Package pal.substmodel
Class GTR
- java.lang.Object
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- pal.substmodel.AbstractRateMatrix
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- pal.substmodel.NucleotideModel
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- pal.substmodel.GTR
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,ExternalParameterListener
,NamedParameterized
,Parameterized
,Report
,RateMatrix
,XMLConstants
public class GTR extends NucleotideModel implements java.io.Serializable, XMLConstants
GTR (general time reversible) model of nucleotide evolution Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J Mol Evol 20: 86-93.- Version:
- $Id: GTR.java,v 1.13 2003/11/30 05:29:22 matt Exp $
Parameters
- A
- B
- C
- D
- E
- Author:
- Korbinian Strimmer
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Field Summary
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Fields inherited from class pal.substmodel.AbstractRateMatrix
format
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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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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 parameterdouble
getLowerLimit(int n)
get lower parameter limitint
getModelID()
get numerical code describing the model typeint
getNumParameters()
get number of parametersjava.lang.String
getParameterName(int i)
java.lang.String
getUniqueName()
double
getUpperLimit(int n)
get upper parameter limitprotected 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
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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
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface pal.misc.Parameterized
getParameter, setParameter
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Methods inherited from interface pal.substmodel.RateMatrix
addPalObjectListener, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale
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Constructor Detail
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GTR
public GTR(double a, double b, double c, double d, double e, double[] freq)
constructor 1- Parameters:
a
- entry in rate matrixb
- entry in rate matrixc
- entry in rate matrixd
- entry in rate matrixe
- entry in rate matrixfreq
- nucleotide frequencies
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GTR
public GTR(double[] params, double[] freq)
constructor 2- Parameters:
params
- parameter listfreq
- nucleotide frequencies
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Method Detail
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clone
public java.lang.Object clone()
- Specified by:
clone
in interfaceRateMatrix
- Overrides:
clone
in classAbstractRateMatrix
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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
public void report(java.io.PrintWriter out)
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)
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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
public java.lang.String getUniqueName()
- Specified by:
getUniqueName
in interfaceRateMatrix
- Returns:
- the name of this rate matrix
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getParameterName
public java.lang.String getParameterName(int i)
- 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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