java.lang.Object
- pal.substmodel.AbstractRateMatrix

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix

Direct Known Subclasses:

AminoAcidModel, CodonModel, NucleotideModel, TwoStateModel
```
public abstract class AbstractRateMatrix
extends java.lang.Object
implements RateMatrix, ExternalParameterListener
```
abstract base class for all rate matrices

Version:

$Id: AbstractRateMatrix.java,v 1.30 2004/04/05 05:14:39 matt Exp $

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

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

Field Summary

Fields
Modifier and Type Field Description

protected FormattedOutput format

Constructor Summary

Constructors
Modifier Constructor Description

protected AbstractRateMatrix(int dim)

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addPalObjectListener(PalObjectListener pol)`	Add a PalObjectListener to be notified of changes to the model.
`java.lang.Object`	`clone()`
`protected void`	`fireParametersChangedEvent()`
`protected void`	`fireParametersChangedEvent(PalObjectEvent pe)`
`DataType`	`getDataType()`	Get the data type of this rate matrix
`int`	`getDimension()`
`double[]`	`getEquilibriumFrequencies()`
`double`	`getEquilibriumFrequency(int i)`
`protected double[]`	`getFrequencies()`
`abstract int`	`getModelID()`	get numerical code describing the model type
`OrthogonalHints`	`getOrthogonalHints()`
`double`	`getParameter(int parameter)`	get model parameter
`double[][]`	`getRelativeRates()`
`void`	`getTransitionProbabilities(double[][] probabilityStore)`	A utility method for speed, transfers trans prob information quickly into store
`double`	`getTransitionProbability(int fromState, int toState)`	Returns the probability of going from one state to another given the current distance
`int`	`getTypeID()`	get numerical code describing the data type
`void`	`parameterChanged(ParameterEvent pe)`	For the external parameter interface.
`protected void`	`printFrequencies(java.io.PrintWriter out)`
`void`	`rebuild()`
`protected abstract void`	`rebuildRateMatrix(double[][] rate, double[] parameters)`
`void`	`removePalObjectListener(PalObjectListener pol)`
`void`	`scale(double scale)`
`protected void`	`setDataType(DataType dt)`
`void`	`setDistance(double distance)`	Sets the distance (such as time/branch length) used when calculating the probabilities.
`void`	`setDistanceTranspose(double distance)`	Sets the distance (such as time/branch length) used when calculating the probabilities.
`protected void`	`setFrequencies(double[] f)`
`void`	`setParameter(double value, int parameter)`	set model parameter
`void`	`setParameters(double[] parameters)`
`double`	`setParametersNoScale(double[] parameters)`
`protected void`	`updateMatrixExp()`

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

Methods inherited from interface pal.misc.NamedParameterized
getParameterName

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

Methods inherited from interface pal.substmodel.RateMatrix
getUniqueName

Methods inherited from interface pal.misc.Report
report

- Field Detail
  - format
```
protected FormattedOutput format
```
- Constructor Detail
  - AbstractRateMatrix
```
protected AbstractRateMatrix(int dim)
```
- Method Detail
  - getTypeID
```
public int getTypeID()
```
    get numerical code describing the data type
    
    Specified by:
    
    getTypeID in interface RateMatrix
    
    Returns:
    
    integer code identifying a data type
  - getModelID
```
public abstract int getModelID()
```
    get numerical code describing the model type
    
    Specified by:
    
    getModelID in interface RateMatrix
    
    Returns:
    
    integer code identifying a substitution model
  - getDimension
```
public int getDimension()
```
    Specified by:
    
    getDimension in interface RateMatrix
    
    Returns:
    
    the dimension of this rate matrix.
  - getEquilibriumFrequencies
```
public double[] getEquilibriumFrequencies()
```
    Specified by:
    
    getEquilibriumFrequencies in interface RateMatrix
    
    Returns:
    
    stationary frequencies (sum = 1.0)
  - getEquilibriumFrequency
```
public double getEquilibriumFrequency(int i)
```
    Specified by:
    
    getEquilibriumFrequency in interface RateMatrix
    
    Returns:
    
    stationary frequencie (sum = 1.0) for ith state
  - getDataType
```
public DataType getDataType()
```
    Description copied from interface: RateMatrix
    
    Get the data type of this rate matrix
    
    Specified by:
    
    getDataType in interface RateMatrix
  - setDataType
```
protected final void setDataType(DataType dt)
```
  - getRelativeRates
```
public double[][] getRelativeRates()
```
    Specified by:
    
    getRelativeRates in interface RateMatrix
    
    Returns:
    
    rate matrix (transition: from 1st index to 2nd index)
  - getTransitionProbability
```
public double getTransitionProbability(int fromState,
                                       int toState)
```
    Returns the probability of going from one state to another given the current distance
    
    Specified by:
    
    getTransitionProbability in interface RateMatrix
    
    Parameters:
    
    fromState - The state from which we are starting
    
    toState - The resulting state
    
    Returns:
    
    the probability of going from one state to another given the current distance
  - rebuild
```
public final void rebuild()
```
  - setDistance
```
public final void setDistance(double distance)
```
    Sets the distance (such as time/branch length) used when calculating the probabilities.
    
    Specified by:
    
    setDistance in interface RateMatrix
  - setDistanceTranspose
```
public final void setDistanceTranspose(double distance)
```
    Sets the distance (such as time/branch length) used when calculating the probabilities.
    
    Specified by:
    
    setDistanceTranspose in interface RateMatrix
  - getTransitionProbabilities
```
public final void getTransitionProbabilities(double[][] probabilityStore)
```
    A utility method for speed, transfers trans prob information quickly into store
    
    Specified by:
    
    getTransitionProbabilities in interface RateMatrix
  - scale
```
public void scale(double scale)
```
    Specified by:
    
    scale in interface RateMatrix
  - printFrequencies
```
protected void printFrequencies(java.io.PrintWriter out)
```
  - setFrequencies
```
protected void setFrequencies(double[] f)
```
  - setParametersNoScale
```
public double setParametersNoScale(double[] parameters)
```
    Specified by:
    
    setParametersNoScale in interface RateMatrix
  - setParameters
```
public void setParameters(double[] parameters)
```
  - setParameter
```
public final void setParameter(double value,
                               int parameter)
```
    Description copied from interface: Parameterized
    
    set model parameter
    
    Specified by:
    
    setParameter in interface Parameterized
    
    Parameters:
    
    value - parameter value
    
    parameter - parameter number
  - getParameter
```
public final double getParameter(int parameter)
```
    Description copied from interface: Parameterized
    
    get model parameter
    
    Specified by:
    
    getParameter in interface Parameterized
    
    Parameters:
    
    parameter - parameter number
    
    Returns:
    
    parameter value
  - rebuildRateMatrix
```
protected abstract void rebuildRateMatrix(double[][] rate,
                                          double[] parameters)
```
  - addPalObjectListener
```
public void addPalObjectListener(PalObjectListener pol)
```
    Description copied from interface: RateMatrix
    
    Add a PalObjectListener to be notified of changes to the model. Only the parametersChanged method will generally be called
    
    Specified by:
    
    addPalObjectListener in interface RateMatrix
  - removePalObjectListener
```
public void removePalObjectListener(PalObjectListener pol)
```
    Specified by:
    
    removePalObjectListener in interface RateMatrix
  - fireParametersChangedEvent
```
protected void fireParametersChangedEvent()
```
  - fireParametersChangedEvent
```
protected void fireParametersChangedEvent(PalObjectEvent pe)
```
  - updateMatrixExp
```
protected void updateMatrixExp()
```
  - parameterChanged
```
public void parameterChanged(ParameterEvent pe)
```
    For the external parameter interface. This can be ignored unless you want to use this Rate Matrix as an external parameter listener This method does two things.First it sets a flag indicating that rebuild method should be called the next time a setDistance method is called, and then it notifies any PalObject listeners that a parameter has changed
    
    Specified by:
    
    parameterChanged in interface ExternalParameterListener
  - clone
```
public java.lang.Object clone()
```
    Specified by:
    
    clone in interface RateMatrix
    
    Overrides:
    
    clone in class java.lang.Object
  - getOrthogonalHints
```
public OrthogonalHints getOrthogonalHints()
```
    Specified by:
    
    getOrthogonalHints in interface RateMatrix
    
    Returns:
    
    null
  - getFrequencies
```
protected final double[] getFrequencies()
```

Class AbstractRateMatrix

Nested Class Summary

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

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface pal.misc.NamedParameterized

Methods inherited from interface pal.misc.Parameterized

Methods inherited from interface pal.substmodel.RateMatrix

Methods inherited from interface pal.misc.Report

Field Detail

format

Constructor Detail

AbstractRateMatrix

Method Detail

getTypeID

getModelID

getDimension

getEquilibriumFrequencies

getEquilibriumFrequency

getDataType

setDataType

getRelativeRates

getTransitionProbability

rebuild

setDistance

setDistanceTranspose

getTransitionProbabilities

scale

printFrequencies

setFrequencies

setParametersNoScale

setParameters

setParameter

getParameter

rebuildRateMatrix

addPalObjectListener

removePalObjectListener

fireParametersChangedEvent

fireParametersChangedEvent

updateMatrixExp

parameterChanged

clone

getOrthogonalHints

getFrequencies