AbstractGeneticAlgorithm (Morphokinetics)

java.lang.Object
- geneticAlgorithm.AbstractGeneticAlgorithm

All Implemented Interfaces:

IGeneticAlgorithm, IProgressable

Direct Known Subclasses:

GeneticAlgorithm, GeneticAlgorithmDcmaEs
```
public abstract class AbstractGeneticAlgorithm
extends java.lang.Object
implements IGeneticAlgorithm
```
Author:

N. Ferrando

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

(package private) class AbstractGeneticAlgorithm.Updater
Inner class responsible to update the interface.

Nested Classes
Modifier and Type	Class and Description
`(package private) class`	`AbstractGeneticAlgorithm.Updater` Inner class responsible to update the interface.

Field Summary

Fields
Modifier and Type	Field and Description
`private int`	`currentIteration`
`private double`	`depositionRatePerSite`
`private int`	`dimensions` Number of different genes.
`private BasicEvaluator`	`evaluator`
`private boolean`	`expDistribution`
`private double`	`expectedSimulationTime`
`private IgaProgressFrame`	`graphics`
`private IInitialisator`	`initialisation`
`private double`	`islandDensity`
`private AbstractPsdEvaluator`	`mainEvaluator`
`private MainInterface`	`mainInterface`
`private double`	`maxValueGene`
`private double`	`minValueGene`
`private IMutation`	`mutation`
`private int`	`offspringSize`
`private java.util.List<IEvaluation>`	`otherEvaluators`
`private Parser`	`parser`
`private Population`	`population`
`private int`	`populationReplacements`
`private int`	`populationSize`
`private IRecombination`	`recombination`
`private IReinsertion`	`reinsertion`
`private RestrictionOperator`	`restriction`
`private ISelection`	`selection`
`private AbstractSimulation`	`simulation`
`private double`	`stopError` The stop error.
`private int`	`totalIterations`
`private AbstractGeneticAlgorithm.Updater`	`updater`

Constructor Summary

Constructors
Constructor and Description
`AbstractGeneticAlgorithm(Parser parser, ISelection selection, IMutation mutation, IRecombination recombination, IReinsertion reinsertion)`

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`private java.util.List<IEvaluation>`	`addNoMoreEvaluators()`
`protected void`	`addToGraphics()`
`protected void`	`clearGraphics()`
`private void`	`configureSiKmc()`
`private AbstractPsdEvaluator`	`createMainEvaluator()` Evaluator evaluation
`boolean`	`exitCondition()` Break if fitness is good enough or condition exceeds 1e14.
`Individual`	`getBestIndividual()`
`int`	`getCurrentIteration()`
`Individual`	`getIndividual(int pos)`
`IKmc`	`getKmc()`
`AbstractPsdEvaluator`	`getMainEvaluator()`
`float[]`	`getProgressPercent()`
`protected double`	`getStopError()`
`int`	`getTotalIterations()`
`IGeneticAlgorithm`	`initialise()`
`protected boolean`	`isDtooLarge()`
`void`	`iterate()`
`void`	`iterateOneStep()`
`protected void`	`scaleIndividualRates(Population population)` Deprecated.
`void`	`setExpectedSimulationTime(double expectedSimulationTime)`
`AbstractGeneticAlgorithm`	`setExperimentalPsd(float[][] experimentalPsd)`
`void`	`setGraphics(IgaProgressFrame graphics)`
`void`	`setHierarchy(double[] rates)`
`void`	`setMainInterface(MainInterface mainInterface)` Sets the main interface, starts a thread which will be responsible to update it and assigns the main interface to the evaluator (to be able to also update it with the current surface and PSD).

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface geneticAlgorithm.IGeneticAlgorithm
reevaluate

Field Detail

parser
```
private Parser parser
```

population
```
private Population population
```

evaluator
```
private BasicEvaluator evaluator
```

mainEvaluator

private AbstractPsdEvaluator mainEvaluator

otherEvaluators

private java.util.List<IEvaluation> otherEvaluators

initialisation
```
private IInitialisator initialisation
```

selection
```
private ISelection selection
```

mutation
```
private IMutation mutation
```

recombination
```
private IRecombination recombination
```

reinsertion
```
private IReinsertion reinsertion
```

restriction

private RestrictionOperator restriction

populationSize
```
private final int populationSize
```

offspringSize
```
private final int offspringSize
```

populationReplacements

private final int populationReplacements

expectedSimulationTime
```
private double expectedSimulationTime
```

dimensions
```
private final int dimensions
```
Number of different genes.

minValueGene
```
private final double minValueGene
```

maxValueGene
```
private final double maxValueGene
```

expDistribution
```
private final boolean expDistribution
```

currentIteration
```
private int currentIteration
```

totalIterations
```
private int totalIterations
```

mainInterface
```
private MainInterface mainInterface
```

simulation
```
private AbstractSimulation simulation
```

depositionRatePerSite
```
private double depositionRatePerSite
```

islandDensity
```
private double islandDensity
```

updater

private AbstractGeneticAlgorithm.Updater updater

stopError
```
private final double stopError
```
The stop error. If the current error is below this number, stop.

graphics
```
private IgaProgressFrame graphics
```

Constructor Detail

AbstractGeneticAlgorithm

public AbstractGeneticAlgorithm(Parser parser,
                                ISelection selection,
                                IMutation mutation,
                                IRecombination recombination,
                                IReinsertion reinsertion)

Method Detail
- initialise
```
public IGeneticAlgorithm initialise()
```
  Specified by:
  
  initialise in interface IGeneticAlgorithm
- iterateOneStep
```
public void iterateOneStep()
```
  Specified by:
  
  iterateOneStep in interface IGeneticAlgorithm
- createMainEvaluator
```
private AbstractPsdEvaluator createMainEvaluator()
```
  Evaluator evaluation
  
  Returns:
  
  threaded or basic evaluator
- configureSiKmc
```
private void configureSiKmc()
```
- iterate
```
public void iterate()
```
  Specified by:
  
  iterate in interface IGeneticAlgorithm
- isDtooLarge
```
protected boolean isDtooLarge()
```
- exitCondition
```
public boolean exitCondition()
```
  Break if fitness is good enough or condition exceeds 1e14. Better termination methods are advisable.
  
  Specified by:
  
  exitCondition in interface IGeneticAlgorithm
  
  Returns:
  
  exit search or not
- setExpectedSimulationTime
```
public void setExpectedSimulationTime(double expectedSimulationTime)
```
- getMainEvaluator
```
public AbstractPsdEvaluator getMainEvaluator()
```
- setExperimentalPsd
```
public AbstractGeneticAlgorithm setExperimentalPsd(float[][] experimentalPsd)
```
- getKmc
```
public IKmc getKmc()
```
- getCurrentIteration
```
public int getCurrentIteration()
```
  Specified by:
  
  getCurrentIteration in interface IGeneticAlgorithm
- getTotalIterations
```
public int getTotalIterations()
```
  Specified by:
  
  getTotalIterations in interface IGeneticAlgorithm
- getIndividual
```
public Individual getIndividual(int pos)
```
  Specified by:
  
  getIndividual in interface IGeneticAlgorithm
- getBestIndividual
```
public Individual getBestIndividual()
```
  Specified by:
  
  getBestIndividual in interface IGeneticAlgorithm
- getProgressPercent
```
public float[] getProgressPercent()
```
  Specified by:
  
  getProgressPercent in interface IProgressable
- addNoMoreEvaluators
```
private java.util.List<IEvaluation> addNoMoreEvaluators()
```
- setMainInterface
```
public void setMainInterface(MainInterface mainInterface)
```
  Sets the main interface, starts a thread which will be responsible to update it and assigns the main interface to the evaluator (to be able to also update it with the current surface and PSD).
  
  Parameters:
  
  mainInterface -
- setGraphics
```
public void setGraphics(IgaProgressFrame graphics)
```
  Specified by:
  
  setGraphics in interface IGeneticAlgorithm
- addToGraphics
```
protected void addToGraphics()
```
- clearGraphics
```
protected void clearGraphics()
```
- setHierarchy
```
public void setHierarchy(double[] rates)
```
- getStopError
```
protected double getStopError()
```
- scaleIndividualRates
```
@Deprecated
protected void scaleIndividualRates(Population population)
```
  Deprecated.
  
  Scales genes (ratios) with respect to the expected simulation time. If expected simulation time is 0, no scaling is done
  
  Parameters:
  
  population - The population to be scaled.

Class AbstractGeneticAlgorithm

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface geneticAlgorithm.IGeneticAlgorithm

Field Detail

parser

population

evaluator

mainEvaluator

otherEvaluators

initialisation

selection

mutation

recombination

reinsertion

restriction

populationSize

offspringSize

populationReplacements

expectedSimulationTime

dimensions

minValueGene

maxValueGene

expDistribution

currentIteration

totalIterations

mainInterface

simulation

depositionRatePerSite

islandDensity

updater

stopError

graphics

Constructor Detail

AbstractGeneticAlgorithm

Method Detail

initialise

iterateOneStep

createMainEvaluator

configureSiKmc

iterate

isDtooLarge

exitCondition

setExpectedSimulationTime

getMainEvaluator

setExperimentalPsd

getKmc

getCurrentIteration

getTotalIterations

getIndividual

getBestIndividual

getProgressPercent

addNoMoreEvaluators

setMainInterface

setGraphics

addToGraphics

clearGraphics

setHierarchy

getStopError

scaleIndividualRates