More Population testing

refs #53

src/main/java/eva2/optimization/operator/cluster/ClusteringKMeans.java

@@ -305,8 +305,8 @@ public class ClusteringKMeans implements InterfaceClustering, java.io.Serializab
     /**
      * This method calculates the distance between two double values
      *
-     * @param d1
-     * @param d2
+     * @param indy
+     * @param p
      * @return The scalar distances between d1 and d2
      */
     private double distance(AbstractEAIndividual indy, double[] p) {
@@ -357,19 +357,8 @@ public class ClusteringKMeans implements InterfaceClustering, java.io.Serializab
         return metric.distance(species1.getBestEAIndividual(), species2.getBestEAIndividual()) < mergeDist;
     }
 
-//    /** This method decides if a unclustered individual belongs to an already established species.
-//     * @param indy          A unclustered individual.
-//     * @param species       A species.
-//     * @return True or False.
-//     */
-//    public boolean belongsToSpecies(AbstractEAIndividual indy, Population species, Population pop) {
-//        // @todo perhaps the same as in convergingSpecies
-//        return false;
-//    }
-
     @Override
     public int[] associateLoners(Population loners, Population[] species, Population referencePop) {
-//		tmpIndy = (AbstractEAIndividual)loners.getEAIndividual(0).clone();
         int[] res = new int[loners.size()];
         System.err.println("Warning, associateLoners not implemented for " + this.getClass());
         Arrays.fill(res, -1);

src/main/java/eva2/optimization/population/Population.java

@@ -375,7 +375,7 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
         this.historyList = new LinkedList<>();
         this.generationCount = 0;
         this.functionCallCount = 0;
-        double[] popSeed = null;
+        double[] popSeed;
         if (this.populationArchive != null) {
             this.populationArchive.clear();
             this.populationArchive.initialize();

src/main/java/eva2/tools/ToolBox.java

@@ -31,7 +31,7 @@ public final class ToolBox {
             ret[i] = fields[i].toString();
         }
 
-        System.arraycopy(additionalValues, enumLen - enumLen, ret, enumLen, ret.length - enumLen);
+        System.arraycopy(additionalValues, 0, ret, enumLen, ret.length - enumLen);
         return ret;
     }
 

src/test/java/eva2/optimization/population/PopulationTest.java

@@ -25,12 +25,36 @@ public class PopulationTest {
 
     @Test
     public void testGetData() throws Exception {
+        // Simple data
+        emptyPopulation.putData("someInt", 12);
+        assertEquals(12, emptyPopulation.getData("someInt"));
 
+        // Arrays
+        double[] doubleArray = new double[]{1.0};
+        emptyPopulation.putData("someDoubleArray", doubleArray);
+        assertArrayEquals(doubleArray, (double[])emptyPopulation.getData("someDoubleArray"), 0.0);
+
+        // Objects
+        Object obj = new Object();
+        emptyPopulation.putData("someObject", obj);
+        assertEquals(obj, emptyPopulation.getData("someObject"));
     }
 
     @Test
     public void testHasData() throws Exception {
+        assertFalse(emptyPopulation.hasData("someKey"));
 
+        // Simple data
+        emptyPopulation.putData("someInt", 12);
+        assertTrue(emptyPopulation.hasData("someInt"));
+
+        // Arrays
+        emptyPopulation.putData("someDoubleArray", new double[]{1.0});
+        assertTrue(emptyPopulation.hasData("someDoubleArray"));
+
+        // Objects
+        emptyPopulation.putData("someObject", new Object());
+        assertTrue(emptyPopulation.hasData("someObject"));
     }
 
     @Test
@@ -70,22 +94,33 @@ public class PopulationTest {
 
     @Test
     public void testSetUseHistory() throws Exception {
+        emptyPopulation.setUseHistory(true);
+        assertTrue(emptyPopulation.isUsingHistory());
 
+        emptyPopulation.setUseHistory(false);
+        assertFalse(emptyPopulation.isUsingHistory());
     }
 
     @Test
     public void testIsUsingHistory() throws Exception {
-
+        // Not using history by default
+        assertFalse(emptyPopulation.isUsingHistory());
     }
 
     @Test
     public void testSetAutoAging() throws Exception {
+        emptyPopulation.setAutoAging(true);
+        assertTrue(emptyPopulation.isAutoAging());
 
+
+        emptyPopulation.setAutoAging(false);
+        assertFalse(emptyPopulation.isAutoAging());
     }
 
     @Test
     public void testIsAutoAging() throws Exception {
-
+        // Is auto-aging by default
+        assertTrue(emptyPopulation.isAutoAging());
     }
 
     @Test