java.lang.Object
- pal.substmodel.AbstractRateMatrix
- - pal.substmodel.NucleotideModel
  - - pal.substmodel.HKY

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants
```
public class HKY
extends NucleotideModel
implements java.io.Serializable, XMLConstants
```
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitchondrial DNA. J. Mol. Evol. 22:160-174.
Version:
$Id: HKY.java,v 1.11 2003/11/30 05:29:22 matt Exp $
Parameters
1. Kappa
Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

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

Field Summary

Fields
Modifier and Type Field Description

static int KAPPA_PARAMETER_INDEX
- 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

HKY(double[] params, double[] freq)
Constructor 2

HKY(double kappa, double[] freq)
Constructor 1

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.lang.Object`	`clone()`
`double`	`getDefaultValue(int n)`	get default value of parameter
`double`	`getLowerLimit(int n)`	get lower parameter limit
`int`	`getModelID()`	get numerical code describing the model type
`int`	`getNumParameters()`	get number of parameters
`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`	`setParameterSE(double paramSE, int n)`	set standard errors for model parameter

Methods inherited from class pal.substmodel.NucleotideModel
getInstance, printFrequencies, printRatios

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

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

- Field Detail
  - KAPPA_PARAMETER_INDEX
```
public static final int KAPPA_PARAMETER_INDEX
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - HKY
```
public HKY(double kappa,
           double[] freq)
```
    Constructor 1
    
    Parameters:
    
    kappa - transition/transversion rate ratio
    
    freq - nucleotide frequencies
  - HKY
```
public HKY(double[] params,
           double[] freq)
```
    Constructor 2
    
    Parameters:
    
    params - parameter list
    
    freq - nucleotide frequencies
- Method Detail
  - clone
```
public java.lang.Object clone()
```
    Specified by:
    
    clone in interface RateMatrix
    
    Overrides:
    
    clone in class AbstractRateMatrix
  - 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
  - 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

Class HKY

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.NucleotideModel

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

KAPPA_PARAMETER_INDEX

Constructor Detail

HKY

HKY

Method Detail

clone

getModelID

report

getNumParameters

setParameterSE

getLowerLimit

getUpperLimit

getDefaultValue

getParameterName

getUniqueName

rebuildRateMatrix

Constructor	Description
`HKY(double[] params, double[] freq)`	Constructor 2
`HKY(double kappa, double[] freq)`	Constructor 1