Added javadocs, made minor changes to the comments

5 files changed, 50 insertions, 36 deletions

diff --git a/src/jcgp/backend/modules/mutator/FixedPointMutator.java b/src/jcgp/backend/modules/mutator/FixedPointMutator.java
index 5d40c57..1efdd2f 100644
--- a/src/jcgp/backend/modules/mutator/FixedPointMutator.java
+++ b/src/jcgp/backend/modules/mutator/FixedPointMutator.java
@@ -25,7 +25,7 @@ public class FixedPointMutator extends PointMutator {
 	 * @param resources a reference to the experiment's resources.
 	 */
 	public FixedPointMutator(final Resources resources) {
-		super();
+		super(resources);
 		genesMutated = new IntegerParameter(5, "Genes mutated", false, false) {
 			@Override
 			public void validate(Number newValue) {
diff --git a/src/jcgp/backend/modules/mutator/Mutator.java b/src/jcgp/backend/modules/mutator/Mutator.java
index 02fd70a..56692ef 100644
--- a/src/jcgp/backend/modules/mutator/Mutator.java
+++ b/src/jcgp/backend/modules/mutator/Mutator.java
@@ -25,14 +25,22 @@ import jcgp.backend.resources.Resources;
  *
  */
 public abstract class Mutator extends Module {
+	
+	/**
+	 * For internal use only, initialises the resources field.
+	 * 
+	 * @param resources the experiment's resources.
+	 */
+	protected Mutator(Resources resources) {
+		super(resources);
+	}
 
 	/**
 	 * Applies mutations to the specified chromosome according
 	 * to the parameter values.
 	 * 
 	 * @param chromosome the chromosome to mutate.
-	 * @param resources parameters and utilities for optional reference.
 	 */
-	public abstract void mutate(Chromosome chromosome, Resources resources);
+	public abstract void mutate(Chromosome chromosome);
 	
 }
diff --git a/src/jcgp/backend/modules/mutator/PercentPointMutator.java b/src/jcgp/backend/modules/mutator/PercentPointMutator.java
index 31a7739..015edf4 100644
--- a/src/jcgp/backend/modules/mutator/PercentPointMutator.java
+++ b/src/jcgp/backend/modules/mutator/PercentPointMutator.java
@@ -24,12 +24,12 @@ public class PercentPointMutator extends PointMutator {
 	private DoubleParameter mutationRate;
 
 	/**
-	 * Creates a new instance of PointMutator. 
+	 * Creates a new instance of PercentPointMutator. 
 	 * 
 	 * @param resources a reference to the experiment's resources.
 	 */
 	public PercentPointMutator(final Resources resources) {
-		super();
+		super(resources);
 		mutationRate = new DoubleParameter(10, "Percent mutation", false, false) {
 			@Override
 			public void validate(Number newValue) {
diff --git a/src/jcgp/backend/modules/mutator/PointMutator.java b/src/jcgp/backend/modules/mutator/PointMutator.java
index 0223a37..9e421c2 100644
--- a/src/jcgp/backend/modules/mutator/PointMutator.java
+++ b/src/jcgp/backend/modules/mutator/PointMutator.java
@@ -24,48 +24,57 @@ public abstract class PointMutator extends Mutator {
 
 	protected IntegerParameter genesMutated;
 	protected BooleanParameter report;
+	
+	/**
+	 * For internal use only, initialises the resources field.
+	 * 
+	 * @param resources the experiment's resources.
+	 */
+	protected PointMutator(Resources resources) {
+		super(resources);
+	}
 
 	@Override
-	public void mutate(Chromosome chromosome, Resources resources) {
-		if (report.get()) resources.reportln("[Mutator] Number of mutations to be performed: " + genesMutated.get());
+	public void mutate(Chromosome chromosome) {
+		if (report.get()) getResources().reportln("[Mutator] Number of mutations to be performed: " + genesMutated.get());
 		
 		// for however many genes must be mutated
 		for (int i = 0; i < genesMutated.get(); i++) {
 			
 			MutableElement m = chromosome.getRandomMutableElement();
 			
-			if (report.get()) resources.report("[Mutator] Mutation " + i + " selected " + m + ", ");
+			if (report.get()) getResources().report("[Mutator] Mutation " + i + " selected " + m + ", ");
 			
 			// outputs and nodes are mutated differently
 			if (m instanceof Output) {
-				if (report.get()) resources.report("changed source from " + ((Output) m).getSource() + " ");
+				if (report.get()) getResources().report("changed source from " + ((Output) m).getSource() + " ");
 				
 				// outputs are easy, simply set to a different random connection, any will do
 				m.setConnection(0, chromosome.getRandomConnection());
 				
-				if (report.get()) resources.reportln("to " + ((Output) m).getSource());
+				if (report.get()) getResources().reportln("to " + ((Output) m).getSource());
 			} else if (m instanceof Node) {
 				/* nodes are more complicated, first we must decide whether to mutate the function
 				 * or a connection
 				 * we do this by generating a random int between 0 and 1 + arity
 				 */
-				int geneType = resources.getRandomInt(1 + resources.arity());
+				int geneType = getResources().getRandomInt(1 + getResources().arity());
 				
 				// if the int is less than 1, mutate function, else mutate connections 
 				if (geneType < 1) {
-					if (report.get()) resources.report("changed function from " + ((Node) m).getFunction() + " ");
+					if (report.get()) getResources().report("changed function from " + ((Node) m).getFunction() + " ");
 					
-					((Node) m).setFunction(resources.getRandomFunction());
+					((Node) m).setFunction(getResources().getRandomFunction());
 					
-					if (report.get()) resources.reportln("to " + ((Node) m).getFunction());
+					if (report.get()) getResources().reportln("to " + ((Node) m).getFunction());
 				} else {
 					// if we decided to mutate connection, subtract 1 from geneType so it fits into the arity range
 					geneType -= 1;
-					if (report.get()) resources.report("changed connection " + geneType + " from " + ((Node) m).getConnection(geneType) + " ");
+					if (report.get()) getResources().report("changed connection " + geneType + " from " + ((Node) m).getConnection(geneType) + " ");
 					
 					m.setConnection(geneType, chromosome.getRandomConnection(((Node) m).getColumn()));
 					
-					if (report.get()) resources.reportln("to " + ((Node) m).getConnection(geneType));
+					if (report.get()) getResources().reportln("to " + ((Node) m).getConnection(geneType));
 				}
 			}
 		}
diff --git a/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java b/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java
index c65fc22..9273558 100644
--- a/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java
+++ b/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java
@@ -25,17 +25,14 @@ public class ProbabilisticMutator extends Mutator {
 
 	private DoubleParameter mutationProbability;
 	private BooleanParameter report;
-	
-	private Resources resources;
-	
+		
 	/**
 	 * Creates a new instance of ProbabilisticMutator. 
 	 * 
 	 * @param resources a reference to the experiment's resources.
 	 */
 	public ProbabilisticMutator(Resources resources) {
-		super();
-		this.resources = resources;
+		super(resources);
 		
 		mutationProbability = new DoubleParameter(10, "Mutation probability", false, false) {
 			@Override
@@ -56,53 +53,53 @@ public class ProbabilisticMutator extends Mutator {
 	}
 
 	@Override
-	public void mutate(Chromosome chromosome, Resources resources) {
-		if (report.get()) resources.reportln("[Mutator] Starting mutations");
+	public void mutate(Chromosome chromosome) {
+		if (report.get()) getResources().reportln("[Mutator] Starting mutations");
 		
 		// go through nodes - [rows][columns]
-		for (int r = 0; r < resources.rows(); r++) {
-			for (int c = 0; c < resources.columns(); c++) {
+		for (int r = 0; r < getResources().rows(); r++) {
+			for (int c = 0; c < getResources().columns(); c++) {
 				// go through all connections
-				for (int a = 0; a < resources.arity(); a++) {
+				for (int a = 0; a < getResources().arity(); a++) {
 					if (mutateGene()) {
 						Node n = chromosome.getNode(r, c);
 						
-						if (report.get()) resources.report("[Mutator] Mutating " + n +
+						if (report.get()) getResources().report("[Mutator] Mutating " + n +
 								", changed connection " + a + " from " + n.getConnection(a) + " ");
 						
 						n.setConnection(a, chromosome.getRandomConnection(c));
 						
-						if (report.get()) resources.reportln("to " + n.getConnection(a));
+						if (report.get()) getResources().reportln("to " + n.getConnection(a));
 						
 					}
 				}
 				// deal with node function next
 				if (mutateGene()) {
 					Node n = chromosome.getNode(r, c);
-					if (report.get()) resources.report("[Mutator] Mutating " + n +
+					if (report.get()) getResources().report("[Mutator] Mutating " + n +
 							", changed function from " + n.getFunction());
 					
-					n.setFunction(resources.getRandomFunction());
+					n.setFunction(getResources().getRandomFunction());
 					
-					if (report.get()) resources.reportln(" to " + n.getFunction());
+					if (report.get()) getResources().reportln(" to " + n.getFunction());
 				}
 			}
 		}
 		// finally, mutate outputs
-		for (int o = 0; o < resources.outputs(); o++) {
+		for (int o = 0; o < getResources().outputs(); o++) {
 			if (mutateGene()) {
 				Output out = chromosome.getOutput(o);
 				
-				if (report.get()) resources.report("[Mutator] Mutating " + out +
+				if (report.get()) getResources().report("[Mutator] Mutating " + out +
 						", changed source from " + out.getSource());
 				
 				out.setConnection(0, chromosome.getRandomConnection());
 				
-				if (report.get()) resources.reportln("to " + out.getSource());
+				if (report.get()) getResources().reportln("to " + out.getSource());
 			}
 		}
 		
-		if (report.get()) resources.reportln("[Mutator] Mutation finished ");
+		if (report.get()) getResources().reportln("[Mutator] Mutation finished ");
 
 	}
 	
@@ -115,6 +112,6 @@ public class ProbabilisticMutator extends Mutator {
 	 * @return true if a mutation should be performed, false if otherwise.
 	 */
 	private boolean mutateGene() {
-		return resources.getRandomDouble(100) < mutationProbability.get();
+		return getResources().getRandomDouble(100) < mutationProbability.get();
 	}
 }