Moved files around to different folders, and commented some more packages. Aiming to have the entire backend fully commented by the end of today

5 files changed, 31 insertions, 13 deletions

diff --git a/src/jcgp/backend/modules/es/MuPlusLambda.java b/src/jcgp/backend/modules/es/MuPlusLambda.java
index 50bf265..754e89b 100644
--- a/src/jcgp/backend/modules/es/MuPlusLambda.java
+++ b/src/jcgp/backend/modules/es/MuPlusLambda.java
@@ -76,6 +76,11 @@ public class MuPlusLambda implements EvolutionaryStrategy {
 	}
 	
 	@Override
+	public Parameter<?>[] getLocalParameters() {
+		return new Parameter[] {mu, lambda, report};
+	}
+	
+	@Override
 	public void evolve(Population population, Mutator mutator, Resources resources) {		
 		/* Population is sorted in ascending order of fitness, so leave the last
 		 * mu chromosomes intact
@@ -95,11 +100,6 @@ public class MuPlusLambda implements EvolutionaryStrategy {
 	}
 
 	@Override
-	public Parameter<?>[] getLocalParameters() {
-		return new Parameter[] {mu, lambda, report};
-	}
-
-	@Override
 	public String toString() {
 		return "(μ + λ)";
 	}
diff --git a/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java b/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java
index e3c1d03..cacb451 100644
--- a/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java
+++ b/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java
@@ -70,7 +70,7 @@ public class ProbabilisticMutator implements Mutator {
 			for (int c = 0; c < resources.columns(); c++) {
 				// go through all connections
 				for (int a = 0; a < resources.arity(); a++) {
-					if (mutate()) {
+					if (mutateGene()) {
 						Node n = chromosome.getNode(r, c);
 						
 						if (report.get()) resources.report("[Mutator] Mutating " + n +
@@ -83,7 +83,7 @@ public class ProbabilisticMutator implements Mutator {
 					}
 				}
 				// deal with node function next
-				if (mutate()) {
+				if (mutateGene()) {
 					Node n = chromosome.getNode(r, c);
 					if (report.get()) resources.report("[Mutator] Mutating " + n +
 							", changed function from " + n.getFunction());
@@ -96,7 +96,7 @@ public class ProbabilisticMutator implements Mutator {
 		}
 		// finally, mutate outputs
 		for (int o = 0; o < resources.outputs(); o++) {
-			if (mutate()) {
+			if (mutateGene()) {
 				Output out = chromosome.getOutput(o);
 				
 				if (report.get()) resources.report("[Mutator] Mutating " + out +
@@ -120,7 +120,7 @@ public class ProbabilisticMutator implements Mutator {
 	 * 
 	 * @return true if a mutation should be performed, false if otherwise.
 	 */
-	private boolean mutate() {
+	private boolean mutateGene() {
 		return resources.getRandomDouble(100) < mutationProbability.get();
 	}
 
diff --git a/src/jcgp/backend/modules/problem/Problem.java b/src/jcgp/backend/modules/problem/Problem.java
index 07183ea..368d512 100644
--- a/src/jcgp/backend/modules/problem/Problem.java
+++ b/src/jcgp/backend/modules/problem/Problem.java
@@ -9,6 +9,25 @@ import jcgp.backend.population.Population;
 import jcgp.backend.resources.ModifiableResources;
 import jcgp.backend.resources.Resources;
 
+/**
+ * Defines the general behaviour of a CGP problem. The primary function of Problem 
+ * is to evaluate a population and assign 
+ * <br><br>
+ * Parameters may be specified to control the implemented problem. Any parameters
+ * returned by {@code getLocalParameters()} should be displayed by the user interface,
+ * if it is being used. See {@link Parameter} for more information. 
+ * <br><br>
+ * It is advisable to use {@code Resources.reportln()} and {@code Resources.report()}
+ * to print any relevant information. Note that reportln() and report() are affected
+ * by the report interval base parameter. Use {@code Resources.println()} and
+ * {@code Resources.print()} to print information regardless of the current generation.
+ * See {@link Resources} for more information.
+ * 
+ * @see Module
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
 public abstract class Problem implements Module {
 
 	protected FunctionSet functionSet;
@@ -23,7 +42,7 @@ public abstract class Problem implements Module {
 	
 	public abstract boolean isPerfectSolution(Chromosome fittest);
 	
-	public abstract void parse(File file, ModifiableResources resources);
+	public abstract void parseProblemData(File file, ModifiableResources resources);
 	
 	public void setFileExtension(String fileExtension) {
 		this.fileExtension = fileExtension;
diff --git a/src/jcgp/backend/modules/problem/TestCaseProblem.java b/src/jcgp/backend/modules/problem/TestCaseProblem.java
index 6c4a7dc..7ce0327 100644
--- a/src/jcgp/backend/modules/problem/TestCaseProblem.java
+++ b/src/jcgp/backend/modules/problem/TestCaseProblem.java
@@ -119,8 +119,7 @@ public abstract class TestCaseProblem<U extends Object> extends Problem {
 		testCases.clear();
 	}
 
-	public void parse(File file, ModifiableResources resources) {
-		TestCaseParser.parseParameters(file, resources);
+	public void parseProblemData(File file, ModifiableResources resources) {
 		TestCaseParser.parse(file, this, resources);
 	}
 }
diff --git a/src/jcgp/backend/modules/problem/TravellingSalesmanProblem.java b/src/jcgp/backend/modules/problem/TravellingSalesmanProblem.java
index 6491ec6..8363ef8 100644
--- a/src/jcgp/backend/modules/problem/TravellingSalesmanProblem.java
+++ b/src/jcgp/backend/modules/problem/TravellingSalesmanProblem.java
@@ -36,7 +36,7 @@ public class TravellingSalesmanProblem extends Problem {
 	}
 
 	@Override
-	public void parse(File file, ModifiableResources resources) {
+	public void parseProblemData(File file, ModifiableResources resources) {
 		// TODO Auto-generated method stub
 		
 	}