Added support for marking edges as permanent or forbidden (via mapping)

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

@@ -23,6 +23,8 @@ public class Core {
 	public static void performYoshiko(
 			int timeLimit,
 			CyColumn weightColumn,
+			CyColumn permanentColumn,
+			CyColumn forbiddenColumn,
 			double insertionCostDefault,
 			double deletionCostDefault
 			) 
@@ -45,6 +47,8 @@ public class Core {
 				currentNetwork,
 				nodeMap,
 				weightColumn,
+				permanentColumn, 
+				forbiddenColumn,
 				deletionCostDefault
 				);
 		
@@ -55,7 +59,6 @@ public class Core {
 		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);
@@ -63,6 +66,7 @@ public class Core {
 		for (long i=0;i<numberOfSolutions;i++) {
 			System.out.println("Processing solution "+(i+1)+" of "+numberOfSolutions);
 			String columnName = "YOSHIKO_SOLUTION_"+(i+1);
+			currentNetwork.getDefaultNodeTable().deleteColumn(columnName);
 			currentNetwork.getDefaultNodeTable().createColumn(columnName, String.class, false);
 			long numberOfClusters = LibraryInterface.ClusterEditingSolutions_getNumberOfClusters(solutions, i);
 			for (long k=0;k<numberOfClusters;k++) {

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

@@ -21,6 +21,8 @@ public class NetworkParser {
 			CyNetwork net,
 			NodeMap nodeMap,
 			CyColumn weightColumn,
+			CyColumn permanentColumn,
+			CyColumn forbiddenColumn,
 			double deletionCostDefault
 			) 
 	{
@@ -36,30 +38,53 @@ public class NetworkParser {
 			
 			//Loop over edges
 			for (CyEdge e : edges) {
+				
 				CyRow edgeEntry = net.getRow(e);
-				//Set to default cost
+				
+				//Parse editing costs
 				double weight = deletionCostDefault;
 				if (weightColumn != null){
+					System.out.println("Using column: "+weightColumn.getName());
 					try {
 						//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());
+						logger.debug("Column has type: "+weightType.getName());
+						if (weightType == Integer.class) {
+							weight = (int)edgeEntry.get(weightColumn.getName(), weightType);
+						}
+						else if(weightType == Double.class) {
 							weight = (double)edgeEntry.get(weightColumn.getName(), weightType);
 						}
+					}
 					catch(Exception ex) {
+						ex.printStackTrace();
 						//Invalid entry (no entry)
 						logger.info("No valid edit costs defined for: "+edgeEntry.get("name", String.class)+", falling back to default value!");
 					}
 				}
 				
+				//Parse Forbidden/Permanent markers
+				boolean forbidden = false;
+				boolean permanent = false;
+				if (permanentColumn != null) {
+					permanent = (boolean)edgeEntry.get(permanentColumn.getName(), boolean.class);
+				}
+				if (forbiddenColumn != null) {
+					forbidden = (boolean)edgeEntry.get(forbiddenColumn.getName(), boolean.class);
+				}
+
 
 				logger.debug("Found Edge: "+edgeEntry.get("name", String.class)+ " with weight:"+weight);
 				
-				LibraryInterface.LibraryInput_addEdge(generatedInput,
+				LibraryInterface.LibraryInput_addEdge(
+						generatedInput,
 						nodeMap.get(e.getSource()),
-						nodeMap.get(e.getTarget())
-						, weight);
+						nodeMap.get(e.getTarget()),
+						weight,
+						permanent,
+						forbidden
+						);
 				
 			}
 		}

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

@@ -10,35 +10,46 @@ 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;
 
 @SuppressWarnings("serial") //will never be serialized
-public class ModificationCostMapper extends ComfortPanel{
+public class ColumnMapper extends ComfortPanel{
 	
 	//Symbolic links
 	private CyApplicationManager cy;
 	
 	//Swing components
-	private JComboBox<CyColumn> tableFields;
-	private JCheckBox useMapping;
+	private JComboBox<CyColumn> editingCostMapper;
+	private JComboBox<CyColumn> permanentMapper;
+	private JComboBox<CyColumn> forbiddenMapper;
 		
-	public ModificationCostMapper() {
-		tableFields = new JComboBox<CyColumn>();
-		useMapping = new JCheckBox("Map modification costs");
-		useMapping.setToolTipText(
+	private JCheckBox useMappingCost;
+	private JCheckBox useMappingPerm;
+	private JCheckBox useMappingForb;
+	
+	public ColumnMapper() {
+		cy = Core.getApplicationManager();
+
+		//SWING COMPONENTS
+		editingCostMapper = new JComboBox<CyColumn>();
+		permanentMapper = new JComboBox<CyColumn>();
+		forbiddenMapper = new JComboBox<CyColumn>();
+
+		useMappingCost = new JCheckBox("Map modification costs");
+		useMappingPerm = new JCheckBox("Map edges as permanent");
+		useMappingForb = new JCheckBox("Map edges as forbidden");
+		
+		useMappingCost.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"
 				);
-		cy = Core.getApplicationManager();
-		this.addAll(useMapping,tableFields);
+		this.addAll(useMappingCost,editingCostMapper,useMappingPerm,permanentMapper,useMappingForb,forbiddenMapper);
 		//Initial call to get table values
 		updateValues();
 		//Add a focus listener to update values
-		tableFields.addFocusListener (new FocusListener() {
+		this.addFocusListener (new FocusListener() {
 
 			@Override
 			public void focusGained(FocusEvent e) {
@@ -53,22 +64,56 @@ public class ModificationCostMapper extends ComfortPanel{
 	}
 	
 	public void updateValues() {
-		//Clear entries
-		tableFields.removeAllItems();
+		
 		CyNetwork net = cy.getCurrentNetwork();
+
 		if (net != null) { //Check if a network is loaded
+	
+			//Clear entries
+			editingCostMapper.removeAllItems();
 			for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
 				//Only add columns with numeric values
 				if (c.getType() == Integer.class || c.getType() == Double.class) {
-					tableFields.addItem(c);
+					editingCostMapper.addItem(c);
+				}
+			}
+			
+			forbiddenMapper.removeAllItems();
+			for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
+				//Only add columns with boolean values
+				if (c.getType() == Boolean.class) {
+					editingCostMapper.addItem(c);
+				}
+			}
+			
+			permanentMapper.removeAllItems();
+			for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
+				//Only add columns with boolean values
+				if (c.getType() == Boolean.class) {
+					permanentMapper.addItem(c);
+				}
+			}
+		
+		}
 	}
+	
+	public CyColumn getEditingCostColumn() {
+		if (useMappingCost.isSelected()) {
+			return editingCostMapper.getItemAt(editingCostMapper.getSelectedIndex());
 		}
+		return null;
 	}
+	
+	public CyColumn getForbiddenColumn() {
+		if (useMappingForb.isSelected()) {
+			return forbiddenMapper.getItemAt(forbiddenMapper.getSelectedIndex());
+		}
+		return null;
 	}
 	
-	public CyColumn getValue() {
-		if (useMapping.isSelected()) {
-			return tableFields.getItemAt(tableFields.getSelectedIndex());
+	public CyColumn getPermanentColumn() {
+		if (useMappingPerm.isSelected()) {
+			return permanentMapper.getItemAt(permanentMapper.getSelectedIndex());
 		}
 		return null;
 	}

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

@@ -10,16 +10,15 @@ import org.cytoscape.model.CyColumn;
 public class EditCostPanel extends ComfortPanel {
 	
 	//SWING COMPONENTS
-	private ModificationCostMapper modCostMapper;
+	private ColumnMapper columnMapper;
 	private DoubleInputField  icField;
 	private DoubleInputField dcField;
 	private JLabel icLabel;
 	private JLabel dcLabel;
 	
 	public EditCostPanel() {
-		
 		//Initialize components
-		modCostMapper = new ModificationCostMapper();
+		columnMapper = new ColumnMapper();
 		icField = new DoubleInputField(Double.NEGATIVE_INFINITY,0);
 		dcField = new DoubleInputField(0,Double.POSITIVE_INFINITY);
 		icField.setText("-1.0");
@@ -28,7 +27,7 @@ public class EditCostPanel extends ComfortPanel {
 		dcLabel = new JLabel("Deletion Cost:");
 		icLabel.setLabelFor(icField);
 		dcLabel.setLabelFor(dcField);
-		this.addAll(modCostMapper,icField,dcField,icLabel,dcLabel);
+		this.addAll(columnMapper,icField,dcField,icLabel,dcLabel);
 		
 		//
 		this.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
@@ -37,7 +36,15 @@ public class EditCostPanel extends ComfortPanel {
 	//SETTER / GETTER
 
 	public CyColumn getWeightColumn() {
-		return modCostMapper.getValue();
+		return columnMapper.getEditingCostColumn();
+	}
+	
+	public CyColumn getPermanentColumn() {
+		return columnMapper.getPermanentColumn();
+	}
+	
+	public CyColumn getForbiddenColumn() {
+		return columnMapper.getForbiddenColumn();
 	}
 
 	public double getDefaultInsertionCost() {
@@ -48,4 +55,6 @@ public class EditCostPanel extends ComfortPanel {
 		return dcField.getValueAsDouble();
 	}
 
+
+	
 }

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

 package de.hhu.ba.yoshikoWrapper.gui;
 
+import java.text.DecimalFormat;
 import java.text.NumberFormat;
 
 import javax.swing.text.NumberFormatter;
@@ -19,7 +20,7 @@ public class FormatHelper {
 	}
 
 	public static NumberFormatter getDoubleFormatter(double minValue, double maxValue) {
-		NumberFormat format = NumberFormat.getInstance();
+		NumberFormat format = DecimalFormat.getInstance();
 	    NumberFormatter formatter = new NumberFormatter(format);
 	    formatter.setValueClass(Double.class);
 	    formatter.setMinimum(minValue);

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

@@ -100,6 +100,8 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 					Core.performYoshiko(
 							timeLimitSetter.getTimeLimit(), 
 							ecPanel.getWeightColumn(),
+							ecPanel.getPermanentColumn(),
+							ecPanel.getForbiddenColumn(),
 							ecPanel.getDefaultInsertionCost(),
 							ecPanel.getDefaultDeletionCost()
 							);

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

@@ -2,6 +2,7 @@ package de.hhu.ba.yoshikoWrapper.gui;
 
 import java.awt.Component;
 
+import javax.swing.BoxLayout;
 import javax.swing.JCheckBox;
 
 @SuppressWarnings("serial")
@@ -15,6 +16,7 @@ public class ReductionRulesChooser extends ComfortPanel{
 	private JCheckBox useSNRule;
 	
 	public ReductionRulesChooser() {
+		this.setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
 		//Initialize subcomponents
 		useCRule = new JCheckBox("Use Clique Rule");
 		useCCRule = new JCheckBox("Use Critical-Clique Rule");