java.lang.Object
- pal.substmodel.PositiveSelectionRateMatrixGroup

All Implemented Interfaces:: java.io.Serializable, RateMatrixGroup

public class PositiveSelectionRateMatrixGroup
extends java.lang.Object
implements RateMatrixGroup

See Also:: Serialized Form

Constructor Summary

Constructors
Constructor	Description
`PositiveSelectionRateMatrixGroup(MutableDouble kappaStore, MutableDouble omegaStore, double[] freqs, CodonTable table)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`DataType`	`getDataType()`
`double[]`	`getEquilibriumFrequencies()`
`int`	`getNumberOfTransitionCategories()`
`java.lang.String`	`getSummary(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)`
`void`	`updateParameters(double[] categoryProbabilities)`	Update internal representation based on any parameters (that are specified externally) and the given category probablitilies.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - PositiveSelectionRateMatrixGroup
```
public PositiveSelectionRateMatrixGroup(MutableDouble kappaStore,
                                        MutableDouble omegaStore,
                                        double[] freqs,
                                        CodonTable table)
```
- Method Detail
  - getNumberOfTransitionCategories
```
public int getNumberOfTransitionCategories()
```
    Specified by:
    
    getNumberOfTransitionCategories in interface RateMatrixGroup
  - updateParameters
```
public void updateParameters(double[] categoryProbabilities)
```
    Description copied from interface: RateMatrixGroup
    
    Update internal representation based on any parameters (that are specified externally) and the given category probablitilies. The controller (user of this class) should be calling this method after the parameters of an external parameterization object have been set.
    
    Specified by:
    
    updateParameters in interface RateMatrixGroup
    
    Parameters:
    
    categoryProbabilities - the probabilities (summing to one) of each category (class) of substitution
  - getEquilibriumFrequencies
```
public double[] getEquilibriumFrequencies()
```
    Specified by:
    
    getEquilibriumFrequencies in interface RateMatrixGroup
  - getDataType
```
public DataType getDataType()
```
    Specified by:
    
    getDataType 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[] categoryProbabilities)
```
    Specified by:
    
    getSummary in interface RateMatrixGroup

Class PositiveSelectionRateMatrixGroup

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PositiveSelectionRateMatrixGroup

Method Detail

getNumberOfTransitionCategories

updateParameters

getEquilibriumFrequencies

getDataType

getTransitionProbabilities

getTransitionProbabilitiesTranspose

getTransitionProbabilities

getTransitionProbabilitiesTranspose

getSummary