pal.substmodel
Class SimpleRateMatrixGroup

java.lang.Object
  extended by pal.substmodel.SimpleRateMatrixGroup
All Implemented Interfaces:
java.io.Serializable, RateMatrixGroup

public abstract class SimpleRateMatrixGroup
extends java.lang.Object
implements RateMatrixGroup

See Also:
Serialized Form

Constructor Summary
SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices, double[] equilibriumFrequencies, double[] initialClassProbabilities, DataType dataType)
           
 
Method Summary
 DataType getDataType()
           
 double getDefaultValue(int n)
           
 double[] getEquilibriumFrequencies()
           
 double getLowerLimit(int n)
           
 int getNumberOfParameters()
           
 int getNumberOfTransitionCategories()
           
 java.lang.String getSummary(double[] parameters, double[] categoryProbabilities)
           
 void getTransitionProbabilities(double branchLength, double[][][] tableStore)
           
 void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
           
 void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
           
 void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
           
 double getUpperLimit(int n)
           
 void setParameters(double[] parameters, double[] categoryProbabilities)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface pal.substmodel.RateMatrixGroup
getSummary, updateParameters
 

Constructor Detail

SimpleRateMatrixGroup

public SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices,
                             double[] equilibriumFrequencies,
                             double[] initialClassProbabilities,
                             DataType dataType)
Method Detail

getNumberOfParameters

public int getNumberOfParameters()

getLowerLimit

public double getLowerLimit(int n)

getUpperLimit

public double getUpperLimit(int n)

getDefaultValue

public double getDefaultValue(int n)

setParameters

public void setParameters(double[] parameters,
                          double[] categoryProbabilities)

getEquilibriumFrequencies

public double[] getEquilibriumFrequencies()
Specified by:
getEquilibriumFrequencies in interface RateMatrixGroup

getDataType

public DataType getDataType()
Specified by:
getDataType in interface RateMatrixGroup

getNumberOfTransitionCategories

public int getNumberOfTransitionCategories()
Specified by:
getNumberOfTransitionCategories in interface RateMatrixGroup

getTransitionProbabilities

public void getTransitionProbabilities(double branchLength,
                                       double[][][] tableStore)
Specified by:
getTransitionProbabilities in interface RateMatrixGroup

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double branchLength,
                                                double[][][] tableStore)
Specified by:
getTransitionProbabilitiesTranspose in interface RateMatrixGroup

getTransitionProbabilities

public void getTransitionProbabilities(double branchLength,
                                       int category,
                                       double[][] tableStore)
Specified by:
getTransitionProbabilities in interface RateMatrixGroup

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double branchLength,
                                                int category,
                                                double[][] tableStore)
Specified by:
getTransitionProbabilitiesTranspose in interface RateMatrixGroup

getSummary

public java.lang.String getSummary(double[] parameters,
                                   double[] categoryProbabilities)