Updated API to Cyto 3.0.1

Some basic work on Meta-Graph

pom.xml

@@ -4,7 +4,7 @@
 	<properties>
 		<bundle.symbolicName>de.hhu.ba.yoshikoWrapper</bundle.symbolicName>
 		<bundle.namespace>de.hhu.ba.yoshikoWrapper</bundle.namespace>
-		<cytoscape.api.version>3.0.0</cytoscape.api.version>
+		<cytoscape.api.version>3.0.1</cytoscape.api.version>
 		
 		<maven-bundle-plugin.version>2.3.4</maven-bundle-plugin.version>
 		<osgi.api.version>4.2.0</osgi.api.version>
@@ -12,7 +12,7 @@
 
 	<groupId>de.hhu.ba</groupId>
 	<artifactId>yoshikoWrapper</artifactId>
-	<version>0.0.2</version>
+	<version>0.0.3</version>
 	
 	<name>YoshikoWrapper</name>
 
@@ -125,6 +125,12 @@
 			<type>test-jar</type>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>layout-api</artifactId>
+			<version>${cytoscape.api.version}</version>
+			<type>bundle</type>
+		</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

@@ -6,6 +6,7 @@ import org.cytoscape.application.CyApplicationManager;
 import org.cytoscape.application.swing.CySwingApplication;
 import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkManager;
 import org.cytoscape.model.events.AddedEdgesListener;
 import org.cytoscape.model.events.ColumnCreatedListener;
 import org.cytoscape.model.events.ColumnDeletedListener;
@@ -15,6 +16,11 @@ import org.cytoscape.service.util.AbstractCyActivator;
 import org.cytoscape.service.util.CyServiceRegistrar;
 import org.cytoscape.session.events.SessionLoadedListener;
 import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
 import org.cytoscape.work.swing.DialogTaskManager;
 import org.osgi.framework.BundleContext;
 
@@ -47,7 +53,12 @@ public class CyActivator extends AbstractCyActivator {
 		CyCore.networkViewFactory = getService(context, CyNetworkViewFactory.class);
 		CyCore.networkFactory = getService(context, CyNetworkFactory.class);
 		CyCore.swing = getService(context, CySwingApplication.class);
-		
+		CyCore.networkViewManager  = getService(context,CyNetworkViewManager.class);
+		CyCore.networkManager = getService(context,CyNetworkManager.class);
+		CyCore.layoutAlgorithmManager = getService(context,CyLayoutAlgorithmManager.class);
+		CyCore.visualMappingManager = getService(context,VisualMappingManager.class);
+		CyCore.visualStyleFactory = getService(context,VisualStyleFactory.class);
+		CyCore.continuousMappingFactory = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
 		//Set language according to settings
 		LocalizationManager.switchLanguage(cm.getProperties().getProperty("locale", "enUS"));
 

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

@@ -137,7 +137,7 @@ public class AlgorithmTask extends AbstractTask {
 		for (long i=0;i<numberOfSolutions;i++) {
 			
 			taskMonitor.setStatusMessage("Processing solution "+(i+1)+" of "+numberOfSolutions);
-			YoshikoSolution solution = new YoshikoSolution();
+			YoshikoSolution solution = new YoshikoSolution(net);
 			String columnName = "YOSHIKO_SOLUTION_"+(i+1);
 			
 			net.getDefaultNodeTable().deleteColumn(columnName);

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

@@ -3,11 +3,18 @@ package de.hhu.ba.yoshikoWrapper.core;
 import org.cytoscape.application.CyApplicationManager;
 import org.cytoscape.application.swing.CySwingApplication;
 import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkManager;
 import org.cytoscape.service.util.CyServiceRegistrar;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
 import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
 import org.cytoscape.work.swing.DialogTaskManager;
 import org.osgi.framework.BundleContext;
 
+
 /**Simple link collection to enable access to Cytoscape instances
  *
  */
@@ -21,6 +28,12 @@ public class CyCore {
 	public static CyNetworkViewFactory networkViewFactory;
 	public static CyNetworkFactory networkFactory;
 	public static CySwingApplication swing;
+	public static CyNetworkViewManager networkViewManager;
+	public static CyNetworkManager networkManager;
+	public static CyLayoutAlgorithmManager layoutAlgorithmManager;
+	public static VisualMappingManager visualMappingManager;
+	public static VisualStyleFactory visualStyleFactory;
+	public static VisualMappingFunctionFactory continuousMappingFactory;
 
 	//
 }

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

 package de.hhu.ba.yoshikoWrapper.graphModel;
 
 import java.util.ArrayList;
+import java.util.HashMap;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+
+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;
 	
-	public YoshikoSolution() {
+	public YoshikoSolution(CyNetwork originalGraph) {
 		cluster = new ArrayList<YoshikoCluster>();
+		this.originalGraph = originalGraph;
+	}
+
+	/**
+	 * Transforms this solution in a meta-graph where each cluster is represented by one node
+	 * @return The meta-graph as CyNetwork
+	 */
+	public CyNetwork toMetaGraph() {
+		
+		CyNetwork metaGraph = CyCore.networkFactory.createNetwork();
+		
+		metaGraph.getRow(metaGraph).set(CyNetwork.NAME, LocalizationManager.get("metaGraph"));
+		
+		metaGraph.getDefaultNodeTable().createColumn("clusterSize", Integer.class, false);
+		
+		//Map Cluster to Nodes for further reference
+		HashMap<YoshikoCluster,CyNode> map = new HashMap<YoshikoCluster,CyNode>();
+		
+		//Add nodes
+		for (YoshikoCluster c: cluster) {
+			CyNode clusterNode = metaGraph.addNode();
+			metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.id);
+			metaGraph.getRow(clusterNode).set("clusterSize",c.nodes.size());
+			map.put(c, clusterNode);
+		}
+		
+		//Add edges (O(|C|^2*|V|^2) can maybe be improved? //TODO
+		for (YoshikoCluster c1:cluster) {
+			for (YoshikoCluster c2:cluster) {
+				if (
+						metaGraph.containsEdge(map.get(c1),map.get(c2))
+						|| c1 == c2
+						) {
+					continue;
+				}
+				clusterloop:
+				for (CyNode c1n : c1.nodes) {
+					for (CyNode c2n : c2.nodes) {
+						if (originalGraph.containsEdge(c1n, c2n) || originalGraph.containsEdge(c2n, c1n)) {
+							metaGraph.addEdge(map.get(c1), map.get(c2), false);
+							break clusterloop;
+						}
+					}
+				}
+			}
+		}
+		return metaGraph;
 	}
 	
 }

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

 package de.hhu.ba.yoshikoWrapper.gui;
 
 import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 
 import javax.swing.Box;
 import javax.swing.BoxLayout;
@@ -8,6 +10,14 @@ 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;
@@ -42,7 +52,45 @@ public class SolutionTab extends ComfortPanel {
 		clusterCount = new JLabel(LocalizationManager.get("clusterFound")+" "+s.cluster.size());
 		
 		createMetaGraph = new JButton(LocalizationManager.get("createMetaGraph"));
-		this.addAll(clusterCount,scrollPane);
+		createMetaGraph.addActionListener(new ActionListener() {
+
+			@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();
+			}
+			
+		});
+		this.addAll(clusterCount,scrollPane,createMetaGraph);
 	}
 	
 }

src/main/resources/YoshikoStrings.properties

@@ -21,3 +21,4 @@ nrSolutions = Number of Solutions:
 redRuleChooserTitle = Reduction Rules
 discardSolution = Discard
 createMetaGraph = Create Meta-Graph
+metaGraph = Meta Graph
\ No newline at end of file