Some work on wrapping parameters

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

@@ -38,7 +38,7 @@ public class CyActivator extends AbstractCyActivator {
 		}
 		
 		CyApplicationManager cyApplicationManager = getService(context, CyApplicationManager.class);
-		Core.registerApplicationManager(cyApplicationManager);
+		Core.setApplicationManager(cyApplicationManager);
 		
 		CySwingApplication cytoscapeDesktopService = getService(context,CySwingApplication.class);
 		

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

@@ -14,9 +14,6 @@ public class Core {
 	
 	private static CyApplicationManager cy;
 	
-	public static void registerApplicationManager(CyApplicationManager cyApplicationManager) {
-		cy = cyApplicationManager;
-	}
 
 	public static void performYoshiko(int timeLimit) {
 		CyNetwork currentNetwork = cy.getCurrentNetwork();
@@ -60,4 +57,15 @@ public class Core {
 		LibraryInterface.delete_LibraryInput(input);		
 	}
 	
+	
+	//SETTER / GETTER METHODS
+	
+	public static void setApplicationManager(CyApplicationManager cyApplicationManager) {
+		cy = cyApplicationManager;
+	}
+	
+	public static CyNetwork getCurrentNetwork() {
+		return cy.getCurrentNetwork();
+	}
+
 }

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

@@ -2,17 +2,23 @@ package de.hhu.ba.yoshikoWrapper.core;
 
 import java.io.File;
 
+import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
+
 public class YoshikoLoader {
 	
-	private static boolean libraryLoaded;
 	private static ConfigurationManager cm;
 	
 	public static void loadLibrary(String libPath) {
+		//TODO: Java has no method to unload a native library :( This means, that reloading the library file on the fly is not possible
+		
+		//Check 1: Library is already loaded
 		
-		if (libraryLoaded) {
+		if (isLibraryLoaded()) {
+			System.out.println("Library is already loaded!");
 			return;
 		}
 		
+		//Attempt to load from a previously stored path
 		File f = new File (libPath);
 		if (!f.exists()) {
 			System.out.println("Could not find a previously saved yoshiko library path, needs to be set manually!");
@@ -24,7 +30,6 @@ public class YoshikoLoader {
 			System.load(libPath);
 			//update cfg
 			cm.getProperties().setProperty("pathToYoshiko", libPath);
-			libraryLoaded = true;
 		}
 		catch(Exception e) {
 			e.printStackTrace();
@@ -34,7 +39,9 @@ public class YoshikoLoader {
 	//SETTER / GETTER
 	
 	public static boolean isLibraryLoaded() {
-		return libraryLoaded;
+
+		if (LibraryInterface.getVersionString() != null) return true;
+		return false;
 	}
 
 

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

+package de.hhu.ba.yoshikoWrapper.gui;
+
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+
+@SuppressWarnings("serial")
+public class ComfortPanel extends JPanel {
+	
+	/**
+	 * Comfort Function
+	 * @param components The components that are to be added to this panel
+	 */
+	protected void addAll(JComponent... components) {
+		for (JComponent c : components){
+			this.add(c);
+		}
+		
+	}
+	
+}

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

+package de.hhu.ba.yoshikoWrapper.gui;
+
+import javax.swing.JFormattedTextField;
+
+/**
+ * Provides a more strict input field that only accepts double
+ */
+@SuppressWarnings("serial")
+public class DoubleInputField extends JFormattedTextField{
+
+	public DoubleInputField() {
+		super(FormatHelper.getDoubleFormatter());
+		this.setColumns(8);
+	}
+
+	public int getTimeLimit() {
+		return Integer.parseInt(getText());
+	}
+}

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

@@ -18,4 +18,16 @@ public class FormatHelper {
 	    return formatter;
 	}
 
+	public static NumberFormatter getDoubleFormatter() {
+		NumberFormat format = NumberFormat.getInstance();
+	    NumberFormatter formatter = new NumberFormatter(format);
+	    formatter.setValueClass(Integer.class);
+	    formatter.setMinimum(0);
+	    formatter.setMaximum(Integer.MAX_VALUE);
+	    formatter.setAllowsInvalid(false);
+	    formatter.setCommitsOnValidEdit(true);
+	    
+	    return formatter;
+	}
+
 }

src/main/java/de/hhu/ba/yoshikoWrapper/gui/NumberInputField.java → src/main/java/de/hhu/ba/yoshikoWrapper/gui/IntegerInputField.java

@@ -5,16 +5,12 @@ import javax.swing.JFormattedTextField;
 /**
  * Provides a more strict input field that only accepts integers
  */
-public class NumberInputField extends JFormattedTextField{
+@SuppressWarnings("serial")
+public class IntegerInputField extends JFormattedTextField{
 
-	/**
-	 * SerialVersionUID
-	 */
-	private static final long serialVersionUID = -1144461027491991050L;
-	
-	
-	public NumberInputField() {
+	public IntegerInputField() {
 		super(FormatHelper.getIntegerFormatter());
+		this.setColumns(8);
 	}
 
 	public int getTimeLimit() {

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

@@ -5,11 +5,14 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
 import javax.swing.BoxLayout;
+import javax.swing.ButtonGroup;
 import javax.swing.Icon;
 import javax.swing.JButton;
+import javax.swing.JCheckBox;
 import javax.swing.JFileChooser;
 import javax.swing.JLabel;
-import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+
 import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.application.swing.CytoPanelName;
 import de.hhu.ba.yoshikoWrapper.core.Core;
@@ -20,36 +23,58 @@ import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
  * @author Philipp Spohr, Aug 6, 2017
  *
  */
-public class MainPanel extends JPanel implements CytoPanelComponent {
-
-	/**
-	 * Unique identifier for serialization
-	 */
-	private static final long serialVersionUID = 6214827920591046457L;
+@SuppressWarnings("serial")
+public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 
 	//SYMBOLIC LINKS
 	private MainPanel self = this; //for lambda function references
-	//SWING COMPONENTS
 	
+	//SWING COMPONENTS
 	private LibStatusPanel libStatusPanel;
 	private JButton searchLibButton;
 	private JLabel yoshikoVersionLabel;
+	
+	private ModificationCostMapper modCostMapper;
+	
+	private ButtonGroup heuristicGroup;
+	private JRadioButton useHeuristic;
+	private JRadioButton useILP;
+	
 	private TimeLimitSetter timeLimitSetter;
 	
+	private ReductionRulesChooser reductionRulesChooser;
+	
+	private JCheckBox useTriangleCutsBox;
+	private JCheckBox usePartitionCutsBox;
+	
+
+
 	/**
 	 * Main constructor, creates a new Panel and initializes subcomponents
 	 */
 	public MainPanel() {
 		
-		
 		this.setLayout(new BoxLayout(this,BoxLayout.PAGE_AXIS));
-		//SWING COMPONENT INITIALIZATION
 		
+		//SWING COMPONENT INITIALIZATION
 		libStatusPanel = new LibStatusPanel();
 		libStatusPanel.setStyle(YoshikoLoader.isLibraryLoaded());
-		this.add(libStatusPanel);
 		
-		searchLibButton = new JButton("SHOW YOSHIKO LIB");
+		yoshikoVersionLabel = new JLabel("YOSHIKO VERSION");
+		if (LibraryInterface.getVersionString() != null) {
+			yoshikoVersionLabel.setText(LibraryInterface.getVersionString());
+		}
+		searchLibButton = new JButton("POINT TO LIB");
+
+		modCostMapper = new ModificationCostMapper();
+		
+		heuristicGroup = new ButtonGroup();
+		useILP = new JRadioButton("Use Integer Linear Programming");
+		useILP.setSelected(true);
+		useHeuristic = new JRadioButton("Use Heuristic");
+		heuristicGroup.add(useILP);
+		heuristicGroup.add(useHeuristic);
+		
 		searchLibButton.addActionListener(new ActionListener() {
 
 			@Override
@@ -64,7 +89,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 			}
 			
 		});
-		this.add(searchLibButton);
 
 		JButton runButton = new JButton("RUN");
 		runButton.addActionListener(new ActionListener() {
@@ -79,20 +103,36 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 			}
 			
 		});
-		this.add(runButton);
 
+		reductionRulesChooser = new ReductionRulesChooser();
 		
 		timeLimitSetter = new TimeLimitSetter();
-		this.add(timeLimitSetter);
 		
+		useTriangleCutsBox = new JCheckBox("Use Triangle Cuts");
+		usePartitionCutsBox = new JCheckBox("Use Partition Cuts");
 
-		yoshikoVersionLabel = new JLabel("YOSHIKO VERSION");
-		this.add(yoshikoVersionLabel);
+		
+		this.addAll(
+				libStatusPanel,
+				yoshikoVersionLabel,
+				searchLibButton,
+				modCostMapper,
+				useILP,
+				useHeuristic,
+				timeLimitSetter,
+				reductionRulesChooser,
+				useTriangleCutsBox,
+				usePartitionCutsBox,
+				runButton
+				);
 		
 		this.setVisible(true);
 	}
 
 	
+	
+	//GETTER / SETTER
+
 	public Component getComponent() {
 		return this;
 	}

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

+package de.hhu.ba.yoshikoWrapper.gui;
+
+
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JPanel;
+
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyNetwork;
+
+import de.hhu.ba.yoshikoWrapper.core.Core;
+
+@SuppressWarnings("serial") //will never be serialized
+public class ModificationCostMapper extends JPanel {
+	
+	//Symbolic links
+	private CyNetwork net;
+	
+	//Swing components
+	private JComboBox<CyColumn> tableFields;
+	private JCheckBox useMapping;
+	
+	public ModificationCostMapper() {
+		tableFields = new JComboBox<CyColumn>();
+		useMapping = new JCheckBox("Map modification costs");
+		useMapping.setToolTipText(
+				"When you use this value you can assign a column in the edge table to represent the modification costs that are to be paid for deleting an edge."
+				+"You can also assign negative values if you have a complete graph to represent insertion costs."
+				+"Note: Any missing values are assumed to be the default values"
+				);
+		net = Core.getCurrentNetwork();
+		//Initial call to get table values
+		updateValues();
+		//Add a focus listener to update values
+		//TODO: This might be a bit inelegant but there is no way to get a callback from CS when a table changes values
+		this.addFocusListener(new FocusListener() {
+
+			@Override
+			public void focusGained(FocusEvent e) {
+				updateValues();
+			}
+
+			@Override
+			public void focusLost(FocusEvent e) {}
+			
+		});
+
+	}
+	
+	public void updateValues() {
+		//Clear entries
+		tableFields.removeAllItems();
+		for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
+			tableFields.addItem(c);
+		}
+	}
+	
+	public CyColumn getValue() {
+		if (useMapping.isSelected()) {
+			return tableFields.getItemAt(tableFields.getSelectedIndex());
+		}
+		return null;
+	}
+
+}

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

+package de.hhu.ba.yoshikoWrapper.gui;
+
+import java.awt.Component;
+
+import javax.swing.JCheckBox;
+
+@SuppressWarnings("serial")
+public class ReductionRulesChooser extends ComfortPanel{
+
+	private JCheckBox useCRule;
+	private JCheckBox useCCRule;
+	private JCheckBox useACRule;
+	private JCheckBox useHERule;
+	private JCheckBox usePDRRule;
+	private JCheckBox useSNRule;
+	
+	public ReductionRulesChooser() {
+		//Initialize subcomponents
+		useCRule = new JCheckBox("Use Clique Rule");
+		useCCRule = new JCheckBox("Use Critical-Clique Rule");
+		useACRule = new JCheckBox("Use Almost-Clique Rule");
+		useHERule = new JCheckBox("Use Heavy-Edge 3 in 1 Rule");
+		usePDRRule = new JCheckBox("Use Parameter Dependent Reduction Rule");
+		useSNRule = new JCheckBox("Use Similar Neighborhood Rule");
+		
+		this.addAll(
+				useCRule,
+				useCCRule,
+				useACRule,
+				useHERule,
+				usePDRRule,
+				useSNRule
+				);
+		//By default all reduction rules should be applied
+		for (Component c :this.getComponents()) {
+			((JCheckBox)c).setSelected(true);
+		}
+	}
+	
+	
+	/** Creates a 6 Bit bitmask representing the currently selected choice of reduction rules.
+	 * @return
+	 */
+	public String getBitMask() {
+		String ret = "";
+		ret += (useCRule.isSelected() ? "1" : "0");
+		ret += (useCCRule.isSelected() ? "1" : "0");
+		ret += (useACRule.isSelected() ? "1" : "0");
+		ret += (useHERule.isSelected() ? "1" : "0");
+		ret += (usePDRRule.isSelected() ? "1" : "0");
+		ret += (useSNRule.isSelected() ? "1" : "0");
+		return ret;
+	}
+}

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

@@ -4,21 +4,16 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
 import javax.swing.JCheckBox;
-import javax.swing.JPanel;
 
-public class TimeLimitSetter extends JPanel{
-	
-	/**
-	 * Unique UID for serialization
-	 */
-	private static final long serialVersionUID = 6617497954814566334L;
+@SuppressWarnings("serial")
+public class TimeLimitSetter extends ComfortPanel{
 
 	private JCheckBox checkBox;
-	private NumberInputField numberField;
+	private IntegerInputField numberField;
 	
 	public TimeLimitSetter() {
 		checkBox = new JCheckBox("Use time limit (s):");
-		numberField = new NumberInputField();
+		numberField = new IntegerInputField();
 		numberField.setEnabled(false); //By default time limit is turned off
 		checkBox.addActionListener(
 				new ActionListener() {
@@ -31,8 +26,7 @@ public class TimeLimitSetter extends JPanel{
 				}
 				);
 		//REGISTER COMPONENTS
-		this.add(checkBox);
-		this.add(numberField);
+		this.addAll(checkBox,numberField);
 	}
 	
 	public int getTimeLimit() {

src/main/java/de/hhu/ba/yoshikoWrapper/gui/package-info.java

-/**
- * 
- */
-/**
- * @author Philipp Spohr, Aug 6, 2017
+/**This package contains all Swing extensions and components (frontend)
  *
  */
 package de.hhu.ba.yoshikoWrapper.gui;
\ No newline at end of file