Package pal.substmodel
Class TN
java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.NucleotideModel
pal.substmodel.TN
- All Implemented Interfaces:
Serializable
,Cloneable
,ExternalParameterListener
,NamedParameterized
,Parameterized
,Report
,RateMatrix
,XMLConstants
Tamura-Nei model of nucleotide evolution
Tamura, K. and M. Nei. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Bio. Evol. 10:512-526.
Parameters
- Kappa
- r
- Version:
- $Id: TN.java,v 1.8 2003/11/13 04:05:39 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
getDefaultValue
(int n) get default value of parameterdouble
getLowerLimit
(int n) get lower parameter limitint
get numerical code describing the model typeint
get number of parametersgetParameterName
(int i) double
getUpperLimit
(int n) get upper parameter limitprotected void
rebuildRateMatrix
(double[][] rate, double[] parameters) void
report
(PrintWriter out) print human readable report (e.g., on parameters and associated model)void
setParameterSE
(double paramSE, int n) set standard errors for model parameterMethods inherited from class pal.substmodel.NucleotideModel
getInstance, printFrequencies, printRatios
Methods inherited from class pal.substmodel.AbstractRateMatrix
addPalObjectListener, clone, 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.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
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Field Details
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KAPPA_PARAMETER_INDEX
public static final int KAPPA_PARAMETER_INDEX- See Also:
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R_PARAMETER_INDEX
public static final int R_PARAMETER_INDEX- See Also:
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Constructor Details
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TN
public TN(double kappa, double r, double[] freq) constructor 1- Parameters:
kappa
- transition/transversion rate ratior
- pyrimidine/purin transition rate ratiofreq
- nucleotide frequencies
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TN
public TN(double[] params, double[] freq) constructor 2- Parameters:
params
- parameter listfreq
- nucleotode frequencies
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Method Details
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getModelID
public int getModelID()Description copied from class:AbstractRateMatrix
get numerical code describing the model type- Specified by:
getModelID
in interfaceRateMatrix
- Specified by:
getModelID
in classAbstractRateMatrix
- Returns:
- integer code identifying a substitution model
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report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model) -
getNumParameters
public int getNumParameters()Description copied from interface:Parameterized
get number of parameters- Specified by:
getNumParameters
in interfaceParameterized
- Returns:
- number of parameters
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setParameterSE
public void setParameterSE(double paramSE, int n) Description copied from interface:Parameterized
set standard errors for model parameter- Specified by:
setParameterSE
in interfaceParameterized
- Parameters:
paramSE
- standard error of parameter valuen
- parameter number
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getLowerLimit
public double getLowerLimit(int n) Description copied from interface:Parameterized
get lower parameter limit- Specified by:
getLowerLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- lower bound
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getUpperLimit
public double getUpperLimit(int n) Description copied from interface:Parameterized
get upper parameter limit- Specified by:
getUpperLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- upper bound
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getDefaultValue
public double getDefaultValue(int n) Description copied from interface:Parameterized
get default value of parameter- Specified by:
getDefaultValue
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- default value
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getUniqueName
- Specified by:
getUniqueName
in interfaceRateMatrix
- Returns:
- a short unique human-readable identifier for this rate matrix.
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getParameterName
- Specified by:
getParameterName
in interfaceNamedParameterized
- Returns:
- a short identifier for this parameter type. Should be the same for all instances of a given class!
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rebuildRateMatrix
protected void rebuildRateMatrix(double[][] rate, double[] parameters) - Specified by:
rebuildRateMatrix
in classAbstractRateMatrix
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