1 files changed, 61 insertions, 14 deletions

diff --git a/src/jcgp/backend/parsers/FunctionParser.java b/src/jcgp/backend/parsers/FunctionParser.java
index cc52ce9..806099e 100644
--- a/src/jcgp/backend/parsers/FunctionParser.java
+++ b/src/jcgp/backend/parsers/FunctionParser.java
@@ -6,21 +6,35 @@ import java.io.FileReader;
 import java.util.Scanner;
 
 import jcgp.backend.function.FunctionSet;
-import jcgp.backend.modules.problem.Problem;
-import jcgp.backend.resources.ModifiableResources;
+import jcgp.backend.resources.Resources;
 
 /**
- * Parses the functions from a .par file. 
- * Functions marked with a 1 are enabled, 
- * and those marked with 0 are disabled.
+ * Contains a static method for parsing functions from a
+ * .par file. 
  * 
  * @author Eduardo Pedroni
  *
  */
 public abstract class FunctionParser {
 
-	public static void parseFunctions(File file, Problem problem, ModifiableResources resources) {
-		
+	/**
+	 * Reads the specified file and attempts to enable 
+	 * and disable the functions in the FunctionSet 
+	 * accordingly.
+	 * <br><br>
+	 * Standard CGP .par files do not contain enough information
+	 * to determine if they match the currently selected function set.
+	 * For this reason, the parser assumes the function set is correct
+	 * and treats functions by their index rather than their name. Any
+	 * index outside the bounds of the function set is ignored and a
+	 * warning message is printed once parsing is complete.
+	 * 
+	 * @param file the .par file to parse.
+	 * @param functionSet the function set whose functions should be modified. 
+	 * @param resources used for printing console messages.
+	 */
+	public static void parse(File file, FunctionSet functionSet, Resources resources) {
+		// create file reader and scanner to parse, return if file does not exist
 		FileReader fr;
 		try {
 			fr = new FileReader(file);
@@ -30,23 +44,56 @@ public abstract class FunctionParser {
 		}
 		
 		Scanner in = new Scanner(fr);
-		FunctionSet functionSet = problem.getFunctionSet();
+		boolean excessFunctions = false;
 		resources.println("[Parser] Parsing file: " + file.getAbsolutePath() + "...");
 		
+		/*
+		 * The encoding used in .par files is quite simple, so regex matches are used to extract
+		 * the values.
+		 * 
+		 * A standard .par file contains functions in the following format:
+		 * 
+		 * 0  1      modulus-0
+		 * 0  1      sqrt-1
+		 * 0  1      reciprocal-2
+		 * 
+		 * The first integer signals whether to enable or disable the function. Any non-zero value
+		 * is treated as "enable". The second integer is the function arity. The integer following
+		 * the function name is the function index. 
+		 * 
+		 * The scanner is used to return each line separately. Every line that ends in a number
+		 * is treated as a function line and split into an array, which holds its composing integers.
+		 * This array is then used to enable or disabled the indexed function.
+		 * 
+		 * A flag is raised if the index exceeds the total number of functions, and a warning is
+		 * printed once parsing is complete regarding the index mismatch.
+		 * 
+		 */
 		while (in.hasNextLine()) {
 			String line = in.nextLine();
 			if (line.substring(line.length() - 1).matches("[0-9]")) {
 				String[] splitString = line.split("[^0-9]+");
 				int functionIndex = Integer.parseInt(splitString[splitString.length - 1]);
-				if (Integer.parseInt(splitString[0]) != 0 && !functionSet.isEnabled(functionSet.getFunction(functionIndex))) {
-					functionSet.enableFunction(functionIndex);
-					resources.println("[Parser] Enabled function: " + functionSet.getFunction(functionIndex));
-				} else if (Integer.parseInt(splitString[0]) == 0 && functionSet.isEnabled(functionSet.getFunction(functionIndex))) {
-					functionSet.disableFunction(functionIndex);
-					resources.println("[Parser] Disabled function: " + functionSet.getFunction(functionIndex));
+				
+				if (functionIndex < functionSet.getTotalFunctionCount()) {
+					if (Integer.parseInt(splitString[0]) != 0) {
+						functionSet.enableFunction(functionIndex);
+						resources.println("[Parser] Enabled function: " + functionSet.getFunction(functionIndex));
+					} else if (Integer.parseInt(splitString[0]) == 0) {
+						functionSet.disableFunction(functionIndex);
+						resources.println("[Parser] Disabled function: " + functionSet.getFunction(functionIndex));
+					}
+				} else {
+					excessFunctions = true;
 				}
 			}
 		}
+		
+		// warn the user function index went out of bounds
+		if (excessFunctions) {
+			resources.println("[Parser] Warning: the parameter file contained more functions than the current function set");
+		}
+		
 		in.close();
 		resources.println("[Parser] Finished parsing functions");
 	}