java.lang.Object
- 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

Constructors
Constructor	Description
`SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices, double[] equilibriumFrequencies, double[] initialClassProbabilities, DataType dataType)`

Method Summary

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

Class SimpleRateMatrixGroup

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface pal.substmodel.RateMatrixGroup

Constructor Detail

SimpleRateMatrixGroup

Method Detail

getNumberOfParameters

getLowerLimit

getUpperLimit

getDefaultValue

setParameters

getEquilibriumFrequencies

getDataType

getNumberOfTransitionCategories

getTransitionProbabilities

getTransitionProbabilitiesTranspose

getTransitionProbabilities

getTransitionProbabilitiesTranspose

getSummary