Package pal.substmodel
Class YangCodonModel
java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.CodonModel
pal.substmodel.YangCodonModel
- All Implemented Interfaces:
Serializable
,Cloneable
,ExternalParameterListener
,NamedParameterized
,Parameterized
,Report
,RateMatrix
,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:
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
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
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 final class
A Utility classNested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final double
static final double
static final int
static final double
static final double
static final double
static final double
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
ConstructorsConstructorDescriptionYangCodonModel
(double[] params, double[] freq) constructor 4 (universal codon table)YangCodonModel
(double[] params, double[] freq, CodonTable codonTable) constructor 3YangCodonModel
(double omega, double kappa, double[] freq) constructor 2 (universal codon table)YangCodonModel
(double omega, double kappa, double[] freq, CodonTable codonTable) constructor 1 -
Method Summary
Modifier and TypeMethodDescriptionstatic final MutableDouble
createKappaStore
(double initialValue) static final MutableDouble
createKappaStore
(double initialValue, String name) static final MutableDouble
createOmegaStore
(double initialValue) static final MutableDouble
createOmegaStore
(double initialValue, String name) double
getDefaultValue
(int n) get default value of parameterfinal double
getKappa()
final double
final double
final double
double
getLowerLimit
(int n) get lower parameter limitint
get numerical code describing the model typeint
get number of parametersfinal double
getOmega()
final double
final double
final double
getParameterName
(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)final void
setKappa
(double value) final void
setKappaSE
(double value) final void
setOmega
(double value) final void
setOmegaSE
(double value) void
setParameterSE
(double paramSE, int n) set standard errors for model parametertoString()
Methods inherited from class pal.substmodel.CodonModel
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, 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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MAXIMUM_OMEGA
public static final double MAXIMUM_OMEGA- See Also:
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MAXIMUM_KAPPA
public static final double MAXIMUM_KAPPA- See Also:
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MINIMUM_OMEGA
public static final double MINIMUM_OMEGA- See Also:
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MINIMUM_KAPPA
public static final double MINIMUM_KAPPA- See Also:
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DEFAULT_KAPPA
public static final double DEFAULT_KAPPA- See Also:
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DEFAULT_OMEGA
public static final double DEFAULT_OMEGA- See Also:
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KAPPA_PARAMETER
public static final int KAPPA_PARAMETER- See Also:
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OMEGA_PARAMETER
public static final int OMEGA_PARAMETER- See Also:
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Constructor Details
-
YangCodonModel
constructor 1- Parameters:
omega
- N/S rate ratiokappa
- transition/transversion rate ratiofreq
- codon frequenciescodonTable
- codon table
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YangCodonModel
public YangCodonModel(double omega, double kappa, double[] freq) constructor 2 (universal codon table)- Parameters:
omega
- N/S rate ratiokappa
- transition/transversion rate ratiofreq
- codon frequencies
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YangCodonModel
public YangCodonModel(double[] params, double[] freq) constructor 4 (universal codon table)- Parameters:
params
- parameter listfreq
- nucleotide frequencies
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YangCodonModel
constructor 3- Parameters:
params
- parameter listfreq
- nucleotide frequenciescodonTable
- codon table
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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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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 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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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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getUniqueName
- Specified by:
getUniqueName
in interfaceRateMatrix
- Returns:
- a short unique human-readable identifier for this rate matrix.
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rebuildRateMatrix
protected void rebuildRateMatrix(double[][] rate, double[] parameters) - Specified by:
rebuildRateMatrix
in classAbstractRateMatrix
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toString
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createKappaStore
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createKappaStore
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createOmegaStore
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createOmegaStore
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