toxtree 0.0.1

data/Toxtree-v2.6.13/src/toxtree/ui/tree/TreeOptions.java

@@ -0,0 +1,253 @@
+/*
+Copyright (C) 2005-2007  
+
+Contact: nina@acad.bg
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
+ */
+
+package toxtree.ui.tree;
+
+import java.awt.Color;
+import java.awt.Desktop;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTextPane;
+import javax.swing.UIManager;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.plaf.ButtonUI;
+import javax.swing.text.html.HTMLEditorKit;
+
+import org.openscience.cdk.interfaces.IAtomContainer;
+
+import toxTree.core.IDecisionInteractive;
+import toxTree.core.IDecisionMethod;
+import toxTree.core.IDecisionRule;
+import toxTree.core.IDecisionRuleList;
+import toxTree.io.Tools;
+import toxtree.ui.PropertyEditor;
+import ambit2.base.config.Preferences;
+import ambit2.base.config.Preferences.VTAGS;
+import ambit2.ui.editors.PreferencesPanel;
+
+import com.l2fprod.common.swing.JOutlookBar;
+import com.l2fprod.common.swing.PercentLayout;
+
+public class TreeOptions extends JSplitPane {
+    /**
+	 * 
+	 */
+    private static final long serialVersionUID = -4430297393022588312L;
+
+    public TreeOptions(IDecisionMethod tree, IAtomContainer atomcontainer) {
+	super(JSplitPane.HORIZONTAL_SPLIT);
+	JOutlookBar outlook = new JOutlookBar();
+	outlook.setBackground(Color.white);
+	outlook.setTabPlacement(JTabbedPane.LEFT);
+	addGenericTab(outlook);
+	if (atomcontainer != null)
+	    addMoleculeTab(outlook, atomcontainer);
+	addTreeTab(outlook, tree);
+	setLeftComponent(outlook);
+	JTextPane details = new JTextPane();
+	details.addHyperlinkListener(new HyperlinkListener() {
+	    public void hyperlinkUpdate(HyperlinkEvent e) {
+		if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+		    try {
+			if (Desktop.isDesktopSupported()) {
+			    Desktop.getDesktop().browse(e.getURL().toURI());
+			} else
+			    Tools.openURL(e.getURL().toString());
+		    } catch (Exception x) {
+			x.printStackTrace();
+		    }
+		}
+	    }
+	});
+	details.setEditorKit(new HTMLEditorKit());
+	details.setText(tree.getExplanation());
+	setRightComponent(new JScrollPane(details));
+	setPreferredSize(new Dimension(450, 400));
+
+    }
+
+    void addGenericTab(JOutlookBar tabs) {
+	JPanel panel = new JPanel();
+	panel.setLayout(new PercentLayout(PercentLayout.VERTICAL, 0));
+	panel.setOpaque(false);
+
+	JButton button = new JButton(new PropertiesAction("Options", "General Toxtree options") {
+	    /**
+	     * 
+	     */
+	    private static final long serialVersionUID = -7838273383616865960L;
+
+	    @Override
+	    public void actionPerformed(ActionEvent e) {
+
+		setRightComponent(new PreferencesPanel(new Preferences.VTAGS[] { VTAGS.General, VTAGS.Structure,
+			VTAGS.RemoteQuery }).getJComponent());
+	    }
+	});
+	try {
+
+	    button.setUI((ButtonUI) Class.forName((String) UIManager.get("OutlookButtonUI")).newInstance());
+	    button.setIcon(Tools.getImage("cog.png"));
+	} catch (Exception e) {
+	    e.printStackTrace();
+	}
+	panel.add(button);
+
+	JScrollPane scroll = tabs.makeScrollPane(panel);
+	tabs.addTab("General", scroll);
+
+    }
+
+    void addMoleculeTab(JOutlookBar tabs, IAtomContainer atomcontainer) {
+	JPanel panel = new JPanel();
+	panel.setLayout(new PercentLayout(PercentLayout.VERTICAL, 0));
+	panel.setOpaque(false);
+
+	JButton button = new JButton(new StructureAction(atomcontainer, "Structure", "Current structure") {
+	    /**
+	     * 
+	     */
+	    private static final long serialVersionUID = 3895237480993153266L;
+
+	    public void actionPerformed(ActionEvent e) {
+		setRightComponent(new PropertyEditor(getMolecule(), null));
+	    }
+	});
+	try {
+	    button.setUI((ButtonUI) Class.forName((String) UIManager.get("OutlookButtonUI")).newInstance());
+	} catch (Exception e) {
+	    e.printStackTrace();
+	}
+	panel.add(button);
+
+	JScrollPane scroll = tabs.makeScrollPane(panel);
+	tabs.addTab("Structure", scroll);
+
+    }
+
+    void addTreeTab(JOutlookBar tabs, IDecisionMethod tree) {
+	JPanel panel = null;
+
+	IDecisionRuleList rules = tree.getRules();
+	for (int i = 0; i < rules.size(); i++) {
+	    IDecisionRule rule = rules.getRule(i);
+	    /*
+	     * if (rule instanceof IDecisionInteractive) { JComponent c =
+	     * ((IDecisionInteractive) rule).optionsPanel(null); if (c == null)
+	     * continue; JButton button = new JButton(new
+	     * RuleAction((IDecisionInteractive)
+	     * rule,rule.getID(),rule.getExplanation()) { public void
+	     * actionPerformed(ActionEvent e) { JComponent c =
+	     * getRule().optionsPanel(null); setPreferredSize(new
+	     * Dimension(200,400)); setRightComponent(c);
+	     * 
+	     * } }); try { button.setUI((ButtonUI)Class.forName(
+	     * (String)UIManager.get("OutlookButtonUI")).newInstance());
+	     * button.setIcon(Tools.getImage("arrow_divide.png")); } catch
+	     * (Exception e) { e.printStackTrace(); } if (panel == null) { panel
+	     * = new JPanel(); panel.setLayout(new
+	     * PercentLayout(PercentLayout.VERTICAL, 0));
+	     * panel.setOpaque(false); } panel.add(button); }
+	     */
+	}
+
+	if (panel != null) {
+	    JScrollPane scroll = tabs.makeScrollPane(panel);
+	    tabs.addTab("", scroll);
+
+	    // this to test the UI gets notified of changes
+	    int index = tabs.indexOfComponent(scroll);
+	    tabs.setTitleAt(index, "Rules options");
+	    tabs.setToolTipTextAt(index, tree.getTitle());
+	}
+
+    }
+}
+
+class StructureAction extends PropertiesAction {
+    protected IAtomContainer molecule = null;
+    /**
+	 * 
+	 */
+    private static final long serialVersionUID = -1074623615249070194L;
+
+    public StructureAction(IAtomContainer molecule, String title, String hint) {
+	super(title, hint);
+	setMolecule(molecule);
+    }
+
+    public IAtomContainer getMolecule() {
+	return molecule;
+    }
+
+    public void setMolecule(IAtomContainer molecule) {
+	this.molecule = molecule;
+    }
+}
+
+class RuleAction extends PropertiesAction {
+    protected IDecisionInteractive rule = null;
+    /**
+	 * 
+	 */
+    private static final long serialVersionUID = -1074623615249070194L;
+
+    public RuleAction(IDecisionInteractive rule, String title, String hint) {
+	super(title, hint);
+	this.rule = rule;
+    }
+
+    public IDecisionInteractive getRule() {
+	return rule;
+    }
+
+    public void setRule(IDecisionInteractive rule) {
+	this.rule = rule;
+    }
+}
+
+class PropertiesAction extends AbstractAction {
+    /**
+	 * 
+	 */
+    private static final long serialVersionUID = -1074623615249070194L;
+
+    public PropertiesAction(String title, String hint) {
+	super(title);
+	putValue(AbstractAction.SHORT_DESCRIPTION, hint);
+
+    }
+
+    public void actionPerformed(ActionEvent e) {
+
+    }
+}

data/Toxtree-v2.6.13/src/toxtree/ui/tree/TreePanel.java

@@ -0,0 +1,194 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007 
+
+Contact: nina@acad.bg
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+*/
+package toxtree.ui.tree;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.util.Observable;
+import java.util.Observer;
+
+import javax.swing.BorderFactory;
+import javax.swing.Icon;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTextArea;
+import javax.swing.JTree;
+import javax.swing.UIManager;
+import javax.swing.event.TreeSelectionEvent;
+import javax.swing.event.TreeSelectionListener;
+import javax.swing.tree.DefaultTreeCellRenderer;
+import javax.swing.tree.TreeSelectionModel;
+
+import toxTree.core.IDecisionCategory;
+import toxTree.core.IDecisionMethod;
+import toxTree.core.IDecisionRule;
+import toxTree.io.Tools;
+import toxtree.ui.tree.rules.RulePanel;
+
+/**
+ * 
+ * Displays decision tree by standart {@link JTree} component.
+ * @author Nina Jeliazkova
+ * <b>Modified</b> 2005-10-23
+ */
+public class TreePanel extends JPanel implements TreeSelectionListener, Observer {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -6284436109070270704L;
+
+	protected DecisionTreeModel treeModel = null;
+	protected JTextArea reference = null;
+	protected JTree tree = null;
+
+	protected RulePanel rulePanel = null;
+
+	DecisionNodePanel nodePanel = null;
+
+	public TreePanel(IDecisionMethod treeMethod) {
+		super(new BorderLayout());
+		this.treeModel = new DecisionTreeModel(treeMethod);
+		addWidgets(treeMethod);
+	}
+
+	protected void addWidgets(IDecisionMethod treeMethod) {
+		JPanel p = new JPanel(new BorderLayout());
+		reference = new JTextArea();
+		reference.setWrapStyleWord(true);
+		reference.setColumns(30);
+		reference.setEditable(treeMethod.isEditable());
+		reference.setAutoscrolls(false);
+		reference.setPreferredSize(new Dimension(500, 24));
+		reference.setText(treeMethod.getExplanation());
+		reference.setToolTipText(treeMethod.getExplanation());
+		JScrollPane referenceView = new JScrollPane(reference);
+		referenceView.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+		referenceView.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
+		
+		p.add(referenceView,BorderLayout.NORTH);
+		
+		if (treeModel == null)
+			this.treeModel = new DecisionTreeModel();
+		tree = new JTree(treeModel);
+		   // Retrieve the three icons
+	    Icon leafIcon = Tools.getImage("tick.png");
+	    Icon openIcon = Tools.getImage("open.gif");
+	    Icon closedIcon = Tools.getImage("open.gif");
+	    
+	    // Update only one tree instance
+	    DefaultTreeCellRenderer renderer = (DefaultTreeCellRenderer)tree.getCellRenderer();
+	    renderer.setLeafIcon(leafIcon);
+	    renderer.setClosedIcon(closedIcon);
+	    renderer.setOpenIcon(openIcon);
+	    
+	    // Change defaults so that all new tree components will have new icons
+	    UIManager.put("Tree.leafIcon", leafIcon);
+	    UIManager.put("Tree.openIcon", openIcon);
+	    UIManager.put("Tree.closedIcon", closedIcon);
+	    
+		tree.getSelectionModel().setSelectionMode(
+				TreeSelectionModel.SINGLE_TREE_SELECTION);
+
+		// Listen for when the selection changes.
+		tree.addTreeSelectionListener(this);
+
+		JScrollPane treeView = new JScrollPane(tree);
+		treeView.setPreferredSize(new Dimension(500, 300));
+
+		rulePanel = new RulePanel(null);
+
+		p.add(treeView, BorderLayout.CENTER);
+		nodePanel = new DecisionNodePanel(null);
+
+		p.add(nodePanel, BorderLayout.SOUTH);
+
+		JSplitPane treePane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, p,
+				rulePanel);
+		treePane.setOneTouchExpandable(false);
+		treePane.setDividerLocation(250);
+
+		// Provide minimum sizes for the two components in the split pane
+		Dimension minimumSize = new Dimension(100, 50);
+		p.setMinimumSize(minimumSize);
+		rulePanel.setMinimumSize(minimumSize);
+
+		treePane.setBorder(BorderFactory.createTitledBorder("Decision Tree"));
+
+		add(treePane, BorderLayout.CENTER);
+	}
+
+	public void valueChanged(TreeSelectionEvent e) {
+		Object node = (Object) tree.getLastSelectedPathComponent();
+
+		if (node == null)
+			return;
+
+		if (node instanceof IDecisionRule) {
+			IDecisionRule nodeR = (IDecisionRule) node;
+			nodePanel.setNode((Observable) node);
+
+			rulePanel.setRule(nodeR);
+			IDecisionCategory category;
+			IDecisionRule branch = treeModel.decisionMethod.getBranch(nodeR,
+					false);
+
+			if (branch != null)
+				nodePanel.setNoBranch((Observable) branch);
+			else {
+				category = treeModel.decisionMethod.getCategory(nodeR, false);
+				if (category == null) {
+					// shouldn't get here
+					System.err.print("ERROR: no branch and no category!");
+					System.err.print(nodeR.toString());
+					System.err.print("\t");
+					System.err.println(nodeR);
+				}
+				nodePanel.setNoBranch((Observable) category);
+			}
+
+			branch = treeModel.decisionMethod.getBranch(nodeR, true);
+			if (branch != null)
+				nodePanel.setYesBranch((Observable) branch);
+
+			else {
+				category = treeModel.decisionMethod.getCategory(nodeR, true);
+				nodePanel.setYesBranch((Observable) category);
+			}
+		}
+	}
+
+	public void setDecisionMethod(IDecisionMethod decisionMethod) {
+		treeModel.decisionMethod = decisionMethod;
+
+	}
+
+	public void update(Observable arg0, Object arg1) {
+		treeModel.fireStructureChanged();
+		
+	}
+
+	
+}

data/Toxtree-v2.6.13/src/toxtree/ui/tree/TreePrefuse.java

@@ -0,0 +1,393 @@
+/*
+Copyright (C) 2005-2007  
+
+Contact: nina@acad.bg
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
+*/
+
+package toxtree.ui.tree;
+
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseEvent;
+import java.awt.geom.Rectangle2D;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+
+import prefuse.Constants;
+import prefuse.Display;
+import prefuse.Visualization;
+import prefuse.action.ActionList;
+import prefuse.action.RepaintAction;
+import prefuse.action.assignment.ColorAction;
+import prefuse.action.assignment.DataColorAction;
+import prefuse.action.layout.Layout;
+import prefuse.action.layout.graph.ForceDirectedLayout;
+import prefuse.action.layout.graph.NodeLinkTreeLayout;
+import prefuse.activity.Activity;
+import prefuse.controls.ControlAdapter;
+import prefuse.controls.DragControl;
+import prefuse.controls.FocusControl;
+import prefuse.controls.NeighborHighlightControl;
+import prefuse.controls.PanControl;
+import prefuse.controls.ToolTipControl;
+import prefuse.controls.WheelZoomControl;
+import prefuse.controls.ZoomControl;
+import prefuse.controls.ZoomToFitControl;
+import prefuse.data.Graph;
+import prefuse.data.Node;
+import prefuse.data.search.PrefixSearchTupleSet;
+import prefuse.data.search.SearchTupleSet;
+import prefuse.render.DefaultRendererFactory;
+import prefuse.render.EdgeRenderer;
+import prefuse.render.LabelRenderer;
+import prefuse.util.ColorLib;
+import prefuse.util.GraphicsLib;
+import prefuse.util.display.DisplayLib;
+import prefuse.util.display.ItemBoundsListener;
+import prefuse.visual.VisualGraph;
+import prefuse.visual.VisualItem;
+import toxTree.core.IDecisionCategories;
+import toxTree.core.IDecisionMethod;
+import toxTree.core.IDecisionRule;
+import toxTree.io.Tools;
+import toxTree.tree.Tree2PrefuseGraph;
+import toxTree.ui.tree.categories.CategoriesRenderer;
+
+public class TreePrefuse extends Display implements ITreeView {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 4945963443432036734L;
+    private static final String LABEL = "short";
+    public static final String GRAPH = "graph";
+    public static final String NODES = "graph.nodes";
+    public static final String EDGES = "graph.edges";
+    
+	protected Graph graph;
+	protected IDecisionMethod tree;
+    protected PropertyChangeSupport propertyChangeSupport;
+	
+    public TreePrefuse(final IDecisionMethod tree, EditTreeActions actions)  {
+    	this(tree,actions,false);
+    }
+	public TreePrefuse(final IDecisionMethod tree, EditTreeActions actions, boolean forcefieldLayout)  {
+        // setup a visualisation
+        super(new Visualization());
+        propertyChangeSupport = new PropertyChangeSupport(this);
+        setSize(700, 750);
+        setDecisionMethod(tree);
+
+        m_vis.setValue(EDGES, null, VisualItem.INTERACTIVE, Boolean.TRUE);
+        
+        LabelRenderer nodeRenderer = new LabelRenderer(LABEL);
+        nodeRenderer.setRoundedCorner(8, 8);
+        EdgeRenderer edgeR = new EdgeRenderer(Constants.EDGE_TYPE_CURVE);
+        edgeR.setDefaultLineWidth(2);        
+
+        DefaultRendererFactory rendererFactory = new DefaultRendererFactory(nodeRenderer,edgeR);
+        m_vis.setRendererFactory(rendererFactory);
+        
+        ColorAction nodeText = new ColorAction(NODES, VisualItem.TEXTCOLOR);
+        nodeText.setDefaultColor(ColorLib.gray(0));
+        ColorAction nodeStroke = new ColorAction(NODES, VisualItem.STROKECOLOR);
+        nodeStroke.setDefaultColor(ColorLib.gray(100));
+        //ColorAction nodeFill = new ColorAction(NODES, VisualItem.FILLCOLOR);
+        //nodeFill.setDefaultColor(ColorLib.gray(255));
+        ColorAction edgeStrokes = new ColorAction(EDGES, VisualItem.STROKECOLOR);
+        edgeStrokes.setDefaultColor(ColorLib.gray(100));
+        /*
+        ColorAction edgeFill = new ColorAction(EDGES, VisualItem.FILLCOLOR);
+        edgeFill.setDefaultColor(ColorLib.gray(100));
+        */
+        
+	    DataColorAction nodeFill = new DataColorAction(NODES, Tree2PrefuseGraph.FIELD_NODETYPE,
+         Constants.NOMINAL, VisualItem.FILLCOLOR,  createPalette(tree));
+	    
+	    nodeFill.add(VisualItem.HIGHLIGHT, ColorLib.rgb(255,0,0)); 	    
+
+        // bundle the color actions
+        ActionList draw = new ActionList();
+        //draw.add(shape);        
+        draw.add(nodeText);
+        draw.add(nodeStroke);
+        draw.add(nodeFill);
+        draw.add(edgeStrokes);
+        
+    	ColorAction edgeStrokeColor = new ColorAction(EDGES, 
+    			VisualItem.STROKECOLOR, ColorLib.gray(200));
+    	ColorAction edgeFillColor = new ColorAction(EDGES, 
+    			VisualItem.FILLCOLOR, ColorLib.gray(200));    	
+/* doesn't compile with current prefuse library
+ * 
+   		edgeStrokeColor.add(ExpressionParser.predicate("answer == '" + AbstractRule.MSG_YES + "'"), ColorLib.rgba(0,255,0,100));
+   		edgeStrokeColor.add(ExpressionParser.predicate("answer == '" + AbstractRule.MSG_NO + "'"), ColorLib.rgba(255,0,0,100));
+
+   		edgeFillColor.add(ExpressionParser.predicate("answer == '" + AbstractRule.MSG_YES + "'"), ColorLib.rgba(0,255,0,100));
+   		edgeFillColor.add(ExpressionParser.predicate("answer == '" + AbstractRule.MSG_NO + "'"), ColorLib.rgba(255,0,0,100));
+*/
+   		
+   		draw.add(edgeStrokeColor);
+   		draw.add(edgeFillColor);
+        
+        m_vis.putAction("draw", draw);
+
+/*
+
+                */
+        
+//      create an action list with an animated layout
+//      the INFINITY parameter tells the action list to run indefinitely
+        if (forcefieldLayout) {
+	        ActionList layout = new ActionList(Activity.INFINITY);
+	        layout.add(new ForceDirectedLayout(GRAPH));
+	        layout.add(new RepaintAction());
+	        m_vis.putAction("treeLayout", layout);
+        } else {
+            Layout treeLayout = new NodeLinkTreeLayout(GRAPH, Constants.ORIENT_TOP_BOTTOM,10,10,10);
+            ((NodeLinkTreeLayout)treeLayout).setRootNodeOffset(10);
+            m_vis.putAction("treeLayout", treeLayout);        	
+        }
+                   
+
+
+        
+        ToolTipControl ttc = new ToolTipControl(Tree2PrefuseGraph.FIELD_EXPLANATION);
+        addControlListener(ttc);
+        FocusControl fc = new FocusControl() {
+        	@Override
+        	public void itemClicked(VisualItem item, MouseEvent e) {
+        		// TODO Auto-generated method stub
+        		super.itemClicked(item, e);
+                Object o = null;
+        		int no = item.getInt(Tree2PrefuseGraph.FIELD_ID);
+        		if (no > 0) 
+                    o = tree.getRule(no-1);                   
+                
+                if (e.getButton() == MouseEvent.BUTTON1) {
+                    if (o instanceof IDecisionRule) {
+                        propertyChangeSupport.firePropertyChange(Tree2PrefuseGraph.FIELD_RULE, null,o);     
+                    }
+                } else {
+                    if (e.isPopupTrigger()) {
+                        JPopupMenu pm = getPopupMenu();
+                        if (pm != null)
+                            pm.show(e.getComponent(),e.getX(), e.getY());
+                    }
+                    
+                }                
+        	}
+        };
+        addControlListener(fc);
+        /*
+        Interactive controls of the display are specified using the Control objects found in prefuse.controls. 
+        These controls might be to handle tool tips (ToolTipControl), hovering the mouse (HoverActionControl), 
+        or the focusing of items the user clicks on (FocusControl). 
+        Other controls that don't affect the data include the DragControl, PanControl, and the ZoomControl.
+        */
+        /*
+        addControlListener(new HoverActionControl("repaint"));
+        ColorAction colorAction = new ColorAction(FIELD_ID, VisualItem.FILLCOLOR, ColorLib.rgba(255,255,255,0));
+        colorAction.add("_hover", ColorLib.gray(200,210));
+        
+//      adds the control
+        addControlListener(new NeighborHighlightControl());
+//         set the _highlight color
+        colorAction = new ColorAction(FIELD_ID, VisualItem.FILLCOLOR, ColorLib.rgba(255,255,255,0));
+        colorAction.add("_highlight", ColorLib.rgb(255,200,125));
+        */
+
+        addControlListener(new FocusControl(1));
+        addControlListener(new DragControl());
+        addControlListener(new PanControl());
+        addControlListener(new ZoomControl());
+        addControlListener(new WheelZoomControl());
+        addControlListener(new ZoomToFitControl());
+        addControlListener(new NeighborHighlightControl());        
+        //addControlListener(new RotationControl());
+        
+        addControlListener(new ControlAdapter() {
+            public void itemEntered(VisualItem item, MouseEvent e) {
+            	
+            	//System.out.println("itemEntered " + item.get);
+            	
+ 
+                    
+            }
+            public void itemExited(VisualItem item, MouseEvent e) {
+            	/*
+            	System.out.println(e.paramString());
+            	
+                if ( item.canGetInt(Tree2PrefuseGraph.FIELD_ID) ) {
+                	int no = item.getInt(Tree2PrefuseGraph.FIELD_ID);
+                	if (no > 0)
+                		System.out.println(Integer.toString(no) + '\t' + tree.getRule(no-1));
+                    
+                } 
+                */  
+            }
+        });
+        
+        SearchTupleSet search = new PrefixSearchTupleSet();
+        m_vis.addFocusGroup(Visualization.SEARCH_ITEMS, search);
+
+        // run actions
+        m_vis.run("treeLayout");
+        m_vis.run("draw");
+	}
+
+	public void setDecisionMethod(IDecisionMethod decisionMethod) {
+		this.tree = decisionMethod;
+		try {
+			initGraph(tree);
+		} catch (Exception x) {
+			x.printStackTrace();
+			graph = new Graph();  
+		}
+		
+	}
+	public JComponent getJComponent() {
+		return this;
+	}
+
+	protected int[] createPalette(IDecisionMethod tree) {
+		if ((tree != null) && (tree.getCategories().size() > 0)) {
+			IDecisionCategories ct = tree.getCategories();
+			CategoriesRenderer r = new CategoriesRenderer(ct);
+			int[] c = new int[ct.size() + 1];
+			c[0] = ColorLib.rgb(250,250,250);
+			for (int i=0; i < ct.size();i++) {
+				Color clr = r.getShowColor(i);
+				c[i+1] = clr.getRGB();
+			}	
+			return c;
+		} else 
+		    return  new int[] {
+			         ColorLib.rgb(250,250,250), ColorLib.rgb(100,100,255),
+			         ColorLib.rgb(100,255,100),ColorLib.rgb(255,100,100),
+			         ColorLib.rgb(100,255,255),ColorLib.rgb(255,100,255),
+			         ColorLib.rgb(255,255,100),ColorLib.rgb(100,100,100),
+			         ColorLib.rgb(0,255,0)
+			     };
+	
+	}
+    private VisualGraph initGraph(IDecisionMethod tree) throws Exception {
+        graph = new Graph(true);
+        /*
+        public Graph(Table nodes, Table edges, boolean directed,
+                String nodeKey, String sourceKey, String targetKey)
+                */
+        Tree2PrefuseGraph tg = new Tree2PrefuseGraph(graph);
+        Node root = tg.walkRules(tree);
+        VisualGraph vg =  m_vis.addGraph(GRAPH, graph);
+        //vg.addColumn(LABEL,"CONCAT([id], [name])");
+        return vg;
+    }
+	
+    public Display getOverview() {
+        // overview display
+        Display overview = new Display(m_vis);
+        overview.setSize(290,290);
+        overview.addItemBoundsListener(new FitOverviewListener());
+        return overview;
+    }
+    
+	public IDecisionMethod getDecisionMethod() {
+		return tree;
+	}
+    public void addSelectRuleListener(PropertyChangeListener listener) {
+        propertyChangeSupport.addPropertyChangeListener(listener);
+    }
+
+    public JPopupMenu getPopupMenu() {
+        // TODO Auto-generated method stub
+        return null;
+    }
+    public Action getHelpAction() {
+        Action a = new AbstractAction("Help",Tools.getImage("help.png")) {
+            
+            /**
+	     * 
+	     */
+	    private static final long serialVersionUID = 6907883029421002289L;
+
+	    public void actionPerformed(ActionEvent arg0) {
+                showHelp();
+            }
+        };
+        a.putValue(Action.SHORT_DESCRIPTION, getHelp());
+        return a;
+    }
+    protected String getHelp() {
+        StringBuffer b = new StringBuffer();
+        b.append("<html>");
+        b.append("<ul>");
+        b.append("<li>");
+        b.append("<b>Panning: </b>Pans the display, changing the viewable region of the visualization.");
+        b.append("<br>Panning is accomplished by clicking on the background of a");
+        b.append(" visualization with the left mouse button and then dragging.");
+        b.append("<li>");
+        b.append("<b>Zooming: </b>");
+        b.append("Zooms the display, changing the scale of the viewable region.<br>");
+        b.append("Zooming is achieved by pressing the right mouse button on the background");
+        b.append("of the visualization and dragging the mouse up or down. <br>Moving the mouse up");
+        b.append("zooms out the display around the spot the mouse was originally pressed.");
+        b.append("<br>Moving the mouse down similarly zooms in the display, making items larger" );
+        b.append("<br>Also the display might be zoomed by using the mouse scroll wheel, changing the scale of the viewable region.");
+        b.append("<li>");
+        b.append("<b>Dragging: </b>Changes a node's location when dragged on screen. ");
+        b.append("<li>");
+        b.append("<b>Fit to screen: </b>Zooms a display such that all items within a given group will fit within ");
+        b.append("the display bounds.<br> Click the right mouse button once, with no dragging.");        
+        b.append("</ul>");
+        b.append("</html>");
+        return b.toString();
+    }
+    protected void showHelp() {
+        JOptionPane.showMessageDialog(this, getHelp(), "Help",JOptionPane.PLAIN_MESSAGE, null);        
+    }
+}
+
+class FitOverviewListener implements ItemBoundsListener {
+    private Rectangle2D m_bounds = new Rectangle2D.Double();
+    private Rectangle2D m_temp = new Rectangle2D.Double();
+    private double m_d = 15;
+    public void itemBoundsChanged(Display d) {
+        d.getItemBounds(m_temp);
+        GraphicsLib.expand(m_temp, 25/d.getScale());
+        
+        double dd = m_d/d.getScale();
+        double xd = Math.abs(m_temp.getMinX()-m_bounds.getMinX());
+        double yd = Math.abs(m_temp.getMinY()-m_bounds.getMinY());
+        double wd = Math.abs(m_temp.getWidth()-m_bounds.getWidth());
+        double hd = Math.abs(m_temp.getHeight()-m_bounds.getHeight());
+        if ( xd>dd || yd>dd || wd>dd || hd>dd ) {
+            m_bounds.setFrame(m_temp);
+            DisplayLib.fitViewToBounds(d, m_bounds, 0);
+        }
+    }
+}
+