Added methods in Chromosome to compare active and all nodes. Associated tests also written.

3 files changed, 81 insertions, 71 deletions

diff --git a/src/jcgp/tests/ChromosomeTests.java b/src/jcgp/tests/ChromosomeTests.java
index ff1de18..d2407a6 100644
--- a/src/jcgp/tests/ChromosomeTests.java
+++ b/src/jcgp/tests/ChromosomeTests.java
@@ -36,6 +36,9 @@ import org.junit.Test;
  *  - It should feature a clone constructor, 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.
  *  
  *  TODO: bashing (strange value ranges, etc)
  *  
@@ -82,29 +85,21 @@ public class ChromosomeTests {
 		// create a clone, check to see if it really is a clone
 		Chromosome clone = new Chromosome(chromosome);
 
-		// set input values
-		testInputs = new int[Parameters.getInputs()];
-		for (int i = 0; i < Parameters.getInputs(); i++) {
-			testInputs[i] = i * 2 - 3;
-		}
-		chromosome.setInputs(testInputs);
-		clone.setInputs(testInputs);
-
 		// compare all elements, one by one
 		// check outputs
 		for (int o = 0; o < Parameters.getOutputs(); o++) {
 			// check that no cross-references exist between chromosomes
-			assertTrue("Cloned chromosome contained a reference to a member of the original chromosome.",
-					c.getOutput(o) != oc.getOutput(o) && 
-					c.getOutput(o).getSource() != oc.getOutput(o).getSource());
+			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 (c.getOutput(o).getSource() instanceof Input && oc.getOutput(o).getSource() instanceof Input) {
+			if (clone.getOutput(o).getSource() instanceof Input && chromosome.getOutput(o).getSource() instanceof Input) {
 				assertTrue("Outputs did not connect to equivalent inputs.", 
-						((Input) c.getOutput(o).getSource()).getIndex() == ((Input) oc.getOutput(o).getSource()).getIndex());
-			} else if (c.getOutput(o).getSource() instanceof Node && oc.getOutput(o).getSource() instanceof Node) {
+						((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) c.getOutput(o).getSource()).getRow() == ((Node) oc.getOutput(o).getSource()).getRow() && 
-						((Node) c.getOutput(o).getSource()).getColumn() == ((Node) oc.getOutput(o).getSource()).getColumn());
+						((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.");
 			}
@@ -112,24 +107,37 @@ public class ChromosomeTests {
 		// check nodes, rows first
 		for (int row = 0; row < Parameters.getRows(); row++) {
 			for (int column = 0; column < Parameters.getColumns(); column++) {
-				// look at each connection
+				// 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 < Parameters.getMaxArity(); connection++) {
-					if (c.getNode(row, column).getConnection(connection) instanceof Input && 
-							oc.getNode(row, column).getConnection(connection) instanceof Input) {
+					// 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) c.getNode(row, column).getConnection(connection)).getIndex() ==
-								((Input) oc.getNode(row, column).getConnection(connection)).getIndex());
+								((Input) clone.getNode(row, column).getConnection(connection)).getIndex() ==
+								((Input) chromosome.getNode(row, column).getConnection(connection)).getIndex());
 
-					} else if (c.getNode(row, column).getConnection(connection) instanceof Node && 
-							oc.getNode(row, column).getConnection(connection) instanceof Node) {
+					} 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) c.getNode(row, column).getConnection(connection)).getRow() ==
-								((Node) oc.getNode(row, column).getConnection(connection)).getRow() &&
+								((Node) clone.getNode(row, column).getConnection(connection)).getRow() ==
+								((Node) chromosome.getNode(row, column).getConnection(connection)).getRow() &&
 
-								((Node) c.getNode(row, column).getConnection(connection)).getColumn() ==
-								((Node) oc.getNode(row, column).getConnection(connection)).getColumn());
+								((Node) clone.getNode(row, column).getConnection(connection)).getColumn() ==
+								((Node) chromosome.getNode(row, column).getConnection(connection)).getColumn());
 
 					} else {
 						fail("Connection types did not match.");
@@ -138,17 +146,27 @@ public class ChromosomeTests {
 			}
 		}
 
-
-		// change clone inputs, outputs should no longer match
+		// set input values
 		testInputs = new int[Parameters.getInputs()];
 		for (int i = 0; i < Parameters.getInputs(); i++) {
-			testInputs[i] = i * 2;
+			testInputs[i] = (i + 1) * 2 - 3;
 		}
+		chromosome.setInputs(testInputs);
 		clone.setInputs(testInputs);
+
+		// check that both chromosomes have the same outputs
 		for (int i = 0; i < Parameters.getOutputs(); i++) {
-			assertTrue("Incorrect output returned.", chromosome.getOutput(i).calculate() != 
+			assertTrue("Incorrect output returned.", chromosome.getOutput(i).calculate() == 
 					clone.getOutput(i).calculate());
 		}
+
+		// mutate an active node in clone, check that the same node in chromosome produces a different output
+		// NOTE: given a small grid this mutation may actually pick the same connection (causing no effective change) and therefore the test would fail.
+		Node node = clone.getActiveNodes().get(Utilities.getRandomInt(clone.getActiveNodes().size()));
+		node.setConnection(clone.getRandomConnection(node.getColumn()));
+
+		assertTrue("Mutation affected both nodes in both chromosomes.", node.getValue() != chromosome.getNode(node.getRow(), node.getColumn()).getValue());
+
 	}
 
 	/**
@@ -282,12 +300,41 @@ public class ChromosomeTests {
 
 		chromosome.getNode(0, 0).setConnection(chromosome.getInput(0));
 
-		assertTrue("Active connection not in list.", chromosome.getActiveNodes().contains(chromosome.getInput(0)));
-		assertTrue("Active connection not in list.", chromosome.getActiveNodes().contains(chromosome.getNode(0, 0)));
+		assertTrue("Active node not in list.", chromosome.getActiveNodes().contains(chromosome.getNode(0, 0)));
 
 		// change outputs, print list
 		chromosome.getOutput(0).setConnection(chromosome.getNode(0, Parameters.getColumns() - 1));
 
 		System.out.println("Active connections: " + chromosome.getActiveNodes().toString() + "\n");
 	}
+	
+	/**
+	 * 
+	 */
+	@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();
+		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();
+		assertTrue("Chromosomes did match.", !chromosome.compareTo(c));
+	}
 }
diff --git a/src/jcgp/tests/NodeTests.java b/src/jcgp/tests/NodeTests.java
index ecc87ff..5b378d2 100644
--- a/src/jcgp/tests/NodeTests.java
+++ b/src/jcgp/tests/NodeTests.java
@@ -2,7 +2,6 @@ package jcgp.tests;
 
 import static org.junit.Assert.assertTrue;
 
-import java.util.ArrayList;
 import java.util.Random;
 
 import jcgp.Parameters;
@@ -92,11 +91,6 @@ public class NodeTests {
 				return arg1;
 			}
 
-			@Override
-			public void getActive(ArrayList<Connection> activeNodes) {
-				// irrelevant for this test
-			}
-
 		},
 		new Connection() {
 
@@ -106,11 +100,6 @@ public class NodeTests {
 				return arg2;
 			}
 
-			@Override
-			public void getActive(ArrayList<Connection> activeNodes) {
-				// irrelevant for this test
-			}
-
 		}});
 	}
 
@@ -189,11 +178,6 @@ public class NodeTests {
 				return 0;
 			}
 
-			@Override
-			public void getActive(ArrayList<Connection> activeNodes) {
-				// blank
-
-			}
 		};
 		conn1 = new Connection() {
 
@@ -203,11 +187,6 @@ public class NodeTests {
 				return 0;
 			}
 
-			@Override
-			public void getActive(ArrayList<Connection> activeNodes) {
-				// blank
-
-			}
 		};
 		node.initialise(null, conn0, conn1);
 		
@@ -222,17 +201,12 @@ public class NodeTests {
 				// blank
 				return 0;
 			}
-
-			@Override
-			public void getActive(ArrayList<Connection> activeNodes) {
-				// blank
-
-			}
 		};
 		node.setConnection(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 06295ae..04eac7f 100644
--- a/src/jcgp/tests/OutputTests.java
+++ b/src/jcgp/tests/OutputTests.java
@@ -2,7 +2,6 @@ package jcgp.tests;
 
 import static org.junit.Assert.assertTrue;
 
-import java.util.ArrayList;
 import java.util.Random;
 
 import jcgp.Parameters;
@@ -69,11 +68,6 @@ public class OutputTests {
 				// test value
 				return outputValue;
 			}
-
-			@Override
-			public void getActive(ArrayList<Connection> activeNodes) {
-				// blank				
-			}
 		});
 
 		assertTrue("Incorrect evaluation.", output.calculate() == outputValue);
@@ -89,11 +83,6 @@ public class OutputTests {
 				// blank
 				return 0;
 			}
-
-			@Override
-			public void getActive(ArrayList<Connection> activeNodes) {
-				// blank				
-			}
 		};
 		output.setConnection(newConn);