pal.substmodel

Class HKY

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

Method Summary

Methods

Modifier and Type	Method and 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 pal.substmodel.AbstractRateMatrix

addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getFrequencies, getOrthogonalHints, getParameter, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, parameterChanged, rebuild, removePalObjectListener, scale, setDataType, setDistance, setDistanceTranspose, setFrequencies, setParameter, setParameters, setParametersNoScale, updateMatrixExp

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface pal.substmodel.RateMatrix

addPalObjectListener, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale

Methods inherited from interface pal.misc.Parameterized

getParameter, setParameter

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