pal.substmodel
Class YangCodonModel

java.lang.Object
  |
  +--pal.substmodel.AbstractRateMatrix
        |
        +--pal.substmodel.CodonModel
              |
              +--pal.substmodel.YangCodonModel
All Implemented Interfaces:
java.lang.Cloneable, NamedParameterized, Parameterized, RateMatrix, Report, java.io.Serializable, XMLConstants

public class YangCodonModel
extends CodonModel
implements java.io.Serializable, XMLConstants

Yang's model of codon evolution

See Also:
Serialized Form

Fields inherited from class pal.substmodel.AbstractRateMatrix
dataType, dimension, format, frequency, rate
 
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_GROWTH, CONSTANT_MUTATION_RATE, CONSTANT_POPULATION, CPREV, DATA_TYPE, DATA_TYPE_ID, DAYHOFF, DAYS, DEMOGRAPHIC_MODEL, DIRECTION, EDGE, EXPONENTIAL_GROWTH, F81, F84, FREQUENCIES, G_TO_T, GENERATIONS, 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, OMEGA, ORIGIN, PARAMETER, POPULATION_SIZE, PYRIMIDINE_PURINE_RATIO, RATE_MATRIX, SEQUENCE, SPACES_PER_LEVEL, STEPPED_MUTATION_RATE, TIME, TIME_DATA, TN, TREE, TS_TV_RATIO, TWO_STATE, TYPE, UNIFORM, UNITS, UNKNOWN, VALUE, VT, WAG, YANG_CODON_MODEL, YEARS
 
Constructor Summary
YangCodonModel(double[] params, double[] freq)
          constructor 4 (universal codon table)
YangCodonModel(double[] params, double[] freq, CodonTable codonTable)
          constructor 3
YangCodonModel(double omega, double kappa, double[] freq)
          constructor 2 (universal codon table)
YangCodonModel(double omega, double kappa, double[] freq, CodonTable codonTable)
          constructor 1
 
Method Summary
 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
 double getParameter(int n)
          get model parameter
 java.lang.String getParameterName(int i)
           
 java.lang.String getUniqueName()
           
 double getUpperLimit(int n)
          get upper parameter limit
 void report(java.io.PrintWriter out)
          print human readable report (e.g., on parameters and associated model)
 void setParameter(double param, int n)
          set model parameter
 void setParameterSE(double paramSE, int n)
          set standard errors for model parameter
 
Methods inherited from class pal.substmodel.CodonModel
getInstance, printFrequencies, printRatios
 
Methods inherited from class pal.substmodel.AbstractRateMatrix
addPalObjectListener, clone, fireParametersChangedEvent, fireParametersChangedEvent, fromQToR, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, setDistance, setFrequencies, 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, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, setDistance
 

Constructor Detail

YangCodonModel

public YangCodonModel(double omega,
                      double kappa,
                      double[] freq,
                      CodonTable codonTable)
constructor 1
Parameters:
omega - N/S rate ratio
kappa - transition/transversion rate ratio
freq - codon frequencies
codonTable - codon table

YangCodonModel

public YangCodonModel(double omega,
                      double kappa,
                      double[] freq)
constructor 2 (universal codon table)
Parameters:
omega - N/S rate ratio
kappa - transition/transversion rate ratio
freq - codon frequencies

YangCodonModel

public YangCodonModel(double[] params,
                      double[] freq)
constructor 4 (universal codon table)
Parameters:
params - parameter list
freq - nucleotide frequencies

YangCodonModel

public YangCodonModel(double[] params,
                      double[] freq,
                      CodonTable codonTable)
constructor 3
Parameters:
params - parameter list
freq - nucleotide frequencies
codonTable - codon table
Method Detail

getModelID

public int getModelID()
Description copied from interface: RateMatrix
get numerical code describing the model type
Overrides:
getModelID in class AbstractRateMatrix
Following copied from interface: pal.substmodel.RateMatrix
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)
Following copied from interface: pal.misc.Report
Parameters:
out - output stream

getNumParameters

public int getNumParameters()
Description copied from interface: Parameterized
get number of parameters
Following copied from interface: pal.misc.Parameterized
Returns:
number of parameters

setParameter

public void setParameter(double param,
                         int n)
Description copied from interface: Parameterized
set model parameter
Following copied from interface: pal.misc.Parameterized
Parameters:
param - parameter value
n - parameter number

getParameter

public double getParameter(int n)
Description copied from interface: Parameterized
get model parameter
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
parameter value

setParameterSE

public void setParameterSE(double paramSE,
                           int n)
Description copied from interface: Parameterized
set standard errors for model parameter
Following copied from interface: pal.misc.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
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
lower bound

getUpperLimit

public double getUpperLimit(int n)
Description copied from interface: Parameterized
get upper parameter limit
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
upper bound

getDefaultValue

public double getDefaultValue(int n)
Description copied from interface: Parameterized
get default value of parameter
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
default value

getParameterName

public java.lang.String getParameterName(int i)
Following copied from interface: pal.misc.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()
Following copied from interface: pal.substmodel.RateMatrix
Returns:
a short unique human-readable identifier for this rate matrix.