Support for retrieving clusters via CyRest

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

@@ -127,6 +127,13 @@ public class CyActivator extends AbstractCyActivator {
 		props_GET_SOLUTIONS.setProperty(COMMAND_DESCRIPTION,"Retrieve solutions associated with a result");
 		registerService(context, commandTaskFactory_GET_SOLUTIONS, TaskFactory.class, props_GET_SOLUTIONS);
 
+		TaskFactory commandTaskFactory_GET_CLUSTERS = new CommandTaskFactory(YoshikoCommand.GET_CLUSTERS);
+		Properties props_GET_CLUSTERS = new Properties();
+		props_GET_CLUSTERS.setProperty(COMMAND_NAMESPACE, "yoshiko");
+		props_GET_CLUSTERS.setProperty(COMMAND, YoshikoCommand.GET_CLUSTERS.toString());
+		props_GET_CLUSTERS.setProperty(COMMAND_DESCRIPTION,"Retrieve clusters associated with a solution");
+		registerService(context, commandTaskFactory_GET_CLUSTERS, TaskFactory.class, props_GET_CLUSTERS);
+
 		//Initialize and register main panel
 		MainPanel mainPanel = new MainPanel();
 		registerService(context,mainPanel,CytoPanelComponent.class, new Properties());

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

@@ -88,4 +88,8 @@ public class YoshikoResult{
 		return id;
 	}
 
+	public YoshikoSolution getSolution(long solutionID) {
+		return solutions.get(solutionID);
+	}
+
 }

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

@@ -22,7 +22,6 @@
 package de.hhu.ba.yoshikoWrapper.graphModel;
 
 import java.util.Collection;
-import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 

src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/CommandTaskFactory.java

@@ -4,9 +4,7 @@ import org.cytoscape.work.TaskFactory;
 import org.cytoscape.work.TaskIterator;
 
 import de.hhu.ba.yoshikoWrapper.core.ParameterSet;
-import de.hhu.ba.yoshikoWrapper.tasks.AlgorithmTask;
-import de.hhu.ba.yoshikoWrapper.tasks.CreateClusterViewsTask;
-import de.hhu.ba.yoshikoWrapper.tasks.GetSolutionsTask;
+import de.hhu.ba.yoshikoWrapper.tasks.*;
 
 public class CommandTaskFactory implements TaskFactory{
 
@@ -39,7 +37,11 @@ public class CommandTaskFactory implements TaskFactory{
 					new GetSolutionsTask()
 					);
 		}
-
+		else if (command == YoshikoCommand.GET_CLUSTERS) {
+			return new TaskIterator(
+					new GetClustersTask()
+					);
+		}
 		else if (command == YoshikoCommand.PERFORM_ALGORITHM) {
 			return new TaskIterator(
 					new AlgorithmTask(

src/main/java/de/hhu/ba/yoshikoWrapper/taskFactories/YoshikoCommand.java

@@ -12,7 +12,8 @@ public enum YoshikoCommand {
 	CREATE_CLUSTER_VIEW,
 	CREATE_META_GRAPH,
 	PERFORM_ALGORITHM,
-	GET_SOLUTIONS;
+	GET_SOLUTIONS,
+	GET_CLUSTERS;
 
 	@Override
 	public String toString() {
@@ -22,6 +23,9 @@ public enum YoshikoCommand {
 		else if (this==CREATE_CLUSTER_VIEW) {
 			return "createcvs";
 		}
+		else if (this==GET_CLUSTERS) {
+			return "clusters"; //TODO: maybe smarter names for the commands
+		}
 		else if (this==GET_SOLUTIONS) {
 			return "solutions";
 		}

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

 package de.hhu.ba.yoshikoWrapper.tasks;
 
-import java.util.ArrayList;
+import java.util.Collection;
 
 import org.cytoscape.work.ObservableTask;
 import org.cytoscape.work.TaskMonitor;
@@ -17,9 +17,9 @@ public class GetClustersTask implements ObservableTask {
 	public int resultID = -1;
 
 	@Tunable(description="The solution ID for which the solutions should be displayed", context="nogui")
-	public int solutionID = -1;
+	public long solutionID = -1;
 
-	private ArrayList<YoshikoCluster> clusters;
+	private Collection<YoshikoCluster> clusters;
 
 	@Override
 	public void run(TaskMonitor taskMonitor) throws Exception {
@@ -27,11 +27,14 @@ public class GetClustersTask implements ObservableTask {
 		if (result == null) {
 			throw new Exception("No result with ID: "+resultID+" was found!"); //TODO: Localization
 		}
+		if (result.getSolution(solutionID)== null) {
+			throw new Exception("No solution with ID: "+solutionID+" was found!"); //TODO: Localization
+		}
+		clusters = result.getSolution(solutionID).getClusters();
 	}
 
 	@Override
 	public void cancel() {
-		// TODO Auto-generated method stub
 
 	}
 
@@ -40,7 +43,9 @@ public class GetClustersTask implements ObservableTask {
 	public <R> R getResults(Class<? extends R> type) {
 		if (type.equals(String.class)) {
 			String ret = "";
-
+			for (YoshikoCluster c: clusters) {
+				ret+="Cluster[ID="+c.getID()+"]: "+c.getSize()+" nodes\n";
+			}
 			return (R) ret;
 		}
 		return null;