1 files changed, 40 insertions, 9 deletions

diff --git a/src/jcgp/backend/population/Output.java b/src/jcgp/backend/population/Output.java
index d876951..ab693e2 100644
--- a/src/jcgp/backend/population/Output.java
+++ b/src/jcgp/backend/population/Output.java
@@ -2,26 +2,39 @@ package jcgp.backend.population;
 
 import java.util.ArrayList;
 
-public class Output extends Gene implements MutableElement {
+/**
+ * This is a chromosome output. Outputs are a special
+ * type of mutable element with a single connection. It
+ * returns the value of its single connection, but it 
+ * may not be connected to - it terminates a chromosome
+ * active connection path. 
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
+public class Output implements MutableElement {
 	
 	private Connection source;
 	private Chromosome chromosome;
 	private int index;
 	
+	/**
+	 * Makes a new instance of {@code Output} with the 
+	 * specified arguments.
+	 * 
+	 * @param chromosome the chromosome this output belongs to.
+	 * @param index the output index.
+	 */
 	public Output(Chromosome chromosome, int index) {
 		this.chromosome = chromosome;
 		this.index = index;
 	}
 
+	/**
+	 * @return the value of the output's source.
+	 */
 	public Object calculate() {
-		Object result = source.getValue();
-		return result;
-	}
-
-	@Override
-	public void setConnection(int index, Connection newConnection) {
-		source = newConnection;
-		chromosome.recomputeActiveNodes();
+		return source.getValue();
 	}
 
 	public int getIndex() {
@@ -38,12 +51,30 @@ public class Output extends Gene implements MutableElement {
 		}
 	}
 	
+	/**
+	 * When mutating an output, the index parameter
+	 * is simply ignored and the output source is
+	 * set. 
+	 * 
+	 * @see jcgp.backend.population.MutableElement#setConnection(int, jcgp.backend.population.Connection)
+	 */
+	@Override
+	public void setConnection(int index, Connection newConnection) {
+		source = newConnection;
+		// trigger active path recomputation
+		chromosome.recomputeActiveNodes();
+	}
+	
 	@Override
 	public boolean copyOf(MutableElement m) {
+		// both cannot be the same instance
 		if (this != m) {
+			// element must be instance of output
 			if (m instanceof Output) {
 				Output o = (Output) m;
+				// index must be the same
 				if (index == o.getIndex()) {
+					// source must be the same
 					if (source != o.getSource()) {
 						if (source instanceof Input && o.getSource() instanceof Input) {
 							if (((Input) source).getIndex() == ((Input) o.getSource()).getIndex()) {