pal.substmodel
Class CodonModel

java.lang.Object
  extended by pal.substmodel.AbstractRateMatrix
      extended by pal.substmodel.CodonModel
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix
Direct Known Subclasses:
YangCodonModel

public abstract class CodonModel
extends AbstractRateMatrix
implements RateMatrix, java.io.Serializable

base class for nucleotide rate matrices

Version:
$Id: CodonModel.java,v 1.5 2003/11/13 04:05:39 matt Exp $
Author:
Andrew Rambaut
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
 
Constructor Summary
protected CodonModel(double[] f)
           
 
Method Summary
static CodonModel getInstance(int modelID, double[] params, double[] freq)
          Create codon 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

CodonModel

protected CodonModel(double[] f)
Method Detail

getInstance

public static CodonModel getInstance(int modelID,
                                     double[] params,
                                     double[] freq)
Create codon substitution model according to model type

Parameters:
modelID - model code
params - model parameters
freq - model frequencies
Returns:
codon rate matrix

printFrequencies

protected void printFrequencies(java.io.PrintWriter out)
Overrides:
printFrequencies in class AbstractRateMatrix

printRatios

protected void printRatios(java.io.PrintWriter out)