Hide several elements from the UI

src/eva2/optimization/individuals/AbstractEAIndividual.java

@@ -275,7 +275,7 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
      *
      * @param opt The optimization problem that is to be solved.
      */
-    public void init(InterfaceOptimizationProblem opt) {
+    public void initialize(InterfaceOptimizationProblem opt) {
         initializationOperator.initialize(this, opt);
         this.mutationOperator.initialize(this, opt);
         this.crossoverOperator.init(this, opt);

src/eva2/optimization/individuals/ESIndividualDoubleData.java

@@ -105,9 +105,6 @@ public class ESIndividualDoubleData extends AbstractEAIndividual implements Inte
         }
     }
 
-/************************************************************************************
- * InterfaceDataTypeDouble methods
- */
     /**
      * This method allows you to request a certain amount of double data
      *
@@ -235,17 +232,14 @@ public class ESIndividualDoubleData extends AbstractEAIndividual implements Inte
         System.arraycopy(doubleData, 0, this.genotype, 0, doubleData.length);
     }
 
-/************************************************************************************
- * AbstractEAIndividual methods
- */
     /**
      * This method will allow a default initialisation of the individual
      *
      * @param opt The optimization problem that is to be solved.
      */
     @Override
-    public void init(InterfaceOptimizationProblem opt) {
+    public void initialize(InterfaceOptimizationProblem opt) {
-        super.init(opt);
+        super.initialize(opt);
         // evil operators may not respect the range, so at least give some hint
         if (!Mathematics.isInRange(genotype, range)) {
             EVAERROR.errorMsgOnce("Warning: Individual out of range after initialization (and potential initial crossover/mutation)!");
@@ -304,9 +298,6 @@ public class ESIndividualDoubleData extends AbstractEAIndividual implements Inte
         return strB.toString();
     }
 
-/************************************************************************************
- * InterfaceESIndividual methods
- */
     /**
      * This method will allow the user to read the ES 'genotype'
      *

src/eva2/optimization/individuals/GAESIndividualBinaryDoubleData.java

@@ -76,9 +76,9 @@ public class GAESIndividualBinaryDoubleData extends AbstractEAIndividual impleme
      * @param opt The optimization problem that is to be solved.
      */
     @Override
-    public void init(InterfaceOptimizationProblem opt) {
+    public void initialize(InterfaceOptimizationProblem opt) {
-        ((AbstractEAIndividual) this.doubleIndividual).init(opt);
+        ((AbstractEAIndividual) this.doubleIndividual).initialize(opt);
-        ((AbstractEAIndividual) this.binaryIndividual).init(opt);
+        ((AbstractEAIndividual) this.binaryIndividual).initialize(opt);
     }
 
     @Override
@@ -105,8 +105,8 @@ public class GAESIndividualBinaryDoubleData extends AbstractEAIndividual impleme
                 ((AbstractEAIndividual) this.binaryIndividual).initByValue(((Object[]) obj)[0], opt);
             }
         } else {
-            ((AbstractEAIndividual) this.doubleIndividual).init(opt);
+            ((AbstractEAIndividual) this.doubleIndividual).initialize(opt);
-            ((AbstractEAIndividual) this.binaryIndividual).init(opt);
+            ((AbstractEAIndividual) this.binaryIndividual).initialize(opt);
             System.out.println("Initial value for GAESIndividualDoubleData is not suitable!");
         }
     }

src/eva2/optimization/individuals/GAIndividualDoubleData.java

@@ -10,6 +10,7 @@ import eva2.optimization.operator.mutation.MutateGAUniform;
 import eva2.problems.InterfaceOptimizationProblem;
 import eva2.tools.math.RNG;
 import eva2.util.annotation.Description;
+import eva2.util.annotation.Parameter;
 
 import java.util.BitSet;
 
@@ -229,10 +230,6 @@ public class GAIndividualDoubleData extends AbstractEAIndividual implements Inte
         }
     }
 
-/************************************************************************************
- * AbstractEAIndividual methods
- */
-
     /**
      * This method will initialize the individual with a given value for the
      * phenotype.
@@ -373,6 +370,7 @@ public class GAIndividualDoubleData extends AbstractEAIndividual implements Inte
      *
      * @param coding The used genotype coding method
      */
+    @Parameter(name = "coding", description = "Choose the coding to use.")
     public void setGACoding(InterfaceGADoubleCoding coding) {
         this.doubleCoding = coding;
     }
@@ -381,16 +379,13 @@ public class GAIndividualDoubleData extends AbstractEAIndividual implements Inte
         return this.doubleCoding;
     }
 
-    public String gADoubleCodingTipText() {
-        return "Choose the coding to use.";
-    }
-
     /**
      * This method allows you to set the number of mulitruns that are to be performed,
      * necessary for stochastic optimizers to ensure reliable results.
      *
      * @param precision The number of multiruns that are to be performed
      */
+    @Parameter(description = "Gives the number of bits to be used to code a double.")
     public void setPrecision(int precision) {
         this.precision = precision;
     }
@@ -398,8 +393,4 @@ public class GAIndividualDoubleData extends AbstractEAIndividual implements Inte
     public int getPrecision() {
         return this.precision;
     }
-
-    public String precisionTipText() {
-        return "Gives the number of bits to be used to code a double.";
-    }
 }

src/eva2/optimization/individuals/GAPIndividualProgramData.java

@@ -72,9 +72,9 @@ public class GAPIndividualProgramData extends AbstractEAIndividual implements In
      * @param opt The optimization problem that is to be solved.
      */
     @Override
-    public void init(InterfaceOptimizationProblem opt) {
+    public void initialize(InterfaceOptimizationProblem opt) {
-        ((AbstractEAIndividual) this.numberData).init(opt);
+        ((AbstractEAIndividual) this.numberData).initialize(opt);
-        ((AbstractEAIndividual) this.programData).init(opt);
+        ((AbstractEAIndividual) this.programData).initialize(opt);
     }
 
     @Override
@@ -101,8 +101,8 @@ public class GAPIndividualProgramData extends AbstractEAIndividual implements In
                 ((AbstractEAIndividual) this.programData).initByValue(((Object[]) obj)[0], opt);
             }
         } else {
-            ((AbstractEAIndividual) this.numberData).init(opt);
+            ((AbstractEAIndividual) this.numberData).initialize(opt);
-            ((AbstractEAIndividual) this.programData).init(opt);
+            ((AbstractEAIndividual) this.programData).initialize(opt);
             System.out.println("Initial value for GAPIndividualDoubleData is not suitable!");
         }
     }

src/eva2/optimization/individuals/GIOBGAIndividualIntegerPermutationData.java

@@ -72,9 +72,9 @@ public class GIOBGAIndividualIntegerPermutationData extends AbstractEAIndividual
      * @param opt The optimization problem that is to be solved.
      */
     @Override
-    public void init(InterfaceOptimizationProblem opt) {
+    public void initialize(InterfaceOptimizationProblem opt) {
-        ((AbstractEAIndividual) this.integerData).init(opt);
+        ((AbstractEAIndividual) this.integerData).initialize(opt);
-        ((AbstractEAIndividual) this.permutationData).init(opt);
+        ((AbstractEAIndividual) this.permutationData).initialize(opt);
     }
 
     @Override
@@ -101,8 +101,8 @@ public class GIOBGAIndividualIntegerPermutationData extends AbstractEAIndividual
                 ((AbstractEAIndividual) this.permutationData).initByValue(((Object[]) obj)[0], opt);
             }
         } else {
-            ((AbstractEAIndividual) this.integerData).init(opt);
+            ((AbstractEAIndividual) this.integerData).initialize(opt);
-            ((AbstractEAIndividual) this.permutationData).init(opt);
+            ((AbstractEAIndividual) this.permutationData).initialize(opt);
             System.out.println("Initial value for GIOBGAIndividualIntegerPermutationData is not suitable!");
         }
     }

src/eva2/optimization/operator/crossover/TestESCrossover.java

@@ -110,12 +110,12 @@ public class TestESCrossover implements java.io.Serializable {
             tmpIndyD.setDoubleRange(newRange);
             for (int i = 0; i < partners.getTargetSize(); i++) {
                 tmpIndyEA = (AbstractEAIndividual) ((AbstractEAIndividual) tmpIndyD).clone();
-                tmpIndyEA.init(optimizationProblem);
+                tmpIndyEA.initialize(optimizationProblem);
                 partners.add(tmpIndyEA);
             }
             partners.init();
             daddy = (AbstractEAIndividual) ((AbstractEAIndividual) tmpIndyD).clone();
-            daddy.init(optimizationProblem);
+            daddy.initialize(optimizationProblem);
             plot.clearAll();
             plot.setUnconnectedPoint(-2, -2, 0);
             plot.setUnconnectedPoint(2, 2, 0);

src/eva2/optimization/population/Population.java

@@ -15,6 +15,7 @@ import eva2.tools.math.Mathematics;
 import eva2.tools.math.RNG;
 import eva2.tools.math.StatisticUtils;
 import eva2.util.annotation.Description;
+import eva2.util.annotation.Hidden;
 import eva2.util.annotation.Parameter;
 
 import java.util.*;
@@ -602,6 +603,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
         return historyList;
     }
 
+    @Hidden
     public void setHistory(LinkedList<AbstractEAIndividual> theHist) {
         historyList = theHist;
     }
@@ -684,6 +686,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      *
      * @param d The new number of functioncalls.
      */
+    @Hidden
     public void setFunctionCalls(int d) {
         this.functionCallCount = d;
     }
@@ -738,6 +741,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      *
      * @param gen the value to set as new generation index
      */
+    @Hidden
     public void setGeneration(int gen) {
         this.generationCount = gen;
     }
@@ -2519,11 +2523,8 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
         return seedCardinality;
     }
 
+    @Parameter(description = "The initial cardinality for binary genotype individuals, given as pair of mean and std.dev.")
     public void setSeedCardinality(Pair<Integer, Integer> seedCardinality) {
         this.seedCardinality = seedCardinality;
     }
-
-    public String seedCardinalityTipText() {
-        return "The initial cardinality for binary genotype individuals, given as pair of mean and std.dev.";
-    }
 }

src/eva2/optimization/strategies/ANPSO.java

@@ -541,7 +541,7 @@ public class ANPSO extends NichePSO implements InterfaceAdditionalPopulationInfo
                     if (reinitSuperfl) {
                         for (int i = 0; i < tmpPop.size(); i++) {
                             AbstractEAIndividual indy = tmpPop.getEAIndividual(i);
-                            indy.init(optimizationProblem);
+                            indy.initialize(optimizationProblem);
                             indy.resetFitness(Double.MAX_VALUE); // TODO this is not so nice... they should be collected in a reinit-list and inserted at the beginning of the next optimize step
                             ParticleSwarmOptimization.initIndividualDefaults(indy, 0.2);
                             ParticleSwarmOptimization.initIndividualMemory(indy);

src/eva2/optimization/strategies/ArtificialBeeColony.java

@@ -194,7 +194,7 @@ public class ArtificialBeeColony extends AbstractOptimizer implements Serializab
          */
         AbstractEAIndividual oldestIndy = getOldestIndividual();
         if (oldestIndy.getAge() > this.maxTrials) {
-            oldestIndy.init(this.optimizationProblem);
+            oldestIndy.initialize(this.optimizationProblem);
             this.optimizationProblem.evaluate(oldestIndy);
             this.population.incrFunctionCalls();
         }

src/eva2/optimization/strategies/MultiObjectiveCMAES.java

@@ -100,7 +100,7 @@ public class MultiObjectiveCMAES extends AbstractOptimizer implements Serializab
     /*
      * (non-Javadoc)
      * 
-     * @see eva2.optimization.strategies.InterfaceOptimizer#init()
+     * @see eva2.optimization.strategies.InterfaceOptimizer#initialize()
      */
     @Override
     public void initialize() {

src/eva2/optimization/strategies/ParticleFilterOptimization.java

@@ -146,7 +146,7 @@ public class ParticleFilterOptimization extends AbstractOptimizer implements jav
             int i;
             for (i = 0; (i + parents.getTargetSize()) < pop.getTargetSize(); i++) {
                 immi = (AbstractEAIndividual) pop.getEAIndividual(0).clone();
-                immi.init(getProblem());
+                immi.initialize(getProblem());
                 parents.add(immi);
             }
             parents.synchSize();

src/eva2/optimization/strategies/ParticleSubSwarmOptimization.java

@@ -481,7 +481,7 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
 
         for (int i = 0; i < tmp.getTargetSize(); i++) {
             tmpIndy = (AbstractEAIndividual) template.clone();
-            tmpIndy.init(prob);
+            tmpIndy.initialize(prob);
             tmp.add(tmpIndy);
         }
         tmp.init();

src/eva2/optimization/strategies/tribes/TribesExplorer.java

@@ -954,7 +954,7 @@ v[d] = cmin * v[d];
     }
 
     @Override
-    public void init(InterfaceOptimizationProblem opt) {
+    public void initialize(InterfaceOptimizationProblem opt) {
         // TODO whats this for?
         for (int i = 0; i < this.position.x.length; i++) {
             this.position.x[0] = 0.;
@@ -983,7 +983,7 @@ v[d] = cmin * v[d];
             }
             this.setDoubleGenotype(x);
         } else {
-            this.init(opt);
+            this.initialize(opt);
             System.err.println("Initial value for ESIndividualDoubleData is not double[]!");
         }
     }

src/eva2/optimization/tools/ImpactOfDimensionOnMOEAs.java

@@ -104,7 +104,7 @@ public class ImpactOfDimensionOnMOEAs {
         ((InterfaceDataTypeDouble) template).setDoubleDataLength(numberOfVariables);
         for (int i = 0; i < popSize; i++) {
             tmpIndy = (AbstractEAIndividual) template.clone();
-            tmpIndy.init(null);
+            tmpIndy.initialize(null);
             pop.add(tmpIndy);
         }
     }

src/eva2/problems/AbstractMultiModalProblemKnown.java

@@ -57,7 +57,7 @@ public abstract class AbstractMultiModalProblemKnown extends AbstractProblemDoub
         ((InterfaceDataTypeDouble) this.template).setDoubleRange(makeRange());
         for (int i = 0; i < population.getTargetSize(); i++) {
             tmpIndy = (AbstractEAIndividual) this.template.clone();
-            tmpIndy.init(this);
+            tmpIndy.initialize(this);
             population.add(tmpIndy);
         }
         // population initialize must be last

src/eva2/problems/AbstractOptimizationProblem.java

@@ -189,7 +189,7 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
 
         for (int i = 0; i < population.getTargetSize(); i++) {
             tmpIndy = (AbstractEAIndividual) template.clone();
-            tmpIndy.init(prob);
+            tmpIndy.initialize(prob);
             population.add(tmpIndy);
         }
         // population initialize must be last

src/eva2/problems/BKnapsackProblem.java

@@ -160,7 +160,7 @@ public class BKnapsackProblem extends AbstractProblemBinary implements java.io.S
     }
 
     protected void initIndy(int k, AbstractEAIndividual indy) {
-        indy.init(this);
+        indy.initialize(this);
         if (RNG.flipCoin(this.problemSpecificInit)) {
             BitSet tmpSet = new BitSet();
             tmpSet.clear();

src/eva2/problems/SimpleProblemWrapper.java

@@ -12,6 +12,7 @@ import eva2.problems.simple.InterfaceSimpleProblem;
 import eva2.problems.simple.SimpleF1;
 import eva2.problems.simple.SimpleProblemBinary;
 import eva2.problems.simple.SimpleProblemDouble;
+import eva2.util.annotation.Parameter;
 
 import java.util.BitSet;
 
@@ -164,6 +165,7 @@ public class SimpleProblemWrapper extends AbstractOptimizationProblem {
     /**
      * @param simProb the simProb to set
      */
+    @Parameter(description = "Set the simple problem class which is to be optimized")
     public void setSimpleProblem(InterfaceSimpleProblem<?> simProb) {
         this.simProb = simProb;
         initTemplate();
@@ -186,19 +188,13 @@ public class SimpleProblemWrapper extends AbstractOptimizationProblem {
         }
     }
 
-    /**
-     *
-     */
-    public String simpleProblemTipText() {
-        return "Set the simple problem class which is to be optimized";
-    }
-
     /**
      * This method allows you to choose how much noise is to be added to the
      * fitness. This can be used to make the optimization problem more difficult.
      *
      * @param noise The sigma for a gaussian random number.
      */
+    @Parameter(description = "Gaussian noise level on the fitness value.")
     public void setNoise(double noise) {
         if (noise < 0) {
             noise = 0;
@@ -210,11 +206,6 @@ public class SimpleProblemWrapper extends AbstractOptimizationProblem {
         return this.noise;
     }
 
-    public String noiseTipText() {
-        return "Gaussian noise level on the fitness value.";
-    }
-
-
     /**
      * A (symmetric) absolute range limit.
      *
@@ -229,15 +220,12 @@ public class SimpleProblemWrapper extends AbstractOptimizationProblem {
      *
      * @param defaultRange
      */
+    @Parameter(name = "range", description =  "Absolute limit for the symmetric range in any dimension")
     public void setDefaultRange(double defaultRange) {
         this.defaultRange = defaultRange;
         initTemplate();
     }
 
-    public String defaultRangeTipText() {
-        return "Absolute limit for the symmetric range in any dimension";
-    }
-
     /**
      * Take care that all properties which may be hidden (and currently are) send a "hide" message to the Java Bean properties.
      * This is called by PropertySheetPanel in use with the GenericObjectEditor.
@@ -246,16 +234,12 @@ public class SimpleProblemWrapper extends AbstractOptimizationProblem {
         setSimpleProblem(getSimpleProblem());
     }
 
+    @Parameter(name = "individual", description = "Set the individual properties for the optimization")
     public void setIndividualTemplate(AbstractEAIndividual indy) {
         resetTemplate = false;
         template = indy;
     }
 
-    @Override
-    public String individualTemplateTipText() {
-        return "Set the individual properties for the optimization";
-    }
-
     /**
      * This method returns a string describing the optimization problem.
      *