Class VariableIndependentSingleSplitDistribution

  • All Implemented Interfaces:
    NeoParameterized, SingleSplitDistribution

    public class VariableIndependentSingleSplitDistribution
    extends java.lang.Object
    implements SingleSplitDistribution

    Title: VariableIndependentSingleSplitDistribution

    Description: Allows for a split in substitution model parameters where the class distribution before the split maybe different after the split (and the probabilities of being in a before class and an after class are independent)

    Author:
    Matthew Goode
    • Constructor Detail

      • VariableIndependentSingleSplitDistribution

        public VariableIndependentSingleSplitDistribution​(int numberOfBaseTransitionCategories)
      • VariableIndependentSingleSplitDistribution

        public VariableIndependentSingleSplitDistribution​(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