Fixed some graphic glitches with SWIG and Cyto API

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

@@ -86,7 +86,6 @@ public class CyActivator extends AbstractCyActivator {
 		CyCore.continuousMappingFactory = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
 		CyCore.rootNetworkManager = getService(context,CyRootNetworkManager.class);
 		CyCore.applyVisualStyleTaskFactory = getService(context,ApplyVisualStyleTaskFactory.class);
-		//TODO: Not sure how to infer type here
 		CyCore.renderingEngineFactory = getService(context,RenderingEngineFactory.class);
 
 		//Set language according to settings

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

@@ -24,7 +24,6 @@ package de.hhu.ba.yoshikoWrapper.core;
 import java.awt.Window;
 import java.util.Properties;
 
-import javax.swing.JDialog;
 import javax.swing.JOptionPane;
 
 import org.cytoscape.application.swing.CytoPanel;

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

@@ -62,6 +62,5 @@ public class CyCore {
 	public static CyRootNetworkManager rootNetworkManager;
 	public static ApplyVisualStyleTaskFactory applyVisualStyleTaskFactory;
 	public static RenderingEngineFactory<CyNetwork> renderingEngineFactory;
-
 	//
 }

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

@@ -31,7 +31,6 @@ import org.slf4j.Logger;
 
 import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
 import de.hhu.ba.yoshikoWrapper.swig.LibraryInput;
-import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
 
 public class NetworkParser {
 	

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

@@ -28,27 +28,25 @@ import javax.swing.JPanel;
 import javax.swing.GroupLayout.Alignment;
 
 import org.cytoscape.model.CyColumn;
-import org.cytoscape.util.swing.BasicCollapsiblePanel;
 
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 
 @SuppressWarnings("serial") //Will never be serialized
-public class EditCostPanel extends BasicCollapsiblePanel {
+public class EditCostPanel extends JPanel {
 	
 	//SWING COMPONENTS
-	private ColumnMapper columnMapper;
+	private final ColumnMapper columnMapper;
 	
-	private DoubleInputField  icField;
-	private DoubleInputField dcField;
+	private final DoubleInputField  icField;
+	private final DoubleInputField dcField;
 	
-	private JLabel icLabel;
-	private JLabel dcLabel;
+	private final JLabel icLabel;
+	private final JLabel dcLabel;
 	
-	private JPanel groupIC;
-	private JPanel groupDC;
+	private final JPanel groupIC;
+	private final JPanel groupDC;
 	
 	public EditCostPanel() {
-		super(LocalizationManager.get("editingCostPanel"));
 
 		//Initialize components
 		columnMapper = new ColumnMapper();
@@ -73,7 +71,7 @@ public class EditCostPanel extends BasicCollapsiblePanel {
 
 		
 		//Layout
-		GroupLayout layout = new GroupLayout(this.getContentPane());
+		GroupLayout layout = new GroupLayout(this);
 		
 		layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING,true)
 				.addComponent(columnMapper)
@@ -87,10 +85,9 @@ public class EditCostPanel extends BasicCollapsiblePanel {
 				.addComponent(groupDC)
 		);
 		
-		this.getContentPane().setLayout(layout);
+		this.setLayout(layout);
 		
 	}
-	
 	//SETTER / GETTER
 
 	public CyColumn getWeightColumn() {

src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageSwitcherPanel.java → src/main/java/de/hhu/ba/yoshikoWrapper/gui/LanguageSwitcherPanelFactory.java

@@ -28,20 +28,19 @@ import org.cytoscape.util.swing.BasicCollapsiblePanel;
 
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 
-@SuppressWarnings("serial")
-public class LanguageSwitcherPanel extends BasicCollapsiblePanel{
+public class LanguageSwitcherPanelFactory{
 	
-	private final LanguageSwitcher switcher;
-	
-	public LanguageSwitcherPanel() {
-		super(LocalizationManager.get("switchLanguage"));
-		this.getContentPane().setLayout(new BoxLayout(this.getContentPane(),BoxLayout.X_AXIS));
+	public static BasicCollapsiblePanel createLanguageSwitcherPanel() {
+		final LanguageSwitcher switcher;
+		final BasicCollapsiblePanel ret = new BasicCollapsiblePanel(LocalizationManager.get("switchLanguage"));
+		ret.getContentPane().setLayout(new BoxLayout(ret.getContentPane(),BoxLayout.X_AXIS));
 		//SWING COMPONENTS INIT
 		switcher = new LanguageSwitcher();
 		
-		SwingUtil.addAll(this,
+		SwingUtil.addAll(ret,
 				switcher
 		);
+		return ret;
 	}
 
 }

src/main/java/de/hhu/ba/yoshikoWrapper/gui/LibraryPanel.java → src/main/java/de/hhu/ba/yoshikoWrapper/gui/LibraryPanelFactory.java

@@ -37,19 +37,16 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
 import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
 
-@SuppressWarnings("serial")
-public class LibraryPanel extends BasicCollapsiblePanel {
+public class LibraryPanelFactory{
 	
-	//SYMBOLIC LINKS
-	private LibraryPanel self = this;
 
-	private LibStatusPanel libStatusPanel;
-	private JButton searchLibButton;
-	private JLabel yoshikoVersionLabel;
+	public static BasicCollapsiblePanel createLibraryPanel() {
+		final BasicCollapsiblePanel ret = new BasicCollapsiblePanel(LocalizationManager.get("libraryPanel"));
 				
+		final LibStatusPanel libStatusPanel;
+		final JButton searchLibButton;
+		final JLabel yoshikoVersionLabel;
 		
-	public LibraryPanel() {
-		super(LocalizationManager.get("libraryPanel"));
 		//SWING COMPONENT INITIALIZATION
 		libStatusPanel = new LibStatusPanel();
 		searchLibButton = new JButton(LocalizationManager.get("resolveLibPath"));
@@ -66,7 +63,7 @@ public class LibraryPanel extends BasicCollapsiblePanel {
 			@Override
 			public void actionPerformed(ActionEvent e) {
 				final YLibChooser c = new YLibChooser();
-				int returnVal = c.showOpenDialog(self);
+				int returnVal = c.showOpenDialog(ret);
 				if (returnVal == JFileChooser.APPROVE_OPTION) {
 					YoshikoLoader.loadLibrary(c.getSelectedFile().getAbsolutePath());
 				}
@@ -76,14 +73,14 @@ public class LibraryPanel extends BasicCollapsiblePanel {
 			}
 		});
 		
-		SwingUtil.addAll(this,
+		SwingUtil.addAll(ret,
 				libStatusPanel,
 				yoshikoVersionLabel,
 				searchLibButton
 		);
 		
 		//Layout
-		GroupLayout layout = new GroupLayout(this.getContentPane());
+		GroupLayout layout = new GroupLayout(ret.getContentPane());
 		
 		layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING,true)
 				.addComponent(libStatusPanel)
@@ -98,7 +95,8 @@ public class LibraryPanel extends BasicCollapsiblePanel {
 		);
 		
 		
-		this.getContentPane().setLayout(layout);
+		ret.getContentPane().setLayout(layout);
 		
+		return ret;
 	}
 }

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

@@ -30,13 +30,6 @@ import java.awt.Dialog.ModalityType;
 import java.awt.Window;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.awt.event.ComponentEvent;
-import java.awt.event.ComponentListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.awt.event.WindowEvent;
-import java.awt.event.WindowFocusListener;
-import java.awt.event.WindowListener;
 import java.util.ArrayList;
 import java.util.Arrays;
 
@@ -49,10 +42,10 @@ import javax.swing.JComponent;
 import javax.swing.JDialog;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
-import javax.swing.SwingUtilities;
 
 import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.application.swing.CytoPanelName;
+import org.cytoscape.util.swing.BasicCollapsiblePanel;
 import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.TaskIterator;
 
@@ -68,8 +61,6 @@ import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
 @SuppressWarnings("serial")
 public class MainPanel extends JPanel implements CytoPanelComponent {
 	
-	private MainPanel self = this;
-	
 	//SWING COMPONENTS
 		
 	private final YoshikoHeader header;
@@ -77,10 +68,19 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 	private final JCheckBox showAdvancedOptions;
 	private final ArrayList<JComponent> advancedOptions;
 
-	private final LanguageSwitcherPanel langPanel;
-	private final LibraryPanel libraryPanel;
+	//Those two work with factories whysoever
+	private final BasicCollapsiblePanel langPanel;
+	private final BasicCollapsiblePanel libraryPanel;
+	
+	//Those don't work really as collapsible panels and cause glitches which forces the workaround of wrapping them
+	//Probably someone used getClass() == instead of instanceof so extending BasicCollapsiblePanel is sadly not possible
+	private final BasicCollapsiblePanel ecPanelWrapper;
 	private final EditCostPanel ecPanel;
+	
+	private final BasicCollapsiblePanel reductionWrapper;
 	private final ReductionRulesChooser reductionRulesChooser;
+	
+	private final BasicCollapsiblePanel opWrapper;
 	private final OperationModePanel opModePanel;	
 	
 	/**
@@ -94,34 +94,38 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 		showAdvancedOptions = new JCheckBox(LocalizationManager.get("showAdvanced"));
 		showAdvancedOptions.addActionListener(toggleAdvancedOptionsListener);
 		
-		langPanel = new LanguageSwitcherPanel();
+		langPanel = LanguageSwitcherPanelFactory.createLanguageSwitcherPanel();
 		
-		libraryPanel = new LibraryPanel();
+		libraryPanel = LibraryPanelFactory.createLibraryPanel();
 		//If no library is loaded yet the obvious panel should be showing up
 		if (!YoshikoLoader.isLibraryLoaded()) {
 			libraryPanel.setCollapsed(false);
 		}
 		
 		ecPanel = new EditCostPanel();
+		ecPanelWrapper = new BasicCollapsiblePanel(LocalizationManager.get("editingCostPanel"));
+		ecPanelWrapper.add(ecPanel);
 		
 		opModePanel = new OperationModePanel();
+		opWrapper = new BasicCollapsiblePanel(LocalizationManager.get("operationMode"));
+		opWrapper.add(opModePanel);
 		
+		reductionWrapper = new BasicCollapsiblePanel(LocalizationManager.get("redRuleChooserTitle"));
 		reductionRulesChooser = new ReductionRulesChooser();
+		reductionWrapper.add(reductionRulesChooser);
 		
 		JButton runButton = new JButton(LocalizationManager.get("run"));
 		runButton.addActionListener(buttonListener);
 
 		//Add components to main panel
-
-		
 		SwingUtil.addAll(this,
 				header,
 				showAdvancedOptions,
 				langPanel,
 				libraryPanel,
-				ecPanel,
-				reductionRulesChooser,
-				opModePanel,
+				ecPanelWrapper,
+				reductionWrapper,
+				opWrapper,
 				runButton
 		);
 		
@@ -129,8 +133,8 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 		advancedOptions = new ArrayList<JComponent>();
 		advancedOptions.addAll(
 				Arrays.asList(
-						opModePanel,
-						reductionRulesChooser
+						opWrapper,
+						reductionWrapper
 						)
 		);
 		
@@ -140,16 +144,14 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 		GroupLayout layout = new GroupLayout(this);
 		layout.setAutoCreateGaps(true);
 		layout.setAutoCreateContainerGaps(true);
-		
 		layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING,true)
-				.addGap(50,50,50)
 				.addComponent(header,DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 				.addComponent(showAdvancedOptions,DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 				.addComponent(langPanel,DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 				.addComponent(libraryPanel,PREFERRED_SIZE, PREFERRED_SIZE, Short.MAX_VALUE)
-				.addComponent(ecPanel,DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
-				.addComponent(reductionRulesChooser,DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
-				.addComponent(opModePanel,DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+				.addComponent(ecPanelWrapper,DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+				.addComponent(reductionWrapper,DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+				.addComponent(opWrapper,DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 				.addComponent(runButton,DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 		);
 		
@@ -158,9 +160,9 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 				.addComponent(showAdvancedOptions,PREFERRED_SIZE,PREFERRED_SIZE,PREFERRED_SIZE)
 				.addComponent(langPanel,PREFERRED_SIZE,PREFERRED_SIZE,PREFERRED_SIZE)
 				.addComponent(libraryPanel,PREFERRED_SIZE,PREFERRED_SIZE,PREFERRED_SIZE)
-				.addComponent(ecPanel,PREFERRED_SIZE,PREFERRED_SIZE,PREFERRED_SIZE)
-				.addComponent(reductionRulesChooser,PREFERRED_SIZE,PREFERRED_SIZE,PREFERRED_SIZE)
-				.addComponent(opModePanel,PREFERRED_SIZE,PREFERRED_SIZE,PREFERRED_SIZE)
+				.addComponent(ecPanelWrapper,PREFERRED_SIZE,PREFERRED_SIZE,PREFERRED_SIZE)
+				.addComponent(reductionWrapper,PREFERRED_SIZE,PREFERRED_SIZE,PREFERRED_SIZE)
+				.addComponent(opWrapper,PREFERRED_SIZE,PREFERRED_SIZE,PREFERRED_SIZE)
 				.addComponent(runButton,PREFERRED_SIZE,PREFERRED_SIZE,PREFERRED_SIZE)	
 		);
 		
@@ -249,6 +251,10 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 	
 	//GETTER / SETTER
 	
+	public ColumnMapper getColumnMapper() {
+		return ecPanel.getColumnMapper();
+	}
+
 	public Component getComponent() {
 		return this;
 	}
@@ -262,17 +268,10 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 	}
 
 	public String getTitle() {
-		//TODO: Be creative I guess
 		return "Yoshiko";
 	}
 	
-	public ColumnMapper getColumnMapper() {
-		return ecPanel.getColumnMapper();
-	}
-	
 	public Icon getIcon() {
 		return GraphicsLoader.getLogo(16);
 	}
-
-
 }

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

@@ -29,17 +29,14 @@ import static javax.swing.GroupLayout.DEFAULT_SIZE;
 import javax.swing.ButtonGroup;
 import javax.swing.GroupLayout;
 import javax.swing.JCheckBox;
+import javax.swing.JPanel;
 import javax.swing.JRadioButton;
 
-import org.cytoscape.util.swing.BasicCollapsiblePanel;
 
 import javax.swing.GroupLayout.Alignment;
 
-
-import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
-
 @SuppressWarnings("serial")
-public class OperationModePanel extends BasicCollapsiblePanel{
+public class OperationModePanel extends JPanel{
 	
 	//SWING COMPONENTS
 	private final JRadioButton useHeuristic;
@@ -53,8 +50,6 @@ public class OperationModePanel extends BasicCollapsiblePanel{
 
 	public OperationModePanel() {
 		
-		super(LocalizationManager.get("operationMode"));
-		
 		heuristicGroup = new ButtonGroup();
 		useILP = new JRadioButton("Use Integer Linear Programming");
 		useILP.setSelected(true);
@@ -84,7 +79,7 @@ public class OperationModePanel extends BasicCollapsiblePanel{
 		);
 
 		//Layout
-		GroupLayout layout = new GroupLayout(this.getContentPane());
+		GroupLayout layout = new GroupLayout(this);
 		
 		layout.setAutoCreateContainerGaps(true);
 		
@@ -106,7 +101,7 @@ public class OperationModePanel extends BasicCollapsiblePanel{
 				.addComponent(usePartitionCutsBox)
 		);
 		
-		this.getContentPane().setLayout(layout);
+		this.setLayout(layout);
 		
 	}
 	

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

@@ -33,12 +33,10 @@ import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.GroupLayout.Alignment;
 
-import org.cytoscape.util.swing.BasicCollapsiblePanel;
-
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 
 @SuppressWarnings("serial")
-public class ReductionRulesChooser extends BasicCollapsiblePanel{
+public class ReductionRulesChooser extends JPanel{
 
 	private final JCheckBox useCRule;
 	private final JCheckBox useCCRule;
@@ -54,7 +52,6 @@ public class ReductionRulesChooser extends BasicCollapsiblePanel{
 	
 	public ReductionRulesChooser() {
 
-		super(LocalizationManager.get("redRuleChooserTitle"));
 		//Initialize subcomponents
 		useCRule = new JCheckBox("Use Clique Rule");
 		useCCRule = new JCheckBox("Use Critical-Clique Rule");
@@ -99,7 +96,7 @@ public class ReductionRulesChooser extends BasicCollapsiblePanel{
 				);
 		
 		//Layout
-		GroupLayout layout = new GroupLayout(this.getContentPane());
+		GroupLayout layout = new GroupLayout(this);
 		
 		layout.setAutoCreateGaps(true);
 		
@@ -123,7 +120,7 @@ public class ReductionRulesChooser extends BasicCollapsiblePanel{
 			.addComponent(SNPanel, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)						
 		);
 		
-		this.getContentPane().setLayout(layout);
+		this.setLayout(layout);
 		
 	}