1 files changed, 0 insertions, 334 deletions
diff --git a/src/jcgp/tests/ChromosomeTests.java b/src/jcgp/tests/ChromosomeTests.java
deleted file mode 100644
index eb4b5d1..0000000
--- a/src/jcgp/tests/ChromosomeTests.java
+++ /dev/null
@@ -1,334 +0,0 @@
-package jcgp.tests;
-
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import jcgp.JCGP.Resources;
-import jcgp.population.Chromosome;
-import jcgp.population.Connection;
-import jcgp.population.Input;
-import jcgp.population.MutableElement;
-import jcgp.population.Node;
-import jcgp.population.Output;
-
-import org.junit.Before;
-import org.junit.BeforeClass;
-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 random MutableElement.
- *  - It should be able to return a random allowed connection given a column.
- *  - It should be able to return a random connection.
- *  - It should contain a freely modifiable fitness value.
- *  - For truth table evaluations, it should be able to have its inputs set.
- *  - For truth table evaluations, the output should return a value according to the inputs.
- *  - It should feature a copy method, which creates a deep copy of a specified Chromosome object.
- *  - It should be able to return a list of active nodes.
- *  - It should contain a method to evaluate whether a given chromosome is identical
- *    to it.
- *  - Same as above, but only looking at the active portion of a chromosome.
- *  
- *  
- *  WARNING: changing parameters may cause the tests to incorrectly fail!
- * 
- * @author Eduardo Pedroni
- *
- */
-public class ChromosomeTests {
-
-	private Chromosome chromosome;
-	private static Resources resources;
-
-	@BeforeClass
-	public static void setUpBeforeClass() {
-		resources = new Resources();
-	}
-
-	@Before
-	public void setUp() throws Exception {
-		chromosome = new Chromosome(resources);
-	}
-
-	/**
-	 * 
-	 */
-	@Test
-	public void cloneTest() {
-		// create a clone, check to see if it really is a clone
-		Chromosome clone = new Chromosome(chromosome);
-
-		// compare all elements, one by one
-		// check outputs
-		for (int o = 0; o < resources.getInt("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) && 
-					clone.getOutput(o).getSource() != chromosome.getOutput(o).getSource());
-			// check that the connections are equivalent
-			if (clone.getOutput(o).getSource() instanceof Input && chromosome.getOutput(o).getSource() instanceof Input) {
-				assertTrue("Outputs did not connect to equivalent inputs.", 
-						((Input) clone.getOutput(o).getSource()).getIndex() == ((Input) chromosome.getOutput(o).getSource()).getIndex());
-			} else if (clone.getOutput(o).getSource() instanceof Node && chromosome.getOutput(o).getSource() instanceof Node) {
-				assertTrue("Outputs did not connect to equivalent nodes.", 
-						((Node) clone.getOutput(o).getSource()).getRow() == ((Node) chromosome.getOutput(o).getSource()).getRow() && 
-						((Node) clone.getOutput(o).getSource()).getColumn() == ((Node) chromosome.getOutput(o).getSource()).getColumn());
-			} else {
-				fail("Output source types did not match.");
-			}
-		}
-		// check nodes, rows first
-		for (int row = 0; row < resources.getInt("rows"); row++) {
-			for (int column = 0; column < resources.getInt("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
-				assertTrue("Equivalent nodes self-reference differently.", clone.getNode(row, column).getRow() == chromosome.getNode(row, column).getRow() &&
-						clone.getNode(row, column).getColumn() == chromosome.getNode(row, column).getColumn());
-				// check that the two nodes have the same function
-				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++) {
-					// 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));
-
-					// if the connections aren't the same instance, check that their addresses are the same
-					if (clone.getNode(row, column).getConnection(connection) instanceof Input && 
-							chromosome.getNode(row, column).getConnection(connection) instanceof Input) {
-
-						assertTrue("Nodes did not connect to equivalent inputs.", 
-								((Input) clone.getNode(row, column).getConnection(connection)).getIndex() ==
-								((Input) chromosome.getNode(row, column).getConnection(connection)).getIndex());
-
-					} else if (clone.getNode(row, column).getConnection(connection) instanceof Node && 
-							chromosome.getNode(row, column).getConnection(connection) instanceof Node) {
-
-						assertTrue("Nodes did not connect to equivalent nodes.", 
-								((Node) clone.getNode(row, column).getConnection(connection)).getRow() ==
-								((Node) chromosome.getNode(row, column).getConnection(connection)).getRow() &&
-
-								((Node) clone.getNode(row, column).getConnection(connection)).getColumn() ==
-								((Node) chromosome.getNode(row, column).getConnection(connection)).getColumn());
-
-					} else {
-						fail("Connection types did not match.");
-					}
-				}
-			}
-		}
-
-		// check cloning given a known topology
-		chromosome = createKnownConfiguration();
-		clone = new Chromosome(chromosome);
-		
-		Integer[] testInputs = new Integer[] {5, 8, 4};
-		chromosome.setInputs((Object[]) testInputs);
-		clone.setInputs((Object[]) testInputs);
-
-		// check that both chromosomes have the same outputs
-		for (int i = 0; i < resources.getInt("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));
-
-		assertTrue("Mutation affected nodes in both chromosomes.",
-				clone.getOutput(1).calculate() != chromosome.getOutput(1).calculate());
-
-	}
-	/**
-	 * 
-	 */
-	@Test
-	public void fitnessTest() {
-		// set a fitness value, check if returned value is the same
-		chromosome.setFitness(10);
-		assertTrue("Incorrect fitness returned.", chromosome.getFitness() == 10);
-	}
-
-	/**
-	 * 
-	 */
-	@Test
-	public void randomConnectionTest() {
-		// get random connections with column 0, check that they are all inputs
-		for (int i = 0; i < 10000; i++) {
-			boolean connectionReturn = chromosome.getRandomConnection(0) instanceof Input;
-			assertTrue("Connection is not an input.", connectionReturn);
-		}
-
-		// 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;
-		for (int i = 0; i < connectionPicks; i++) {
-			Connection c = chromosome.getRandomConnection(chosenColumn);
-			if (c instanceof Node) {
-				connectionNodes++;
-				if (((Node) c).getColumn() >= chosenColumn) {
-					connectionOutOfRange++;
-				}
-				assertTrue("Connection is not allowed : " + ((Node) c).getColumn(), ((Node) c).getColumn() < chosenColumn && ((Node) c).getColumn() < chosenColumn);
-			} else if (c instanceof Input) {
-				connectionInputs++;
-			} else {
-				fail("Return is neither Node nor Input.");
-
-			}	
-		}
-		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("Node/input ratio: " + (chosenColumn >= resources.getInt("levelsBack") ? resources.getInt("levelsBack") : chosenColumn) * resources.getDouble("rows") / resources.getDouble("inputs") +
-				", picked ratio: " + (double) connectionNodes / (double) connectionInputs);
-
-		System.out.println(connectionOutOfRange + " nodes that disrespected levels back were picked.");
-	}
-	/**
-	 * 
-	 */
-	@Test
-	public void randomMutableTest() {
-		// get mutable elements, check Node to Output ratio
-		int mutablePicks = 100000;
-		int mutableNodes = 0, mutableOutputs = 0;
-		for (int i = 0; i < mutablePicks; i++) {
-			MutableElement m = chromosome.getRandomMutableElement();
-
-			if (m instanceof Node) {
-				mutableNodes++;
-			} else if (m instanceof Output) {
-				mutableOutputs++;
-			} else {
-				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 " +
-				mutableOutputs + " were outputs.");
-		System.out.println("Node/output ratio: " + resources.getDouble("nodes") / resources.getDouble("outputs") +
-				", picked ratio: " + (double) mutableNodes / (double) mutableOutputs + "\n");
-	}
-
-	/**
-	 * 
-	 */
-	@Test
-	public void getOutputsTest() {
-		chromosome = createKnownConfiguration();
-
-		chromosome.setInputs(5, 8, 4);
-
-		// with this configuration, the outputs should be 13 and 25.
-		assertTrue("Incorrect output returned.", (Integer) chromosome.getOutput(0).calculate() == 13);
-		assertTrue("Incorrect output returned.", (Integer) chromosome.getOutput(1).calculate() == 25);
-	}
-
-	/**
-	 * 
-	 */
-	@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++) {
-			testInputs[i] = i * 2 - 3;
-		}
-		chromosome.setInputs((Object[]) testInputs);
-		for (int i = 0; i < resources.getInt("inputs"); i++) {
-			assertTrue("Incorrect input returned.", ((Integer) chromosome.getInput(i).getValue()) == i * 2 - 3);
-		}
-	}
-
-	/**
-	 * 
-	 */
-	@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++) {
-				assertTrue("Incorrect node returned.", chromosome.getNode(r, c).getColumn() == c &&
-						chromosome.getNode(r, c).getRow() == r);
-			}
-		}
-	}
-
-	/**
-	 * 
-	 */
-	@Test
-	public void activeNodeTest() {
-		// active node detection happens recursively, the user only calls a single method
-		// set connections to a known configuration
-		chromosome = createKnownConfiguration();
-		
-		assertTrue("Active node missing from list.", chromosome.getActiveNodes().contains(chromosome.getNode(0, 0)));
-		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);
-	}
-
-	/**
-	 * 
-	 */
-	@Test
-	public void compareActiveTest() {
-		// create a clone of the chromosome, compare active nodes - should return true
-		Chromosome c = new Chromosome(chromosome);
-		assertTrue("Active nodes did not match.", chromosome.compareActiveTo(c));
-		assertTrue("Symmetry not obeyed.", c.compareActiveTo(chromosome));
-
-		// create a new random chromosome, this time they should not match
-		c = new Chromosome(resources);
-		assertTrue("Active nodes did match.", !chromosome.compareActiveTo(c));
-	}
-
-	/**
-	 * 
-	 */
-	@Test
-	public void compareTest() {
-		// create a clone of the chromosome, compare - should return true
-		Chromosome c = new Chromosome(chromosome);
-		assertTrue("Chromosomes did not match.", chromosome.compareTo(c));
-		assertTrue("Symmetry not obeyed.", c.compareTo(chromosome));
-
-		// create a new random chromosome, this time they should not match
-		c = new Chromosome(resources);
-		assertTrue("Chromosomes did match.", !chromosome.compareTo(c));
-	}
-	/**
-	 * Utility for creating a chromosome of known configuration.
-	 * Topology is 3x3, with 3 inputs and 2 outputs.
-	 * Given inputs 5, 8 and 4 outputs should be 13 and 25.
-	 * 
-	 * Active nodes (r, c): [0, 0], [1, 1], [1, 2]
-	 * 
-	 * @return the configured chromosome
-	 */
-	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);
-
-		Chromosome c = new Chromosome(resources);
-
-		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(0, c.getNode(0, 0));
-		c.getOutput(1).setConnection(0, c.getNode(1, 2));
-
-		return c;
-	}
-}