Some refactor

.settings/org.eclipse.core.resources.prefs

 eclipse.preferences.version=1
 encoding//src/main/java=UTF-8
 encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
 encoding/<project>=UTF-8

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

@@ -59,6 +59,8 @@ public class YoshikoCluster {
 	private ArrayList<CyNode> nodes;
 	private CySubNetwork net;
 
+	private Image img;
+
 	//SYMBOLIC LINKS
 	private final CyNetwork originalGraph;
 	private Logger logger = YoshikoLogger.getInstance().getLogger();
@@ -70,9 +72,8 @@ public class YoshikoCluster {
 		this.nodes = new ArrayList<CyNode>();
 	}
 
-	private void createSubNetwork() {
+	public void createSubNetwork() {
 
-		if (net == null) {
 		CyRootNetwork originalGraphAsRoot = CyCore.rootNetworkManager.getRootNetwork(originalGraph);
 
 		//Create nested graph and cluster subnet
@@ -92,7 +93,6 @@ public class YoshikoCluster {
 
 		net = subnet; //Save for further reference
 	}
-	}
 
 	/**
 	 * Attempt to select the nodes belonging to this cluster in the original Graph given that they still exist
@@ -114,12 +114,20 @@ public class YoshikoCluster {
 	}
 
 
-	public void generateImage(JLabel label, int width, int height) {
+	public void applyImage(JLabel label, int width, int height) {
 
 		if (net == null) {
-			createSubNetwork();
+			return;
+		}
+
+		if (img != null) {
+			getImage(width,height,label);
+			label.setIcon(new ImageIcon(img));
+			return;
+		}
 	}
 
+	private void getImage(int width, int height,JLabel label) {
 		final CyNetworkView view = CyCore.networkViewFactory.createNetworkView(net);
 
 		//layout cluster
@@ -150,7 +158,7 @@ public class YoshikoCluster {
 
 						@Override
 						public void run() {
-							Image img = renderingEngine.createImage(width,height);
+							img = renderingEngine.createImage(width,height);
 							label.setIcon(new ImageIcon(img));
 
 							renderingEngine.dispose();
@@ -161,11 +169,8 @@ public class YoshikoCluster {
 
 
 				}
-
 				@Override
-				public void cancel() {
-					//Nothing to do as GC is handled by JAVA
-				}
+				public void cancel() {}
 
 			}
 	    );
@@ -173,8 +178,6 @@ public class YoshikoCluster {
 		CyCore.dialogTaskManager.execute(
 				createLayout
 		);
-
-
 	}
 
 	public int getSize() {
@@ -186,9 +189,6 @@ public class YoshikoCluster {
 	}
 
 	public CySubNetwork getSubNetwork() {
-		if (net == null) {
-			createSubNetwork();
-		}
 		return net;
 	}
 

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

@@ -46,130 +46,33 @@ 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;
+	private final CyNetwork originalGraph;
 
 	public ArrayList<YoshikoCluster> cluster;
-	public int id;
 
-	public YoshikoSolution(CyNetwork originalGraph) {
+	private final long id;
+
+	public YoshikoSolution(CyNetwork originalGraph, long id) {
 		cluster = new ArrayList<YoshikoCluster>();
 		this.originalGraph = originalGraph;
+		this.id = id;
 	}
 
-	/**
-	 * Transforms this solution in a meta-graph where each cluster is represented by one node
-	 * The nodes are linked to subgraphs representing the cluster and also their size is scaled relative to cluster size
-	 */
-	public void exportMetaGraph() {
-
-		CyNetwork metaGraph = CyCore.networkFactory.createNetwork();
-
-		metaGraph.getRow(metaGraph).set(CyNetwork.NAME, LocalizationManager.get("metaGraph"));
-
-		metaGraph.getDefaultNodeTable().createColumn("clusterSize", Integer.class, false);
-		metaGraph.getDefaultEdgeTable().createColumn("edgeStrength", Integer.class, false);
-
-		CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
-
-
-		//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();
-			CySubNetwork subnet = c.getSubNetwork();
-			CyCore.networkManager.addNetwork(subnet);
-			//Create network view and register it
-			CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
-			//layout cluster
-			CyCore.dialogTaskManager.execute(
-				layout.createTaskIterator(
-						subnetView,
-						layout.getDefaultLayoutContext(),
-						CyLayoutAlgorithm.ALL_NODE_VIEWS,
-						null
-				)
-			);
-
-			StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
-
-			CyCore.networkViewManager.addNetworkView(subnetView);
-
-			clusterNode.setNetworkPointer(subnet);
-			//Set node attributes
-			metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.getID());
-			metaGraph.getRow(clusterNode).set(StyleManager.CLUSTERSIZE_COLUMN_NAME,c.getSize());
-			map.put(c, clusterNode);
-		}
+	//_____________GETTER / SETTER ________________//
 
-		//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;
+	public ArrayList<YoshikoCluster> getCluster() {
+		return cluster;
 	}
-				for (CyNode c1n : c1.getSubNetwork().getNodeList()) {
-					for (CyNode c2n : c2.getSubNetwork().getNodeList()) {
-						if (originalGraph.containsEdge(c1n, c2n) || originalGraph.containsEdge(c2n, c1n)) {
-							if (!metaGraph.containsEdge(map.get(c1), map.get(c2))){
-								CyEdge edge = metaGraph.addEdge(map.get(c1), map.get(c2), false);
-								metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,1);
-							}
-							else {
-								CyEdge edge = metaGraph.getConnectingEdgeList(map.get(c1), map.get(c2), Type.ANY).get(0);
-								metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,
-								metaGraph.getRow(edge).get(StyleManager.EDGESTRENGTH_COLUMN_NAME, Integer.class)+1
-										);
-							}
-						}
-					}
-				}
-			}
-		}
-
-		CyNetworkView view = CyCore.networkViewFactory.createNetworkView(metaGraph);
-
-		//Layout and style solution
 
-		TaskIterator it = 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());
+	public CyNetwork getOriginalGraph() {
+		return originalGraph;
 	}
 
-			@Override
-			public void cancel() {}
-
-		});
-
-		CyCore.dialogTaskManager.execute(
-				it
-		);
-
-		CyCore.networkManager.addNetwork(metaGraph);
-		CyCore.networkViewManager.addNetworkView(
-				view
-		);
-
-		view.updateView();
-
-		CyCore.cy.setCurrentNetworkView(view);
+	/**
+	 * @return the id
+	 */
+	public long getId() {
+		return id;
 	}
 
 }

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

@@ -48,8 +48,9 @@ public class ClusterView extends JPanel {
 	private final JLabel icon;
 	private final BasicCollapsiblePanel nodeList;
 
-	private final Border regularBorder = BorderFactory.createLineBorder(Color.GRAY,3);
+	private final Border regularBorder = BorderFactory.createLineBorder(Color.GRAY,1);
 	private final Border highlightBorder = BorderFactory.createLineBorder(GraphicsLoader.yoshikoGreen,3);
+	private final Border selectedBorder = BorderFactory.createLineBorder(Color.BLUE,3);
 
 	//SYMBOLIC LINKS
 
@@ -69,7 +70,7 @@ public class ClusterView extends JPanel {
 		clusterSize = new JLabel(LocalizationManager.get("clusterSize")+" "+c.getSize());
 		icon = new JLabel();
 		icon.setBorder(BorderFactory.createLineBorder(Color.BLACK));
-		cluster.generateImage(icon,128, 128);
+		cluster.applyImage(icon,128, 128);
 
 		SwingUtil.addAll(this,title,clusterSize,icon);
 		this.add(Box.createVerticalStrut(4));

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

@@ -53,7 +53,6 @@ import org.cytoscape.util.swing.BasicCollapsiblePanel;
 import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.TaskIterator;
 
-import de.hhu.ba.yoshikoWrapper.core.AlgorithmTask;
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
@@ -63,6 +62,7 @@ import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
 import de.hhu.ba.yoshikoWrapper.swing.LanguageSwitcherPanelFactory;
 import de.hhu.ba.yoshikoWrapper.swing.LibraryPanelFactory;
 import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
+import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
 
 /**This class describes the Swing Panel that the user interacts with in cytoscape
  *

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

@@ -162,7 +162,7 @@ public class ResultPanel extends JPanel implements CytoPanelComponent{
 	private void addSolutionTab(YoshikoSolution s) {
 		SolutionTab tab = new SolutionTab(s);
 		solutionTabs.add(
-				LocalizationManager.get("solution")+" "+(s.id+1),
+				LocalizationManager.get("solution")+" "+(s.getId()+1),
 				tab
 		);
 	}

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

@@ -32,10 +32,14 @@ import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 
+import org.cytoscape.work.TaskIterator;
+
+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;
 import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
+import de.hhu.ba.yoshikoWrapper.tasks.CreateMetaGraphTask;
 
 @SuppressWarnings("serial")
 public class SolutionTab extends JPanel {
@@ -88,7 +92,11 @@ public class SolutionTab extends JPanel {
 
 			@Override
 			public void actionPerformed(ActionEvent e) {
-				solution.exportMetaGraph();
+				CyCore.dialogTaskManager.execute(
+						new TaskIterator(1,
+								new CreateMetaGraphTask(solution)
+						)
+				);
 			}
 
 		});

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

@@ -19,7 +19,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  ******************************************************************************/
-package de.hhu.ba.yoshikoWrapper.core;
+package de.hhu.ba.yoshikoWrapper.tasks;
 
 import java.awt.Window;
 import java.util.Properties;
@@ -34,6 +34,11 @@ import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.TaskMonitor;
 import org.slf4j.Logger;
 
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
+import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.core.NetworkParser;
+import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
+import de.hhu.ba.yoshikoWrapper.core.StatusInformer;
 import de.hhu.ba.yoshikoWrapper.cytoUtil.NodeMap;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
@@ -49,6 +54,7 @@ import de.hhu.ba.yoshikoWrapper.swing.components.ResultPanel;
 
 public class AlgorithmTask extends AbstractTask {
 
+	private String SOLUTION_COLUMN_PREFIX = "yoshikoSolution_";
 
 	//Symbolic links
 	private static Logger logger = YoshikoLogger.getInstance().getLogger();
@@ -137,20 +143,18 @@ public class AlgorithmTask extends AbstractTask {
 
 		long numberOfSolutions = result.getNumberOfSolutions();
 
-
 		taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO localize
 
 		YoshikoResult yoshikoResult = new YoshikoResult();
 		yoshikoResult.flags = result.getFlags();
 
-		System.out.print("ILP FLAG: "+yoshikoResult.flags.getIlpGenerated());
 
 		//Loop over (multiple) solutions
 		for (long i=0;i<numberOfSolutions;i++) {
 
 			taskMonitor.setStatusMessage("Processing solution "+(i+1)+" of "+numberOfSolutions);
-			YoshikoSolution solution = new YoshikoSolution(net);
-			String columnName = "YOSHIKO_SOLUTION_"+(i+1);
+			YoshikoSolution solution = new YoshikoSolution(net,i);
+			String columnName = SOLUTION_COLUMN_PREFIX+(i+1);
 
 			net.getDefaultNodeTable().deleteColumn(columnName);
 			net.getDefaultNodeTable().createColumn(columnName, String.class, false);
@@ -170,16 +174,18 @@ public class AlgorithmTask extends AbstractTask {
 
 				long sizeOfCluster = clusterVector.size();
 				for (int l=0;l<sizeOfCluster;l++) { //Unsafe mismatch int long
-					taskMonitor.setStatusMessage("Processing entry "+(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?)
 				}
-				cluster.getSubNetwork();
+				cluster.createSubNetwork();
+				//Register cluster with solution for further reference
 				solution.cluster.add(cluster);
 			}
+			//Register solution with result for further reference
 			yoshikoResult.solutions.add(solution);
 		}
 

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

+package de.hhu.ba.yoshikoWrapper.tasks;
+
+import java.util.HashMap;
+
+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.work.AbstractTask;
+import org.cytoscape.work.Task;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskMonitor;
+
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
+import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.StyleManager;
+import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
+import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
+
+public class CreateMetaGraphTask extends AbstractTask {
+
+	private final YoshikoSolution solution;
+
+	public CreateMetaGraphTask(YoshikoSolution s) {
+		this.solution = s;
+	}
+
+	@Override
+	public void run(TaskMonitor taskMonitor) throws Exception {
+		CyNetwork metaGraph = CyCore.networkFactory.createNetwork();
+
+		metaGraph.getRow(metaGraph).set(CyNetwork.NAME, LocalizationManager.get("metaGraph"));
+
+		metaGraph.getDefaultNodeTable().createColumn("clusterSize", Integer.class, false);
+		metaGraph.getDefaultEdgeTable().createColumn("edgeStrength", Integer.class, false);
+
+		CyLayoutAlgorithm layout = CyCore.layoutAlgorithmManager.getDefaultLayout();
+
+
+		//Map Cluster to Nodes for further reference
+		HashMap<YoshikoCluster,CyNode> map = new HashMap<YoshikoCluster,CyNode>();
+
+
+		//Add nodes
+		for (YoshikoCluster c: solution.getCluster()) {
+
+
+
+			CyNode clusterNode = metaGraph.addNode();
+			CySubNetwork subnet = c.getSubNetwork();
+			CyCore.networkManager.addNetwork(subnet);
+			//Create network view and register it
+			CyNetworkView subnetView = CyCore.networkViewFactory.createNetworkView(subnet);
+			//layout cluster
+			CyCore.dialogTaskManager.execute(
+				layout.createTaskIterator(
+						subnetView,
+						layout.getDefaultLayoutContext(),
+						CyLayoutAlgorithm.ALL_NODE_VIEWS,
+						null
+				)
+			);
+
+			StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
+
+			CyCore.networkViewManager.addNetworkView(subnetView);
+
+			clusterNode.setNetworkPointer(subnet);
+			//Set node attributes
+			metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("cluster")+" "+c.getID());
+			metaGraph.getRow(clusterNode).set(StyleManager.CLUSTERSIZE_COLUMN_NAME,c.getSize());
+			map.put(c, clusterNode);
+		}
+
+		//Add edges (O(|C|^2*|V|^2) can maybe be improved? //TODO
+		for (YoshikoCluster c1:solution.getCluster()) {
+			for (YoshikoCluster c2:solution.getCluster()) {
+				if (
+						metaGraph.containsEdge(map.get(c1),map.get(c2))
+						|| c1 == c2
+						) {
+					continue;
+				}
+				for (CyNode c1n : c1.getSubNetwork().getNodeList()) {
+					for (CyNode c2n : c2.getSubNetwork().getNodeList()) {
+						if (solution.getOriginalGraph().containsEdge(c1n, c2n) || solution.getOriginalGraph().containsEdge(c2n, c1n)) {
+							if (!metaGraph.containsEdge(map.get(c1), map.get(c2))){
+								CyEdge edge = metaGraph.addEdge(map.get(c1), map.get(c2), false);
+								metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,1);
+							}
+							else {
+								CyEdge edge = metaGraph.getConnectingEdgeList(map.get(c1), map.get(c2), Type.ANY).get(0);
+								metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,
+								metaGraph.getRow(edge).get(StyleManager.EDGESTRENGTH_COLUMN_NAME, Integer.class)+1
+										);
+							}
+						}
+					}
+				}
+			}
+		}
+
+		CyNetworkView view = CyCore.networkViewFactory.createNetworkView(metaGraph);
+
+		//Layout and style solution
+
+		TaskIterator it = 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);
+		CyCore.networkViewManager.addNetworkView(
+				view
+		);
+
+		view.updateView();
+
+		CyCore.cy.setCurrentNetworkView(view);
+	}
+
+}

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

+/**
+ * 
+ */
+/**
+ * @author Philipp Spohr, Sep 14, 2017
+ *
+ */
+package de.hhu.ba.yoshikoWrapper.tasks;
\ No newline at end of file