java.lang.Object
- 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

Constructors
Constructor Description

RateMatrixHandler(NeoRateMatrix rateMatrix, double[] equilibriumFrequencies)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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

Class RateMatrixHandler

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

RateMatrixHandler

Method Detail

getCopy

getEquilibriumFrequencies

getTransitionProbabilities

getTransitionProbabilitiesTranspose

report

getNumParameters

setParameter

getParameter

setParameterSE

getLowerLimit

getUpperLimit

getDefaultValue