Majorly refactored, node grid is fully implemented. About to attempt active path locking.

4 files changed, 92 insertions, 162 deletions

diff --git a/src/jcgp/tests/ChromosomeTests.java b/src/jcgp/tests/ChromosomeTests.java
index c61785e..6323b88 100644
--- a/src/jcgp/tests/ChromosomeTests.java
+++ b/src/jcgp/tests/ChromosomeTests.java
@@ -1,13 +1,8 @@
 package jcgp.tests;
 
-import static org.junit.Assert.*;
-
-import java.util.Random;
-
-import jcgp.Utilities;
-import jcgp.modules.function.Arithmetic;
-import jcgp.modules.function.FunctionSet;
-import jcgp.parameters.Parameters;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import jcgp.CGP.Resources;
 import jcgp.population.Chromosome;
 import jcgp.population.Connection;
 import jcgp.population.Input;
@@ -45,30 +40,16 @@ import org.junit.Test;
 public class ChromosomeTests {
 
 	private Chromosome chromosome;
+	private static Resources resources;
 
 	@BeforeClass
 	public static void setUpBeforeClass() {
-		// initialise function set
-		FunctionSet functionSet = new FunctionSet(new Arithmetic.Addition(), new Arithmetic.Subtraction());
-
-		// initialise utilities
-		Utilities.setResources(new Random(1234), functionSet);
-
-		// initialise parameters
-		Parameters.setMutationRate(10);
-		Parameters.setTotalGenerations(10);
-		Parameters.setTotalRuns(5);
-		Parameters.setMaxArity(functionSet.getMaxArity());
+		resources = new Resources();
 	}
 
 	@Before
 	public void setUp() throws Exception {
-		Parameters.setColumns(5);
-		Parameters.setRows(2);
-		Parameters.setInputs(2);
-		Parameters.setOutputs(4);
-		Parameters.setLevelsBack(5);
-		chromosome = new Chromosome();
+		chromosome = new Chromosome(resources);
 	}
 
 	/**
@@ -81,7 +62,7 @@ public class ChromosomeTests {
 
 		// compare all elements, one by one
 		// check outputs
-		for (int o = 0; o < Parameters.getOutputs(); o++) {
+		for (int o = 0; o < (int) resources.get("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) && 
@@ -99,8 +80,8 @@ public class ChromosomeTests {
 			}
 		}
 		// check nodes, rows first
-		for (int row = 0; row < Parameters.getRows(); row++) {
-			for (int column = 0; column < Parameters.getColumns(); column++) {
+		for (int row = 0; row < (int) resources.get("rows"); row++) {
+			for (int column = 0; column < (int) resources.get("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
@@ -110,7 +91,7 @@ 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 < Parameters.getMaxArity(); connection++) {
+				for (int connection = 0; connection < (int) resources.get("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));
@@ -149,12 +130,12 @@ public class ChromosomeTests {
 		clone.setInputs((Object[]) testInputs);
 
 		// check that both chromosomes have the same outputs
-		for (int i = 0; i < Parameters.getOutputs(); i++) {
+		for (int i = 0; i < (int) resources.get("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(clone.getInput(2));
+		clone.getOutput(1).setConnection(resources.getRandomInt((int) resources.get("arity")), clone.getInput(2));
 
 		assertTrue("Mutation affected nodes in both chromosomes.",
 				clone.getOutput(1).calculate() != chromosome.getOutput(1).calculate());
@@ -183,7 +164,7 @@ 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 = Parameters.getColumns() - 1;
+		int chosenColumn = (int) resources.get("columns") - 1;
 		for (int i = 0; i < connectionPicks; i++) {
 			Connection c = chromosome.getRandomConnection(chosenColumn);
 			if (c instanceof Node) {
@@ -199,10 +180,10 @@ public class ChromosomeTests {
 
 			}	
 		}
-		System.out.println("Out of " + connectionPicks + " connections picked from " + ((chosenColumn >= Parameters.getLevelsBack()) ? Parameters.getLevelsBack() : chosenColumn) * Parameters.getRows() +
-				" allowed nodes and " + Parameters.getInputs() + " inputs, " + connectionNodes + " were nodes and " + connectionInputs + " were inputs.");
+		System.out.println("Out of " + connectionPicks + " connections picked from " + ((chosenColumn >= (int) resources.get("levelsBack")) ? (int) resources.get("levelsBack") : chosenColumn) * (int) resources.get("rows") +
+				" allowed nodes and " + (int) resources.get("inputs") + " inputs, " + connectionNodes + " were nodes and " + connectionInputs + " were inputs.");
 
-		System.out.println("Node/input ratio: " + ((double) ((chosenColumn >= Parameters.getLevelsBack()) ? Parameters.getLevelsBack() : chosenColumn) * Parameters.getRows()) / (double) Parameters.getInputs() +
+		System.out.println("Node/input ratio: " + ((Integer) (((chosenColumn >= (int) resources.get("levelsBack")) ? (int) resources.get("levelsBack") : chosenColumn) * (Integer) resources.get("rows"))).doubleValue() / ((Integer) resources.get("inputs")).doubleValue() +
 				", picked ratio: " + (double) connectionNodes / (double) connectionInputs);
 
 		System.out.println(connectionOutOfRange + " nodes that disrespected levels back were picked.");
@@ -226,10 +207,10 @@ public class ChromosomeTests {
 				fail("Return is neither Node nor Output.");
 			}
 		}
-		System.out.println("Out of " + mutablePicks + " mutable elements picked from " + Parameters.getNodeCount() +
-				" nodes and " + Parameters.getOutputs() + " outputs, " + mutableNodes + " were nodes and " +
+		System.out.println("Out of " + mutablePicks + " mutable elements picked from " + (int) resources.get("nodes") +
+				" nodes and " + (int) resources.get("outputs") + " outputs, " + mutableNodes + " were nodes and " +
 				mutableOutputs + " were outputs.");
-		System.out.println("Node/output ratio: " + (double) Parameters.getNodeCount() / (double) Parameters.getOutputs() +
+		System.out.println("Node/output ratio: " + ((Integer) resources.get("nodes")).doubleValue() / ((Integer) resources.get("outputs")).doubleValue() +
 				", picked ratio: " + (double) mutableNodes / (double) mutableOutputs + "\n");
 	}
 
@@ -253,12 +234,12 @@ public class ChromosomeTests {
 	@Test
 	public void setInputTest() {
 		// set input values, check that acquired values are correct
-		Integer[] testInputs = new Integer[Parameters.getInputs()];
-		for (int i = 0; i < Parameters.getInputs(); i++) {
+		Integer[] testInputs = new Integer[(int) resources.get("inputs")];
+		for (int i = 0; i < (int) resources.get("inputs"); i++) {
 			testInputs[i] = i * 2 - 3;
 		}
 		chromosome.setInputs((Object[]) testInputs);
-		for (int i = 0; i < Parameters.getInputs(); i++) {
+		for (int i = 0; i < (int) resources.get("inputs"); i++) {
 			assertTrue("Incorrect input returned.", ((Integer) chromosome.getInput(i).getValue()) == i * 2 - 3);
 		}
 	}
@@ -269,8 +250,8 @@ public class ChromosomeTests {
 	@Test
 	public void getNodeTest() {
 		// get all nodes one by one, check that they are all correct
-		for (int r = 0; r < Parameters.getRows(); r++) {
-			for (int c = 0; c < Parameters.getColumns(); c++) {
+		for (int r = 0; r < (int) resources.get("rows"); r++) {
+			for (int c = 0; c < (int) resources.get("columns"); c++) {
 				assertTrue("Incorrect node returned.", chromosome.getNode(r, c).getColumn() == c &&
 						chromosome.getNode(r, c).getRow() == r);
 			}
@@ -304,7 +285,7 @@ public class ChromosomeTests {
 		assertTrue("Symmetry not obeyed.", c.compareActiveTo(chromosome));
 
 		// create a new random chromosome, this time they should not match
-		c = new Chromosome();
+		c = new Chromosome(resources);
 		assertTrue("Active nodes did match.", !chromosome.compareActiveTo(c));
 	}
 
@@ -319,7 +300,7 @@ public class ChromosomeTests {
 		assertTrue("Symmetry not obeyed.", c.compareTo(chromosome));
 
 		// create a new random chromosome, this time they should not match
-		c = new Chromosome();
+		c = new Chromosome(resources);
 		assertTrue("Chromosomes did match.", !chromosome.compareTo(c));
 	}
 	/**
@@ -333,20 +314,20 @@ public class ChromosomeTests {
 	 */
 	private Chromosome createKnownConfiguration() {
 		// with a small topology, build a chromosome of known connections and check outputs
-		Parameters.setColumns(3);
-		Parameters.setRows(3);
-		Parameters.setInputs(3);
-		Parameters.setOutputs(2);
-		Parameters.setLevelsBack(3);
+		resources.set("columns", 3);
+		resources.set("rows", 3);
+		resources.set("inputs", 3);
+		resources.set("outputs", 2);
+		resources.set("levelsBack", 3);
 
-		Chromosome c = new Chromosome();
+		Chromosome c = new Chromosome(resources);
 
-		c.getNode(0, 0).initialise(Utilities.getFunction(0), c.getInput(0), c.getInput(1));
-		c.getNode(1, 1).initialise(Utilities.getFunction(0), c.getNode(0, 0), c.getInput(1));
-		c.getNode(1, 2).initialise(Utilities.getFunction(0), c.getNode(1, 1), c.getInput(2));
+		c.getNode(0, 0).initialise(resources.getFunction(0), c.getInput(0), c.getInput(1));
+		c.getNode(1, 1).initialise(resources.getFunction(0), c.getNode(0, 0), c.getInput(1));
+		c.getNode(1, 2).initialise(resources.getFunction(0), c.getNode(1, 1), c.getInput(2));
 
-		c.getOutput(0).setConnection(c.getNode(0, 0));
-		c.getOutput(1).setConnection(c.getNode(1, 2));
+		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/tests/NodeTests.java b/src/jcgp/tests/NodeTests.java
index 74b8140..330ef7a 100644
--- a/src/jcgp/tests/NodeTests.java
+++ b/src/jcgp/tests/NodeTests.java
@@ -1,13 +1,9 @@
 package jcgp.tests;
 
 import static org.junit.Assert.assertTrue;
-
-import java.util.Random;
-
-import jcgp.Utilities;
-import jcgp.modules.function.Arithmetic;
-import jcgp.modules.function.Function;
-import jcgp.parameters.Parameters;
+import jcgp.CGP.Resources;
+import jcgp.function.Arithmetic;
+import jcgp.function.Function;
 import jcgp.population.Chromosome;
 import jcgp.population.Connection;
 import jcgp.population.Node;
@@ -35,32 +31,22 @@ public class NodeTests {
 
 	private Node node;
 	private static Chromosome chromosome;
+	private static Resources resources;
 	// these numbers will be used by the node under test
 	private final int arg1 = 2;
 	private final int arg2 = 5;
 
 	@BeforeClass
 	public static void setUpBeforeClass() {
-		// initialise utilities
-		Utilities.setResources(new Random(1234), null);
-
-		// initialise parameters
-		Parameters.setColumns(0);
-		Parameters.setRows(0);
-		Parameters.setInputs(0);
-		Parameters.setOutputs(0);
-		Parameters.setLevelsBack(0);
-		Parameters.setMutationRate(10);
-		Parameters.setTotalGenerations(100);
-		Parameters.setTotalRuns(5);
-		Parameters.setMaxArity(2);
-
-		chromosome = new Chromosome();
+		
+		resources = new Resources();
+
+		chromosome = new Chromosome(resources);
 	}
 
 	@Before
 	public void setUp() throws Exception {
-		node = new Node(chromosome, 0, 0);
+		node = new Node(chromosome, 0, 0, (int) resources.get("arity"));
 		// make node with anonymous addition function and hard-coded value connections
 		node.initialise(new Arithmetic.Addition(),
 				new Connection[]{new Connection() {
@@ -117,6 +103,12 @@ public class NodeTests {
 				// blank
 				return 0;
 			}
+
+			@Override
+			public String getName() {
+				// blank
+				return null;
+			}
 		};
 
 		node.setFunction(f);
@@ -194,7 +186,7 @@ public class NodeTests {
 				return null;
 			}
 		};
-		node.setConnection(conn2);
+		node.setConnection(resources.getRandomInt((int) resources.get("arity")), conn2);
 
 		assertTrue("Connection was not found in node.", node.getConnection(0) == conn2 || node.getConnection(1) == conn2);
 
diff --git a/src/jcgp/tests/OutputTests.java b/src/jcgp/tests/OutputTests.java
index b8f7d96..00cfea3 100644
--- a/src/jcgp/tests/OutputTests.java
+++ b/src/jcgp/tests/OutputTests.java
@@ -2,10 +2,7 @@ package jcgp.tests;
 
 import static org.junit.Assert.assertTrue;
 
-import java.util.Random;
-
-import jcgp.Utilities;
-import jcgp.parameters.Parameters;
+import jcgp.CGP.Resources;
 import jcgp.population.Chromosome;
 import jcgp.population.Connection;
 import jcgp.population.Output;
@@ -30,27 +27,15 @@ public class OutputTests {
 
 	private Output output;
 	private static Chromosome chromosome;
+	private static Resources resources;
 	// these are the test values
 	private final int outputValue = 10;
 	private final int outputIndex = 2;
 
 	@BeforeClass
 	public static void setUpBeforeClass() {
-		// initialise utilities
-		Utilities.setResources(new Random(1234), null);
-
-		// initialise parameters
-		Parameters.setColumns(0);
-		Parameters.setRows(0);
-		Parameters.setInputs(0);
-		Parameters.setOutputs(0);
-		Parameters.setLevelsBack(0);
-		Parameters.setMutationRate(10);
-		Parameters.setTotalGenerations(100);
-		Parameters.setTotalRuns(5);
-		Parameters.setMaxArity(2);
-
-		chromosome = new Chromosome();
+		resources = new Resources();
+		chromosome = new Chromosome(resources);
 	}
 
 	@Before
@@ -61,7 +46,7 @@ public class OutputTests {
 	@Test
 	public void evaluationsTest() {
 		// set source connection, check that the appropriate value is returned
-		output.setConnection(new Connection() {
+		output.setConnection(0, new Connection() {
 
 			@Override
 			public Object getValue() {
@@ -96,7 +81,7 @@ public class OutputTests {
 				return null;
 			}
 		};
-		output.setConnection(newConn);
+		output.setConnection(0, newConn);
 
 		assertTrue("Incorrect connection returned.", output.getSource() == newConn);
 	}
diff --git a/src/jcgp/tests/PopulationTests.java b/src/jcgp/tests/PopulationTests.java
index d646b90..474b8d5 100644
--- a/src/jcgp/tests/PopulationTests.java
+++ b/src/jcgp/tests/PopulationTests.java
@@ -1,13 +1,7 @@
 package jcgp.tests;
 
-import static org.junit.Assert.*;
-
-import java.util.Random;
-
-import jcgp.Utilities;
-import jcgp.modules.function.Arithmetic;
-import jcgp.modules.function.FunctionSet;
-import jcgp.parameters.Parameters;
+import static org.junit.Assert.assertTrue;
+import jcgp.CGP.Resources;
 import jcgp.population.Chromosome;
 import jcgp.population.Population;
 
@@ -19,9 +13,7 @@ import org.junit.Test;
  * 
  * Tests which cover the behaviour specified for a population.
  * 
- *  - A population should be able to return parents and offspring separately. 
- *  - It should be possible to iterate through all the chromosomes in a population
- *    with one indexing system - parents then offspring.
+ *  - It should be possible to iterate through all the chromosomes in a population.
  *  - When constructed with no arguments, it should generate populationSize
  *    random chromosomes, distributed according to the EA parameters.
  *  - If one or more chromosomes are passed into the constructor, it should use them
@@ -34,81 +26,61 @@ import org.junit.Test;
 public class PopulationTests {
 
 	private Population population;
+	private static Resources resources;
 
 	@BeforeClass
 	public static void setUpBeforeClass() throws Exception {
-		// initialise function set
-		FunctionSet functionSet = new FunctionSet(new Arithmetic.Addition(), new Arithmetic.Subtraction());
-
-		// initialise utilities
-		Utilities.setResources(new Random(1234), functionSet);
-
-		// initialise parameters
-		Parameters.setColumns(20);
-		Parameters.setRows(20);
-		Parameters.setInputs(2);
-		Parameters.setOutputs(4);
-		Parameters.setLevelsBack(1);
-		Parameters.setMutationRate(10);
-		Parameters.setTotalGenerations(100);
-		Parameters.setTotalRuns(5);
-		Parameters.setPopulationSize(1, 4);
-		Parameters.setMaxArity(functionSet.getMaxArity());
+		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());
 	}
 
 	@Before
 	public void setUp() throws Exception {
-		population = new Population();
+		population = new Population(resources);
 	}
 
 	@Test
 	public void defaultPopulationTest() {
 		// check that the constructor really generates populationSize chromosomes when none is given
-		int offspring = 0, parent = 0;
-		while (true) {
-			try {
-				population.getOffspring(offspring);
-			} catch (IndexOutOfBoundsException e) {
-				break;
-			}
-			offspring++;
-		}
+		int chromosomes = 0;
 		while (true) {
 			try {
-				population.getParent(parent);
+				population.getChromosome(chromosomes);
 			} catch (IndexOutOfBoundsException e) {
 				break;
 			}
-			parent++;
+			chromosomes++;
 		}
-		assertTrue("Incorrect number of chromosomes generated.", offspring + parent == Parameters.getPopulationSize());
-	}
-	
-	@Test
-	public void offspringParentTest() {
-		// the first parent should not be the same as the first offspring
-		assertTrue("Same chromosome returned as parent and offspring", population.getOffspring(0) != population.getParent(0));
+
+		assertTrue("Incorrect number of chromosomes generated.", chromosomes == (int) resources.get("popSize"));
 	}
 	
 	@Test
-	public void singleIndexTest() {
-		// assuming 1+4
-		// the first chromosome should be the first (and only) parent
-		assertTrue("Incorrect chromosome returned.", population.getChromosome(0) == population.getParent(0));
-		// the next 4 chromosomes should be the offspring, in order
-		for (int i = 0; i < Parameters.getOffspringCount(); i++) {
-			assertTrue("Incorrect chromosome returned.", population.getChromosome(i + 1) == population.getOffspring(i));
-		}
-	}
-
-	@Test
 	public void preinitialisedChromosomeTest() {
 		// the original chromosome that will be cloned
-		Chromosome oc = new Chromosome();
+		Chromosome oc = new Chromosome(resources);
 
 		// initialise a population with a copy of it
-		population = new Population(oc);
+		population = new Population(oc, resources);
 		// check that the first parent chromosome is identical to, but not the same instance as, the one given
-		assertTrue("Incorrect chromosome in population.", population.getParent(0).compareTo(oc) && population.getParent(0) != oc);
+		assertTrue("Incorrect chromosome in population.", population.getChromosome(0).compareTo(oc) && population.getChromosome(0) != oc);
 	}
 }