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org.jaga.exampleApplications.proteinLocation
Class ProgressiveTestGroupSizeHook

java.lang.Object
  extended by org.jaga.hooks.SimpleGAHook
      extended by org.jaga.exampleApplications.proteinLocation.ProgressiveTestGroupSizeHook

public class ProgressiveTestGroupSizeHook
extends SimpleGAHook

TODO: Complete these comments.

Project: JAGA - Java API for Genetic Algorithms.

Company: University College London and JAGA.Org (http://www.jaga.org).

Copyright: (c) 2004 by G. Paperin.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, ONLY if you include a note of the original author(s) in any redistributed/modified copy.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA or see http://www.gnu.org/licenses/gpl.html

Version:
JAGA public release 1.0 beta
Author:
Greg Paperin (greg@jaga.org)

Field Summary
private  ProteinGroup allNegatives
           
private  int allNegativesIndex
           
private  ProteinGroup allPositives
           
private  int allPositivesIndex
           
private  double averagePatternLen
           
private  int averagePatternLenGen
           
private  boolean boosting
           
private  int boostStartTimeout
           
private  int boostStopTimeout
           
private  AnalysisHook cooperator
           
private  int lastSizeIncreaseGen
           
private  double mutationBoost
           
private  double mutProb
           
private  ProteinGroup testNegatives
           
private  ProteinGroup testPositives
           
private  int testSetSizeDelta
           
private  int timeToBoost
           
private  int timeToStopBoost
           
private  double triggerFitness
           
 
Constructor Summary
private ProgressiveTestGroupSizeHook()
           
  ProgressiveTestGroupSizeHook(ProteinGroup allPositives, ProteinGroup allNegatives, ProteinGroup testPositives, ProteinGroup testNegatives, int initialTestSetSize, int testSetSizeDelta, double triggerFitness, double mutationBoost, int boostStartTimeout, int boostStopTimeout, GAParameterSet params)
           
 
Method Summary
 void foundNewResult(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
           
 void generationChanged(SimpleGA caller, Population pop, int age, GAResult result, GAParameterSet params)
           
private  void printInfo()
           
 void setAnalysisHookForCooperation(AnalysisHook cooperator)
           
private  void startBoost(GAParameterSet params)
           
private  void stopBoost(GAParameterSet params)
           
 
Methods inherited from class org.jaga.hooks.SimpleGAHook
fitnessCalculated, initialisationDone, reproduced, selectedForReproduction, terminationConditionApplies
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

mutationBoost

private double mutationBoost

boostStartTimeout

private int boostStartTimeout

boostStopTimeout

private int boostStopTimeout

allPositives

private ProteinGroup allPositives

allNegatives

private ProteinGroup allNegatives

testPositives

private ProteinGroup testPositives

testNegatives

private ProteinGroup testNegatives

testSetSizeDelta

private int testSetSizeDelta

triggerFitness

private double triggerFitness

allPositivesIndex

private int allPositivesIndex

allNegativesIndex

private int allNegativesIndex

cooperator

private AnalysisHook cooperator

averagePatternLen

private double averagePatternLen

averagePatternLenGen

private int averagePatternLenGen

mutProb

private double mutProb

lastSizeIncreaseGen

private int lastSizeIncreaseGen

boosting

private boolean boosting

timeToBoost

private int timeToBoost

timeToStopBoost

private int timeToStopBoost
Constructor Detail

ProgressiveTestGroupSizeHook

private ProgressiveTestGroupSizeHook()

ProgressiveTestGroupSizeHook

public ProgressiveTestGroupSizeHook(ProteinGroup allPositives,
                                    ProteinGroup allNegatives,
                                    ProteinGroup testPositives,
                                    ProteinGroup testNegatives,
                                    int initialTestSetSize,
                                    int testSetSizeDelta,
                                    double triggerFitness,
                                    double mutationBoost,
                                    int boostStartTimeout,
                                    int boostStopTimeout,
                                    GAParameterSet params)
Method Detail

startBoost

private void startBoost(GAParameterSet params)

stopBoost

private void stopBoost(GAParameterSet params)

foundNewResult

public void foundNewResult(SimpleGA caller,
                           Population pop,
                           int age,
                           GAResult result,
                           GAParameterSet params)
Overrides:
foundNewResult in class SimpleGAHook

generationChanged

public void generationChanged(SimpleGA caller,
                              Population pop,
                              int age,
                              GAResult result,
                              GAParameterSet params)
Overrides:
generationChanged in class SimpleGAHook

setAnalysisHookForCooperation

public void setAnalysisHookForCooperation(AnalysisHook cooperator)

printInfo

private void printInfo()

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