Remove unneccesary EvA class prefixes from GUI classes.

src/eva2/gui/MainFrame.java

@@ -68,7 +68,7 @@ public class MainFrame extends JFrame implements OptimizationStateListener {
     private long startTime = 0;
     private boolean withGUI = true;
     private boolean withTreeView = false;
-    private EvATabbedFrameMaker frameMaker = null;
+    private TabbedFrameMaker frameMaker = null;
     private Window parentWindow;
 
     private java.util.List<OptimizationStateListener> superListenerList = null;
@@ -719,7 +719,7 @@ public class MainFrame extends JFrame implements OptimizationStateListener {
             newModuleAdapter.addOptimizationStateListener(this);
             try {
                 if (withGUI) {
-                    // this (or rather: EvAModuleButtonPanelMaker) is where the start button etc come from!
+                    // this (or rather: ModuleButtonPanelMaker) is where the start button etc come from!
                     frameMaker = newModuleAdapter.getModuleFrame();
 
                     /* This is the left TabPane on the main frame */
@@ -772,21 +772,21 @@ public class MainFrame extends JFrame implements OptimizationStateListener {
     }
 
     /**
-     * Create a tree view of an object based on EvATreeNode. It is encapsulated
+     * Create a tree view of an object based on TreeNode. It is encapsulated
      * in a JScrollPane.
      *
      * @param goPanel
      * @param title
      * @param object
      * @return
-     * @see eva2.gui.EvATreeNode
+     * @see TreeNode
      */
     public JComponent getEvATreeView(JParaPanel goPanel, String title, Object object) {
-        EvATreeNode root = new EvATreeNode(title, object); // the root of the tree
+        TreeNode root = new TreeNode(title, object); // the root of the tree
         JTree jtree = new JTree(root);
         JScrollPane treeView = new JScrollPane(jtree);
 
-        EvATreeSelectionListener treeListener = new EvATreeSelectionListener(root, goPanel.getEditor(), jtree);
+        TreeSelectionListener treeListener = new TreeSelectionListener(root, goPanel.getEditor(), jtree);
         // hooks itself up as the tree listener. It reacts both to changes in the selection
         // state of the tree (to update the parameter panel) and to changes in the
         // parameters to update the tree

src/eva2/gui/ModuleButtonPanelMaker.java

@@ -16,9 +16,9 @@ import java.util.logging.Logger;
  * Contains the GUI elements of start and stop buttons and optionally a help
  * button.
  */
-public class EvAModuleButtonPanelMaker implements OptimizationStateListener, Serializable, PanelMaker {
+public class ModuleButtonPanelMaker implements OptimizationStateListener, Serializable, PanelMaker {
 
-    private static final Logger LOGGER = Logger.getLogger(EvAModuleButtonPanelMaker.class.getName());
+    private static final Logger LOGGER = Logger.getLogger(ModuleButtonPanelMaker.class.getName());
     private String name = "undefined";
     private ModuleAdapter moduleAdapter;
     private boolean runningState;
@@ -33,7 +33,7 @@ public class EvAModuleButtonPanelMaker implements OptimizationStateListener, Ser
     /**
      *
      */
-    public EvAModuleButtonPanelMaker(ModuleAdapter adapter, boolean state) {
+    public ModuleButtonPanelMaker(ModuleAdapter adapter, boolean state) {
         name = "GENERAL";
         runningState = state;
         moduleAdapter = adapter;

src/eva2/gui/OptimizationEditorPanel.java

@@ -220,7 +220,7 @@ public class OptimizationEditorPanel extends JPanel implements ItemListener {
     }
 
     /**
-     * This method is duplicated from EvAModuleButtonPanelMaker. ToDo: Refactor
+     * This method is duplicated from ModuleButtonPanelMaker. ToDo: Refactor
      * this.
      *
      * @param iconSrc Source path of icon

src/eva2/gui/TabbedFrameMaker.java

@@ -15,16 +15,16 @@ import java.util.logging.Logger;
 /**
  * Produces the main EvA2 frame and a tool bar instance.
  */
-public class EvATabbedFrameMaker implements Serializable, PanelMaker, InterfaceNotifyOnInformers {
+public class TabbedFrameMaker implements Serializable, PanelMaker, InterfaceNotifyOnInformers {
 
-    private static final Logger LOGGER = Logger.getLogger(EvATabbedFrameMaker.class.getName());
+    private static final Logger LOGGER = Logger.getLogger(TabbedFrameMaker.class.getName());
     private static final long serialVersionUID = 2637376545826821423L;
     private ArrayList<PanelMaker> pmContainer = null;
     private JExtToolBar extToolBar;
-    EvAModuleButtonPanelMaker butPanelMkr = null;
+    ModuleButtonPanelMaker butPanelMkr = null;
     private JTabbedPane tabbedPane;
 
-    public EvATabbedFrameMaker() {
+    public TabbedFrameMaker() {
         pmContainer = null;
     }
 
@@ -59,9 +59,9 @@ public class EvATabbedFrameMaker implements Serializable, PanelMaker, InterfaceN
 
         for (PanelMaker element : pmContainer) {
             JComponent panel = element.makePanel();
-            if (element instanceof EvAModuleButtonPanelMaker) {
+            if (element instanceof ModuleButtonPanelMaker) {
                 extToolBar.add(panel);
-                butPanelMkr = (EvAModuleButtonPanelMaker) element;
+                butPanelMkr = (ModuleButtonPanelMaker) element;
             } else if (element instanceof JParaPanel) {
                 tabbedPane.addTab(((JParaPanel) element).getName(), panel);
             }
@@ -95,7 +95,7 @@ public class EvATabbedFrameMaker implements Serializable, PanelMaker, InterfaceN
         if (butPanelMkr != null) {
             butPanelMkr.onUserStart();
         } else {
-            System.err.println("Error: button panel was null (EvATabbedFrameMaker)");
+            System.err.println("Error: button panel was null (TabbedFrameMaker)");
         }
     }
 

src/eva2/gui/TreeNode.java

@@ -13,10 +13,10 @@ import javax.swing.tree.DefaultMutableTreeNode;
  * @see PropertySheetPanel
  * @see eva2.optimization.OptimizationParameters
  */
-public class EvATreeNode extends DefaultMutableTreeNode {
+public class TreeNode extends DefaultMutableTreeNode {
     private String[] childrenNames = null;
     private Object[] childrenValues = null;
-    private String myName = "EvATreeNode";
+    private String myName = "TreeNode";
     private boolean doListPrimitives = false;
 
     /**
@@ -28,7 +28,7 @@ public class EvATreeNode extends DefaultMutableTreeNode {
      * @param name   title of the node
      * @param target
      */
-    public EvATreeNode(String name, Object target) {
+    public TreeNode(String name, Object target) {
         super(target);
         myName = name;
         setObject(target, true);
@@ -67,7 +67,7 @@ public class EvATreeNode extends DefaultMutableTreeNode {
         for (int i = 0; i < childrenValues.length; i++) {
             if (childrenValues[i] != null) {
                 if (doListPrimitives || !(BeanInspector.isJavaPrimitive(childrenValues[i].getClass()))) {
-                    super.add(new EvATreeNode(childrenNames[i], childrenValues[i]));
+                    super.add(new TreeNode(childrenNames[i], childrenValues[i]));
                 }
             }
         }

src/eva2/gui/TreeSelectionListener.java

@@ -2,7 +2,6 @@ package eva2.gui;
 
 import javax.swing.*;
 import javax.swing.event.TreeSelectionEvent;
-import javax.swing.event.TreeSelectionListener;
 import javax.swing.tree.DefaultTreeModel;
 import javax.swing.tree.TreePath;
 import java.awt.*;
@@ -11,16 +10,16 @@ import java.beans.PropertyChangeListener;
 import java.beans.PropertyEditor;
 
 /**
- * Listener for use with the EvATreeNode class. It implements both the tree selection listener
+ * Listener for use with the TreeNode class. It implements both the tree selection listener
  * to react to selection changes in the tree view (and update the parameter panel),
  * and the property change listener to
  * react to changes in the parameters (and update the tree).
  *
  * @author mkron
  */
-public class EvATreeSelectionListener implements TreeSelectionListener, PropertyChangeListener {
+public class TreeSelectionListener implements javax.swing.event.TreeSelectionListener, PropertyChangeListener {
     private PropertyEditor goe = null;
-    private EvATreeNode root = null;
+    private TreeNode root = null;
     private JTree jtree = null;
 
     /**
@@ -31,7 +30,7 @@ public class EvATreeSelectionListener implements TreeSelectionListener, Property
      * @param goEditor the editor containing the parameter panel
      * @param jt       the GUI view of the tree
      */
-    public EvATreeSelectionListener(EvATreeNode rootNode, PropertyEditor goEditor, JTree jt) {
+    public TreeSelectionListener(TreeNode rootNode, PropertyEditor goEditor, JTree jt) {
         goe = goEditor;
         root = rootNode;
         jtree = jt;
@@ -48,13 +47,13 @@ public class EvATreeSelectionListener implements TreeSelectionListener, Property
     public void valueChanged(TreeSelectionEvent e) {
         TreePath tp = e.getPath();
 
-        EvATreeNode leafNode = (EvATreeNode) tp.getLastPathComponent();
+        TreeNode leafNode = (TreeNode) tp.getLastPathComponent();
         Component editComp = goe.getCustomEditor();
         if (editComp instanceof OptimizationEditorPanel) {
             // update the object in the main OptimizationEditorPanel
             ((OptimizationEditorPanel) editComp).setTarget(leafNode.getUserObject());
         } else {
-            System.err.println("Error, unable to notify custom editor of type " + editComp.getClass() + ", expected OptimizationEditorPanel (EvATreeSelectionListener)");
+            System.err.println("Error, unable to notify custom editor of type " + editComp.getClass() + ", expected OptimizationEditorPanel (TreeSelectionListener)");
         }
     }
 

src/eva2/optimization/modules/GenericModuleAdapter.java

@@ -1,8 +1,8 @@
 package eva2.optimization.modules;
 
 
-import eva2.gui.EvAModuleButtonPanelMaker;
+import eva2.gui.ModuleButtonPanelMaker;
-import eva2.gui.EvATabbedFrameMaker;
+import eva2.gui.TabbedFrameMaker;
 import eva2.gui.JParaPanel;
 import eva2.gui.editor.GenericObjectEditor;
 import eva2.optimization.InterfaceOptimizationParameters;
@@ -67,21 +67,21 @@ public class GenericModuleAdapter extends AbstractModuleAdapter implements Seria
      * If the statistics are not of type StatisticsWithGUI, it is assumed that no GUI is
      * desired (and this method should not be called).
      *
-     * @return the EvATabbedFrameMaker
+     * @return the TabbedFrameMaker
      * @see JParaPanel
-     * @see EvAModuleButtonPanelMaker
+     * @see ModuleButtonPanelMaker
      * @see StatisticsWithGUI
      */
     @Override
-    public EvATabbedFrameMaker getModuleFrame() {
+    public TabbedFrameMaker getModuleFrame() {
         if (!(statisticsModule instanceof StatisticsWithGUI)) {
             System.err.println("Error: Unable to create Frame when started with noGUI option (GenericModuleAdapter)!");
             return null;
         }
-        EvATabbedFrameMaker frmMkr = new EvATabbedFrameMaker();
+        TabbedFrameMaker frmMkr = new TabbedFrameMaker();
 
         InterfaceStatisticsParameters Stat = statisticsModule.getStatisticsParameters();
-        EvAModuleButtonPanelMaker buttonPanel = new EvAModuleButtonPanelMaker(remoteModuleAdapter, ((Processor) processor).isOptimizationRunning());
+        ModuleButtonPanelMaker buttonPanel = new ModuleButtonPanelMaker(remoteModuleAdapter, ((Processor) processor).isOptimizationRunning());
         buttonPanel.setHelperFilename(helperFilename);
         frmMkr.addPanelMaker(buttonPanel);
         InterfaceOptimizationParameters optimizationParameters = ((Processor) processor).getOptimizationParameters();

src/eva2/optimization/modules/ModuleAdapter.java

@@ -1,5 +1,5 @@
 package eva2.optimization.modules;
-import eva2.gui.EvATabbedFrameMaker;
+import eva2.gui.TabbedFrameMaker;
 import eva2.optimization.OptimizationStateListener;
 import eva2.optimization.statistics.OptimizationJob;
 
@@ -8,7 +8,7 @@ import eva2.optimization.statistics.OptimizationJob;
  */
 public interface ModuleAdapter extends OptimizationStateListener {
 
-    EvATabbedFrameMaker getModuleFrame();
+    TabbedFrameMaker getModuleFrame();
 
     void startOptimization(); // called from client
 

src/eva2/optimization/operator/postprocess/PostProcess.java

@@ -120,7 +120,7 @@ public class PostProcess {
      * @param epsilon     the threshold up to which an optimum is considered found.
      * @param bTakeFitter if true, the fitter of two close individuals is selected, otherwise the closer one
      * @return a Population of individuals corresponding to the given optima
-     * @see getFoundOptimaArray(Population pop, Population optima, double epsilon, boolean bTakeFitter)
+     * @see #getFoundOptimaArray(Population pop, Population optima, double epsilon, boolean bTakeFitter)
      */
     public static Population getFoundOptima(Population pop, Population optima, double epsilon, boolean bTakeFitter) {
         Population result = new Population(5);
@@ -136,10 +136,10 @@ public class PostProcess {
     }
 
     /**
-     * Calls clusterBest with a ClusteringDensitiyBased clustering object with the given sigma and a
+     * Calls clusterBest with a ClusteringDensityBased clustering object with the given sigma and a
      * minimum group size of 2.
      *
-     * @param pop
+     * @param pop           A population of possible solutions.
      * @param sigmaCluster
      * @param returnQuota
      * @param lonerMode
@@ -265,9 +265,9 @@ public class PostProcess {
      * Returns shallow copies!
      *
      * @param pop
-     * @param fitNorm
+     * @param fitThresh
-     * @param bSmaller if true, return individuals with lower or equal, else with higher fitness only
+     * @param bSmallerEq    if true, return individuals with lower or equal, else with higher fitness only
-     * @param crit     index of the fitness criterion or -1 to use the norm
+     * @param crit          index of the fitness criterion or -1 to use the norm
      * @return
      */
     public static Population filterFitness(Population pop, double fitThresh, boolean bSmallerEq, int crit) {
@@ -363,8 +363,6 @@ public class PostProcess {
      * @return the number of evaluations actually performed
      */
     public static int processWithHC(Population pop, AbstractOptimizationProblem problem, int maxSteps, double stepSize, double minStepSize) {
-//		pop.setFunctionCalls(0); // or else optimization wont restart on an "old" population
-//		pop.setGeneration(0);
         int stepsBef = pop.getFunctionCalls();
         processWithHC(pop, problem, new EvaluationTerminator(pop.getFunctionCalls() + maxSteps), new MutateESMutativeStepSizeControl(stepSize, minStepSize, stepSize));
         return pop.getFunctionCalls() - stepsBef;
@@ -377,7 +375,7 @@ public class PostProcess {
      * @param problem
      * @param maxSteps
      * @return the number of evaluations actually performed
-     * @see processWithHC(Population pop, AbstractOptimizationProblem problem, int maxSteps, double stepSize, double minStepSize)
+     * @see #processWithHC(Population pop, AbstractOptimizationProblem problem, int maxSteps, double stepSize, double minStepSize)
      */
     public static int processWithHC(Population pop, AbstractOptimizationProblem problem, int maxSteps) {
         return processWithHC(pop, problem, maxSteps, defaultMutationStepSize, minMutationStepSize);
@@ -402,7 +400,6 @@ public class PostProcess {
             System.err.println("warning: population size and vector size dont match! (PostProcess::processWithHC)");
         }
         hc.setPopulation(pop);
-//		hc.initializeByPopulation(pop, false);
         OptimizerRunnable ppRunnable = new OptimizerRunnable(OptimizerFactory.makeParams(hc, pop, problem, 0, term), true);
 
         runPP(ppRunnable);
@@ -528,7 +525,7 @@ public class PostProcess {
      * @param initPerturbation
      * @param prob
      * @return
-     * @see NelderMeadSimplex.createNMSPopulation(candidate, perturbRatio, range, includeCand)
+     * @see NelderMeadSimplex#createNMSPopulation(candidate, perturbRatio, range, includeCand)
      */
     public static Pair<AbstractEAIndividual, Integer> localSolverNMS(AbstractEAIndividual cand, int hcSteps,
                                                                      double initPerturbation, AbstractOptimizationProblem prob) {
@@ -549,10 +546,10 @@ public class PostProcess {
      * @param problem
      * @param candidates
      * @param index           index of the individual for which to produce the sub population
-     * @param maxPerturbation
+     * @param maxRelativePerturbation
      * @param includeCand
      * @see #createPopInSubRange(double, AbstractOptimizationProblem, AbstractEAIndividual)
-     * @see #NelderMeadSimplex.createNMSPopulation(AbstractEAIndividual, double, double[][], boolean)
+     * @see NelderMeadSimplex#createNMSPopulation(AbstractEAIndividual, double, double[][], boolean)
      */
     public static Population createLSSupPopulation(PostProcessMethod method, AbstractOptimizationProblem problem, Population candidates, int index, double maxRelativePerturbation, boolean includeCand) {
         Population subPop = null;
@@ -980,7 +977,6 @@ public class PostProcess {
      * @param prob
      * @param hist
      * @param accuracy
-     * @param maxPPEvalsPerIndy
      * @return
      */
     public static Population clusterBestUpdateHistogram(Population pop, AbstractOptimizationProblem prob, SolutionHistogram hist, int crit, double accuracy) {
@@ -1137,8 +1133,8 @@ public class PostProcess {
      * @param treatAsUnknown
      * @param listener
      * @return
-     * @see {@link AbstractOptimizationProblem.extractPotentialOptima}
+     * @see {@link AbstractOptimizationProblem#extractPotentialOptima}
-     * @see AbstractOptimizationProblem.isPotentialOptimumNMS(AbstractEAIndividual, double, double, int)
+     * @see AbstractOptimizationProblem#isPotentialOptimumNMS(AbstractEAIndividual, double, double, int)
      */
     public static int[] checkAccuracy(AbstractOptimizationProblem prob, Population sols, double[] epsilonPhenoSpace,
                                       double extrOptEpsFitConf, double extrOptClustSig, int maxEvals, SolutionHistogram[] solHists, boolean treatAsUnknown,
@@ -1260,9 +1256,9 @@ public class PostProcess {
      * In this case, return the third of the minimum distance to the next neighbor in the population.
      * The maxPerturb can be given as upper bound of the perturbation if it is > 0.
      *
-     * @param candidates population of solutions to look at
+     * @param candidates    population of solutions to look at
-     * @param i          index of the individual in the population to look at
+     * @param i             index of the individual in the population to look at
-     * @param maxPerturb optional upper bound of the returned perturbation
+     * @param maxAbsPerturb optional upper bound of the returned perturbation
      * @return
      */
     public static double findNMSPerturb(Population candidates, int i, double maxAbsPerturb) {
@@ -1400,9 +1396,7 @@ public class PostProcess {
      */
     public static void stopAllPP() {
         synchronized (ppRunnables) {
-            for (OptimizerRunnable rnbl : ppRunnables) {
+            ppRunnables.forEach(OptimizerRunnable::stopOpt);
-                rnbl.stopOpt();
-            }
         }
     }
 }