Package pal.misc

Class ParameterizedDoubleBundle

java.lang.Object
pal.misc.ParameterizedDoubleBundle
All Implemented Interfaces:
NeoParameterized
public class ParameterizedDoubleBundle extends 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 Details

    • ParameterizedDoubleBundle

      public ParameterizedDoubleBundle(MutableDouble[] parameters)

  • Method Details

    • getNumberOfParameters

      public int getNumberOfParameters()
      Description copied from interface: NeoParameterized
      get number of parameters
      Specified by:
      getNumberOfParameters in interface NeoParameterized
      Returns:
      number of parameters

    • 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

    • getDefaultValues

      public void getDefaultValues(double[] store, int startIndex)
      Description copied from interface: NeoParameterized
      get default value parameter values
      Specified by:
      getDefaultValues in interface NeoParameterized

    • toString

      public String toString()
      Overrides:
      toString in class Object