pal.substmodel
Class NucleotideModel

java.lang.Object
  pal.substmodel.AbstractRateMatrix
      pal.substmodel.NucleotideModel

All Implemented Interfaces:

java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, RateMatrix, Report, java.io.Serializable

Direct Known Subclasses:

F81, F84, GTR, HKY, TN

public abstract class NucleotideModel

extends AbstractRateMatrix

implements RateMatrix, java.io.Serializable

base class for nucleotide rate matrices

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary

Fields inherited from class pal.substmodel.AbstractRateMatrix

format

Constructor Summary

protected

NucleotideModel(double[] f)

Method Summary

static NucleotideModel	getInstance(int modelID, double[] params, double[] freq) Create nucleotide substitution model according to model type
protected void	printFrequencies(java.io.PrintWriter out)
protected void	printRatios(java.io.PrintWriter out)

Methods inherited from class pal.substmodel.AbstractRateMatrix

addPalObjectListener, clone, fireParametersChangedEvent, fireParametersChangedEvent, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getFrequencies, getModelID, getOrthogonalHints, getParameter, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, parameterChanged, rebuild, rebuildRateMatrix, 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.substmodel.RateMatrix

addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale

Methods inherited from interface pal.misc.NamedParameterized

getParameterName

Methods inherited from interface pal.misc.Parameterized

getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE

Methods inherited from interface pal.misc.Report

report

Constructor Detail

NucleotideModel

protected NucleotideModel(double[] f)

Method Detail

getInstance

public static NucleotideModel getInstance(int modelID,
                                          double[] params,
                                          double[] freq)

Create nucleotide substitution model according to model type

Parameters:

modelID - model code

params - model parameters

freq - model frequencies

Returns:

nucleotide rate matrix

printFrequencies

protected void printFrequencies(java.io.PrintWriter out)

Overrides:

printFrequencies in class AbstractRateMatrix

printRatios

protected void printRatios(java.io.PrintWriter out)