Moved non-ea stuff back to core.main (#19)

src/core/de.evoal.approximative.density/src/main/java/de/evoal/approximative/density/ea/fitness/DensityBasedFitness.java

@@ -114,7 +114,7 @@ public abstract class DensityBasedFitness extends OptimisationFunctionDecorator
             final double predictedValue = current[i];
             final double probability = probabilityCalculator.apply(sourceData, targetData, candidate, predictedValue);
 
-            fitness[i] = current[i] * Math.pow(probability, rootExponent) + (1 - probability) * 1.0 / Math.pow(probability, exponent);
+            fitness[i] = current[i] * Math.pow(probability, rootExponent) + (1 - probability) / Math.pow(probability, exponent);
         }
 
         return fitness;

src/core/de.evoal.approximative.density/src/main/java/de/evoal/approximative/density/model/CustomKernelDensity.java

@@ -12,7 +12,7 @@ public class CustomKernelDensity {
      * The kernel -- a symmetric but not necessarily positive function that
      * integrates to one. Here we just Gaussian density function.
      */
-    private GaussianDistribution gaussian;
+    private final GaussianDistribution gaussian;
 
     /**
      * Constructor. The bandwidth of kernel will be estimated by the rule of thumb.

src/core/de.evoal.approximative.density/src/main/java/de/evoal/approximative/density/model/DensityData.java

@@ -4,7 +4,7 @@ import de.evoal.surrogate.api.configuration.PartialFunctionConfiguration;
 
 public interface DensityData {
 
-    public void attachTo(final PartialFunctionConfiguration configuration, final String propertyName);
+    void attachTo(final PartialFunctionConfiguration configuration, final String propertyName);
 
-    public double probability(final double value);
+    double probability(final double value);
 }

src/core/de.evoal.core.arff/src/main/java/de/evoal/core/arff/io/ArffPropertiesReader.java

@@ -21,7 +21,7 @@ import java.util.Arrays;
 @Dependent
 @Named("arff-reader")
 public class ArffPropertiesReader implements PropertiesReader {
-    private static interface TriFunction<S,T,U,R> {
+    private interface TriFunction<S,T,U,R> {
         /**
          * Applies this function to the given arguments.
          *

src/core/de.evoal.core.arff/src/main/java/de/evoal/core/arff/main/ConvertArff.java

@@ -52,8 +52,8 @@ public class ConvertArff implements MainClass {
         final PropertiesSpecification specification = readSpecification();
 
         try (final PropertiesReader reader = PropertiesIOFactory.reader(arffFile, specification);
-             final PropertiesWriter writer = PropertiesIOFactory.writer(jsonFile, specification);
-            ) {
+             final PropertiesWriter writer = PropertiesIOFactory.writer(jsonFile, specification)
+        ) {
 
             while(reader.hasNext()) {
                 writer.add(reader.next());

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/api/cdi/Fitness.java

@@ -15,5 +15,5 @@ public @interface Fitness {
     /**
      * @return Name of the fitness calculator.
      */
-    public String value();
+    String value();
 }

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/api/codec/CustomCodec.java

@@ -18,5 +18,5 @@ public interface CustomCodec<G extends Gene<?, G>> extends Codec<Properties, G>
      * @param p The individual to code.
      * @return The generated (non-null) genotype.
      */
-    public Genotype<G> encode(final Properties p);
+    Genotype<G> encode(final Properties p);
 }

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/api/initial/InitialPopulation.java

@@ -8,5 +8,5 @@ import io.jenetics.engine.EvolutionStream;
 public interface InitialPopulation<G extends Gene<?, G>, C extends Comparable<C>> {
     InitialPopulation init(final Instance initialization);
 
-    public EvolutionStream<G, C> create(final Engine<G, C> engine);
+    EvolutionStream<G, C> create(final Engine<G, C> engine);
 }

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/AltererFactory.java

@@ -3,12 +3,13 @@ package de.evoal.core.ea.main.alterer;
 import java.util.function.BiFunction;
 
 import de.evoal.core.api.optimisation.OptimisationValue;
+import de.evoal.core.ea.api.codec.CustomCodec;
 import de.evoal.core.ea.main.alterer.internal.MeanCorrelationAlterer;
 import de.evoal.core.ea.main.alterer.mutator.SingleBitFlipMutator;
 import de.evoal.core.ea.main.alterer.crossover.*;
 import de.evoal.core.ea.main.alterer.mutator.SingleBitFlipCorrelationMutator;
 import de.evoal.core.ea.main.alterer.mutator.SwapCorrelationMutator;
-import de.evoal.core.ea.api.correlations.Correlations;
+import de.evoal.core.api.correlations.Correlations;
 import de.evoal.languages.model.instance.Instance;
 import de.evoal.core.api.utils.LanguageHelper;
 import io.jenetics.*;
@@ -28,6 +29,9 @@ public class AltererFactory {
 	@Inject
 	private BiFunction<Double, Double, Alterer> factory;
 
+	@Inject
+	private CustomCodec codec;
+
 	/**
 	 * Creates an alterer based on the heuristic configuration.
 	 *
@@ -79,7 +83,7 @@ public class AltererFactory {
 		final Double crossoverProbability = LanguageHelper.lookup(config, "crossover-probability");
 		final Double swapProbability = LanguageHelper.lookup(config,"swap-probability");
 		
-		return new UniformCorrelationCrossover(crossoverProbability, swapProbability, correlations);
+		return new UniformCorrelationCrossover(crossoverProbability, swapProbability, correlations, codec);
 	}
 
 	private <G extends Gene<?, G>> Alterer<G, OptimisationValue> createBitFlipMutator (final Instance config) {
@@ -92,7 +96,7 @@ public class AltererFactory {
 		final Double probability = LanguageHelper.lookup(config, "probability");
 		final Double threshold = LanguageHelper.lookup(config, "threshold");
 
-		return new SingleBitFlipCorrelationMutator(probability, threshold, correlations);
+		return new SingleBitFlipCorrelationMutator(probability, threshold, correlations, codec);
 	}
 
 	private <G extends Gene<?, G>> Alterer<G, OptimisationValue> createSwapMutator (final Instance config) {
@@ -105,7 +109,7 @@ public class AltererFactory {
 		final Double probability = LanguageHelper.lookup(config, "probability");
 		final Double threshold = LanguageHelper.lookup(config, "threshold");
 
-		return new SwapCorrelationMutator<>(probability, threshold, correlations);
+		return new SwapCorrelationMutator<>(probability, threshold, correlations, codec);
 	}
 
 	private <G extends Gene<?, G>> Alterer<G, OptimisationValue> createSinglePointCrossover(final Instance config) {
@@ -117,7 +121,7 @@ public class AltererFactory {
 	private <G extends Gene<?, G>> Alterer<G, OptimisationValue> createCorrelationSinglePointCrossover(final Instance config) {
 		final Double probability = LanguageHelper.lookup(config, "probability");
 
-		return new SinglePointCorrelationCrossover(probability, correlations);
+		return new SinglePointCorrelationCrossover(probability, correlations, codec);
 	}
 
 	private <G extends Gene<?, G>> Alterer<G, OptimisationValue> createPartiallyMatchedAlterer(final Instance config) {
@@ -129,7 +133,7 @@ public class AltererFactory {
 	private <G extends Gene<?, G>> Alterer<G, OptimisationValue> createCorrelationPartiallyMatchedAlterer(final Instance config) {
 		final Double probability = LanguageHelper.lookup(config, "probability");
 
-		return (Alterer<G, OptimisationValue>) new PartiallyMatchedCorrelationCrossover<G, OptimisationValue>(probability, correlations);
+		return (Alterer<G, OptimisationValue>) new PartiallyMatchedCorrelationCrossover<G, OptimisationValue>(probability, correlations, codec);
 	}
 
 	private <G extends Gene<?, G>> Alterer<G, OptimisationValue> createMultiPointCrossover(final Instance config) {
@@ -143,7 +147,7 @@ public class AltererFactory {
 		final Double probability = LanguageHelper.lookup(config, "probability");
 		final Integer count = LanguageHelper.lookup(config, "count");
 
-		return new MultiPointCorrelationCrossover<>(probability, count, correlations);
+		return new MultiPointCorrelationCrossover<>(probability, count, correlations, codec);
 	}
 
 	private <G extends Gene<?, G>> Alterer<G, OptimisationValue> createMeanAlterer(final Instance config) {
@@ -155,7 +159,7 @@ public class AltererFactory {
 	private <G extends NumericGene<?, G> & Mean<G>> Alterer<G, OptimisationValue> createCorrelationMeanAlterer(final Instance config) {
 		final Double probability = LanguageHelper.lookup(config, "probability");
 
-		return  (Alterer<G, OptimisationValue>) new MeanCorrelationAlterer<G, OptimisationValue>(probability, correlations);
+		return new MeanCorrelationAlterer<G, OptimisationValue>(probability, correlations, codec);
 	}
 
 	private <G extends Gene<?, G>> Alterer<G, OptimisationValue> createLineCrossover(final Instance config) {
@@ -169,7 +173,7 @@ public class AltererFactory {
 		final Double probability = LanguageHelper.lookup(config, "probability");
 		final Double position = LanguageHelper.lookup(config, "position");
 
-		return new LineCorrelationCrossover(probability, position, correlations);
+		return new LineCorrelationCrossover(probability, position, correlations, codec);
 	}
 
 	private <G extends Gene<?, G>> Alterer<G, OptimisationValue> createIntermediateCrossover(final Instance config) {

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/CorrelationCrossover.java

 package de.evoal.core.ea.main.alterer.crossover;
 
-import de.evoal.core.ea.api.correlations.Correlation;
-import de.evoal.core.ea.api.correlations.Correlations;
+import de.evoal.core.api.correlations.Correlation;
+import de.evoal.core.api.correlations.Correlations;
+import de.evoal.core.ea.api.codec.CustomCodec;
 import io.jenetics.*;
 import io.jenetics.util.MSeq;
 import io.jenetics.util.RandomRegistry;
@@ -17,7 +18,9 @@ public abstract class CorrelationCrossover<
         >
         extends Recombinator<G, C> {
 
-    private final Correlations<G> correlations;
+    private final Correlations correlations;
+
+    private final CustomCodec<G> codec;
 
     /**
      * Constructs an alterer with a given recombination probability.
@@ -26,10 +29,11 @@ public abstract class CorrelationCrossover<
      * @throws IllegalArgumentException if the {@code probability} is not in the
      *          valid range of {@code [0, 1]}
      */
-    protected CorrelationCrossover(final double probability, final Correlations correlations) {
+    protected CorrelationCrossover(final double probability, final Correlations correlations, final CustomCodec<G> codec) {
         super(probability, 2);
         
         this.correlations = correlations;
+        this.codec = codec;
     }
 
     @Override
@@ -48,7 +52,7 @@ public abstract class CorrelationCrossover<
 
         //Choosing the Chromosome index for crossover.
         final int chIndex = random.nextInt(min(gt1.length(), gt2.length()));
-        final int rootIndex = correlations.findCorrelationRoot(gt1, chIndex);
+        final int rootIndex = correlations.findCorrelationRoot(codec.decode(gt1), chIndex);
 
         final var c1 = MSeq.of(gt1);
         final var c2 = MSeq.of(gt2);
@@ -79,7 +83,7 @@ public abstract class CorrelationCrossover<
         c1.set(chIndex, c1.get(chIndex).newInstance(genes1.toISeq()));
         c2.set(chIndex, c2.get(chIndex).newInstance(genes2.toISeq()));
 
-        for(final Correlation correlation : correlations.find(gt1, chIndex)) {
+        for(final Correlation correlation : correlations.find(codec.decode(gt1), chIndex)) {
             final int targetIndex = correlation.getChromosomeTwo();
 
             correlationOrder += crossover(gt1, gt2, c1, c2, targetIndex, newCrossoverMemento().apply(memento, correlation)); // sum up correlations

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/CorrelationCrossoverMemento.java

 package de.evoal.core.ea.main.alterer.crossover;
 
-import de.evoal.core.ea.api.correlations.Correlation;
+import de.evoal.core.api.correlations.Correlation;
 
 public interface CorrelationCrossoverMemento<T extends CorrelationCrossoverMemento<T>> {
 
     /**
      * Applies the given memento with according to the correlation to this memento.
      */
-    public T apply(final T memento, final Correlation correlation);
+    T apply(final T memento, final Correlation correlation);
 }

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/LineCorrelationCrossover.java

 package de.evoal.core.ea.main.alterer.crossover;
 
 import de.evoal.core.api.utils.Requirements;
-import de.evoal.core.ea.api.correlations.Correlations;
+import de.evoal.core.api.correlations.Correlations;
+import de.evoal.core.ea.api.codec.CustomCodec;
 import io.jenetics.NumericGene;
 import io.jenetics.util.MSeq;
 
@@ -27,8 +28,8 @@ public class LineCorrelationCrossover<
      * @throws IllegalArgumentException if the {@code probability} is not in the
      *         valid range of {@code [0, 1]} or if {@code p} is smaller then zero
      */
-    public LineCorrelationCrossover(final double probability, final double p, final Correlations correlations) {
-        super(probability, correlations);
+    public LineCorrelationCrossover(final double probability, final double p, final Correlations correlations, final CustomCodec<G> codec) {
+        super(probability, correlations, codec);
         _p = Requirements.nonNegative(p);
     }
 
@@ -42,8 +43,8 @@ public class LineCorrelationCrossover<
      * @throws IllegalArgumentException if the {@code probability} is not in the
      *         valid range of {@code [0, 1]}
      */
-    public LineCorrelationCrossover(final double probability, final Correlations correlations) {
-        this(probability, 0, correlations);
+    public LineCorrelationCrossover(final double probability, final Correlations correlations, final CustomCodec<G> codec) {
+        this(probability, 0, correlations, codec);
     }
 
     @Override

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/LineCorrelationCrossoverMemento.java

 package de.evoal.core.ea.main.alterer.crossover;
 
-import de.evoal.core.ea.api.correlations.Correlation;
+import de.evoal.core.api.correlations.Correlation;
 import io.jenetics.util.RandomRegistry;
 import lombok.Data;
 

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/MultiPointCorrelationCrossover.java

 package de.evoal.core.ea.main.alterer.crossover;
 
-import de.evoal.core.ea.api.correlations.Correlations;
+import de.evoal.core.api.correlations.Correlations;
+import de.evoal.core.ea.api.codec.CustomCodec;
 import io.jenetics.Gene;
 import io.jenetics.util.MSeq;
 
@@ -22,8 +23,8 @@ public class MultiPointCorrelationCrossover<
      * @throws IllegalArgumentException if the {@code probability} is not in the
      *         valid range of {@code [0, 1]} or {@code n &lt; 1}.
      */
-    public MultiPointCorrelationCrossover(final double probability, final int n, final Correlations correlations) {
-        super(probability, correlations);
+    public MultiPointCorrelationCrossover(final double probability, final int n, final Correlations correlations, final CustomCodec<G> codec) {
+        super(probability, correlations, codec);
         if (n < 1) {
             throw new IllegalArgumentException(format(
                     "n must be at least 1 but was %d.", n
@@ -39,8 +40,8 @@ public class MultiPointCorrelationCrossover<
      * @throws IllegalArgumentException if the {@code probability} is not in the
      *         valid range of {@code [0, 1]}.
      */
-    public MultiPointCorrelationCrossover(final double probability, final Correlations correlations) {
-        this(probability, 2, correlations);
+    public MultiPointCorrelationCrossover(final double probability, final Correlations correlations, final CustomCodec<G> codec) {
+        this(probability, 2, correlations, codec);
     }
 
     /**
@@ -50,16 +51,16 @@ public class MultiPointCorrelationCrossover<
      * @param n the number of crossover points.
      * @throws IllegalArgumentException if {@code n &lt; 1}.
      */
-    public MultiPointCorrelationCrossover(final int n, final Correlations correlations) {
-        this(0.05, n, correlations);
+    public MultiPointCorrelationCrossover(final int n, final Correlations correlations, final CustomCodec<G> codec) {
+        this(0.05, n, correlations, codec);
     }
 
     /**
      * Create a new crossover instance with two crossover points and crossover
      * probability 0.05.
      */
-    public MultiPointCorrelationCrossover(final Correlations correlations) {
-        this(0.05, 2, correlations);
+    public MultiPointCorrelationCrossover(final Correlations correlations, final CustomCodec<G> codec) {
+        this(0.05, 2, correlations, codec);
     }
 
     /**

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/MultiPointCorrelationCrossoverMemento.java

 package de.evoal.core.ea.main.alterer.crossover;
 
-import de.evoal.core.ea.api.correlations.Correlation;
+import de.evoal.core.api.correlations.Correlation;
 import io.jenetics.internal.math.Subset;
 import io.jenetics.util.RandomRegistry;
 

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/PartiallyMatchedCorrelationCrossover.java

 package de.evoal.core.ea.main.alterer.crossover;
 
-import de.evoal.core.ea.api.correlations.Correlations;
+import de.evoal.core.api.correlations.Correlations;
+import de.evoal.core.ea.api.codec.CustomCodec;
 import io.jenetics.EnumGene;
 import io.jenetics.util.MSeq;
 
@@ -12,8 +13,8 @@ public class PartiallyMatchedCorrelationCrossover<
 > extends CorrelationCrossover<EnumGene<T>, C, PartiallyMatchedCorrelationCrossoverMemento>
 {
 
-    public PartiallyMatchedCorrelationCrossover(final double probability, final Correlations correlations) {
-        super(probability, correlations);
+    public PartiallyMatchedCorrelationCrossover(final double probability, final Correlations correlations, final CustomCodec<EnumGene<T>> codec) {
+        super(probability, correlations, codec);
     }
 
     @Override

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/PartiallyMatchedCorrelationCrossoverMemento.java

 package de.evoal.core.ea.main.alterer.crossover;
 
-import de.evoal.core.ea.api.correlations.Correlation;
+import de.evoal.core.api.correlations.Correlation;
 import io.jenetics.internal.math.Subset;
 import io.jenetics.util.RandomRegistry;
 

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/SinglePointCorrelationCrossover.java

 package de.evoal.core.ea.main.alterer.crossover;
 
-import de.evoal.core.ea.api.correlations.Correlations;
+import de.evoal.core.api.correlations.Correlations;
+import de.evoal.core.ea.api.codec.CustomCodec;
 import io.jenetics.Gene;
 import io.jenetics.util.MSeq;
 
@@ -20,8 +21,8 @@ public class SinglePointCorrelationCrossover<
      * @throws IllegalArgumentException if the {@code probability} is not in the
      *         valid range of {@code [0, 1]}.
      */
-    public SinglePointCorrelationCrossover(final double probability, final Correlations correlations) {
-        super(probability, 1, correlations);
+    public SinglePointCorrelationCrossover(final double probability, final Correlations correlations, final CustomCodec<G> codec) {
+        super(probability, 1, correlations, codec);
     }
 
     @Override

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/SinglePointCorrelationCrossoverMemento.java

 package de.evoal.core.ea.main.alterer.crossover;
 
-import de.evoal.core.ea.api.correlations.Correlation;
+import de.evoal.core.api.correlations.Correlation;
 import io.jenetics.util.RandomRegistry;
 import lombok.Getter;
 import lombok.Setter;

src/core/de.evoal.core.ea/src/main/java/de/evoal/core/ea/main/alterer/crossover/UniformCorrelationCrossover.java

 package de.evoal.core.ea.main.alterer.crossover;
 
 import de.evoal.core.api.utils.Requirements;
-import de.evoal.core.ea.api.correlations.Correlations;
+import de.evoal.core.api.correlations.Correlations;
+import de.evoal.core.ea.api.codec.CustomCodec;
 import io.jenetics.Gene;
 import io.jenetics.util.MSeq;
 
@@ -28,9 +29,10 @@ public class UniformCorrelationCrossover<
     public UniformCorrelationCrossover(
             final double crossoverProbability,
             final double swapProbability,
-            final Correlations correlations
+            final Correlations correlations,
+            final CustomCodec<G> codec
     ) {
-        super(crossoverProbability, correlations);
+        super(crossoverProbability, correlations, codec);
 
         Requirements.requireProbability(swapProbability);
         _swapProbability = swapProbability;