4 files changed, 278 insertions, 0 deletions
diff --git a/src/jcgp/backend/parser/ChromosomeParser.java b/src/jcgp/backend/parser/ChromosomeParser.java
new file mode 100644
index 0000000..74f638c
--- /dev/null
+++ b/src/jcgp/backend/parser/ChromosomeParser.java
@@ -0,0 +1,131 @@
+package jcgp.backend.parser;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.util.Scanner;
+
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Connection;
+import jcgp.backend.population.Node;
+import jcgp.backend.resources.Resources;
+
+/**
+ * This class includes a method for parsing .chr files and another
+ * for writing .chr files from given chromosomes.
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
+public class ChromosomeParser {
+
+	/**
+	 * Use this method to parse .chr files into a given chromosome.
+	 * <br><br>
+	 * This is not fully defensive as it doesn't check for number of inputs, 
+	 * doesn't compare rows and columns individually and doesn't account for levels back. It
+	 * is not viable to implement these defensive measures with the chromosome format used 
+	 * by CGP.
+	 * 
+	 * @param file the .chr file to parse from
+	 * @param chromosome the chromosome to configure
+	 * @param resources the experiment resources
+	 */
+	public static void parse(File file, Chromosome chromosome, Resources resources) {
+		/* 
+		 * Count the nodes to make sure the size of the .chr file matches the experiment parameters.
+		 * 
+		 * We do this by using the scanner to get the node and output portions of the file as they
+		 * are separated by 3 tab characters. Every number is replaced by a single known character, 
+		 * and the length of the string with the new characters is compared with that of a string
+		 * where the new known character has been removed, yielding the total number of values.
+		 * 
+		 */
+		FileReader fr;
+		try {
+			fr = new FileReader(file);
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+			return;
+		}
+		Scanner in = new Scanner(fr);
+		in.useDelimiter("\\t\\t\\t");
+		String geneString = in.next().replaceAll("[0-9]+", "g");
+		String outString = in.next().replaceAll("[0-9]+", "o");
+		int geneCount = geneString.length() - geneString.replace("g", "").length();
+		int outCount = outString.length() - outString.replace("o", "").length();
+		in.close();
+		
+		
+		// if the acquired values match the current parameters, apply them to the chromosome
+		if ((geneCount == resources.nodes() * (resources.arity() + 1))
+				&& outCount == resources.outputs()) {
+			// prepare a new scanner
+			try {
+				fr = new FileReader(file);
+			} catch (FileNotFoundException e) {
+				e.printStackTrace();
+				return;
+			}
+			in = new Scanner(fr);
+			
+			int gene;
+			Connection newConnection;
+			Node changingNode;
+			// for all nodes, columns first
+			for (int c = 0; c < resources.columns(); c ++) {
+				for (int r = 0; r < resources.rows(); r ++) {
+					// store the changing node
+					changingNode = chromosome.getNode(r, c);
+
+					// for every connection
+					for (int i = 0; i < resources.arity(); i ++) {
+						// get connection number from the .chr file
+						gene = in.nextInt();
+						if (gene < resources.inputs()) {
+							// connection was an input
+							newConnection = chromosome.getInput(gene);
+						} else {
+							// connection was another node, calculate which from its number
+							newConnection = chromosome.getNode((gene - resources.inputs()) % resources.rows(), 
+									(gene - resources.inputs()) / resources.rows());
+						}
+						changingNode.setConnection(i, newConnection);
+					}
+
+					// set the function, straight indexing should work - this is not entirely
+					// safe, but it is not viable to check for functionset compatibility
+					changingNode.setFunction(resources.getFunction(in.nextInt()));
+				}
+			}
+
+			// outputs
+			for (int o = 0; o < resources.outputs(); o ++) {
+				gene = in.nextInt();
+				if (gene < resources.inputs()) {
+					// connection was an input
+					newConnection = chromosome.getInput(gene);
+				} else {
+					// connection was another node, calculate which from its number
+					newConnection = chromosome.getNode((gene - resources.inputs()) % resources.rows(), 
+							(gene - resources.inputs()) / resources.rows());
+				}
+				chromosome.getOutput(o).setConnection(0, newConnection);
+			}
+			in.close();
+		}
+	}
+	
+	/**
+	 * Writes a chromosome into the specified .chr file.
+	 * 
+	 * 
+	 * 
+	 * @param file
+	 * @param chromosome
+	 */
+	public static void save(File file, Chromosome chromosome) {
+		
+	}
+	
+}
diff --git a/src/jcgp/backend/parser/FunctionParser.java b/src/jcgp/backend/parser/FunctionParser.java
new file mode 100644
index 0000000..64a095c
--- /dev/null
+++ b/src/jcgp/backend/parser/FunctionParser.java
@@ -0,0 +1,58 @@
+package jcgp.backend.parser;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.util.Scanner;
+
+import jcgp.backend.function.FunctionSet;
+import jcgp.backend.modules.problem.Problem;
+
+public class FunctionParser {
+
+private FunctionSet functionSet;
+	
+	private FunctionParser(Problem problem) {
+		this.functionSet = problem.getFunctionSet();
+	}
+
+	public static void parseFunctions(File file, Problem problem) {
+		FunctionParser pp = new FunctionParser(problem);
+		
+		FileReader fr;
+		try {
+			fr = new FileReader(file);
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+			return;
+		}
+		
+		Scanner in = new Scanner(fr);
+		
+		while (in.hasNextLine()) {
+			String line = in.nextLine();
+			if (line.substring(line.length() - 1).matches("[0-9]")) {
+				pp.parseAndSet(line.split("[^0-9]+"));
+			}
+		}
+		
+		in.close();
+	}
+	
+	private void parseAndSet(String[] splitString) {
+//		System.out.println("new line");
+//		for (int i= 0; i < splitString.length; i++) {
+//			System.out.println(i + ": " + splitString[i]);
+//		}
+		int functionIndex = Integer.parseInt(splitString[splitString.length - 1]);
+		System.out.println("index: " + functionIndex);
+		if (Integer.parseInt(splitString[0]) != 0) {
+			System.out.println("enabling: " + functionSet.getFunction(functionIndex).getName());
+			functionSet.enableFunction(functionIndex);
+		} else {
+			System.out.println("disabling: " + functionSet.getFunction(functionIndex).getName());
+			functionSet.disableFunction(functionIndex);
+		}
+		
+	}	
+}
diff --git a/src/jcgp/backend/parser/ParameterParser.java b/src/jcgp/backend/parser/ParameterParser.java
new file mode 100644
index 0000000..473b632
--- /dev/null
+++ b/src/jcgp/backend/parser/ParameterParser.java
@@ -0,0 +1,76 @@
+package jcgp.backend.parser;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.util.Scanner;
+import jcgp.backend.resources.ModifiableResources;
+
+public class ParameterParser {
+	
+	private ModifiableResources resources;
+	
+	private ParameterParser(ModifiableResources resources) {
+		this.resources = resources;
+	}
+
+	public static void parseParameters(File file, ModifiableResources resources) {
+		ParameterParser pp = new ParameterParser(resources);
+		
+		FileReader fr;
+		try {
+			fr = new FileReader(file);
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+			return;
+		}
+		
+		Scanner in = new Scanner(fr);
+		
+		while (in.hasNextLine()) {
+			pp.parseAndSet(in.nextLine().split("( |\t)+"));
+		}
+		
+		in.close();
+	}
+	
+	private void parseAndSet(String[] splitString) {
+		switch (splitString[1]) {
+		
+		case "population_size":
+			resources.setPopulationSize(Integer.parseInt(splitString[0]));
+			break;
+			
+		case "num_generations":
+			resources.setGenerations(Integer.parseInt(splitString[0]));
+			break;
+			
+		case "num_runs_total":
+			resources.setRuns(Integer.parseInt(splitString[0]));
+			break;
+			
+		case "num_rows":
+			resources.setRows(Integer.parseInt(splitString[0]));
+			break;
+			
+		case "num_cols":
+			resources.setColumns(Integer.parseInt(splitString[0]));
+			break;
+
+		case "levels_back":
+			resources.setLevelsBack(Integer.parseInt(splitString[0]));
+			break;
+		
+		case "report_interval":
+			resources.setReportInterval(Integer.parseInt(splitString[0]));
+			break;
+		
+		case "global_seed":
+			resources.setSeed(Integer.parseInt(splitString[0]));
+			break;
+
+		default:
+			break;
+		}
+	}
+}
diff --git a/src/jcgp/backend/parser/TestCaseParser.java b/src/jcgp/backend/parser/TestCaseParser.java
new file mode 100644
index 0000000..c997177
--- /dev/null
+++ b/src/jcgp/backend/parser/TestCaseParser.java
@@ -0,0 +1,13 @@
+package jcgp.backend.parser;
+
+import java.io.File;
+
+import jcgp.backend.modules.problem.TestCaseProblem;
+
+public class TestCaseParser {
+
+	public static void parse(File file, TestCaseProblem<?> problem) {
+		
+	}
+
+}