-Improved Meta-Graph performance

-Fixed bug using ILP when selecting heuristic mode
-Fixed bug with discarding solution sometimes not removing subgraphs/metagraph
-Fixed bug with infinite gap values being formatted incorrectly
-Enabled highlighting of clusters in meta-graph
-Enabled returning to original network view upon result destruction
-Fixed bugs with cluster-view sometimes using incorrect styles/layout
-Reworked concurrency / synchronization
-Various smaller performance issues

pom.xml

@@ -33,7 +33,7 @@
 
 	<groupId>de.hhu.ba</groupId>
 	<artifactId>yoshikoWrapper</artifactId>
-	<version>0.1.2</version>
+	<version>0.1.3</version>
 
 	<name>YoshikoWrapper</name>
 

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

@@ -21,6 +21,8 @@
  ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.core;
 
+import java.util.concurrent.CountDownLatch;
+
 import org.cytoscape.application.CyApplicationManager;
 import org.cytoscape.application.swing.CySwingApplication;
 import org.cytoscape.model.CyNetwork;
@@ -36,6 +38,10 @@ import org.cytoscape.view.presentation.RenderingEngineFactory;
 import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
 import org.cytoscape.view.vizmap.VisualMappingManager;
 import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.work.FinishStatus;
+import org.cytoscape.work.ObservableTask;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskObserver;
 import org.cytoscape.work.swing.DialogTaskManager;
 import org.osgi.framework.BundleContext;
 
@@ -68,4 +74,25 @@ public class CyCore {
 	public static String getConfig(String key) {
 		return cm.getProperties().getProperty(key);
 	}
+
+	/**
+	 * Convenience function that runs all tasks in a task iterator but blocks until all tasks are finished
+	 * @param taskIterator
+	 * @throws InterruptedException
+	 */
+	public static synchronized void runAndWait(TaskIterator taskIterator) throws InterruptedException {
+		CountDownLatch blockLatch = new CountDownLatch(1);
+		dialogTaskManager.execute(taskIterator,new TaskObserver() {
+
+			@Override
+			public void taskFinished(ObservableTask task) {}
+
+			@Override
+			public void allFinished(FinishStatus finishStatus) {
+				blockLatch.countDown();
+			}
+
+		});
+		blockLatch.await();
+	}
 }

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

@@ -44,9 +44,11 @@ public class StatusInformer extends CplexInformer {
 	@Override
 	public void updateStatus(YoshikoState state, double value) {
 		if (state == YoshikoState.SOLVING_ILP){
+			if (value <= 1.0) {
 				taskMonitor.setStatusMessage(LocalizationManager.get("currentGap")+": "+SwingUtil.twoDecimals.format(value)+"%");
 			}
 		}
+	}
 
 	@Override
 	public void updateStatus(YoshikoState state) {

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

 package de.hhu.ba.yoshikoWrapper.core;
 
+
 import org.osgi.framework.Version;
 
 public class YoshUtil {

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

@@ -28,7 +28,6 @@ import java.util.List;
 
 import javax.swing.ImageIcon;
 import javax.swing.JLabel;
-import javax.swing.SwingUtilities;
 
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
@@ -39,9 +38,10 @@ import org.cytoscape.model.subnetwork.CySubNetwork;
 import org.cytoscape.view.layout.CyLayoutAlgorithm;
 import org.cytoscape.view.model.CyNetworkView;
 import org.cytoscape.view.presentation.RenderingEngine;
-import org.cytoscape.work.Task;
+import org.cytoscape.work.FinishStatus;
+import org.cytoscape.work.ObservableTask;
 import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.TaskObserver;
 import org.slf4j.Logger;
 
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
@@ -61,6 +61,9 @@ public class YoshikoCluster {
 
 	private Image img;
 
+	private CySubNetwork subnet;
+
+
 	//SYMBOLIC LINKS
 	private final YoshikoSolution solution;
 	private Logger logger = YoshikoLogger.getInstance().getLogger();
@@ -90,19 +93,21 @@ public class YoshikoCluster {
 	}
 
 	/**
-	 * Generates a subgraph for this cluster by choosing the nodes and induced edges from the original graph
+	 * Generates a subgraph for this clusters by choosing the nodes and induced edges from the original graph if such a graph doesn't exist yet.
 	 * @return
 	 */
 	public CySubNetwork getSubNetwork() {
 
+		if (subnet == null) {
 			CyRootNetwork originalGraphAsRoot =
 					CyCore.rootNetworkManager.getRootNetwork(solution.getOriginalGraph());
 
-		//Create nested graph and cluster subnet
+			//Create nested graph and clusters subnet
 			ArrayList<CyEdge> inducedEdges = new ArrayList<CyEdge>();
 			for (CyNode n: nodes) {
 				//Sadly Cytoscape doesnt provide a comfort function here
 				List<CyEdge> adjacentEdges = solution.getOriginalGraph().getAdjacentEdgeList(n, CyEdge.Type.ANY);
+
 				for (CyEdge e: adjacentEdges) {
 					if (nodes.contains(e.getSource()) && nodes.contains(e.getTarget())) {
 						inducedEdges.add(e);
@@ -110,23 +115,32 @@ public class YoshikoCluster {
 				}
 			}
 
-		CySubNetwork subnet = originalGraphAsRoot.addSubNetwork(nodes ,inducedEdges);
-
-		subnet.getRow(subnet).set(CyNetwork.NAME, LocalizationManager.get("cluster")+" "+(id+1));
+			subnet = originalGraphAsRoot.addSubNetwork(nodes ,inducedEdges);
+			subnet.getRow(subnet).set(CyNetwork.NAME, LocalizationManager.get("clusters")+" "+(id+1));
+		}
 
 		return subnet;
 	}
 
+	public void highlight() {
+		if (CyCore.cy.getCurrentNetwork() == solution.getOriginalGraph()) {
+			highlightInOriginalGraph();
+		}
+		else if (CyCore.cy.getCurrentNetwork() == solution.getMetaGraph()) {
+			solution.highlightInMetaGraph(this);
+		}
+	}
+
 	/**
-	 * Attempt to select the nodes belonging to this cluster in the original Graph given that they still exist
+	 * Attempt to select the nodes belonging to this clusters in the original Graph given that they still exist
 	 */
-	public void highlightInOriginalGraph() {
+	private void highlightInOriginalGraph() {
 		try {
 			List<CyRow> allRows = solution.getOriginalGraph().getDefaultNodeTable().getAllRows();
 			for (CyRow r: allRows) {
 				r.set("selected", false);
 			}
-			//Select nodes corresponding to the cluster
+			//Select nodes corresponding to the clusters
 			for (CyNode n : nodes) {
 				solution.getOriginalGraph().getRow(n).set("selected", true);
 			}
@@ -136,37 +150,19 @@ public class YoshikoCluster {
 		}
 	}
 
-
-	public void applyImage(JLabel label, int width, int height) throws Exception {
-
-		if (img != null) {
-			label.setIcon(new ImageIcon(img));
-		}
-		else {
-			getImage(width,height,label);
-		}
-	}
-
-	private void getImage(int width, int height,JLabel label) {
+	public void generateClusterIcon(int width, int height,JLabel label) throws InterruptedException {
 		final CyNetworkView view = CyCore.networkViewFactory.createNetworkView(getSubNetwork());
 
-		//layout cluster
+		//layout clusters
 		final CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
-		final TaskIterator createLayout = layout.createTaskIterator(
+		CyCore.runAndWait(layout.createTaskIterator(
 			view,
 			layout.getDefaultLayoutContext(),
 			CyLayoutAlgorithm.ALL_NODE_VIEWS,
 			null
+			)
 		);
 
-		createLayout.append(
-			new Task() {
-
-				@Override
-				public void run(TaskMonitor taskMonitor) throws Exception {
-					taskMonitor.setStatusMessage("Generating cluster view for C:"+id);
-
-
 		view.setVisualProperty(NETWORK_WIDTH, new Double(width));
 		view.setVisualProperty(NETWORK_HEIGHT, new Double(height));
 		view.fitContent();
@@ -174,29 +170,18 @@ public class YoshikoCluster {
 		StyleManager.style(view, CyCore.visualMappingManager.getCurrentVisualStyle());
 
 		RenderingEngine<CyNetwork> renderingEngine = CyCore.renderingEngineFactory.createRenderingEngine(label, view);
-					SwingUtilities.invokeLater(new Runnable() {
 
-						@Override
-						public void run() {
 		img = renderingEngine.createImage(width,height);
 		label.setIcon(new ImageIcon(img));
+
 		renderingEngine.dispose();
 		view.dispose();
 	}
 
-					});
-
-
+	public void delete() {
+		if (subnet != null) {
+			CyCore.networkManager.destroyNetwork(subnet);
 		}
-				@Override
-				public void cancel() {}
-
-			}
-	    );
-
-		CyCore.dialogTaskManager.execute(
-				createLayout
-		);
 	}
 
 	public int getSize() {
@@ -215,4 +200,8 @@ public class YoshikoCluster {
 		return solution.getOriginalGraph().getRow(n).get("name", String.class);
 	}
 
+
+
+
+
 }

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

@@ -71,5 +71,11 @@ public class YoshikoResult {
 		return originalGraph;
 	}
 
+	public void delete() {
+		for (YoshikoSolution s: solutions) {
+			s.delete();
+		}
+	}
+
 
 }

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

@@ -22,19 +22,36 @@
 package de.hhu.ba.yoshikoWrapper.graphModel;
 
 import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+import javax.swing.JOptionPane;
 
 import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
+import org.slf4j.Logger;
+
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
+import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
 
 public class YoshikoSolution {
 
 	private final YoshikoResult result;
 
-	public ArrayList<YoshikoCluster> cluster;
+	private CyNetwork metaGraph;
+	private HashMap<YoshikoCluster, CyNode> metaGraphMap;
+
+
+	public ArrayList<YoshikoCluster> clusters;
 
 	private final long id;
 
+	private Logger logger = YoshikoLogger.getInstance().getLogger();
+
+
 	public YoshikoSolution(YoshikoResult yoshikoResult, long id) {
-		cluster = new ArrayList<YoshikoCluster>();
+		clusters = new ArrayList<YoshikoCluster>();
 		this.result = yoshikoResult;
 		this.id = id;
 	}
@@ -42,7 +59,7 @@ public class YoshikoSolution {
 	//_____________GETTER / SETTER ________________//
 
 	public ArrayList<YoshikoCluster> getClusters() {
-		return cluster;
+		return clusters;
 	}
 
 	/**
@@ -56,4 +73,37 @@ public class YoshikoSolution {
 		return result.getOriginalGraph();
 	}
 
+	public void delete() {
+		for (YoshikoCluster c: clusters) {
+			c.delete();
+		}
+		if (this.metaGraph != null) {
+			CyCore.networkManager.destroyNetwork(metaGraph);
+		}
+	}
+
+	public void setMetaGraph(CyNetwork metaGraph, HashMap<YoshikoCluster, CyNode> map) {
+		this.metaGraph = metaGraph;
+		this.metaGraphMap = map;
+	}
+
+	public CyNetwork getMetaGraph() {
+		return metaGraph;
+	}
+
+	public void highlightInMetaGraph(YoshikoCluster yoshikoCluster) {
+		try {
+			List<CyRow> allRows = metaGraph.getDefaultNodeTable().getAllRows();
+			for (CyRow r: allRows) {
+				r.set("selected", false);
+			}
+
+			metaGraph.getRow(metaGraphMap.get(yoshikoCluster)).set("selected", true);
+		}
+		catch (Exception e) {
+			logger.warn("The graph doesn't exist anymore, can't highlight nodes!");
+		}
+
+	}
+
 }

src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ClusterView.java

@@ -42,6 +42,7 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
 import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
 import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
+import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
 
 @SuppressWarnings("serial")
 public class ClusterView extends JPanel {
@@ -76,17 +77,17 @@ public class ClusterView extends JPanel {
 
 		//Swing init
 
-		title = new JLabel(LocalizationManager.get("cluster")+" "+(c.getID()+1));
+		title = new JLabel(LocalizationManager.get("clusters")+" "+(c.getID()+1));
 		clusterSize = new JLabel(LocalizationManager.get("clusterSize")+" "+c.getSize());
 		icon = new JLabel();
 		//icon.setBorder(BorderFactory.createLineBorder(Color.BLACK));
-		cluster.applyImage(icon,CLUSTER_ICON_SIZE, CLUSTER_ICON_SIZE);
+		cluster.generateClusterIcon(CLUSTER_ICON_SIZE, CLUSTER_ICON_SIZE,icon);
 
 		SwingUtil.addAll(this,title,clusterSize,icon);
 
 		nodeList = new BasicCollapsiblePanel(LocalizationManager.get("nodes"));
 
-		//Loop over nodes in the cluster and add them to the view
+		//Loop over nodes in the clusters and add them to the view
 		for (CyNode n : c.getSubNetwork().getNodeList()) {
 			nodeList.add(
 				new JLabel(
@@ -147,7 +148,7 @@ public class ClusterView extends JPanel {
 
 		@Override
 		public void mouseEntered(MouseEvent e) {
-			cluster.highlightInOriginalGraph();
+			cluster.highlight();
 			setBorder(isSelected ? selectedBorder : highlightBorder);
 		}
 

src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/ResultPanel.java

@@ -25,9 +25,11 @@ import static javax.swing.GroupLayout.*;
 
 import java.awt.Color;
 import java.awt.Component;
+import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Properties;
 
 import javax.swing.BoxLayout;
@@ -58,6 +60,7 @@ import org.cytoscape.model.events.AddedNodesListener;
 import org.cytoscape.model.events.NetworkAboutToBeDestroyedEvent;
 import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
 import org.cytoscape.util.swing.BasicCollapsiblePanel;
+import org.cytoscape.view.model.CyNetworkView;
 
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
@@ -123,11 +126,16 @@ NetworkAboutToBeDestroyedListener
 			solutionTabs.add(tab);
 		}
 
+		marker = new BasicCollapsiblePanel(LocalizationManager.get("solutionMarker"));
+		marker.setLayout(new BoxLayout(marker,BoxLayout.Y_AXIS));
+
+		JLabel costLabel = new JLabel(LocalizationManager.get("cost")+" "+result.getFlags().getTotalCost());
+		marker.add(costLabel);
+
 		if (result.getFlags().getIlpGenerated()) {
 			//TODO: Move to MarkerPanel for better codestyle
 			//Optional Markers
-			marker = new BasicCollapsiblePanel(LocalizationManager.get("ilpMarker"));
-			marker.setLayout(new BoxLayout(marker,BoxLayout.Y_AXIS));
+
 			if(result.getFlags().getOptimal()) {
 				JLabel optimalLabel;
 				optimalLabel = new JLabel(LocalizationManager.get("optimal"));
@@ -142,15 +150,15 @@ NetworkAboutToBeDestroyedListener
 				marker.add(new JLabel(result.getFlags().getSolvedInstances()+"/"+result.getFlags().getReducedInstances()+" "+LocalizationManager.get("redSolved")));
 				marker.add(new JLabel(LocalizationManager.get("lastInstanceGap")+" "+(int)(100*result.getFlags().getLastGap())+"%"));
 			}
-			JLabel costLabel = new JLabel(LocalizationManager.get("cost")+" "+result.getFlags().getTotalCost());
-			marker.add(costLabel);
+
 			if (result.getFlags().getTimedOut()) {
 				marker.add(new JLabel(LocalizationManager.get("timeoutMarker")));
 			}
 			marker.setCollapsed(false);
-			this.add(marker);
 		}
 
+		this.add(marker);
+
 		destroyButton = new JButton(LocalizationManager.get("discardSolution"));
 		destroyButton.addActionListener(new ActionListener() {
 
@@ -172,16 +180,13 @@ NetworkAboutToBeDestroyedListener
 		layout.setHorizontalGroup(horizontalGroup);
 		layout.setVerticalGroup(verticalGroup);
 
-		if (result.getFlags().getIlpGenerated()) {
-			horizontalGroup.addComponent(marker,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE);
-			verticalGroup.addComponent(marker,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE);
-		}
-
 		horizontalGroup
+			.addComponent(marker,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
 			.addComponent(invalidLabel,DEFAULT_SIZE, PREFERRED_SIZE,Short.MAX_VALUE)
 			.addComponent(tabbedPane,HACKFIX_FIXED_WIDTH, PREFERRED_SIZE,Short.MAX_VALUE)
 			.addComponent(destroyButton,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE);
 		verticalGroup
+			.addComponent(marker,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
 			.addComponent(invalidLabel,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
 			.addComponent(tabbedPane,DEFAULT_SIZE, DEFAULT_SIZE,PREFERRED_SIZE)
 			.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED, DEFAULT_SIZE, Short.MAX_VALUE)
@@ -190,6 +195,8 @@ NetworkAboutToBeDestroyedListener
 		layout.setAutoCreateGaps(true);
 		layout.setAutoCreateContainerGaps(true);
 
+		//SWING BLACK MAGIC FOR ADEPTS
+		this.setMinimumSize(new Dimension(HACKFIX_FIXED_WIDTH,this.getMinimumSize().height));
 
 		this.setLayout(layout);
 
@@ -206,6 +213,7 @@ NetworkAboutToBeDestroyedListener
 	}
 
 	public void deleteSolution() {
+
 		int dialogResult = JOptionPane.showConfirmDialog (
 				null,
 				LocalizationManager.get("deleteSolution"),
@@ -215,9 +223,19 @@ NetworkAboutToBeDestroyedListener
 		if (dialogResult != JOptionPane.YES_OPTION) {
 			return;
 		}
+
+		//Restore view
+		if (result.getOriginalGraph() != null) {
+			Collection<CyNetworkView> viewsToReturn = CyCore.networkViewManager.getNetworkViews(result.getOriginalGraph());
+			if (!viewsToReturn.isEmpty()) {
+				CyCore.cy.setCurrentNetworkView(viewsToReturn.iterator().next());
+			}
+		}
+
 		CyCore.registrar.unregisterService(this,CytoPanelComponent.class);
-		removeAll();
+		result.delete();
 		super.setVisible(false);
+
 	}
 
 	private void invalidateResult() {

src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/SolutionTab.java

@@ -86,14 +86,14 @@ public class SolutionTab extends JPanel {
 		//Declaration of Swing Components
 		clusterViewList = new ClusterViewList();
 
-		for (YoshikoCluster c: solution.cluster) {
+		for (YoshikoCluster c: solution.clusters) {
 			ClusterView clusterView = new ClusterView(c);
 			clusterViewList.add(clusterView);
 		}
 
 		scrollPane = new JScrollPane(clusterViewList);
 
-		clusterCount = new JLabel(LocalizationManager.get("clusterFound")+" "+s.cluster.size());
+		clusterCount = new JLabel(LocalizationManager.get("clusterFound")+" "+s.clusters.size());
 
 		createClusterView = new JButton(LocalizationManager.get("createClusterView"));
 		createMetaGraph = new JButton(LocalizationManager.get("createMetaGraph"));
@@ -170,7 +170,7 @@ public class SolutionTab extends JPanel {
 				.addGap(8)
 				.addComponent(clusterCount,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
 				.addGap(8)
-				.addComponent(scrollPane,PREFERRED_SIZE,DEFAULT_SIZE,Short.MAX_VALUE)
+				.addComponent(scrollPane,DEFAULT_SIZE,DEFAULT_SIZE,Short.MAX_VALUE)
 				.addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
 				.addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
 		);

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

@@ -71,7 +71,7 @@ public class AlgorithmTask extends AbstractTask {
 
 	private ResultPanel resultPanel;
 
-	public AlgorithmTask(// <<< Too many variables here, some should be grouped later TODO:
+	public AlgorithmTask(
 			Window statusWindow,
 			CyNetwork net,
 			ParameterSet parameterSet
@@ -85,6 +85,7 @@ public class AlgorithmTask extends AbstractTask {
 	@Override
 	public void run(TaskMonitor taskMonitor) throws Exception {
 
+		//TODO: Improve setProgress values
 
 		taskMonitor.setTitle(LocalizationManager.get("yoshTask"));
 		taskMonitor.setProgress(0.0);
@@ -127,9 +128,9 @@ public class AlgorithmTask extends AbstractTask {
 				parameterSet.solCount,
 				parameterSet.reductionRulesBitMask,
 				parameterSet.snrMultFactor,
+				parameterSet.useHeuristic,
 				parameterSet.usePartitionCuts,
-				parameterSet.useTriangleCuts,
-				parameterSet.useHeuristic
+				parameterSet.useTriangleCuts
 		);
 
 
@@ -162,30 +163,30 @@ public class AlgorithmTask extends AbstractTask {
 			//Fetch number of clusters in the solution
 			long numberOfClusters = result.getNumberOfClusters(i);
 
-			//Loop over cluster
+			//Loop over clusters
 			for (long k=0;k<numberOfClusters;k++) {
 				//Create java instance
 				YoshikoCluster cluster = new YoshikoCluster(solution,k);
 
 
-				taskMonitor.setStatusMessage("Processing cluster "+(k+1)+" of "+numberOfClusters);
+				taskMonitor.setStatusMessage("Processing clusters "+(k+1)+" of "+numberOfClusters);
 
 				IntVector clusterVector = result.getCluster(i, k);
 
 				long sizeOfCluster = clusterVector.size();
 				for (int l=0;l<sizeOfCluster;l++) { //Unsafe mismatch int long
-					taskMonitor.setStatusMessage("Processing node "+(l+1)+ " of "+sizeOfCluster);
+					//taskMonitor.setStatusMessage("Processing node "+(l+1)+ " of "+sizeOfCluster);
 					int nodeID = clusterVector.get(l);
 					CyNode node = nodeMap.indexOf(nodeID); //<<< Another int/long conversion
 					cluster.addNode(node);
 
 					net.getRow(node).set(columnName, ""+(k+1)); //Add Cluster ID in table (Remove in final version?)
 				}
-				//Register cluster with solution for further reference
-				solution.cluster.add(cluster);
+				//Register clusters with solution for further reference
+				solution.clusters.add(cluster);
 			}
 			//Sort clusters by size, descending as the biggest clusters are usually the most relevant
-			solution.cluster.sort(YoshikoCluster.lessThanComparator);
+			solution.clusters.sort(YoshikoCluster.lessThanComparator);
 			//Register solution with result for further reference
 			yoshikoResult.addSolution(solution);
 		}

src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateClusterViews.java

@@ -5,8 +5,11 @@ import java.util.ArrayList;
 import org.cytoscape.model.subnetwork.CySubNetwork;
 import org.cytoscape.view.layout.CyLayoutAlgorithm;
 import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.work.FinishStatus;
+import org.cytoscape.work.ObservableTask;
 import org.cytoscape.work.Task;
 import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.TaskObserver;
 
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
@@ -56,20 +59,30 @@ public class CreateClusterViews implements Task {
 			CyCore.networkManager.addNetwork(subnet,false);
 			//Create network view and register it
 			CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
-			//layout cluster
+			//layout clusters
 			CyCore.dialogTaskManager.execute(
 				layout.createTaskIterator(
 						subnetView,
 						layout.getDefaultLayoutContext(),
 						CyLayoutAlgorithm.ALL_NODE_VIEWS,
 						null
-				)
-			);
+				),
+				new TaskObserver() {
 
-			StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
+					@Override
+					public void taskFinished(ObservableTask task) {}
 
+					@Override
+					public void allFinished(FinishStatus finishStatus) {
+						StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
 						CyCore.networkViewManager.addNetworkView(subnetView);
 					}
+
+				}
+			);
+
+
+		}
 	}
 
 	@Override

src/main/java/de/hhu/ba/yoshikoWrapper/tasks/CreateMetaGraphTask.java

@@ -3,6 +3,8 @@ package de.hhu.ba.yoshikoWrapper.tasks;
 import java.util.ArrayList;
 import java.util.HashMap;
 
+import javax.swing.SwingUtilities;
+
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
@@ -11,9 +13,11 @@ import org.cytoscape.model.subnetwork.CySubNetwork;
 import org.cytoscape.view.layout.CyLayoutAlgorithm;
 import org.cytoscape.view.model.CyNetworkView;
 import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.FinishStatus;
+import org.cytoscape.work.ObservableTask;
 import org.cytoscape.work.Task;
-import org.cytoscape.work.TaskIterator;
 import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.TaskObserver;
 
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
@@ -76,8 +80,10 @@ public class CreateMetaGraphTask extends AbstractTask {
 			CyCore.networkManager.addNetwork(subnet,false);
 			//Create network view and register it
 			CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
-			//layout cluster
-			CyCore.dialogTaskManager.execute(
+
+			//Apply layout
+			CyCore.runAndWait(
+
 				layout.createTaskIterator(
 						subnetView,
 						layout.getDefaultLayoutContext(),
@@ -90,17 +96,23 @@ public class CreateMetaGraphTask extends AbstractTask {
 
 			CyCore.networkViewManager.addNetworkView(subnetView,false);
 
-			//Link cluster node in meta graph and subnet graph to use Cytoscape Nested Network feature
+			//Link clusters node in meta graph and subnet graph to use Cytoscape Nested Network feature
 			clusterNode.setNetworkPointer(subnet);
 			//Set node attributes
-			metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.getID());
+			metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("clusters")+" "+c.getID());
 			metaGraph.getRow(clusterNode).set(StyleManager.CLUSTERSIZE_COLUMN_NAME,c.getSize());
 			map.put(c, clusterNode);
 		}
+
+		//EDGE_PROCESSING
+		//We are checking if any edges in the original graph connect clusters, if so we count them
+
 		taskMonitor.setStatusMessage(LocalizationManager.get("metaGraph_edges"));
-		//Add edges (O(|C|^2*|V|^2) can maybe be improved? //TODO
-		for (YoshikoCluster c1:solution.getClusters()) {
-			for (YoshikoCluster c2:solution.getClusters()) {
+
+		for (int x = 0; x <solution.getClusters().size(); x ++) {
+			YoshikoCluster c1 = solution.getClusters().get(x);
+			for (int y = x; y <solution.getClusters().size(); y ++) {
+				YoshikoCluster c2 = solution.getClusters().get(y);
 
 				if(isTerminated) {
 					throw new Exception("Terminated by user!");
@@ -112,6 +124,7 @@ public class CreateMetaGraphTask extends AbstractTask {
 						) {
 					continue;
 				}
+				//TODO: Improve running time here?
 				for (CyNode c1n : c1.getSubNetwork().getNodeList()) {
 					for (CyNode c2n : c2.getSubNetwork().getNodeList()) {
 						if (solution.getOriginalGraph().containsEdge(c1n, c2n) || solution.getOriginalGraph().containsEdge(c2n, c1n)) {
@@ -131,32 +144,22 @@ public class CreateMetaGraphTask extends AbstractTask {
 			}
 		}
 
+		solution.setMetaGraph(metaGraph,map);
+
 		CyNetworkView view = CyCore.networkViewFactory.createNetworkView(metaGraph);
 
 		//Layout and style solution
-
-		TaskIterator it = layout.createTaskIterator(
+		CyCore.runAndWait(
+			layout.createTaskIterator(
 					view,
 					layout.getDefaultLayoutContext(),
 					CyLayoutAlgorithm.ALL_NODE_VIEWS,
 					null
+			)
 		);
 
-		it.append(new Task() {
-
-			@Override
-			public void run(TaskMonitor taskMonitor) throws Exception {
 		StyleManager.styleWithMapping(view, CyCore.visualMappingManager.getCurrentVisualStyle());
-			}
 
-			@Override
-			public void cancel() {}
-
-		});
-
-		CyCore.dialogTaskManager.execute(
-			it
-		);
 
 		CyCore.networkManager.addNetwork(metaGraph,false);
 		CyCore.networkViewManager.addNetworkView(
@@ -166,6 +169,7 @@ public class CreateMetaGraphTask extends AbstractTask {
 		view.updateView();
 
 		CyCore.cy.setCurrentNetworkView(view);
+
 	}
 
 	@Override

src/main/resources/YoshikoStrings.properties

@@ -26,7 +26,7 @@
 about = INSERT SOME AMAZING INFO ABOUT THIS APPLICATION,\n THE AUTHOR AND WHERE TO FIND MORE INFO HERE\n <a href=\"www.hhu.de\" >LINK</a>
 aboutButton = About Yoshiko
 aboutTitle = Yoshiko Plugin Info
-cluster = Cluster
+clusters = Cluster
 clusterFound = Clusters found:
 clusterSize = Cluster Size:
 continueTimeout = The ILP has exceeded the given time limit. Do you want to continue? (This may take a long time)
@@ -46,7 +46,6 @@ firstStart = Thanks for using the Yoshiko Clustering Tool!\nIt appears, that thi
 gap = Gap
 getYoshiko = Get Yoshiko Library
 icTooltip = This value is used to determine what the algorithm pays when inserting an edge.\nExisting mappings overwrite this value.\nA higher value means that the algorithm is less likely to insert edges in order to generate a cluster.
-ilpMarker = ILP Properties
 incompleteResult = This run yielded no usable result!
 instance = Instance
 invalidated = No longer valid, original graph changed!
@@ -77,6 +76,7 @@ resultsPanelTitle = Yoshiko Results
 run = Perform Algorithm
 showAdvanced = Show advanced options
 solution = Solution
+solutionMarker = Solution Properties
 
 status_createCV = Creating cluster view for cluster:
 

thesis/tex/Thesis.tex

@@ -30,6 +30,14 @@
 \cleardoublepage
 
 \begin{abstract}
+This paper describes an implementation of the Yoshiko-alorithm,
+which clusters data based on the weighted cluster-editing problem,
+as a plugin for Cytoscape.
+
+Cytoscape is a network visualization and analysis tool (insert info)
+
+Yoshiko is based on work from (insert info)
+
 
 \end{abstract}
 
@@ -40,6 +48,8 @@
 \section{Introduction}
 \section{The Yoshiko-App for Cytoscape}
 	\subsection{Technical Details}
+		\subsubsection{Program Structure}
+		\subsubsection{JNI}
 	\subsection{Algorithm}
 		\input{Chapter/alg_overview}
 		\subsubsection{Data Modeling}
@@ -49,4 +59,6 @@
 			\input{Chapter/dm_impl}
 \section{Evaluation of the Yoshiko Algorithm}
 \section{Outlook}
+	\subsection{Multigraph Analysis}
+	\subsection{Integration in other frameworks}
 \end{document}
\ No newline at end of file