Some refactoring // cleanup

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

@@ -3,6 +3,7 @@ package de.hhu.ba.yoshikoWrapper;
 import java.util.Properties;
 
 import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.application.events.SetCurrentNetworkListener;
 import org.cytoscape.application.swing.CySwingApplication;
 import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.model.CyNetworkFactory;
@@ -88,6 +89,7 @@ public class CyActivator extends AbstractCyActivator {
 		registerService(context,netChangeListener, ColumnCreatedListener.class, new Properties());
 		registerService(context,netChangeListener, ColumnDeletedListener.class, new Properties());
 		registerService(context,netChangeListener, SessionLoadedListener.class, new Properties());
+		registerService(context,netChangeListener, SetCurrentNetworkListener.class, new Properties());
 
 	}
 

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

+package de.hhu.ba.yoshikoWrapper.core;
+
+import javax.swing.ImageIcon;
+
+public class GraphicsLoader {
+	private static ImageIcon yoshikoLogo;
+	private static ImageIcon yoshikoText;
+	
+	public static ImageIcon getLogo() {
+		if (yoshikoLogo == null) {
+			yoshikoLogo = new ImageIcon("/resources/graphics/YoshikoAlphaLogo.png");
+		}
+		return yoshikoLogo;
+	}
+	
+	public static ImageIcon getText() {
+		if (yoshikoLogo == null) {
+			yoshikoLogo = new ImageIcon("/graphics/YoshikoAlphaText.png");
+		}
+		return yoshikoText;
+	}
+}

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

 package de.hhu.ba.yoshikoWrapper.core;
 
+import org.cytoscape.application.events.SetCurrentNetworkEvent;
+import org.cytoscape.application.events.SetCurrentNetworkListener;
 import org.cytoscape.model.events.AddedEdgesEvent;
 import org.cytoscape.model.events.AddedEdgesListener;
 import org.cytoscape.model.events.ColumnCreatedEvent;
@@ -22,7 +24,8 @@ AddedEdgesListener,
 RemovedEdgesListener,
 ColumnCreatedListener,
 ColumnDeletedListener,
-SessionLoadedListener
+SessionLoadedListener,
+SetCurrentNetworkListener
 {
 	private ColumnMapper columnMapper;
 	
@@ -60,4 +63,9 @@ SessionLoadedListener
 		columnMapper.updateValues();
 	}
 
+	@Override
+	public void handleEvent(SetCurrentNetworkEvent e) {
+		columnMapper.updateValues();
+	}
+
 }

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

 package de.hhu.ba.yoshikoWrapper.gui;
 
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
+import java.awt.FlowLayout;
+
 import javax.swing.BoxLayout;
-import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 
@@ -18,43 +17,64 @@ public class ColumnMapper extends ComfortPanel{
 	
 
 	//Swing components
-	private JComboBox<CyColumn> editingCostMapper;
-	private JComboBox<CyColumn> permanentMapper;
-	private JComboBox<CyColumn> forbiddenMapper;
+	private final JComboBox<CyColumn> editingCostMapper;
+	private final JComboBox<CyColumn> permanentMapper;
+	private final JComboBox<CyColumn> forbiddenMapper;
 		
-	private JCheckBox useMappingCost;
-	private JCheckBox useMappingPerm;
-	private JCheckBox useMappingForb;
+	private final JCheckBox useMappingCost;
+	private final JCheckBox useMappingPerm;
+	private final JCheckBox useMappingForb;
 	
-	private JButton updateColumns;
+	private final ComfortPanel costGroup;
+	private final ComfortPanel permGroup;
+	private final ComfortPanel forbGroup;
 		
 	public ColumnMapper() {
 		this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
 
 		//SWING COMPONENTS
+		
+		//Combo-Boxes that map to the CyColumns
 		editingCostMapper = new JComboBox<CyColumn>();
 		permanentMapper = new JComboBox<CyColumn>();
 		forbiddenMapper = new JComboBox<CyColumn>();
 		
+		//Should only be enabled if the option is checked
+		editingCostMapper.setEnabled(false);
+		permanentMapper.setEnabled(false);
+		forbiddenMapper.setEnabled(false);
+
 		useMappingCost = new JCheckBox("Map modification costs");
 		useMappingPerm = new JCheckBox("Map edges as permanent");
 		useMappingForb = new JCheckBox("Map edges as forbidden");
 		
-		updateColumns = new JButton("Update Columns!");
+		useMappingCost.addActionListener(
+			new EnableWhenSelectedListener(useMappingCost, editingCostMapper)
+		);
+		useMappingPerm.addActionListener(
+			new EnableWhenSelectedListener(useMappingPerm, permanentMapper)
+			);
+		useMappingForb.addActionListener(
+			new EnableWhenSelectedListener(useMappingForb, forbiddenMapper)
+		);
 		
-		this.addAll(useMappingCost,editingCostMapper,useMappingPerm,permanentMapper,useMappingForb,forbiddenMapper,updateColumns);
-		//Initial call to get table values
-		updateValues();
-		//Add a focus listener to update values
-		updateColumns.addActionListener(new ActionListener() {
+		costGroup = new ComfortPanel();
+		permGroup = new ComfortPanel();
+		forbGroup = new ComfortPanel();
+		
+		costGroup.setLayout(new FlowLayout());
+		permGroup.setLayout(new FlowLayout());
+		forbGroup.setLayout(new FlowLayout());
+
+		costGroup.addAll(useMappingCost,editingCostMapper);
+		permGroup.addAll(useMappingPerm,permanentMapper);
+		forbGroup.addAll(useMappingForb,forbiddenMapper);
 
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				updateValues(); //shitty temporary solution
-			}
 		
-		});
+		this.addAll(costGroup,permGroup,forbGroup);
 		
+		//Initial call to get table values
+		updateValues();
 
 	}
 	

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

 package de.hhu.ba.yoshikoWrapper.gui;
 
+import java.awt.FlowLayout;
+
 import javax.swing.BorderFactory;
 import javax.swing.BoxLayout;
 import javax.swing.JLabel;
+import javax.swing.border.Border;
 import javax.swing.border.EtchedBorder;
 
 import org.cytoscape.model.CyColumn;
 
+import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+
 @SuppressWarnings("serial") //Will never be serialized
 public class EditCostPanel extends ComfortPanel {
 	
 	//SWING COMPONENTS
 	private ColumnMapper columnMapper;
+	
 	private DoubleInputField  icField;
 	private DoubleInputField dcField;
+	
 	private JLabel icLabel;
 	private JLabel dcLabel;
 	
@@ -25,23 +32,33 @@ public class EditCostPanel extends ComfortPanel {
 		this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
 		//Initialize components
 		columnMapper = new ColumnMapper();
+		
 		icField = new DoubleInputField(Double.NEGATIVE_INFINITY,0);
 		dcField = new DoubleInputField(0,Double.POSITIVE_INFINITY);
+		
 		icField.setText("-1.0");
+		icField.setToolTipText(LocalizationManager.get("icTooltip"));
 		dcField.setText("1.0");
-		icLabel = new JLabel("Insertion Cost:");
-		dcLabel = new JLabel("Deletion Cost:");
+		
+		icLabel = new JLabel(LocalizationManager.get("defaultInsertion"));
+		dcLabel = new JLabel(LocalizationManager.get("defaultDeletion"));
 		//Group the labels with their text fields
 		groupIC = new ComfortPanel();
 		groupDC = new ComfortPanel();
 		
+		groupIC.setLayout(new FlowLayout());
+		groupDC.setLayout(new FlowLayout());
+
 		groupIC.addAll(icLabel,icField);
 		groupDC.addAll(dcLabel,dcField);
 		
 		this.addAll(columnMapper,groupIC,groupDC);
 		
 		//Decoration/Visual
-		this.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
+		Border border = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
+		border = BorderFactory.createTitledBorder(border,LocalizationManager.get("editingCostPanel"));
+
+		this.setBorder(border);
 	}
 	
 	//SETTER / GETTER

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

+package de.hhu.ba.yoshikoWrapper.gui;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+
+
+public class EnableWhenSelectedListener implements ActionListener {
+	
+	private final JComponent component;
+	private final JCheckBox checkBox;
+
+	public EnableWhenSelectedListener(JCheckBox cb, JComponent c) {
+		this.component = c;
+		this.checkBox = cb;
+	}
+
+	@Override
+	public void actionPerformed(ActionEvent e) {
+		if (checkBox.isSelected()) {
+			component.setEnabled(true);
+		}
+		else {
+			component.setEnabled(false);
+		}
+	}
+
+}

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

 package de.hhu.ba.yoshikoWrapper.gui;
 
 import java.awt.Component;
+import java.awt.FlowLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Arrays;
 
-import javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
 import javax.swing.Icon;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
 import javax.swing.JOptionPane;
-import javax.swing.JRadioButton;
 
 import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.application.swing.CytoPanelName;
@@ -19,6 +21,7 @@ import org.cytoscape.work.TaskIterator;
 
 import de.hhu.ba.yoshikoWrapper.core.AlgorithmTask;
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
+import de.hhu.ba.yoshikoWrapper.core.GraphicsLoader;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
 
@@ -30,81 +33,101 @@ import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
 public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 
 	//SWING COMPONENTS
+	
+	private final YoshikoHeader header;
+	
+	/**
+	 * Swing is a bit special sometimes, so a panel is used to wrap the lang-switcher.
+	 * This prevents stretching of the component
+	 */
+	private final ComfortPanel langSwitcherWrapper;
 	private final LanguageSwitcher langSwitcher;
 	
 	private final LibraryPanel libraryPanel;
 
 	private final EditCostPanel ecPanel;
 	
-	private final ButtonGroup heuristicGroup;
-	private final JRadioButton useHeuristic;
-	private final JRadioButton useILP;
-	
-	private final TimeLimitSetter timeLimitSetter;
 	
 	private final ReductionRulesChooser reductionRulesChooser;
 
-	private final JCheckBox useTriangleCutsBox;
-	private final JCheckBox usePartitionCutsBox;
+	private final OperationModePanel opModePanel;
+	
+	private final JCheckBox showAdvancedOptions;
 	
 
-	private final SolutionNumberChooser solutionNumberChooser;
+	private final ArrayList<JComponent> advancedOptions;
 
 	/**
 	 * Main constructor, creates a new Panel and initializes subcomponents
-	 * @param solPanel 
 	 */
 	public MainPanel() {
 				
 		//SWING INIT
-		this.setLayout(new BoxLayout(this,BoxLayout.PAGE_AXIS));
+		this.setLayout(new FlowLayout());
 		
 		//Initialize Swing components
+		header = new YoshikoHeader();
+		
+		langSwitcherWrapper = new ComfortPanel();
 		langSwitcher = new LanguageSwitcher();
+		langSwitcherWrapper.addAll(new JLabel(LocalizationManager.get("switchLanguage")),langSwitcher);
+		langSwitcherWrapper.setLayout(new FlowLayout());
+		
 		libraryPanel = new LibraryPanel();
 		
 		ecPanel = new EditCostPanel();
 		
-		heuristicGroup = new ButtonGroup();
-		useILP = new JRadioButton("Use Integer Linear Programming");
-		useILP.setSelected(true);
-
-		useHeuristic = new JRadioButton("Use Heuristic");
-		heuristicGroup.add(useILP);
-		heuristicGroup.add(useHeuristic);
-		
-		solutionNumberChooser = new SolutionNumberChooser();
+		opModePanel = new OperationModePanel();
 		
 		reductionRulesChooser = new ReductionRulesChooser();
 		
-		timeLimitSetter = new TimeLimitSetter();
-				
-		useTriangleCutsBox = new JCheckBox("Use Triangle Cuts");
-		usePartitionCutsBox = new JCheckBox("Use Partition Cuts");
-
 		JButton runButton = new JButton("RUN");
 		runButton.addActionListener(buttonListener);
-		//Link time limit option to ILP
-		useILP.addActionListener(ilpHeuristicSwitch);
-		useHeuristic.addActionListener(ilpHeuristicSwitch);
+
+		
+		showAdvancedOptions = new JCheckBox(LocalizationManager.get("showAdvanced"));
+		showAdvancedOptions.addActionListener(toggleAdvancedOptionsListener);
 
 		this.addAll(
-				langSwitcher,
+				header,
+				langSwitcherWrapper,
+				showAdvancedOptions,
 				libraryPanel,
 				ecPanel,
-				useILP,
-				useHeuristic,
-				timeLimitSetter,
 				reductionRulesChooser,
-				useTriangleCutsBox,
-				usePartitionCutsBox,
-				solutionNumberChooser,
+				opModePanel,
 				runButton
 				);
 		
+		advancedOptions = new ArrayList<JComponent>();
+		//Manage all advanced components separately to enable toggling
+		advancedOptions.addAll(
+				Arrays.asList(
+						opModePanel,
+						reductionRulesChooser
+						)
+		);
+		
+		showAdvancedOptions(false);
+
 		this.setVisible(true);
 	}
 	
+	private ActionListener toggleAdvancedOptionsListener = new ActionListener() {
+
+		@Override
+		public void actionPerformed(ActionEvent e) {
+			showAdvancedOptions(showAdvancedOptions.isSelected());
+		}
+		
+	};
+	
+	private void showAdvancedOptions(boolean show) {
+		for (JComponent j : advancedOptions) {
+			j.setVisible(show);
+		}
+	}
+
 	/**
 	 * ButtonListener for the "Run" Button
 	 * Handles calling the algorithm and fetching/passing the arguments from swing components
@@ -116,7 +139,7 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 			if (YoshikoLoader.isLibraryLoaded()){
 				AbstractTask yoshiko = new AlgorithmTask(
 					CyCore.cy.getCurrentNetwork(),
-					timeLimitSetter.getTimeLimit(), 
+					opModePanel.getTimeLimit(),
 					ecPanel.getWeightColumn(),
 					ecPanel.getPermanentColumn(),
 					ecPanel.getForbiddenColumn(),
@@ -124,16 +147,15 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 					ecPanel.getDefaultDeletionCost(),
 					reductionRulesChooser.getBitMask(),
 					reductionRulesChooser.getMultFactor(),
-					useTriangleCutsBox.isSelected(),
-					usePartitionCutsBox.isSelected(), 
-					useHeuristic.isSelected(), 
-					solutionNumberChooser.getSolCount()
+					opModePanel.useTriangleCuts(),
+					opModePanel.usePartitionCuts(), 
+					opModePanel.useHeuristic(),
+					opModePanel.getSolCount()
 				);
 				CyCore.dialogTaskManager.execute(new TaskIterator(1,yoshiko));
 			}
 			else {
 				JOptionPane.showMessageDialog(	
-						
 					null,
 					LocalizationManager.get("noLibTitle"),
 					LocalizationManager.get("noLibMessage"),
@@ -143,21 +165,6 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 		}
 	};
 	
-	ActionListener ilpHeuristicSwitch = new ActionListener() {
-		@Override
-		public void actionPerformed(ActionEvent e) {
-			if (useILP.isSelected()) {
-				timeLimitSetter.setEnabled(true);
-			}
-			else {
-				timeLimitSetter.setEnabled(false);
-			}
-		}	
-	};
-	
-	public ColumnMapper getColumnMapper() {
-		return ecPanel.getColumnMapper();
-	}
 
 	
 	//GETTER / SETTER
@@ -179,10 +186,12 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 		return "Yoshiko";
 	}
 	
+	public ColumnMapper getColumnMapper() {
+		return ecPanel.getColumnMapper();
+	}
 	
 	public Icon getIcon() {
-		//TODO: 
-		return null;
+		return GraphicsLoader.getLogo();
 	}
 
 

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

+package de.hhu.ba.yoshikoWrapper.gui;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBox;
+import javax.swing.JRadioButton;
+import javax.swing.border.Border;
+import javax.swing.border.EtchedBorder;
+
+import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+
+@SuppressWarnings("serial")
+public class OperationModePanel extends ComfortPanel{
+	private final JRadioButton useHeuristic;
+	private final JRadioButton useILP;
+	private final TimeLimitSetter timeLimitSetter;
+	private final SolutionNumberChooser solutionNumberChooser;
+	private final JCheckBox useTriangleCutsBox;
+	private final JCheckBox usePartitionCutsBox;
+	
+	private final ButtonGroup heuristicGroup;
+
+	public OperationModePanel() {
+		
+		this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
+		
+		heuristicGroup = new ButtonGroup();
+		useILP = new JRadioButton("Use Integer Linear Programming");
+		useILP.setSelected(true);
+
+		useHeuristic = new JRadioButton("Use Heuristic");
+		heuristicGroup.add(useILP);
+		heuristicGroup.add(useHeuristic);
+		
+		solutionNumberChooser = new SolutionNumberChooser();
+		
+
+		timeLimitSetter = new TimeLimitSetter();
+				
+		useTriangleCutsBox = new JCheckBox("Use Triangle Cuts");
+		usePartitionCutsBox = new JCheckBox("Use Partition Cuts");
+		
+		//Link time limit option to ILP
+		useILP.addActionListener(ilpHeuristicSwitch);
+		useHeuristic.addActionListener(ilpHeuristicSwitch);
+		
+
+		this.addAll(useILP,useHeuristic,solutionNumberChooser,timeLimitSetter,useTriangleCutsBox,usePartitionCutsBox);
+		
+		Border border = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
+		border = BorderFactory.createTitledBorder(border,LocalizationManager.get("operationMode"));
+		this.setBorder(border);
+	}
+	
+	ActionListener ilpHeuristicSwitch = new ActionListener() {
+		@Override
+		public void actionPerformed(ActionEvent e) {
+			if (useILP.isSelected()) {
+				timeLimitSetter.setEnabled(true);
+				useTriangleCutsBox.setEnabled(true);
+				usePartitionCutsBox.setEnabled(true);
+				solutionNumberChooser.setEnabled(true);
+			}
+			else {
+				timeLimitSetter.setEnabled(false);
+				useTriangleCutsBox.setEnabled(false);
+				usePartitionCutsBox.setEnabled(false);
+				solutionNumberChooser.setEnabled(false);
+			}
+		}	
+	};
+	
+	//SETTER GETTER
+
+	public int getTimeLimit() {
+		return timeLimitSetter.getTimeLimit();
+	}
+
+	public boolean useTriangleCuts() {
+		return useTriangleCutsBox.isSelected();
+	}
+
+	public boolean usePartitionCuts() {
+		return usePartitionCutsBox.isSelected();
+	}
+
+	public boolean useHeuristic() {
+		return useHeuristic.isSelected();
+	}
+
+	public int getSolCount() {
+		return solutionNumberChooser.getSolCount();
+	}
+}

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

@@ -17,7 +17,11 @@ public class SolutionNumberChooser extends ComfortPanel {
 		numSolutionsSetter.setModel(new SpinnerNumberModel(1,1,Integer.MAX_VALUE,1));
 		label = new JLabel(LocalizationManager.get("nrSolutions"));
 		this.addAll(label, numSolutionsSetter);	 
+	}
 	
+	@Override
+	public void setEnabled(boolean enabled) {
+		numSolutionsSetter.setEnabled(enabled);
 	}
 
 	public int getSolCount() {

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

@@ -32,6 +32,7 @@ public class TimeLimitSetter extends ComfortPanel{
 		this.addAll(checkBox,numberField);
 	}
 	
+	@Override
 	public void setEnabled(boolean enabled) {
 		if (enabled) {
 			this.checkBox.setEnabled(enabled);

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

+package de.hhu.ba.yoshikoWrapper.gui;
+
+
+import javax.swing.BoxLayout;
+import javax.swing.JLabel;
+
+import de.hhu.ba.yoshikoWrapper.core.GraphicsLoader;
+
+@SuppressWarnings("serial")
+public class YoshikoHeader extends ComfortPanel {
+	
+	private JLabel logo;
+	private JLabel text;
+	
+	public YoshikoHeader() {
+		this.setLayout(new BoxLayout(this,BoxLayout.X_AXIS));
+
+		logo = new JLabel(GraphicsLoader.getLogo());
+		text = new JLabel(GraphicsLoader.getText());
+
+		this.addAll(logo,text);
+		
+	}
+}

src/main/resources/YoshikoStrings.properties

@@ -22,3 +22,10 @@ redRuleChooserTitle = Reduction Rules
 discardSolution = Discard
 createMetaGraph = Create Meta-Graph
 metaGraph = Meta Graph
+showAdvanced = Show advanced options
+editingCostPanel = Editing Costs
+defaultInsertion = Default insertion cost:
+defaultDeletion = Default deletion cost:
+switchLanguage = Plugin language:
+icTooltip = This value is used to determine what the algorithm pays when inserting an edge. Existing mappings overwrite this value. A higher value means that the algorithm is less likely to insert edges in order to generate a cluster.
+operationMode = Operation Mode
\ No newline at end of file

src/main/resources/graphics/package-info.java

+package graphics;
\ No newline at end of file