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

@@ -71,12 +71,12 @@ public class LocalizationManager {
 	}
 
 	//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

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

@@ -34,12 +34,12 @@ 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();

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;