Package pal.misc

Class ParameterizedDoubleBundle

  • All Implemented Interfaces:
    NeoParameterized

    public class ParameterizedDoubleBundle
    extends java.lang.Object
    implements NeoParameterized

    Title: ParameterizedDoubleBundle

    Description: A parameterized double bundle is simple a parameterized collection of mutable double objects. The idea is, all the changable attributes of the phylogenetic entities that are being accessed (eg the branch lengths of a tree, and the parameters of a model) can be grouped together externally (the point of this approach will become more apparent over time as PAL evolves)

    Version:
    1.0
    Author:
    Matthew Goode
    • Constructor Detail

      • ParameterizedDoubleBundle

        public ParameterizedDoubleBundle​(MutableDouble[] parameters)
    • Method Detail

      • setParameters

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

        public void getParameters​(double[] parameterStore,
                                  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