pal.substmodel.GTR

All Implemented Interfaces:: Serializable, Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants

public class GTR extends NucleotideModel implements 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

Nested Class Summary

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

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

GTR(double[] params, double[] freq)

constructor 2

GTR(double a, double b, double c, double d, double e, double[] freq)

constructor 1
Method Summary

Modifier and Type

Method

Description

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

String

getParameterName(int i)

String

getUniqueName()

double

getUpperLimit(int n)

get upper parameter limit

protected 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 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.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

Constructor Details
- GTR
  
  public GTR(double a, double b, double c, double d, double e, double[] freq)
  
  constructor 1
  
  Parameters:
  
  a - entry in rate matrix
  
  b - entry in rate matrix
  
  c - entry in rate matrix
  
  d - entry in rate matrix
  
  e - entry in rate matrix
  
  freq - nucleotide frequencies
- GTR
  
  public GTR(double[] params, double[] freq)
  
  constructor 2
  
  Parameters:
  
  params - parameter list
  
  freq - nucleotide frequencies
Method Details
- clone
  
  public 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(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
- getUniqueName
  
  public String getUniqueName()
  
  Specified by:
  
  getUniqueName in interface RateMatrix
  
  Returns:
  
  the name of this rate matrix
- getParameterName
  
  public 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!
- rebuildRateMatrix
  
  protected void rebuildRateMatrix(double[][] rate, double[] parameters)
  
  Specified by:
  
  rebuildRateMatrix in class AbstractRateMatrix

Class GTR

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

Constructor Details

GTR

GTR

Method Details

clone

getModelID

report

getNumParameters

setParameterSE

getLowerLimit

getUpperLimit

getDefaultValue

getUniqueName

getParameterName

rebuildRateMatrix