more logical sorting of parameters

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

@@ -32,6 +32,10 @@ public class AlgorithmTask extends AbstractTask {
 	private int timeLimit;
 	private CyNetwork net;
 	private String bitMaskRules;
+	private double multiplicativeFactor;
+	private boolean separatePartitionCuts;
+	private boolean separateTriangles;
+	private boolean useHeuristic;
 	private SolutionsPanel solutionsPanel;
 
 	public AlgorithmTask(
@@ -60,7 +64,7 @@ public class AlgorithmTask extends AbstractTask {
 		this.bitMaskRules = bitMaskRules;
 		this.multiplicativeFactor = multiplicativeFactor;
 		this.separatePartitionCuts = separatePartitionCuts;
-		this.separateTriangles =separateTriangle;
+		this.separateTriangles = separateTriangles;
 		this.useHeuristic = useHeuristic;
 		this.solutionsPanel = solutionsPanel;
 	}

src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java

@@ -44,6 +44,7 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 	
 	private final ReductionRulesChooser reductionRulesChooser;
 	
+	
 	private final JCheckBox useTriangleCutsBox;
 	private final JCheckBox usePartitionCutsBox;
 	
@@ -75,6 +76,14 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 		heuristicGroup.add(useHeuristic);
 		
 
+		reductionRulesChooser = new ReductionRulesChooser();
+		
+		timeLimitSetter = new TimeLimitSetter();
+				
+		useTriangleCutsBox = new JCheckBox("Use Triangle Cuts");
+		usePartitionCutsBox = new JCheckBox("Use Partition Cuts");
+		
+
 		JButton runButton = new JButton("RUN");
 		runButton.addActionListener(new ActionListener() {
 
@@ -90,8 +99,12 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 						ecPanel.getForbiddenColumn(),
 						ecPanel.getDefaultInsertionCost(),
 						ecPanel.getDefaultDeletionCost(),
-							ReductionRulesChooser.getBitMask(),
-							name, alignmentX, autoscrolls, autoscrolls, autoscrolls, solutionsPanel
+						reductionRulesChooser.getBitMask(),
+						reductionRulesChooser.getMultFactor(),
+						useTriangleCutsBox.isSelected(),
+						usePartitionCutsBox.isSelected(), 
+						useHeuristic.isSelected(), 
+						solutionsPanel
 					);
 					CyCore.dialogTaskManager.execute(new TaskIterator(1,yoshiko));
 					solutionsPanel.setVisible(true);
@@ -108,13 +121,6 @@ public class MainPanel extends ComfortPanel implements CytoPanelComponent {
 			
 		});
 
-		reductionRulesChooser = new ReductionRulesChooser();
-		
-		timeLimitSetter = new TimeLimitSetter();
-		
-		useTriangleCutsBox = new JCheckBox("Use Triangle Cuts");
-		usePartitionCutsBox = new JCheckBox("Use Partition Cuts");
-
 		
 		this.addAll(
 				langSwitcher,

src/main/java/de/hhu/ba/yoshikoWrapper/gui/ReductionRulesChooser.java

 package de.hhu.ba.yoshikoWrapper.gui;
 
 import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 
 import javax.swing.BoxLayout;
 import javax.swing.JCheckBox;
@@ -8,12 +10,17 @@ import javax.swing.JCheckBox;
 @SuppressWarnings("serial")
 public class ReductionRulesChooser extends ComfortPanel{
 
-	private JCheckBox useCRule;
-	private JCheckBox useCCRule;
-	private JCheckBox useACRule;
-	private JCheckBox useHERule;
-	private JCheckBox usePDRRule;
-	private JCheckBox useSNRule;
+	private final JCheckBox useCRule;
+	private final JCheckBox useCCRule;
+	private final JCheckBox useACRule;
+	private final JCheckBox useHERule;
+	private final JCheckBox usePDRRule;
+	private final JCheckBox useSNRule;
+	
+	private final DoubleInputField multFactor;
+	
+	private final ComfortPanel SNPanel;
+
 	
 	public ReductionRulesChooser() {
 		this.setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
@@ -24,6 +31,25 @@ public class ReductionRulesChooser extends ComfortPanel{
 		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 ComfortPanel();
+		
+		SNPanel.addAll(useSNRule,multFactor);
+		useSNRule.setSelected(true);
+
+		useSNRule.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				if (useSNRule.isSelected()) {
+					multFactor.setEnabled(true);
+				}
+				else {
+					multFactor.setEnabled(false);
+				}
+			}
+		});
+		
 		
 		this.addAll(
 				useCRule,
@@ -31,13 +57,15 @@ public class ReductionRulesChooser extends ComfortPanel{
 				useACRule,
 				useHERule,
 				usePDRRule,
-				useSNRule
+				SNPanel
 				);
 		//By default all reduction rules should be applied
 		for (Component c :this.getComponents()) {
+			if (c instanceof JCheckBox) {
 				((JCheckBox)c).setSelected(true);
 			}
 		}
+	}
 	
 	
 	/** Creates a 6 Bit bitmask representing the currently selected choice of reduction rules.
@@ -53,4 +81,11 @@ public class ReductionRulesChooser extends ComfortPanel{
 		ret += (useSNRule.isSelected() ? "1" : "0");
 		return ret;
 	}
+	
+	public double getMultFactor() {
+		if (useSNRule.isSelected()) {
+			return multFactor.getValueAsDouble();
+		}
+		return 1.0d;
+	}
 }