GUIParameters all refactored and commented.

4 files changed, 46 insertions, 57 deletions

diff --git a/src/jcgp/backend/tests/ChromosomeTests.java b/src/jcgp/backend/tests/ChromosomeTests.java
index a16ba75..07326a7 100644
--- a/src/jcgp/backend/tests/ChromosomeTests.java
+++ b/src/jcgp/backend/tests/ChromosomeTests.java
@@ -2,6 +2,7 @@ package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
+import jcgp.backend.function.IntegerArithmetic;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
 import jcgp.backend.population.Input;
@@ -45,6 +46,7 @@ public class ChromosomeTests {
 	@BeforeClass
 	public static void setUpBeforeClass() {
 		resources = new ModifiableResources();
+		resources.setFunctionSet(new IntegerArithmetic());
 	}
 
 	@Before
@@ -62,7 +64,7 @@ public class ChromosomeTests {
 
 		// compare all elements, one by one
 		// check outputs
-		for (int o = 0; o < resources.getInt("outputs"); o++) {
+		for (int o = 0; o < resources.outputs(); o++) {
 			// check that no cross-references exist between chromosomes
 			assertTrue("Cloned chromosome contains a reference to a member of the original chromosome.",
 					clone.getOutput(o) != chromosome.getOutput(o) && 
@@ -80,8 +82,8 @@ public class ChromosomeTests {
 			}
 		}
 		// check nodes, rows first
-		for (int row = 0; row < resources.getInt("rows"); row++) {
-			for (int column = 0; column < resources.getInt("columns"); column++) {
+		for (int row = 0; row < resources.rows(); row++) {
+			for (int column = 0; column < resources.columns(); column++) {
 				// check that nodes are not pointers to the same instance
 				assertTrue("Both chromosomes contain a reference to the same node.", clone.getNode(row, column) != chromosome.getNode(row, column));
 				// check that both nodes reference their own position in the grid correctly
@@ -91,7 +93,7 @@ public class ChromosomeTests {
 				assertTrue("Equivalent nodes have different functions.", clone.getNode(row, column).getFunction() == chromosome.getNode(row, column).getFunction());
 
 				// compare each connection
-				for (int connection = 0; connection < resources.getInt("arity"); connection++) {
+				for (int connection = 0; connection < resources.arity(); connection++) {
 					// first look at whether they are actually the same instance
 					assertTrue("Nodes are connected to the same connection instance.", 
 							clone.getNode(row, column).getConnection(connection) !=	chromosome.getNode(row, column).getConnection(connection));
@@ -130,12 +132,12 @@ public class ChromosomeTests {
 		clone.setInputs((Object[]) testInputs);
 
 		// check that both chromosomes have the same outputs
-		for (int i = 0; i < resources.getInt("outputs"); i++) {
+		for (int i = 0; i < resources.outputs(); i++) {
 			assertTrue("Incorrect output returned", ((Integer) chromosome.getOutput(i).calculate()) == ((Integer) clone.getOutput(i).calculate()));
 		}
 
 		// mutate an output in clone, check that the same node in chromosome produces a different output
-		clone.getOutput(1).setConnection(resources.getRandomInt(resources.getInt("arity")), clone.getInput(2));
+		clone.getOutput(1).setConnection(resources.getRandomInt(resources.arity()), clone.getInput(2));
 
 		assertTrue("Mutation affected nodes in both chromosomes.",
 				clone.getOutput(1).calculate() != chromosome.getOutput(1).calculate());
@@ -164,7 +166,7 @@ public class ChromosomeTests {
 
 		// get random connections with the last column as reference, check that they're all within range
 		int connectionNodes = 0, connectionOutOfRange = 0, connectionInputs = 0, connectionPicks = 100000;
-		int chosenColumn = resources.getInt("columns") - 1;
+		int chosenColumn = resources.columns() - 1;
 		for (int i = 0; i < connectionPicks; i++) {
 			Connection c = chromosome.getRandomConnection(chosenColumn);
 			if (c instanceof Node) {
@@ -180,10 +182,10 @@ public class ChromosomeTests {
 
 			}	
 		}
-		System.out.println("Out of " + connectionPicks + " connections picked from " + ((chosenColumn >= resources.getInt("levelsBack")) ? resources.getInt("levelsBack") : chosenColumn) * resources.getInt("rows") +
-				" allowed nodes and " + resources.getInt("inputs") + " inputs, " + connectionNodes + " were nodes and " + connectionInputs + " were inputs.");
+		System.out.println("Out of " + connectionPicks + " connections picked from " + ((chosenColumn >= resources.levelsBack()) ? resources.levelsBack() : chosenColumn) * resources.rows() +
+				" allowed nodes and " + resources.inputs() + " inputs, " + connectionNodes + " were nodes and " + connectionInputs + " were inputs.");
 
-		System.out.println("Node/input ratio: " + (chosenColumn >= resources.getInt("levelsBack") ? resources.getInt("levelsBack") : chosenColumn) * resources.getDouble("rows") / resources.getDouble("inputs") +
+		System.out.println("Node/input ratio: " + (chosenColumn >= resources.levelsBack() ? resources.levelsBack() : chosenColumn) * (double) resources.rows() / (double) resources.inputs() +
 				", picked ratio: " + (double) connectionNodes / (double) connectionInputs);
 
 		System.out.println(connectionOutOfRange + " nodes that disrespected levels back were picked.");
@@ -207,10 +209,10 @@ public class ChromosomeTests {
 				fail("Return is neither Node nor Output.");
 			}
 		}
-		System.out.println("Out of " + mutablePicks + " mutable elements picked from " + resources.getInt("nodes") +
-				" nodes and " + resources.getInt("outputs") + " outputs, " + mutableNodes + " were nodes and " +
+		System.out.println("Out of " + mutablePicks + " mutable elements picked from " + resources.nodes() +
+				" nodes and " + resources.outputs() + " outputs, " + mutableNodes + " were nodes and " +
 				mutableOutputs + " were outputs.");
-		System.out.println("Node/output ratio: " + resources.getDouble("nodes") / resources.getDouble("outputs") +
+		System.out.println("Node/output ratio: " + (double) resources.nodes() / (double) resources.outputs() +
 				", picked ratio: " + (double) mutableNodes / (double) mutableOutputs + "\n");
 	}
 
@@ -234,12 +236,12 @@ public class ChromosomeTests {
 	@Test
 	public void setInputTest() {
 		// set input values, check that acquired values are correct
-		Integer[] testInputs = new Integer[resources.getInt("inputs")];
-		for (int i = 0; i < resources.getInt("inputs"); i++) {
+		Integer[] testInputs = new Integer[resources.inputs()];
+		for (int i = 0; i < resources.inputs(); i++) {
 			testInputs[i] = i * 2 - 3;
 		}
 		chromosome.setInputs((Object[]) testInputs);
-		for (int i = 0; i < resources.getInt("inputs"); i++) {
+		for (int i = 0; i < resources.inputs(); i++) {
 			assertTrue("Incorrect input returned.", ((Integer) chromosome.getInput(i).getValue()) == i * 2 - 3);
 		}
 	}
@@ -250,8 +252,8 @@ public class ChromosomeTests {
 	@Test
 	public void getNodeTest() {
 		// get all nodes one by one, check that they are all correct
-		for (int r = 0; r < resources.getInt("rows"); r++) {
-			for (int c = 0; c < resources.getInt("columns"); c++) {
+		for (int r = 0; r < resources.rows(); r++) {
+			for (int c = 0; c < resources.columns(); c++) {
 				assertTrue("Incorrect node returned.", chromosome.getNode(r, c).getColumn() == c &&
 						chromosome.getNode(r, c).getRow() == r);
 			}
@@ -271,7 +273,9 @@ public class ChromosomeTests {
 		assertTrue("Active node missing from list.", chromosome.getActiveNodes().contains(chromosome.getNode(1, 1)));
 		assertTrue("Active node missing from list.", chromosome.getActiveNodes().contains(chromosome.getNode(1, 2)));
 		
-		assertTrue("List has the wrong number of nodes.", chromosome.getActiveNodes().size() == 3);
+		chromosome.printNodes();
+		
+		assertTrue("List has the wrong number of nodes: " + chromosome.getActiveNodes(), chromosome.getActiveNodes().size() == 3);
 	}
 
 	/**
@@ -314,11 +318,11 @@ public class ChromosomeTests {
 	 */
 	private Chromosome createKnownConfiguration() {
 		// with a small topology, build a chromosome of known connections and check outputs
-		resources.set("columns", 3);
-		resources.set("rows", 3);
-		resources.set("inputs", 3);
-		resources.set("outputs", 2);
-		resources.set("levelsBack", 3);
+		resources.setColumns(3);
+		resources.setRows(3);
+		resources.setInputs(3);
+		resources.setOutputs(2);
+		resources.setLevelsBack(3);
 
 		Chromosome c = new Chromosome(resources);
 
@@ -328,7 +332,7 @@ public class ChromosomeTests {
 
 		c.getOutput(0).setConnection(0, c.getNode(0, 0));
 		c.getOutput(1).setConnection(0, c.getNode(1, 2));
-
+		
 		return c;
 	}
 }
diff --git a/src/jcgp/backend/tests/NodeTests.java b/src/jcgp/backend/tests/NodeTests.java
index e8fe02f..0e08d92 100644
--- a/src/jcgp/backend/tests/NodeTests.java
+++ b/src/jcgp/backend/tests/NodeTests.java
@@ -7,7 +7,7 @@ import jcgp.backend.function.IntegerArithmetic;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
 import jcgp.backend.population.Node;
-import jcgp.backend.resources.Resources;
+import jcgp.backend.resources.ModifiableResources;
 
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -32,7 +32,7 @@ public class NodeTests {
 
 	private Node node;
 	private static Chromosome chromosome;
-	private static Resources resources;
+	private static ModifiableResources resources;
 	// these numbers will be used by the node under test
 	private final int arg1 = 2;
 	private final int arg2 = 5;
@@ -40,14 +40,14 @@ public class NodeTests {
 	@BeforeClass
 	public static void setUpBeforeClass() {
 		
-		resources = new Resources();
-
+		resources = new ModifiableResources();
+		resources.setFunctionSet(new IntegerArithmetic());
 		chromosome = new Chromosome(resources);
 	}
 
 	@Before
 	public void setUp() throws Exception {
-		node = new Node(chromosome, 0, 0, resources.getInt("arity"));
+		node = new Node(chromosome, 0, 0, resources.arity());
 		// make node with anonymous addition function and hard-coded value connections
 		node.initialise(new IntegerArithmetic.Addition(),
 				new Connection[]{new Connection() {
@@ -174,7 +174,7 @@ public class NodeTests {
 				return 0;
 			}
 		};
-		node.setConnection(resources.getRandomInt(resources.getInt("arity")), conn2);
+		node.setConnection(resources.getRandomInt(resources.arity()), conn2);
 
 		assertTrue("Connection was not found in node.", node.getConnection(0) == conn2 || node.getConnection(1) == conn2);
 
diff --git a/src/jcgp/backend/tests/OutputTests.java b/src/jcgp/backend/tests/OutputTests.java
index afe44a7..a331f2d 100644
--- a/src/jcgp/backend/tests/OutputTests.java
+++ b/src/jcgp/backend/tests/OutputTests.java
@@ -1,10 +1,11 @@
 package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
+import jcgp.backend.function.IntegerArithmetic;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
 import jcgp.backend.population.Output;
-import jcgp.backend.resources.Resources;
+import jcgp.backend.resources.ModifiableResources;
 
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -26,14 +27,15 @@ public class OutputTests {
 
 	private Output output;
 	private static Chromosome chromosome;
-	private static Resources resources;
+	private static ModifiableResources resources;
 	// these are the test values
 	private final int outputValue = 10;
 	private final int outputIndex = 2;
 
 	@BeforeClass
 	public static void setUpBeforeClass() {
-		resources = new Resources();
+		resources = new ModifiableResources();
+		resources.setFunctionSet(new IntegerArithmetic());
 		chromosome = new Chromosome(resources);
 	}
 
diff --git a/src/jcgp/backend/tests/PopulationTests.java b/src/jcgp/backend/tests/PopulationTests.java
index 31df8b9..fb8ced4 100644
--- a/src/jcgp/backend/tests/PopulationTests.java
+++ b/src/jcgp/backend/tests/PopulationTests.java
@@ -1,9 +1,10 @@
 package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
+import jcgp.backend.function.IntegerArithmetic;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Population;
-import jcgp.backend.resources.Resources;
+import jcgp.backend.resources.ModifiableResources;
 
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -26,30 +27,12 @@ import org.junit.Test;
 public class PopulationTests {
 
 	private Population population;
-	private static Resources resources;
+	private static ModifiableResources resources;
 
 	@BeforeClass
 	public static void setUpBeforeClass() throws Exception {
-		resources = new Resources();
-		
-		
-//		// initialise function set
-//		FunctionSet functionSet = new FunctionSet(new Arithmetic.Addition(), new Arithmetic.Subtraction());
-//
-//		// initialise utilities
-//		Utilities.setResources(new Random(1234), functionSet);
-//
-//		// initialise parameters
-//		Resources.setColumns(20);
-//		Resources.setRows(20);
-//		Resources.setInputs(2);
-//		Resources.setOutputs(4);
-//		Resources.setLevelsBack(1);
-//		Resources.setMutationRate(10);
-//		Resources.setTotalGenerations(100);
-//		Resources.setTotalRuns(5);
-//		Resources.setPopulationSize(1, 4);
-//		Resources.setMaxArity(functionSet.getMaxArity());
+		resources = new ModifiableResources();
+		resources.setFunctionSet(new IntegerArithmetic());
 	}
 
 	@Before
@@ -70,7 +53,7 @@ public class PopulationTests {
 			chromosomes++;
 		}
 
-		assertTrue("Incorrect number of chromosomes generated.", chromosomes == resources.getInt("popSize"));
+		assertTrue("Incorrect number of chromosomes generated.", chromosomes == resources.populationSize());
 	}
 	
 	@Test