stuff

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

@@ -28,6 +28,6 @@ public class ConfigurationManager extends AbstractConfigDirPropsReader{
 
 	public ConfigurationManager(String appName, String fileName){
 		super(appName, fileName, CyProperty.SavePolicy.CONFIG_DIR);
-		this.getProperties().list(System.out);
+		//this.getProperties().list(System.out);
 	}
 }

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

@@ -4,12 +4,16 @@ package de.hhu.ba.yoshikoWrapper.core;
 import java.io.IOException;
 
 import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyNetwork;
 import org.cytoscape.work.Tunable;
 import org.cytoscape.work.TunableValidator;
 
 public class ParameterSet implements TunableValidator
 {
 
+	@Tunable(description="Network to analyze for clusters", context="nogui")
+	public CyNetwork net = CyCore.cy.getCurrentNetwork();
+
 	@Tunable(description="Time Limit for the ILP mode", context="nogui")
 	public int timeLimit = -1;
 
@@ -50,17 +54,27 @@ public class ParameterSet implements TunableValidator
 
 	@Override
 	public ValidationState getValidationState(Appendable errMsg) {
-		if (!checkBitmask(reductionRulesBitMask)) {
+		System.out.println("DEBUG: Running VALIDATION of tunables"); //TODO: Move to logger (if it would work)
 		try {
-				errMsg.append("The Bitmask provided is invalid! Needs to be six bit binary (example: 011001)");
+			if (net!= null) {
+				//Verify column validity
+				CyColumn weightColumn = net.getDefaultEdgeTable().getColumn(weightColumnName);
+				if (weightColumn == null) {
+					errMsg.append("Could not find a column named: "+weightColumnName+"\n");
+					return ValidationState.INVALID;
+				}
+			}
+			if (!checkBitmask(reductionRulesBitMask)) {
+				errMsg.append("The Bitmask provided is invalid! Needs to be six bit binary (example: 011001)\n");
+				return ValidationState.INVALID;
+			}
+			return ValidationState.OK;
 		} catch (IOException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
 		return ValidationState.INVALID;
 	}
-		return ValidationState.OK;
-	}
 
 	/**
 	 * Helper function that verifies a String and checks if it represents a 6-bit bitmask
@@ -79,4 +93,5 @@ public class ParameterSet implements TunableValidator
 		return true;
 	}
 
+
 }

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

@@ -314,7 +314,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 			if (YoshikoLoader.isLibraryLoaded()){
 				AbstractTask yoshiko = new AlgorithmTask(
 					popupLevel,
-					networkToBeProcessed,
 					fetchParameters(networkToBeProcessed)
 				);
 				/**
@@ -345,6 +344,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 	 */
 	private ParameterSet fetchParameters(CyNetwork net) {
 		ParameterSet ret = new ParameterSet();
+		ret.net = net;
 		ret.timeLimit = opModePanel.getTimeLimit();
 		ret.weightColumnName = ecPanel.getWeightColumn().getName();
 		ret.permanentColumn = ecPanel.getPermanentColumn();

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

@@ -185,7 +185,7 @@ NetworkAboutToBeDestroyedListener
 		verticalGroup
 			.addComponent(marker,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
 			.addComponent(invalidLabel,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
-			.addComponent(tabbedPane,PREFERRED_SIZE, DEFAULT_SIZE,Short.MAX_VALUE)
+			.addComponent(tabbedPane,DEFAULT_SIZE, DEFAULT_SIZE,DEFAULT_SIZE)
 			.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED, DEFAULT_SIZE, Short.MAX_VALUE)
 			.addComponent(destroyButton,DEFAULT_SIZE, DEFAULT_SIZE,PREFERRED_SIZE);
 

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

@@ -218,8 +218,8 @@ public class SolutionTab extends JPanel {
 				.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)
+				.addGap(4)
+				.addComponent(scrollPane,DEFAULT_SIZE,DEFAULT_SIZE,PREFERRED_SIZE)
 				.addGap(4)
 		);
 

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

@@ -45,7 +45,6 @@ public class CommandTaskFactory implements TaskFactory{
 		else if (command == YoshikoCommand.PERFORM_ALGORITHM) {
 			return new TaskIterator(
 					new AlgorithmTask(
-							null,
 							null,
 							new ParameterSet()
 							)

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

@@ -77,8 +77,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
 	@ContainsTunables
 	public ParameterSet parameterSet = null;
 
-	@Tunable(description="Network to analyze for clusters", context="nogui")
-	public CyNetwork net = CyCore.cy.getCurrentNetwork();
+
 
 	//Temps, pointing to and need to be freed in C++
 	private LibraryInput c_input;
@@ -98,12 +97,10 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
 	 */
 	public AlgorithmTask(
 			Window statusWindow,
-			CyNetwork net,
 			ParameterSet parameterSet
 			)
 	{
 		this.statusWindow = statusWindow;
-		this.net = net;
 		this.parameterSet = parameterSet;
 	}
 
@@ -115,8 +112,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
 		taskMonitor.setTitle(LocalizationManager.get("yoshTask"));
 		taskMonitor.setProgress(0.0);
 
-		//Get current network
-		if (net == null) {
+		//Check current network
+		if (parameterSet.net == null) {
 			logger.warn("CoreAlgorithm called on a net that is NULL!");
 			throw new Exception("CoreAlgorithm called on a net that is NULL!"); //TODO: Localize
 		}
@@ -131,14 +128,14 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
 		}
 
 		//Create a node map to identify nodes and eges in the solution
-		NodeMap nodeMap  = new NodeMap(net);
+		NodeMap nodeMap  = new NodeMap(parameterSet.net);
 		taskMonitor.setProgress(0.1);
 
 		//Generate an c_input instance from the network
 		c_input = NetworkParser.parseNetwork(
-				net,
+				parameterSet.net,
 				nodeMap,
-				net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName),
+				parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName), //Simplify
 				parameterSet.permanentColumn,
 				parameterSet.forbiddenColumn,
 				parameterSet.defaultDeletionCost
@@ -146,8 +143,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
 		taskMonitor.setProgress(0.2);
 
 		boolean containsRealValues = GraphAnalyzer.containsRealValues(
-				net,
-				net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName),
+				parameterSet.net,
+				parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName),
 				parameterSet.permanentColumn,
 				parameterSet.forbiddenColumn,
 				parameterSet.defaultInsertionCost,
@@ -184,7 +181,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
 
 		taskMonitor.setStatusMessage("Found: "+numberOfSolutions+" solutions!"); //TODO: Localize
 
-		result = new YoshikoResult(net,c_result.getFlags());
+		result = new YoshikoResult(parameterSet.net,c_result.getFlags());
 
 		//Loop over (multiple) solutions
 		for (long i=0;i<numberOfSolutions;i++) {
@@ -195,8 +192,8 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
 
 			String columnName = SOLUTION_COLUMN_PREFIX+(i+1);
 
-			net.getDefaultNodeTable().deleteColumn(columnName);
-			net.getDefaultNodeTable().createColumn(columnName, String.class, false);
+			parameterSet.net.getDefaultNodeTable().deleteColumn(columnName);
+			parameterSet.net.getDefaultNodeTable().createColumn(columnName, String.class, false);
 
 			//Fetch number of clusters in the solution
 			long numberOfClusters = c_result.getNumberOfClusters(i);
@@ -218,7 +215,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
 					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?)
+					parameterSet.net.getRow(node).set(columnName, ""+(k+1)); //Add Cluster ID in table (Remove in final version?)
 				}
 				//Register clusters with solution for further reference
 				solution.addCluster(cluster);