From 8f7874fa75c532bab994af8e6553d37afe42ec4c Mon Sep 17 00:00:00 2001
From: Eduardo Pedroni <ep625@york.ac.uk>
Date: Thu, 30 Jan 2014 21:41:33 +0000
Subject: Chromosome data structure partially refactored, also added higher
 level classes.

---
 src/jcgp/chromosome/Chromosome.java             | 66 ++++++++++++++++++++++++-
 src/jcgp/chromosome/Population.java             | 16 ++++++
 src/jcgp/chromosome/element/MutableElement.java |  7 ---
 src/jcgp/chromosome/element/Node.java           | 18 +++----
 src/jcgp/chromosome/element/Output.java         | 14 ------
 5 files changed, 86 insertions(+), 35 deletions(-)
 create mode 100644 src/jcgp/chromosome/Population.java

(limited to 'src/jcgp/chromosome')

diff --git a/src/jcgp/chromosome/Chromosome.java b/src/jcgp/chromosome/Chromosome.java
index 19d7e77..cdf2e4b 100644
--- a/src/jcgp/chromosome/Chromosome.java
+++ b/src/jcgp/chromosome/Chromosome.java
@@ -2,16 +2,78 @@ package jcgp.chromosome;
 
 import java.util.ArrayList;
 
-import jcgp.chromosome.element.ChromosomeElement;
+import jcgp.CGP;
+import jcgp.chromosome.element.Input;
+import jcgp.chromosome.element.Node;
+import jcgp.chromosome.element.Output;
 
 public class Chromosome {
 
-	private ArrayList<ArrayList<? extends ChromosomeElement>> nodes;
+	private ArrayList<Input> inputs;
+	private ArrayList<ArrayList<Node>> nodes;
+	private ArrayList<Output> outputs;
 	
+	/**
+	 * Good citizen.
+	 * 
+	 */
 	public Chromosome() {
 		
+		inputs = new ArrayList<Input>(CGP.INPUTS);
+		for (int i = 0; i < CGP.INPUTS; i++) {
+			inputs.add(new Input());
+		}
 		
+		// rows first
+		nodes = new ArrayList<ArrayList<Node>>(CGP.ROWS);
+		for (int r = 0; r < CGP.ROWS; r++) {
+			nodes.add(new ArrayList<Node>(CGP.COLUMNS));
+			for (int c = 0; c < CGP.COLUMNS; c++) {
+				nodes.get(r).add(new Node());
+			}
+		}
 		
+		outputs = new ArrayList<Output>(CGP.OUTPUTS);
+		for (int o = 0; o < CGP.OUTPUTS; o++) {
+			outputs.add(new Output());
+		}
+	}
+	
+	public int getActiveNodeCount() {
+		return 0;
+	}
+
+	/**
+	 * @return the inputs
+	 */
+	public final ArrayList<Input> getInputs() {
+		return inputs;
+	}
+
+	/**
+	 * @return the nodes
+	 */
+	public final ArrayList<ArrayList<Node>> getNodes() {
+		return nodes;
+	}
+
+	/**
+	 * @return the outputs
+	 */
+	public final ArrayList<Output> getOutputs() {
+		return outputs;
+	}
+	
+	public final Node getNode(int row, int column) {
+		return nodes.get(row).get(column);
+	}
+	
+	public final Output getOutput(int index) {
+		return outputs.get(index);
+	}
+	
+	public final Input getInputs(int index) {
+		return inputs.get(index);
 	}
 	
 }
diff --git a/src/jcgp/chromosome/Population.java b/src/jcgp/chromosome/Population.java
new file mode 100644
index 0000000..e720a24
--- /dev/null
+++ b/src/jcgp/chromosome/Population.java
@@ -0,0 +1,16 @@
+package jcgp.chromosome;
+
+import java.util.ArrayList;
+
+public class Population {
+	
+	private ArrayList<Chromosome> population;
+	
+	public Population(int size) {
+		population = new ArrayList<Chromosome>(size);
+		for (int c = 0; c < size; c++) {
+			population.add(new Chromosome());
+		}
+	}
+
+}
diff --git a/src/jcgp/chromosome/element/MutableElement.java b/src/jcgp/chromosome/element/MutableElement.java
index ed7e23c..0122c69 100644
--- a/src/jcgp/chromosome/element/MutableElement.java
+++ b/src/jcgp/chromosome/element/MutableElement.java
@@ -1,12 +1,5 @@
 package jcgp.chromosome.element;
 
-import jcgp.chromosome.Chromosome;
-import jcgp.chromosome.functions.FunctionSet;
-
 public interface MutableElement {
 	
-	public void initialise(Chromosome chromosome, FunctionSet functions);
-	
-	public void mutate(Chromosome chromosome, FunctionSet functions);
-
 }
diff --git a/src/jcgp/chromosome/element/Node.java b/src/jcgp/chromosome/element/Node.java
index f97c680..761c3c9 100644
--- a/src/jcgp/chromosome/element/Node.java
+++ b/src/jcgp/chromosome/element/Node.java
@@ -1,22 +1,16 @@
 package jcgp.chromosome.element;
 
-import jcgp.chromosome.Chromosome;
-import jcgp.chromosome.functions.FunctionSet;
+import jcgp.chromosome.functions.Function;
 
-public class Node extends ChromosomeElement implements MutableElement {
 
-	@Override
-	public void initialise(Chromosome chromosome, FunctionSet functions) {
-		// TODO Auto-generated method stub
-		
-	}
+public class Node extends ChromosomeElement implements MutableElement {
+	
+	private Function function;
 
-	@Override
-	public void mutate(Chromosome chromosome, FunctionSet functions) {
-		// TODO Auto-generated method stub
+	public Node() {
 		
 	}
-
+	
 	@Override
 	public int evaluate() {
 		// TODO Auto-generated method stub
diff --git a/src/jcgp/chromosome/element/Output.java b/src/jcgp/chromosome/element/Output.java
index 261e77d..ee4d204 100644
--- a/src/jcgp/chromosome/element/Output.java
+++ b/src/jcgp/chromosome/element/Output.java
@@ -1,22 +1,8 @@
 package jcgp.chromosome.element;
 
-import jcgp.chromosome.Chromosome;
-import jcgp.chromosome.functions.FunctionSet;
 
 public class Output extends ChromosomeElement implements MutableElement {
 
-	@Override
-	public void initialise(Chromosome chromosome, FunctionSet functions) {
-		// TODO Auto-generated method stub
-		
-	}
-
-	@Override
-	public void mutate(Chromosome chromosome, FunctionSet functions) {
-		// TODO Auto-generated method stub
-		
-	}
-
 	@Override
 	public int evaluate() {
 		// TODO Auto-generated method stub
-- 
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