CachedRateMatrix

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pal.substmodel
Class 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
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
`CachedRateMatrix(CachedRateMatrix cachedRateMatrix)`
`CachedRateMatrix(RateMatrix rateMatrix, DoubleKeyCache cache)`
`CachedRateMatrix(RateMatrix rateMatrix, int maxCacheSize)`

Method Summary
`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