java.lang.Object
- pal.misc.PalObjectListener.EventGenerator
- - pal.misc.Parameterized.ParameterizedUser
  - - pal.substmodel.SingleClassSubstitutionModel

All Implemented Interfaces:: java.io.Serializable, Parameterized, Report, SubstitutionModel

public class SingleClassSubstitutionModel
extends Parameterized.ParameterizedUser
implements SubstitutionModel

See Also:: Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from interface pal.misc.Parameterized
  Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
- Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel
  SubstitutionModel.Utils

Constructor Summary

Constructors
Constructor Description

SingleClassSubstitutionModel(NeoRateMatrix base, DataType dt, double[] frequencies)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addPalObjectListener(PalObjectListener l)`
`java.lang.Object`	`clone()`
`SubstitutionModel`	`getCopy()`
`DataType`	`getDataType()`
`double[]`	`getEquilibriumFrequencies()`	Should return a double[] array of the related equilibrium frequencies.
`int`	`getNumberOfTransitionCategories()`
`OrthogonalHints`	`getOrthogonalHints()`	May return null
`double[]`	`getTransitionCategoryProbabilities()`
`double`	`getTransitionCategoryProbability(int category)`
`void`	`getTransitionProbabilities(double branchLength, double[][][] store)`	Table is organized as [transition_group][from][to]
`void`	`getTransitionProbabilities(double branchLength, int category, double[][] store)`	Table is organized as [transition_group][from][to]
`void`	`getTransitionProbabilitiesTranspose(double branchLength, double[][][] store)`	Table is organized as [transition_group][to][from]
`void`	`getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] store)`	Table is organized as [transition_group][to][from]
`void`	`removePalObjectListener(PalObjectListener l)`
`void`	`report(java.io.PrintWriter out)`	print human readable report (e.g., on parameters and associated model)
`java.lang.String`	`toString()`

Methods inherited from class pal.misc.Parameterized.ParameterizedUser
getAllParameters, getDefaultValue, getLowerLimit, getNumParameters, getParameter, getRandomParameterValue, getUpperLimit, randomiseParameters, setParameter, setParameterizedBase, setParameterSE

Methods inherited from class pal.misc.PalObjectListener.EventGenerator
fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent

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

Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE

- Constructor Detail
  - SingleClassSubstitutionModel
```
public SingleClassSubstitutionModel(NeoRateMatrix base,
                                    DataType dt,
                                    double[] frequencies)
```
- Method Detail
  - getDataType
```
public DataType getDataType()
```
    Specified by:
    
    getDataType in interface SubstitutionModel
  - getNumberOfTransitionCategories
```
public int getNumberOfTransitionCategories()
```
    Specified by:
    
    getNumberOfTransitionCategories in interface SubstitutionModel
  - getTransitionCategoryProbability
```
public double getTransitionCategoryProbability(int category)
```
    Specified by:
    
    getTransitionCategoryProbability in interface SubstitutionModel
  - getTransitionCategoryProbabilities
```
public double[] getTransitionCategoryProbabilities()
```
    Specified by:
    
    getTransitionCategoryProbabilities in interface SubstitutionModel
    
    Returns:
    
    all the category probabilites for each category respectively.
  - getEquilibriumFrequencies
```
public double[] getEquilibriumFrequencies()
```
    Description copied from interface: SubstitutionModel
    
    Should return a double[] array of the related equilibrium frequencies. As a rule, callers should not alter the returned array (it may be used internally)
    
    Specified by:
    
    getEquilibriumFrequencies in interface SubstitutionModel
  - getTransitionProbabilities
```
public void getTransitionProbabilities(double branchLength,
                                       double[][][] store)
```
    Description copied from interface: SubstitutionModel
    
    Table is organized as [transition_group][from][to]
    
    Specified by:
    
    getTransitionProbabilities in interface SubstitutionModel
  - getTransitionProbabilities
```
public void getTransitionProbabilities(double branchLength,
                                       int category,
                                       double[][] store)
```
    Description copied from interface: SubstitutionModel
    
    Table is organized as [transition_group][from][to]
    
    Specified by:
    
    getTransitionProbabilities in interface SubstitutionModel
  - getTransitionProbabilitiesTranspose
```
public void getTransitionProbabilitiesTranspose(double branchLength,
                                                double[][][] store)
```
    Description copied from interface: SubstitutionModel
    
    Table is organized as [transition_group][to][from]
    
    Specified by:
    
    getTransitionProbabilitiesTranspose in interface SubstitutionModel
  - getTransitionProbabilitiesTranspose
```
public void getTransitionProbabilitiesTranspose(double branchLength,
                                                int category,
                                                double[][] store)
```
    Description copied from interface: SubstitutionModel
    
    Table is organized as [transition_group][to][from]
    
    Specified by:
    
    getTransitionProbabilitiesTranspose in interface SubstitutionModel
  - addPalObjectListener
```
public void addPalObjectListener(PalObjectListener l)
```
    Specified by:
    
    addPalObjectListener in interface SubstitutionModel
    
    Overrides:
    
    addPalObjectListener in class PalObjectListener.EventGenerator
  - removePalObjectListener
```
public void removePalObjectListener(PalObjectListener l)
```
    Specified by:
    
    removePalObjectListener in interface SubstitutionModel
    
    Overrides:
    
    removePalObjectListener in class PalObjectListener.EventGenerator
  - getOrthogonalHints
```
public OrthogonalHints getOrthogonalHints()
```
    Description copied from interface: SubstitutionModel
    
    May return null
    
    Specified by:
    
    getOrthogonalHints in interface SubstitutionModel
  - report
```
public void report(java.io.PrintWriter out)
```
    Description copied from interface: Report
    
    print human readable report (e.g., on parameters and associated model)
    
    Specified by:
    
    report in interface Report
    
    Parameters:
    
    out - output stream
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - clone
```
public java.lang.Object clone()
```
    Specified by:
    
    clone in interface SubstitutionModel
    
    Overrides:
    
    clone in class java.lang.Object
  - getCopy
```
public SubstitutionModel getCopy()
```

Class SingleClassSubstitutionModel

Nested Class Summary

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

Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel

Constructor Summary

Method Summary

Methods inherited from class pal.misc.Parameterized.ParameterizedUser

Methods inherited from class pal.misc.PalObjectListener.EventGenerator

Methods inherited from class java.lang.Object

Methods inherited from interface pal.misc.Parameterized

Constructor Detail

SingleClassSubstitutionModel

Method Detail

getDataType

getNumberOfTransitionCategories

getTransitionCategoryProbability

getTransitionCategoryProbabilities

getEquilibriumFrequencies

getTransitionProbabilities

getTransitionProbabilities

getTransitionProbabilitiesTranspose

getTransitionProbabilitiesTranspose

addPalObjectListener

removePalObjectListener

getOrthogonalHints

report

toString

clone

getCopy