pal.misc
Class Parameterized.ParameterizedUser

java.lang.Object
  extended by pal.misc.PalObjectListener.EventGenerator
      extended by pal.misc.Parameterized.ParameterizedUser
Direct Known Subclasses:
GeneralRateDistributionSubstitutionModel, SingleClassSubstitutionModel
Enclosing interface:
Parameterized

public abstract static class Parameterized.ParameterizedUser
extends PalObjectListener.EventGenerator

A Utility class for using as the superclass to subclasses which work by adding functionality to a general Parameterized object (the base Parameterized object)


Constructor Summary
protected Parameterized.ParameterizedUser()
          Sub class should call setParameterizedBase() at some point if using this constructor...
protected Parameterized.ParameterizedUser(Parameterized base)
           
 
Method Summary
 double[] getAllParameters()
          Obtain a fresh array containing the current parameter values
 double getDefaultValue(int n)
           
 double getLowerLimit(int n)
           
 int getNumParameters()
           
 double getParameter(int n)
           
protected  double getRandomParameterValue(int parameter)
           
 double getUpperLimit(int n)
           
protected  void randomiseParameters()
           
 void setParameter(double param, int n)
           
protected  void setParameterizedBase(Parameterized base)
          Set's the base parameterized object...
 void setParameterSE(double paramSE, int n)
           
 
Methods inherited from class pal.misc.PalObjectListener.EventGenerator
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Parameterized.ParameterizedUser

protected Parameterized.ParameterizedUser(Parameterized base)

Parameterized.ParameterizedUser

protected Parameterized.ParameterizedUser()
Sub class should call setParameterizedBase() at some point if using this constructor... otherwise many explosions and the flashing of lights.

Method Detail

setParameterizedBase

protected void setParameterizedBase(Parameterized base)
Set's the base parameterized object...


getNumParameters

public final int getNumParameters()

setParameter

public final void setParameter(double param,
                               int n)

getRandomParameterValue

protected double getRandomParameterValue(int parameter)

randomiseParameters

protected void randomiseParameters()

getParameter

public final double getParameter(int n)

setParameterSE

public final void setParameterSE(double paramSE,
                                 int n)

getLowerLimit

public final double getLowerLimit(int n)

getUpperLimit

public final double getUpperLimit(int n)

getDefaultValue

public final double getDefaultValue(int n)

getAllParameters

public final double[] getAllParameters()
Obtain a fresh array containing the current parameter values

Returns:
a newly created double array of the parameter values