Merge remote-tracking branch 'origin/master' into dev_general

pom.xml

@@ -33,7 +33,7 @@
 
 	<groupId>de.hhu.ba</groupId>
 	<artifactId>yoshikoWrapper</artifactId>
-	<version>0.1.1</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

@@ -44,7 +44,9 @@ public class StatusInformer extends CplexInformer {
 	@Override
 	public void updateStatus(YoshikoState state, double value) {
 		if (state == YoshikoState.SOLVING_ILP){
-			taskMonitor.setStatusMessage(LocalizationManager.get("currentGap")+": "+SwingUtil.twoDecimals.format(value)+"%");
+			if (value <= 1.0) {
+				taskMonitor.setStatusMessage(LocalizationManager.get("currentGap")+": "+SwingUtil.twoDecimals.format(value)+"%");
+			}
 		}
 	}
 

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/cytoUtil/GraphAnalyzer.java

+package de.hhu.ba.yoshikoWrapper.cytoUtil;
+
+import java.util.List;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+
+public class GraphAnalyzer {
+	public static boolean isMultiGraph(CyNetwork net) {
+		//TODO: Better algorithm?
+
+
+		int n = net.getNodeCount();
+		List<CyEdge> edges = net.getEdgeList();
+
+		//Easiest check: Check if the graph contains more edges than a complete graph
+		if (edges.size() > (n*(n-1))/2) {
+			return true;
+		}
+
+		for (int i = 0; i < edges.size()-1; i++) {
+			for (int j=i+1; j<edges.size();j++) {
+				if (connectSameNodes(edges.get(i),edges.get(j))){
+					return true;
+				}
+			}
+		}
+
+		return false;
+	}
+
+	private static boolean connectSameNodes(CyEdge e1, CyEdge e2) {
+		if (//Treating all edges as undirected here
+				(e1.getSource() == e2.getTarget() && e1.getTarget() == e2.getSource()) ||
+				(e1.getSource() == e2.getSource() && e1.getTarget() == e2.getTarget())
+				) {
+			return true;
+		}
+		return false;
+	}
+
+	public static boolean isDirected(CyNetwork net) {
+		for (CyEdge e: net.getEdgeList()) {
+			if (e.isDirected()) {
+				return true;
+			}
+		}
+		return false;
+	}
+}

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();
@@ -90,43 +93,54 @@ 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() {
 
-		CyRootNetwork originalGraphAsRoot =
-				CyCore.rootNetworkManager.getRootNetwork(solution.getOriginalGraph());
-
-		//Create nested graph and cluster 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);
+		if (subnet == null) {
+			CyRootNetwork originalGraphAsRoot =
+					CyCore.rootNetworkManager.getRootNetwork(solution.getOriginalGraph());
+
+			//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);
+					}
 				}
 			}
-		}
-
-		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);
 			}
@@ -136,67 +150,38 @@ 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();
+		view.setVisualProperty(NETWORK_WIDTH, new Double(width));
+		view.setVisualProperty(NETWORK_HEIGHT, new Double(height));
+		view.fitContent();
 
-					StyleManager.style(view, CyCore.visualMappingManager.getCurrentVisualStyle());
+		StyleManager.style(view, CyCore.visualMappingManager.getCurrentVisualStyle());
 
-					RenderingEngine<CyNetwork> renderingEngine = CyCore.renderingEngineFactory.createRenderingEngine(label, view);
-					SwingUtilities.invokeLater(new Runnable() {
+		RenderingEngine<CyNetwork> renderingEngine = CyCore.renderingEngineFactory.createRenderingEngine(label, view);
 
-						@Override
-						public void run() {
-							img = renderingEngine.createImage(width,height);
-							label.setIcon(new ImageIcon(img));
-							renderingEngine.dispose();
-							view.dispose();
-						}
-
-					});
-
-
-				}
-				@Override
-				public void cancel() {}
+		img = renderingEngine.createImage(width,height);
+		label.setIcon(new ImageIcon(img));
 
-			}
-	    );
+		renderingEngine.dispose();
+		view.dispose();
+	}
 
-		CyCore.dialogTaskManager.execute(
-				createLayout
-		);
+	public void delete() {
+		if (subnet != null) {
+			CyCore.networkManager.destroyNetwork(subnet);
+		}
 	}
 
 	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/help/HelpLinks.java

@@ -49,7 +49,8 @@ public final class HelpLinks {
 	/**
 	 * The base location of the bachelor thesis paper
 	 */
-	private static final String docLocation = "file:///home/philipp/workspace/cs/BachelorThesis/YoshikoWrapper/thesis/tex/Thesis.pdf";
+	//TODO: Add final location when published
+	private static final String docLocation = "https://gitlab.cs.uni-duesseldorf.de/spohr/YoshikoWrapper/tree/master";
 
 	/**
 	 * A HashMap linking Classes to a link, pointing to a specific subsection of the BachelorThesis paper that is relevant for understanding the Class

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/MainPanel.java

@@ -49,6 +49,7 @@ import javax.swing.ScrollPaneConstants;
 
 import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.application.swing.CytoPanelName;
+import org.cytoscape.model.CyNetwork;
 import org.cytoscape.util.swing.BasicCollapsiblePanel;
 import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.TaskIterator;
@@ -57,6 +58,7 @@ import de.hhu.ba.yoshikoWrapper.core.CyCore;
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
 import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.GraphAnalyzer;
 import de.hhu.ba.yoshikoWrapper.swing.AboutDialogFactory;
 import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
 import de.hhu.ba.yoshikoWrapper.swing.LanguageSwitcherPanel;
@@ -263,6 +265,32 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 		@Override
 		public void actionPerformed(ActionEvent e) {
 
+			CyNetwork networkToBeProcessed = CyCore.cy.getCurrentNetwork();
+
+			//WARNINGS FOR FEATURES THAT ARE NOT RESEARCHED
+			//TODO: (Obviously) research!
+			if (GraphAnalyzer.isMultiGraph(networkToBeProcessed)) {
+				JOptionPane.showMessageDialog(
+						null,
+						LocalizationManager.get("multiGraphWarning"),
+						LocalizationManager.get("optionpane_title"),
+						JOptionPane.WARNING_MESSAGE
+				);
+			}
+
+			//Annotation: Currently Cytoscape is really weird concerning directed/undirected edges
+			//There is an API function isDirected() for edges but all edges are directed
+			//I'll leave this commented out until CS makes sense
+
+//			if (GraphAnalyzer.isDirected(networkToBeProcessed)) {
+//				JOptionPane.showMessageDialog(
+//						null,
+//						LocalizationManager.get("directedGraphWarning"),
+//						LocalizationManager.get("optionpane_title"),
+//						JOptionPane.WARNING_MESSAGE
+//				);
+//			}
+
 			//SWING BLACK MAGIC
 			Window noWindow = null;
 			JDialog statusWindow = new JDialog(noWindow);
@@ -277,7 +305,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 			if (YoshikoLoader.isLibraryLoaded()){
 				AbstractTask yoshiko = new AlgorithmTask(
 					popupLevel,
-					CyCore.cy.getCurrentNetwork(),
+					networkToBeProcessed,
 					fetchParameter()
 				);
 				/**

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

@@ -25,20 +25,26 @@ 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;
 import javax.swing.GroupLayout;
-import javax.swing.GroupLayout.Group;
+import javax.swing.GroupLayout.ParallelGroup;
+import javax.swing.GroupLayout.SequentialGroup;
 import javax.swing.Icon;
 import javax.swing.JButton;
 import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JTabbedPane;
+import javax.swing.LayoutStyle;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
 
 import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.application.swing.CytoPanelName;
@@ -55,6 +61,7 @@ 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;
@@ -78,9 +85,6 @@ NetworkAboutToBeDestroyedListener
 
 	//MACRO
 
-	//TODO: (Nächstes Leben) find a good solution with Swing that scales the panel and respects layout
-	private static final int HACKFIX_FIXED_WIDTH = 128+256;
-
 	private final JTabbedPane tabbedPane;
 
 	private final JButton destroyButton;
@@ -93,6 +97,11 @@ NetworkAboutToBeDestroyedListener
 
 	private boolean isValid;
 
+	//SWING LAYOUT
+
+	private ParallelGroup horizontalGroup;
+	private SequentialGroup verticalGroup;
+
 	public ResultPanel(YoshikoResult result) throws Exception {
 
 		this.result = result;
@@ -101,6 +110,7 @@ NetworkAboutToBeDestroyedListener
 
 		//Init subcomponents
 		invalidLabel = new JLabel();
+		invalidLabel.setHorizontalAlignment(SwingConstants.CENTER);
 		tabbedPane = new JTabbedPane();