added a lot of comments and got rid of some minor bugs

NeoSuit/src/main/java/controller/DatabaseController.java

@@ -7,6 +7,10 @@ import org.neo4j.graphdb.GraphDatabaseService;
 import de.chw.sdg.db.Neo4Jdb;
 import logging.Logger;
 
+/**
+ * Manages the database access. This includes starting and stopping in a safe
+ * manner
+ */
 public class DatabaseController {
 	private String path;
 	private GraphDatabaseService db;
@@ -35,11 +39,22 @@ public class DatabaseController {
 		return path;
 	}
 
+	/**
+	 * Stops the current DB instance and sets the path for the next
+	 * 
+	 * @param path
+	 *            path of next DB
+	 */
 	public void setPath(String path) {
 		stopDB();
 		this.path = path;
 	}
 
+	/**
+	 * Starts the DB registers shutdown hook
+	 * 
+	 * @return Database handle
+	 */
 	public GraphDatabaseService startDB() {
 		if (db == null) {
 

NeoSuit/src/main/java/controller/ExportController.java

@@ -5,6 +5,10 @@ import org.neo4j.graphdb.Node;
 
 import de.chw.parallax.java.GeneratorExecutor;
 
+/**
+ * Wraps SDG2Java, which exports a database node to java code
+ *
+ */
 public class ExportController {
 	GeneratorExecutor generator;
 

NeoSuit/src/main/java/controller/FileSystemController.java

@@ -7,12 +7,17 @@ import java.nio.file.Files;
 
 import logging.Logger;
 
+/**
+ * Wraps every interaction with the File System, such as deleting or copying a
+ * directory
+ *
+ */
 public class FileSystemController {
 
-	private final static String basepath = "tmp";
+	private final static String BASE_PATH = "tmp";
 
 	public static File initializeFolder(String dirName) {
-		File dbDir = new File(basepath, dirName);
+		File dbDir = new File(BASE_PATH, dirName);
 		Logger.info("Initializing DB Folder: " + dbDir.getAbsolutePath());
 		if (dbDir.exists()) {
 			deleteDir(dbDir);
@@ -37,7 +42,7 @@ public class FileSystemController {
 
 	public static File copyDirToLocal(final String src) {
 		File srcFile = new File(src);
-		File targetFile = new File(basepath, srcFile.getName());
+		File targetFile = new File(BASE_PATH, srcFile.getName());
 		if (targetFile.exists()) {
 			deleteDir(targetFile);
 		}

NeoSuit/src/main/java/controller/SootController.java → NeoSuit/src/main/java/controller/Java2SDGController.java

@@ -10,9 +10,13 @@ import org.neo4j.graphdb.GraphDatabaseService;
 import de.chw.sdg.Sdg;
 import logging.Logger;
 
-public class SootController {
+/**
+ * Generates a SDG from given Java code
+ *
+ */
+public class Java2SDGController {
 
-	private Sdg soot;
+	private Sdg sdg;
 
 	public String[] buildArguments(String pathToJava, String classpath, String mainClass) {
 		ArrayList<String> args = new ArrayList<String>();
@@ -73,24 +77,24 @@ public class SootController {
 	}
 
 	public GraphDatabaseService getDB() {
-		return soot.getGraphDatabaseService();
+		return sdg.getGraphDatabaseService();
 	}
 
 	public void startUp(String pathToDB) {
-		soot = new Sdg(pathToDB);
-		soot.connect();
+		sdg = new Sdg(pathToDB);
+		sdg.connect();
 
-		soot.deleteContent();
+		sdg.deleteContent();
 	}
 
-	public void startSoot(String[] args) throws IOException {
+	public void startJava2SDG(String[] args) throws IOException {
 
-		soot.transform(args);
+		sdg.transform(args);
 	}
 
-	public void startSoot(String javaSrc, String classpath, String mainClass, String pathToDB) throws Exception {
+	public void startJava2SDG(String javaSrc, String classpath, String mainClass, String pathToDB) throws Exception {
 		startUp(pathToDB);
-		startSoot(buildArguments(javaSrc, classpath, mainClass));
+		startJava2SDG(buildArguments(javaSrc, classpath, mainClass));
 
 	}
 }

NeoSuit/src/main/java/controller/LazyQueryController.java

@@ -19,6 +19,11 @@ import model.ParallelizationPattern;
 import model.Pattern;
 import model.Query;
 
+/**
+ * Handles the database queries and code export in a lazy manner and has a cache
+ * layer to reduce the amount of queries for the database
+ *
+ */
 public class LazyQueryController {
 
 	private Pattern activeCandidatePattern;

NeoSuit/src/main/java/controller/QueryController.java

@@ -21,6 +21,11 @@ import model.ParallelizationPattern;
 import model.Pattern;
 import model.Query;
 
+/**
+ * Handles the database queries and wraps the result in matches; also generates
+ * the java code for the update pattern
+ *
+ */
 public class QueryController {
 
 	public static List<Match> getResultsForPattern(Pattern pattern, boolean applyPP) {

NeoSuit/src/main/java/controller/SourceFinder.java

@@ -11,6 +11,10 @@ import java.util.List;
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
 
+/**
+ * Locates a given class in a java project path and returns the files content
+ *
+ */
 public class SourceFinder {
 	private File srcDirectory;
 	private List<String> srcLines;

NeoSuit/src/main/java/logging/LabelLogger.java

@@ -2,6 +2,10 @@ package logging;
 
 import javafx.scene.control.Label;
 
+/**
+ * Logs into a Label field, to show messages to user
+ *
+ */
 public class LabelLogger implements GraphicLogger {
 
 	private final Label textField;
@@ -40,7 +44,7 @@ public class LabelLogger implements GraphicLogger {
 	}
 
 	@Override
-	public void exception(Throwable exception) {
+	public void exception(final Throwable exception) {
 		textField.setText(exception.getMessage());
 		Logger.exception(exception);
 	}

NeoSuit/src/main/java/logging/Logger.java

@@ -4,6 +4,10 @@ import java.io.PrintStream;
 
 import logging.LoggerInterface.Level;
 
+/**
+ * Handles the logging
+ *
+ */
 public final class Logger {
 
 	private Logger() {

NeoSuit/src/main/java/model/CandidatePatternMatches.java

@@ -2,6 +2,10 @@ package model;
 
 import java.util.List;
 
+/**
+ * Represents the candidate pattern machtches for a given pattern
+ *
+ */
 public class CandidatePatternMatches {
 	private final Pattern pattern;
 	private final List<Match> matches;

NeoSuit/src/main/java/model/CandidatePatternResult.java

@@ -4,6 +4,10 @@ import java.util.Map;
 
 import org.neo4j.graphdb.Node;
 
+/**
+ * Holds the result of a candidate pattern
+ *
+ */
 public class CandidatePatternResult {
 
 	private Node displayNode;

NeoSuit/src/main/java/model/CompareState.java

@@ -15,6 +15,10 @@ import preferences.PreferenceConstants;
 import preferences.Preferences;
 import tasks.Java2SDGTask;
 
+/**
+ * Holds the complete state of the ui.wizard.CompareScreen
+ *
+ */
 public class CompareState {
 
 	private List<CandidatePatternMatches> patternMatches;

NeoSuit/src/main/java/model/Match.java

@@ -4,6 +4,11 @@ import java.util.HashMap;
 import java.util.Map;
 import java.util.UUID;
 
+/**
+ * Holds all information regarding a Pattern match, including the candidate and
+ * update pattern result.
+ *
+ */
 public class Match {
 	private final String matchId = UUID.randomUUID().toString();
 	private Pattern pattern;

NeoSuit/src/main/java/model/ParallelizationPattern.java

@@ -7,6 +7,10 @@ import java.util.List;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
+/**
+ * Handles a parallelization pattern and parses the query node in it
+ *
+ */
 public class ParallelizationPattern {
 
 	private String javaVersion;

NeoSuit/src/main/java/model/Pattern.java

@@ -20,6 +20,10 @@ import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 import logging.Logger;
 
+/**
+ * Handles everything related to patterns including the parsing of such
+ *
+ */
 public class Pattern {
 
 	private String name;

NeoSuit/src/main/java/model/PatternList.java

@@ -29,9 +29,9 @@ import javafx.collections.ObservableList;
 import logging.Logger;
 
 /**
- * manages Candidate and Update Patterns
+ * manages patterns in a list regarding order and active state. Keeps the
+ * patterns only as reference and does not maintain a local copy.
  * 
- * @author danielschmidt
  *
  */
 

NeoSuit/src/main/java/model/Query.java

@@ -19,9 +19,8 @@ import logging.Logger;
 import preferences.Preferences;
 
 /**
- * Manages parsing / var replacement and everything related to queries
- * 
- * @author danielschmidt
+ * Manages parsing / temporary variable replacement and everything related to
+ * queries, including parsing and loading from another file
  *
  */
 

NeoSuit/src/main/java/preferences/PreferenceConstants.java

 package preferences;
 
+/**
+ * The place to store the preference constants
+ *
+ */
 public final class PreferenceConstants {
 	public final static String DEFAULT_PATH = "WIZARD_DEF_PATH", DEFAULT_TARGET_PATH = "EXPERT_TARGET_PATH",
 			DEFAULT_DB = "EXPERT_DB", DEFAULT_CLASS = "WIZARD_DEF_CLASS", CLASS_PATH = "CLASS_PATH",

NeoSuit/src/main/java/preferences/Preferences.java

@@ -11,6 +11,10 @@ import java.util.Map;
 
 import logging.Logger;
 
+/**
+ * Handles the preferences as a simple persistent key value store
+ *
+ */
 public final class Preferences {
 
 	private static Map<String, String> prefs;

NeoSuit/src/main/java/tasks/CandidatePatternListTask.java

@@ -7,9 +7,13 @@ import javafx.concurrent.Task;
 import model.CandidatePatternMatches;
 import model.PatternList;
 
+/**
+ * Queries the database to get a list of matched candidate patterns
+ *
+ */
 public class CandidatePatternListTask extends Task<Void> {
 
-	private ObservableList<String> cpMatches;
+	private ObservableList<String> candidatePatternMatches;
 
 	@Override
 	protected Void call() {
@@ -20,10 +24,10 @@ public class CandidatePatternListTask extends Task<Void> {
 		java.util.List<CandidatePatternMatches> matches = QueryController
 				.getResultsForPatternList(patterns.getActivePatterns(), false);
 
-		cpMatches = FXCollections.observableArrayList();
+		candidatePatternMatches = FXCollections.observableArrayList();
 		for (CandidatePatternMatches pm : matches) {
 			if (pm.getMatches().size() > 0) {
-				cpMatches.add(pm.getPattern().getName());
+				candidatePatternMatches.add(pm.getPattern().getName());
 			}
 		}
 		this.updateMessage("Pattern applied!");
@@ -32,7 +36,7 @@ public class CandidatePatternListTask extends Task<Void> {
 	}
 
 	public ObservableList<String> getMatches() {
-		return this.cpMatches;
+		return this.candidatePatternMatches;
 	}
 
 }