Commented lots of packages.

4 files changed, 0 insertions, 395 deletions

diff --git a/src/jcgp/backend/parser/ChromosomeParser.java b/src/jcgp/backend/parser/ChromosomeParser.java
deleted file mode 100644
index fd03b7d..0000000
--- a/src/jcgp/backend/parser/ChromosomeParser.java
+++ /dev/null
@@ -1,177 +0,0 @@
-package jcgp.backend.parser;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.PrintWriter;
-import java.util.Scanner;
-
-import jcgp.backend.population.Chromosome;
-import jcgp.backend.population.Connection;
-import jcgp.backend.population.Input;
-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 abstract 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();
-						System.out.println("r: " + r + " c: " + c + " i: " + i + " gene: " + gene);
-						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();
-		} else {
-			throw new IllegalArgumentException("The topology of the chromosome in " + file.getName() + " does not match that of the experiment.");
-		}
-	}
-	
-	/**
-	 * Writes a chromosome into the specified .chr file.
-	 * 
-	 * 
-	 * @param file the file to write to
-	 * @param chromosome the chromosome to save
-	 */
-	public static void save(File file, Chromosome chromosome, Resources resources) {
-		PrintWriter writer;
-		try {
-			writer = new PrintWriter(file);
-		} catch (FileNotFoundException e) {
-			// something bad happened
-			return;
-		}
-		
-		// for all nodes, columns first
-		for (int c = 0; c < resources.columns(); c++) {
-			for (int r = 0; r < resources.rows(); r++) {
-				for (int i = 0; i < resources.arity(); i++) {
-					// print the connections, separated by spaces
-					Connection conn = chromosome.getNode(r, c).getConnection(i);
-					if (conn instanceof Input) {
-						writer.print(" " + ((Input) conn).getIndex());
-					} else if (conn instanceof Node) {
-						writer.print(" " + (((((Node) conn).getColumn() + 1) * resources.inputs()) + ((Node) conn).getRow()));
-					} else {
-						throw new ClassCastException("Could not handle " + conn.getClass() + " as a subclass of Connection");
-					}
-				}
-				// print the function numbers
-				writer.print(" " + resources.getFunctionIndex(chromosome.getNode(r, c).getFunction()));
-				// node is done, print tab
-				writer.print("\t");
-			}
-		}
-		// nodes are done, print two tabs to separate from output
-		writer.print("\t\t");
-		for (int o = 0; o < resources.outputs(); o ++) {
-			Connection source = chromosome.getOutput(o).getSource();
-			if (source instanceof Input) {
-				writer.print(" " + ((Input) source).getIndex());
-			} else if (source instanceof Node) {
-				writer.print(" " + (((((Node) source).getColumn() + 1) * resources.inputs()) + ((Node) source).getRow()));
-			} else {
-				throw new ClassCastException("Could not handle " + source.getClass() + " as a subclass of Connection");
-			}
-		}
-		
-		writer.close();
-		System.out.println("writer is closed");
-	}
-	
-}
diff --git a/src/jcgp/backend/parser/FunctionParser.java b/src/jcgp/backend/parser/FunctionParser.java
deleted file mode 100644
index ab94899..0000000
--- a/src/jcgp/backend/parser/FunctionParser.java
+++ /dev/null
@@ -1,51 +0,0 @@
-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) {
-		int functionIndex = Integer.parseInt(splitString[splitString.length - 1]);
-		if (Integer.parseInt(splitString[0]) != 0) {
-			functionSet.enableFunction(functionIndex);
-		} else {
-			functionSet.disableFunction(functionIndex);
-		}
-		
-	}	
-}
diff --git a/src/jcgp/backend/parser/ParameterParser.java b/src/jcgp/backend/parser/ParameterParser.java
deleted file mode 100644
index f96ebf9..0000000
--- a/src/jcgp/backend/parser/ParameterParser.java
+++ /dev/null
@@ -1,77 +0,0 @@
-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
deleted file mode 100644
index d47d663..0000000
--- a/src/jcgp/backend/parser/TestCaseParser.java
+++ /dev/null
@@ -1,90 +0,0 @@
-package jcgp.backend.parser;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.util.Scanner;
-
-import jcgp.backend.modules.problem.TestCaseProblem;
-import jcgp.backend.resources.ModifiableResources;
-
-public class TestCaseParser {
-
-	private TestCaseProblem<?> problem;
-	
-	public TestCaseParser(TestCaseProblem<?> problem) {
-		this.problem = problem;
-	}
-	
-	public void parse(File file) {
-		FileReader fr;
-		try {
-			fr = new FileReader(file);
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-			return;
-		}
-		
-		Scanner in = new Scanner(fr);
-		boolean readingTestCases = false;
-		int inputs = 0, outputs = 0;
-		
-		problem.clearTestCases();
-		
-		while (in.hasNextLine()) {
-			String nextLine = in.nextLine();
-			
-			if (nextLine.startsWith(".i")) {
-				String[] split = nextLine.split(" +");
-				inputs = Integer.parseInt(split[1]);
-			} else if (nextLine.startsWith(".o")) {
-				String[] split = nextLine.split(" +");
-				outputs = Integer.parseInt(split[1]);
-			} else if (nextLine.startsWith(".p") || nextLine.startsWith(".t")) {
-				readingTestCases = true;
-			} else if (nextLine.startsWith(".e")) {
-				readingTestCases = false;
-				// set test cases? not safe probably
-			} else if (readingTestCases) {
-				String[] split = nextLine.split("( |\t)+");
-				String[] inputCases = new String[inputs];
-				String[] outputCases = new String[outputs];
-				for (int i = 0; i < inputs; i++) {
-					inputCases[i] = split[i];
-				}
-				for (int o = 0; o < outputs; o++) {
-					outputCases[o] = split[o + inputs];
-				}
-				
-				problem.addTestCase(inputCases, outputCases);
-			}
-		}
-		
-		in.close();
-	}
-
-	public static void parseParameters(File file, ModifiableResources resources) {
-		
-		FileReader fr;
-		try {
-			fr = new FileReader(file);
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-			return;
-		}
-		
-		Scanner in = new Scanner(fr);
-
-		while (in.hasNextLine()) {
-			String nextLine = in.nextLine();
-			if (nextLine.startsWith(".i")) {
-				String[] split = nextLine.split(" +");
-				resources.setInputs(Integer.parseInt(split[1]));
-			} else if (nextLine.startsWith(".o")) {
-				String[] split = nextLine.split(" +");
-				resources.setOutputs(Integer.parseInt(split[1]));
-			}
-		}
-		in.close();
-	}
-}