Fixes to meta-graph bugs introduced recently

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

@@ -203,22 +203,24 @@ public class SolutionTab extends JPanel {
 		layout = new GroupLayout(this);
 
 		layout.setHorizontalGroup(layout.createParallelGroup(Alignment.CENTER,true)
+				.addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
+				.addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
 				.addGap(8)
 				.addComponent(clusterCount,DEFAULT_SIZE,DEFAULT_SIZE,Short.MAX_VALUE)
 				.addComponent(hideSingles,DEFAULT_SIZE,DEFAULT_SIZE,Short.MAX_VALUE)
 				.addGap(8)
 				.addComponent(scrollPane,PREFERRED_SIZE,PREFERRED_SIZE,Short.MAX_VALUE)
-				.addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
-				.addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
+				.addGap(4)
 		);
 		layout.setVerticalGroup(layout.createSequentialGroup()
+				.addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
+				.addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
 				.addGap(8)
 				.addComponent(clusterCount,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
 				.addComponent(hideSingles,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
 				.addGap(8)
 				.addComponent(scrollPane,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
-				.addComponent(createClusterView,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
-				.addComponent(createMetaGraph,DEFAULT_SIZE,DEFAULT_SIZE,DEFAULT_SIZE)
+				.addGap(4)
 		);
 
 		this.setLayout(layout);

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

@@ -22,6 +22,10 @@ public class CreateClusterViewsTask implements Task {
 	@Tunable
 	public ArrayList<YoshikoCluster> clusters; //TODO: Make Tunable, reference by ID?
 
+	/**
+	 * Killswitch, used to determine if the algorithm has been terminated.
+	 * We can use this to cancel at a given point (so we don't need to finish the entire task)
+	 */
 	private boolean isTerminated;
 
 	/**
@@ -77,11 +81,8 @@ public class CreateClusterViewsTask implements Task {
 						StyleManager.style(subnetView,CyCore.visualMappingManager.getCurrentVisualStyle());
 						CyCore.networkViewManager.addNetworkView(subnetView);
 					}
-
 				}
 			);
-
-
 		}
 	}
 

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

@@ -94,7 +94,7 @@ public class CreateMetaGraphTask extends AbstractTask{
 			//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("clusters")+" "+c.getID());
+			metaGraph.getRow(clusterNode).set("name", LocalizationManager.get("clusters")+" "+(c.getID()+1));
 			metaGraph.getRow(clusterNode).set(StyleManager.CLUSTERSIZE_COLUMN_NAME,c.getSize());
 			map.put(c, clusterNode);
 		}
@@ -105,12 +105,13 @@ public class CreateMetaGraphTask extends AbstractTask{
 		taskMonitor.setStatusMessage(LocalizationManager.get("metaGraph_edges"));
 
 		Iterator<YoshikoCluster> it1 = solution.getClusters().iterator();
-		Iterator<YoshikoCluster> it2 = solution.getClusters().iterator();
 
 		while (it1.hasNext()) {
 			YoshikoCluster c1 = it1.next();
+			Iterator<YoshikoCluster> it2 = solution.getClusters().iterator();
 			while(it2.hasNext()) {
 				YoshikoCluster c2 = it2.next();
+				System.out.println("Debug: Processing edges between cluster "+c1.getID()+" and "+c2.getID());
 
 				if(isTerminated) {
 					throw new Exception("Terminated by user!");
@@ -126,7 +127,9 @@ public class CreateMetaGraphTask extends AbstractTask{
 				for (CyNode c1n : c1.getSubNetwork().getNodeList()) {
 					for (CyNode c2n : c2.getSubNetwork().getNodeList()) {
 						if (solution.getOriginalGraph().containsEdge(c1n, c2n) || solution.getOriginalGraph().containsEdge(c2n, c1n)) {
+							System.out.println("Debug: Found relevant edge from "+c1n.getSUID()+ " to "+c2n.getSUID());
 							if (!metaGraph.containsEdge(map.get(c1), map.get(c2))){
+								System.out.println("We create a new edge for it");
 								CyEdge edge = metaGraph.addEdge(map.get(c1), map.get(c2), false);
 								metaGraph.getRow(edge).set(StyleManager.EDGESTRENGTH_COLUMN_NAME,1);
 							}

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

@@ -9,16 +9,32 @@ import org.cytoscape.work.Tunable;
 import de.hhu.ba.yoshikoWrapper.core.ResultList;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
-import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
 
+/**
+ * A task that retrieves the clusters associated with a given solution in a given result. This is meant to be used via CyRest / command line functionality exclusively
+ *
+ * @author Philipp Spohr, Dec 12, 2017
+ *
+ */
 public class GetClustersTask implements ObservableTask {
 
+
+	/**
+	 * The ID of the result for which the clusters are to be retrieved
+	 */
 	@Tunable(description="The result ID for which the solutions should be displayed", context="nogui")
 	public int resultID = -1;
 
+	/**
+	 * The ID of the solution for which the clusters are to be retrieved
+	 */
 	@Tunable(description="The solution ID for which the solutions should be displayed", context="nogui")
 	public long solutionID = -1;
 
+
+	/**
+	 * The clusters as a collection when they are retrieved
+	 */
 	private Collection<YoshikoCluster> clusters;
 
 	@Override

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

@@ -10,11 +10,23 @@ import de.hhu.ba.yoshikoWrapper.core.ResultList;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoSolution;
 
+/**
+ * Basic task that retrieves solutions associated with a run (result)
+ * This is meant to be invoked from cmd / CyRest exclusively to receive solution IDs
+ * @author Philipp Spohr, Dec 12, 2017
+ *
+ */
 public class GetSolutionsTask implements ObservableTask {
 
+	/**
+	 * The result ID for the result/run for which the solutions are to be retrieved
+	 */
 	@Tunable(description="The result ID for which the solutions should be displayed", context="nogui")
 	public int resultID = -1;
 
+	/**
+	 * The solutions as a collection in case the task was successful
+	 */
 	private Collection<YoshikoSolution> solutions;
 
 	@Override
@@ -27,9 +39,7 @@ public class GetSolutionsTask implements ObservableTask {
 	}
 
 	@Override
-	public void cancel() {
-		// TODO Auto-generated method stub
-	}
+	public void cancel() {} //There is nothing here that remains in an instable state as we are simply reading / retrieving data
 
 	@SuppressWarnings("unchecked")
 	@Override
@@ -44,4 +54,5 @@ public class GetSolutionsTask implements ObservableTask {
 		return null;
 	}
 
+
 }