Implemented meta-graph

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

@@ -12,9 +12,11 @@ import org.cytoscape.model.events.ColumnCreatedListener;
 import org.cytoscape.model.events.ColumnDeletedListener;
 import org.cytoscape.model.events.NetworkAddedListener;
 import org.cytoscape.model.events.RemovedEdgesListener;
+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.visualize.ApplyVisualStyleTaskFactory;
 import org.cytoscape.view.model.CyNetworkViewFactory;
 import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
 import org.cytoscape.view.model.CyNetworkViewManager;
@@ -59,6 +61,9 @@ public class CyActivator extends AbstractCyActivator {
 		CyCore.visualMappingManager = getService(context,VisualMappingManager.class);
 		CyCore.visualStyleFactory = getService(context,VisualStyleFactory.class);
 		CyCore.continuousMappingFactory = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
+		CyCore.rootNetworkManager = getService(context,CyRootNetworkManager.class);
+		CyCore.applyVisualStyleTaskFactory = getService(context,ApplyVisualStyleTaskFactory.class);
+		
 		//Set language according to settings
 		LocalizationManager.switchLanguage(cm.getProperties().getProperty("locale", "enUS"));
 

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

@@ -149,7 +149,9 @@ public class AlgorithmTask extends AbstractTask {
 			//Loop over cluster
 			for (long k=0;k<numberOfClusters;k++) {
 				//Create java instance
-				YoshikoCluster cluster = new YoshikoCluster(k);
+				YoshikoCluster cluster = new YoshikoCluster(k,net);
+
+				
 				taskMonitor.setStatusMessage("Processing cluster "+(k+1)+" of "+numberOfClusters);
 				
 				SWIGTYPE_p_std__vectorT_int_t clusterVector = LibraryInterface.ClusterEditingSolutions_getCluster(result, i, k);

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

@@ -4,7 +4,9 @@ import org.cytoscape.application.CyApplicationManager;
 import org.cytoscape.application.swing.CySwingApplication;
 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.visualize.ApplyVisualStyleTaskFactory;
 import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
 import org.cytoscape.view.model.CyNetworkViewFactory;
 import org.cytoscape.view.model.CyNetworkViewManager;
@@ -34,6 +36,8 @@ public class CyCore {
 	public static VisualMappingManager visualMappingManager;
 	public static VisualStyleFactory visualStyleFactory;
 	public static VisualMappingFunctionFactory continuousMappingFactory;
+	public static CyRootNetworkManager rootNetworkManager;
+	public static ApplyVisualStyleTaskFactory applyVisualStyleTaskFactory;
 
 	//
 }

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

@@ -2,14 +2,22 @@ package de.hhu.ba.yoshikoWrapper.graphModel;
 
 import java.util.ArrayList;
 
+import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
 
+
 public class YoshikoCluster {
-	public long id;
+	
+	
+	public final long id;
+	public final CyNetwork originalGraph;
+	
 	public ArrayList<CyNode> nodes;
 	
-	public YoshikoCluster(long id) {
+	public YoshikoCluster(long id, CyNetwork originalGraph) {
 		this.id = id;
+		this.originalGraph = originalGraph;
 		this.nodes = new ArrayList<CyNode>();		
 	}
+
 }

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

@@ -2,17 +2,25 @@ package de.hhu.ba.yoshikoWrapper.graphModel;
 
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
-
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+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 {
 	
 	private CyNetwork originalGraph;
+	
 	public ArrayList<YoshikoCluster> cluster;
 	public int id;
 	
@@ -23,9 +31,9 @@ public class YoshikoSolution {
 
 	/**
 	 * Transforms this solution in a meta-graph where each cluster is represented by one node
-	 * @return The meta-graph as CyNetwork
+	 * The nodes are linked to subgraphs representing the cluster and also their size is scaled relative to cluster size
 	 */
-	public CyNetwork toMetaGraph() {
+	public void exportMetaGraph() {
 		
 		CyNetwork metaGraph = CyCore.networkFactory.createNetwork();
 		
@@ -33,12 +41,48 @@ public class YoshikoSolution {
 		
 		metaGraph.getDefaultNodeTable().createColumn("clusterSize", Integer.class, false);
 		
+		CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
+
+		
 		//Map Cluster to Nodes for further reference
 		HashMap<YoshikoCluster,CyNode> map = new HashMap<YoshikoCluster,CyNode>();
 		
+		//Convert original graph to root graph to allow embedding of nodes
+		CyRootNetwork originalGraphAsRoot = CyCore.rootNetworkManager.getRootNetwork(originalGraph);
+		
 		//Add nodes
 		for (YoshikoCluster c: cluster) {
 			CyNode clusterNode = metaGraph.addNode();
+			//Create nested graph and cluster subnet
+			ArrayList<CyEdge> inducedEdges = new ArrayList<CyEdge>();
+			for (CyNode n: c.nodes) {
+				//Sadly Cytoscape doesnt provide a comfort function here
+				List<CyEdge> adjacentEdges = originalGraph.getAdjacentEdgeList(n, CyEdge.Type.ANY);
+				for (CyEdge e: adjacentEdges) {
+					if (c.nodes.contains(e.getSource()) && c.nodes.contains(e.getTarget())) {
+						inducedEdges.add(e);
+					}
+				}
+			}
+			CySubNetwork subnet = originalGraphAsRoot.addSubNetwork(c.nodes ,inducedEdges);
+
+			subnet.getRow(subnet).set(CyNetwork.NAME, LocalizationManager.get("cluster")+" "+(c.id+1));
+			
+			CyCore.networkManager.addNetwork(subnet);
+			//Create network view and register it
+			CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
+			CyCore.networkViewManager.addNetworkView(subnetView);
+			//layout cluster
+			CyCore.dialogTaskManager.execute(
+				layout.createTaskIterator(
+						subnetView, 
+						layout.getDefaultLayoutContext(), 
+						CyLayoutAlgorithm.ALL_NODE_VIEWS,
+						null
+				)
+			);
+			clusterNode.setNetworkPointer(subnet);
+			//Set node attributes
 			metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.id);
 			metaGraph.getRow(clusterNode).set("clusterSize",c.nodes.size());
 			map.put(c, clusterNode);
@@ -64,7 +108,38 @@ public class YoshikoSolution {
 				}
 			}
 		}
-		return metaGraph;
+		
+		CyNetworkView view = CyCore.networkViewFactory.createNetworkView(metaGraph);
+		//layout solution
+		CyCore.dialogTaskManager.execute(
+			layout.createTaskIterator(
+					view, 
+					layout.getDefaultLayoutContext(), 
+					CyLayoutAlgorithm.ALL_NODE_VIEWS,
+					null
+			)
+		);
+		
+		CyCore.networkManager.addNetwork(metaGraph);
+		CyCore.networkViewManager.addNetworkView(
+				view
+		);
+		
+		//define style for solution
+		ContinuousMapping<Integer, Double> contMap = (ContinuousMapping<Integer, Double>)CyCore.continuousMappingFactory.createVisualMappingFunction(
+				"clusterSize",
+				Integer.class,
+				BasicVisualLexicon.NODE_SIZE
+			);
+		VisualStyle vs= CyCore.visualStyleFactory.createVisualStyle("Meta-Graph Style");
+		vs.addVisualMappingFunction(contMap);
+		CyCore.visualMappingManager.addVisualStyle(vs);
+		CyCore.cy.setCurrentNetworkView(view);
+		//Apply visual style
+		CyCore.visualMappingManager.setVisualStyle(vs, view);
+		vs.apply(view);
+		view.updateView();
+
 	}
 	
 }

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

@@ -11,12 +11,9 @@ import javax.swing.BoxLayout;
 import javax.swing.JLabel;
 import javax.swing.border.Border;
 
-import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
 import org.cytoscape.model.CyRow;
-import org.cytoscape.view.model.CyNetworkView;
 
-import de.hhu.ba.yoshikoWrapper.core.CyCore;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
 
@@ -26,10 +23,6 @@ public class ClusterView extends ComfortPanel {
 	private final JLabel title;
 	private final JLabel clusterSize;
 	
-	private final CyNetworkView clusterView;
-	
-	private CyNetwork clusterSubNet;
-	
 	private final Border regularBorder = BorderFactory.createLineBorder(Color.GRAY);
 	private final Border highlightBorder = BorderFactory.createLineBorder(Color.RED);
 	
@@ -43,15 +36,13 @@ public class ClusterView extends ComfortPanel {
 	public ClusterView(YoshikoCluster c) {
 		
 		this.cluster = c;		
+		
 		//Swing init
 		this.setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
 		
 		title = new JLabel(LocalizationManager.get("cluster")+" "+(c.id+1));
 		clusterSize = new JLabel(LocalizationManager.get("clusterSize")+" "+c.nodes.size());
 				
-		this.clusterSubNet = CyCore.networkFactory.createNetwork();
-		this.clusterView = CyCore.networkViewFactory.createNetworkView(this.clusterSubNet); 
-		
 		this.addAll(title,clusterSize);
 		this.add(Box.createVerticalStrut(4));
 		
@@ -59,7 +50,7 @@ public class ClusterView extends ComfortPanel {
 		for (CyNode n : c.nodes) {
 			this.add(
 					new JLabel(
-						CyCore.cy.getCurrentNetwork().getRow(n).get("name", String.class)
+							c.originalGraph.getRow(n).get("name", String.class)
 					)
 				);
 		}
@@ -79,13 +70,13 @@ public class ClusterView extends ComfortPanel {
 		public void mousePressed(MouseEvent e) {
 			//Undo previous selection
 			
-			List<CyRow> allRows = CyCore.cy.getCurrentNetwork().getDefaultNodeTable().getAllRows();
+			List<CyRow> allRows = cluster.originalGraph.getDefaultNodeTable().getAllRows();
 			for (CyRow r: allRows) {
 				r.set("selected", false);
 			}
 			//Select nodes corresponding to the cluster
 			for (CyNode n : cluster.nodes) {
-				CyCore.cy.getCurrentNetwork().getRow(n).set("selected", true);
+				cluster.originalGraph.getRow(n).set("selected", true);
 			}
 		}
 		

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

@@ -10,14 +10,6 @@ import javax.swing.JButton;
 import javax.swing.JLabel;
 import javax.swing.JScrollPane;
 
-import org.cytoscape.model.CyNetwork;
-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;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
@@ -56,37 +48,7 @@ public class SolutionTab extends ComfortPanel {
 
 			@Override
 			public void actionPerformed(ActionEvent e) {
-				CyNetwork metaGraph = solution.toMetaGraph();
-				CyNetworkView view = CyCore.networkViewFactory.createNetworkView(metaGraph);
-				//layout solution
-				CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
-				CyCore.dialogTaskManager.execute(
-					layout.createTaskIterator(
-							view, 
-							layout.getDefaultLayoutContext(), 
-							CyLayoutAlgorithm.ALL_NODE_VIEWS,
-							null
-					)
-				);
-				//define style for solution
-				ContinuousMapping<Integer, Double> contMap = (ContinuousMapping<Integer, Double>)CyCore.continuousMappingFactory.createVisualMappingFunction(
-						"clusterSize",
-						Integer.class,
-						BasicVisualLexicon.NODE_SIZE
-					);
-				VisualStyle vs= CyCore.visualStyleFactory.createVisualStyle("Meta-Graph Style");
-				vs.addVisualMappingFunction(contMap);
-				CyCore.visualMappingManager.addVisualStyle(vs);
-
-				
-				CyCore.networkManager.addNetwork(metaGraph);
-				CyCore.networkViewManager.addNetworkView(
-						view
-				);
-
-				CyCore.cy.setCurrentNetworkView(view);
-				vs.apply(CyCore.cy.getCurrentNetworkView());
-				CyCore.cy.getCurrentNetworkView().updateView();
+				solution.exportMetaGraph();
 			}
 			
 		});