Package pal.substmodel

Class 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

    • 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

      • getUniqueName

        public final java.lang.String getUniqueName()
        Specified by:
        getUniqueName in interface RateMatrix
        Returns:
        a short unique human-readable identifier for this rate matrix.

      • 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