pal.substmodel
Class F81
java.lang.Object
|
+--pal.substmodel.AbstractRateMatrix
|
+--pal.substmodel.NucleotideModel
|
+--pal.substmodel.F81
- All Implemented Interfaces:
- java.lang.Cloneable, NamedParameterized, Parameterized, RateMatrix, Report, java.io.Serializable, XMLConstants
- public class F81
- extends NucleotideModel
- implements java.io.Serializable, XMLConstants
Felsenstein 1981 model of nucleotide evolution
- See Also:
- Serialized Form
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 |
F81(double[] freq)
constructor |
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 |
F81
public F81(double[] freq)
- constructor
- Parameters:
freq
- nucleotide frequencies
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 valuen
- 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 valuen
- 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()
- Returns:
- the name of this rate matrix