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pom.xml

@@ -157,6 +157,11 @@
 			<artifactId>swing-util-api</artifactId>
 			<version>${cytoscape.api.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>group-api</artifactId>
+			<version>${cytoscape.api.version}</version>
+		</dependency>
 	</dependencies>
 
 	<description>A Cytoscape plugin for graph-based clustering that wraps the yoshiko algorithm.</description>

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

@@ -38,6 +38,7 @@ import org.cytoscape.model.subnetwork.CyRootNetworkManager;
 import org.cytoscape.service.util.AbstractCyActivator;
 import org.cytoscape.service.util.CyServiceRegistrar;
 import org.cytoscape.session.events.SessionLoadedListener;
+import org.cytoscape.task.create.CloneNetworkTaskFactory;
 import org.cytoscape.task.visualize.ApplyVisualStyleTaskFactory;
 import org.cytoscape.view.model.CyNetworkViewFactory;
 import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
@@ -87,6 +88,7 @@ public class CyActivator extends AbstractCyActivator {
 		CyCore.rootNetworkManager = getService(context,CyRootNetworkManager.class);
 		CyCore.applyVisualStyleTaskFactory = getService(context,ApplyVisualStyleTaskFactory.class);
 		CyCore.renderingEngineFactory = getService(context,RenderingEngineFactory.class);
+		CyCore.cloneNetworkTaskFactory = getService(context,CloneNetworkTaskFactory.class);
 
 		//Set language according to settings
 		LocalizationManager.switchLanguage(cm.getProperties().getProperty("locale", "enUS"));

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

@@ -30,7 +30,6 @@ import org.cytoscape.application.swing.CytoPanel;
 import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.application.swing.CytoPanelName;
 import org.cytoscape.application.swing.CytoPanelState;
-import org.cytoscape.model.CyColumn;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
 import org.cytoscape.work.AbstractTask;
@@ -58,19 +57,8 @@ public class AlgorithmTask extends AbstractTask {
 	private Window statusWindow;
 
 	//Parameters
-	private final double insertionCostDefault;
-	private final double deletionCostDefault;
-	private final CyColumn permanentColumn;
-	private final CyColumn forbiddenColumn;
-	private CyColumn weightColumn;
-	private int timeLimit;
-	private CyNetwork net;
-	private String bitMaskRules;
-	private double multiplicativeFactor;
-	private boolean separatePartitionCuts;
-	private boolean separateTriangles;
-	private boolean useHeuristic;
-	private int numberOfSolutions;
+	private final ParameterSet parameterSet;
+	private final CyNetwork net;
 	
 	//Temps, need to be freed in C++
 	private LibraryInput input;
@@ -82,34 +70,12 @@ public class AlgorithmTask extends AbstractTask {
 	public AlgorithmTask(// <<< Too many variables here, some should be grouped later TODO:
 			Window statusWindow,
 			CyNetwork net,
-			int timeLimit,
-			CyColumn weightColumn,
-			CyColumn permanentColumn,
-			CyColumn forbiddenColumn,
-			double insertionCostDefault,
-			double deletionCostDefault,
-			String bitMaskRules,
-			double multiplicativeFactor,
-			boolean separatePartitionCuts,
-			boolean separateTriangles,
-			boolean useHeuristic,
-			int numberOfSolutions
+			ParameterSet parameterSet
 			) 
 	{
 		this.statusWindow = statusWindow;
 		this.net = net;
-		this.timeLimit = timeLimit;
-		this.weightColumn = weightColumn;
-		this.permanentColumn = permanentColumn;
-		this.forbiddenColumn = forbiddenColumn;
-		this.insertionCostDefault = insertionCostDefault;
-		this.deletionCostDefault = deletionCostDefault;
-		this.bitMaskRules = bitMaskRules;
-		this.multiplicativeFactor = multiplicativeFactor;
-		this.separatePartitionCuts = separatePartitionCuts;
-		this.separateTriangles = separateTriangles;
-		this.useHeuristic = useHeuristic;
-		this.numberOfSolutions = numberOfSolutions;
+		this.parameterSet = parameterSet;
 	}
 
 	@Override
@@ -125,7 +91,7 @@ public class AlgorithmTask extends AbstractTask {
 		}
 		
 		//Set time limit
-		LibraryInterface.setTimeLimit(timeLimit);
+		LibraryInterface.setTimeLimit(parameterSet.timeLimit);
 
 		//Create a node map to identify nodes and eges in the solution
 		NodeMap nodeMap  = new NodeMap(net);
@@ -135,24 +101,24 @@ public class AlgorithmTask extends AbstractTask {
 		input = NetworkParser.parseNetwork(
 				net,
 				nodeMap,
-				weightColumn,
-				permanentColumn, 
-				forbiddenColumn,
-				deletionCostDefault
+				parameterSet.weightColumn,
+				parameterSet.permanentColumn, 
+				parameterSet.forbiddenColumn,
+				parameterSet.defaultDeletionCost
 				);
 		taskMonitor.setProgress(0.2);
 
 		//Set the default value for insertion cost
-		input.setDefaultInsertionCost(insertionCostDefault);
+		input.setDefaultInsertionCost(parameterSet.defaultInsertionCost);
 		
 		//Call Yoshiko <<< Algorithm is performed here
 		ca = LibraryInterface.getRun(input, 
-				numberOfSolutions,
-				bitMaskRules,
-				multiplicativeFactor, 
-				separatePartitionCuts,
-				separateTriangles,
-				useHeuristic
+				parameterSet.solCount,
+				parameterSet.reductionRulesBitMask,
+				parameterSet.snrMultFactor, 
+				parameterSet.usePartitionCuts,
+				parameterSet.useTriangleCuts,
+				parameterSet.useHeuristic
 		);
 		class CallbackHandler extends CplexInformer{
 			

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

@@ -28,6 +28,7 @@ import org.cytoscape.model.CyNetworkFactory;
 import org.cytoscape.model.CyNetworkManager;
 import org.cytoscape.model.subnetwork.CyRootNetworkManager;
 import org.cytoscape.service.util.CyServiceRegistrar;
+import org.cytoscape.task.create.CloneNetworkTaskFactory;
 import org.cytoscape.task.visualize.ApplyVisualStyleTaskFactory;
 import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
 import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -62,5 +63,7 @@ public class CyCore {
 	public static CyRootNetworkManager rootNetworkManager;
 	public static ApplyVisualStyleTaskFactory applyVisualStyleTaskFactory;
 	public static RenderingEngineFactory<CyNetwork> renderingEngineFactory;
+	public static CloneNetworkTaskFactory cloneNetworkTaskFactory;
+
 	//
 }

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

+package de.hhu.ba.yoshikoWrapper.core;
+
+import org.cytoscape.model.CyColumn;
+
+public class ParameterSet {
+
+	public int timeLimit;
+	public CyColumn weightColumn;
+	public CyColumn permanentColumn;
+	public CyColumn forbiddenColumn;
+	public double defaultInsertionCost;
+	public double defaultDeletionCost;
+	public String reductionRulesBitMask;
+	public double snrMultFactor;
+	public boolean useTriangleCuts;
+	public boolean usePartitionCuts;
+	public boolean useHeuristic;
+	public int solCount;
+	
+}

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

+/**
+ * 
+ */
+/**
+ * @author Philipp Spohr, Sep 5, 2017
+ *
+ */
+package de.hhu.ba.yoshikoWrapper.cytoUtil;
\ No newline at end of file

src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.java

@@ -94,8 +94,11 @@ public class YoshikoCluster {
 		}
 	}
 	
+	/**
+	 * Attempt to select the nodes belonging to this cluster in the original Graph given that they still exist
+	 */
 	public void select() {
-		if (originalGraph.getDefaultNodeTable() != null) {
+		try {
 			List<CyRow> allRows = originalGraph.getDefaultNodeTable().getAllRows();
 			for (CyRow r: allRows) {
 				r.set("selected", false);
@@ -105,21 +108,23 @@ public class YoshikoCluster {
 				originalGraph.getRow(n).set("selected", true);
 			}
 		}
-		else {
+		catch (Exception e) {
 			logger.warn("The graph doesn't exist anymore, can't highlight nodes!");
 		}
 	}
 	
 
 	public void generateImage(JLabel label, int width, int height) {
+		
 		if (net == null) {
 			createSubNetwork();
 		}
-		CyNetworkView view = CyCore.networkViewFactory.createNetworkView(net);
+		
+		final CyNetworkView view = CyCore.networkViewFactory.createNetworkView(net);
 		
 		//layout cluster
-		CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
-		TaskIterator createLayout = layout.createTaskIterator(
+		final CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
+		final TaskIterator createLayout = layout.createTaskIterator(
 			view, 
 			layout.getDefaultLayoutContext(), 
 			CyLayoutAlgorithm.ALL_NODE_VIEWS,
@@ -161,7 +166,7 @@ public class YoshikoCluster {
 
 				@Override
 				public void cancel() {
-					// TODO Auto-generated method stub
+					//Nothing to do as GC is handled by JAVA
 				}
 				
 			}
@@ -197,6 +202,4 @@ public class YoshikoCluster {
 		return originalGraph.getRow(n).get("name", String.class);
 	}
 
-
-
 }

src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoSolution.java

@@ -28,17 +28,23 @@ import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
 import org.cytoscape.model.CyEdge.Type;
+
 import org.cytoscape.model.subnetwork.CySubNetwork;
 import org.cytoscape.view.layout.CyLayoutAlgorithm;
 import org.cytoscape.view.model.CyNetworkView;
 import org.cytoscape.view.presentation.property.BasicVisualLexicon;
 import org.cytoscape.view.vizmap.VisualStyle;
 import org.cytoscape.view.vizmap.mappings.ContinuousMapping;
+
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 
 public class YoshikoSolution {
 	
+	/**
+	 * The original Graph from which the solution was generated.
+	 * NOTE: This can be destroyed or modified during runtime while the solution still exists and may become invalid
+	 */
 	private CyNetwork originalGraph;
 	
 	public ArrayList<YoshikoCluster> cluster;

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

@@ -53,6 +53,7 @@ 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.ParameterSet;
 import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
 
 /**This class describes the Swing Panel that the user interacts with in cytoscape
@@ -212,18 +213,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 				AbstractTask yoshiko = new AlgorithmTask(
 					popupLevel,
 					CyCore.cy.getCurrentNetwork(),
-					opModePanel.getTimeLimit(),
-					ecPanel.getWeightColumn(),
-					ecPanel.getPermanentColumn(),
-					ecPanel.getForbiddenColumn(),
-					ecPanel.getDefaultInsertionCost(),
-					ecPanel.getDefaultDeletionCost(),
-					reductionRulesChooser.getBitMask(),
-					reductionRulesChooser.getMultFactor(),
-					opModePanel.useTriangleCuts(),
-					opModePanel.usePartitionCuts(), 
-					opModePanel.useHeuristic(),
-					opModePanel.getSolCount()
+					fetchParameter()
 				);
 				/**
 				 * Don't queue multiple runs at once because that will get messy
@@ -247,6 +237,26 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 		}
 	};
 	
+	/**
+	 * Fetches all the parameters from the various swing components and packs them into a neat abstract wrapper class
+	 * @return The currently selected parameter wrapped in a ParameterSet
+	 */
+	private ParameterSet fetchParameter() {
+		ParameterSet ret = new ParameterSet();
+		ret.timeLimit = opModePanel.getTimeLimit();
+		ret.weightColumn = ecPanel.getWeightColumn();
+		ret.permanentColumn = ecPanel.getPermanentColumn();
+		ret.forbiddenColumn = ecPanel.getForbiddenColumn();
+		ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
+		ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
+		ret.reductionRulesBitMask = reductionRulesChooser.getBitMask();
+		ret.snrMultFactor = reductionRulesChooser.getMultFactor();
+		ret.useTriangleCuts = opModePanel.useTriangleCuts();
+		ret.usePartitionCuts = opModePanel.usePartitionCuts(); 
+		ret.useHeuristic = opModePanel.useHeuristic();
+		ret.solCount = opModePanel.getSolCount();
+		return ret;
+	}
 
 	
 	//GETTER / SETTER