Some updates, mainly GP stuff...

src/eva2/gui/GOEPanel.java

@@ -221,6 +221,7 @@ public class GOEPanel extends JPanel implements ItemListener {
 //			System.out.println("Copying " + BeanInspector.toString(source));
 			SerializedObject so = new SerializedObject(source);
 			result = so.getObject();
+			so=null;
 		} catch (Exception ex) {
 			System.err.println("GenericObjectEditor: Problem making backup object");
 			System.err.println(source.getClass().getName());

src/eva2/gui/GenericArrayEditor.java

@@ -114,6 +114,7 @@ implements PropertyEditor {
 				try {
 					SerializedObject so = new SerializedObject(addObj);
 					addObj = so.getObject();
+					so=null;
 					if (selected != -1) {
 						m_ListModel.insertElementAt(addObj, selected);
 					} else {

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

@@ -949,7 +949,7 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
                 if ((i+1) < b.length) sb.append(separator);
             }
         } else if (individual instanceof InterfaceDataTypeProgram) {
-            InterfaceProgram[] b = ((InterfaceDataTypeProgram)individual).getProgramData();
+            InterfaceProgram[] b = ((InterfaceDataTypeProgram)individual).getProgramDataWithoutUpdate();
             for (int i = 0; i < b.length; i++) {
                 sb.append(b[i].getStringRepresentation());
                 if ((i+1) < b.length) sb.append(separator);

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

@@ -27,7 +27,7 @@ public class GPIndividualProgramData extends AbstractEAIndividual implements Int
     protected GPArea[]                    m_Area;
     protected double                      m_InitFullGrowRatio   = 0.5;
     protected int                         m_InitDepth           = 4;
-    protected int                         m_maxDepth         = 8;
+    protected int                         m_maxAllowedDepth         = 8;
     protected boolean                     m_CheckMaxDepth    = true;
 
     public GPIndividualProgramData() {
@@ -58,7 +58,7 @@ public class GPIndividualProgramData extends AbstractEAIndividual implements Int
         }
         this.m_InitFullGrowRatio        = individual.m_InitFullGrowRatio;
         this.m_InitDepth                = individual.m_InitDepth;
-        this.m_maxDepth              = individual.m_maxDepth;
+        this.m_maxAllowedDepth              = individual.m_maxAllowedDepth;
         this.m_CheckMaxDepth         = individual.m_CheckMaxDepth;
 
         // cloning the members of AbstractEAIndividual
@@ -90,7 +90,7 @@ public class GPIndividualProgramData extends AbstractEAIndividual implements Int
         if (individual instanceof GPIndividualProgramData) {
             GPIndividualProgramData indy = (GPIndividualProgramData) individual;
             //@todo Eigendlich k<EFBFBD>nnte ich noch die Areas vergleichen
-            if (this.m_maxDepth != indy.m_maxDepth)
+            if (this.m_maxAllowedDepth != indy.m_maxAllowedDepth)
                 return false;
             if ((this.m_Genotype == null) || (indy.m_Genotype == null))
                 return false;
@@ -134,9 +134,13 @@ public class GPIndividualProgramData extends AbstractEAIndividual implements Int
         this.m_Phenotype = new AbstractGPNode[this.m_Genotype.length];
         for (int i = 0; i < this.m_Genotype.length; i++) {
             this.m_Phenotype[i] = (AbstractGPNode)this.m_Genotype[i].clone();
-            if ((this.m_CheckMaxDepth) && (this.m_Phenotype[i].isMaxDepthViolated(this.m_maxDepth))) {
+            // if (!m_Phenotype[0].checkDepth(0)) {
-                //System.out.println("Trying to meet the Target Depth!");
+            // 	System.err.println("error... " + m_Genotype[0].checkDepth(0));
-                this.m_Phenotype[i].repairMaxDepth(this.m_Area[i], this.m_maxDepth);
+            // }
+
+            if ((this.m_CheckMaxDepth) && (this.m_Phenotype[i].isMaxDepthViolated(this.m_maxAllowedDepth))) {
+                System.err.println("Trying to meet the Target Depth! " + this.m_Phenotype[i].isMaxDepthViolated(this.m_maxAllowedDepth) + " "+ m_Phenotype[i].getMaxDepth());
+                this.m_Phenotype[i].repairMaxDepth(this.m_Area[i], this.m_maxAllowedDepth);
                 //System.out.println("TragetDepth: " + this.m_TargetDepth + " : " + this.m_Program.getMaxDepth());
             }
         }
@@ -148,7 +152,8 @@ public class GPIndividualProgramData extends AbstractEAIndividual implements Int
      * @return InterfaceProgram[] representing the Program.
      */
     public InterfaceProgram[] getProgramDataWithoutUpdate() {
-        return this.m_Phenotype;
+    	if (this.m_Phenotype==null) return getProgramData();
+    	else return this.m_Phenotype;
     }
 
     /** This method allows you to set the program phenotype.
@@ -244,6 +249,7 @@ public class GPIndividualProgramData extends AbstractEAIndividual implements Int
      */
     public void SetPGenotype(AbstractGPNode[] b) {
         this.m_Genotype = b;
+        this.m_Phenotype=null;
     }
 
     /** This method will allow the user to set the current program 'genotype'.
@@ -252,28 +258,41 @@ public class GPIndividualProgramData extends AbstractEAIndividual implements Int
      */
     public void SetPGenotype(AbstractGPNode b, int i) {
         this.m_Genotype[i] = b;
+        m_Genotype[i].updateDepth(0);
+//        System.out.println("Setting pheno of depth " + b.getMaxDepth() + " " + b.getStringRepresentation());
+        this.m_Phenotype=null;
     }
 
-    /** This method performs a simple one element mutation on the program
+    /** 
+     * This method performs a simple one element mutation on the program
      */
     public void defaultMutate() {
-        ArrayList allNodes = new ArrayList();
         for (int i = 0; i < this.m_Genotype.length; i++) {
-            this.m_Genotype[i].addNodesTo(allNodes);
+            AbstractGPNode nodeToMutate = this.m_Genotype[i].getRandomNode();
-            AbstractGPNode nodeToMutate = (AbstractGPNode) allNodes.get(RNG.randomInt(0, allNodes.size()-1));
+            if (nodeToMutate.getParent() == null) { // mutate at root
-            if (nodeToMutate.getParent() == null) {
                 this.defaultInit(null);
             } else {
                 AbstractGPNode parent = nodeToMutate.getParent();
-                AbstractGPNode newNode = (AbstractGPNode)(((AbstractGPNode)this.m_Area[i].getRandomNode().clone()));
+            	if (m_CheckMaxDepth && (nodeToMutate.getDepth()==m_maxAllowedDepth)) { // mutate with a constant
-                newNode.setDepth(nodeToMutate.getDepth());
+            		AbstractGPNode newNode = (AbstractGPNode)(((AbstractGPNode)this.m_Area[i].getRandomNodeWithArity(0).clone()));
-                newNode.initGrow(this.m_Area[i], this.m_maxDepth);
+            		newNode.setDepth(nodeToMutate.getDepth());
-                parent.setNode(newNode, nodeToMutate);
+            		parent.setNode(newNode, nodeToMutate);
+            	} else {
+            		AbstractGPNode newNode = (AbstractGPNode)(((AbstractGPNode)this.m_Area[i].getRandomNode().clone()));
+            		newNode.setDepth(nodeToMutate.getDepth());
+            		newNode.initGrow(this.m_Area[i], this.m_maxAllowedDepth);
+            		parent.setNode(newNode, nodeToMutate);
+            	}
+                //if (!m_Genotype[i].checkDepth(0) || (m_Genotype[i].isMaxDepthViolated(m_maxAllowedDepth))) {
+                //	System.err.println("Error in GPIndividualProgramData.defaultMutate!");
+                //}
             }
         }
+        m_Phenotype=null; // reset pheno
     }
 
     public void defaultInit(InterfaceOptimizationProblem prob) {
+        m_Phenotype=null; // reset pheno
         for (int i = 0; i < this.m_Area.length; i++) {
             if (this.m_Area[i] == null) {
             	EVAERROR.errorMsgOnce("Error in GPIndividualProgramData.defaultInit(): Area["+i+"] == null !!");
@@ -339,9 +358,9 @@ public class GPIndividualProgramData extends AbstractEAIndividual implements Int
      * @param b     The new init Depth of the GP Tree.
      */
     public void setInitDepth(int b) {
-        if (b > this.m_maxDepth) {
+        if (b > this.m_maxAllowedDepth) {
             System.out.println("Waring Init Depth will be set to Target Depth!");
-            b = this.m_maxDepth;
+            b = this.m_maxAllowedDepth;
         }
         this.m_InitDepth = b;
     }
@@ -355,17 +374,29 @@ public class GPIndividualProgramData extends AbstractEAIndividual implements Int
     /** This method set/get the target depth.
      * @param b     The new target Depth of the GP Tree.
      */
-    public void setMaxDepth(int b) {
+    public void setMaxAllowedDepth(int b) {
-        this.m_maxDepth = b;
+        this.m_maxAllowedDepth = b;
     }
-    public int getMaxDepth() {
+    public int getMaxAllowedDepth() {
-        return this.m_maxDepth;
+        return this.m_maxAllowedDepth;
     }
-    public String maxDepthTipText() {
+    public String maxAllowedDepthTipText() {
-        return "The maximum depth of the GP tree.";
+        return "The maximum depth allowed for the GP tree.";
     }
     
     public String[] customPropertyOrder() {
-    	return new String[] {"initDepth", "checkMaxDepth", "maxDepth"};
+    	return new String[] {"initDepth", "checkMaxDepth", "maxAllowedDepth"};
     }
+
+	public void updateDepth() {
+		for (int i=0; i<m_Genotype.length; i++) {
+			m_Genotype[i].updateDepth(0);
+		}
+	}
+	
+	public void checkDepth() {
+		for (int i=0; i<m_Genotype.length; i++) {
+			m_Genotype[i].checkDepth(0);
+		}
+	}
 }

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

@@ -33,4 +33,9 @@ public interface InterfaceGPIndividual {
      */
     public Object[] getFunctionArea();
 
+    /**
+     * Return the maximal allowed depth of a GP tree (or -1 if it does not apply).
+     * @return
+     */
+    public int getMaxAllowedDepth();
 }

src/eva2/server/go/individuals/codings/gp/AbstractGPNode.java

@@ -12,6 +12,7 @@ import eva2.server.go.problems.InterfaceProgramProblem;
 import eva2.tools.Pair;
 import eva2.tools.ReflectPackage;
 import eva2.tools.math.Mathematics;
+import eva2.tools.math.RNG;
 
 
 /** This gives an abstract node, with default functionality for get and set methods.
@@ -56,6 +57,18 @@ public abstract class AbstractGPNode implements InterfaceProgram, java.io.Serial
     	return sb.toString();
     }
     
+    /**
+     * Recursively perform deep cloning of the members of this instance and all sub-nodes.
+     *
+     * @param node the node to clone values from
+     **/
+    protected void cloneMembers(AbstractGPNode node) {
+        this.m_Depth    = node.m_Depth;
+        this.m_Parent   = node.m_Parent;
+        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
+        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
+    }
+    
     private static void appendStringRepresentation(AbstractGPNode node, StringBuffer sbuf) {
     	String op = node.getOpIdentifier(); 
     	sbuf.append(op);
@@ -350,14 +363,20 @@ public abstract class AbstractGPNode implements InterfaceProgram, java.io.Serial
         this.m_Nodes[index] = node;
     }
 
-    /** This method allows you to set a node specified by the index
+    /** 
+     * This method allows you to set a node specified by the reference.
      * @param newnode      The new node.
      * @param oldnode      The old node.
      */
     public void setNode(AbstractGPNode newnode, AbstractGPNode oldnode) {
         newnode.setParent(this);
-        newnode.setDepth(this.m_Depth+1);
+        newnode.updateDepth(this.m_Depth+1);
-        for (int i = 0; i < this.m_Nodes.length; i++) if (this.m_Nodes[i].equals(oldnode)) this.m_Nodes[i] = newnode;
+        for (int i = 0; i < this.m_Nodes.length; i++) {
+        	if (this.m_Nodes[i] == oldnode) {
+        		this.m_Nodes[i] = newnode;
+//        		System.out.println("SWITCHED " + i);
+        	}
+        }
     }
     /** This method returns all nodes begining with the current node.
      * @param ListOfNodes   This ArrayList will contain all nodes
@@ -367,6 +386,27 @@ public abstract class AbstractGPNode implements InterfaceProgram, java.io.Serial
         for (int i = 0; i < this.m_Nodes.length; i++) this.m_Nodes[i].addNodesTo(ListOfNodes);
     }
 
+    /**
+     * Return a shallow reference to a random node within this tree.
+     * @return
+     */
+    public AbstractGPNode getRandomNode() {
+    	ArrayList allNodes = new ArrayList(10);
+        addNodesTo(allNodes);
+        return (AbstractGPNode) allNodes.get(RNG.randomInt(allNodes.size()));
+    }
+    
+    /**
+     * Return a shallow reference to a random leaf of this tree.
+     * @return
+     */
+    public AbstractGPNode getRandomLeaf() {
+    	if (m_Nodes.length>0) {
+    		int k=RNG.randomInt(m_Nodes.length);
+    		return m_Nodes[k].getRandomLeaf();
+    	} else return this;
+    }
+    
     /** This method allows you to set the parent of the node
      * @param parent    The new parent
      */
@@ -435,7 +475,8 @@ public abstract class AbstractGPNode implements InterfaceProgram, java.io.Serial
         return result;
     }
 
-    /** This method will return the max depth of the tree
+    /**
+     * Return the maximal depth of the tree starting here, but relating to the whole tree.
      * @return The max depth.
      */
     public int getMaxDepth() {
@@ -446,6 +487,16 @@ public abstract class AbstractGPNode implements InterfaceProgram, java.io.Serial
         return result;
     }
 
+    /**
+     * Return the depth of the subtree only.
+     * 
+     * @return
+     */
+    public int getSubtreeDepth() {
+        int maxDepth = getMaxDepth();
+        return maxDepth-m_Depth;
+    }
+    
     /** This method will check if maxdepth is violated
      * @param maxDepth     The max depth.
      * @return True if MaxDepth is violated
@@ -503,4 +554,32 @@ public abstract class AbstractGPNode implements InterfaceProgram, java.io.Serial
             return false;
         }
     }
+    
+    /**
+     * Update the depth of this node tree starting with the given initial depth of the root.
+     * 
+     * @param myDepth
+     */
+	public void updateDepth(int myDepth) {
+		m_Depth=myDepth;
+		for (int i=0; i<m_Nodes.length; i++) {
+			m_Nodes[i].updateDepth(myDepth+1);
+		}
+	}
+	
+    /**
+     * Check the depth of this node tree starting with the given initial depth of the root.
+     * 
+     * @param myDepth
+     */
+	public boolean checkDepth(int myDepth) {
+		if (m_Depth!=myDepth) {
+			System.err.println("Depth was wrong at level " + myDepth);
+			return false;
+		}
+		for (int i=0; i<m_Nodes.length; i++) {
+			if (!m_Nodes[i].checkDepth(myDepth+1)) return false;
+		}
+		return true;
+	}
 }

src/eva2/server/go/individuals/codings/gp/GPNodeAbs.java

@@ -12,10 +12,7 @@ public class GPNodeAbs extends AbstractGPNode implements java.io.Serializable {
     public GPNodeAbs() {
     }
     public GPNodeAbs(GPNodeAbs node) {
-        this.m_Depth    = node.m_Depth;
+        this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeAdd.java

@@ -18,10 +18,7 @@ public class GPNodeAdd extends AbstractGPNode implements java.io.Serializable {
     }
 
     public GPNodeAdd(GPNodeAdd node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeConst.java

@@ -16,10 +16,7 @@ public class GPNodeConst extends AbstractGPNode implements java.io.Serializable
 
     public GPNodeConst(GPNodeConst node) {
     	value = node.value;
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     @Override

src/eva2/server/go/individuals/codings/gp/GPNodeCos.java

@@ -14,10 +14,7 @@ public class GPNodeCos extends AbstractGPNode implements java.io.Serializable {
     public GPNodeCos() {
     }
     public GPNodeCos(GPNodeCos node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeDiv.java

@@ -22,10 +22,7 @@ public class GPNodeDiv extends AbstractGPNode implements java.io.Serializable {
 
     public GPNodeDiv(GPNodeDiv node) {
         this.m_LowerBorderForSec = node.m_LowerBorderForSec;
-        this.m_Depth    = node.m_Depth;
+        this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeExp.java

@@ -14,10 +14,7 @@ public class GPNodeExp extends AbstractGPNode implements java.io.Serializable {
     public GPNodeExp() {
     }
     public GPNodeExp(GPNodeExp node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeFlowExec2.java

@@ -15,10 +15,7 @@ public class GPNodeFlowExec2 extends AbstractGPNode implements java.io.Serializa
 
     }
     public GPNodeFlowExec2(GPNodeFlowExec2 node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeFlowExec3.java

@@ -15,10 +15,7 @@ public class GPNodeFlowExec3 extends AbstractGPNode implements java.io.Serializa
 
     }
     public GPNodeFlowExec3(GPNodeFlowExec3 node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeInput.java

@@ -30,10 +30,7 @@ public class GPNodeInput extends AbstractGPNode implements java.io.Serializable
 
     public GPNodeInput(GPNodeInput node) {
         this.m_Identifier   = node.m_Identifier;
-        this.m_Depth    = node.m_Depth;
+        this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
     
     public void setIdentifier(String str) {

src/eva2/server/go/individuals/codings/gp/GPNodeMult.java

@@ -15,10 +15,7 @@ public class GPNodeMult extends AbstractGPNode implements java.io.Serializable {
     public GPNodeMult() {
     }
     public GPNodeMult(GPNodeMult node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeNeg.java

@@ -15,10 +15,7 @@ public class GPNodeNeg extends AbstractGPNode implements java.io.Serializable {
     public GPNodeNeg() {
     }
     public GPNodeNeg(GPNodeNeg node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeOne.java

@@ -9,10 +9,14 @@ public class GPNodeOne extends GPNodeConst implements java.io.Serializable {
     	super(1.);
     }
     
+    public GPNodeOne(GPNodeOne node) {
+    	super(node);
+	}
+    
     /** This method allows you to clone the Nodes
      * @return the clone
      */
     public Object clone() {
-        return (Object) new GPNodeOne();
+        return (Object) new GPNodeOne(this);
     }
 }

src/eva2/server/go/individuals/codings/gp/GPNodeOutput.java

@@ -29,10 +29,7 @@ public class GPNodeOutput extends AbstractGPNode implements java.io.Serializable
 
     public GPNodeOutput(GPNodeOutput node) {
         this.m_Identifier   = node.m_Identifier;
-        this.m_Depth    = node.m_Depth;
+        this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     @Override

src/eva2/server/go/individuals/codings/gp/GPNodePi.java

@@ -9,11 +9,15 @@ public class GPNodePi extends GPNodeConst implements java.io.Serializable {
     	super(Math.PI);
     }
     
-    /** This method allows you to clone the Nodes
+    public GPNodePi(GPNodePi node) {
+    	super(node);
+	}
+
+	/** This method allows you to clone the Nodes
      * @return the clone
      */
     public Object clone() {
-        return (Object) new GPNodePi();
+        return (Object) new GPNodePi(this);
     }
     
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodePow2.java

@@ -14,10 +14,7 @@ public class GPNodePow2 extends AbstractGPNode implements java.io.Serializable {
     public GPNodePow2() {
     }
     public GPNodePow2(GPNodePow2 node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodePow3.java

@@ -14,10 +14,7 @@ public class GPNodePow3 extends AbstractGPNode implements java.io.Serializable {
     public GPNodePow3() {
     }
     public GPNodePow3(GPNodePow3 node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeProd.java

@@ -14,10 +14,7 @@ public class GPNodeProd extends AbstractGPNode implements java.io.Serializable {
     }
 
     public GPNodeProd(GPNodeProd node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeSin.java

@@ -14,10 +14,7 @@ public class GPNodeSin extends AbstractGPNode implements java.io.Serializable {
     public GPNodeSin() {
     }
     public GPNodeSin(GPNodeSin node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeSqrt.java

@@ -15,10 +15,7 @@ public class GPNodeSqrt extends AbstractGPNode implements java.io.Serializable {
     public GPNodeSqrt() {
     }
     public GPNodeSqrt(GPNodeSqrt node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeSub.java

@@ -15,10 +15,7 @@ public class GPNodeSub extends AbstractGPNode implements java.io.Serializable {
     public GPNodeSub() {
     }
     public GPNodeSub(GPNodeSub node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/individuals/codings/gp/GPNodeSum.java

@@ -14,10 +14,7 @@ public class GPNodeSum extends AbstractGPNode implements java.io.Serializable {
     }
 
     public GPNodeSum(GPNodeSum node) {
-        this.m_Depth    = node.m_Depth;
+    	this.cloneMembers(node);
-        this.m_Parent   = node.m_Parent;
-        this.m_Nodes    = new AbstractGPNode[node.m_Nodes.length];
-        for (int i = 0; i < node.m_Nodes.length; i++) this.m_Nodes[i] = (AbstractGPNode) node.m_Nodes[i].clone();
     }
 
     /** This method will be used to identify the node in the GPAreaEditor

src/eva2/server/go/operators/crossover/CrossoverGPDefault.java

@@ -4,6 +4,7 @@ package eva2.server.go.operators.crossover;
 import java.util.ArrayList;
 
 import eva2.server.go.individuals.AbstractEAIndividual;
+import eva2.server.go.individuals.GPIndividualProgramData;
 import eva2.server.go.individuals.InterfaceGPIndividual;
 import eva2.server.go.individuals.codings.gp.AbstractGPNode;
 import eva2.server.go.populations.Population;
@@ -18,12 +19,18 @@ import eva2.tools.math.RNG;
  * To change this template use Options | File Templates.
  */
 public class CrossoverGPDefault implements InterfaceCrossover, java.io.Serializable {
-    private InterfaceOptimizationProblem    m_OptimizationProblem;
+    /**
+	 * 
+	 */
+	private static final long serialVersionUID = 8900427365914281930L;
+	private InterfaceOptimizationProblem    m_OptimizationProblem;
+    private boolean maintainMaxDepth = true;
+	private static final boolean TRACE=false;
 
     public CrossoverGPDefault() {
-
     }
     public CrossoverGPDefault(CrossoverGPDefault c) {
+    	this.maintainMaxDepth = c.maintainMaxDepth;
         this.m_OptimizationProblem      = c.m_OptimizationProblem;
     }
     /** This method will enable you to clone a given mutation operator
@@ -33,53 +40,67 @@ public class CrossoverGPDefault implements InterfaceCrossover, java.io.Serializa
         return new CrossoverGPDefault(this);
     }
 
-    /** This method performs crossover on two individuals. If the individuals do
+    /** 
-     * not implement InterfaceGAIndividual, then nothing will happen.
+     * Exchange subtrees of two GP nodes. Allows to keep the depth restriction.
+     * 
      * @param indy1 The first individual
      * @param partners The second individual
      */
     public AbstractEAIndividual[] mate(AbstractEAIndividual indy1, Population partners) {
+    	if (partners.size()>1) System.err.println("Warning, crossover may not work on more than one partner! " + this.getClass());
         AbstractEAIndividual[] result = null;
         result = new AbstractEAIndividual[partners.size()+1];
         result[0] = (AbstractEAIndividual) (indy1).clone();
         for (int i = 0; i < partners.size(); i++) result[i+1] = (AbstractEAIndividual) ((AbstractEAIndividual)partners.get(i)).clone();
-        //for (int i = 0; i < result.length; i++) System.out.println("Before Crossover: " +result[i].getSolutionRepresentationFor());
+        if (TRACE) for (int i = 0; i < result.length; i++) System.out.println("Before Crossover: " +result[i].getStringRepresentation());
         if (partners.size() == 0) return result;
         if ((indy1 instanceof InterfaceGPIndividual) && (partners.get(0) instanceof InterfaceGPIndividual)) {
-
+        	int allowedDepth = ((InterfaceGPIndividual)indy1).getMaxAllowedDepth();
-            //select node from 0 and memorize parent
+        	
-            ArrayList allNodes = new ArrayList();
             AbstractGPNode[] nodes = ((InterfaceGPIndividual)result[0]).getPGenotype();
-            for (int t = 0; t < nodes.length; t++) {
+            for (int t = 0; t < nodes.length; t++) { // for each of the genotypes (multiploidy??)
-                allNodes = new ArrayList();
+                ((InterfaceGPIndividual)result[0]).getPGenotype()[t].getRandomNode();
-                ((InterfaceGPIndividual)result[0]).getPGenotype()[t].addNodesTo(allNodes);
+                AbstractGPNode selNodeThis     = ((InterfaceGPIndividual)result[0]).getPGenotype()[t].getRandomNode();
-                AbstractGPNode oldNode     = (AbstractGPNode) allNodes.get(RNG.randomInt(0, allNodes.size()-1));
+                AbstractGPNode selNodeOther = ((InterfaceGPIndividual)result[1]).getPGenotype()[t].getRandomNode();
-                AbstractGPNode newNode, memorizingNode = oldNode, tmpNode;
+                if (maintainMaxDepth) {//System.err.print(".");
-                AbstractGPNode oldParent, newParent;
+                	int maxTries=10;
-                oldParent = oldNode.getParent();
+                		// if the echange would violate the depth restriction, choose new nodes for a few times...
-                for (int i = 1; i < result.length; i++) {
+                		while (maxTries>=0 && ((selNodeOther.getSubtreeDepth()+selNodeThis.getDepth()>allowedDepth) || 
-                    // choose Node from i and add it to i-1
+                				(selNodeThis.getSubtreeDepth()+selNodeOther.getDepth()>allowedDepth))) {
-                    allNodes = new ArrayList();
+                            if (RNG.flipCoin(0.5)) selNodeThis  = ((InterfaceGPIndividual)result[0]).getPGenotype()[t].getRandomNode();
-                    ((InterfaceGPIndividual)result[i]).getPGenotype()[t].addNodesTo(allNodes);
+                            else selNodeOther = ((InterfaceGPIndividual)result[1]).getPGenotype()[t].getRandomNode();
-                    newNode = (AbstractGPNode) allNodes.get(RNG.randomInt(0, allNodes.size()-1));
+                            maxTries--;
-                    tmpNode = newNode;
+                		}
-                    newParent = tmpNode.getParent();
+                	if (maxTries<0) { // on a failure, at least exchange two leaves, which always works
-                    if (oldParent == null) ((InterfaceGPIndividual)result[i-1]).SetPGenotype(newNode, t);
+//                		System.err.println("Unable to select fitting nodes! Just switch leaves...");
-                    else oldParent.setNode(newNode, oldNode);
+                        selNodeThis     = ((InterfaceGPIndividual)result[0]).getPGenotype()[t].getRandomLeaf();
-                    oldNode = tmpNode;
+                        selNodeOther = ((InterfaceGPIndividual)result[1]).getPGenotype()[t].getRandomLeaf();
-                    oldParent = newParent;
+                	}
                 }
-                // add node from 0 to result.length-1
+                if (TRACE) {
-                if (oldParent == null) {
+                	System.out.println("Selected t " + selNodeThis.getStringRepresentation());
-                    ((InterfaceGPIndividual)result[result.length-1]).SetPGenotype(memorizingNode, t);
+                	System.out.println("Selected o " + selNodeOther.getStringRepresentation());
-                } else {
-                    oldParent.setNode(memorizingNode, oldNode);
                 }
+                
+                AbstractGPNode selNodeThisParent, selNodeOtherParent;
+                selNodeThisParent = selNodeThis.getParent();
+                selNodeOtherParent = selNodeOther.getParent();
+                
+                // actually switch individuals!
+                if (selNodeThisParent == null) ((InterfaceGPIndividual)result[0]).SetPGenotype((AbstractGPNode)selNodeOther.clone(), t);
+                else selNodeThisParent.setNode((AbstractGPNode)selNodeOther.clone(), selNodeThis);
+//                for (int i = 0; i < result.length; i++) System.out.println("-- Betw Crossover: " +result[i].getStringRepresentation());
+                if (selNodeOtherParent == null) ((InterfaceGPIndividual)result[1]).SetPGenotype((AbstractGPNode)selNodeThis.clone(), t);
+                else selNodeOtherParent.setNode((AbstractGPNode)selNodeThis.clone(), selNodeOther);
+
             }
         }
         //in case the crossover was successfull lets give the mutation operators a chance to mate the strategy parameters
-        for (int i = 0; i < result.length; i++) result[i].getMutationOperator().crossoverOnStrategyParameters(indy1, partners);
+        for (int i = 0; i < result.length; i++) {
-        //for (int i = 0; i < result.length; i++) System.out.println("After Crossover: " +result[i].getSolutionRepresentationFor());
+        	((GPIndividualProgramData)result[i]).checkDepth();
+        	result[i].getMutationOperator().crossoverOnStrategyParameters(indy1, partners);
+        }
+        if (TRACE) for (int i = 0; i < result.length; i++) System.out.println("After Crossover: " +result[i].getStringRepresentation());
         return result;
     }
 

src/eva2/server/go/problems/PSymbolicRegression.java

@@ -575,7 +575,7 @@ public class PSymbolicRegression extends AbstractOptimizationProblem implements
 	 */
 	public static int getIndySize(AbstractEAIndividual indy) {
 		if (indy instanceof InterfaceDataTypeProgram) {
-			InterfaceProgram prog = ((InterfaceDataTypeProgram)indy).getProgramData()[0];
+			InterfaceProgram prog = ((InterfaceDataTypeProgram)indy).getProgramDataWithoutUpdate()[0];
 			if (prog instanceof AbstractGPNode) {
 				AbstractGPNode gpNode = (AbstractGPNode)prog;
 				return gpNode.getNumberOfNodes();
@@ -584,7 +584,7 @@ public class PSymbolicRegression extends AbstractOptimizationProblem implements
 	}
 	
 	/**
-	 * Return the depth of an individual representing a program or null
+	 * Return the maximal depth of an individual representing a program or null
 	 * if it is of an incompatible type.
 	 * 
 	 * @param indy
@@ -592,10 +592,14 @@ public class PSymbolicRegression extends AbstractOptimizationProblem implements
 	 */
 	public static int getIndyDepth(AbstractEAIndividual indy) {
 		if (indy instanceof InterfaceDataTypeProgram) {
-			InterfaceProgram prog = ((InterfaceDataTypeProgram)indy).getProgramData()[0];
+			InterfaceProgram prog = ((InterfaceDataTypeProgram)indy).getProgramDataWithoutUpdate()[0];
 			if (prog instanceof AbstractGPNode) {
 				AbstractGPNode gpNode = (AbstractGPNode)prog;
-				return gpNode.getMaxDepth();
+				int d = gpNode.getMaxDepth();
+				//if (!gpNode.checkDepth(0)) {
+				//	System.out.println(d + "\n" + gpNode.getStringRepresentation());
+				//}
+				return d;
 			} else return 0;
 		} else return 0;
 	}

src/eva2/server/stat/StatisticsWithGUI.java

@@ -242,7 +242,7 @@ public class StatisticsWithGUI extends AbstractStatistics implements Serializabl
 				// plot the column as indicated by the graph description
 				if (currentStatDoubleData[colIndex]!=null) plotFitnessPoint(0, subGraph++, functionCalls, currentStatDoubleData[colIndex]);
 				else {
-					EVAERROR.errorMsgOnce("Error, data field " + graphDesc.get(i).head + " does not contain primitive data and cannot be plotted.");
+//					EVAERROR.errorMsgOnce("Error, data field " + graphDesc.get(i).head + " does not contain primitive data and cannot be plotted.");
 					subGraph++; // increase index anyways or the name assignment gets inconsistent
 				}
 			}