOfTransitionCategories()
int	getNumParameters() Five parameters, three proportions, kappa, omega.
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 [transition_group][from][to]
void	getTransitionProbabilities(double branchLength, int category, double[][] tableStore) Table is organized as [tree_group][from][to]
void	getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore) Table is organized as [tree_group][to][from]
void	getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore) Table is organized as [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
void	setTransitionCategoryProbabilities(double p0, double p1, double p2) We use three parameters instead of two to make opimisation easier (there are effectively only *two* parameters though)
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

Constructor Detail

YangCodonModel.SimplePositiveSelection

protected YangCodonModel.SimplePositiveSelection(YangCodonModel.SimplePositiveSelection toCopy)

YangCodonModel.SimplePositiveSelection

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

YangCodonModel.SimplePositiveSelection

public YangCodonModel.SimplePositiveSelection(CodonTable translator,
                                              double[] codonProbabilities,
                                              double startingKappa,
                                              double startingFreeOmega,
                                              double p0,
                                              double p1)

YangCodonModel.SimplePositiveSelection

public YangCodonModel.SimplePositiveSelection(CodonTable translator,
                                              double[] codonProbabilities,
                                              double startingKappa,
                                              double startingFreeOmega,
                                              double p0,
                                              double p1,
                                              double p2)

Method Detail

clone

public java.lang.Object clone()

Specified by:

clone in interface SubstitutionModel

Overrides:

clone in class java.lang.Object

getCopy

public SubstitutionModel getCopy()

getDataType

public DataType getDataType()

Specified by:

getDataType in interface SubstitutionModel

getNumberOfTransitionCategories

public int getNumberOfTransitionCategories()

Specified by:

getNumberOfTransitionCategories in interface SubstitutionModel

Returns:

3

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.

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

getTransitionProbabilities

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

Description copied from interface: SubstitutionModel

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

Specified by:

getTransitionProbabilities in interface SubstitutionModel

getTransitionProbabilities

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

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

Specified by:

getTransitionProbabilities in interface SubstitutionModel

getTransitionProbabilitiesTranspose

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

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

Specified by:

getTransitionProbabilitiesTranspose in interface SubstitutionModel

getTransitionProbabilitiesTranspose

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

Table is organized as [to][from]

Specified by:

getTransitionProbabilitiesTranspose in interface SubstitutionModel

setTransitionCategoryProbabilities

public final void setTransitionCategoryProbabilities(double p0,
                                                     double p1,
                                                     double p2)

We use three parameters instead of two to make opimisation easier (there are effectively only *two* parameters though)

Parameters:

p0 -

p1 -

p2 -

getNumParameters

public int getNumParameters()

Five parameters, three proportions, kappa, omega. Even though the probabilities could be represented by two parameters we use three for ease of optimisation

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