Minor refactorings

11 files changed, 42 insertions, 73 deletions

diff --git a/src/jcgp/JCGP.java b/src/jcgp/JCGP.java
index 5a86303..99ed556 100644
--- a/src/jcgp/JCGP.java
+++ b/src/jcgp/JCGP.java
@@ -20,7 +20,6 @@ import jcgp.backend.parsers.TestCaseParser;
 import jcgp.backend.population.Population;
 import jcgp.backend.resources.Console;
 import jcgp.backend.resources.ModifiableResources;
-import jcgp.backend.resources.Resources;
 import jcgp.backend.statistics.StatisticsLogger;
 
 /**
@@ -234,7 +233,7 @@ public class JCGP {
 	 */
 	public void nextGeneration() {
 		if (!finished) {
-			problem.evaluate(population, (Resources) resources);
+			problem.evaluate(population);
 
 			if (resources.currentGeneration() < resources.generations()) {
 				
diff --git a/src/jcgp/backend/function/Function.java b/src/jcgp/backend/function/Function.java
index 2e1f3c6..f277228 100644
--- a/src/jcgp/backend/function/Function.java
+++ b/src/jcgp/backend/function/Function.java
@@ -17,7 +17,7 @@ public abstract class Function {
 	 * @param args the function arguments.
 	 * @return the function result.
 	 */
-	public abstract Object run(Object... args);
+	public abstract Object run(Object... arguments);
 	
 	/**
 	 * @return the arity of the function.
diff --git a/src/jcgp/backend/function/UnsignedInteger.java b/src/jcgp/backend/function/UnsignedInteger.java
index d23862c..553f934 100644
--- a/src/jcgp/backend/function/UnsignedInteger.java
+++ b/src/jcgp/backend/function/UnsignedInteger.java
@@ -39,15 +39,6 @@ public class UnsignedInteger {
 	}
 	
 	/**
-	 * Makes a new instance of UnsignedInteger with a specified value.
-	 * 
-	 * @param i the value with which to initialise.
-	 */
-	public UnsignedInteger(Integer i) {
-		value = i;
-	}
-	
-	/**
 	 * Makes a new instance of UnsignedInteger from the string representation
 	 * of an unsigned integer.
 	 * 
diff --git a/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java b/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java
index e2f17c3..ff77a0d 100644
--- a/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java
+++ b/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java
@@ -31,9 +31,9 @@ public class DigitalCircuitProblem extends TestCaseProblem<UnsignedInteger> {
 	}
 
 	@Override
-	public void evaluate(Population population, Resources resources) {
+	public void evaluate(Population population) {
 		// for every chromosome in the population
-		for (int i = 0; i < resources.populationSize(); i++) {
+		for (int i = 0; i < getResources().populationSize(); i++) {
 			// assume an initial fitness of 0
 			int fitness = 0;
 
@@ -41,13 +41,13 @@ public class DigitalCircuitProblem extends TestCaseProblem<UnsignedInteger> {
 			for (int t = 0; t < testCases.size(); t++) {
 				population.get(i).setInputs((Object[]) testCases.get(t).getInputs());
 				// check each output
-				for (int o = 0; o < resources.outputs(); o++) {
+				for (int o = 0; o < getResources().outputs(); o++) {
 					Integer output = ((UnsignedInteger) population.get(i).getOutput(o).calculate()).get();
-					Integer matches = ~(output ^ testCases.get(t).getOutput(o).get());
+					Integer matches = ~(output ^ testCases.get(t).getOutputs()[o].get());
 					// check only the relevant bits
 					int bits;
-					if (resources.inputs() < 5) {
-						bits = (int) Math.pow(2.0, (double) resources.inputs());
+					if (getResources().inputs() < 5) {
+						bits = (int) Math.pow(2.0, (double) getResources().inputs());
 					} else {
 						bits = 32;
 					}
diff --git a/src/jcgp/backend/modules/problem/Problem.java b/src/jcgp/backend/modules/problem/Problem.java
index 2af2373..6785733 100644
--- a/src/jcgp/backend/modules/problem/Problem.java
+++ b/src/jcgp/backend/modules/problem/Problem.java
@@ -74,7 +74,7 @@ public abstract class Problem extends Module {
 	 * @param population the population to be evaluated.
 	 * @param resources parameters and utilities for optional reference.
 	 */
-	public abstract void evaluate(Population population, Resources resources);
+	public abstract void evaluate(Population population);
 	
 	/**
 	 * Used to assert whether a given population contains a perfect solution
diff --git a/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java b/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java
index 3b5f539..6bc4790 100644
--- a/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java
+++ b/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java
@@ -84,7 +84,7 @@ public class SymbolicRegressionProblem extends TestCaseProblem<Double> {
 	}
 	
 	@Override
-	public void evaluate(Population population, Resources resources) {
+	public void evaluate(Population population) {
 		// for every chromosome in the population
 		for (int i = 0; i < getResources().populationSize(); i++) {
 			// assume an initial fitness of 0
@@ -95,7 +95,7 @@ public class SymbolicRegressionProblem extends TestCaseProblem<Double> {
 				// check each output
 				for (int o = 0; o < getResources().outputs(); o++) {
 					Double cgpValue = (Double) population.get(i).getOutput(o).calculate();
-					Double dataValue = testCases.get(t).getOutput(o);
+					Double dataValue = testCases.get(t).getOutputs()[o];
 					if (hitsBasedFitness.get()) {
 						if (Math.abs(cgpValue - dataValue) <= errorThreshold.get()) {
 							fitness++;
diff --git a/src/jcgp/backend/modules/problem/TestCaseProblem.java b/src/jcgp/backend/modules/problem/TestCaseProblem.java
index 188e236..964860c 100644
--- a/src/jcgp/backend/modules/problem/TestCaseProblem.java
+++ b/src/jcgp/backend/modules/problem/TestCaseProblem.java
@@ -50,22 +50,6 @@ public abstract class TestCaseProblem<T> extends Problem {
 		}
 		
 		/**
-		 * @param index the index to return.
-		 * @return the indexed input.
-		 */
-		public U getInput(int index) {
-			return inputs[index];
-		}
-		
-		/**
-		 * @param index the index to return.
-		 * @return the indexed output.
-		 */
-		public U getOutput(int index) {
-			return outputs[index];
-		}
-		
-		/**
 		 * @return the complete array of inputs.
 		 */
 		public U[] getInputs() {
diff --git a/src/jcgp/backend/population/Chromosome.java b/src/jcgp/backend/population/Chromosome.java
index e28032c..d84c5f0 100644
--- a/src/jcgp/backend/population/Chromosome.java
+++ b/src/jcgp/backend/population/Chromosome.java
@@ -112,13 +112,11 @@ public class Chromosome implements Comparable<Chromosome> {
 			inputs[i] = new Input(i);
 		}
 
-		int arity = resources.arity();
-		
 		// rows first
 		nodes = new Node[(resources.rows())][(resources.columns())];
 		for (int r = 0; r < nodes.length; r++) {
 			for (int c = 0; c < nodes[r].length; c++) {
-				nodes[r][c] = new Node(this, r, c, arity);
+				nodes[r][c] = new Node(this, r, c);
 			}
 		}
 		outputs = new Output[resources.outputs()];
diff --git a/src/jcgp/backend/population/Node.java b/src/jcgp/backend/population/Node.java
index 7712c50..6696694 100644
--- a/src/jcgp/backend/population/Node.java
+++ b/src/jcgp/backend/population/Node.java
@@ -40,24 +40,14 @@ public class Node implements Mutable, Connection {
 	 * @param chromosome the chromosome this node belongs to.
 	 * @param row the node's row.
 	 * @param column the node's column.
-	 * @param arity the maximum arity of the experiment.
 	 */
-	public Node(Chromosome chromosome, int row, int column, int arity) {
+	public Node(Chromosome chromosome, int row, int column) {
 		this.chromosome = chromosome;
 		this.column = column;
 		this.row = row;
 	}
 	
 	/**
-	 * Sets the node function.
-	 * 
-	 * @param newFunction the new function to set.
-	 */
-	public void setFunction(Function newFunction) {
-		function = newFunction;
-	}
-
-	/**
 	 * Initialises the node with the specified values.
 	 * The number of connections passed as argument must
 	 * be exactly the same as the experiment arity, or 
@@ -66,7 +56,7 @@ public class Node implements Mutable, Connection {
 	 * @param newFunction the node function to set.
 	 * @param newConnections the node connections to set.
 	 */
-	public void initialise(Function newFunction, Connection ... newConnections) {
+	public void initialise(Function newFunction, Connection... newConnections) {
 		function = newFunction;
 		if (newConnections.length == chromosome.getResources().arity()) {
 			connections = newConnections;
@@ -97,12 +87,37 @@ public class Node implements Mutable, Connection {
 	}
 	
 	/**
+	 * Sets the node function.
+	 * 
+	 * @param newFunction the new function to set.
+	 */
+	public void setFunction(Function newFunction) {
+		function = newFunction;
+	}
+	
+	/**
 	 * @param index the connection to return.
 	 * @return the indexed connection.
 	 */
 	public Connection getConnection(int index) {
 		return connections[index];
 	}
+	
+	/**
+	 * This method sets the indexed connection to the specified new connection.
+	 * If the given connection is null or disrespects levels back, it is discarded
+	 * and no connections are changed.
+	 * 
+	 * @param index the connection index to set.
+	 * @param newConnection the {@code Connection} to connect to.
+	 */
+	public void setConnection(int index, Connection newConnection) {
+		// connection must not be null
+		if (newConnection != null) {
+			connections[index] = newConnection;
+			chromosome.recomputeActiveNodes();
+		}
+	}
 
 	/**
 	 * For package use, this is a recursive method
@@ -127,24 +142,6 @@ public class Node implements Mutable, Connection {
 			}
 		}
 	}
-	
-	/**
-	 * This method sets the indexed connection to the specified new connection.
-	 * If the given connection is null or disrespects levels back, it is discarded
-	 * and no connections are changed.
-	 * 
-	 * @param index the connection index to set.
-	 * @param newConnection the {@code Connection} to connect to.
-	 */
-	public void setConnection(int index, Connection newConnection) {
-		// connection must not be null
-		if (newConnection != null) {
-			//if () {
-				connections[index] = newConnection;
-			chromosome.recomputeActiveNodes();
-			//}
-		}
-	}
 
 	@Override
 	public boolean copyOf(Mutable element) {
diff --git a/src/jcgp/backend/tests/NodeTests.java b/src/jcgp/backend/tests/NodeTests.java
index ee940a0..4daa6d3 100644
--- a/src/jcgp/backend/tests/NodeTests.java
+++ b/src/jcgp/backend/tests/NodeTests.java
@@ -45,7 +45,7 @@ public class NodeTests {
 
 	@Before
 	public void setUp() throws Exception {
-		node = new Node(chromosome, 0, 0, resources.arity());
+		node = new Node(chromosome, 0, 0);
 		// make node with addition function and hard-coded value connections
 		node.initialise(resources.getFunction(0),
 				new Connection[]{new Connection() {
diff --git a/src/jcgp/gui/settings/testcase/TestCaseTable.java b/src/jcgp/gui/settings/testcase/TestCaseTable.java
index d4f789c..605b75e 100644
--- a/src/jcgp/gui/settings/testcase/TestCaseTable.java
+++ b/src/jcgp/gui/settings/testcase/TestCaseTable.java
@@ -62,7 +62,7 @@ public class TestCaseTable extends Stage {
 				@Override
 				public ObservableValue<String> call(CellDataFeatures<TestCase<Object>, String> param) {
 					// create a new string property and give it the test case value, no need for dynamic binding - this wont change often
-					return new SimpleStringProperty(param.getValue().getInput(index).toString());
+					return new SimpleStringProperty(param.getValue().getInputs()[index].toString());
 				}
 			});
 			tc.setSortable(false);
@@ -79,7 +79,7 @@ public class TestCaseTable extends Stage {
 				@Override
 				public ObservableValue<String> call(CellDataFeatures<TestCase<Object>, String> param) {
 					// create a new string property and give it the test case value, no need for dynamic binding - this wont change often
-					return new SimpleStringProperty(param.getValue().getOutput(index).toString());
+					return new SimpleStringProperty(param.getValue().getOutputs()[index].toString());
 				}
 			});
 			tc.setSortable(false);