Minor clean-up

src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java

@@ -52,7 +52,6 @@ import static org.cytoscape.work.ServiceProperties.COMMAND_NAMESPACE;
 import de.hhu.ba.yoshikoWrapper.core.ConfigurationManager;
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
-import de.hhu.ba.yoshikoWrapper.core.YoshUtil;
 import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
 import de.hhu.ba.yoshikoWrapper.swing.components.MainPanel;
 import de.hhu.ba.yoshikoWrapper.taskFactories.CommandTaskFactory;
@@ -94,11 +93,11 @@ public class CyActivator extends AbstractCyActivator {
 		CyCore.rootNetworkManager = getService(context,CyRootNetworkManager.class);
 		//TODO: Not sure how to correctly infer arguments here
 		CyCore.renderingEngineFactory = getService(context,RenderingEngineFactory.class);
-		CyCore.cloneNetworkTaskFactory = getService(context,CloneNetworkTaskFactory.class);
+		//CyCore.cloneNetworkTaskFactory = getService(context,CloneNetworkTaskFactory.class);
 		CyCore.commandExecutorTaskFactory = getService(context,CommandExecutorTaskFactory.class);
 
 		//Store a reference to the Version for easier access
-		YoshUtil.version = context.getBundle().getVersion();
+		//YoshUtil.version = context.getBundle().getVersion();
 
 		//Set language according to settings -> Default to enUS
 		LocalizationManager.switchLanguage(cm.getProperties().getProperty("locale", "enUS"));

src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.java

@@ -55,7 +55,7 @@ public class CyCore {
 	public static CyApplicationManager cy;
 	public static DialogTaskManager dialogTaskManager;
 	public static ConfigurationManager cm;
-	public static BundleContext context;
+	//public static BundleContext context;
 	public static CyServiceRegistrar registrar;
 	public static CyNetworkViewFactory networkViewFactory;
 	public static CyNetworkFactory networkFactory;
@@ -68,7 +68,7 @@ public class CyCore {
 	public static VisualMappingFunctionFactory continuousMappingFactory;
 	public static CyRootNetworkManager rootNetworkManager;
 	public static RenderingEngineFactory<CyNetwork> renderingEngineFactory;
-	public static CloneNetworkTaskFactory cloneNetworkTaskFactory;
+	//public static CloneNetworkTaskFactory cloneNetworkTaskFactory;
 	public static CommandExecutorTaskFactory commandExecutorTaskFactory;
 	//
 

src/main/java/de/hhu/ba/yoshikoWrapper/core/LocalizationManager.java

 /*******************************************************************************
  * Copyright (C) 2017 Philipp Spohr
- * 
+ *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
  * in the Software without restriction, including without limitation the rights
  * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  * copies of the Software, and to permit persons to whom the Software is
  * furnished to do so, subject to the following conditions:
- * 
+ *
  * The above copyright notice and this permission notice shall be included in
  * all copies or substantial portions of the Software.
- * 
+ *
  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -30,21 +30,21 @@ import java.util.ResourceBundle;
  *  This class should never be initialized
  */
 public class LocalizationManager {
-	
+
 	/**
 	 * Default constructor, hidden to prevent invocation
 	 */
 	private LocalizationManager() {};
-	
+
 	//Locales
-	
+
 	static public final Locale usEnglish = new Locale("en","US");
 	static public final Locale german = new Locale("de","DE");
 	static public final Locale serbocroatianLatin = new Locale("hr","HR");
 	static public final Locale modernGreek = new Locale("el","EL");
 
 	//Map
-	
+
     static private final HashMap<String, Locale> locales;
     static
     {
@@ -56,12 +56,12 @@ public class LocalizationManager {
 
     }
 
-	
+
 	static private ResourceBundle currentBundle;
-	
+
 	static private Locale currentLocale = usEnglish;
 
-	
+
 	private static void updateBundle() {
 		currentBundle = ResourceBundle.getBundle("YoshikoStrings",currentLocale);
 		CyCore.cm.getProperties().setProperty(
@@ -69,22 +69,22 @@ public class LocalizationManager {
 				currentLocale.getLanguage()+currentLocale.getCountry()
 				);
 	}
-	
+
 	//https://en.wikipedia.org/wiki/Regional_Indicator_Symbol -> Right now there are not enough fonts support this
-	public static  String localeToUnicodeFlag(Locale locale) {
-		String countryCode = locale.getCountry();
-		int firstLetter = Character.codePointAt(countryCode, 0)-0x41+0x1F1E6;
-		int secondLetter = Character.codePointAt(countryCode, 1)-0x41+0x1F1E6;
-		return new String(Character.toChars(firstLetter))+new String(Character.toChars(secondLetter));
-	}
+//	public static  String localeToUnicodeFlag(Locale locale) {
+//		String countryCode = locale.getCountry();
+//		int firstLetter = Character.codePointAt(countryCode, 0)-0x41+0x1F1E6;
+//		int secondLetter = Character.codePointAt(countryCode, 1)-0x41+0x1F1E6;
+//		return new String(Character.toChars(firstLetter))+new String(Character.toChars(secondLetter));
+//	}
 
 
 	//SETTER/GETTER methods
-	
+
 	static public Collection<Locale> getLocales(){
 		return locales.values();
 	}
-	
+
 	/**
 	 * Returns the localized string corresponding to the given key.
 	 * This is the main method that should be used for accessing strings and is preferable to any use of constant strings.
@@ -97,7 +97,7 @@ public class LocalizationManager {
 		}
 		return currentBundle.getString(key);
 	}
-	
+
 	static public void switchLanguage(Locale lcl) {
 		currentLocale = lcl;
 		updateBundle();

src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshUtil.java

-package de.hhu.ba.yoshikoWrapper.core;
-
-
-import org.osgi.framework.Version;
-
-public class YoshUtil {
-	public static Version version;
-
-	public static final String ABOUT_LINK = "https://spqrph.github.io/cytoscape-tutorials/presentations/yoshiko/yoshiko.html#/title";
-}

src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java

@@ -55,14 +55,14 @@ public class GraphAnalyzer {
 		return false;
 	}
 
-	public static boolean isDirected(CyNetwork net) {
-		for (CyEdge e: net.getEdgeList()) {
-			if (e.isDirected()) {
-				return true;
-			}
-		}
-		return false;
-	}
+//	public static boolean isDirected(CyNetwork net) {
+//		for (CyEdge e: net.getEdgeList()) {
+//			if (e.isDirected()) {
+//				return true;
+//			}
+//		}
+//		return false;
+//	}
 
 	/**
 	 * Generates a fitting bitmask by choosing the reduction rules that appear to be the best choice based on current research

src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/HelpButton.java

@@ -4,16 +4,11 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
-import java.io.IOException;
-import java.net.URI;
-import java.util.HashMap;
 
 import javax.swing.BorderFactory;
 import javax.swing.ImageIcon;
 import javax.swing.JButton;
-import javax.swing.JOptionPane;
 
-import org.cytoscape.command.CommandExecutorTaskFactory;
 
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 import de.hhu.ba.yoshikoWrapper.cytoUtil.CommandExecutor;

src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/IntegerInputField.java

 /*******************************************************************************
  * Copyright (C) 2017 Philipp Spohr
- * 
+ *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
  * in the Software without restriction, including without limitation the rights
  * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  * copies of the Software, and to permit persons to whom the Software is
  * furnished to do so, subject to the following conditions:
- * 
+ *
  * The above copyright notice and this permission notice shall be included in
  * all copies or substantial portions of the Software.
- * 
+ *
  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -31,21 +31,21 @@ import de.hhu.ba.yoshikoWrapper.swing.FormatHelper;
  */
 @SuppressWarnings("serial")
 public class IntegerInputField extends JFormattedTextField{
-	
+
 	private final NumberFormatter formatter;
 
-	public IntegerInputField(int minValue, int maxValue) {
-		super();
-		formatter = FormatHelper.getIntegerFormatter(minValue,maxValue);
-		this.setFormatter(formatter);
-		this.setColumns(8);
-	}
+//	public IntegerInputField(int minValue, int maxValue) {
+//		super();
+//		formatter = FormatHelper.getIntegerFormatter(minValue,maxValue);
+//		this.setFormatter(formatter);
+//		this.setColumns(8);
+//	}
 
 	public IntegerInputField() {
 		super();
 		formatter = FormatHelper.getIntegerFormatter();
 		this.setFormatter(formatter);
-		this.setColumns(8);	
+		this.setColumns(8);
 	}
 
 	public int getValueAsInt() {

src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetClustersTask.java

@@ -34,9 +34,7 @@ public class GetClustersTask implements ObservableTask {
 	}
 
 	@Override
-	public void cancel() {
-
-	}
+	public void cancel() {}
 
 	@SuppressWarnings("unchecked")
 	@Override

src/main/java/de/hhu/ba/yoshikoWrapper/tasks/GetSolutionsTask.java

 package de.hhu.ba.yoshikoWrapper.tasks;
 
-import java.util.ArrayList;
 import java.util.Collection;
 
 import org.cytoscape.work.ObservableTask;