pal.substmodel
Class MultiRateMatrixHandler

java.lang.Object
  extended by pal.substmodel.MultiRateMatrixHandler
All Implemented Interfaces:
java.io.Serializable, NeoParameterized

public class MultiRateMatrixHandler
extends java.lang.Object
implements NeoParameterized, java.io.Serializable

See Also:
Serialized Form

Constructor Summary
MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices, double[] equilibriumFrequencies, double[] initialClassProportions)
           
 
Method Summary
 MultiRateMatrixHandler getCopy()
           
 double getDefaultValue(int n)
           
 void getDefaultValues(double[] store, int startIndex)
          get default value parameter values
 double[] getEquilibriumFrequencies()
           
 double getLowerLimit(int n)
          get lower parameter limit
 int getNumberOfParameters()
          get number of parameters
 int getNumberOfSubstitutionClasses()
           
 void getParameters(double[] parameterStore, int startIndex)
          get model parameter
 double getSubstitutionClassDefaultValue()
           
 double getSubstitutionClassLowerLimit()
           
 double getSubstitutionClassUpperLimit()
           
 void getTransitionProbabilities(double distance, double[][][] store)
           
 void getTransitionProbabilities(double distance, int category, double[][] store)
           
 void getTransitionProbabilitiesTranspose(double distance, double[][][] store)
           
 void getTransitionProbabilitiesTranspose(double distance, int category, double[][] store)
           
 double getUpperLimit(int n)
          get upper parameter limit
 void report(java.io.PrintWriter out)
          Reporting stuff
 void setAllParameters(double[] rateParameters, double[] classProportions)
           
 void setParameters(double[] parameters, int startIndex)
          set model parameter
 void setSubstitutionClassProbabilities(double[] classProportions)
           
 void setSubstitutionClassProbabilities(double[] classProportions, int startIndex)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MultiRateMatrixHandler

public MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices,
                              double[] equilibriumFrequencies,
                              double[] initialClassProportions)
Method Detail

setSubstitutionClassProbabilities

public void setSubstitutionClassProbabilities(double[] classProportions)

setSubstitutionClassProbabilities

public void setSubstitutionClassProbabilities(double[] classProportions,
                                              int startIndex)

getNumberOfSubstitutionClasses

public final int getNumberOfSubstitutionClasses()

getCopy

public final MultiRateMatrixHandler getCopy()

getEquilibriumFrequencies

public final double[] getEquilibriumFrequencies()

getTransitionProbabilities

public void getTransitionProbabilities(double distance,
                                       double[][][] store)

getTransitionProbabilities

public void getTransitionProbabilities(double distance,
                                       int category,
                                       double[][] store)

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double distance,
                                                double[][][] store)

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double distance,
                                                int category,
                                                double[][] store)

report

public void report(java.io.PrintWriter out)
Reporting stuff

Parameters:
out - where to report too

getSubstitutionClassLowerLimit

public final double getSubstitutionClassLowerLimit()

getSubstitutionClassUpperLimit

public final double getSubstitutionClassUpperLimit()

getSubstitutionClassDefaultValue

public final double getSubstitutionClassDefaultValue()

getLowerLimit

public double getLowerLimit(int n)
Description copied from interface: NeoParameterized
get lower parameter limit

Specified by:
getLowerLimit in interface NeoParameterized
Parameters:
n - parameter number
Returns:
lower bound

getUpperLimit

public double getUpperLimit(int n)
Description copied from interface: NeoParameterized
get upper parameter limit

Specified by:
getUpperLimit in interface NeoParameterized
Parameters:
n - parameter number
Returns:
upper bound

getDefaultValue

public double getDefaultValue(int n)

getNumberOfParameters

public int getNumberOfParameters()
Description copied from interface: NeoParameterized
get number of parameters

Specified by:
getNumberOfParameters in interface NeoParameterized
Returns:
number of parameters

setAllParameters

public void setAllParameters(double[] rateParameters,
                             double[] classProportions)

setParameters

public void setParameters(double[] parameters,
                          int startIndex)
Description copied from interface: NeoParameterized
set model parameter

Specified by:
setParameters in interface NeoParameterized
Parameters:
parameters - the array holding the parameters
startIndex - the index into the array that the related parameters start at

getParameters

public void getParameters(double[] parameterStore,
                          int startIndex)
Description copied from interface: NeoParameterized
get model parameter

Specified by:
getParameters in interface NeoParameterized
startIndex - the index into the array that the related parameters start at

getDefaultValues

public void getDefaultValues(double[] store,
                             int startIndex)
Description copied from interface: NeoParameterized
get default value parameter values

Specified by:
getDefaultValues in interface NeoParameterized