Added an abstraction over individual initialization methods.

src/eva2/server/go/individuals/AbstractEAIndividual.java

@@ -13,6 +13,8 @@ import eva2.server.go.individuals.codings.gp.InterfaceProgram;
 import eva2.server.go.operators.constraint.InterfaceConstraint;
 import eva2.server.go.operators.crossover.InterfaceCrossover;
 import eva2.server.go.operators.crossover.NoCrossover;
+import eva2.server.go.operators.initialization.DefaultInitialization;
+import eva2.server.go.operators.initialization.InterfaceInitialization;
 import eva2.server.go.operators.mutation.InterfaceMutation;
 import eva2.server.go.operators.mutation.NoMutation;
 import eva2.server.go.populations.Population;
@@ -58,7 +60,9 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
     protected double                           m_MutationProbability   = 0.2;
     protected InterfaceMutation             m_MutationOperator      = new NoMutation();
     protected InterfaceCrossover            m_CrossoverOperator     = new NoCrossover();
-//    protected String[]                      m_Identifiers           = new String[m_ObjectIncrement];
+    protected InterfaceInitialization		m_InitOperator		= new DefaultInitialization();
+
+	//    protected String[]                      m_Identifiers           = new String[m_ObjectIncrement];
 //    protected Object[]                      m_Objects               = new Object[m_ObjectIncrement];
     protected HashMap<String,Object> 		m_dataHash 				= new HashMap<String,Object>();
     
@@ -148,6 +152,7 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
         m_Marked            = individual.m_Marked;
         m_isPenalized		= individual.m_isPenalized;
         individualIndex = individual.individualIndex;
+        m_InitOperator = individual.m_InitOperator.clone();
         if (individual.parentIDs != null) {
         	parentIDs = new Long[individual.parentIDs.length];
         	System.arraycopy(individual.parentIDs, 0, parentIDs, 0, parentIDs.length);
@@ -271,7 +276,8 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
      * @param opt   The optimization problem that is to be solved.
      */
     public void init(InterfaceOptimizationProblem opt) {
-        this.defaultInit(opt);
+    	m_InitOperator.initialize(this, opt);
+//        this.defaultInit(opt);
         this.m_MutationOperator.init(this, opt);
         this.m_CrossoverOperator.init(this, opt);
     }
@@ -815,6 +821,16 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
         return "The chance that crossover occurs.";
     }
 
+    public InterfaceInitialization getInitOperator() {
+		return m_InitOperator;
+	}
+	public void setInitOperator(InterfaceInitialization mInitOperator) {
+		m_InitOperator = mInitOperator;
+	}
+    public String initOperatorTipText() {
+    	return "An initialization method for the individual";
+    }
+	
     /** This method allows you to store an arbitrary value under an arbitrary
      * name.
      * @param name      The identifying name.

src/eva2/server/go/operators/initialization/DefaultInitialization.java

@@ -0,0 +1,32 @@
+package eva2.server.go.operators.initialization;
+
+import eva2.server.go.individuals.AbstractEAIndividual;
+import eva2.server.go.problems.InterfaceOptimizationProblem;
+
+/**
+ * A dummy initialization method which only calls the default init method of the individual.
+ * 
+ * @author mkron
+ *
+ */
+public class DefaultInitialization implements InterfaceInitialization, java.io.Serializable { 
+	private static final long serialVersionUID = 1L;
+
+	public DefaultInitialization() {}
+	
+	public void initialize(AbstractEAIndividual indy, InterfaceOptimizationProblem problem) {
+		indy.defaultInit(problem);
+	}
+	
+	public InterfaceInitialization clone() {
+		return new DefaultInitialization();
+	}
+	
+	public String getName() {
+		return "DefaultInitialization";
+	}
+	
+	public String globalInfo() {
+		return "Uses the standard initialization of the individual implementation";
+	}
+}

src/eva2/server/go/operators/initialization/GAInitializeSegmentwise.java

@@ -0,0 +1,125 @@
+package eva2.server.go.operators.initialization;
+
+import java.util.BitSet;
+
+import eva2.server.go.individuals.AbstractEAIndividual;
+import eva2.server.go.individuals.InterfaceGAIndividual;
+import eva2.server.go.problems.InterfaceOptimizationProblem;
+import eva2.tools.EVAERROR;
+import eva2.tools.math.RNG;
+
+/**
+ * An initialization method which sets a fixed number of bits per segment,
+ * where a segment is a connected subsequence of the genotype.
+ * This is usable for GA individuals only.
+ * 
+ * The initialization may be parameterized in two ways, where each takes a fixed
+ * segment length s. Firstly, a fixed number of bits (k<=s) is set per segment,
+ * so each segment has equal cardinality.
+ * Secondly, an int-array can be specified which defines possibly varying k_i for
+ * each segment i, so different segments may have different cardinaltiy. The array
+ * must comply to the binary genotype length of the problem. The array definition
+ * has strict priority over the fixed cardinality definition.  
+ * 
+ * @author mkron
+ *
+ */
+public class GAInitializeSegmentwise implements InterfaceInitialization, java.io.Serializable {
+	protected int[] bitsPerSegmentArray = new int[0];
+	private int bitsPerSegment=1;
+	private int segmentLength=4;
+	
+	public GAInitializeSegmentwise() {}
+	
+	public GAInitializeSegmentwise(GAInitializeSegmentwise o) {
+		bitsPerSegment = o.bitsPerSegment;
+		segmentLength = o.segmentLength;
+		if (o.bitsPerSegmentArray!=null) {
+			bitsPerSegmentArray = new int[o.bitsPerSegmentArray.length];
+			System.arraycopy(o.bitsPerSegmentArray, 0, bitsPerSegmentArray, 0, bitsPerSegmentArray.length);
+		}
+	}
+	
+	public GAInitializeSegmentwise(int segLen, int[] bitsPerSeg) {
+		segmentLength = segLen;
+		bitsPerSegmentArray = bitsPerSeg;
+	}
+	
+	public InterfaceInitialization clone() {
+		return new GAInitializeSegmentwise(this);
+	}
+	
+	@Override
+	public void initialize(AbstractEAIndividual indy,
+			InterfaceOptimizationProblem problem) {
+		if (indy instanceof InterfaceGAIndividual) {
+			InterfaceGAIndividual gaIndy =  ((InterfaceGAIndividual)indy);
+			int genotypeLen = gaIndy.getGenotypeLength();
+			BitSet genotype = gaIndy.getBGenotype();
+			if (bitsPerSegmentArray==null || (bitsPerSegmentArray.length==0)) {
+				// regard only a fixed number of bits per segment
+				for (int i=0; i<genotypeLen; i+=segmentLength) {
+					// create the next segment
+					BitSet nextSeg=RNG.randomBitSet(bitsPerSegment, segmentLength);
+					for (int k=i;k<i+segmentLength; k++) {
+						// transfer the new segment to the genotype
+						if (k<genotypeLen) genotype.set(k, nextSeg.get(k-i));
+					}
+				}
+				// write back the genotype (it may have been cloned, who knows...)
+				gaIndy.SetBGenotype(genotype);
+			} else { // the number of bits to set may vary from segment to segment.
+				if (bitsPerSegmentArray.length * segmentLength != genotypeLen) EVAERROR.errorMsgOnce("Warning, potential mismatch between segment lengths and genotype length in " + this.getClass());
+				if (bitsPerSegmentArray.length * segmentLength < genotypeLen) System.err.println("Warning, " + (genotypeLen - bitsPerSegmentArray.length * segmentLength) + " bits will not be initialized!");
+				for (int s=0; s<bitsPerSegmentArray.length; s++) {
+					// look at each segment individually
+					BitSet nextSeg=RNG.randomBitSet(bitsPerSegmentArray[s], bitsPerSegment);
+					for (int k=(s)*bitsPerSegment; k<(s+1)*bitsPerSegment; k++) {
+						if (k<genotypeLen) genotype.set(k, nextSeg.get(k-(s*bitsPerSegment)));
+					}
+				}
+			}
+		} else throw new RuntimeException("Error: "+ this.getClass() + " must be used with individuals of type " + InterfaceGAIndividual.class + "!");
+	}
+
+	
+	public int[] getBitsPerSegmentArray() {
+		return bitsPerSegmentArray;
+	}
+	public void setBitsPerSegmentArray(int[] bitsPerSegmentArray) {
+		this.bitsPerSegmentArray = bitsPerSegmentArray;
+	}
+	public String bitsPerSegmentArrayTipText() {
+		return "A value per segment defining the number of bits to set for that segment, or null if fixed";
+	}
+
+	public int getBitsPerSegment() {
+		return bitsPerSegment;
+	}
+	public void setBitsPerSegment(int bitsPerSegment) {
+		this.bitsPerSegment = bitsPerSegment;
+	}
+	public String bitsPerSegmentTipText() {
+		return "If not array-wise defined, this fixed number of bits is set per segment";
+	}
+
+	public int getSegmentLength() {
+		return segmentLength;
+	}
+	public void setSegmentLength(int segmentLength) {
+		this.segmentLength = segmentLength;
+	}
+	public String segmentLengthTipText() {
+		return "The fixed length of a segment, which is a substring of the binary genotype";
+	}
+	
+	////////
+	public String getName() {
+		return "GA segment-wise init";
+	}
+	
+	public String globalInfo() {
+		return "A method which initializes a fixed number of bits per binary segment, which is a fixed number" +
+				"of bits for substrings of equal length"; 
+	}
+}

src/eva2/server/go/operators/initialization/InterfaceInitialization.java

@@ -0,0 +1,31 @@
+package eva2.server.go.operators.initialization;
+
+import eva2.server.go.individuals.AbstractEAIndividual;
+import eva2.server.go.problems.InterfaceOptimizationProblem;
+
+/**
+ * An abstraction over individual initialization methods in analogy
+ * to mutation and crossover. It is member of every abstract individual
+ * but the specific implementation may depend on the data type of the
+ * individual.
+ * 
+ * @author mkron
+ *
+ */
+public interface InterfaceInitialization {
+	
+	/**
+	 * Perform initialization of a given individual, which may potentially depend on 
+	 * a problem instance.
+	 * 
+	 * @param indy 	the target individual to initialize
+	 * @param problem	the problem instance under consideration
+	 */
+	public void initialize(AbstractEAIndividual indy, InterfaceOptimizationProblem problem);
+
+	/**
+	 * A specific cloning method.
+	 * @return
+	 */
+	public InterfaceInitialization clone();
+}

src/eva2/tools/math/RNG.java

@@ -4,6 +4,8 @@ import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.Random;
 
+import eva2.tools.EVAERROR;
+
 
 public class RNG {
 	private static Random random;
@@ -289,6 +291,10 @@ public class RNG {
 	 * Create a random bitset with given cardinality and lengths, 
 	 */
 	public static BitSet randomBitSet(int cardinality, int length) {
+		if (cardinality>length) {
+			EVAERROR.errorMsgOnce("Error, invalid cardinality " + cardinality + " requested for bit length "+ length +", cardinality will be reduced.");
+			cardinality=length;
+		}
 		BitSet bs = new BitSet(length);
 		int[] perm = randomPerm(length);
 		for (int i=0; i<cardinality; i++) {