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 +++++++++++++++++++++++++++++++++++--
 1 file changed, 64 insertions(+), 2 deletions(-)

(limited to 'src/jcgp/chromosome/Chromosome.java')

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);
 	}
 	
 }
-- 
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