Added support for auto config of reduction rules

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

@@ -22,5 +22,7 @@ public class ParameterSet {
 	public boolean useHeuristic;
 	public int solCount;
 	public boolean disableMultiThreading;
+	/**Describes whether auto configuration of the reduction rules is to be used. Overrides the bit mask.**/
+	public boolean suggestReduction;
 
 }

src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/GraphAnalyzer.java

@@ -2,10 +2,19 @@ package de.hhu.ba.yoshikoWrapper.cytoUtil;
 
 import java.util.List;
 
+import org.cytoscape.model.CyColumn;
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyRow;
+import org.slf4j.Logger;
+
+import de.hhu.ba.yoshikoWrapper.logging.YoshikoLogger;
+
 
 public class GraphAnalyzer {
+
+	private static Logger logger = YoshikoLogger.getInstance().getLogger();
+
 	public static boolean isMultiGraph(CyNetwork net) {
 		//TODO: Better algorithm?
 
@@ -47,4 +56,87 @@ public class GraphAnalyzer {
 		}
 		return false;
 	}
+
+	/**
+	 * Generates a fitting bitmask by choosing the reduction rules that appear to be the best choice based on current research
+	 * @param containsRealValues
+	 * @param heuristic
+	 * @return
+	 */
+	public static String suggestReductionRules(boolean containsRealValues, boolean heuristic) {
+
+		//TODO: Maybe also choose SNR Factor?
+		//TODO: More research, identify good rules
+
+		boolean useCRule = false,useCCRule= false,useACRule= false,useHERule= false,usePDRRule= false,useSNRule = false;
+		String ret = "";
+
+		//First of all: We don't choose any rules when in heuristic mode
+		if (!heuristic) {
+			//We check if the graph contains real weights
+			if (!containsRealValues) {
+				useCRule = true;
+				useCCRule = true;
+				useACRule = true;
+				useHERule = true;
+			}
+			usePDRRule = true;
+			useSNRule = true;
+		}
+
+		ret += (useCRule ? "1" : "0");
+		ret += (useCCRule ? "1" : "0");
+		ret += (useACRule ? "1" : "0");
+		ret += (useHERule ? "1" : "0");
+		ret += (usePDRRule ? "1" : "0");
+		ret += (useSNRule ? "1" : "0");
+
+		//logger.info("Suggesting the following reduction-rules bitmask: "+ret);
+		System.out.println("Suggesting the following reduction-rules bitmask: "+ret);
+
+		return ret;
+	}
+
+	public static boolean containsRealValues(
+			CyNetwork net,
+			CyColumn weightColumn,
+			CyColumn permanentColumn,
+			CyColumn forbiddenColumn,
+			double defaultInsertionCost,
+			double defaultDeletionCost)
+	{
+		//Simple checks: Deletion and Insertion Costs
+		if (defaultInsertionCost % 1 != 0 || defaultDeletionCost % 1 != 0) {
+			return true;
+		}
+
+		if (net != null){
+			//Fetch edges
+			List<CyEdge> edges = net.getEdgeList();
+
+			//Loop over edges
+			for (CyEdge e : edges) {
+
+				//Fetch entry and check if it exists
+				CyRow edgeEntry = net.getRow(e);
+
+				//Check if there is a weight column defined, else skip
+				if (weightColumn != null){
+					//Check if the column contains an entry for the respective edge
+					//It is possible, that there are missing entries
+					if (edgeEntry.get(weightColumn.getName(), weightColumn.getType()) != null){
+						if (weightColumn.getType() == Double.class) {
+							double weight = edgeEntry.get(weightColumn.getName(), Double.class);
+							if (weight%1!=0) {
+								return true;
+							}
+						}
+					}
+				}
+			}
+		}
+		return false;
+	}
+
+
 }

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

@@ -44,12 +44,12 @@ public class EditCostPanel extends JPanel {
 	private final JLabel icLabel;
 	private final JLabel dcLabel;
 
-	private final HelpButton helpButton;
+	//private final HelpButton helpButton;
 
 	public EditCostPanel() {
 
 		//Initialize components
-		helpButton = new HelpButton();
+		//helpButton = new HelpButton();
 
 		columnMapper = new ColumnMapper();
 
@@ -66,7 +66,7 @@ public class EditCostPanel extends JPanel {
 		//Add components
 		SwingUtil.addAll(this,icLabel,icField);
 		SwingUtil.addAll(this,dcLabel,dcField);
-		SwingUtil.addAll(helpButton);
+		//SwingUtil.addAll(helpButton);
 		SwingUtil.addAll(this,columnMapper);
 
 
@@ -74,7 +74,7 @@ public class EditCostPanel extends JPanel {
 		GroupLayout layout = new GroupLayout(this);
 
 		layout.setHorizontalGroup(layout.createParallelGroup()
-				.addComponent(helpButton,Alignment.TRAILING)
+				//.addComponent(helpButton,Alignment.TRAILING)
 				.addComponent(columnMapper)
 				.addGroup(layout.createSequentialGroup()
 						.addGroup(layout.createParallelGroup(Alignment.LEADING)
@@ -90,7 +90,7 @@ public class EditCostPanel extends JPanel {
 		);
 
 		layout.setVerticalGroup(layout.createSequentialGroup()
-				.addComponent(helpButton)
+				//.addComponent(helpButton)
 				.addComponent(columnMapper)
 				.addGroup(layout.createParallelGroup(Alignment.BASELINE)
 						.addComponent(icLabel)

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

@@ -58,7 +58,9 @@ 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.CommandExecutor;
 import de.hhu.ba.yoshikoWrapper.cytoUtil.GraphAnalyzer;
+import de.hhu.ba.yoshikoWrapper.help.HelpLinks;
 import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
 import de.hhu.ba.yoshikoWrapper.swing.LibraryPanelFactory;
 import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
@@ -117,7 +119,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 
 			@Override
 			public void actionPerformed(ActionEvent e) {
-				//CommandExecutorTaskFactory fac;
+				CommandExecutor.executeCommand("cybrowser", "show",HelpLinks.mainInfo , null);
 			}
 
 		});
@@ -312,7 +314,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 				AbstractTask yoshiko = new AlgorithmTask(
 					popupLevel,
 					networkToBeProcessed,
-					fetchParameter()
+					fetchParameters(networkToBeProcessed)
 				);
 				/**
 				 * Don't queue multiple runs at once because that will get messy
@@ -340,7 +342,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 	 * Fetches all the parameters from the various swing components and packs them into a neat abstract wrapper class
 	 * @return The currently selected parameter wrapped in a ParameterSet
 	 */
-	private ParameterSet fetchParameter() {
+	private ParameterSet fetchParameters(CyNetwork net) {
 		ParameterSet ret = new ParameterSet();
 		ret.timeLimit = opModePanel.getTimeLimit();
 		ret.weightColumn = ecPanel.getWeightColumn();
@@ -348,11 +350,12 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 		ret.forbiddenColumn = ecPanel.getForbiddenColumn();
 		ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
 		ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
+		ret.useHeuristic = opModePanel.useHeuristic();
 		ret.reductionRulesBitMask = reductionRulesChooser.getBitMask();
+		ret.suggestReduction = reductionRulesChooser.useAutoConfig();
 		ret.snrMultFactor = reductionRulesChooser.getMultFactor();
 		ret.useTriangleCuts = opModePanel.useTriangleCuts();
 		ret.usePartitionCuts = opModePanel.usePartitionCuts();
-		ret.useHeuristic = opModePanel.useHeuristic();
 		ret.solCount = opModePanel.getSolCount();
 		ret.disableMultiThreading = opModePanel.isMultiThreadingDisabled();
 		return ret;

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

@@ -25,12 +25,16 @@ import static javax.swing.GroupLayout.DEFAULT_SIZE;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
 
 import javax.swing.BoxLayout;
 import javax.swing.GroupLayout;
 import javax.swing.JCheckBox;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
+import javax.swing.JSeparator;
+import javax.swing.SwingConstants;
 import javax.swing.GroupLayout.Alignment;
 
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
@@ -39,6 +43,10 @@ import de.hhu.ba.yoshikoWrapper.swing.SwingUtil;
 @SuppressWarnings("serial")
 public class ReductionRulesChooser extends JPanel{
 
+	private final JCheckBox useAutoConfig;
+
+	private final JSeparator separator;
+
 	private final JCheckBox useCRule;
 	private final JCheckBox useCCRule;
 	private final JCheckBox useACRule;
@@ -54,24 +62,34 @@ public class ReductionRulesChooser extends JPanel{
 	public ReductionRulesChooser() {
 
 		//Initialize subcomponents
+		useAutoConfig = new JCheckBox(LocalizationManager.get("autoConfig"));
+		useAutoConfig.addItemListener(new ItemListener() {
+
+			@Override
+			public void itemStateChanged(ItemEvent e) {
+				enableRuleSelection(e.getStateChange()== ItemEvent.DESELECTED ? true : false);
+			}
+
+		});
+		separator = new JSeparator(SwingConstants.HORIZONTAL);
+		//TODO: Localization
 		useCRule = new JCheckBox("Use Clique Rule");
 		useCCRule = new JCheckBox("Use Critical-Clique Rule");
 		useACRule = new JCheckBox("Use Almost-Clique Rule");
 		useHERule = new JCheckBox("Use Heavy-Edge 3 in 1 Rule");
 		usePDRRule = new JCheckBox("Use Parameter Dependent Reduction Rule");
 		useSNRule = new JCheckBox("Use Similar Neighborhood Rule");
+
 		multFactor = new DoubleInputField(1, Double.POSITIVE_INFINITY);
 		multFactor.setText("1.0");
+
 		SNPanel = new JPanel();
 		SNPanel.setLayout(new BoxLayout(SNPanel,BoxLayout.X_AXIS));
+
 		SwingUtil.addAll(SNPanel,new JLabel(LocalizationManager.get("multFactor")),multFactor);
 
-		useSNRule.setSelected(true);
-		useCRule.setSelected(true);
-		useCCRule.setSelected(true);
-		useACRule.setSelected(true);
-		useHERule.setSelected(true);
-		usePDRRule.setSelected(true);
+		enableRuleSelection(false);
+		useAutoConfig.setSelected(true);
 
 		useSNRule.addActionListener(new ActionListener() {
 			@Override
@@ -87,6 +105,8 @@ public class ReductionRulesChooser extends JPanel{
 
 
 		SwingUtil.addAll(this,
+				useAutoConfig,
+				separator,
 				useCRule,
 				useCCRule,
 				useACRule,
@@ -102,6 +122,8 @@ public class ReductionRulesChooser extends JPanel{
 		layout.setAutoCreateGaps(true);
 
 		layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING,true)
+			.addComponent(useAutoConfig, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+			.addComponent(separator, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 			.addComponent(useCRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 			.addComponent(useCCRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 			.addComponent(useACRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
@@ -112,6 +134,8 @@ public class ReductionRulesChooser extends JPanel{
 		);
 
 		layout.setVerticalGroup(layout.createSequentialGroup()
+			.addComponent(useAutoConfig, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
+			.addComponent(separator, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 			.addComponent(useCRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 			.addComponent(useCCRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
 			.addComponent(useACRule, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
@@ -126,6 +150,17 @@ public class ReductionRulesChooser extends JPanel{
 	}
 
 
+	protected void enableRuleSelection(boolean enable) {
+		useCRule.setEnabled(enable);
+		useCCRule.setEnabled(enable);
+		useACRule.setEnabled(enable);
+		useHERule.setEnabled(enable);
+		usePDRRule.setEnabled(enable);
+		useSNRule.setEnabled(enable);
+		multFactor.setEnabled(enable);
+	}
+
+
 	/** Creates a 6 Bit bitmask representing the currently selected choice of reduction rules.
 	 * @return
 	 */
@@ -140,6 +175,10 @@ public class ReductionRulesChooser extends JPanel{
 		return ret;
 	}
 
+	public boolean useAutoConfig() {
+		return useAutoConfig.isSelected();
+	}
+
 	public double getMultFactor() {
 		if (useSNRule.isSelected()) {
 			return multFactor.getValueAsDouble();

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

@@ -51,7 +51,7 @@ 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.CreateClusterViews;
+import de.hhu.ba.yoshikoWrapper.tasks.CreateClusterViewsTask;
 import de.hhu.ba.yoshikoWrapper.tasks.CreateMetaGraphTask;
 /**
  * Swing Component, that represents one solution of a Yoshiko result and displays it
@@ -149,7 +149,7 @@ public class SolutionTab extends JPanel {
 				}
 				CyCore.dialogTaskManager.execute(
 						new TaskIterator(1,
-							new CreateClusterViews(
+							new CreateClusterViewsTask(
 								selectedClusters
 							)
 						)

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

@@ -3,7 +3,9 @@ package de.hhu.ba.yoshikoWrapper.taskFactories;
 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;
 
 public class CommandTaskFactory implements TaskFactory{
 
@@ -21,7 +23,11 @@ public class CommandTaskFactory implements TaskFactory{
 	public TaskIterator createTaskIterator() {
 		//We simply switch between the possible commands
 		if (command == YoshikoCommand.CREATE_CLUSTER_VIEW) {
-			return null;
+			return new TaskIterator(
+					new CreateClusterViewsTask(
+							null
+							)
+					);
 		}
 		else if (command == YoshikoCommand.CREATE_META_GRAPH) {
 			return null;
@@ -31,7 +37,7 @@ public class CommandTaskFactory implements TaskFactory{
 					new AlgorithmTask(
 							null,
 							null,
-							null
+							new ParameterSet()
 							)
 					);
 		}

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

@@ -32,6 +32,7 @@ import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
 import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.ContainsTunables;
+import org.cytoscape.work.ObservableTask;
 import org.cytoscape.work.TaskMonitor;
 import org.cytoscape.work.Tunable;
 import org.slf4j.Logger;
@@ -41,6 +42,7 @@ 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.GraphAnalyzer;
 import de.hhu.ba.yoshikoWrapper.cytoUtil.NodeMap;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoResult;
@@ -54,7 +56,7 @@ import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
 import de.hhu.ba.yoshikoWrapper.swing.components.ResultPanel;
 
 
-public class AlgorithmTask extends AbstractTask {
+public class AlgorithmTask extends AbstractTask implements ObservableTask {
 
 	//Constants
 	private static final String SOLUTION_COLUMN_PREFIX = "yoshikoSolution_"; //TODO: Make customizable?
@@ -77,12 +79,15 @@ public class AlgorithmTask extends AbstractTask {
 	public CyNetwork net;
 
 	//Temps, pointing to and need to be freed in C++
-	private LibraryInput input;
-	private ClusterEditingSolutions result;
-	private CoreAlgorithm ca;
+	private LibraryInput c_input;
+	private ClusterEditingSolutions c_result;
+	private CoreAlgorithm c_algorithm;
 
 	private ResultPanel resultPanel;
 
+	private YoshikoResult result;
+
+
 	/**
 	 * Default constructor, creates a new AlgorithmTask
 	 * @param statusWindow The Window in which the status-bar is to be shown, can be null
@@ -111,7 +116,7 @@ public class AlgorithmTask extends AbstractTask {
 		//Get current network
 		if (net == null) {
 			logger.warn("CoreAlgorithm called on a net that is NULL!");
-			throw new Exception("CoreAlgorithm called on a net that is NULL!");
+			throw new Exception("CoreAlgorithm called on a net that is NULL!"); //TODO: Localize
 		}
 
 		//Set time limit
@@ -127,8 +132,8 @@ public class AlgorithmTask extends AbstractTask {
 		NodeMap nodeMap  = new NodeMap(net);
 		taskMonitor.setProgress(0.1);
 
-		//Generate an input instance from the network
-		input = NetworkParser.parseNetwork(
+		//Generate an c_input instance from the network
+		c_input = NetworkParser.parseNetwork(
 				net,
 				nodeMap,
 				parameterSet.weightColumn,
@@ -138,11 +143,24 @@ public class AlgorithmTask extends AbstractTask {
 				);
 		taskMonitor.setProgress(0.2);
 
+		boolean containsRealValues = GraphAnalyzer.containsRealValues(
+				net,
+				parameterSet.weightColumn,
+				parameterSet.permanentColumn,
+				parameterSet.forbiddenColumn,
+				parameterSet.defaultInsertionCost,
+				parameterSet.defaultDeletionCost);
+
+		//Suggest reduction rules
+		if (parameterSet.suggestReduction) {
+			parameterSet.reductionRulesBitMask = GraphAnalyzer.suggestReductionRules(containsRealValues, parameterSet.useHeuristic);
+		}
+
 		//Set the default value for insertion cost
-		input.setDefaultInsertionCost(parameterSet.defaultInsertionCost);
+		c_input.setDefaultInsertionCost(parameterSet.defaultInsertionCost);
 
 		//Call Yoshiko <<< Algorithm is performed here
-		ca = LibraryInterface.getRun(input,
+		c_algorithm = LibraryInterface.getRun(c_input,
 				parameterSet.solCount,
 				parameterSet.reductionRulesBitMask,
 				parameterSet.snrMultFactor,
@@ -152,26 +170,26 @@ public class AlgorithmTask extends AbstractTask {
 		);
 
 
-		ca.registerCplexInformer(new StatusInformer(statusWindow,taskMonitor));
+		c_algorithm.registerCplexInformer(new StatusInformer(statusWindow,taskMonitor));
 
-		result  = ca.run();
+		c_result  = c_algorithm.run();
 
 		taskMonitor.setProgress(0.9);
 
-		checkForInvalidSolutions(result);
+		checkForInvalidSolutions(c_result);
 
-		long numberOfSolutions = result.getNumberOfSolutions();
+		long numberOfSolutions = c_result.getNumberOfSolutions();
 
 		taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO: Localize
 
-		YoshikoResult yoshikoResult = new YoshikoResult(net,result.getFlags());
+		result = new YoshikoResult(net,c_result.getFlags());
 
 		//Loop over (multiple) solutions
 		for (long i=0;i<numberOfSolutions;i++) {
 
 			taskMonitor.setStatusMessage("Processing solution "+(i+1)+" of "+numberOfSolutions);
 
-			YoshikoSolution solution = new YoshikoSolution(yoshikoResult,i);
+			YoshikoSolution solution = new YoshikoSolution(result,i);
 
 			String columnName = SOLUTION_COLUMN_PREFIX+(i+1);
 
@@ -179,7 +197,7 @@ public class AlgorithmTask extends AbstractTask {
 			net.getDefaultNodeTable().createColumn(columnName, String.class, false);
 
 			//Fetch number of clusters in the solution
-			long numberOfClusters = result.getNumberOfClusters(i);
+			long numberOfClusters = c_result.getNumberOfClusters(i);
 
 			//Loop over clusters
 			for (long k=0;k<numberOfClusters;k++) {
@@ -189,7 +207,7 @@ public class AlgorithmTask extends AbstractTask {
 
 				taskMonitor.setStatusMessage("Processing clusters "+(k+1)+" of "+numberOfClusters);
 
-				IntVector clusterVector = result.getCluster(i, k);
+				IntVector clusterVector = c_result.getCluster(i, k);
 
 				long sizeOfCluster = clusterVector.size();
 				for (int l=0;l<sizeOfCluster;l++) { //Unsafe mismatch int long
@@ -205,18 +223,18 @@ public class AlgorithmTask extends AbstractTask {
 			}
 			//Sort clusters by size, descending as the biggest clusters are usually the most relevant
 			solution.clusters.sort(YoshikoCluster.lessThanComparator);
-			//Register solution with result for further reference
-			yoshikoResult.addSolution(solution);
+			//Register solution with c_result for further reference
+			result.addSolution(solution);
 		}
 
 		taskMonitor.setProgress(0.99);
 		//At this point the C++ objects can be freed, in case that the algorithm terminates beforehand they need to be cleaned-up elsewhere
-		ca.delete();
-		input.delete();
-		result.delete();
+		c_algorithm.delete();
+		c_input.delete();
+		c_result.delete();
 
 		//Generate solutionsPanel
-		resultPanel = new ResultPanel(yoshikoResult);
+		resultPanel = new ResultPanel(result);
 
 		//Show solution panel
 		CyCore.registrar.registerService(resultPanel,CytoPanelComponent.class, new Properties());
@@ -231,16 +249,16 @@ public class AlgorithmTask extends AbstractTask {
 
 	private void checkForInvalidSolutions(ClusterEditingSolutions result) throws Exception {
 		if (result == null) {
-			//There was no result object generated at all
+			//There was no c_result object generated at all
 			throw new Exception(LocalizationManager.get("noFeasible"));
 		}
 
 		if (result.getNumberOfSolutions() == 0) {
-			//The result object is empty
+			//The c_result object is empty
 			throw new Exception(LocalizationManager.get("noFeasible"));
 		}
 		if (result.getNumberOfSolutions() == 1) {
-			//The result doesn't contain any clusters
+			//The c_result doesn't contain any clusters
 			if (result.getNumberOfClusters(0) == 0) {
 				throw new Exception(LocalizationManager.get("noFeasible"));
 			}
@@ -251,21 +269,30 @@ public class AlgorithmTask extends AbstractTask {
 	@Override
 	public void cancel() {
 		//Free C++ resources
-		if (ca != null) {
+		if (c_algorithm != null) {
 			System.out.println("Deleting CoreAlgorithm instance!");
-			ca.cancel();
-			ca.delete();
+			c_algorithm.cancel();
+			c_algorithm.delete();
 		}
-		if (input != null) {
-			input.delete();
+		if (c_input != null) {
+			c_input.delete();
 		}
-		if (result != null) {
-			result.delete();
+		if (c_result != null) {
+			c_result.delete();
 		}
-		//Delete (incomplete) result panel
+		//Delete (incomplete) c_result panel
 		if (resultPanel != null) {
 			resultPanel.deleteSolution();
 		}
 		super.cancel();
 	}
+
+	@Override
+	public <R> R getResults(Class<? extends R> type) {
+		//TODO:
+		if (type.equals(YoshikoResult.class)) {
+			return (R) (result!=null ? result : null);
+		}
+		return null;
+	}
 }

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

@@ -17,10 +17,10 @@ import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 import de.hhu.ba.yoshikoWrapper.cytoUtil.StyleManager;
 import de.hhu.ba.yoshikoWrapper.graphModel.YoshikoCluster;
 
-public class CreateClusterViews implements Task {
+public class CreateClusterViewsTask implements Task {
 
 	@Tunable
-	public ArrayList<YoshikoCluster> clusters;
+	public ArrayList<YoshikoCluster> clusters; //TODO: Make Tunable, reference by ID?
 
 	private boolean isTerminated;
 
@@ -35,7 +35,7 @@ public class CreateClusterViews implements Task {
 	 */
 	private ArrayList<CySubNetwork> initializedSubNetworks;
 
-	public CreateClusterViews(ArrayList<YoshikoCluster> clusters) {
+	public CreateClusterViewsTask(ArrayList<YoshikoCluster> clusters) {
 		this.clusters = clusters;
 
 		this.previousView = CyCore.cy.getCurrentNetworkView();

src/main/resources/YoshikoStrings.properties

@@ -26,6 +26,8 @@
 about = Yoshiko Cytoscape App
 aboutButton = About Yoshiko
 aboutTitle = Yoshiko Plugin Info
+autoConfig = Choose reduction rules automatically
+
 clusters = Cluster
 clusterFound = Clusters found:
 clusterSize = Cluster Size: