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	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	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	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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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 java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pal.misc.Parameterized
getParameter, setParameter

Methods inherited from interface pal.substmodel.RateMatrix
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale

- 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)
```

Class YangCodonModel

Nested Class Summary

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

Field Summary

Fields inherited from class pal.substmodel.AbstractRateMatrix

Fields inherited from interface pal.util.XMLConstants

Constructor Summary

Method Summary

Methods inherited from class pal.substmodel.CodonModel

Methods inherited from class pal.substmodel.AbstractRateMatrix

Methods inherited from class java.lang.Object

Methods inherited from interface pal.misc.Parameterized

Methods inherited from interface pal.substmodel.RateMatrix

Field Detail

MAXIMUM_OMEGA

MAXIMUM_KAPPA

MINIMUM_OMEGA

MINIMUM_KAPPA

DEFAULT_KAPPA

DEFAULT_OMEGA

KAPPA_PARAMETER

OMEGA_PARAMETER

Constructor Detail

YangCodonModel

YangCodonModel

YangCodonModel

YangCodonModel

Method Detail

getModelID

report

getNumParameters

setParameterSE

getKappaLowerLimit

getOmegaLowerLimit

getKappaUpperLimit

getOmegaUpperLimit

getKappaDefaultValue

getOmegaDefaultValue

getOmega

getKappa

setKappaSE

setOmegaSE

setKappa

setOmega

getLowerLimit

getUpperLimit

getDefaultValue

getParameterName

getUniqueName

rebuildRateMatrix

toString

createKappaStore

createKappaStore

createOmegaStore

createOmegaStore