Cleanup and documentation update.

refs #2

src/eva2/client/package-info.java

@@ -1 +0,0 @@
-package eva2.client;

src/eva2/examples/package-info.java

@@ -1 +1,4 @@
+/**
+ * Contains example implementations for custom Terminators and Optimizations.
+ */
 package eva2.examples;

src/eva2/gui/BeanInspector.java

@@ -511,7 +511,7 @@ public class BeanInspector {
      * For a primitive type, return the boxed referenced type. Return null for
      * any non-primitive type.
      *
-     * @param clz1
+     * @param cls
      * @return
      */
     public static Class getBoxedType(Class cls) {

src/eva2/gui/EvATreeNode.java

@@ -11,7 +11,7 @@ import javax.swing.tree.DefaultMutableTreeNode;
  *
  * @author mkron
  * @see PropertySheetPanel
- * @see GOParameters
+ * @see eva2.optimization.modules.OptimizationParameters
  */
 public class EvATreeNode extends DefaultMutableTreeNode {
     private String[] childrenNames = null;

src/eva2/gui/Main.java

@@ -1,8 +1,8 @@
 package eva2.gui;
 
 import eva2.EvAInfo;
-import eva2.client.ClassPreloader;
+import eva2.util.ClassPreloader;
-import eva2.client.EvAComAdapter;
+import eva2.util.EvAComAdapter;
 import eva2.optimization.OptimizationStateListener;
 import eva2.optimization.go.InterfaceOptimizationParameters;
 import eva2.optimization.modules.AbstractModuleAdapter;
@@ -90,7 +90,7 @@ public class Main extends JFrame implements OptimizationStateListener {
 
     /**
      * Constructor of GUI of EvA2. Works as client for the EvA2 server. Note
-     * that the Main initialized multi-threaded for efficiency. Use {@link #awaitGuiInitialized()}
+     * that the Main initialized multi-threaded for efficiency. Use {@link #awaitClientInitialized()} }
      * to await full initialization if necessary.
      */
     public Main(final String hostName) {
@@ -100,7 +100,7 @@ public class Main extends JFrame implements OptimizationStateListener {
     /**
      * A constructor. Splash screen is optional, Gui is activated, no parent
      * window. Note that the Main initialized multi-threaded for
-     * efficiency. Use {@link #awaitGuiInitialized()} to await full
+     * efficiency. Use {@link #awaitClientInitialized()} to await full
      * initialization if necessary.
      *
      * @param hostName
@@ -114,7 +114,7 @@ public class Main extends JFrame implements OptimizationStateListener {
 
     /**
      * A constructor with optional spash screen. Note that the Main is
-     * initialized multi-threaded for efficiency. Use {@link #awaitGuiInitialized()}
+     * initialized multi-threaded for efficiency. Use {@link #awaitClientInitialized()}
      * to await full initialization if necessary.
      *
      * @param hostName
@@ -128,7 +128,7 @@ public class Main extends JFrame implements OptimizationStateListener {
 
     /**
      * A constructor with optional splash screen. Note that the Main
-     * initialized multi-threaded for efficiency. Use {@link #awaitGuiInitialized()}
+     * initialized multi-threaded for efficiency. Use {@link #awaitClientInitialized()}
      * to await full initialization if necessary.
      *
      * @param hostName
@@ -144,11 +144,11 @@ public class Main extends JFrame implements OptimizationStateListener {
 
     /**
      * A constructor with optional splash screen. Note that the Main
-     * initialized multi-threaded for efficiency. Use {@link #awaitGuiInitialized()}
+     * initialized multi-threaded for efficiency. Use {@link #awaitClientInitialized()}
      * to await full initialization if necessary.
      *
      * @param hostName
-     * @param paramsFile
+     * @param optimizationParameters
      * @param autorun
      * @param noSplash
      * @param noGui
@@ -179,7 +179,7 @@ public class Main extends JFrame implements OptimizationStateListener {
      * from a file (paramsFile) or given directly as a java instance. Both may
      * be null to start with standard parameters. If both are non null, the java
      * instance has the higher priority. Note that the Main initialized
-     * multi-threaded for efficiency. Use {@link #awaitGuiInitialized()} to
+     * multi-threaded for efficiency. Use {@link #awaitClientInitialized()} to
      * await full initialization if necessary.
      *
      * @param hostName

src/eva2/gui/package-info.java

@@ -1 +1,4 @@
+/**
+ * Base package for the EvA2 GUI.
+ */
 package eva2.gui;

src/eva2/json/package-info.java

@@ -0,0 +1,4 @@
+/**
+ * JSON package for serializing and deserializing optimization configurations.
+ */
+package eva2.json;

src/eva2/optimization/ModuleServer.java

@@ -26,6 +26,7 @@ public final class ModuleServer {
 
     /**
      *
+     * @param EvAProps
      */
     public ModuleServer(Properties EvAProps) {
         if (instanceCounter > 0) {
@@ -93,6 +94,9 @@ public final class ModuleServer {
      * module classes; if necessary through a remote proxy. Try to load a given
      * parameter file in case its a GOModuleAdapter.
      *
+     * @param selectedModuleName
+     * @param optimizationParameters
+     * @param noGuiLogFile
      * @return the loaded module adapter instance
      */
     public ModuleAdapter createModuleAdapter(String selectedModuleName, InterfaceOptimizationParameters optimizationParameters, String noGuiLogFile) {

src/eva2/optimization/go/SwingWorker.java

@@ -7,11 +7,11 @@ import javax.swing.*;
  * SwingWorker 3), an abstract class that you subclass to
  * perform GUI-related work in a dedicated thread.  For
  * instructions on using this class, see:
- * <p/>
+ * </p><p>
  * http://java.sun.com/products/jfc/tsc/articles/threads/threads2.html
  * or
  * http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html
- * <p/>
+ * </p><p>
  * Note that the API changed slightly in the 3rd version:
  * You must now invoke start() on the SwingWorker after
  * creating it.

src/eva2/optimization/modules/GOModuleAdapter.java

@@ -8,6 +8,7 @@ import java.io.Serializable;
 /**
  * Starts a statistics GUI and the GOProcessor thread.
  */
+@SuppressWarnings("unused")
 public class GOModuleAdapter extends GenericModuleAdapter implements ModuleAdapter, Serializable {
 
     private static final String moduleName = "Genetic_Optimization";

src/eva2/optimization/modules/GenericModuleAdapter.java

@@ -56,7 +56,6 @@ public class GenericModuleAdapter extends AbstractModuleAdapter implements Seria
      *
      * @param adapterName     The AdapterName
      * @param helperFName     name of a html help file name
-     * @param Client          The client to serve
      * @param params          a parameter set describing the optimizer module
      * @param optimizerExpert set to true if setting the optimizer is an expert option being hidden from the gui
      */

src/eva2/optimization/modules/OptimizationParameters.java

@@ -20,7 +20,7 @@ import java.util.logging.Level;
 /**
  * OptimizationParameters for configuration of an
  * optimization run.
- * <p/>
+ * </p><p>
  * This class is used to generate the default GUI
  * configuration panel for optimizations.
  */

src/eva2/optimization/modules/Processor.java

@@ -40,8 +40,6 @@ import java.util.logging.Logger;
  * interface, it is applied to the instance that returned it directly. For
  * arrays of objects each array entry is again handled by checking for
  * getParamControl, thus recursive controllable structures are possible.
- *
- * @author mkron
  */
 public class Processor extends Thread implements InterfaceProcessor, InterfacePopulationChangedEventListener {
 
@@ -227,7 +225,6 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo
         optimizationParameters.getOptimizer().addPopulationChangedEventListener(this);
 
         runCounter = 0;
-        String popLog = null; //"populationLog.txt";
 
         while (isOptimizationRunning() && (runCounter < statistics.getStatisticsParameter().getMultiRuns())) {
             LOGGER.info(String.format("Starting Optimization %d/%d", runCounter + 1, statistics.getStatisticsParameter().getMultiRuns()));
@@ -244,19 +241,11 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo
             if (optimizationStateListener != null) {
                 optimizationStateListener.updateProgress(getStatusPercent(optimizationParameters.getOptimizer().getPopulation(), runCounter, statistics.getStatisticsParameter().getMultiRuns()), null);
             }
-            if (popLog != null) {
-                EVAHELP.clearLog(popLog);
-            }
 
             do {    // main loop
                 maybeUpdateParamCtrl(optimizationParameters);
 
                 this.optimizationParameters.getOptimizer().optimize();
-                // registerPopulationStateChanged *SHOULD* be fired by the optimizer or resp. the population
-                // as we are event listener
-                if (popLog != null) {
-                    EVAHELP.logString(this.optimizationParameters.getOptimizer().getPopulation().getIndyList(), popLog);
-                }
             }
             while (isOptimizationRunning() && !this.optimizationParameters.getTerminator().isTerminated(this.optimizationParameters.getOptimizer().getAllSolutions()));
 

src/eva2/optimization/package-info.java

@@ -1 +1,4 @@
+/**
+ *
+ */
 package eva2.optimization;

src/eva2/optimization/population/Population.java

@@ -955,7 +955,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * population. If the population is empty, -1 is returned.
      *
      * @return The index of the best individual.
-     * @see getIndexOfBestOrWorstIndividual()
+     * @see #getIndexOfBestOrWorstIndividual(boolean, java.util.Comparator)
      */
     public int getIndexOfBestIndividualPrefFeasible() {
         if (size() < 1) {
@@ -969,7 +969,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * the population.
      *
      * @return The index of the worst individual.
-     * @see getIndexOfBestOrWorstIndividual()
+     * @see #getIndexOfBestOrWorstIndividual(boolean, java.util.Comparator)
      */
     public int getIndexOfWorstIndividualNoConstr() {
         return getIndexOfBestOrWorstIndy(false, false, -1);
@@ -981,7 +981,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * fitIndex < 0). If the population is empty, -1 is returned.
      *
      * @return The index of the best individual.
-     * @see getIndexOfBestOrWorstIndividual()
+     * @see #getIndexOfBestOrWorstIndividual(boolean, java.util.Comparator)
      */
     public int getIndexOfBestIndividualPrefFeasible(int fitIndex) {
         if (size() < 1) {
@@ -996,7 +996,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * fitIndex < 0).
      *
      * @return The index of the best individual.
-     * @see getIndexOfBestOrWorstIndividual()
+     * @see #getIndexOfBestOrWorstIndividual(boolean, java.util.Comparator)
      */
     public int getIndexOfWorstIndividualNoConstr(int fitIndex) {
         return getIndexOfBestOrWorstIndy(false, false, fitIndex);
@@ -1257,7 +1257,6 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * instance.
      *
      * @param n
-     * @param l
      */
     public Population toTail(int n) {
         Population retPop = new Population(n);
@@ -1310,8 +1309,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * the population has not been modified. The returned array must not be
      * altered!
      *
-     * @param fitIndex the fitness criterion to be used or -1 for pareto
+     * @param comp The comparator
-     *                 dominance
      * @return
      */
     public ArrayList<AbstractEAIndividual> getSorted(Comparator<Object> comp) {
@@ -1332,7 +1330,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
     /**
      * Returns the sorted population as a new population instance.
      *
-     * @see getSorted(Comparator)
+     * @see #getSorted(java.util.Comparator)
      */
     public Population getSortedPop(Comparator<Object> comp) {
         Population pop = this.cloneWithoutInds();
@@ -1386,8 +1384,8 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * returns dst Population.
      *
      * @param n
-     * @param from
+     * @param src
-     * @param to
+     * @param dst
      * @return
      */
     public static Population moveNInds(int n, Population src, Population dst) {
@@ -1402,8 +1400,8 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
     /**
      * Move one random individual from src to dst population.
      *
-     * @param from
+     * @param src
-     * @param to
+     * @param dst
      */
     public static void moveRandIndFromTo(Population src, Population dst) {
         int k = RNG.randomInt(src.size());
@@ -1762,7 +1760,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * individual to be removed is not contained in the instance. Otherwise,
      * this is ignored.
      *
-     * @param tmpPop
+     * @param popToRemove
      * @param errorOnMissing
      */
     public void removeMembers(Population popToRemove, boolean errorOnMissing) {
@@ -1843,7 +1841,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
     /**
      * Returns the average, minimal and maximal individual distance as diversity
      * measure for the population. If the given metric argument is null, the
-     * euclidian distance of individual positions is used, which presumes that {@link AbstractEAIndividual.getDoublePosition(indy)}
+     * euclidian distance of individual positions is used, which presumes that {@link eva2.optimization.individuals.AbstractEAIndividual#getDoublePosition(eva2.optimization.individuals.AbstractEAIndividual)}
      * returns a valid double position for the individuals of the population.
      * This is of course rather expensive computationally.
      *
@@ -1859,7 +1857,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
     /**
      * Returns the average, minimal and maximal individual distance as diversity
      * measure for the population. If the given metric argument is null, the
-     * euclidian distance of individual positions is used, which presumes that {@link AbstractEAIndividual.getDoublePosition(indy)}
+     * euclidian distance of individual positions is used, which presumes that {@link AbstractEAIndividual#getDoublePosition(eva2.optimization.individuals.AbstractEAIndividual)}
      * returns a valid double position for the individuals of the population.
      * This is of course rather expensive computationally.
      *
@@ -2046,7 +2044,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * Return a Pair of the individuals index and distance. If the population is
      * empty, a Pair of (-1,-1) is returned.
      *
-     * @param pos
+     * @param refIndy
      * @param pop
      * @param closestOrFarthest if true, the closest individual is retrieved,
      *                          otherwise the farthest
@@ -2073,8 +2071,8 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * population.
      *
      * @param indy
-     * @param pop
      * @param d
+     * @param metric
      * @return true if d(indy,pop)<=d, else false
      */
     public boolean isWithinPopDist(AbstractEAIndividual indy, double d, InterfaceDistanceMetric metric) {
@@ -2140,7 +2138,6 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      *
      * @param criterion
      * @return
-     * @see AbstractEAIndidivual.getDoublePosition(individual)
      */
     public double[] getCenterWeighted(AbstractSelProb selProb, int criterion, boolean obeyConst) {
         selProb.computeSelectionProbability(this, "Fitness", obeyConst);
@@ -2162,7 +2159,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * Search for the closest individual to the indexed individual within the
      * population. Return its index or -1 if none could be found.
      *
-     * @param indy
+     * @param neighborIndex
      * @return closest neighbor (euclidian measure) of the given individual in
      *         the given population
      */
@@ -2309,8 +2306,8 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * true and the individuals are out of range, they are projected into the
      * range by force.
      *
-     * @param modRange
+     * @param range
-     * @param b
+     * @param forceRange
      */
     public void updateRange(double[][] range, boolean forceRange) {
         for (int i = 0; i < size(); i++) {
@@ -2337,19 +2334,6 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
     public String initMethodTipText() {
         return "Define the initial sampling method. Note that anything other than inidividualDefault will override the individual initialization concerning the positions in solution space.";
     }
-//	/**
-//	 * Check whether the population at the current state has been marked as
-//	 * evaluated. This allows to avoid double evaluations. 
-//	 * 
-//	 * @return true if the population has been marked as evaluated in its current state, else false 
-//	 */
-//	public boolean isEvaluated() {
-//		if (evaluationTimeModCount != modCount) return false;
-//		Pair<Integer,Integer> hashes = getIndyHashSums();
-//		
-//		if (evaluationTimeHashes == null) return false;
-//		else return ((hashes.head().equals(evaluationTimeHashes.head())) && (hashes.tail().equals(evaluationTimeHashes.tail())) && (evaluationTimeModCount == modCount));
-//	}
 
     /**
      * Add the population data of a given population to this instance. Note that
@@ -2435,7 +2419,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * Return true if the current instance is a subset of the given population,
      * otherwise false.
      *
-     * @param offspring
+     * @param set
      * @return
      */
     public boolean isSubSet(Population set) {

src/eva2/optimization/stat/AbstractStatistics.java

@@ -97,7 +97,7 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
     private List<InterfaceAdditionalPopulationInformer> lastInformerList = null;
     private PopulationInterface lastSols = null;
     private String textFieldDelimiter = "\t";
-    private int defaultFitCriterion = 0; // TODO this might be a user chosen int - or even more elegantly, a MOSOConverter
+    private int defaultFitCriterion = 0; // ToDo this might be a user chosen int - or even more elegantly, a MOSOConverter
 
     protected StringSelection lastFieldSelection = null; // store the graph selection at the beginning of a multi-run
     protected boolean lastIsShowFull = false; // store the "show full text" stats property at the beginning of a multi-run
@@ -891,7 +891,6 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
             }
         }
         return values;
-//		return StringTools.concatValues(values, textFieldDelimiter);
     }
 
     /**
@@ -899,7 +898,6 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
      * The length of this list depends on the field selection state.
      *
      * @param informerList
-     * @param pop
      * @param metaInfo     if non null, the meta info strings are returned in this list
      * @return
      */
@@ -913,7 +911,6 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
             if (metaInfo != null) {
                 metaInfo.addAll(Arrays.asList(informer.getAdditionalDataInfo()));
             }
-//			hdr = hdr + "\t " + informer.getAdditionalDataHeader(pop);
         }
         Iterator<String> hIter = headers.iterator();
         Iterator<String> mIter = (metaInfo != null) ? metaInfo.iterator() : null;
@@ -950,48 +947,15 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
         return new Pair<>(statValuesString, statValues.toArray(new Object[statValues.size()]));
     }
 
-//	/**
-//	 * Append additional informer informations to the given StringBuffer.
-//	 * 
-//	 * @param informerList
-//	 * @param pop
-//	 * @param sbuf
-//	 */
-//	protected Double[] appendAdditionalInfo(List<InterfaceAdditionalPopulationInformer> informerList, PopulationInterface pop, StringBuffer sbuf) {
-//		if (informerList != null) {
-//			ArrayList<Object> additionalObjects = new ArrayList<Object>(5);
-//			
-//			for (InterfaceAdditionalPopulationInformer informer : informerList) {
-//				additionalObjects.addAll(Arrays.asList(informer.getAdditionalDataValue(pop)));
-//			}
-//			String addInfo = StringTools.concatValues(additionalObjects, textFieldDelimiter);
-//			Double[] retVals = parseDoubles(additionalObjects);
-//			if (sbuf!=null) sbuf.append(addInfo);
-//			return retVals;
-//			
-////			StringBuffer addBuffer = new StringBuffer();
-////			for (InterfaceAdditionalPopulationInformer informer : informerList) {
-////				addBuffer.append(" \t ");
-////				addBuffer.append(informer.getAdditionalDataValue(pop));
-////			}
-////			String addInfo = addBuffer.toString().trim();
-////			if (addInfo.startsWith("\t")) addInfo.substring(2); // remove first separator to avoid returning empty field as double
-////			Double[] retVals = parseDoubles(addInfo, "\t");
-////			if (sbuf!=null) sbuf.append(addInfo);
-////			return retVals;
-//		}
-//		return null;
-//	}	
-
     /**
-     * @deprecated The method {@link #createNextGenerationPerformed(PopulationInterface, List)} should be used instead.
+     * @deprecated The method {@link #createNextGenerationPerformed(eva2.optimization.population.PopulationInterface, eva2.optimization.strategies.InterfaceOptimizer, java.util.List)} should be used instead.
      */
     @Override
-    public synchronized void createNextGenerationPerformed(double[] bestfit,
+    public synchronized void createNextGenerationPerformed(double[] bestFit,
-                                                           double[] worstfit, int calls) {
+                                                           double[] worstFit, int calls) {
         functionCalls = calls;
-        currentBestFit = bestfit;
+        currentBestFit = bestFit;
-        currentWorstFit = worstfit;
+        currentWorstFit = worstFit;
         currentBestFeasibleFit = null;
         currentMeanFit = null;
 
@@ -1044,7 +1008,7 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
      * If the population returns a specific data array, this method is called instead of doing standard output
      *
      * @param pop
-     * @param informer
+     * @param informerList
      */
     public abstract void plotSpecificData(PopulationInterface pop, List<InterfaceAdditionalPopulationInformer> informerList);
 

src/eva2/optimization/stat/GenericStatistics.java

@@ -52,17 +52,16 @@ public class GenericStatistics implements Serializable {
             states = new boolean[fields.length];
             for (int i = 0; i < fields.length; i++) {
                 String desc = fields[i].toString(); //System.out.println("desc "+desc);
-                int istransient = desc.indexOf("transient");
+                int isTransient = desc.indexOf("transient");
                 Object FieldValue = null;
-                if (istransient == -1 || fields[i].getName().equals("elementData")) {  // the elementdatahack
+                if (isTransient == -1 || fields[i].getName().equals("elementData")) {  // the elementdatahack
                     fields[i].setAccessible(true);
                     FieldValue = fields[i].get(target);
                 }
                 propertyNames[i] = fields[i].getName();
             }
         } catch (Exception ex) {
-            System.out.println("ERROR in GenericStatistics:" + ex.getMessage());
+            LOGGER.severe("GenericStatistics:" + ex.getMessage());
-            ex.printStackTrace();
         }
     }
 
@@ -98,7 +97,6 @@ public class GenericStatistics implements Serializable {
      *
      */
     public void setState(boolean[] x) {
-        System.out.println("in statistics setState !!!!!!!!!!!!!!!!!!");
         states = x;
     }
 
@@ -149,8 +147,7 @@ public class GenericStatistics implements Serializable {
         try {
             fields = getDeclaredFields(target);
         } catch (Exception ex) {
-            System.out.println("ERROR in GenericStatistics:" + ex.getMessage());
+            LOGGER.severe("ERROR in GenericStatistics:" + ex.getMessage());
-            ex.printStackTrace();
         }
         int index = 0;
         for (int i = 0; i < fields.length; i++) {
@@ -159,11 +156,11 @@ public class GenericStatistics implements Serializable {
                     continue;
                 }
                 if (fields[i].getName().equals(propertyNames[n])) {
-                    String desc = fields[i].toString(); //System.out.println("desc "+desc);
+                    String desc = fields[i].toString();
-                    int istransient = desc.indexOf("transient");
+                    int isTransient = desc.indexOf("transient");
 
                     Object fieldValue = null;
-                    if (istransient == -1 || fields[i].getName().equals("elementData")) {  // the elementdatahack
+                    if (isTransient == -1 || fields[i].getName().equals("elementData")) {  // the elementdatahack
                         fields[i].setAccessible(true);
                         try {
                             fieldValue = fields[i].get(target);
@@ -175,8 +172,7 @@ public class GenericStatistics implements Serializable {
                             }
                             index++;
                         } catch (Exception ex) {
-                            System.out.println("ERROR in GenericStatistics:" + ex.getMessage());
+                            LOGGER.severe("ERROR in GenericStatistics:" + ex.getMessage());
-                            ex.printStackTrace();
                         }
                     }
                     break;

src/eva2/optimization/stat/GraphSelectionEnum.java

@@ -5,11 +5,10 @@ import eva2.tools.StringSelection;
 /**
  * An Enum to be used in the statistics classes for identifying data fields.
  *
- * @author mkron
  * @see AbstractStatistics
  */
 public enum GraphSelectionEnum {
-    // DONT change this order, or the relation to AbstractStatistics will be lost
+    // DON'T change this order, or the relation to AbstractStatistics will be lost
     currentBest, meanFit, currentWorst, runBest, currentBestFeasible, runBestFeasible,
     avgEucPopDistance, maxEucPopDistance, avgPopMetricDist, maxPopMetricDist;
 

src/eva2/optimization/stat/InterfaceStatistics.java

@@ -15,7 +15,7 @@ public interface InterfaceStatistics {
     /**
      * Initialize statistics computations.
      */
-    void startOptimizationPerformed(String InfoString, int runnumber, Object params, List<InterfaceAdditionalPopulationInformer> informerList); // called from processor
+    void startOptimizationPerformed(String infoString, int runNumber, Object params, List<InterfaceAdditionalPopulationInformer> informerList); // called from processor
 
     /**
      * Finalize statistics computations.
@@ -34,7 +34,7 @@ public interface InterfaceStatistics {
 
     void createNextGenerationPerformed(PopulationInterface Pop, InterfaceOptimizer opt, List<InterfaceAdditionalPopulationInformer> informerList);
 
-    void createNextGenerationPerformed(double[] bestfit, double[] worstfit, int calls);
+    void createNextGenerationPerformed(double[] bestFit, double[] worstFit, int calls);
 
     InterfaceStatisticsParameter getStatisticsParameter(); // called from moduleadapter
 

src/eva2/optimization/stat/OptimizationJobList.java

@@ -183,7 +183,6 @@ public class OptimizationJobList extends PropertySelectableList<OptimizationJob>
         genericArrayEditor.addUpperActionButton("Test Stats", al);
         genericArrayEditor.addLowerActionButton("Save selected", sal);
 
-//    	edi.addPopupItem("Reset selected", getClearSelectedActionListener(parent, jobList)); // this option does not make much sense - instead of deleting data, taking over the settings for a new run is more plausible
         genericArrayEditor.addPopupItem("Reuse as current settings", getReuseActionListener(parent, jobList));
         genericArrayEditor.setAdditionalCenterPane(createStatsPanel(jobList, genericArrayEditor));
         genericArrayEditor.setValue(jobList);
@@ -193,12 +192,11 @@ public class OptimizationJobList extends PropertySelectableList<OptimizationJob>
 
     private static JComponent createStatsPanel(final OptimizationJobList jobList, final GenericArrayEditor edi) {
         JParaPanel pan = new JParaPanel(EvAStatisticalEvaluation.statsParams, "Statistics");
-        JComponent paraPan = pan.makePanel();
+        return pan.makePanel();
-        return paraPan;
     }
 
     private static ActionListener getReuseActionListener(final Component parent, final OptimizationJobList jobList) {
-        ActionListener al = new ActionListener() {
+        return new ActionListener() {
 
             @Override
             public void actionPerformed(ActionEvent e) {
@@ -215,11 +213,10 @@ public class OptimizationJobList extends PropertySelectableList<OptimizationJob>
                 }
             }
         };
-        return al;
     }
 
     private static ActionListener getClearSelectedActionListener(final Component parent, final OptimizationJobList jobList) {
-        ActionListener al = new ActionListener() {
+        return new ActionListener() {
 
             @Override
             public void actionPerformed(ActionEvent e) {
@@ -229,13 +226,12 @@ public class OptimizationJobList extends PropertySelectableList<OptimizationJob>
                 }
             }
         };
-        return al;
     }
 
     /**
      * Link a processor to the job list for re-scheduling jobs.
      *
-     * @param processor
+     * @param mod
      */
     public void setModule(ModuleAdapter mod) {
         module = mod;
@@ -251,16 +247,9 @@ public class OptimizationJobList extends PropertySelectableList<OptimizationJob>
     }
 
     public boolean removeTextListener(InterfaceTextListener tListener) {
-        if (listeners != null) {
+        return listeners != null && listeners.remove(tListener);
-            return listeners.remove(tListener);
-        } else {
-            return false;
-        }
     }
 
-    /*
-     * (non-Javadoc) @see eva2.server.stat.InterfaceTextListener#print(java.lang.String)
-     */
     @Override
     public void print(String str) {
         if (listeners != null) {
@@ -270,9 +259,6 @@ public class OptimizationJobList extends PropertySelectableList<OptimizationJob>
         }
     }
 
-    /*
-     * (non-Javadoc) @see eva2.server.stat.InterfaceTextListener#println(java.lang.String)
-     */
     @Override
     public void println(String str) {
         if (listeners != null) {

src/eva2/optimization/stat/StatisticsDummy.java

@@ -51,8 +51,8 @@ public class StatisticsDummy implements InterfaceStatistics, InterfaceTextListen
     }
 
     @Override
-    public void createNextGenerationPerformed(double[] bestfit,
+    public void createNextGenerationPerformed(double[] bestFit,
-                                              double[] worstfit, int calls) {
+                                              double[] worstFit, int calls) {
     }
 
     @Override
@@ -93,9 +93,9 @@ public class StatisticsDummy implements InterfaceStatistics, InterfaceTextListen
     }
 
     @Override
-    public void startOptimizationPerformed(String InfoString, int runnumber,
+    public void startOptimizationPerformed(String infoString, int runNumber,
                                            Object params, List<InterfaceAdditionalPopulationInformer> informerList) {
-        if (runnumber == 0) {
+        if (runNumber == 0) {
             bestIndividualAllover = null;
         }
         bestRunIndy = null;

src/eva2/optimization/strategies/ANPSO.java

@@ -424,7 +424,6 @@ public class ANPSO extends NichePSO implements InterfaceOptimizer, InterfaceAddi
     /**
      * The returned array may contain null entries (for indies scheduled for reinitialization).
      *
-     * @param pop
      * @return an array of references sorted according to the particle indices
      *         (i.e. returnedArray[i] = individual with individualIndex i)
      */
@@ -569,11 +568,7 @@ public class ANPSO extends NichePSO implements InterfaceOptimizer, InterfaceAddi
         useAsMainSwarm(newMainPop);
     }
 
-/**********************************************************************************************************************
- * Optimization
- */
     /**
-     * @tested (non-Javadoc) @see javaeva.server.oa.go.Strategies.InterfaceOptimizer#optimize()
      */
     @Override
     public void optimize() {
@@ -674,7 +669,6 @@ public class ANPSO extends NichePSO implements InterfaceOptimizer, InterfaceAddi
  */
     /**
      * @param size
-     * @tested ps
      * sets the !initial! size of the mainswarm population
      * use this instead of getPopulation.setPopulationSize()
      */
@@ -709,7 +703,6 @@ public class ANPSO extends NichePSO implements InterfaceOptimizer, InterfaceAddi
 
     /**
      * @return a population consisting of copies from the mainswarm and all subswarms.
-     * @tested junit
      * returns a population consisting of copies from the mainswarm and all subswarms
      * (active and inactive, so the size of this Population is not necessarily constant).
      * Especially important for the call back regarding the output file...
@@ -748,7 +741,6 @@ public class ANPSO extends NichePSO implements InterfaceOptimizer, InterfaceAddi
 
     /**
      * @return array with copies of the gbest individuals
-     * @tested junit
      * returns the cloned global best individuals (ie best of all time) from every subswarm
      */
     public Population getSubswarmRepresentatives() {
@@ -769,7 +761,6 @@ public class ANPSO extends NichePSO implements InterfaceOptimizer, InterfaceAddi
 
     /**
      * @return descriptive string of the elite
-     * @tested emp
      * returns a string that lists the global best individuals (ie best of all time) from every subswarm
      */
     public String getSubswarmRepresentativesAsString() {
@@ -782,7 +773,6 @@ public class ANPSO extends NichePSO implements InterfaceOptimizer, InterfaceAddi
     }
 
     /**
-     * @tested plots all subswarms as connected lines to their respective best individual
      */
     @Override
     protected void plotSubSwarms() {
@@ -845,7 +835,6 @@ public class ANPSO extends NichePSO implements InterfaceOptimizer, InterfaceAddi
      * @return inactive particles with given index
      *         (may return more than one particle for a given index because indizes are reused during deactivation
      *         and the reinitialized particle may be deactivated again...)
-     * @tested method not used any more
      */
     public Vector<AbstractEAIndividual> getInactiveIndiesByParticleIndex(Integer index) {
         Vector<AbstractEAIndividual> indies = null;
@@ -862,7 +851,6 @@ public class ANPSO extends NichePSO implements InterfaceOptimizer, InterfaceAddi
 
     /**
      * @return The name of the algorithm
-     * @tested nn
      * This method will return a naming String
      */
     @Override
@@ -1031,22 +1019,6 @@ public class ANPSO extends NichePSO implements InterfaceOptimizer, InterfaceAddi
         return representatives;
     }
 
-/*
-    public String[] getAdditionalDataHeader(PopulationInterface pop) {
-		return new String[]{"mainSwarmSize","numActSpec","numArchived", "archivedMedCorr"};
-	}
-
-	public Object[] getAdditionalDataValue(PopulationInterface pop) {
-		int actSwarms = countActiveSubswarms();
-		double medCor = (getSubswarmRepresentatives(true)).getCorrelations()[3]; // median correlation of best indies of inactive subswarms
-		return new Object[]{getMainSwarm().getPopulation().size(),
-				actSwarms,
-				(getSubSwarms().size()-actSwarms),
-				medCor};
-	}
-
-*/
-
     /**
      * Return the median correlation of the best individuals of the given set of swarms.
      */

src/eva2/optimization/strategies/DifferentialEvolution.java

@@ -195,7 +195,7 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
                 }
                 isEmpty = (isEmpty && (result[i] == 0));
             }
-            // single parent! dont add another one
+            // single parent! don't add another one
         }
 
         return result;
@@ -250,7 +250,7 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
                 }
                 isEmpty = (isEmpty && (result[i] == 0));
             }
-            // single parent! dont add another one
+            // single parent! don't add another one
         }
 
         return result;
@@ -538,8 +538,7 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
         optimizationProblem.evaluate(children);
 
         /**
-         * MdP: added a reevalutation mechanism for dynamically changing
+         * Re-evalutation mechanism for dynamically changing problems
-         * problems
          */
         if (isReEvaluate()) {
             for (int i = 0; i < this.population.size(); i++) {
@@ -594,8 +593,7 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
 
 
         /**
-         * MdP: added a reevalutation mechanism for dynamically changing
+         * Reevalutation mechanism for dynamically changing problems
-         * problems
          */
         if (isReEvaluate()) {
             nextDoomed = -1;

src/eva2/package-info.java

@@ -1,4 +1,4 @@
 /**
- * Base package of the project that contains globally important classes.
+ * Base package of EvA2
  */
 package eva2;

src/eva2/problems/AbstractOptimizationProblem.java

@@ -56,7 +56,6 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
             population.incrFunctionCalls();
             semaphore.release();
         }
-
     }
 
     /**
@@ -68,7 +67,7 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
      */
     public static final String OLD_FITNESS_KEY = "oldFitness";
 
-    private int parallelthreads = 1;
+    private int parallelThreads = 1;
 
     protected AbstractEAIndividual template = null;
 
@@ -83,11 +82,11 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
     public abstract Object clone();
 
     public int getParallelThreads() {
-        return parallelthreads;
+        return parallelThreads;
     }
 
-    public void setParallelThreads(int parallelthreads) {
+    public void setParallelThreads(int parallelThreads) {
-        this.parallelthreads = parallelthreads;
+        this.parallelThreads = parallelThreads;
     }
 
     public String parallelThreadsTipText() {
@@ -120,10 +119,10 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
         AbstractEAIndividual tmpIndy;
         evaluatePopulationStart(population);
 
-        if (this.parallelthreads > 1) {
+        if (this.parallelThreads > 1) {
             Vector<AbstractEAIndividual> queue = new Vector<>(population.size());
             Semaphore sema = new Semaphore(0);
-            ExecutorService pool = Executors.newFixedThreadPool(parallelthreads);
+            ExecutorService pool = Executors.newFixedThreadPool(parallelThreads);
             int cntIndies = 0;
             for (; cntIndies < population.size(); cntIndies++) {
                 AbstractEAIndividual tmpindy = (AbstractEAIndividual) population.get(cntIndies);
@@ -160,17 +159,14 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
      *
      * @param population
      */
-
+    public void evaluatePopulationStart(Population population) {}
-    public void evaluatePopulationStart(Population population) {
-    }
 
     /**
      * Empty thunk for implementation in subclasses. This is called after a population was evaluated.
      *
      * @param population
      */
-    public void evaluatePopulationEnd(Population population) {
+    public void evaluatePopulationEnd(Population population) {}
-    }
 
     /**
      * This method evaluate a single individual and sets the fitness values
@@ -224,7 +220,7 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
      */
     @Override
     public Double getDoublePlotValue(Population pop) {
-        return new Double(pop.getBestEAIndividual().getFitness(0));
+        return pop.getBestEAIndividual().getFitness(0);
     }
 
     /**

src/eva2/tools/BasicResourceLoader.java

@@ -40,17 +40,15 @@ import java.util.zip.ZipEntry;
 import java.util.zip.ZipFile;
 import java.util.zip.ZipInputStream;
 
-
 /**
  * Loads resource file from directory OR jar file. Now it is easier possible to
  * access resource files in a directory structure or a .jar/.zip file.
  *
- * @.author		Marcel Kronfeld
+ * @author Marcel Kronfeld
- * @.author wegnerj
+ * @author wegnerj
- * @.author Robin Friedman, rfriedman@TriadTherapeutics.com
+ * @author Robin Friedman, rfriedman@TriadTherapeutics.com
- * @.author Gerd Mueller
+ * @author Gerd Mueller
- * @.license GPL
+ * @license GPL
- * @.cvsversion $Revision: 1.3 $, $Date: 2005/02/17 16:48:44 $
  */
 public class BasicResourceLoader implements ResourceLoader {
     /**
@@ -81,7 +79,7 @@ public class BasicResourceLoader implements ResourceLoader {
     /**
      * Description of the Method
      *
-     * @param resourceFile Description of the Parameter
+     * @param resourceFile Source file to read
      * @return Description of the Return Value
      */
     public static List<String> readLines(String resourceFile) {
@@ -91,8 +89,8 @@ public class BasicResourceLoader implements ResourceLoader {
     /**
      * Description of the Method
      *
-     * @param resourceFile   Description of the Parameter
+     * @param resourceFile   Source file to read
-     * @param ignoreComments Description of the Parameter
+     * @param ignoreCommentedLines Whether to ignore commented lines
      * @return Description of the Return Value
      */
     public static List<String> readLines(String resourceFile,
@@ -106,7 +104,7 @@ public class BasicResourceLoader implements ResourceLoader {
      * @param resourceFile File to read
      * @param ignorePrefix array of prefixes which mark a line to be ignored
      * @param lOffset      offset of the first line to read
-     * @param lCnt         number of lines to read, if <= 0, all lines are read
+     * @param lCnt         number of lines to read, if less than 0, all lines are read
      * @return List of lines which were read or null on an error
      */
     public static List<String> readLines(String resourceFile,

src/eva2/tools/CubicSpline.java

@@ -1,210 +0,0 @@
-package eva2.tools;
-
-/**
- * *******************************************************
- * <p/>
- * Class CubicSpline
- * <p/>
- * Class for performing an interpolation using a cubic spline
- * setTabulatedArrays and interpolate adapted from Numerical Recipes in C
- * <p/>
- * WRITTEN BY: Mick Flanagan
- * <p/>
- * DATE:	May 2002
- * <p/>
- * DOCUMENTATION:
- * See Michael T Flanagan's JAVA library on-line web page:
- * CubicSpline.html
- * <p/>
- * ********************************************************
- */
-
-public class CubicSpline {
-
-    private int npoints = 0;        // no. of tabulated points
-    private double[] y = null;      // y=f(x) tabulated function
-    private double[] x = null;      // x in tabulated function f(x)
-    private double[] y2 = null;     // returned second derivatives of y
-    private double yp1 = 0.0D;      // first derivative at point one
-    // default value = zero (natural spline)
-    private double ypn = 0.0D;      // first derivative at point n
-    // default value = zero (natural spline)
-
-    // Constructors
-    // Constructor with data arrays initialised to arrays x and y
-    public CubicSpline(double[] x, double[] y) {
-        this.npoints = x.length;
-        if (this.npoints != y.length) {
-            throw new IllegalArgumentException("Arrays x and y are of different length");
-        }
-        this.x = new double[npoints];
-        this.y = new double[npoints];
-        this.y2 = new double[npoints];
-        for (int i = 0; i < this.npoints; i++) {
-            this.x[i] = x[i];
-            this.y[i] = y[i];
-        }
-        this.yp1 = 1e40;
-        this.ypn = 1e40;
-    }
-
-    // Constructor with data arrays initialised to zero
-    // Primarily for use by BiCubicSpline
-    CubicSpline(int npoints) {
-        this.npoints = npoints;
-        this.x = new double[npoints];
-        this.y = new double[npoints];
-        this.y2 = new double[npoints];
-        this.yp1 = 1e40;
-        this.ypn = 1e40;
-    }
-
-    //  METHODS
-    // Resets the x y data arrays - primarily for use in BiCubicSpline
-    public void resetData(double[] x, double[] y) {
-        if (x.length != y.length) {
-            throw new IllegalArgumentException("Arrays x and y are of different length");
-        }
-        if (this.npoints != x.length) {
-            throw new IllegalArgumentException("Original array length not matched by new array length");
-        }
-        for (int i = 0; i < this.npoints; i++) {
-            this.x[i] = x[i];
-            this.y[i] = y[i];
-        }
-    }
-
-    // Returns a new CubicSpline setting array lengths to n and all array values to zero with natural spline default
-    // Primarily for use in BiCubicSpline
-    public static CubicSpline zero(int n) {
-        CubicSpline aa = new CubicSpline(n);
-        return aa;
-    }
-
-    // Create a one dimensional array of cubic spline objects of length n each of array length m
-    // Primarily for use in BiCubicSpline
-    public static CubicSpline[] oneDarray(int n, int m) {
-        CubicSpline[] a = new CubicSpline[n];
-        for (int i = 0; i < n; i++) {
-            a[i] = CubicSpline.zero(m);
-        }
-        return a;
-    }
-
-    // Enters the first derivatives of the cubic spline at
-    // the first and last point of the tabulated data
-    // Overrides a natural spline
-    public void setDerivLimits(double yp1, double ypn) {
-        this.yp1 = yp1;
-        this.ypn = ypn;
-    }
-
-    // Returns the internal array of second derivatives
-    public double[] getDeriv() {
-        return this.y2;
-    }
-
-    //  Calculates the second derivatives of the tabulated function
-    //  for use by the cubic spline interpolation method (.interpolate)
-    public void calcDeriv() {
-        int i = 0, k = 0;
-        double p = 0.0D, qn = 0.0D, sig = 0.0D, un = 0.0D;
-        double[] u = new double[npoints];
-
-        if (yp1 > 0.99e30) {
-            y2[0] = u[0] = 0.0;
-        } else {
-            this.y2[0] = -0.5;
-            u[0] = (3.0 / (this.x[1] - this.x[0])) * ((this.y[1] - this.y[0]) / (this.x[1] - this.x[0]) - this.yp1);
-        }
-
-        for (i = 1; i <= this.npoints - 2; i++) {
-            sig = (this.x[i] - this.x[i - 1]) / (this.x[i + 1] - this.x[i - 1]);
-            p = sig * this.y2[i - 1] + 2.0;
-            this.y2[i] = (sig - 1.0) / p;
-            u[i] = (this.y[i + 1] - this.y[i]) / (this.x[i + 1] - this.x[i]) - (this.y[i] - this.y[i - 1]) / (this.x[i] - this.x[i - 1]);
-            u[i] = (6.0 * u[i] / (this.x[i + 1] - this.x[i - 1]) - sig * u[i - 1]) / p;
-        }
-
-        if (this.ypn > 0.99e30) {
-            qn = un = 0.0;
-        } else {
-            qn = 0.5;
-            un = (3.0 / (this.x[npoints - 1] - this.x[this.npoints - 2])) * (this.ypn - (this.y[this.npoints - 1] - this.y[this.npoints - 2]) / (this.x[this.npoints - 1] - x[this.npoints - 2]));
-        }
-
-        this.y2[this.npoints - 1] = (un - qn * u[this.npoints - 2]) / (qn * this.y2[this.npoints - 2] + 1.0);
-        for (k = this.npoints - 2; k >= 0; k--) {
-            this.y2[k] = this.y2[k] * this.y2[k + 1] + u[k];
-        }
-    }
-
-    //  INTERPOLATE
-    //  Returns an interpolated value of y for a value of xfrom a tabulated function y=f(x)
-    //  after the data has been entered via a constructor and the derivatives calculated and
-    //  stored by calcDeriv().
-    public double interpolate(double xx) {
-        int klo = 0, khi = 0, k = 0;
-        double h = 0.0D, b = 0.0D, a = 0.0D, yy = 0.0D;
-
-        if (xx < this.x[0] || xx > this.x[this.npoints - 1]) {
-//                        System.out.println(xx);
-            xx -= 0.00001;
-            //throw new IllegalArgumentException("x is outside the range of data points");
-        }
-
-        klo = 0;
-        khi = this.npoints - 1;
-        while (khi - klo > 1) {
-            k = (khi + klo) >> 1;
-            if (this.x[k] > xx) {
-                khi = k;
-            } else {
-                klo = k;
-            }
-        }
-        h = this.x[khi] - this.x[klo];
-
-        if (h == 0.0) {
-            throw new IllegalArgumentException("Two values of x are identical");
-        } else {
-            a = (this.x[khi] - xx) / h;
-            b = (xx - this.x[klo]) / h;
-            yy = a * this.y[klo] + b * this.y[khi] + ((a * a * a - a) * this.y2[klo] + (b * b * b - b) * this.y2[khi]) * (h * h) / 6.0;
-        }
-        return yy;
-    }
-
-    //  Returns an interpolated value of y for a value of x (xx) from a tabulated function y=f(x)
-    //  after the derivatives (deriv) have been calculated independently of and calcDeriv().
-    public static double interpolate(double xx, double[] x, double[] y, double[] deriv) {
-        if (((x.length != y.length) || (x.length != deriv.length)) || (y.length != deriv.length)) {
-            throw new IllegalArgumentException("array lengths are not all equal");
-        }
-        int n = x.length;
-        int klo = 0, khi = 0, k = 0;
-        double h = 0.0D, b = 0.0D, a = 0.0D, yy = 0.0D;
-
-        klo = 0;
-        khi = n - 1;
-        while (khi - klo > 1) {
-            k = (khi + klo) >> 1;
-            if (x[k] > xx) {
-                khi = k;
-            } else {
-                klo = k;
-            }
-        }
-        h = x[khi] - x[klo];
-
-        if (h == 0.0) {
-            throw new IllegalArgumentException("Two values of x are identical");
-        } else {
-            a = (x[khi] - xx) / h;
-            b = (xx - x[klo]) / h;
-            yy = a * y[klo] + b * y[khi] + ((a * a * a - a) * deriv[klo] + (b * b * b - b) * deriv[khi]) * (h * h) / 6.0;
-        }
-        return yy;
-    }
-
-}

src/eva2/tools/JarResources.java

@@ -1,21 +1,7 @@
 package eva2.tools;
-/**
- * Title:        EvA2
- * Description:
- * Copyright:    Copyright (c) 2003
- * Company:      University of Tuebingen, Computer Architecture
- * @author Holger Ulmer, Felix Streichert, Hannes Planatscher
- * @version: $Revision: 10 $
- *            $Date: 2006-01-18 11:02:22 +0100 (Wed, 18 Jan 2006) $
- *            $Author: streiche $
- */
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
 
 import java.io.BufferedInputStream;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -25,7 +11,7 @@ import java.util.zip.ZipInputStream;
 
 /**
  * JarResources: JarResources maps all resources included in a
- * Zip or Jar file. Additionaly, it provides a method to extract one
+ * Zip or Jar file. Additionally, it provides a method to extract one
  * as a blob.
  */
 public final class JarResources {
@@ -34,15 +20,15 @@ public final class JarResources {
     public boolean debugOn = false;
 
     // jar resource mapping tables
-    private Hashtable htSizes = new Hashtable();
+    private Hashtable<String,Integer> htSizes = new Hashtable<>();
-    private Hashtable htJarContents = new Hashtable();
+    private Hashtable<String,byte[]> htJarContents = new Hashtable<>();
 
     // a jar file
     private String jarFileName;
 
     /**
      * creates a JarResources. It extracts all resources from a Jar
-     * into an internal hashtable, keyed by resource names.
+     * into an internal HashTable, keyed by resource names.
      *
      * @param jarFileName a jar or zip file
      */
@@ -57,7 +43,7 @@ public final class JarResources {
      * @param name a resource name.
      */
     public byte[] getResource(String name) {
-        return (byte[]) htJarContents.get(name);
+        return htJarContents.get(name);
     }
 
     /**
@@ -73,15 +59,15 @@ public final class JarResources {
                 if (debugOn) {
                     System.out.println(dumpZipEntry(ze));
                 }
-                htSizes.put(ze.getName(), new Integer((int) ze.getSize()));
+                htSizes.put(ze.getName(), (int) ze.getSize());
             }
             zf.close();
 
-            // extract resources and put them into the hashtable.
+            // extract resources and put them into the HashTable.
             FileInputStream fis = new FileInputStream(jarFileName);
             BufferedInputStream bis = new BufferedInputStream(fis);
             ZipInputStream zis = new ZipInputStream(bis);
-            ZipEntry ze = null;
+            ZipEntry ze;
             while ((ze = zis.getNextEntry()) != null) {
                 if (ze.isDirectory()) {
                     continue;
@@ -94,11 +80,11 @@ public final class JarResources {
                 int size = (int) ze.getSize();
                 // -1 means unknown size.
                 if (size == -1) {
-                    size = ((Integer) htSizes.get(ze.getName())).intValue();
+                    size = htSizes.get(ze.getName());
                 }
                 byte[] b = new byte[size];
                 int rb = 0;
-                int chunk = 0;
+                int chunk;
                 while ((size - rb) > 0) {
                     chunk = zis.read(b, rb, size - rb);
                     if (chunk == -1) {
@@ -106,7 +92,7 @@ public final class JarResources {
                     }
                     rb += chunk;
                 }
-                // add to internal resource hashtable
+                // add to internal resource HashTable
                 htJarContents.put(ze.getName(), b);
                 if (debugOn) {
                     System.out.println(
@@ -118,8 +104,6 @@ public final class JarResources {
             }
         } catch (NullPointerException e) {
             System.out.println("done.");
-        } catch (FileNotFoundException e) {
-            e.printStackTrace();
         } catch (IOException e) {
             e.printStackTrace();
         }
@@ -144,15 +128,15 @@ public final class JarResources {
         }
         sb.append(ze.getName());
         sb.append("\t");
-        sb.append("" + ze.getSize());
+        sb.append("").append(ze.getSize());
         if (ze.getMethod() == ZipEntry.DEFLATED) {
-            sb.append("/" + ze.getCompressedSize());
+            sb.append("/").append(ze.getCompressedSize());
         }
         return (sb.toString());
     }
 
     /**
-     * Is a test driver. Given a jar file and a resource name, it trys to
+     * Is a test driver. Given a jar file and a resource name, it tries to
      * extract the resource and then tells us whether it could or not.
      * <p/>
      * <strong>Example</strong>
@@ -185,4 +169,4 @@ public final class JarResources {
         }
     }
 
-}    // End of JarResources class.
+}

src/eva2/tools/ReflectPackage.java

@@ -41,7 +41,6 @@ public class ReflectPackage {
      *
      * @param pckgname
      * @return
-     * @throws ClassNotFoundException
      */
     public static int getClassesFromFilesFltr(HashSet<Class> set, String path, String pckgname, boolean includeSubs, Class reqSuperCls) {
         try {
@@ -91,9 +90,7 @@ public class ReflectPackage {
                         } else {
                             cntAdded += addClass(set, cls);
                         }
-                    } catch (Exception e) {
+                    } catch (Exception | Error e) {
-                        System.err.println("ReflectPackage: Couldnt get Class from jar for " + pckgname + '.' + file + ": " + e.getMessage());
-                    } catch (Error e) {
                         System.err.println("ReflectPackage: Couldnt get Class from jar for " + pckgname + '.' + file + ": " + e.getMessage());
                     }
                 } else if (includeSubs) {

src/eva2/tools/SelectedTag.java

@@ -4,7 +4,6 @@ package eva2.tools;
  * This serves as activation state of one item in an array of Tags
  * identified by integer IDs. String names should be unique as well as integer IDs.
  */
-
 public class SelectedTag implements java.io.Serializable {
     protected int selectedId;
     protected Tag[] tags;
@@ -30,7 +29,7 @@ public class SelectedTag implements java.io.Serializable {
      * Constructor from a String array, creates a Tag array where the IDs correspond to array index.
      *
      * @param selID
-     * @param tagStrings
+     * @param strings
      */
     public SelectedTag(int selID, String... strings) {
         init(selID, strings);

src/eva2/tools/SerializedObject.java

@@ -26,7 +26,6 @@ public class SerializedObject implements Serializable {
      *
      * @param obj the Object to serialize.
      * @throws IOException
-     * @throws Exception   if the object is not Serializable.
      */
     public SerializedObject(Object obj) throws IOException {
         this(obj, false);
@@ -38,7 +37,6 @@ public class SerializedObject implements Serializable {
      * @param obj      the Object to serialize.
      * @param compress true if the object should be stored compressed.
      * @throws IOException
-     * @throws Exception   if the object is not Serializable.
      */
     public SerializedObject(Object obj, boolean compress) throws IOException {
         isCompressed = compress;
@@ -51,8 +49,7 @@ public class SerializedObject implements Serializable {
      * @param obj      the Object to serialize
      * @param compress true if the object should be compressed.
      * @return the byte array containing the serialized object.
-     * @throws IOException
+     * @throws IOException   if the object is not Serializable.
-     * @throws Exception   if the object is not Serializable.
      */
     protected static byte[] toByteArray(Object obj, boolean compress) throws IOException {
         ByteArrayOutputStream bo = new ByteArrayOutputStream();
@@ -86,10 +83,6 @@ public class SerializedObject implements Serializable {
         Object result = oi.readObject();
         oi.close();
         return result;
-//		} catch (Exception ex) {
-//			ex.printStackTrace();
-//		}
-//		return null;
     }
 
     /**

src/eva2/tools/StringTools.java

@@ -22,8 +22,8 @@ public final class StringTools {
      * Returns a HTML formatted String, in which each line is at most lineBreak
      * symbols long.
      *
-     * @param string
+     * @param string Text to be converted to HTML
-     * @param lineBreak
+     * @param lineBreak Number of characters until a line break is inserted
      * @return
      */
     public static String toHTML(String string, int lineBreak) {
@@ -129,7 +129,7 @@ public final class StringTools {
                         || (!ignoreCase && (args[i].equals(keys[k])))) { // if the key was found
                     found = true;
                     if (arities[k] == 0) {
-                        values[k] = new String("true");
+                        values[k] = "true";
                     } // and its zero-arity, just return true as its value
                     else { // else return an array of size arity with following strings
                         try {
@@ -302,7 +302,7 @@ public final class StringTools {
      * Concatenate a list of Objects using a given delimiter string.
      * The objects are converted to strings using the BeanInspector class.
      *
-     * @param headlineFields
+     * @param objects
      * @param delim
      * @return
      */
@@ -337,7 +337,7 @@ public final class StringTools {
     /**
      * Remove or replace blanks, braces, etc. from a string for use as a file name.
      *
-     * @param predefName
+     * @param str
      * @return
      */
     public static String simplifySymbols(String str) {

src/eva2/tools/ToolBox.java

@@ -7,8 +7,6 @@ import java.util.List;
 
 /**
  * Collection of miscellaneous static helper methods.
- *
- * @author mkron
  */
 public final class ToolBox {
     /**
@@ -20,28 +18,29 @@ public final class ToolBox {
     /**
      * Convert all items of an enum to a String array and append the given String array at the end.
      *
-     * @param additionals
+     * @param e The enum to convert
+     * @param additionalValues Additional string values
      * @return
      */
-    public static String[] appendEnumAndArray(Enum<?> e, String[] additionals) {
+    public static String[] appendEnumAndArray(Enum<?> e, String[] additionalValues) {
         Enum<?>[] fields = e.getClass().getEnumConstants();
         int enumLen = fields.length; //values().length;
-        int len = enumLen + additionals.length;
+        int len = enumLen + additionalValues.length;
         String[] ret = new String[len];
         for (int i = 0; i < enumLen; i++) {
             ret[i] = fields[i].toString();
         }
 
-        System.arraycopy(additionals, enumLen - enumLen, ret, enumLen, ret.length - enumLen);
+        System.arraycopy(additionalValues, enumLen - enumLen, ret, enumLen, ret.length - enumLen);
         return ret;
     }
 
     /**
      * Append two String arrays. If both are null, null is returned.
      *
-     * @param strArr1
+     * @param strArr1 First array
-     * @param strArr2
+     * @param strArr2 Second array
-     * @return
+     * @return A single array containing the merged set of values
      */
     public static String[] appendArrays(String[] strArr1, String[] strArr2) {
         if (strArr1 == null) {
@@ -82,16 +81,15 @@ public final class ToolBox {
      * converted double arrays whenever this is directly possible, or null otherwise.
      * The length of the array will correspond to the length of the given list.
      *
-     * @param l
+     * @param l A list of Objects
-     * @return
+     * @return A double array containing the converted object values
-     * @see BeanInspector.toString(Object)
      */
     public static Double[] parseDoubles(List<Object> l) {
-        ArrayList<Double> vals = new ArrayList<>();
+        ArrayList<Double> values = new ArrayList<>();
         for (Object o : l) {
-            vals.add(toDouble(o)); // null if unsuccessfull
+            values.add(toDouble(o)); // null if unsuccessful
         }
-        return vals.toArray(new Double[vals.size()]);
+        return values.toArray(new Double[values.size()]);
     }
 
     /**
@@ -107,8 +105,7 @@ public final class ToolBox {
             return ((Number) o).doubleValue();
         } else {
             try {
-                Double d = Double.parseDouble(BeanInspector.toString(o));
+                return Double.parseDouble(BeanInspector.toString(o));
-                return d;
             } catch (Exception e) {
                 // Here be dragons!
             }
@@ -120,9 +117,8 @@ public final class ToolBox {
      * For an array of objects, generate an array of Double which contains the
      * converted double arrays whenever this is directly possible, or null otherwise.
      *
-     * @param l
+     * @param os
-     * @return
+     * @return Double array containing the converted object values.
-     * @see BeanInspector.toString(Object)
      */
     public static Double[] parseDoubles(Object[] os) {
         Double[] vals = new Double[os.length];

src/eva2/tools/chart2d/DArea.java

@@ -94,10 +94,10 @@ public class DArea extends JComponent implements DParent, Printable {
 
     /**
      * method 'adds' a certain border around the contained rectangle that means
-     * that it takes the old border and takes the maxima of the old and the new
+     * that it takes the old border and takes the maximum of the old and the new
      * values
      *
-     * @param clip the java.awt.Insets object of the new clip
+     * @param b The border
      */
     @Override
     public void addDBorder(DBorder b) {
@@ -146,7 +146,7 @@ public class DArea extends JComponent implements DParent, Printable {
 
     /**
      * returns the measures of the DArea The DMeasures object calculates the
-     * different coodinates and contains a Graphics object to paint the
+     * different coordinates and contains a Graphics object to paint the
      * DElements of the area
      *
      * @return the measures of the DArea
@@ -424,8 +424,7 @@ public class DArea extends JComponent implements DParent, Printable {
      * @param pf the @see java.awt.print.PageFormat
      * @param pi the page index
      * @return int @see java.awt.print.Printable
-     * @see java.awt.print.Printable and
+     * @see java.awt.print.Printable
-     * @see java.awt.print.PrintJob
      */
     @Override
     public int print(Graphics g, PageFormat pf, int pi) {

src/eva2/tools/chart2d/DArray.java

@@ -97,7 +97,7 @@ public class DArray implements DIntDoubleMap {
      * the given image value becomes the image of (highest source value + 1)
      *
      * @param image the new image value
-     * @return <code>true<\code> when the minmal or the maximal image value
+     * @return <code>true</code> when the minimal or the maximal image value
      *         has been changed by this method call, else it returns
      *         <code>false</code> @see #getMinImageValue(), #getMaxImageValue()
      */

src/eva2/tools/chart2d/DComponent.java

@@ -6,7 +6,7 @@ import java.awt.*;
  * <code>DComponent</code> is the mother of all objects which can be displayed
  * by a <code>DArea</code> object, even when it would be also enough to
  * implement the <code>DElement</code> interface to an class
- * <p/>
+ * </p>
  * DComponent is abstract because the paint method has to be overridden
  */
 public abstract class DComponent implements DElement {

src/eva2/tools/chart2d/DIntDoubleMap.java

@@ -16,7 +16,7 @@ public interface DIntDoubleMap {
      *
      * @param source the preimage of the image
      * @param image  the new image of the source value
-     * @return <code>true<\code> when the minmal or the maximal image value
+     * @return <code>true</code> when the minimal or the maximal image value
      *         has been changed by this method call, else it returns
      *         <code>false</code> @see #getMinImageValue(), #getMaxImageValue()
      */
@@ -34,7 +34,7 @@ public interface DIntDoubleMap {
      * the image of the highest source value + 1 should be the given image value
      *
      * @param image the new image value
-     * @return <code>true<\code> when the minmal or the maximal image value
+     * @return <code>true</code> when the minimal or the maximal image value
      *         has been changed by this method call, else it returns
      *         <code>false</code> @see #getMinImageValue(), #getMaxImageValue()
      */
@@ -51,23 +51,23 @@ public interface DIntDoubleMap {
      * returns the maximal image value
      *
      * @return the maximal image value
-     * @throw an IllegalArgumentException when it has no image values
+     * @throws IllegalArgumentException when it has no image values
      */
     double getMaxImageValue();
 
     /**
      * returns the minimal image value
      *
-     * @return the minmal image value
+     * @return the minimal image value
-     * @throw an IllegalArgumentException when it has no image values
+     * @throws IllegalArgumentException when it has no image values
      */
     double getMinImageValue();
 
     /**
      * returns the minimal image value
      *
-     * @return the minmal image value
+     * @return the minimal image value
-     * @throw an IllegalArgumentException when it has no image values
+     * @throws IllegalArgumentException when it has no image values
      */
     double getMinPositiveImageValue();
 
@@ -76,7 +76,7 @@ public interface DIntDoubleMap {
      * when at least one of them has changed
      *
      * @return <code>true</code> when either the maximal image value or the
-     *         minmal image value has changed
+     *         minimal image value has changed
      */
     boolean restore();
 

src/eva2/tools/chart2d/DRectangle.java

@@ -202,7 +202,7 @@ public class DRectangle extends DComponent {
     /**
      * method resizes the rectangle to insert p
      *
-     * @param the dPoint p to insert
+     * @param p the dPoint p to insert
      * @return true when the size of the rectangle changed
      */
     public boolean insert(DPoint p) {

src/eva2/tools/chart2d/ScaledBorder.java

@@ -144,8 +144,8 @@ public class ScaledBorder implements Border {
     }
 
     /**
-     * constructor creates a new <code>ScaledBorder<code/>
+     * constructor creates a new <code>ScaledBorder</code>
-     * surrounded by the specified <code>Border<code/>
+     * surrounded by the specified <code>Border</code>
      */
     public ScaledBorder(Border outer) {
         outerBorder = outer;
@@ -171,7 +171,6 @@ public class ScaledBorder implements Border {
     /**
      * method sets the differences between source x-values of the displayed values
      *
-     * @see setAutoScaleX().
      * If scale functions are used there might be a difference between the shown values
      * and the source values
      */
@@ -183,7 +182,6 @@ public class ScaledBorder implements Border {
     /**
      * method sets the differences between source y-values of the displayed values
      *
-     * @see setAutoScaleY().
      * If scale functions are used there might be a difference between the shown values
      * and the source values
      */

src/eva2/tools/math/Jama/util/Maths.java

@@ -3,9 +3,12 @@ package eva2.tools.math.Jama.util;
 public class Maths {
 
     /**
-     * sqrt(a^2 + b^2) without under/overflow. *
+     * sqrt(a^2 + b^2) without under/overflow.
+     *
+     * @param a
+     * @param b
+     * @return
      */
-
     public static double hypot(double a, double b) {
         double r;
         double aa = Math.abs(a);

src/eva2/tools/matlab/JMatLink.java

@@ -20,11 +20,11 @@
 
  * 13.08.1999  thread implementation due to ActiveX thread problem     (0.05) *
 
- * 15.08.1999  intruduced 2 locking mechanisms to lock the engine and         *
+ * 15.08.1999  introduced 2 locking mechanisms to lock the engine and         *
 
  *                wait for data to be return to caller.                (0.06) *
 
- * 16.08.1999  wait for all engine calls to return savely              (0.06a)*
+ * 16.08.1999  wait for all engine calls to return safely              (0.06a)*
 
  * 29.08.1999  made all engine routines "synchronized"                 (0.07) *
 
@@ -113,15 +113,10 @@
 package eva2.tools.matlab;
 
 // **** Thread programming. Notify and start and stop ****
-
 // Look at
-
 // file:///e%7C/jdk1.2/docs/guide/misc/threadPrimitiveDeprecation.html
-
+// on how to suspend, start, stop, interrupt a thread safely in JDK1.2.x
-// on how to suspend, start, stop, interrupt a thread savely in JDK1.2.x
-
 // The problem is ActiveX: one only can make calls to the engine library
-
 // (especially engEvalString) from ONE single thread.
 
 import java.io.UnsupportedEncodingException;

src/eva2/util/ClassPreloader.java

@@ -1,4 +1,4 @@
-package eva2.client;
+package eva2.util;
 
 import eva2.gui.editor.GenericObjectEditor;
 
@@ -6,8 +6,6 @@ import eva2.gui.editor.GenericObjectEditor;
  * This Runnable just requests a number of classes as does the
  * GenericObjectEditor so that they are loaded into the system cache. It can be
  * done at startup time and accelerates later reloading.
- *
- * @author mkron
  */
 public class ClassPreloader implements Runnable {
 

src/eva2/util/EvAComAdapter.java

@@ -1,4 +1,4 @@
-package eva2.client;
+package eva2.util;
 
 
 import eva2.gui.LoggingPanel;

src/eva2/util/package-info.java

@@ -1 +1,4 @@
+/**
+ * Utility classes used in EvA
+ */
 package eva2.util;