pal.substmodel
Class RateMatrixHandler

java.lang.Object
  extended by pal.substmodel.RateMatrixHandler
All Implemented Interfaces:
java.io.Serializable, Parameterized

public class RateMatrixHandler
extends java.lang.Object
implements Parameterized, java.io.Serializable

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
 
Constructor Summary
RateMatrixHandler(NeoRateMatrix rateMatrix, double[] equilibriumFrequencies)
           
 
Method Summary
 RateMatrixHandler getCopy()
           
 double getDefaultValue(int n)
          get default value of parameter
 double[] getEquilibriumFrequencies()
           
 double getLowerLimit(int n)
          get lower parameter limit
 int getNumParameters()
          get number of parameters
 double getParameter(int n)
          get model parameter
 void getTransitionProbabilities(double distance, double[][] store)
           
 void getTransitionProbabilitiesTranspose(double distance, double[][] store)
           
 double getUpperLimit(int n)
          get upper parameter limit
 void report(java.io.PrintWriter out)
          Reporting stuff
 void setParameter(double param, int n)
          set model parameter
 void setParameterSE(double paramSE, int n)
          set standard errors for model parameter
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

RateMatrixHandler

public RateMatrixHandler(NeoRateMatrix rateMatrix,
                         double[] equilibriumFrequencies)
Method Detail

getCopy

public final RateMatrixHandler getCopy()

getEquilibriumFrequencies

public final double[] getEquilibriumFrequencies()

getTransitionProbabilities

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

getTransitionProbabilitiesTranspose

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

report

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

Parameters:
out - where to report too

getNumParameters

public int getNumParameters()
Description copied from interface: Parameterized
get number of parameters

Specified by:
getNumParameters in interface Parameterized
Returns:
number of parameters

setParameter

public void setParameter(double param,
                         int n)
Description copied from interface: Parameterized
set model parameter

Specified by:
setParameter in interface Parameterized
Parameters:
param - parameter value
n - parameter number

getParameter

public double getParameter(int n)
Description copied from interface: Parameterized
get model parameter

Specified by:
getParameter in interface 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

Specified by:
setParameterSE in interface Parameterized
Parameters:
paramSE - standard error of parameter value
n - parameter number

getLowerLimit

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

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

getUpperLimit

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

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

getDefaultValue

public double getDefaultValue(int n)
Description copied from interface: Parameterized
get default value of parameter

Specified by:
getDefaultValue in interface Parameterized
Parameters:
n - parameter number
Returns:
default value