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

Fields
Modifier and Type Field and Description

static double P_DEFAULT_VALUE

static double P_LOWER_LIMIT

static double P_UPPER_LIMIT

Fields
Modifier and Type	Field and Description
`static double`	`P_DEFAULT_VALUE`
`static double`	`P_LOWER_LIMIT`
`static double`	`P_UPPER_LIMIT`

Constructor Summary

Constructors
Constructor and Description
`SimpleNeutralSelection(CodonTable translator, double[] codonProbabilities, double startingKappa)`
`SimpleNeutralSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double proportionZero)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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[]`	`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
  - SimpleNeutralSelection
```
public SimpleNeutralSelection(CodonTable translator,
                              double[] codonProbabilities,
                              double startingKappa)
```
  - SimpleNeutralSelection
```
public 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

Class YangCodonModel.SimpleNeutralSelection

Nested Class Summary

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

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

Field Summary

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

Field Detail

P_UPPER_LIMIT

P_LOWER_LIMIT

P_DEFAULT_VALUE

Constructor Detail

SimpleNeutralSelection

SimpleNeutralSelection

Method Detail

clone

getEquilibriumFrequencies

getCopy

getEquilibriumProbabilities

getDataType

getNumberOfTransitionCategories

getTransitionCategoryProbability

getTransitionCategoryProbabilities

getTransitionProbabilities

getTransitionProbabilities

getTransitionProbabilitiesTranspose

getTransitionProbabilitiesTranspose

getNumParameters

setParameter

getParameter

setParameterSE

getLowerLimit

getUpperLimit

getDefaultValue

getOrthogonalHints

toString

report