Changed column mapping parameters to Cytoscape ListSingleSelection -> easier...

Changed column mapping parameters to Cytoscape ListSingleSelection -> easier and more intuitive for automation users

Updated some license headers

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

+/*******************************************************************************
+ * Copyright (C) 2018 Philipp Spohr
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
+
 package de.hhu.ba.yoshikoWrapper.core;
 
 
 import java.io.IOException;
+import java.util.ArrayList;
 
 import org.cytoscape.model.CyColumn;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.work.Tunable;
 import org.cytoscape.work.TunableValidator;
+import org.cytoscape.work.util.ListSingleSelection;
 
 public class ParameterSet implements TunableValidator
 {
@@ -17,12 +41,14 @@ public class ParameterSet implements TunableValidator
 	@Tunable(description="Time Limit for the ILP mode", context="nogui")
 	public int timeLimit = -1;
 	
+	//COLUMN-MAPPINGS
+
 	@Tunable(description="A column in the edge table containing weights", context="nogui")
-	public String weightColumnName;
+	public ListSingleSelection<String> weightColumnName = null;
 	@Tunable(description="A column containing boolean entries for edges that are to be treated as permanent",context="nogui")
-	public String permanentColumnName;
+	public ListSingleSelection<String> permanentColumnName = null;
 	@Tunable(description="A column containing boolean entries for edges that are to be treated as forbidden",context="nogui")
-	public String forbiddenColumnName;
+	public ListSingleSelection<String> forbiddenColumnName = null;
 
 	@Tunable(description="The default insertion cost that is to be used for non-existing edges",context="nogui")
 	public double defaultInsertionCost = -1;
@@ -55,13 +81,40 @@ public class ParameterSet implements TunableValidator
 	@Tunable(description="Determines the number of clusters that are to be generated. -1 generates the optimal amount of clusters in the sense of WCE",context="nogui")
 	public int clusterCount = -1;
 	
+	/**
+	 * Default constructor, initializes the column mappings to provide a selection of fitting columns
+	 */
+	public ParameterSet() {
+		
+		ArrayList<String> columnNames = new ArrayList<String>();
+		
+		//Only numeric columns are relevant for weight mapping
+		for (CyColumn col : net.getDefaultEdgeTable().getColumns()) {
+			if (Number.class.isAssignableFrom(col.getType())) {
+				columnNames.add(col.getName());
+			}
+		}
+		weightColumnName = new ListSingleSelection<String>(columnNames);
+		
+		columnNames = new ArrayList<String>();
+		
+		//Only boolean columns are relevant for forbidden/permanent mapping
+		for (CyColumn col : net.getDefaultEdgeTable().getColumns()) {
+			if (col.getType() == Boolean.class) {
+				columnNames.add(col.getName());
+			}
+		}
+		forbiddenColumnName = new ListSingleSelection<String>(columnNames);
+		permanentColumnName = new ListSingleSelection<String>(columnNames);
+	}
+
 	@Override
 	public ValidationState getValidationState(Appendable errMsg) {
 		System.out.println("DEBUG: Running VALIDATION of tunables"); //TODO: Move to logger (if it would work)
 		try {
 			if (net!= null) {
 				//Verify column validity
-				CyColumn weightColumn = net.getDefaultEdgeTable().getColumn(weightColumnName);
+				CyColumn weightColumn = net.getDefaultEdgeTable().getColumn(weightColumnName.getSelectedValue());
 				if (weightColumn == null) {
 					errMsg.append("Could not find a column named: "+weightColumnName+"\n");
 					return ValidationState.INVALID;
@@ -109,4 +162,50 @@ public class ParameterSet implements TunableValidator
 		return ret;
 	}
 	
+	//SETTER & GETTER
+	
+	//TODO: Code Redundancy, might be smart to insert the three columns into some sort of super structure and then remove the redundant setters/getters, pass column type as argument
+
+	public void setWeightColumnName(String columnName) {
+		if (weightColumnName.getPossibleValues().contains(columnName)) {
+			weightColumnName.setSelectedValue(columnName);
+		}
+		else {
+			//Attempting to set a column that is not part of the possible values
+			//TODO: Output debug/warning if Cytoscape logger will eventually work
+		}
+	}
+	
+	public void setPermanentColumnName(String columnName) {
+		if (permanentColumnName.getPossibleValues().contains(columnName)) {
+			permanentColumnName.setSelectedValue(columnName);
+		}
+		else {
+			//Attempting to set a column that is not part of the possible values
+			//TODO: Output debug/warning if Cytoscape logger will eventually work
+		}		
+	}
+	
+	public void setForbiddenColumnName(String columnName) {
+		if (forbiddenColumnName.getPossibleValues().contains(columnName)) {
+			forbiddenColumnName.setSelectedValue(columnName);
+		}
+		else {
+			//Attempting to set a column that is not part of the possible values
+			//TODO: Output debug/warning if Cytoscape logger will eventually work
+		}		
+	}
+
+	public String getWeightColumnName() {
+		return weightColumnName.getSelectedValue();
+	}
+	
+	public String getPermanentColumnName() {
+		return permanentColumnName.getSelectedValue();
+	}
+	
+	public String getForbiddenColumnName() {
+		return forbiddenColumnName.getSelectedValue();
+	}
+
 }

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

 /*******************************************************************************
- * Copyright (C) 2017 Philipp Spohr
+ * Copyright (C) 2018 Philipp Spohr
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java

 /*******************************************************************************
- * Copyright (C) 2017 Philipp Spohr
+ * Copyright (C) 2018 Philipp Spohr
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

src/main/java/de/hhu/ba/yoshikoWrapper/swing/SwingUtil.java

 /*******************************************************************************
- * Copyright (C) 2017 Philipp Spohr
+ * Copyright (C) 2018 Philipp Spohr
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

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.getWeightColumnName();
-		ret.permanentColumnName = ecPanel.getPermanentColumnName();
-		ret.forbiddenColumnName = ecPanel.getForbiddenColumnName();
+		ret.setWeightColumnName(ecPanel.getWeightColumnName());
+		ret.setPermanentColumnName(ecPanel.getPermanentColumnName());
+		ret.setForbiddenColumnName(ecPanel.getForbiddenColumnName());
 		ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
 		ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
 		ret.useHeuristic = opModePanel.useHeuristic();

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

 /*******************************************************************************
- * Copyright (C) 2017 Philipp Spohr
+ * Copyright (C) 2018 Philipp Spohr
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

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

@@ -132,9 +132,9 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
 		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;
+		CyColumn weightColumn = parameterSet.getWeightColumnName() != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.getWeightColumnName()) : null;
+		CyColumn permanentColumn = parameterSet.permanentColumnName != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.getPermanentColumnName()) : null;
+		CyColumn forbiddenColumn = parameterSet.forbiddenColumnName != null ? parameterSet.net.getDefaultEdgeTable().getColumn(parameterSet.getForbiddenColumnName()) : null;
 
 		//Generate an c_input instance from the network
 		c_input = NetworkParser.parseNetwork(