Resolve numerous warnings

src/main/java/microsim/alignment/multiple/LogitScalingAlignment.java

@@ -2,11 +2,8 @@
 
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.List;
 import java.util.function.Predicate;
 
-import org.apache.commons.collections4.CollectionUtils;
-
 /**
  * Logit Scaling alignment (as introduced by P. Stephensen in International
  * Journal of Microsimulation (2016) 9(3) 89-102),

src/main/java/microsim/data/ExperimentManager.java

@@ -166,7 +166,7 @@ public Experiment setupExperiment(Experiment experiment, Object... models) throw
             // expandODB(experiment.inputFolder + File.separator + inputDatabaseName,
             // outFolder);
 
-            File inputDir = new File(experiment.inputFolder);
+            File inputDir = new File(Experiment.inputFolder);
             if (inputDir.exists()) {
                 String[] files = inputDir.list();
                 for (String file : files) {
@@ -181,7 +181,7 @@ public Experiment setupExperiment(Experiment experiment, Object... models) throw
         } else if (isMultiRun) {
             log.info("Persisting database connection at: " + DatabaseUtils.databaseInputUrl);
         } else {
-            DatabaseUtils.databaseInputUrl = experiment.inputFolder + File.separator + "input";
+            DatabaseUtils.databaseInputUrl = Experiment.inputFolder + File.separator + "input";
         }
 
         if (saveExperimentOnDatabase) {

src/main/java/microsim/data/MultiKeyCoefficientMap.java

@@ -13,12 +13,13 @@
  *
  * @author Ross Richardson
  */
-public class MultiKeyCoefficientMap extends MultiKeyMap {// implements Cloneable {
+// FIXME: this should be generic over <K, V> and leverage composition
+public class MultiKeyCoefficientMap extends MultiKeyMap<Object, Object> {
 
     private static final long serialVersionUID = 5049597007431364596L;
 
     protected String[] keys;
     protected Map<String, Integer> valuesMap;
 
     /**
      * Creates an empty new MultiKeyCoefficientMap with the names of the keys and
@@ -50,7 +51,7 @@
      * @param keys   - a String array listing the names of the categories of keys
      * @param values - a String array listing the names of the categories of values
      */
-    public MultiKeyCoefficientMap(AbstractHashedMap map, String[] keys, String[] values) {
+    public MultiKeyCoefficientMap(AbstractHashedMap<MultiKey<?>, Object> map, String[] keys, String[] values) {
         super(map);
         this.keys = keys;
         if (values != null) {
@@ -107,7 +108,7 @@
                     if (key[0] instanceof MultiKey)
                         return super.get(key[0]);
                     else
-                        return super.get(new MultiKey(new Object[] { key[0] }));
+                        return super.get(new MultiKey<>(new Object[] { key[0] }));
                 case 2:
                     return super.get(key[0], key[1]);
                 case 3:
@@ -131,7 +132,7 @@
                                                     // of the type MultiKey(MultiKey()).
                         value = (Object[]) super.get(key[0]);
                     else
-                        value = (Object[]) super.get(new MultiKey(new Object[] { key[0] }));
+                        value = (Object[]) super.get(new MultiKey<>(new Object[] { key[0] }));
                     return extractValueFromVector(toStringKey(key[1]), value);
                 case 3:
                     value = (Object[]) super.get(key[0], key[1]);
@@ -184,9 +185,9 @@
                                                           // MultiKey is created unnecessarily, which then leads to a
                                                           // null pointer exception as the MultKeyCoefficientMap does
                                                           // not have a key entry of the type MultiKey(MultiKey()).
-                        super.put((MultiKey) keyValues[0], keyValues[1]);
+                        super.put((MultiKey<?>) keyValues[0], keyValues[1]);
                     else {
-                        super.put(new MultiKey(new Object[] { keyValues[0] }), keyValues[1]);
+                        super.put(new MultiKey<>(new Object[] { keyValues[0] }), keyValues[1]);
                     }
                     break;
                 case 3:
@@ -215,7 +216,7 @@
                     if (value == null)
                         value = new Object[valuesMap.size()];
                     putValueToVector((String) keyValues[1], value, keyValues[2]);
-                    super.put(new MultiKey(new Object[] { keyValues[0] }), value);
+                    super.put(new MultiKey<>(new Object[] { keyValues[0] }), value);
                     break;
                 case 4:
                     value = (Object[]) super.get(keyValues[0], keyValues[1]);
@@ -259,14 +260,14 @@
             case 1:
                 throw new IllegalArgumentException("Wrong number of key parameters");
             case 2:
-                MultiKey key0;
+                MultiKey<?> key0;
                 if (keyValues[0] instanceof MultiKey) { // Ross: If we don't do this check, a new MultiKey of a MultiKey
                                                         // is created unnecessarily, which then leads to a null pointer
                                                         // exception as the MultKeyCoefficientMap does not have a key
                                                         // entry of the type MultiKey(MultiKey()).
-                    key0 = (MultiKey) keyValues[0];
+                    key0 = (MultiKey<?>) keyValues[0];
                 } else {
-                    key0 = new MultiKey(new Object[] { keyValues[0] });
+                    key0 = new MultiKey<>(new Object[] { keyValues[0] });
                 }
                 if (super.containsKey(key0))
                     super.remove(key0);
@@ -325,7 +326,7 @@
      */
     @Override
     public MultiKeyCoefficientMap clone() {
-        HashedMap mapClone = new HashedMap(this.decorated());
+        var mapClone = new HashedMap<>(this.decorated());
         return new MultiKeyCoefficientMap(mapClone, this.getKeysNames(), this.getValuesNames());
     }
 }

src/main/java/microsim/data/db/DatabaseUtils.java

@@ -5,7 +5,6 @@
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -253,7 +252,7 @@ public static EntityManager getEntityManger(boolean autoUpdate) {
             try {
                 // Create the EntityManagerFactory
 
-                Map propertyMap = new HashMap();
+                var propertyMap = new HashMap<String, String>();
                 propertyMap.put("hibernate.connection.url", "jdbc:h2:file:" + databaseInputUrl);
                 entityManagerFactory = Persistence.createEntityManagerFactory("sim-model", propertyMap);
 
@@ -273,7 +272,7 @@ public static void inputSchemaUpdateEntityManger() {
             try {
 
                 // Create the EntityManagerFactory
-                Map propertyMap = new HashMap();
+                var propertyMap = new HashMap<String, String>();
                 propertyMap.put("hibernate.connection.url", "jdbc:h2:file:" + DatabaseUtils.databaseInputUrl);
                 EntityManager em = Persistence.createEntityManagerFactory("sim-model", propertyMap)
                         .createEntityManager();
@@ -309,7 +308,7 @@ public static EntityManager getOutEntityManger(String persistenceUnitName) {
             try {
 
                 // Create the EntityManagerFactory
-                Map propertyMap = new HashMap();
+                var propertyMap = new HashMap<String, String>();
                 propertyMap.put("hibernate.connection.url", "jdbc:h2:file:" + DatabaseUtils.databaseOutputUrl);
                 outEntityManagerFactory = Persistence.createEntityManagerFactory(persistenceUnitName, propertyMap);
 

src/main/java/microsim/engine/SimulationEngine.java

@@ -139,13 +139,6 @@ public class SimulationEngine extends Thread {
 
     private ExperimentBuilder experimentBuilder = null;
 
-    /**
-     * @link dependency
-     * @stereotype use
-     * @supplierRole 1..
-     **/
-    /* #SimModel lnkSimModel; */
-
     /**
      * Build a new SimEngine with the given time unit.
      */
@@ -434,7 +427,7 @@ public void buildModels() {
 
         try {
             currentExperiment = ExperimentManager.getInstance().setupExperiment(currentExperiment,
-                    models.toArray(new SimulationManager[models.size()]));
+                    models.toArray());
         } catch (Exception e) {
             e.printStackTrace();
         }
@@ -467,13 +460,14 @@ public boolean getModelBuildStatus() {
      * 
      * @return The list of disposed models.
      */
+    // FIXME: this should return a List<Class<SimulationManager>>
     public synchronized Class<?>[] disposeModels() {
         eventQueue.clear();
 
         modelBuild = false;
 
         // Get models' class type and dispose
-        Class<?>[] cls = new Class[models.size()];
+        var cls = new Class<?>[models.size()];
         for (int i = 0; i < models.size(); i++) {
             SimulationManager model = models.get(i);
             cls[i] = model.getClass();

src/main/java/microsim/event/CollectionTargetEvent.java

@@ -52,7 +52,7 @@
      */
     public CollectionTargetEvent(Collection<?> elements, Class<?> objectType,
             String method, boolean readOnly) throws SimulationException {
         setForObject(elements, objectType, method, readOnly);
     }
 
     /** Create a collection event using early binding method call. */
@@ -75,7 +75,7 @@
         Class<?> cl = objectType;
         while (cl != null)
             try {
-                methodInvoker = cl.getDeclaredMethod(method, null);
+                methodInvoker = cl.getDeclaredMethod(method);
                 return;
             } catch (NoSuchMethodException e) {
                 cl = cl.getSuperclass();
@@ -112,7 +112,7 @@
         if (methodInvoker != null) {
             while (itr.hasNext()) {
                 try {
-                    methodInvoker.invoke(itr.next(), null);
+                    methodInvoker.invoke(itr.next());
                 } catch (InvocationTargetException e) {
                     System.out.println("Object " + methodInvoker + " Method: "
                             + methodInvoker.getName());

src/main/java/microsim/event/EventQueue.java

@@ -59,12 +59,6 @@ public class EventQueue {
     double time = 0;
     // protected List<ISimEventListener> stepListeners;
 
-    /**
-     * @link dependency
-     * @supplierRole 1..
-     **/
-    /* #SimEvent lnkSimEvent; */
-
     /** Build new event queue with TIME_TICKS time unit. */
     public EventQueue() {
         eventQueue = new PriorityQueue<Event>(10);

src/main/java/microsim/event/SingleTargetEvent.java

@@ -70,7 +70,7 @@ public void setForObject(Object o, String method) throws SimulationException {
         Class<?> cl = o.getClass();
         while (cl != null)
             try {
-                methodInvoker = cl.getDeclaredMethod(method, null);
+                methodInvoker = cl.getDeclaredMethod(method);
                 return;
             } catch (NoSuchMethodException e) {
                 cl = cl.getSuperclass();
@@ -105,7 +105,7 @@ public String toString() {
     public void fireEvent() {
         if (methodInvoker != null) {
             try {
-                methodInvoker.invoke(object, null);
+                methodInvoker.invoke(object);
             } catch (InvocationTargetException e) {
                 System.out.println("Object " + methodInvoker + " Method: "
                         + methodInvoker.getName());

src/main/java/microsim/gui/colormap/DoubleRangeColorMap.java

@@ -43,9 +43,9 @@ public DoubleRangeColorMap(int gradients, Color bottomColor, Color topColor,
         for (int i = 0; i < gradients; i++) {
             // int[] c = getComponents(getBoundedCol(i * gap));
             int[] c = new int[] { 0, 0, 0 };
-            c[0] = redStart + (int) ((redEnd - redStart) * i / gradients);
-            c[1] = greenStart + (int) ((greenEnd - redStart) * i / gradients);
-            c[2] = blueStart + (int) ((blueEnd - redStart) * i / gradients);
+            c[0] = redStart + ((redEnd - redStart) * i / gradients);
+            c[1] = greenStart + ((greenEnd - redStart) * i / gradients);
+            c[2] = blueStart + ((blueEnd - redStart) * i / gradients);
 
             addColor(i, new Color(c[0], c[1], c[2]));
         }

src/main/java/microsim/gui/colormap/TripleRangeColorMap.java

@@ -71,19 +71,19 @@ public TripleRangeColorMap(int gradients, Color bottomColor, Color middleColor,
         for (int i = 0; i < lowGradients; i++) {
             // int[] c = getComponents(getBoundedCol(i * gap));
             int[] c = new int[] { 0, 0, 0 };
-            c[0] = redStart + (int) ((redMiddle - redStart) * i / gradients);
-            c[1] = greenStart + (int) ((greenMiddle - greenStart) * i / gradients);
-            c[2] = blueStart + (int) ((blueMiddle - blueStart) * i / gradients);
+            c[0] = redStart + ((redMiddle - redStart) * i / gradients);
+            c[1] = greenStart + ((greenMiddle - greenStart) * i / gradients);
+            c[2] = blueStart + ((blueMiddle - blueStart) * i / gradients);
 
             addColor(i, new Color(c[0], c[1], c[2]));
         }
 
         for (int i = lowGradients; i < gradients; i++) {
             // int[] c = getComponents(getBoundedCol(i * gap));
             int[] c = new int[] { 0, 0, 0 };
-            c[0] = redMiddle + (int) ((redEnd - redMiddle) * i / gradients);
-            c[1] = greenMiddle + (int) ((greenEnd - greenMiddle) * i / gradients);
-            c[2] = blueMiddle + (int) ((blueEnd - blueMiddle) * i / gradients);
+            c[0] = redMiddle + ((redEnd - redMiddle) * i / gradients);
+            c[1] = greenMiddle + ((greenEnd - greenMiddle) * i / gradients);
+            c[2] = blueMiddle + ((blueEnd - blueMiddle) * i / gradients);
 
             addColor(i, new Color(c[0], c[1], c[2]));
         }

src/main/java/microsim/gui/plot/CollectionBarSimulationPlotter.java

@@ -236,7 +236,7 @@ public void onEvent(Enum<?> type) {
 
     public void update() {
         for (int i = 0; i < sources.size(); i++) {
-            ArraySource cs = (ArraySource) sources.get(i);
+            var cs = sources.get(i);
             final String category = categories.get(i);
 
             double[] vals = cs.getDoubleArray();

src/main/java/microsim/gui/plot/HistogramSimulationPlotter.java

@@ -226,7 +226,7 @@ public void update() {
         // chart.getXYPlot().getRenderer().setSeriesPaint(s, new Color(r, g, b, 130));
 
         for (int i = 0; i < sources.size(); i++) {
-            ArraySource cs = (ArraySource) sources.get(i);
+            var cs = sources.get(i);
             double[] vals = cs.getDoubleArray();
 
             if (minimum != null && maximum != null) {

src/main/java/microsim/gui/plot/IndividualBarSimulationPlotter.java

@@ -8,7 +8,6 @@
 
 import microsim.event.CommonEventType;
 import microsim.event.EventListener;
-import microsim.gui.colormap.ColorMap;
 import microsim.gui.colormap.FixedColorMap;
 import microsim.reflection.ReflectionUtils;
 import microsim.statistics.IDoubleSource;

src/main/java/microsim/gui/plot/ScatterplotSimulationPlotterRefreshable.java

@@ -1,10 +1,7 @@
 package microsim.gui.plot;
 
-//package microsim.gui.plot;
-
 import java.awt.Color;
 import java.util.ArrayList;
-import java.util.List;
 
 import javax.swing.JInternalFrame;
 
@@ -773,10 +770,8 @@ public void setMaxSamples(int maxSamples) {
 
     public void refresh() {
 
-        List data = dataset.getSeries();
-        for (int i = 0; i < data.size(); i++) {
-            XYSeries series = (XYSeries) data.get(i);
-            series.clear();
+        for (int i = 0; i < dataset.getSeriesCount(); i++) {
+            dataset.getSeries(i).clear();
         }
 
     }