Worked on more tests, finished restructuring resources

3 files changed, 34 insertions, 29 deletions

diff --git a/src/jcgp/Utilities.java b/src/jcgp/Utilities.java
index 7de701a..76f996e 100644
--- a/src/jcgp/Utilities.java
+++ b/src/jcgp/Utilities.java
@@ -132,6 +132,8 @@ public class Utilities {
 	 * 
 	 * It will pick outputs or nodes fairly.
 	 * 
+	 * TODO probably remove this
+	 * 
 	 * @param chromosome the chromosome to pick from
 	 * @return a random mutable element
 	 */
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index 328a608..195b95c 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -9,9 +9,9 @@ public class Chromosome {
 	private Input[] inputs;
 	private Node[][] nodes;
 	private Output[] outputs;
-	
+
 	private int fitness = 0;
-	
+
 	/**
 	 * Good citizen.
 	 * 
@@ -22,11 +22,11 @@ public class Chromosome {
 	 * 
 	 */
 	public Chromosome(int inputCount, int rows, int columns, int outputCount) {
-		
+
 		instantiateElements(inputCount, rows, columns, outputCount);
-		
+
 		initialiseConnections();
-	
+
 	}
 
 	/**
@@ -40,7 +40,7 @@ public class Chromosome {
 		for (int i = 0; i < inputCount; i++) {
 			inputs[i] = new Input();
 		}
-		
+
 		// rows first
 		nodes = new Node[rows][columns];
 		for (int r = 0; r < rows; r++) {
@@ -54,9 +54,9 @@ public class Chromosome {
 			outputs[o] = new Output(o);
 		}
 	}
-	
+
 	private void initialiseConnections() {
-		
+
 		// initialise nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
 			for (int c = 0; c < nodes.length; c++) {
@@ -67,13 +67,13 @@ public class Chromosome {
 				nodes[r][c].initialise(Utilities.getRandomFunction(), connections);
 			}
 		}
-		
+
 		for (Output output : outputs) {
 			output.setConnection(Utilities.getRandomNode(this));
 		}
-		
+
 	}
-	
+
 	public int getActiveNodeCount() {
 		return 0;
 	}
@@ -81,23 +81,23 @@ public class Chromosome {
 	public Node getNode(int row, int column) {
 		return nodes[row][column];
 	}
-	
+
 	public Output getOutput(int index) {
 		return outputs[index];
 	}
-	
+
 	public Input getInput(int index) {
 		return inputs[index];
 	}
-	
+
 	public int getFitness() {
 		return fitness;
 	}
-	
+
 	public void setFitness(int newFitness) {
 		fitness = newFitness;
 	}
-	
+
 	public void setInputs(int ... values) throws ParameterMismatchException {
 		// if the values provided don't match the specified number of inputs, the user should be warned
 		if (values.length == inputs.length) {
@@ -110,13 +110,18 @@ public class Chromosome {
 		}
 	}
 
-	public MutableElement getMutableElement(int row, int column) {
-		if (column < Parameters.getColumns() && column >= 0) {
-			return nodes[row][column];
-		} else if (column == Parameters.getColumns()) {
-			return outputs[row];
+	public MutableElement getRandomMutableElement() {
+		// choose output or node
+		int index = Utilities.getRandomInt(outputs.length + Parameters.getNodeCount());
+
+		if (index < outputs.length) {
+			// outputs
+			return outputs[index];
+		} else {
+			// node	
+			index -= outputs.length;
+			return nodes[index / Parameters.getColumns()][index % Parameters.getColumns()];
 		}
-		return null;
 	}
-	
+
 }
diff --git a/src/jcgp/tests/ChromosomeTests.java b/src/jcgp/tests/ChromosomeTests.java
index 123cbd1..75e3596 100644
--- a/src/jcgp/tests/ChromosomeTests.java
+++ b/src/jcgp/tests/ChromosomeTests.java
@@ -22,10 +22,8 @@ import org.junit.Test;
  * Tests which cover the behaviour specified for a chromosome.
  * 
  *  - The chromosome should be able to return a specified node, input or output.
- *  - It should be able to return a MutableElement indexed by row and column, 
- *    where column NodeCount returns outputs.
- *  - It should be able to return a Connection indexed by row and column, where
- *    column 0 returns inputs.
+ *  - It should be able to return a random MutableElement.
+ *  - It should be able to return a random Connection 
  *  - It should contain a freely modifiable fitness value.
  *  - It should be a good citizen - fully initialised upon instantiation.
  *  - It should feature a clone constructor, which creates a deep copy of a 
@@ -91,8 +89,8 @@ public class ChromosomeTests {
 				&& chromosome.getOutput(2).calculate() ==  4 && chromosome.getOutput(0) instanceof Output;
 		assertTrue("Incorrect output returned.", outputReturn);
 
-		// get a mutable element, that that it is a Mutable
-		boolean mutableReturn = chromosome.getMutable() instanceof Output;
+		// get a mutable element, check that it is a Mutable
+		boolean mutableReturn = chromosome.getRandomMutableElement() instanceof Output;
 		
 		// set a fitness value, check if returned value is the same
 		chromosome.setFitness(10);