9 files changed, 99 insertions, 23 deletions
diff --git a/src/jcgp/Main.java b/src/jcgp/Main.java
index 39f3c4b..598c720 100644
--- a/src/jcgp/Main.java
+++ b/src/jcgp/Main.java
@@ -4,7 +4,7 @@ public class Main {
 
 	public static void main(String[] args) {
 		CGP cgp = new CGP();
-
+		cgp.getClass();
 	}
 
 }
diff --git a/src/jcgp/ea/StandardMutator.java b/src/jcgp/ea/StandardMutator.java
index 6a4af1a..447338a 100644
--- a/src/jcgp/ea/StandardMutator.java
+++ b/src/jcgp/ea/StandardMutator.java
@@ -15,17 +15,17 @@ public class StandardMutator implements Mutator {
 		
 		for (int i = 0; i < mutations; i++) {
 			MutableElement m = chromosome.getRandomMutableElement();
-//			
-//			if (m instanceof Output) {
-//				m.setConnection(chromosome.getRandomConnection(m.getColumn()));
-//			} else if (m instanceof Node) {
-//				int geneType = Utilities.getRandomInt(1 + Parameters.getMaxArity());
-//				if (geneType < 1) {
-//					((Node) m).setFunction(Utilities.getRandomFunction());
-//				} else {
-//					m.setConnection(chromosome.getRandomConnection(m.getColumn()));
-//				}
-//			}
+			
+			if (m instanceof Output) {
+				m.setConnection(chromosome.getRandomConnection());
+			} else if (m instanceof Node) {
+				int geneType = Utilities.getRandomInt(1 + Parameters.getMaxArity());
+				if (geneType < 1) {
+					((Node) m).setFunction(Utilities.getRandomFunction());
+				} else {
+					m.setConnection(chromosome.getRandomConnection(((Node) m).getColumn()));
+				}
+			}
 		}
 	}
 }
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index 1f264f2..08ff9b9 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -104,7 +104,7 @@ public class Chromosome {
 				// populate with connections equivalent to clone
 				Connection copyConnection;
 				for (int i = 0; i < connections.length; i++) {
-					copyConnection = clone.getNode(r, c).getConnections(i);
+					copyConnection = clone.getNode(r, c).getConnection(i);
 					if (copyConnection instanceof Input) {
 						connections[i] = inputs[((Input) copyConnection).getIndex()];
 					} else if (copyConnection instanceof Node) {
@@ -251,12 +251,11 @@ public class Chromosome {
 			recomputeActiveNodes = false;
 			activeNodes = new ArrayList<Connection>();
 			
-			for (int r = 0; r < nodes.length; r++) {
-				for (int c = 0; c < nodes[r].length; c++) {
-					
-				}
+			for (Output output : outputs) {
+				output.getActiveNodes(activeNodes);
 			}
-		}		
+			
+		}
 		return activeNodes;
 	}
 
diff --git a/src/jcgp/population/Connection.java b/src/jcgp/population/Connection.java
index 4e69e99..12e92d6 100644
--- a/src/jcgp/population/Connection.java
+++ b/src/jcgp/population/Connection.java
@@ -1,6 +1,11 @@
 package jcgp.population;
 
+import java.util.ArrayList;
+
 public interface Connection {
 
-	public abstract int getValue();
+	public int getValue();
+
+	public void getActive(ArrayList<Connection> activeNodes);
+
 }
diff --git a/src/jcgp/population/Input.java b/src/jcgp/population/Input.java
index ee008ce..f3199b8 100644
--- a/src/jcgp/population/Input.java
+++ b/src/jcgp/population/Input.java
@@ -1,5 +1,7 @@
 package jcgp.population;
 
+import java.util.ArrayList;
+
 public class Input implements Connection {
 	
 	private int value = 0, index;
@@ -21,4 +23,11 @@ public class Input implements Connection {
 		return index;
 	}
 
+	@Override
+	public void getActive(ArrayList<Connection> activeNodes) {
+		if (!activeNodes.contains(this)) {
+			activeNodes.add(this);
+		}
+	}
+
 }
diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java
index 40ffa52..c09532c 100644
--- a/src/jcgp/population/Node.java
+++ b/src/jcgp/population/Node.java
@@ -1,5 +1,7 @@
 package jcgp.population;
 
+import java.util.ArrayList;
+
 import jcgp.Parameters;
 import jcgp.Utilities;
 import jcgp.function.Function;
@@ -58,7 +60,17 @@ public class Node implements MutableElement, Connection {
 		return function;
 	}
 
-	public Connection getConnections(int index) {
+	public Connection getConnection(int index) {
 		return connections[index];
 	}
+
+	@Override
+	public void getActive(ArrayList<Connection> activeNodes) {
+		if (!activeNodes.contains(this)) {
+			activeNodes.add(this);
+		}
+		for (int i = 0; i < function.getArity(); i++) {
+			connections[i].getActive(activeNodes);
+		}
+	}
 }
diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java
index 68045b0..b3cb648 100644
--- a/src/jcgp/population/Output.java
+++ b/src/jcgp/population/Output.java
@@ -1,5 +1,7 @@
 package jcgp.population;
 
+import java.util.ArrayList;
+
 
 public class Output implements MutableElement {
 	
@@ -29,7 +31,8 @@ public class Output implements MutableElement {
 	public Connection getSource() {
 		return source;
 	}
-	
-	
 
+	public void getActiveNodes(ArrayList<Connection> activeNodes) {
+		source.getActive(activeNodes);
+	}
 }
diff --git a/src/jcgp/tests/ChromosomeTests.java b/src/jcgp/tests/ChromosomeTests.java
index ece8203..3b7319f 100644
--- a/src/jcgp/tests/ChromosomeTests.java
+++ b/src/jcgp/tests/ChromosomeTests.java
@@ -146,7 +146,7 @@ public class ChromosomeTests {
 			}	
 		}
 		System.out.println("Out of " + connectionPicks + " connections picked from " + ((chosenColumn >= Parameters.getLevelsBack()) ? Parameters.getLevelsBack() : chosenColumn) * Parameters.getRows() +
-				" nodes and " + Parameters.getInputs() + " allowed nodes, " + connectionNodes + " were nodes and " + connectionInputs + " were inputs.");
+				" allowed nodes and " + Parameters.getInputs() + " inputs, " + connectionNodes + " were nodes and " + connectionInputs + " were inputs.");
 
 		System.out.println("Node/input ratio: " + ((double) ((chosenColumn >= Parameters.getLevelsBack()) ? Parameters.getLevelsBack() : chosenColumn) * Parameters.getRows()) / (double) Parameters.getInputs() +
 				", picked ratio: " + (double) connectionNodes / (double) connectionInputs);
@@ -228,6 +228,20 @@ public class ChromosomeTests {
 	 */
 	@Test
 	public void activeNodeTest() {
+		// active node detection happens recursively, the user only calls a single method
+		// set connections to a known configuration
+		for (int i = 0; i < Parameters.getOutputs(); i++) {
+			chromosome.getOutput(i).setConnection(chromosome.getNode(0, 0));
+		}
+		
+		chromosome.getNode(0, 0).setConnection(chromosome.getInput(0));
 		
+		assertTrue("Active connection not in list.", chromosome.getActiveNodes().contains(chromosome.getInput(0)));
+		assertTrue("Active connection not in list.", chromosome.getActiveNodes().contains(chromosome.getNode(0, 0)));
+		
+		// change outputs, print list
+		chromosome.getOutput(0).setConnection(chromosome.getNode(0, Parameters.getColumns() - 1));
+
+		System.out.println("Active connections: " + chromosome.getActiveNodes().toString() + "\n");
 	}
 }
diff --git a/src/jcgp/tests/NodeTests.java b/src/jcgp/tests/NodeTests.java
new file mode 100644
index 0000000..921879f
--- /dev/null
+++ b/src/jcgp/tests/NodeTests.java
@@ -0,0 +1,34 @@
+package jcgp.tests;
+
+import static org.junit.Assert.*;
+
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * 
+ * Tests which cover the behaviour specified for a node.
+ * 
+ *  - A node should contain read-only row and column values which are set upon construction.
+ *  - It should contain a fully accessible Function object.
+ *  - It should contain a set of connections which can be initialised and randomly 
+ *    modified.
+ *  
+ *  WARNING: changing parameters may cause the tests to incorrectly fail!
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
+public class NodeTests {
+
+	@Before
+	public void setUp() throws Exception {
+		
+	}
+
+	@Test
+	public void test() {
+		
+	}
+
+}