Started refactoring backend in preparation for integration with the GUI

4 files changed, 34 insertions, 67 deletions

diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index df2a9d4..1f0b312 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -52,20 +52,20 @@ public class Chromosome {
 	 *
 	 */
 	private void instantiateElements() {
-		inputs = new Input[Parameters.getInputs()];
-		for (int i = 0; i < Parameters.getInputs(); i++) {
+		inputs = new Input[((int) Parameters.get("inputs").getValue())];
+		for (int i = 0; i < ((int) Parameters.get("inputs").getValue()); i++) {
 			inputs[i] = new Input(i);
 		}
 
 		// rows first
-		nodes = new Node[Parameters.getRows()][Parameters.getColumns()];
-		for (int r = 0; r < Parameters.getRows(); r++) {
-			for (int c = 0; c < Parameters.getColumns(); c++) {
+		nodes = new Node[((int) Parameters.get("rows").getValue())][((int) Parameters.get("columns").getValue())];
+		for (int r = 0; r < ((int) Parameters.get("rows").getValue()); r++) {
+			for (int c = 0; c < ((int) Parameters.get("columns").getValue()); c++) {
 				nodes[r][c] = new Node(this, r, c);
 			}
 		}
-		outputs = new Output[Parameters.getOutputs()];
-		for (int o = 0; o < Parameters.getOutputs(); o++) {
+		outputs = new Output[((int) Parameters.get("outputs").getValue())];
+		for (int o = 0; o < ((int) Parameters.get("outputs").getValue()); o++) {
 			outputs[o] = new Output(this, o);
 		}
 	}
@@ -78,7 +78,7 @@ public class Chromosome {
 		// initialise nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
 			for (int c = 0; c < nodes[r].length; c++) {
-				Connection[] connections = new Connection[Parameters.getMaxArity()];
+				Connection[] connections = new Connection[((int) Parameters.get("maxArity").getValue())];
 				for (int i = 0; i < connections.length; i++) {
 					connections[i] = getRandomConnection(c);
 				}
@@ -100,7 +100,7 @@ public class Chromosome {
 		for (int r = 0; r < nodes.length; r++) {
 			for (int c = 0; c < nodes[r].length; c++) {
 				// make array of connections to initialise with
-				Connection[] connections = new Connection[Parameters.getMaxArity()];
+				Connection[] connections = new Connection[((int) Parameters.get("maxArity").getValue())];
 				// populate with connections equivalent to clone
 				Connection copyConnection;
 				for (int i = 0; i < connections.length; i++) {
@@ -177,7 +177,7 @@ public class Chromosome {
 	 */
 	public MutableElement getRandomMutableElement() {
 		// choose output or node
-		int index = Utilities.getRandomInt(outputs.length + Parameters.getNodeCount());
+		int index = Utilities.getRandomInt(outputs.length + ((int) Parameters.get("rows").getValue()) * ((int) Parameters.get("columns").getValue()));
 
 		if (index < outputs.length) {
 			// outputs
@@ -185,7 +185,7 @@ public class Chromosome {
 		} else {
 			// node	
 			index -= outputs.length;
-			return nodes[index / Parameters.getColumns()][index % Parameters.getColumns()];
+			return nodes[index / ((int) Parameters.get("columns").getValue())][index % ((int) Parameters.get("columns").getValue())];
 		}
 	}
 
@@ -199,7 +199,7 @@ public class Chromosome {
 	 */
 	public Connection getRandomConnection(int column) {
 		// work out the allowed range obeying levels back
-		int allowedColumns = ((column >= Parameters.getLevelsBack()) ? Parameters.getLevelsBack() : column);
+		int allowedColumns = ((column >= ((int) Parameters.get("levelsBack").getValue())) ? ((int) Parameters.get("levelsBack").getValue()) : column);
 		int offset = ((column - allowedColumns) * nodes.length) - inputs.length;
 
 		// choose input or allowed node
@@ -226,7 +226,7 @@ public class Chromosome {
 	 */
 	public Connection getRandomConnection() {
 		// choose output or node
-		int index = Utilities.getRandomInt(inputs.length + Parameters.getNodeCount());
+		int index = Utilities.getRandomInt(inputs.length + ((int) Parameters.get("columns").getValue()) * ((int) Parameters.get("rows").getValue()));
 
 		if (index < inputs.length) {
 			// outputs
@@ -234,7 +234,7 @@ public class Chromosome {
 		} else {
 			// node	
 			index -= inputs.length;
-			return nodes[index / Parameters.getColumns()][index % Parameters.getColumns()];
+			return nodes[index / ((int) Parameters.get("columns").getValue())][index % ((int) Parameters.get("columns").getValue())];
 		}
 	}
 
@@ -269,15 +269,15 @@ public class Chromosome {
 	}
 
 	public boolean compareTo(Chromosome chromosome) {
-		for (int r = 0; r < Parameters.getRows(); r++) {
-			for (int c = 0; c < Parameters.getColumns(); c++) {
+		for (int r = 0; r < ((int) Parameters.get("rows").getValue()); r++) {
+			for (int c = 0; c < ((int) Parameters.get("columns").getValue()); c++) {
 				if (!(nodes[r][c].copyOf(chromosome.getNode(r, c)))) {
 					return false;
 				}
 			}
 		}
 		
-		for (int o = 0; o < Parameters.getOutputs(); o++) {
+		for (int o = 0; o < ((int) Parameters.get("outputs").getValue()); o++) {
 			if (!(outputs[o].copyOf(chromosome.getOutput(o)))) {
 				return false;
 			}
@@ -302,11 +302,11 @@ public class Chromosome {
 	}
 	
 	public void printNodes() {
-		for (int r = 0; r < Parameters.getRows(); r++) {
+		for (int r = 0; r < ((int) Parameters.get("rows").getValue()); r++) {
 			System.out.print("r: " + r + "\t");
-			for (int c = 0; c < Parameters.getColumns(); c++) {
+			for (int c = 0; c < ((int) Parameters.get("columns").getValue()); c++) {
 				System.out.print("N: (" + r + ", " + c + ") ");
-				for (int i = 0; i < Parameters.getMaxArity(); i++) {
+				for (int i = 0; i < ((int) Parameters.get("maxArity").getValue()); i++) {
 					System.out.print("C" + i + ": (" + nodes[r][c].getConnection(i).getDescription() + ") ");
 				}
 				System.out.print("F: " + nodes[r][c].getFunction().toString() + "\t");
@@ -314,7 +314,7 @@ public class Chromosome {
 			System.out.print("\n");
 		}
 		
-		for (int o = 0; o < Parameters.getOutputs(); o++) {
+		for (int o = 0; o < ((int) Parameters.get("outputs").getValue()); o++) {
 			System.out.print("o: " + o + " (" + outputs[o].getSource().getDescription() + ")\t");
 		}
 	}
diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java
index 4203f25..9fafe32 100644
--- a/src/jcgp/population/Node.java
+++ b/src/jcgp/population/Node.java
@@ -20,7 +20,7 @@ public class Node implements MutableElement, Connection {
 		this.chromosome = chromosome;
 		this.column = column;
 		this.row = row;
-		this.connections = new Connection[Parameters.getMaxArity()];
+		this.connections = new Connection[((int) Parameters.get("maxArity").getValue())];
 	}
 
 	@Override
@@ -44,7 +44,7 @@ public class Node implements MutableElement, Connection {
 
 		function = newFunction;
 
-		if (newConnections.length >= Parameters.getMaxArity()) {
+		if (newConnections.length >= ((int) Parameters.get("maxArity").getValue())) {
 			connections = newConnections;
 		} else {
 			throw new InsufficientConnectionsException();
diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java
index 89ca13c..ccecae0 100644
--- a/src/jcgp/population/Output.java
+++ b/src/jcgp/population/Output.java
@@ -2,8 +2,6 @@ package jcgp.population;
 
 import java.util.ArrayList;
 
-import jcgp.parameters.Parameters;
-
 public class Output implements MutableElement {
 	
 	private Connection source;
@@ -17,9 +15,6 @@ public class Output implements MutableElement {
 
 	public Object calculate() {
 		Object result = source.getValue();
-		if (Parameters.getDebug()) {
-			System.out.println("Output " + index + ": " + result);
-		}
 		return result;
 	}
 
diff --git a/src/jcgp/population/Population.java b/src/jcgp/population/Population.java
index 3e7b590..5718515 100644
--- a/src/jcgp/population/Population.java
+++ b/src/jcgp/population/Population.java
@@ -4,46 +4,26 @@ import jcgp.parameters.Parameters;
 
 public class Population {
 	
-	private Chromosome[] parents;
-	private Chromosome[] offspring;
+	private Chromosome[] chromosomes;
 	private Chromosome bestIndividual;
 	
 	public Population(Chromosome parent) {
-		parents = new Chromosome[Parameters.getParentCount()];
+		chromosomes = new Chromosome[((int) Parameters.get("population").getValue())];
 		// make a clone for safety
-		this.parents[0] = new Chromosome(parent);
-		// generate the rest of parents
-		for (int c = 1; c < parents.length; c++) {
-			parents[c] = new Chromosome();
-		}
-		
-		offspring = new Chromosome[Parameters.getOffspringCount()];
-		for (int c = 0; c < offspring.length; c++) {
-			// completely random offspring? depending on EA, this means the given parent won't be selected
-			offspring[c] = new Chromosome();
+		this.chromosomes[0] = new Chromosome(parent);
+		// generate the rest of the individuals
+		for (int c = 1; c < chromosomes.length; c++) {
+			chromosomes[c] = new Chromosome(chromosomes[0]);
 		}
 	}
 	
 	public Population() {
-		parents = new Chromosome[Parameters.getParentCount()];
-		for (int c = 0; c < parents.length; c++) {
-			parents[c] = new Chromosome();
-		}
-
-		offspring = new Chromosome[Parameters.getOffspringCount()];
-		for (int c = 0; c < offspring.length; c++) {
-			offspring[c] = new Chromosome();
+		chromosomes = new Chromosome[((int) Parameters.get("population").getValue())];
+		for (int c = 0; c < chromosomes.length; c++) {
+			chromosomes[c] = new Chromosome();
 		}
 	}
 
-	public Chromosome getOffspring(int index) {
-		return offspring[index];
-	}
-	
-	public Chromosome getParent(int index) {
-		return parents[index];
-	}
-	
 	/**
 	 * Returns all chromosomes, parents first, then offspring.
 	 * 
@@ -51,19 +31,11 @@ public class Population {
 	 * @return
 	 */
 	public Chromosome getChromosome(int index) {
-		if (index < parents.length) {
-			return parents[index];
-		} else {
-			return offspring[index - parents.length];
-		}
+		return chromosomes[index];
 	}
 	
 	public void setBestIndividual(int index) {
-		if (index < parents.length) {
-			bestIndividual = parents[index];
-		} else {
-			bestIndividual = offspring[index - parents.length];
-		}
+		bestIndividual = chromosomes[index];
 	}
 	
 	public Chromosome getBestIndividual() {