Some more work on the GUI

pom.xml

@@ -24,8 +24,8 @@
 				<artifactId>maven-compiler-plugin</artifactId>
 				<version>3.0</version>
 				<configuration>
-					<source>1.6</source>
-					<target>1.6</target>
+					<source>1.8</source>
+					<target>1.8</target>
 					<optimize>true</optimize>
 					<showWarnings>true</showWarnings>
 					<showDeprecation>true</showDeprecation>

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

@@ -2,9 +2,12 @@ package de.hhu.ba.yoshikoWrapper.core;
 //TODO: ADD LOGGER SYSTEM
 
 import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.model.CyColumn;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
+import org.slf4j.Logger;
 
+import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
 import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
 import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_std__vectorT_int_t;
 import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_yskInput__LibraryInput;
@@ -12,22 +15,47 @@ import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_ysk__ClusterEditingSolutions;
 
 public class Core {
 	
-	private static CyApplicationManager cy;
 	
+	//Symbolic links
+	private static CyApplicationManager cy;
+	private static Logger logger = YoshikoLogger.getInstance().getLogger();
 
-	public static void performYoshiko(int timeLimit) {
+	public static void performYoshiko(
+			int timeLimit,
+			CyColumn weightColumn,
+			double insertionCostDefault,
+			double deletionCostDefault
+			) 
+	{
+		//Get current network
 		CyNetwork currentNetwork = cy.getCurrentNetwork();
 		if (currentNetwork == null) {
-			//TODO
+			logger.warn("There is no network loaded. You need to load a network first!");
 			return;
 		}
 		
+		//Set time limit
 		LibraryInterface.setTimeLimit(timeLimit);
 
+		//Create a node map to identify nodes and eges in the solution
 		NodeMap nodeMap  = new NodeMap(currentNetwork);
 
-		SWIGTYPE_p_yskInput__LibraryInput input = NetworkParser.parseNetwork(currentNetwork,nodeMap);
+		//Generate an input instance from the network
+		SWIGTYPE_p_yskInput__LibraryInput input = NetworkParser.parseNetwork(
+				currentNetwork,
+				nodeMap,
+				weightColumn,
+				deletionCostDefault
+				);
+		
+		//Set the default value for insertion cost
+		LibraryInterface.LibraryInput_setDefaultInsertionCost(input, insertionCostDefault);
+
+		//Call Yoshiko <<< Algorithm is performed here
 		SWIGTYPE_p_ysk__ClusterEditingSolutions solutions = LibraryInterface.processLibraryInput(input);
+		
+		
+		
 		long numberOfSolutions = LibraryInterface.ClusterEditingSolutions_getNumberOfSolutions(solutions);
 		System.out.println("Found: "+numberOfSolutions+" solutions!");
 		double modificationCost = LibraryInterface.ClusterEditingSolutions_getTotalCost(solutions);

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

@@ -2,35 +2,54 @@ package de.hhu.ba.yoshikoWrapper.core;
 
 import java.util.List;
 
+import org.cytoscape.model.CyColumn;
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyRow;
+import org.slf4j.Logger;
 
+import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
 import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
 import de.hhu.ba.yoshikoWrapper.swig.SWIGTYPE_p_yskInput__LibraryInput;
 
 public class NetworkParser {
 	
-	//**TODO MAKE DYNAMIC
-	private static String weightIndex = "Weight";
-	
-
-	
-	
-	public static SWIGTYPE_p_yskInput__LibraryInput parseNetwork(CyNetwork net,NodeMap nodeMap) {
+	//Symbolic Links
+	private static Logger logger = YoshikoLogger.getInstance().getLogger();
+
+	public static SWIGTYPE_p_yskInput__LibraryInput parseNetwork(
+			CyNetwork net,
+			NodeMap nodeMap,
+			CyColumn weightColumn,
+			double deletionCostDefault
+			) 
+	{
+		//Create an empty instance / fetch C++ object pointer
 		SWIGTYPE_p_yskInput__LibraryInput generatedInput = LibraryInterface.new_LibraryInput();
 		if (net != null){
+			//Create an empty full graph with a given size
 			LibraryInterface.LibraryInput_setSize(generatedInput,  net.getNodeCount());
+			//Fetch edges
 			List<CyEdge> edges = net.getEdgeList();
-			Class<?> weightType = net.getDefaultEdgeTable().getColumn(weightIndex).getType();
-			System.out.println("Column has type:"+weightType.getName());
+			
+			//Find out if the weights are double or int
+			@SuppressWarnings("unchecked")
+			Class<? extends Number> weightType = (Class<? extends Number>) weightColumn.getType();
+			
+			logger.info("Column has type: "+weightType.getName());
+			//Loop over edges
 			for (CyEdge e : edges) {
 				CyRow edgeEntry = net.getRow(e);
-				double weight = 0.0;
-				if (weightType == Integer.class) {
-					weight = (double)edgeEntry.get(weightIndex, Integer.class);
+				double weight = deletionCostDefault;
+				try {
+					weight = (double)edgeEntry.get(weightColumn.getName(), weightType);
 				}
-				System.out.println("Found Edge: "+edgeEntry.get("name", String.class)+ "with weight:"+weight);
+				catch(Exception ex) {
+					//Invalid entry (no entry)
+					logger.info("No valid edit costs defined for: "+edgeEntry.get("name", String.class)+", falling back to default value!");
+				}
+
+				logger.debug("Found Edge: "+edgeEntry.get("name", String.class)+ "with weight:"+weight);
 				
 				LibraryInterface.LibraryInput_addEdge(generatedInput,
 						nodeMap.get(e.getSource()),

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

@@ -13,7 +13,7 @@ public class DoubleInputField extends JFormattedTextField{
 		this.setColumns(8);
 	}
 
-	public int getTimeLimit() {
-		return Integer.parseInt(getText());
+	public double getValueAsDouble() {
+		return Double.parseDouble(getText());
 	}
 }

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

 package de.hhu.ba.yoshikoWrapper.gui;
 
+import javax.swing.BorderFactory;
 import javax.swing.JLabel;
+import javax.swing.border.EtchedBorder;
+
+import org.cytoscape.model.CyColumn;
 
 @SuppressWarnings("serial") //Will never be serialized
 public class EditCostPanel extends ComfortPanel {
@@ -13,14 +17,35 @@ public class EditCostPanel extends ComfortPanel {
 	private JLabel dcLabel;
 	
 	public EditCostPanel() {
+		
+		//Initialize components
 		modCostMapper = new ModificationCostMapper();
-		icField = new DoubleInputField(0,Double.NEGATIVE_INFINITY);
+		icField = new DoubleInputField(Double.NEGATIVE_INFINITY,0);
 		dcField = new DoubleInputField(0,Double.POSITIVE_INFINITY);
+		icField.setText("-1.0");
+		dcField.setText("1.0");
 		icLabel = new JLabel("Insertion Cost:");
 		dcLabel = new JLabel("Deletion Cost:");
 		icLabel.setLabelFor(icField);
 		dcLabel.setLabelFor(dcField);
 		this.addAll(modCostMapper,icField,dcField,icLabel,dcLabel);
+		
+		//
+		this.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
+	}
+	
+	//SETTER / GETTER
+
+	public CyColumn getWeightColumn() {
+		return modCostMapper.getValue();
+	}
+
+	public double getDefaultInsertionCost() {
+		return icField.getValueAsDouble();
+	}
+	
+	public double getDefaultDeletionCost() {
+		return dcField.getValueAsDouble();
 	}
 	
 }

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

@@ -21,7 +21,7 @@ public class FormatHelper {
 	public static NumberFormatter getDoubleFormatter(double minValue, double maxValue) {
 		NumberFormat format = NumberFormat.getInstance();
 	    NumberFormatter formatter = new NumberFormatter(format);
-	    formatter.setValueClass(Integer.class);
+	    formatter.setValueClass(Double.class);
 	    formatter.setMinimum(minValue);
 	    formatter.setMaximum(maxValue);
 	    formatter.setAllowsInvalid(false);

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

@@ -97,7 +97,12 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 			@Override
 			public void actionPerformed(ActionEvent e) {
 				if (YoshikoLoader.isLibraryLoaded()){
-					Core.performYoshiko(timeLimitSetter.getTimeLimit());
+					Core.performYoshiko(
+							timeLimitSetter.getTimeLimit(), 
+							ecPanel.getWeightColumn(),
+							ecPanel.getDefaultInsertionCost(),
+							ecPanel.getDefaultDeletionCost()
+							);
 
 				}
 			}

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

@@ -10,6 +10,8 @@ import javax.swing.JComboBox;
 import org.cytoscape.application.CyApplicationManager;
 import org.cytoscape.model.CyColumn;
 import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.events.ColumnCreatedEvent;
+import org.cytoscape.model.events.ColumnDeletedListener;
 
 import de.hhu.ba.yoshikoWrapper.core.Core;
 
@@ -36,7 +38,6 @@ public class ModificationCostMapper extends ComfortPanel {
 		//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
 		tableFields.addFocusListener (new FocusListener() {
 
 			@Override
@@ -57,10 +58,13 @@ public class ModificationCostMapper extends ComfortPanel {
 		CyNetwork net = cy.getCurrentNetwork();
 		if (net != null) { //Check if a network is loaded
 			for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
+				//Only add columns with numeric values
+				if (c.getType() == Integer.class || c.getType() == Double.class) {
 					tableFields.addItem(c);
 				}
 			}
 		}
+	}
 	
 	public CyColumn getValue() {
 		if (useMapping.isSelected()) {

src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterface.java

@@ -93,10 +93,6 @@ public class LibraryInterface {
     LibraryInterfaceJNI.delete_LibraryInput(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self));
   }
 
-  public static void LibraryInput_setSize(SWIGTYPE_p_yskInput__LibraryInput self, long id) {
-    LibraryInterfaceJNI.LibraryInput_setSize(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self), id);
-  }
-
   public static void LibraryInput_addEdge(SWIGTYPE_p_yskInput__LibraryInput self, long sourceID, long targetID, double cost) {
     LibraryInterfaceJNI.LibraryInput_addEdge__SWIG_0(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self), sourceID, targetID, cost);
   }
@@ -105,6 +101,14 @@ public class LibraryInterface {
     LibraryInterfaceJNI.LibraryInput_addEdge__SWIG_1(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self), sourceID, targetID, cost, permanent, forbidden);
   }
 
+  public static void LibraryInput_setSize(SWIGTYPE_p_yskInput__LibraryInput self, long id) {
+    LibraryInterfaceJNI.LibraryInput_setSize(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self), id);
+  }
+
+  public static void LibraryInput_setDefaultInsertionCost(SWIGTYPE_p_yskInput__LibraryInput self, double cost) {
+    LibraryInterfaceJNI.LibraryInput_setDefaultInsertionCost(SWIGTYPE_p_yskInput__LibraryInput.getCPtr(self), cost);
+  }
+
   public static String getVersionString() {
     return LibraryInterfaceJNI.getVersionString();
   }

src/main/java/de/hhu/ba/yoshikoWrapper/swig/LibraryInterfaceJNI.java

@@ -29,9 +29,10 @@ public class LibraryInterfaceJNI {
   public final static native void delete_ClusterEditingSolutions(long jarg1);
   public final static native long new_LibraryInput();
   public final static native void delete_LibraryInput(long jarg1);
-  public final static native void LibraryInput_setSize(long jarg1, long jarg2);
   public final static native void LibraryInput_addEdge__SWIG_0(long jarg1, long jarg2, long jarg3, double jarg4);
   public final static native void LibraryInput_addEdge__SWIG_1(long jarg1, long jarg2, long jarg3, double jarg4, boolean jarg5, boolean jarg6);
+  public final static native void LibraryInput_setSize(long jarg1, long jarg2);
+  public final static native void LibraryInput_setDefaultInsertionCost(long jarg1, double jarg2);
   public final static native String getVersionString();
   public final static native long processLibraryInput(long jarg1);
   public final static native void setTimeLimit(int jarg1);