Package pal.substmodel

Interface RateMatrix

    • Method Detail

      • getTypeID

        int getTypeID()
        get numerical code describing the data type
        Returns:
        integer code identifying a data type

      • getModelID

        int getModelID()
        get numerical code describing the model type
        Returns:
        integer code identifying a substitution model

      • getUniqueName

        java.lang.String getUniqueName()
        Returns:
        a short unique human-readable identifier for this rate matrix.

      • getDimension

        int getDimension()
        Returns:
        the dimension of this rate matrix.

      • getEquilibriumFrequencies

        double[] getEquilibriumFrequencies()
        Returns:
        stationary frequencies (sum = 1.0)

      • getEquilibriumFrequency

        double getEquilibriumFrequency​(int i)
        Returns:
        stationary frequency (sum = 1.0) for ith state Preferred method for infrequent use.

      • getDataType

        DataType getDataType()
        Get the data type of this rate matrix

      • getRelativeRates

        double[][] getRelativeRates()
        Deprecated.
        try not to use.
        Returns:
        rate matrix (transition: from 1st index to 2nd index)

      • getTransitionProbability

        double getTransitionProbability​(int fromState,
                                int toState)
        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

      • getTransitionProbabilities

        void getTransitionProbabilities​(double[][] probabilityStore)
        A utility method for speed, transfers trans prob information quickly into store

      • setDistance

        void setDistance​(double distance)
        Sets the distance (such as time/branch length) used when calculating the probabilities. This method may well take the most time!

      • setDistanceTranspose

        void setDistanceTranspose​(double distance)
        Sets the distance (such as time/branch length) used when calculating the probabilities.

      • addPalObjectListener

        void addPalObjectListener​(PalObjectListener pol)
        Add a PalObjectListener to be notified of changes to the model. Only the parametersChanged method will generally be called

      • getOrthogonalHints

        OrthogonalHints getOrthogonalHints()
        Returns:
        an orthogonal hints object for orthogonal optimisation (may return null for no hints)

      • clone

        java.lang.Object clone()

      • setParametersNoScale

        double setParametersNoScale​(double[] parameters)

      • scale

        void scale​(double scaleValue)