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.misc.Parameterized
  Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
- Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel
  SubstitutionModel.Utils

Constructor Summary

Constructors
Modifier	Constructor	Description
	`SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega)`
	`SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1)`
	`SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1, double p2)`
`protected`	`SimplePositiveSelection(YangCodonModel.SimplePositiveSelection toCopy)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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
  - SimplePositiveSelection
```
protected SimplePositiveSelection(YangCodonModel.SimplePositiveSelection toCopy)
```
  - SimplePositiveSelection
```
public SimplePositiveSelection(CodonTable translator,
                               double[] codonProbabilities,
                               double startingKappa,
                               double startingFreeOmega)
```
  - SimplePositiveSelection
```
public SimplePositiveSelection(CodonTable translator,
                               double[] codonProbabilities,
                               double startingKappa,
                               double startingFreeOmega,
                               double p0,
                               double p1)
```
  - SimplePositiveSelection
```
public 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

Class YangCodonModel.SimplePositiveSelection

Nested Class Summary

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

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

Constructor Summary

Method Summary

Methods inherited from class pal.misc.PalObjectListener.EventGenerator

Methods inherited from class java.lang.Object

Methods inherited from interface pal.substmodel.SubstitutionModel

Constructor Detail

SimplePositiveSelection

SimplePositiveSelection

SimplePositiveSelection

SimplePositiveSelection

Method Detail

clone

getCopy

getDataType

getNumberOfTransitionCategories

getTransitionCategoryProbability

getTransitionCategoryProbabilities

getEquilibriumFrequencies

getTransitionProbabilities

getTransitionProbabilities

getTransitionProbabilitiesTranspose

getTransitionProbabilitiesTranspose

setTransitionCategoryProbabilities

getNumParameters

setParameter

getParameter

setParameterSE

getLowerLimit

getUpperLimit

getDefaultValue

getOrthogonalHints

toString

report