Package pal.substmodel

Class SaturatedSingleSplitDistribution

  • All Implemented Interfaces:
    NeoParameterized, SingleSplitDistribution
    public class SaturatedSingleSplitDistribution
extends java.lang.Object
implements SingleSplitDistribution

    Title: SaturatedSingleSplitDistribution

    Description: A model

    Copyright: Copyright (c) 2003

    Company:

    Version:
    1.0
    Author:
    not attributable

    • Constructor Detail

      • SaturatedSingleSplitDistribution

        public SaturatedSingleSplitDistribution​(int numberOfBaseTransitionCategories)

      • SaturatedSingleSplitDistribution

        public SaturatedSingleSplitDistribution​(int numberOfBaseTransitionCategories,
                                        double[] initialParameters)

    • Method Detail

      • getDistribution

        public double[] getDistribution()

      • getDistributionInfo

        public double[][] getDistributionInfo()
        Description copied from interface: SingleSplitDistribution
        Obtain the distribution information stored in the following format: [beforeclass][afterclass] For example, the probability of evolving in class 0 before the split, and class 1 after the split - [0][1]
        Specified by:
        getDistributionInfo in interface SingleSplitDistribution
        Returns:
        an appropriate matrix representing the probability of evolving in the different combinations of before and after classes

      • setParameters

        public void setParameters​(double[] store,
                          int startIndex)
        Description copied from interface: NeoParameterized
        set model parameter
        Specified by:
        setParameters in interface NeoParameterized
        Parameters:
        store - the array holding the parameters
        startIndex - the index into the array that the related parameters start at

      • getParameters

        public void getParameters​(double[] store,
                          int startIndex)
        Description copied from interface: NeoParameterized
        get model parameter
        Specified by:
        getParameters in interface NeoParameterized
        startIndex - the index into the array that the related parameters start at

      • getLowerLimit

        public double getLowerLimit​(int n)
        Description copied from interface: NeoParameterized
        get lower parameter limit
        Specified by:
        getLowerLimit in interface NeoParameterized
        Parameters:
        n - parameter number
        Returns:
        lower bound

      • getUpperLimit

        public double getUpperLimit​(int n)
        Description copied from interface: NeoParameterized
        get upper parameter limit
        Specified by:
        getUpperLimit in interface NeoParameterized
        Parameters:
        n - parameter number
        Returns:
        upper bound

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object