package jcgp.population;

import java.util.ArrayList;

import jcgp.CGP.Utilities;

public class Chromosome {

	private final ArrayList<Input> inputs = new ArrayList<Input>();
	private final ArrayList<ArrayList<Node>> nodes = new ArrayList<ArrayList<Node>>();;
	private final ArrayList<Output> outputs = new ArrayList<Output>();
	
	private int fitness = 0;
	
	/**
	 * Good citizen.
	 * 
	 * @param outputs 
	 * @param columns 
	 * @param rows 
	 * @param inputs 
	 * 
	 */
	public Chromosome(int inputCount, int rows, int columns, int outputCount) {
		
		instantiateElements(inputCount, rows, columns, outputCount);
		
		initialiseConnections();
	
	}

	private void initialiseConnections() {
		
		// initialise nodes
		for (int r = 0; r < nodes.size(); r++) {
			for (int c = 0; c < nodes.size(); c++) {
				Connection[] connections = new Connection[Utilities.getMaxArity()];
				for (int i = 0; i < connections.length; i++) {
					connections[i] = Utilities.getRandomConnection(this, c);
				}
				nodes.get(r).get(c).initialise(Utilities.getRandomFunction(), connections);
			}
		}
		
		for (Output output : outputs) {
			output.setConnection(Utilities.getRandomNode(this));
		}
		
	}

	/**
	 * @param inputCount
	 * @param rows
	 * @param columns
	 * @param outputCount
	 */
	private void instantiateElements(int inputCount, int rows, int columns,	int outputCount) {
		for (int i = 0; i < inputCount; i++) {
			inputs.add(new Input());
		}
		
		// rows first
		for (int r = 0; r < rows; r++) {
			nodes.add(new ArrayList<Node>(columns));
			for (int c = 0; c < columns; c++) {
				nodes.get(r).add(new Node());
			}
		}
		
		for (int o = 0; o < outputCount; o++) {
			outputs.add(new Output());
		}
	}
	
	public int getActiveNodeCount() {
		return 0;
	}

	/**
	 * @return the inputs
	 */
	public ArrayList<Input> getInputs() {
		return inputs;
	}

	/**
	 * @return the nodes
	 */
	public ArrayList<ArrayList<Node>> getNodes() {
		return nodes;
	}

	/**
	 * @return the outputs
	 */
	public ArrayList<Output> getOutputs() {
		return outputs;
	}
	
	public Node getNode(int row, int column) {
		return nodes.get(row).get(column);
	}
	
	public Output getOutput(int index) {
		return outputs.get(index);
	}
	
	public Input getInput(int index) {
		return inputs.get(index);
	}
	
	public int getFitness() {
		return fitness;
	}
	
	public void setFitness(int newFitness) {
		fitness = newFitness;
	}
	
}