Swing is everything but fun

LICENSE

+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
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pom.xml

+<!--
+  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
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+  SOFTWARE.
+-->
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	
@@ -131,6 +152,11 @@
 			<version>${cytoscape.api.version}</version>
 			<type>bundle</type>
 		</dependency>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>swing-util-api</artifactId>
+			<version>${cytoscape.api.version}</version>
+		</dependency>
 	</dependencies>
 
 	<description>A Cytoscape plugin for graph-based clustering that wraps the yoshiko algorithm.</description>

src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper;
 
 import java.util.Properties;

src/main/java/de/hhu/ba/yoshikoWrapper/core/AlgorithmTask.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.core;
 
 import java.util.Properties;

src/main/java/de/hhu/ba/yoshikoWrapper/core/ConfigurationManager.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.core;
 
 import org.cytoscape.property.AbstractConfigDirPropsReader;

src/main/java/de/hhu/ba/yoshikoWrapper/core/CyCore.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.core;
 
 import org.cytoscape.application.CyApplicationManager;

src/main/java/de/hhu/ba/yoshikoWrapper/core/GraphicsLoader.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.core;
 
+import java.awt.Image;
+import java.awt.image.BufferedImage;
+import java.io.IOException;
+
+import javax.imageio.ImageIO;
 import javax.swing.ImageIcon;
 
 public class GraphicsLoader {
-	private static ImageIcon yoshikoLogo;
-	private static ImageIcon yoshikoText;
+	private static BufferedImage yoshikoLogo;
+	private static BufferedImage yoshikoText;
+	
+	private final static ClassLoader classLoader = GraphicsLoader.class.getClassLoader();
 	
-	public static ImageIcon getLogo() {
+	public static ImageIcon getLogo(int size) {
 		if (yoshikoLogo == null) {
-			yoshikoLogo = new ImageIcon("/resources/graphics/YoshikoAlphaLogo.png");
+			try {
+				yoshikoLogo = ImageIO.read(
+						classLoader.getResource("graphics/YoshikoAlphaLogo.png")
+				);
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
 		}
-		return yoshikoLogo;
+		return new ImageIcon(yoshikoLogo.getScaledInstance(size, size, Image.SCALE_SMOOTH));
 	}
 	
-	public static ImageIcon getText() {
-		if (yoshikoLogo == null) {
-			yoshikoLogo = new ImageIcon("/graphics/YoshikoAlphaText.png");
+	public static ImageIcon getText(int height) {
+		if (yoshikoText == null) {
+			try {
+				yoshikoText = ImageIO.read(
+						classLoader.getResource("graphics/YoshikoAlphaText.png")
+				);
+			} catch (IOException e) {
+				e.printStackTrace();
+			}		
 		}
-		return yoshikoText;
+		return new ImageIcon(yoshikoText.getScaledInstance(height*4, height, Image.SCALE_SMOOTH));
 	}
 }

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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.core;
 
 import java.util.Collection;

src/main/java/de/hhu/ba/yoshikoWrapper/core/NetChangeListener.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.core;
 
 import org.cytoscape.application.events.SetCurrentNetworkEvent;

src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.core;
 
 import java.util.List;

src/main/java/de/hhu/ba/yoshikoWrapper/core/NodeMap.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.core;
 
 import java.util.HashMap;

src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.core;
 
 import java.io.File;

src/main/java/de/hhu/ba/yoshikoWrapper/core/package-info.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 /**
  * 
  */

src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.graphModel;
 
 import java.util.ArrayList;

src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.graphModel;
 
 import java.util.ArrayList;

src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.graphModel;
 
 import java.util.ArrayList;

src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/package-info.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 /**
  * 
  */

src/main/java/de/hhu/ba/yoshikoWrapper/gui/ClusterView.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.gui;
 
 import java.awt.Color;
@@ -9,6 +30,7 @@ import javax.swing.BorderFactory;
 import javax.swing.Box;
 import javax.swing.BoxLayout;
 import javax.swing.JLabel;
+import javax.swing.JPanel;
 import javax.swing.border.Border;
 
 import org.cytoscape.model.CyNode;
@@ -18,7 +40,7 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
 
 @SuppressWarnings("serial")
-public class ClusterView extends ComfortPanel {
+public class ClusterView extends JPanel {
 	
 	private final JLabel title;
 	private final JLabel clusterSize;
@@ -43,7 +65,7 @@ public class ClusterView extends ComfortPanel {
 		title = new JLabel(LocalizationManager.get("cluster")+" "+(c.id+1));
 		clusterSize = new JLabel(LocalizationManager.get("clusterSize")+" "+c.nodes.size());
 				
-		this.addAll(title,clusterSize);
+		SwingUtil.addAll(this,title,clusterSize);
 		this.add(Box.createVerticalStrut(4));
 		
 		//Loop over nodes in the cluster and add them to the view

src/main/java/de/hhu/ba/yoshikoWrapper/gui/ColumnMapper.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
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.gui;
 
 
@@ -6,6 +27,7 @@ import java.awt.FlowLayout;
 import javax.swing.BoxLayout;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
+import javax.swing.JPanel;
 
 import org.cytoscape.model.CyColumn;
 import org.cytoscape.model.CyNetwork;
@@ -13,7 +35,7 @@ import org.cytoscape.model.CyNetwork;
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
 
 @SuppressWarnings("serial") //will never be serialized
-public class ColumnMapper extends ComfortPanel{
+public class ColumnMapper extends JPanel{
 	
 
 	//Swing components
@@ -25,9 +47,9 @@ public class ColumnMapper extends ComfortPanel{
 	private final JCheckBox useMappingPerm;
 	private final JCheckBox useMappingForb;
 	
-	private final ComfortPanel costGroup;
-	private final ComfortPanel permGroup;
-	private final ComfortPanel forbGroup;
+	private final JPanel costGroup;
+	private final JPanel permGroup;
+	private final JPanel forbGroup;
 		
 	public ColumnMapper() {
 		this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
@@ -58,20 +80,20 @@ public class ColumnMapper extends ComfortPanel{
 			new EnableWhenSelectedListener(useMappingForb, forbiddenMapper)
 		);
 		
-		costGroup = new ComfortPanel();
-		permGroup = new ComfortPanel();
-		forbGroup = new ComfortPanel();
+		costGroup = new JPanel();
+		permGroup = new JPanel();
+		forbGroup = new JPanel();
 		
 		costGroup.setLayout(new FlowLayout());
 		permGroup.setLayout(new FlowLayout());
 		forbGroup.setLayout(new FlowLayout());
 
-		costGroup.addAll(useMappingCost,editingCostMapper);
-		permGroup.addAll(useMappingPerm,permanentMapper);
-		forbGroup.addAll(useMappingForb,forbiddenMapper);
+		SwingUtil.addAll(costGroup,useMappingCost,editingCostMapper);
+		SwingUtil.addAll(permGroup,useMappingPerm,permanentMapper);
+		SwingUtil.addAll(forbGroup,useMappingForb,forbiddenMapper);
 
 		
-		this.addAll(costGroup,permGroup,forbGroup);
+		SwingUtil.addAll(this,costGroup,permGroup,forbGroup);
 		
 		//Initial call to get table values
 		updateValues();

src/main/java/de/hhu/ba/yoshikoWrapper/gui/ComfortCollapsiblePanel.java

+package de.hhu.ba.yoshikoWrapper.gui;
+
+import org.cytoscape.util.swing.BasicCollapsiblePanel;
+
+@SuppressWarnings("serial")
+public class ComfortCollapsiblePanel extends BasicCollapsiblePanel {
+
+	public ComfortCollapsiblePanel(String text) {
+		super(text);
+	}
+
+	@Override
+	public void setCollapsed(boolean collapse) {
+		super.setCollapsed(collapse);
+		//Force resize of parent
+		if (getParent() != null) {
+			getParent().revalidate();
+		}
+	}
+}