net.maizegenetics.taxa.tree.Parameterized Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of tassel6 Show documentation
Show all versions of tassel6 Show documentation
TASSEL 6 is a software package to evaluate traits association. Feature Tables are at the heart of the package where, a feature is a range of positions or a single position. Row in the that table are taxon.
// Parameterized.java
//
// (c) 1999-2001 PAL Development Core Team
//
// This package may be distributed under the
// terms of the Lesser GNU General Public License (LGPL)
package net.maizegenetics.taxa.tree;
/**
* interface for class with (optimizable) parameters
*
* @version $Id: Parameterized.java,v 1.1 2007/01/12 03:26:18 tcasstevens Exp $
*
* @author Korbinian Strimmer
*/
public interface Parameterized
{
/**
* get number of parameters
*
* @return number of parameters
*/
int getNumParameters();
/**
* set model parameter
*
* @param param parameter value
* @param n parameter number
*/
void setParameter(double param, int n);
/**
* get model parameter
*
* @param n parameter number
*
* @return parameter value
*/
double getParameter(int n);
/**
* set standard errors for model parameter
*
* @param paramSE standard error of parameter value
* @param n parameter number
*/
void setParameterSE(double paramSE, int n);
/**
* get lower parameter limit
*
* @param n parameter number
*
* @return lower bound
*/
double getLowerLimit(int n);
/**
* get upper parameter limit
*
* @param n parameter number
*
* @return upper bound
*/
double getUpperLimit(int n);
/**
* get default value of parameter
*
* @param n parameter number
*
* @return default value
*/
double getDefaultValue(int n);
// ============================================================================
/**
* A Utility class for using as the superclass to subclasses which work by adding functionality to
* a general Parameterized object (the base Parameterized object)
*/
abstract public static class ParameterizedUser //extends PalObjectListener.EventGenerator
{
private Parameterized base_;
protected ParameterizedUser(Parameterized base) {
this.base_ = base;
}
/**
* Sub class should call setParameterizedBase() at some point if using this constructor... otherwise many explosions and the flashing of lights.
*/
protected ParameterizedUser() {}
/**
* Set's the base parameterized object...
*/
protected void setParameterizedBase(Parameterized base) {
this.base_ = base;
}
public int getNumParameters() { return base_.getNumParameters(); }
public void setParameter(double param, int n) {
base_.setParameter(param,n);
//fireParametersChangedEvent();
}
protected double getRandomParameterValue(int parameter) {
double min = base_.getLowerLimit(parameter);
double max = base_.getUpperLimit(parameter);
return Math.random()*(max-min)+min;
}
protected void randomiseParameters() {
final int numberParameters = base_.getNumParameters();
for(int i = 0 ; i < numberParameters ; i++) {
base_.setParameter(getRandomParameterValue(i),i);
}
}
public double getParameter(int n) { return base_.getParameter(n); }
public void setParameterSE(double paramSE, int n) { base_.setParameterSE(paramSE,n); }
public double getLowerLimit(int n) { return base_.getLowerLimit(n); }
public double getUpperLimit(int n) { return base_.getUpperLimit(n); }
public double getDefaultValue(int n) { return base_.getDefaultValue(n); }
}
/**
* A Utility class for using as the superclass to subclasses which are based on double arrays
*/
abstract public static class ParameterizedBase //extends PalObjectListener.EventGenerator
{
private double[] parameters_;
private double[] lowerLimits_;
private double[] upperLimits_;
private double[] defaultValues_;
private double[] parametersSE_;
/**
* Builds a parameterized objects around a set of double arrays
* @note uses the actual passed objects, so subclasses can maintain references
* to the arrays and their values will be refected in the parameterized interface
*/
protected ParameterizedBase(
double[] parameters,
double[] lowerLimits,
double[] upperLimits,
double[] defaultValues
) {
setSource(parameters,lowerLimits,upperLimits,defaultValues);
}
/**
* Builds a parameterized objects around a set of double arrays
* @note uses the actual passed objects, so subclasses can maintain references
* to the arrays and their values will be refected in the parameterized interface
*/
protected ParameterizedBase(
double[] parameters,
double[] lowerLimits,
double[] upperLimits,
double[] defaultValues,
double[] parametersSE
) {
setSource(parameters,lowerLimits,upperLimits,defaultValues, parametersSE);
}
/**
* Builds a parameterized objects around a set of double arrays. The user needs
* to call setSource() at some point to correctly set things up
* @note uses the actual passed objects, so subclasses can maintain references
* to the arrays and their values will be refected in the parameterized interface
*/
protected ParameterizedBase() { }
/**
* Set's the base arrays...
* @throws IllegalArgumentException if arrays are not the same size
*/
protected void setSource(
double[] parameters,
double[] lowerLimits,
double[] upperLimits,
double[] defaultValues
) {
setSource(parameters,lowerLimits,upperLimits,defaultValues,new double[parameters.length]);
}
/**
* Set's the base arrays...
* @throws IllegalArgumentException if arrays are not the same size
*/
protected void setSource(
double[] parameters,
double[] lowerLimits,
double[] upperLimits,
double[] defaultValues,
double[] parametersSE
) {
this.parameters_ = parameters;
this.lowerLimits_ = lowerLimits;
this.upperLimits_ = upperLimits;
this.defaultValues_ = defaultValues;
this.parametersSE_ = parametersSE;
int length = parameters_.length;
if(lowerLimits.length!=length) { sizeError(); }
if(upperLimits.length!=length) { sizeError(); }
if(defaultValues.length!=length) { sizeError(); }
if(parametersSE.length!=length) { sizeError(); }
}
private final void sizeError() {
throw new IllegalArgumentException("All arrays do not match in size");
}
public int getNumParameters() { return parameters_.length; }
public void setParameter(double param, int n) {
this.parameters_[n] = param;
//fireParametersChangedEvent();
}
public double getParameter(int n) { return this.parameters_[n]; }
public void setParameterSE(double paramSE, int n) { this.parametersSE_[n] = paramSE; }
public double getLowerLimit(int n) { return lowerLimits_[n]; }
public double getUpperLimit(int n) { return upperLimits_[n]; }
public double getDefaultValue(int n) { return defaultValues_[n]; }
protected double[] getParametersSE() { return parametersSE_; }
}
/**
* NullParameterized Object
* Can be used by subclasses to implement parameterized without actually having paramters
*/
abstract public static class Null implements Parameterized {
protected Null() { }
public int getNumParameters() { return 0; }
private double error() { throw new RuntimeException("Assertion error : should not be called as no parameters!"); }
public void setParameter(double param, int n) { error(); }
public double getParameter(int n) { return error(); }
public void setParameterSE(double paramSE, int n) { error(); }
public double getLowerLimit(int n) { return error(); }
public double getUpperLimit(int n) { return error(); }
public double getDefaultValue(int n) { return error(); }
}
// ============================================================================
// ============ Utils ==========================================================
public static final class Utils {
/**
* @return the current paramters of source in a double array
*/
public static final double[] getParameters(Parameterized source) {
double[] params = new double[source.getNumParameters()];
for(int i = 0 ; i < params.length ; i++) {
params[i] = source.getParameter(i);
}
return params;
}
/**
* Create a wrapper around a set of double arrays to create a parameterized object
* (changes to parameterized object change given arrays)
*/
public static final Parameterized createParametizedWrapper(double[] parameters, double[] lowerLimits, double[] upperLimits, double[] defaultValues) {
return new ParameterizedWrapper(parameters,lowerLimits,upperLimits,defaultValues);
}
/**
* Create a wrapper around a set of double arrays to create a parameterized object
* (changes to parameterized object change given arrays)
*/
public static final Parameterized createParametizedWrapper(double[] parameters, double[] lowerLimits, double[] upperLimits, double[] defaultValues, double[] parametersSE) {
return new ParameterizedWrapper(parameters,lowerLimits,upperLimits,defaultValues, parametersSE);
}
/**
* Combine multiple parameterized objects into one
*/
public static final Parameterized combine(Parameterized[] bases) {
return new MultiParameterized(bases);
}
/**
* Combine multiple parameterized objects into one
*/
public static final Parameterized combine(Parameterized baseOne, Parameterized baseTwo) {
return new MultiParameterized(new Parameterized[] {baseOne, baseTwo});
}
// ============================================================================
// ============ ParameterizedWrapper ============================================
private static final class ParameterizedWrapper extends ParameterizedBase implements Parameterized {
public ParameterizedWrapper(double[] parameters, double[] lowerLimits, double[] upperLimits, double[] defaultValues) {
super(parameters,lowerLimits,upperLimits,defaultValues);
}
public ParameterizedWrapper(double[] parameters, double[] lowerLimits, double[] upperLimits, double[] defaultValues, double[] parametersSE) {
super(parameters,lowerLimits,upperLimits,defaultValues, parametersSE);
}
}
}
}