From be15f8880236453de72399d959ea53fd1b0dd38a Mon Sep 17 00:00:00 2001
From: Marcel Kronfeld <makron@gmx.net>
Date: Mon, 17 Jan 2011 16:03:30 +0000
Subject: [PATCH] Some adaptions and a new GA mutation operator

---
 .../individuals/GAIndividualBinaryData.java   |   1 +
 .../individuals/GAIndividualIntegerData.java  |   2 +-
 .../crossover/CrossoverGANPoint.java          |   6 +
 .../GAInitializeSegmentwise.java              |   1 -
 .../go/operators/mutation/MutateEAMixer.java  |   9 +-
 .../mutation/MutateGAShiftSubstring.java      | 158 ++++++++++++++++++
 .../operators/selection/SelectTournament.java |   5 +
 .../server/go/populations/Population.java     |  13 ++
 8 files changed, 192 insertions(+), 3 deletions(-)
 create mode 100644 src/eva2/server/go/operators/mutation/MutateGAShiftSubstring.java

diff --git a/src/eva2/server/go/individuals/GAIndividualBinaryData.java b/src/eva2/server/go/individuals/GAIndividualBinaryData.java
index 31dbfc24..e22d61d2 100644
--- a/src/eva2/server/go/individuals/GAIndividualBinaryData.java
+++ b/src/eva2/server/go/individuals/GAIndividualBinaryData.java
@@ -131,6 +131,7 @@ public class GAIndividualBinaryData extends AbstractEAIndividual implements Inte
         result += "})\n Value: ";
         result += "{";
         for (int i = 0; i < this.m_GenotypeLength; i++) {
+            if (i%10==0) result+="|";
             if (this.m_Genotype.get(i)) result += "1";
             else result += "0";
         }
diff --git a/src/eva2/server/go/individuals/GAIndividualIntegerData.java b/src/eva2/server/go/individuals/GAIndividualIntegerData.java
index 1229aef3..18536fb9 100644
--- a/src/eva2/server/go/individuals/GAIndividualIntegerData.java
+++ b/src/eva2/server/go/individuals/GAIndividualIntegerData.java
@@ -28,7 +28,7 @@ public class GAIndividualIntegerData extends AbstractEAIndividual implements Int
     private InterfaceGAIntegerCoding    m_IntegerCoding          = new GAStandardCodingInteger();
 
     public GAIndividualIntegerData() {
-        this.m_MutationProbability  = 0.1;
+        this.m_MutationProbability  = 0.2;
         this.m_MutationOperator     = new MutateGANBit();
         this.m_CrossoverProbability = 0.7;
         this.m_CrossoverOperator    = new CrossoverGANPoint();
diff --git a/src/eva2/server/go/operators/crossover/CrossoverGANPoint.java b/src/eva2/server/go/operators/crossover/CrossoverGANPoint.java
index 74dd0caf..782610fe 100644
--- a/src/eva2/server/go/operators/crossover/CrossoverGANPoint.java
+++ b/src/eva2/server/go/operators/crossover/CrossoverGANPoint.java
@@ -23,6 +23,12 @@ public class CrossoverGANPoint implements InterfaceCrossover, java.io.Serializab
     public CrossoverGANPoint() {
 
     }
+    
+    public CrossoverGANPoint(int nPoints) {
+    	this();
+    	setNumberOfCrossovers(nPoints);
+    }
+    
     public CrossoverGANPoint(CrossoverGANPoint mutator) {
         this.m_OptimizationProblem    = mutator.m_OptimizationProblem;
         this.m_NumberOfCrossovers     = mutator.m_NumberOfCrossovers;
diff --git a/src/eva2/server/go/operators/initialization/GAInitializeSegmentwise.java b/src/eva2/server/go/operators/initialization/GAInitializeSegmentwise.java
index d33facd7..f1b3e23d 100644
--- a/src/eva2/server/go/operators/initialization/GAInitializeSegmentwise.java
+++ b/src/eva2/server/go/operators/initialization/GAInitializeSegmentwise.java
@@ -49,7 +49,6 @@ public class GAInitializeSegmentwise implements InterfaceInitialization, java.io
 		return new GAInitializeSegmentwise(this);
 	}
 	
-	@Override
 	public void initialize(AbstractEAIndividual indy,
 			InterfaceOptimizationProblem problem) {
 		if (indy instanceof InterfaceGAIndividual) {
diff --git a/src/eva2/server/go/operators/mutation/MutateEAMixer.java b/src/eva2/server/go/operators/mutation/MutateEAMixer.java
index 439310ef..7d27e669 100644
--- a/src/eva2/server/go/operators/mutation/MutateEAMixer.java
+++ b/src/eva2/server/go/operators/mutation/MutateEAMixer.java
@@ -56,7 +56,14 @@ public class MutateEAMixer implements InterfaceMutation, java.io.Serializable  {
      */
     public MutateEAMixer(InterfaceMutation ... mutators) {
         this.m_Mutators         = new PropertyMutationMixer(mutators, true);
-        this.m_UseSelfAdaption  = false;
+    }
+    
+    public MutateEAMixer(InterfaceMutation m1, InterfaceMutation m2) {
+    	this(new InterfaceMutation[] {m1, m2});
+    }
+    
+    public MutateEAMixer(InterfaceMutation m1, InterfaceMutation m2, InterfaceMutation m3) {
+    	this(new InterfaceMutation[] {m1, m2, m3});
     }
     
     public MutateEAMixer(MutateEAMixer mutator) {
diff --git a/src/eva2/server/go/operators/mutation/MutateGAShiftSubstring.java b/src/eva2/server/go/operators/mutation/MutateGAShiftSubstring.java
new file mode 100644
index 00000000..41bed7e1
--- /dev/null
+++ b/src/eva2/server/go/operators/mutation/MutateGAShiftSubstring.java
@@ -0,0 +1,158 @@
+package eva2.server.go.operators.mutation;
+
+
+import java.util.BitSet;
+
+import eva2.server.go.individuals.AbstractEAIndividual;
+import eva2.server.go.individuals.InterfaceGAIndividual;
+import eva2.server.go.populations.Population;
+import eva2.server.go.problems.InterfaceOptimizationProblem;
+import eva2.tools.math.RNG;
+
+/**
+ * Shift a certain substring within the individual. The length and shift distance
+ * can be predefined or will be selected at random. The shift is performed cyclic.
+ * 
+ * @author mkron
+ *
+ */
+public class MutateGAShiftSubstring implements InterfaceMutation, java.io.Serializable {
+
+	private int         m_subStringLength = 0;
+    private int         m_shiftDistance   = 0;
+
+	public MutateGAShiftSubstring() {
+
+	}
+	public MutateGAShiftSubstring(MutateGAShiftSubstring mutator) {
+        this.m_subStringLength        = mutator.m_subStringLength;
+        this.m_shiftDistance        = mutator.m_shiftDistance;
+	}
+
+	/** This method will enable you to clone a given mutation operator
+	 * @return The clone
+	 */
+	public Object clone() {
+		return new MutateGAShiftSubstring(this);
+	}
+    
+    /** This method allows you to evaluate wether two mutation operators
+     * are actually the same.
+     * @param mutator   The other mutation operator
+     */
+    public boolean equals(Object mutator) {
+        if (mutator instanceof MutateGAShiftSubstring) {
+            MutateGAShiftSubstring mut = (MutateGAShiftSubstring)mutator;
+            if (this.m_subStringLength != mut.m_subStringLength) return false;
+            if (this.m_shiftDistance != mut.m_shiftDistance) return false;
+            return true;
+        } else return false;
+    }
+
+	/** This method allows you to init the mutation operator
+	 * @param individual      The individual that will be mutated.
+     * @param opt               The optimization problem.
+     */
+    public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
+
+	}
+
+	/** 
+	 * This method will mutate a given AbstractEAIndividual. If the individual
+	 * doesn't implement InterfaceGAIndividual nothing happens.
+	 * @param individual    The individual that is to be mutated
+	 */
+	public void mutate(AbstractEAIndividual individual) {
+//		System.out.println("Before Mutate: " +(individual.getStringRepresentation()));
+		if (individual instanceof InterfaceGAIndividual) {
+			BitSet      tmpBitSet   = (BitSet)((InterfaceGAIndividual)individual).getBGenotype().clone();
+			int len = ((InterfaceGAIndividual)individual).getGenotypeLength();
+//			System.out.println(tmpBitSet.cardinality());
+			int[] substr = selectSubstring(tmpBitSet, len);
+			int a=substr[0];
+			int b=substr[1];
+			int d = selectShiftDist(len);
+//			System.out.println("a, b, d: " + a + " " + b + " " + d);
+			for (int i = 0; i <b-a+1; i++) {
+//                System.out.println("Indices: " + (len+a-d+i)%len + "<-"  + (len+a+i)%len );
+                tmpBitSet.set((len+a-d+i)%len, tmpBitSet.get((len+a+i)%len));
+            }
+			BitSet      origBitSet   = (BitSet)((InterfaceGAIndividual)individual).getBGenotype();
+			for (int i = 0; i <d; i++) {
+//                System.out.println("Indices: " + (len+b-d+i+1)%len + "<-" + ((len+a-d+i)%len));
+                tmpBitSet.set((len+b-d+i+1)%len, origBitSet.get((len+a-d+i)%len));
+            }
+//			System.out.println(tmpBitSet.cardinality());
+			((InterfaceGAIndividual)individual).SetBGenotype(tmpBitSet);
+		}
+//		System.out.println("After Mutate: " +(individual.getStringRepresentation()));
+	}
+
+    private int selectShiftDist(int len) {
+    	if (m_shiftDistance<=0) return RNG.randomInt(len);
+    	else return m_shiftDistance;
+	}
+    
+	private int[] selectSubstring(BitSet tmpBitSet, int len) {
+		int[] str = new int[2];
+		if (m_subStringLength<=0) {
+			str[0]=RNG.randomInt(len); // TODO check for collision? Not a problem in higher dims...
+			str[1]=RNG.randomInt(len);
+		} else {
+			str[0]=RNG.randomInt(len);
+			str[1]=m_subStringLength+str[0]-1; // this may be larger than len, but its modulo-ed away in mutate
+		}
+		return str;
+	}
+	/** This method allows you to perform either crossover on the strategy parameters
+     * or to deal in some other way with the crossover event.
+     * @param indy1     The original mother
+     * @param partners  The original partners
+     */
+    public void crossoverOnStrategyParameters(AbstractEAIndividual indy1, Population partners) {
+        // nothing to do here
+    }
+
+	/** This method allows you to get a string representation of the mutation
+	 * operator
+	 * @return A descriptive string.
+	 */
+	public String getStringRepresentation() {
+		return "GA inversion mutation";
+	}
+
+/**********************************************************************************************************************
+ * These are for GUI
+ */
+	/** This method allows the CommonJavaObjectEditorPanel to read the
+	 * name to the current object.
+	 * @return The name.
+	 */
+	public String getName() {
+		return "GA shift bitstring mutation";
+	}
+	/** This method returns a global info string
+	 * @return description
+	 */
+	public static String globalInfo() {
+		return "This mutation operator shifts n successive along the genotype (cyclic).";
+	}
+	public int getSubStringLength() {
+		return m_subStringLength;
+	}
+	public void setSubStringLength(int stringLength) {
+		m_subStringLength = stringLength;
+	}
+	public String subStringLengthTipText() {
+		return "Length of substring to shift or zero to select it at random";
+	}
+	public int getShiftDistance() {
+		return m_shiftDistance;
+	}
+	public void setShiftDistance(int distance) {
+		m_shiftDistance = distance;
+	}
+	public String shiftDistanceTipText() {
+		return "Distance by which to shift (to the left) or zero to select it at random";
+	}
+}
\ No newline at end of file
diff --git a/src/eva2/server/go/operators/selection/SelectTournament.java b/src/eva2/server/go/operators/selection/SelectTournament.java
index 0cdc102e..f79d5eaf 100644
--- a/src/eva2/server/go/operators/selection/SelectTournament.java
+++ b/src/eva2/server/go/operators/selection/SelectTournament.java
@@ -22,6 +22,11 @@ public class SelectTournament implements InterfaceSelection, java.io.Serializabl
     public SelectTournament() {
     }
 
+    public SelectTournament(int tSize) {
+    	this();
+    	setTournamentSize(tSize);
+    }
+    
     public SelectTournament(SelectTournament a) {
         this.m_TournamentSize       = a.m_TournamentSize;
         this.m_ObeyDebsConstViolationPrinciple = a.m_ObeyDebsConstViolationPrinciple;
diff --git a/src/eva2/server/go/populations/Population.java b/src/eva2/server/go/populations/Population.java
index 329c7c57..5d19ac0d 100644
--- a/src/eva2/server/go/populations/Population.java
+++ b/src/eva2/server/go/populations/Population.java
@@ -142,6 +142,19 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
 		}
 	}
 
+	/**
+	 * Initialize a population with a binCardinality initialization, meaning that
+	 * the individuals are initialized with N(binCard, binStdDev) bits set.
+	 * @param targetSize
+	 * @param binCard
+	 * @param binStdDev
+	 */
+	public Population(int targetSize, int binCard, int binStdDev) {
+		this(targetSize);
+		this.setSeedCardinality(new Pair<Integer,Integer>(binCard, binStdDev));
+		this.setInitMethod(PopulationInitMethod.binCardinality);
+	}
+	
 	public void hideHideable() {
 		setInitMethod(getInitMethod());
 	}