CachedRateMatrix

java.lang.Object
- pal.substmodel.CachedRateMatrix

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, NamedParameterized, PalObjectListener, Parameterized, Report, RateMatrix
```
public abstract class CachedRateMatrix
extends java.lang.Object
implements RateMatrix, PalObjectListener
```
a cached rate matrix. This model caches transition probabilities by distance in order to increase speed of likelihood calculations for repeated calls with same/similar branch lengths.
AS OF 11 November 2003 this class has been made abstract and will be removed at a later point (as it never really helped much)

Version:

$Id: CachedRateMatrix.java,v 1.13 2003/11/13 04:05:39 matt Exp $

Author:

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
- Nested classes/interfaces inherited from interface pal.misc.PalObjectListener
  PalObjectListener.EventGenerator

Constructor Summary

Constructors
Constructor and Description
`CachedRateMatrix(CachedRateMatrix cachedRateMatrix)`
`CachedRateMatrix(RateMatrix rateMatrix, DoubleKeyCache cache)`
`CachedRateMatrix(RateMatrix rateMatrix, int maxCacheSize)`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addPalObjectListener(PalObjectListener pol)` Add a PalObjectListener to be notified of changes to the model.
`java.lang.Object`	`clone()` A non shallow implementation of clone()
`DataType`	`getDataType()` Get the data type of this rate matrix
`double`	`getDefaultValue(int n)` get default value of parameter
`int`	`getDimension()`
`double[]`	`getEquilibriumFrequencies()`
`double`	`getEquilibriumFrequency(int i)`
`double`	`getLowerLimit(int n)` get lower parameter limit
`int`	`getModelID()` get numerical code describing the model type
`int`	`getNumParameters()` get number of parameters
`OrthogonalHints`	`getOrthogonalHints()`
`double`	`getParameter(int n)` get model parameter
`java.lang.String`	`getParameterName(int i)`
`double[][]`	`getRelativeRates()`
`void`	`getTransitionProbabilities(double[][] probs)` A utility method for speed, transfers trans prob information quickly into store
`double`	`getTransitionProbability(int i, int j)` get transition probability for the preselected model and the previously specified distance
`int`	`getTypeID()` get numerical code describing the data type
`java.lang.String`	`getUniqueName()`
`double`	`getUpperLimit(int n)` get upper parameter limit
`void`	`parametersChanged(PalObjectEvent pe)` Signifies that parametric valued governing the state of this Object have changed.
`void`	`removePalObjectListener(PalObjectListener pol)`
`void`	`report(java.io.PrintWriter out)` print human readable report (e.g., on parameters and associated model)
`void`	`setDistance(double k)` set distance and corresponding computation transition probabilities
`void`	`setDistanceTranspose(double k)` Sets the distance (such as time/branch length) used when calculating the probabilities.
`void`	`setParameter(double param, int n)` set model parameter
`void`	`setParameterSE(double paramSE, int n)` set standard errors for model parameter
`void`	`structureChanged(PalObjectEvent pe)` Signifies that the structure of the object has changed (for example in trees to topology has changed)
`java.lang.String`	`toString()` Return string representation of substitution model.

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

Methods inherited from interface pal.substmodel.RateMatrix
scale, setParametersNoScale

- Constructor Detail
  - CachedRateMatrix
```
public CachedRateMatrix(RateMatrix rateMatrix,
                DoubleKeyCache cache)
```
    Parameters:
    model - the underlying substitution model
    cache - the caching method used
  - CachedRateMatrix
```
public CachedRateMatrix(RateMatrix rateMatrix,
                int maxCacheSize)
```
    Parameters:
    model - the underlying substitution model
  - CachedRateMatrix
```
public CachedRateMatrix(CachedRateMatrix cachedRateMatrix)
```
    Parameters:
    model - the previous cached model.
- Method Detail
  - report
```
public final 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
  - getTypeID
```
public final int getTypeID()
```
    Description copied from interface: RateMatrix
    
    get numerical code describing the data type
    
    Specified by:
    
    getTypeID in interface RateMatrix
    
    Returns:
    integer code identifying a data type
  - getModelID
```
public final int getModelID()
```
    Description copied from interface: RateMatrix
    
    get numerical code describing the model type
    
    Specified by:
    
    getModelID in interface RateMatrix
    
    Returns:
    integer code identifying a substitution model
  - getDimension
```
public final int getDimension()
```
    Specified by:
    
    getDimension in interface RateMatrix
    
    Returns:
    the dimension of this rate matrix.
  - getEquilibriumFrequencies
```
public final double[] getEquilibriumFrequencies()
```
    Specified by:
    
    getEquilibriumFrequencies in interface RateMatrix
    
    Returns:
    stationary frequencies (sum = 1.0)
  - getEquilibriumFrequency
```
public final double getEquilibriumFrequency(int i)
```
    Specified by:
    
    getEquilibriumFrequency in interface RateMatrix
    
    Returns:
    stationary frequency (sum = 1.0) for ith state Preferred method for infrequent use.
  - getRelativeRates
```
public final double[][] getRelativeRates()
```
    Specified by:
    
    getRelativeRates in interface RateMatrix
    
    Returns:
    rate matrix (transition: from 1st index to 2nd index)
  - toString
```
public java.lang.String toString()
```
    Return string representation of substitution model.
    
    Overrides:
    
    toString in class java.lang.Object
  - getNumParameters
```
public final int getNumParameters()
```
    Description copied from interface: Parameterized
    
    get number of parameters
    
    Specified by:
    
    getNumParameters in interface Parameterized
    
    Returns:
    number of parameters
  - setParameter
```
public final 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 final 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 final 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 final 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 final 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 final 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
  - getParameterName
```
public final java.lang.String getParameterName(int i)
```
    Specified by:
    
    getParameterName in interface NamedParameterized
    
    Returns:
    a short identifier for this parameter type. Should be the same for all instances of a given class!
  - setDistance
```
public final void setDistance(double k)
```
    set distance and corresponding computation transition probabilities
    
    Specified by:
    
    setDistance in interface RateMatrix
    
    Parameters:
    k - distance
  - setDistanceTranspose
```
public final void setDistanceTranspose(double k)
```
    Description copied from interface: RateMatrix
    
    Sets the distance (such as time/branch length) used when calculating the probabilities.
    
    Specified by:
    
    setDistanceTranspose in interface RateMatrix
  - getTransitionProbability
```
public final double getTransitionProbability(int i,
                              int j)
```
    get transition probability for the preselected model and the previously specified distance
    
    Specified by:
    
    getTransitionProbability in interface RateMatrix
    
    Parameters:
    i - start state
    j - end state
    
    Returns:
    transition probability
  - getTransitionProbabilities
```
public final void getTransitionProbabilities(double[][] probs)
```
    Description copied from interface: RateMatrix
    
    A utility method for speed, transfers trans prob information quickly into store
    
    Specified by:
    
    getTransitionProbabilities in interface RateMatrix
  - clone
```
public final java.lang.Object clone()
```
    A non shallow implementation of clone()
    
    Specified by:
    
    clone in interface RateMatrix
    
    Overrides:
    
    clone in class java.lang.Object
  - getDataType
```
public final DataType getDataType()
```
    Description copied from interface: RateMatrix
    
    Get the data type of this rate matrix
    
    Specified by:
    
    getDataType in interface RateMatrix
  - getUniqueName
```
public final java.lang.String getUniqueName()
```
    Specified by:
    
    getUniqueName in interface RateMatrix
    
    Returns:
    a short unique human-readable identifier for this rate matrix.
  - structureChanged
```
public void structureChanged(PalObjectEvent pe)
```
    Description copied from interface: PalObjectListener
    
    Signifies that the structure of the object has changed (for example in trees to topology has changed)
    
    Specified by:
    
    structureChanged in interface PalObjectListener
  - parametersChanged
```
public void parametersChanged(PalObjectEvent pe)
```
    Description copied from interface: PalObjectListener
    
    Signifies that parametric valued governing the state of this Object have changed. Parameters don't have to be visible ones For example, in trees the branch lengths have changed.
    
    Specified by:
    
    parametersChanged in interface PalObjectListener
  - 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
  - getOrthogonalHints
```
public OrthogonalHints getOrthogonalHints()
```
    Specified by:
    
    getOrthogonalHints in interface RateMatrix
    
    Returns:
    null

Class CachedRateMatrix

Nested Class Summary

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

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface pal.substmodel.RateMatrix

Constructor Detail

CachedRateMatrix

CachedRateMatrix

CachedRateMatrix

Method Detail

report

getTypeID

getModelID

getDimension

getEquilibriumFrequencies

getEquilibriumFrequency

getRelativeRates

toString

getNumParameters

setParameter

getParameter

setParameterSE

getLowerLimit

getUpperLimit

getDefaultValue

getParameterName

setDistance

setDistanceTranspose

getTransitionProbability

getTransitionProbabilities

clone

getDataType

getUniqueName

structureChanged

parametersChanged

addPalObjectListener

removePalObjectListener

getOrthogonalHints