Some work on making CyColumns tunable via their name

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

@@ -20,9 +20,9 @@ public class ParameterSet implements TunableValidator
 	@Tunable(description="A column in the edge table containing weights", context="nogui")
 	public String weightColumnName;
 	@Tunable(description="A column containing boolean entries for edges that are to be treated as permanent",context="nogui")
-	public CyColumn permanentColumn;
+	public String permanentColumnName;
 	@Tunable(description="A column containing boolean entries for edges that are to be treated as forbidden",context="nogui")
-	public CyColumn forbiddenColumn;
+	public String forbiddenColumnName;
 
 	@Tunable(description="The default insertion cost that is to be used for non-existing edges",context="nogui")
 	public double defaultInsertionCost = -1;

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

@@ -60,7 +60,7 @@ SetCurrentNetworkListener
 {
 
 	//Swing components
-	private final JComboBox<CyColumn> editingCostMapper;
+	private final JComboBox<CyColumn> weightMapper;
 	private final JComboBox<CyColumn> permanentMapper;
 	private final JComboBox<CyColumn> forbiddenMapper;
 
@@ -79,12 +79,12 @@ SetCurrentNetworkListener
 		//SWING COMPONENTS
 
 		//Combo-Boxes that map to the CyColumns
-		editingCostMapper = new JComboBox<CyColumn>();
+		weightMapper = new JComboBox<CyColumn>();
 		permanentMapper = new JComboBox<CyColumn>();
 		forbiddenMapper = new JComboBox<CyColumn>();
 
 		//Should only be enabled if the option is checked
-		editingCostMapper.setEnabled(false);
+		weightMapper.setEnabled(false);
 		permanentMapper.setEnabled(false);
 		forbiddenMapper.setEnabled(false);
 
@@ -93,7 +93,7 @@ SetCurrentNetworkListener
 		useMappingForb = new JCheckBox("Map edges as forbidden");
 
 		useMappingCost.addActionListener(
-			new EnableWhenSelectedListener(useMappingCost, editingCostMapper)
+			new EnableWhenSelectedListener(useMappingCost, weightMapper)
 		);
 		useMappingPerm.addActionListener(
 			new EnableWhenSelectedListener(useMappingPerm, permanentMapper)
@@ -103,7 +103,7 @@ SetCurrentNetworkListener
 		);
 
 
-		SwingUtil.addAll(this,useMappingCost,editingCostMapper);
+		SwingUtil.addAll(this,useMappingCost,weightMapper);
 		SwingUtil.addAll(this,useMappingPerm,permanentMapper);
 		SwingUtil.addAll(this,useMappingForb,forbiddenMapper);
 
@@ -117,7 +117,7 @@ SetCurrentNetworkListener
 					.addComponent(useMappingForb)
 			)
 			.addGroup(layout.createParallelGroup(Alignment.LEADING)
-					.addComponent(editingCostMapper)
+					.addComponent(weightMapper)
 					.addComponent(permanentMapper)
 					.addComponent(forbiddenMapper)
 			)
@@ -127,7 +127,7 @@ SetCurrentNetworkListener
 		layout.setVerticalGroup(layout.createSequentialGroup()
 				.addGroup(layout.createParallelGroup()
 						.addComponent(useMappingCost)
-						.addComponent(editingCostMapper)
+						.addComponent(weightMapper)
 				)
 				.addGroup(layout.createParallelGroup()
 						.addComponent(useMappingPerm)
@@ -153,18 +153,18 @@ SetCurrentNetworkListener
 		if (net != null) { //Check if a network is loaded
 
 			//Clear entries
-			editingCostMapper.removeAllItems();
+			weightMapper.removeAllItems();
 			for (CyColumn c : net.getDefaultEdgeTable().getColumns()){
 				//Only add columns with numeric values
 				if (c.getType() == Integer.class || c.getType() == Double.class) {
-					editingCostMapper.addItem(c);
+					weightMapper.addItem(c);
 				}
 			}
-			boolean enable = (editingCostMapper.getItemCount() > 0) ? true : false;
+			boolean enable = (weightMapper.getItemCount() > 0) ? true : false;
 			useMappingCost.setEnabled(enable);
 			if (!useMappingCost.isEnabled()) {
 				useMappingCost.setSelected(false);
-				editingCostMapper.setEnabled(false);
+				weightMapper.setEnabled(false);
 			}
 
 			forbiddenMapper.removeAllItems();
@@ -247,7 +247,7 @@ SetCurrentNetworkListener
 
 	public CyColumn getEditingCostColumn() {
 		if (useMappingCost.isSelected()) {
-			return editingCostMapper.getItemAt(editingCostMapper.getSelectedIndex());
+			return weightMapper.getItemAt(weightMapper.getSelectedIndex());
 		}
 		return null;
 	}

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

@@ -109,17 +109,11 @@ public class EditCostPanel extends JPanel {
 	}
 	//SETTER / GETTER
 
-	public CyColumn getWeightColumn() {
-		return columnMapper.getEditingCostColumn();
-	}
-
-	public CyColumn getPermanentColumn() {
-		return columnMapper.getPermanentColumn();
-	}
+	public String getPermanentColumnName() {
+		return columnMapper.getPermanentColumn() != null ? columnMapper.getPermanentColumn().getName() : null;	}
 
-	public CyColumn getForbiddenColumn() {
-		return columnMapper.getForbiddenColumn();
-	}
+	public String getForbiddenColumnName() {
+		return columnMapper.getForbiddenColumn() != null ? columnMapper.getForbiddenColumn().getName() : null;	}
 
 	public double getDefaultInsertionCost() {
 		return icField.getValueAsDouble();
@@ -133,4 +127,8 @@ public class EditCostPanel extends JPanel {
 		return columnMapper;
 	}
 
+	public String getWeightColumnName() {
+		return columnMapper.getEditingCostColumn() != null ? columnMapper.getEditingCostColumn().getName() : null;
+	}
+
 }

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

@@ -346,9 +346,9 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 		ParameterSet ret = new ParameterSet();
 		ret.net = net;
 		ret.timeLimit = opModePanel.getTimeLimit();
-		ret.weightColumnName = ecPanel.getWeightColumn().getName();
-		ret.permanentColumn = ecPanel.getPermanentColumn();
-		ret.forbiddenColumn = ecPanel.getForbiddenColumn();
+		ret.weightColumnName = ecPanel.getWeightColumnName();
+		ret.permanentColumnName = ecPanel.getPermanentColumnName();
+		ret.forbiddenColumnName = ecPanel.getForbiddenColumnName();
 		ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
 		ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
 		ret.useHeuristic = opModePanel.useHeuristic();

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

@@ -30,13 +30,13 @@ import org.cytoscape.application.swing.CytoPanel;
 import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.application.swing.CytoPanelName;
 import org.cytoscape.application.swing.CytoPanelState;
-import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyColumn;
 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.cytoscape.work.TunableValidator;
 import org.slf4j.Logger;
 
 import de.hhu.ba.yoshikoWrapper.core.CyCore;
@@ -58,7 +58,7 @@ import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
 import de.hhu.ba.yoshikoWrapper.swing.components.ResultPanel;
 
 
-public class AlgorithmTask extends AbstractTask implements ObservableTask {
+public class AlgorithmTask extends AbstractTask implements ObservableTask, TunableValidator {
 
 	//Constants
 	private static final String SOLUTION_COLUMN_PREFIX = "yoshikoSolution_"; //TODO: Make customizable?
@@ -131,22 +131,27 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
 		NodeMap nodeMap  = new NodeMap(parameterSet.net);
 		taskMonitor.setProgress(0.1);
 
+		//We identify the columns if they exist from their given names
+		CyColumn weightColumn = parameterSet.weightColumnName != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName) : null;
+		CyColumn permanentColumn = parameterSet.permanentColumnName != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.permanentColumnName) : null;
+		CyColumn forbiddenColumn = parameterSet.forbiddenColumnName != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.forbiddenColumnName) : null;
+
 		//Generate an c_input instance from the network
 		c_input = NetworkParser.parseNetwork(
 				parameterSet.net,
 				nodeMap,
-				parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName), //Simplify
-				parameterSet.permanentColumn,
-				parameterSet.forbiddenColumn,
+				weightColumn,
+				permanentColumn,
+				forbiddenColumn,
 				parameterSet.defaultDeletionCost
 				);
 		taskMonitor.setProgress(0.2);
 
 		boolean containsRealValues = GraphAnalyzer.containsRealValues(
 				parameterSet.net,
-				parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.weightColumnName),
-				parameterSet.permanentColumn,
-				parameterSet.forbiddenColumn,
+				weightColumn,
+				permanentColumn,
+				forbiddenColumn,
 				parameterSet.defaultInsertionCost,
 				parameterSet.defaultDeletionCost);
 
@@ -305,4 +310,10 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask {
 		}
 		return null;
 	}
+
+	@Override
+	public ValidationState getValidationState(Appendable errMsg) {
+		//In order to validate the arguments for this task we simply check the ParameterSet
+		return parameterSet.getValidationState(errMsg);
+	}
 }