Commented lots of packages.

4 files changed, 19 insertions, 31 deletions

diff --git a/src/jcgp/backend/tests/ChromosomeTests.java b/src/jcgp/backend/tests/ChromosomeTests.java
index 36278ba..bc0c57d 100644
--- a/src/jcgp/backend/tests/ChromosomeTests.java
+++ b/src/jcgp/backend/tests/ChromosomeTests.java
@@ -2,7 +2,7 @@ package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
-import jcgp.backend.function.DoubleArithmetic;
+import jcgp.backend.function.SymbolicRegressionFunctions;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
 import jcgp.backend.population.Input;
@@ -46,7 +46,7 @@ public class ChromosomeTests {
 	@BeforeClass
 	public static void setUpBeforeClass() {
 		resources = new ModifiableResources();
-		resources.setFunctionSet(new DoubleArithmetic());
+		resources.setFunctionSet(new SymbolicRegressionFunctions());
 	}
 
 	@Before
@@ -285,12 +285,12 @@ public class ChromosomeTests {
 	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));
+		assertTrue("Active nodes did not match.", chromosome.compareActiveGenesTo(c));
+		assertTrue("Symmetry not obeyed.", c.compareActiveGenesTo(chromosome));
 
 		// create a new random chromosome, this time they should not match
 		c = new Chromosome(resources);
-		assertTrue("Active nodes did match.", !chromosome.compareActiveTo(c));
+		assertTrue("Active nodes did match.", !chromosome.compareActiveGenesTo(c));
 	}
 
 	/**
@@ -300,12 +300,12 @@ public class ChromosomeTests {
 	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));
+		assertTrue("Chromosomes did not match.", chromosome.compareGenesTo(c));
+		assertTrue("Symmetry not obeyed.", c.compareGenesTo(chromosome));
 
 		// create a new random chromosome, this time they should not match
 		c = new Chromosome(resources);
-		assertTrue("Chromosomes did match.", !chromosome.compareTo(c));
+		assertTrue("Chromosomes did match.", !chromosome.compareGenesTo(c));
 	}
 	/**
 	 * Utility for creating a chromosome of known configuration.
diff --git a/src/jcgp/backend/tests/NodeTests.java b/src/jcgp/backend/tests/NodeTests.java
index 4054661..c63b41e 100644
--- a/src/jcgp/backend/tests/NodeTests.java
+++ b/src/jcgp/backend/tests/NodeTests.java
@@ -2,7 +2,7 @@ package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
 import jcgp.backend.exceptions.InvalidArgumentsException;
-import jcgp.backend.function.DoubleArithmetic;
+import jcgp.backend.function.SymbolicRegressionFunctions;
 import jcgp.backend.function.Function;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
@@ -41,7 +41,7 @@ public class NodeTests {
 	public static void setUpBeforeClass() {
 		
 		resources = new ModifiableResources();
-		resources.setFunctionSet(new DoubleArithmetic());
+		resources.setFunctionSet(new SymbolicRegressionFunctions());
 		chromosome = new Chromosome(resources);
 	}
 
@@ -49,7 +49,7 @@ public class NodeTests {
 	public void setUp() throws Exception {
 		node = new Node(chromosome, 0, 0, resources.arity());
 		// make node with anonymous addition function and hard-coded value connections
-		node.initialise(new DoubleArithmetic.Addition(),
+		node.initialise(new SymbolicRegressionFunctions.Addition(),
 				new Connection[]{new Connection() {
 
 					@Override
@@ -80,7 +80,7 @@ public class NodeTests {
 		Function f = new Function() {
 
 			@Override
-			public Object run(Connection... connections) {
+			public Object run(Object... connections) {
 				// blank
 				return 0;
 			}
@@ -90,12 +90,6 @@ public class NodeTests {
 				// blank
 				return 0;
 			}
-
-			@Override
-			public String getName() {
-				// blank
-				return null;
-			}
 		};
 
 		node.setFunction(f);
@@ -113,7 +107,7 @@ public class NodeTests {
 				((int) node.getValue()) == arg1 + arg2);
 
 		// put in a different function, check the output has changed appropriately
-		node.setFunction(new DoubleArithmetic.Subtraction());
+		node.setFunction(new SymbolicRegressionFunctions.Subtraction());
 
 		assertTrue("Node did not return expected value (difference of arguments).", ((Integer) node.getValue()) == arg1 - arg2);
 
@@ -142,7 +136,7 @@ public class NodeTests {
 		
 		Function function = new Function() {
 			@Override
-			public Object run(Connection... connections)
+			public Object run(Object... connections)
 					throws InvalidArgumentsException {
 				// blank
 				return null;
@@ -152,12 +146,6 @@ public class NodeTests {
 			public int getArity() {
 				return 2;
 			}
-
-			@Override
-			public String getName() {
-				// blank
-				return null;
-			}
 		};
 		
 		node.initialise(function, conn0, conn1);
diff --git a/src/jcgp/backend/tests/OutputTests.java b/src/jcgp/backend/tests/OutputTests.java
index 95b7fc7..8cc10a8 100644
--- a/src/jcgp/backend/tests/OutputTests.java
+++ b/src/jcgp/backend/tests/OutputTests.java
@@ -1,7 +1,7 @@
 package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
-import jcgp.backend.function.DoubleArithmetic;
+import jcgp.backend.function.SymbolicRegressionFunctions;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
 import jcgp.backend.population.Output;
@@ -35,7 +35,7 @@ public class OutputTests {
 	@BeforeClass
 	public static void setUpBeforeClass() {
 		resources = new ModifiableResources();
-		resources.setFunctionSet(new DoubleArithmetic());
+		resources.setFunctionSet(new SymbolicRegressionFunctions());
 		chromosome = new Chromosome(resources);
 	}
 
diff --git a/src/jcgp/backend/tests/PopulationTests.java b/src/jcgp/backend/tests/PopulationTests.java
index fca9c4f..2f36ce1 100644
--- a/src/jcgp/backend/tests/PopulationTests.java
+++ b/src/jcgp/backend/tests/PopulationTests.java
@@ -1,7 +1,7 @@
 package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
-import jcgp.backend.function.DoubleArithmetic;
+import jcgp.backend.function.SymbolicRegressionFunctions;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Population;
 import jcgp.backend.resources.ModifiableResources;
@@ -32,7 +32,7 @@ public class PopulationTests {
 	@BeforeClass
 	public static void setUpBeforeClass() throws Exception {
 		resources = new ModifiableResources();
-		resources.setFunctionSet(new DoubleArithmetic());
+		resources.setFunctionSet(new SymbolicRegressionFunctions());
 	}
 
 	@Before
@@ -64,6 +64,6 @@ public class PopulationTests {
 		// initialise a population with a copy of it
 		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.getChromosome(0).compareTo(oc) && population.getChromosome(0) != oc);
+		assertTrue("Incorrect chromosome in population.", population.getChromosome(0).compareGenesTo(oc) && population.getChromosome(0) != oc);
 	}
 }