More elegant handling of CyColumn tunable, removed workaround via String completely

Updated some headers, some Javadoc

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

@@ -44,11 +44,11 @@ public class ParameterSet implements TunableValidator
 	//COLUMN-MAPPINGS
 
 	@Tunable(description="A column in the edge table containing weights", context="nogui")
-	public ListSingleSelection<String> weightColumnName = null;
+	public ListSingleSelection<CyColumn> weightColumn = null;
 	@Tunable(description="A column containing boolean entries for edges that are to be treated as permanent",context="nogui")
-	public ListSingleSelection<String> permanentColumnName = null;
+	public ListSingleSelection<CyColumn> permanentColumn = null;
 	@Tunable(description="A column containing boolean entries for edges that are to be treated as forbidden",context="nogui")
-	public ListSingleSelection<String> forbiddenColumnName = null;
+	public ListSingleSelection<CyColumn> forbiddenColumn = null;
 
 	@Tunable(description="The default insertion cost that is to be used for non-existing edges",context="nogui")
 	public double defaultInsertionCost = -1;
@@ -86,40 +86,32 @@ public class ParameterSet implements TunableValidator
 	 */
 	public ParameterSet() {
 		
-		ArrayList<String> columnNames = new ArrayList<String>();
+		ArrayList<CyColumn> columns = new ArrayList<CyColumn>();
 		
 		//Only numeric columns are relevant for weight mapping
 		for (CyColumn col : net.getDefaultEdgeTable().getColumns()) {
 			if (Number.class.isAssignableFrom(col.getType())) {
-				columnNames.add(col.getName());
+				columns.add(col);
 			}
 		}
-		weightColumnName = new ListSingleSelection<String>(columnNames);
+		weightColumn = new ListSingleSelection<CyColumn>(columns);
 		
-		columnNames = new ArrayList<String>();
+		columns.clear();
 		
 		//Only boolean columns are relevant for forbidden/permanent mapping
 		for (CyColumn col : net.getDefaultEdgeTable().getColumns()) {
 			if (col.getType() == Boolean.class) {
-				columnNames.add(col.getName());
+				columns.add(col);
 			}
 		}
-		forbiddenColumnName = new ListSingleSelection<String>(columnNames);
-		permanentColumnName = new ListSingleSelection<String>(columnNames);
+		forbiddenColumn = new ListSingleSelection<CyColumn>(columns);
+		permanentColumn = new ListSingleSelection<CyColumn>(columns);
 	}
 
 	@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.getSelectedValue());
-				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;
@@ -156,8 +148,11 @@ public class ParameterSet implements TunableValidator
 
 	@Override
 	public String toString(){
-		String ret = "";
+		String ret = "[ParameterSet]:\n";
 		ret += "Target Cluster Count: "+clusterCount+"\n";
+		ret += "Weight mapped to column: "+(weightColumn.getSelectedValue() != null ? weightColumn.getSelectedValue().getName() : "[NONE]")+"\n";
+		ret += "Permanent edges mapped to column: "+(permanentColumn.getSelectedValue() != null ? permanentColumn.getSelectedValue().getName() : "[NONE]")+"\n";
+		ret += "Forbidden edges mapped to column: "+(forbiddenColumn.getSelectedValue() != null ? forbiddenColumn.getSelectedValue().getName() : "[NONE]")+"\n";
 		//TODO
 		return ret;
 	}
@@ -166,46 +161,28 @@ public class ParameterSet implements TunableValidator
 	
 	//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 setWeightColumn(CyColumn column) {
+		weightColumn.setSelectedValue(column);
 	}
 	
-	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 setPermanentColumn(CyColumn column) {
+		permanentColumn.setSelectedValue(column);
 	}
 	
-	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 void setForbiddenColumn(CyColumn column) {
+		forbiddenColumn.setSelectedValue(column);
 	}
 
-	public String getWeightColumnName() {
-		return weightColumnName.getSelectedValue();
+	public CyColumn getWeightColumn() {
+		return weightColumn.getSelectedValue();
 	}
 	
-	public String getPermanentColumnName() {
-		return permanentColumnName.getSelectedValue();
+	public CyColumn getPermanentColumn() {
+		return permanentColumn.getSelectedValue();
 	}
 	
-	public String getForbiddenColumnName() {
-		return forbiddenColumnName.getSelectedValue();
+	public CyColumn getForbiddenColumn() {
+		return forbiddenColumn.getSelectedValue();
 	}
 
 }

src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoCluster.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
@@ -50,9 +50,14 @@ import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NETWOR
 
 public class YoshikoCluster {
 
-
+	/**
+	 * The internal id used to uniquely identify the cluster
+	 */
 	private final long id;
 
+	/**
+	 * All nodes associated with this cluster
+	 */
 	private ArrayList<CyNode> nodes;
 
 	private Image img;

src/main/java/de/hhu/ba/yoshikoWrapper/graphModel/YoshikoResult.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/graphModel/YoshikoSolution.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/EditCostPanel.java

@@ -26,6 +26,9 @@ import javax.swing.GroupLayout;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JSeparator;
+
+import org.cytoscape.model.CyColumn;
+
 import javax.swing.GroupLayout.Alignment;
 
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
@@ -113,12 +116,6 @@ public class EditCostPanel extends JPanel {
 	}
 	//SETTER / GETTER
 
-	public String getPermanentColumnName() {
-		return columnMapper.getPermanentColumn() != null ? columnMapper.getPermanentColumn().getName() : null;	}
-
-	public String getForbiddenColumnName() {
-		return columnMapper.getForbiddenColumn() != null ? columnMapper.getForbiddenColumn().getName() : null;	}
-
 	public double getDefaultInsertionCost() {
 		return icField.getValueAsDouble();
 	}
@@ -131,8 +128,14 @@ public class EditCostPanel extends JPanel {
 		return columnMapper;
 	}
 
-	public String getWeightColumnName() {
-		return columnMapper.getEditingCostColumn() != null ? columnMapper.getEditingCostColumn().getName() : null;
+	public CyColumn getWeightColumn() {
+		return columnMapper.getEditingCostColumn() != null ? columnMapper.getEditingCostColumn() : null;
 	}
 	
+	public CyColumn getPermanentColumn() {
+		return columnMapper.getPermanentColumn() != null ? columnMapper.getPermanentColumn() : null;	}
+
+	public CyColumn getForbiddenColumn() {
+		return columnMapper.getForbiddenColumn() != null ? columnMapper.getForbiddenColumn(): 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.setWeightColumnName(ecPanel.getWeightColumnName());
-		ret.setPermanentColumnName(ecPanel.getPermanentColumnName());
-		ret.setForbiddenColumnName(ecPanel.getForbiddenColumnName());
+		ret.setWeightColumn(ecPanel.getWeightColumn());
+		ret.setPermanentColumn(ecPanel.getPermanentColumn());
+		ret.setForbiddenColumn(ecPanel.getForbiddenColumn());
 		ret.defaultInsertionCost = ecPanel.getDefaultInsertionCost();
 		ret.defaultDeletionCost = ecPanel.getDefaultDeletionCost();
 		ret.useHeuristic = opModePanel.useHeuristic();

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.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;
+		CyColumn weightColumn = parameterSet.getWeightColumn();
+		CyColumn permanentColumn = parameterSet.getPermanentColumn();
+		CyColumn forbiddenColumn = parameterSet.getForbiddenColumn();
 
 		//Generate an c_input instance from the network
 		c_input = NetworkParser.parseNetwork(