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source: src/main/java/weka/classifiers/bayes/net/GUI.java @ 9

Last change on this file since 9 was 4, checked in by gnappo, 14 years ago
Import di weka.
File size: 109.5 KB

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1	/*
2	* This program is free software; you can redistribute it and/or modify
3	* it under the terms of the GNU General Public License as published by
4	* the Free Software Foundation; either version 2 of the License, or
5	* (at your option) any later version.
6	*
7	* This program is distributed in the hope that it will be useful,
8	* but WITHOUT ANY WARRANTY; without even the implied warranty of
9	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
10	* GNU General Public License for more details.
11	*
12	* You should have received a copy of the GNU General Public License
13	* along with this program; if not, write to the Free Software
14	* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
15	*/
16
17	/*
18	* GUI.java
19	* Copyright (C) 2007 University of Waikato, Hamilton, New Zealand
20	*
21	*/
22	package weka.classifiers.bayes.net;
23
24	import weka.classifiers.bayes.net.MarginCalculator.JunctionTreeNode;
25	import weka.core.FastVector;
26	import weka.core.Instances;
27	import weka.core.OptionHandler;
28	import weka.core.SerializedObject;
29	import weka.core.Utils;
30	import weka.core.converters.AbstractFileLoader;
31	import weka.core.converters.AbstractFileSaver;
32	import weka.core.converters.ArffSaver;
33	import weka.core.converters.ConverterUtils;
34	import weka.gui.ConverterFileChooser;
35	import weka.gui.ExtensionFileFilter;
36	import weka.gui.GenericObjectEditor;
37	import weka.gui.LookAndFeel;
38	import weka.gui.PropertyDialog;
39	import weka.gui.graphvisualizer.BIFFormatException;
40	import weka.gui.graphvisualizer.BIFParser;
41	import weka.gui.graphvisualizer.GraphNode;
42	import weka.gui.graphvisualizer.HierarchicalBCEngine;
43	import weka.gui.graphvisualizer.LayoutCompleteEvent;
44	import weka.gui.graphvisualizer.LayoutCompleteEventListener;
45	import weka.gui.graphvisualizer.LayoutEngine;
46	import weka.gui.visualize.PrintablePanel;
47
48	import java.awt.BorderLayout;
49	import java.awt.Color;
50	import java.awt.Container;
51	import java.awt.Dimension;
52	import java.awt.Font;
53	import java.awt.FontMetrics;
54	import java.awt.Frame;
55	import java.awt.Graphics;
56	import java.awt.Graphics2D;
57	import java.awt.GridBagConstraints;
58	import java.awt.GridBagLayout;
59	import java.awt.GridLayout;
60	import java.awt.Insets;
61	import java.awt.Rectangle;
62	import java.awt.RenderingHints;
63	import java.awt.event.ActionEvent;
64	import java.awt.event.ActionListener;
65	import java.awt.event.MouseAdapter;
66	import java.awt.event.MouseEvent;
67	import java.awt.event.MouseMotionAdapter;
68	import java.awt.event.WindowAdapter;
69	import java.awt.event.WindowEvent;
70	import java.awt.image.BufferedImage;
71	import java.awt.print.PageFormat;
72	import java.awt.print.Printable;
73	import java.awt.print.PrinterException;
74	import java.awt.print.PrinterJob;
75	import java.beans.PropertyEditor;
76	import java.io.File;
77	import java.io.FileReader;
78	import java.io.FileWriter;
79	import java.io.IOException;
80	import java.util.Random;
81
82	import javax.swing.AbstractAction;
83	import javax.swing.Action;
84	import javax.swing.BorderFactory;
85	import javax.swing.ImageIcon;
86	import javax.swing.JButton;
87	import javax.swing.JCheckBox;
88	import javax.swing.JCheckBoxMenuItem;
89	import javax.swing.JDialog;
90	import javax.swing.JFileChooser;
91	import javax.swing.JFrame;
92	import javax.swing.JLabel;
93	import javax.swing.JMenu;
94	import javax.swing.JMenuBar;
95	import javax.swing.JMenuItem;
96	import javax.swing.JOptionPane;
97	import javax.swing.JPanel;
98	import javax.swing.JPopupMenu;
99	import javax.swing.JScrollPane;
100	import javax.swing.JTable;
101	import javax.swing.JTextField;
102	import javax.swing.JToolBar;
103	import javax.swing.KeyStroke;
104	import javax.swing.table.AbstractTableModel;
105
106	/**
107	* GUI interface to Bayesian Networks. Allows editing Bayesian networks
108	* on screen and provides GUI interface to various Bayesian network facilities
109	* in Weka, including random network generation, data set generation and
110	* Bayesion network inference.
111	*
112	* @author Remco Bouckaert (remco@cs.waikato.ac.nz)
113	* @version $Revision: 4902 $
114	*/
115	public class GUI extends JPanel implements LayoutCompleteEventListener {
116
117	/** for serialization */
118	private static final long serialVersionUID = -2038911085935515624L;
119
120	/** The current LayoutEngine */
121	protected LayoutEngine m_layoutEngine;
122
123	/** Panel actually displaying the graph */
124	protected GraphPanel m_GraphPanel;
125
126	/** Container of Bayesian network */
127	EditableBayesNet m_BayesNet = new EditableBayesNet(true);
128
129	/** String containing file name storing current network */
130	protected String m_sFileName = "";
131	/** used for calculating marginals in Bayesian netwowrks */
132	MarginCalculator m_marginCalculator = null;
133
134	/**
135	* used for calculating marginals in Bayesian netwowrks when evidence is
136	* present
137	*/
138	MarginCalculator m_marginCalculatorWithEvidence = null;
139
140	/** flag indicating whether marginal distributions of each of the nodes
141	* should be shown in display.
142	*/
143	boolean m_bViewMargins = false;
144	boolean m_bViewCliques = false;
145
146	/** The menu bar */
147	private JMenuBar m_menuBar;
148
149	/** data selected from file. Used to train a Bayesian network on */
150	Instances m_Instances = null;
151
152	/** Text field for specifying zoom */
153	final JTextField m_jTfZoom;
154	/** toolbar containing buttons at top of window */
155	final JToolBar m_jTbTools;
156	/** status bar at bottom of window */
157	final JLabel m_jStatusBar;
158	/** TextField for node's width */
159	private final JTextField m_jTfNodeWidth = new JTextField(3);
160	/** TextField for nodes height */
161	private final JTextField m_jTfNodeHeight = new JTextField(3);
162	/** this contains the m_GraphPanel GraphPanel */
163	JScrollPane m_jScrollPane;
164
165	/** path for icons */
166	private final String ICONPATH = "weka/classifiers/bayes/net/icons/";
167
168	/** current zoom value */
169	private double m_fScale = 1;
170
171	/** standard width of node */
172	private int m_nNodeHeight = 2 * getFontMetrics(getFont()).getHeight();
173	/** standard height of node */
174	final static int DEFAULT_NODE_WIDTH = 50;
175	private int m_nNodeWidth = DEFAULT_NODE_WIDTH;
176	/** width of node, allowing for some padding */
177	final static int PADDING = 10;
178	private int m_nPaddedNodeWidth = DEFAULT_NODE_WIDTH + PADDING;
179
180
181	/** used when using zoomIn and zoomOut buttons */
182	private int [] m_nZoomPercents = { 10, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 350, 400, 450, 500,
183	550, 600, 650, 700, 800, 900, 999 };
184
185	/** actions triggered by GUI events */
186	Action a_new = new ActionNew();
187
188	Action a_quit = new ActionQuit();
189	Action a_save = new ActionSave();
190	ActionExport a_export = new ActionExport();
191	ActionPrint a_print = new ActionPrint();
192	Action a_load = new ActionLoad();
193	Action a_zoomin = new ActionZoomIn();
194	Action a_zoomout = new ActionZoomOut();
195	Action a_layout = new ActionLayout();
196
197	Action a_saveas = new ActionSaveAs();
198
199	Action a_viewtoolbar = new ActionViewToolbar();
200
201	Action a_viewstatusbar = new ActionViewStatusbar();
202
203	Action a_networkgenerator = new ActionGenerateNetwork();
204
205	Action a_datagenerator = new ActionGenerateData();
206
207	Action a_datasetter = new ActionSetData();
208
209	Action a_learn = new ActionLearn();
210	Action a_learnCPT = new ActionLearnCPT();
211
212	Action a_help = new ActionHelp();
213
214	Action a_about = new ActionAbout();
215
216	ActionAddNode a_addnode = new ActionAddNode();
217
218	Action a_delnode = new ActionDeleteNode();
219	Action a_cutnode = new ActionCutNode();
220	Action a_copynode = new ActionCopyNode();
221	Action a_pastenode = new ActionPasteNode();
222	Action a_selectall = new ActionSelectAll();
223
224	Action a_addarc = new ActionAddArc();
225
226	Action a_delarc = new ActionDeleteArc();
227
228	Action a_undo = new ActionUndo();
229
230	Action a_redo= new ActionRedo();
231
232	Action a_alignleft = new ActionAlignLeft();
233	Action a_alignright = new ActionAlignRight();
234	Action a_aligntop = new ActionAlignTop();
235	Action a_alignbottom = new ActionAlignBottom();
236	Action a_centerhorizontal = new ActionCenterHorizontal();
237	Action a_centervertical = new ActionCenterVertical();
238	Action a_spacehorizontal = new ActionSpaceHorizontal();
239	Action a_spacevertical = new ActionSpaceVertical();
240
241	/** node currently selected through right clicking */
242	int m_nCurrentNode = -1;
243	/** selection of nodes */
244	Selection m_Selection = new Selection();
245	/** selection rectangle drawn through dragging with left mouse button */
246	Rectangle m_nSelectedRect = null;
247
248
249	class Selection {
250	FastVector m_selected;
251	public Selection() {
252	m_selected = new FastVector();
253	} // c'tor
254	public FastVector getSelected() {return m_selected;}
255	void updateGUI() {
256	if (m_selected.size() > 0) {
257	a_cutnode.setEnabled(true);
258	a_copynode.setEnabled(true);
259	} else {
260	a_cutnode.setEnabled(false);
261	a_copynode.setEnabled(false);
262	}
263	if (m_selected.size() > 1) {
264	a_alignleft.setEnabled(true);
265	a_alignright.setEnabled(true);
266	a_aligntop.setEnabled(true);
267	a_alignbottom.setEnabled(true);
268	a_centerhorizontal.setEnabled(true);
269	a_centervertical.setEnabled(true);
270	a_spacehorizontal.setEnabled(true);
271	a_spacevertical.setEnabled(true);
272	} else {
273	a_alignleft.setEnabled(false);
274	a_alignright.setEnabled(false);
275	a_aligntop.setEnabled(false);
276	a_alignbottom.setEnabled(false);
277	a_centerhorizontal.setEnabled(false);
278	a_centervertical.setEnabled(false);
279	a_spacehorizontal.setEnabled(false);
280	a_spacevertical.setEnabled(false);
281	}
282	} // updateGUI
283
284	public void addToSelection(int nNode) {
285	for (int iNode = 0; iNode < m_selected.size(); iNode++) {
286	if (nNode == (Integer) m_selected.elementAt(iNode)) {
287	return;
288	}
289	}
290	m_selected.addElement(nNode);
291	updateGUI();
292	} // addToSelection
293
294	public void addToSelection(int [] iNodes) {
295	for (int iNode = 0; iNode < iNodes.length; iNode++) {
296	addToSelection(iNodes[iNode]);
297	}
298	updateGUI();
299	} // addToSelection
300
301	public void addToSelection(Rectangle selectedRect) {
302	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
303	if (contains(selectedRect, iNode)) {
304	addToSelection(iNode);
305	}
306	}
307	} // addToSelection
308
309	public void selectAll() {
310	m_selected.removeAllElements();
311	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
312	m_selected.addElement(iNode);
313	}
314	updateGUI();
315	} // selectAll
316
317	boolean contains(Rectangle rect, int iNode) {
318	return rect.intersects((m_BayesNet.getPositionX(iNode)) * m_fScale,
319	(m_BayesNet.getPositionY(iNode)) * m_fScale,
320	m_nPaddedNodeWidth * m_fScale, m_nNodeHeight * m_fScale);
321	} // contains
322
323	public void removeFromSelection(int nNode) {
324	for (int iNode = 0; iNode < m_selected.size(); iNode++) {
325	if (nNode == (Integer) m_selected.elementAt(iNode)) {
326	m_selected.removeElementAt(iNode);
327	}
328	}
329	updateGUI();
330	} // removeFromSelection
331
332	public void toggleSelection(int nNode) {
333	for (int iNode = 0; iNode < m_selected.size(); iNode++) {
334	if (nNode == (Integer) m_selected.elementAt(iNode)) {
335	m_selected.removeElementAt(iNode);
336	updateGUI();
337	return;
338	}
339	}
340	addToSelection(nNode);
341	} // toggleSelection
342
343	public void toggleSelection(Rectangle selectedRect) {
344	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
345	if (contains(selectedRect, iNode)) {
346	toggleSelection(iNode);
347	}
348	}
349	} // toggleSelection
350
351	public void clear() {
352	m_selected.removeAllElements();
353	updateGUI();
354	}
355
356	public void draw(Graphics g) {
357	if (m_selected.size() == 0) {
358	return;
359	}
360
361	for (int iNode = 0; iNode < m_selected.size(); iNode++) {
362	int nNode = (Integer) m_selected.elementAt(iNode);
363	int nPosX = m_BayesNet.getPositionX(nNode);
364	int nPosY = m_BayesNet.getPositionY(nNode);
365	g.setColor(Color.BLACK);
366	int nXRC = nPosX + m_nPaddedNodeWidth - m_nNodeWidth - (m_nPaddedNodeWidth - m_nNodeWidth) / 2;
367	int nYRC = nPosY;
368	int d = 5;
369	g.fillRect(nXRC, nYRC, d, d);
370	g.fillRect(nXRC, nYRC + m_nNodeHeight, d, d);
371	g.fillRect(nXRC + m_nNodeWidth, nYRC, d, d);
372	g.fillRect(nXRC + m_nNodeWidth, nYRC + m_nNodeHeight, d, d);
373	}
374	} // draw
375	} // Selection
376
377	ClipBoard m_clipboard = new ClipBoard();
378
379	class ClipBoard {
380	String m_sText = null;
381	public ClipBoard() {
382	if (a_pastenode != null) {
383	a_pastenode.setEnabled(false);
384	}
385	}
386	public boolean hasText() {return m_sText != null;}
387	public String getText() {
388	return m_sText;
389	}
390	public void setText(String sText) {
391	m_sText = sText;
392	a_pastenode.setEnabled(true);
393	}
394	} // class ClipBoard
395
396	/** Base class used for definining actions
397	* with a name, tool tip text, possibly an icon and accelerator key.
398	* */
399	class MyAction extends AbstractAction {
400	/** for serialization */
401	private static final long serialVersionUID = -2038911111935517L;
402
403	public MyAction(String sName, String sToolTipText, String sIcon, String sAcceleratorKey) {
404	super(sName);
405	//setToolTipText(sToolTipText);
406	putValue(Action.SHORT_DESCRIPTION, sToolTipText);
407	putValue(Action.LONG_DESCRIPTION, sToolTipText);
408	if (sAcceleratorKey.length() > 0) {
409	KeyStroke keyStroke = KeyStroke.getKeyStroke(sAcceleratorKey);
410	putValue(Action.ACCELERATOR_KEY, keyStroke);
411	}
412	putValue(Action.MNEMONIC_KEY, (int) sName.charAt(0));
413	java.net.URL tempURL = ClassLoader.getSystemResource(ICONPATH + sIcon + ".png");
414	if (tempURL != null) {
415	putValue(Action.SMALL_ICON, new ImageIcon(tempURL));
416	} else {
417	putValue(Action.SMALL_ICON, new ImageIcon(new BufferedImage(20,20, BufferedImage.TYPE_4BYTE_ABGR)));
418	//System.err.println(ICONPATH + sIcon + ".png not found for weka.gui.graphvisualizer.Graph");
419	}
420	} // c'tor
421
422	/* Place holder. Should be implemented by derived classes.
423	* (non-Javadoc)
424	* @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
425	*/
426	public void actionPerformed(ActionEvent ae) {}
427	} // class MyAction
428
429	class ActionGenerateNetwork extends MyAction {
430	/** for serialization */
431	private static final long serialVersionUID = -2038911085935517L;
432
433	public ActionGenerateNetwork() {
434	super("Generate Network", "Generate Random Bayesian Network", "generate.network", "ctrl N");
435	} // c'tor
436
437	int m_nNrOfNodes = 10;
438
439	int m_nNrOfArcs = 15;
440
441	int m_nCardinality = 2;
442
443	int m_nSeed = 123;
444
445	JDialog dlg = null;
446
447	public void actionPerformed(ActionEvent ae) {
448	if (dlg == null) {
449	dlg = new JDialog();
450	dlg.setTitle("Generate Random Bayesian Network Options");
451
452	final JLabel jLbNrOfNodes = new JLabel("Nr of nodes");
453	final JTextField jTfNrOfNodes = new JTextField(3);
454	jTfNrOfNodes.setHorizontalAlignment(JTextField.CENTER);
455	jTfNrOfNodes.setText("" + m_nNrOfNodes);
456	final JLabel jLbNrOfArcs = new JLabel("Nr of arcs");
457	final JTextField jTfNrOfArcs = new JTextField(3);
458	jTfNrOfArcs.setHorizontalAlignment(JTextField.CENTER);
459	jTfNrOfArcs.setText("" + m_nNrOfArcs);
460	final JLabel jLbCardinality = new JLabel("Cardinality");
461	final JTextField jTfCardinality = new JTextField(3);
462	jTfCardinality.setHorizontalAlignment(JTextField.CENTER);
463	jTfCardinality.setText("" + m_nCardinality);
464	final JLabel jLbSeed = new JLabel("Random seed");
465	final JTextField jTfSeed = new JTextField(3);
466	jTfSeed.setHorizontalAlignment(JTextField.CENTER);
467	jTfSeed.setText("" + m_nSeed);
468
469	JButton jBtGo;
470	jBtGo = new JButton("Generate Network");
471
472	jBtGo.addActionListener(new ActionListener() {
473	public void actionPerformed(ActionEvent ae) {
474	try {
475	BayesNetGenerator generator = new BayesNetGenerator();
476	m_BayesNet = generator;
477	m_BayesNet.clearUndoStack();
478
479	String[] options = new String[8];
480	options[0] = "-N";
481	options[1] = "" + jTfNrOfNodes.getText();
482	options[2] = "-A";
483	options[3] = "" + jTfNrOfArcs.getText();
484	options[4] = "-C";
485	options[5] = "" + jTfCardinality.getText();
486	options[6] = "-S";
487	options[7] = "" + jTfSeed.getText();
488	generator.setOptions(options);
489	generator.generateRandomNetwork();
490	// Convert to EditableBayesNet
491	// This ensures the getOptions() called by GenericObjectEditor to get the correct result.
492	BIFReader bifReader = new BIFReader();
493	bifReader.processString(m_BayesNet.toXMLBIF03());
494	m_BayesNet = new EditableBayesNet(bifReader);
495
496	updateStatus();
497	layoutGraph();
498	a_datagenerator.setEnabled(true);
499	m_Instances = null;;
500	a_learn.setEnabled(false);
501	a_learnCPT.setEnabled(false);
502
503	dlg.setVisible(false);
504	} catch (Exception e) {
505	e.printStackTrace();
506	}
507	}
508	});
509
510	JButton jBtCancel;
511	jBtCancel = new JButton("Cancel");
512	jBtCancel.setMnemonic('C');
513	jBtCancel.addActionListener(new ActionListener() {
514	public void actionPerformed(ActionEvent ae) {
515	dlg.setVisible(false);
516	}
517	});
518	GridBagConstraints gbc = new GridBagConstraints();
519	dlg.setLayout(new GridBagLayout());
520
521	Container c = new Container();
522	c.setLayout(new GridBagLayout());
523	gbc.gridwidth = 2;
524	gbc.insets = new Insets(8, 0, 0, 0);
525	gbc.anchor = GridBagConstraints.NORTHWEST;
526	gbc.gridwidth = GridBagConstraints.RELATIVE;
527	gbc.fill = GridBagConstraints.HORIZONTAL;
528	c.add(jLbNrOfNodes, gbc);
529	gbc.gridwidth = GridBagConstraints.REMAINDER;
530	c.add(jTfNrOfNodes, gbc);
531	gbc.gridwidth = GridBagConstraints.RELATIVE;
532	c.add(jLbNrOfArcs, gbc);
533	gbc.gridwidth = GridBagConstraints.REMAINDER;
534	c.add(jTfNrOfArcs, gbc);
535	gbc.gridwidth = GridBagConstraints.RELATIVE;
536	c.add(jLbCardinality, gbc);
537	gbc.gridwidth = GridBagConstraints.REMAINDER;
538	c.add(jTfCardinality, gbc);
539	gbc.gridwidth = GridBagConstraints.RELATIVE;
540	c.add(jLbSeed, gbc);
541	gbc.gridwidth = GridBagConstraints.REMAINDER;
542	c.add(jTfSeed, gbc);
543
544	gbc.fill = GridBagConstraints.HORIZONTAL;
545	dlg.add(c, gbc);
546	dlg.add(jBtGo);
547	gbc.gridwidth = GridBagConstraints.REMAINDER;
548	dlg.add(jBtCancel);
549	}
550	dlg.pack();
551	dlg.setLocation(100, 100);
552	dlg.setVisible(true);
553	dlg.setSize(dlg.getPreferredSize());
554	dlg.setVisible(false);
555	dlg.setVisible(true);
556	dlg.repaint();
557	} // actionPerformed
558	} // class ActionGenerate
559
560	class ActionGenerateData extends MyAction {
561	/** for serialization */
562	private static final long serialVersionUID = -2038911085935516L;
563
564	public ActionGenerateData() {
565	super("Generate Data", "Generate Random Instances from Network", "generate.data", "ctrl D");
566	} // c'tor
567
568	int m_nNrOfInstances = 100;
569
570	int m_nSeed = 1234;
571
572	String m_sFile = "";
573
574	JDialog dlg = null;
575
576	public void actionPerformed(ActionEvent ae) {
577	if (dlg == null) {
578	dlg = new JDialog();
579	dlg.setTitle("Generate Random Data Options");
580
581	final JLabel jLbNrOfInstances = new JLabel("Nr of instances");
582	final JTextField jTfNrOfInstances = new JTextField(3);
583	jTfNrOfInstances.setHorizontalAlignment(JTextField.CENTER);
584	jTfNrOfInstances.setText("" + m_nNrOfInstances);
585	final JLabel jLbSeed = new JLabel("Random seed");
586	final JTextField jTfSeed = new JTextField(3);
587	jTfSeed.setHorizontalAlignment(JTextField.CENTER);
588	jTfSeed.setText("" + m_nSeed);
589	final JLabel jLbFile = new JLabel("Output file (optional)");
590	final JTextField jTfFile = new JTextField(12);
591	jTfFile.setHorizontalAlignment(JTextField.CENTER);
592	jTfFile.setText(m_sFile);
593
594	JButton jBtGo;
595	jBtGo = new JButton("Generate Data");
596
597	jBtGo.addActionListener(new ActionListener() {
598	public void actionPerformed(ActionEvent ae) {
599	try {
600	String tmpfilename = "tmp.bif.file.xml";
601	BayesNetGenerator generator = new BayesNetGenerator();
602	String[] options = new String[4];
603	options[0] = "-M";
604	options[1] = "" + jTfNrOfInstances.getText();
605	options[2] = "-F";
606	options[3] = tmpfilename;
607	FileWriter outfile = new FileWriter(tmpfilename);
608	StringBuffer text = new StringBuffer();
609	if (m_marginCalculator == null) {
610	m_marginCalculator = new MarginCalculator();
611	m_marginCalculator.calcMargins(m_BayesNet);
612	}
613	text.append(m_marginCalculator.toXMLBIF03());
614	outfile.write(text.toString());
615	outfile.close();
616
617	generator.setOptions(options);
618	generator.generateRandomNetwork();
619	generator.generateInstances();
620	m_Instances = generator.m_Instances;
621	a_learn.setEnabled(true);
622	a_learnCPT.setEnabled(true);
623
624	m_sFile = jTfFile.getText();
625	if (m_sFile != null && !m_sFile.equals("")) {
626	AbstractFileSaver saver = ConverterUtils.getSaverForFile(m_sFile);
627	// no idea what the format is, so let's save it as ARFF file
628	if (saver == null)
629	saver = new ArffSaver();
630	saver.setFile(new File(m_sFile));
631	saver.setInstances(m_Instances);
632	saver.writeBatch();
633	}
634
635	} catch (Exception e) {
636	e.printStackTrace();
637	}
638	dlg.setVisible(false);
639	}
640	});
641
642	JButton jBtFile = new JButton("Browse");
643	jBtFile.addActionListener(new ActionListener() {
644	public void actionPerformed(ActionEvent ae) {
645	ConverterFileChooser fc = new ConverterFileChooser(System.getProperty("user.dir"));
646	fc.setDialogTitle("Save Instances As");
647	int rval = fc.showSaveDialog(GUI.this);
648
649	if (rval == JFileChooser.APPROVE_OPTION) {
650	String filename = fc.getSelectedFile().toString();
651	jTfFile.setText(filename);
652	}
653	dlg.setVisible(true);
654	}
655	});
656	JButton jBtCancel;
657	jBtCancel = new JButton("Cancel");
658	jBtCancel.setMnemonic('C');
659	jBtCancel.addActionListener(new ActionListener() {
660	public void actionPerformed(ActionEvent ae) {
661	dlg.setVisible(false);
662	}
663	});
664	GridBagConstraints gbc = new GridBagConstraints();
665	dlg.setLayout(new GridBagLayout());
666
667	Container c = new Container();
668	c.setLayout(new GridBagLayout());
669	gbc.gridwidth = 2;
670	gbc.insets = new Insets(8, 0, 0, 0);
671	gbc.anchor = GridBagConstraints.NORTHWEST;
672	gbc.gridwidth = GridBagConstraints.RELATIVE;
673	gbc.fill = GridBagConstraints.HORIZONTAL;
674	c.add(jLbNrOfInstances, gbc);
675	gbc.gridwidth = GridBagConstraints.REMAINDER;
676	c.add(jTfNrOfInstances, gbc);
677	gbc.gridwidth = GridBagConstraints.RELATIVE;
678	c.add(jLbSeed, gbc);
679	gbc.gridwidth = GridBagConstraints.REMAINDER;
680	c.add(jTfSeed, gbc);
681	gbc.gridwidth = GridBagConstraints.RELATIVE;
682	c.add(jLbFile, gbc);
683	gbc.gridwidth = GridBagConstraints.REMAINDER;
684	c.add(jTfFile, gbc);
685	gbc.gridwidth = GridBagConstraints.REMAINDER;
686	c.add(jBtFile, gbc);
687
688	gbc.fill = GridBagConstraints.HORIZONTAL;
689	dlg.add(c, gbc);
690	dlg.add(jBtGo);
691	gbc.gridwidth = GridBagConstraints.REMAINDER;
692	dlg.add(jBtCancel);
693	}
694	dlg.setLocation(100, 100);
695	dlg.setVisible(true);
696	dlg.setSize(dlg.getPreferredSize());
697	dlg.setVisible(false);
698	dlg.setVisible(true);
699	dlg.repaint();
700
701	} // actionPerformed
702	} // class ActionGenerateData
703
704	class ActionLearn extends MyAction {
705	/** for serialization */
706	private static final long serialVersionUID = -2038911085935516L;
707
708	public ActionLearn() {
709	super("Learn Network", "Learn Bayesian Network", "learn", "ctrl L");
710	setEnabled(false);
711	} // c'tor
712
713	JDialog dlg = null;
714
715	public void actionPerformed(ActionEvent ae) {
716	if (dlg == null) {
717	dlg = new JDialog();
718	dlg.setTitle("Learn Bayesian Network");
719
720	final JButton jBtOptions = new JButton("Options");
721	jBtOptions.addActionListener(new ActionListener() {
722	public void actionPerformed(ActionEvent ae) {
723	//m_BayesNet = new EditableBayesNet();
724	try {
725	GenericObjectEditor.registerEditors();
726	GenericObjectEditor ce = new GenericObjectEditor(true);
727	ce.setClassType(weka.classifiers.Classifier.class);
728	ce.setValue(m_BayesNet);
729
730	PropertyDialog pd;
731	if (PropertyDialog.getParentDialog(GUI.this) != null)
732	pd = new PropertyDialog(PropertyDialog.getParentDialog(GUI.this), ce, 100, 100);
733	else
734	pd = new PropertyDialog(PropertyDialog.getParentFrame(GUI.this), ce, 100, 100);
735	pd.addWindowListener(new WindowAdapter() {
736	public void windowClosing(WindowEvent e) {
737	PropertyEditor pe = ((PropertyDialog) e.getSource()).getEditor();
738	Object c = (Object) pe.getValue();
739	String options = "";
740	if (c instanceof OptionHandler) {
741	options = Utils.joinOptions(((OptionHandler) c).getOptions());
742	try {
743	m_BayesNet.setOptions(((OptionHandler) c).getOptions());
744	} catch (Exception e2) {
745	e2.printStackTrace();
746	}
747	}
748	System.out.println(c.getClass().getName() + " " + options);
749	System.exit(0);
750	}
751	});
752	pd.setVisible(true);
753	} catch (Exception ex) {
754	ex.printStackTrace();
755	System.err.println(ex.getMessage());
756	}
757	m_BayesNet.clearUndoStack();
758	a_undo.setEnabled(false);
759	a_redo.setEnabled(false);
760	}
761	});
762
763	final JTextField jTfOptions = new JTextField(40);
764	jTfOptions.setHorizontalAlignment(JTextField.CENTER);
765	jTfOptions.setText("" + Utils.joinOptions(m_BayesNet.getOptions()));
766
767	JButton jBtGo;
768	jBtGo = new JButton("Learn");
769
770	jBtGo.addActionListener(new ActionListener() {
771	public void actionPerformed(ActionEvent ae) {
772	try {
773	m_BayesNet.buildClassifier(m_Instances);
774	layoutGraph();
775	updateStatus();
776	m_BayesNet.clearUndoStack();
777
778	dlg.setVisible(false);
779	} catch (Exception e) {
780	e.printStackTrace();
781	}
782	dlg.setVisible(false);
783	}
784	});
785
786	JButton jBtCancel;
787	jBtCancel = new JButton("Cancel");
788	jBtCancel.setMnemonic('C');
789	jBtCancel.addActionListener(new ActionListener() {
790	public void actionPerformed(ActionEvent ae) {
791	dlg.setVisible(false);
792	}
793	});
794	GridBagConstraints gbc = new GridBagConstraints();
795	dlg.setLayout(new GridBagLayout());
796
797	Container c = new Container();
798	c.setLayout(new GridBagLayout());
799	gbc.gridwidth = 2;
800	gbc.insets = new Insets(8, 0, 0, 0);
801	gbc.anchor = GridBagConstraints.NORTHWEST;
802	gbc.gridwidth = GridBagConstraints.RELATIVE;
803	gbc.fill = GridBagConstraints.HORIZONTAL;
804	c.add(jBtOptions, gbc);
805	gbc.gridwidth = GridBagConstraints.REMAINDER;
806	c.add(jTfOptions, gbc);
807
808	gbc.fill = GridBagConstraints.HORIZONTAL;
809	dlg.add(c, gbc);
810	dlg.add(jBtGo);
811	gbc.gridwidth = GridBagConstraints.REMAINDER;
812	dlg.add(jBtCancel);
813	}
814	dlg.setLocation(100, 100);
815	dlg.setVisible(true);
816	dlg.setSize(dlg.getPreferredSize());
817	dlg.setVisible(false);
818	dlg.setVisible(true);
819	dlg.repaint();
820	} // actionPerformed
821	} // class ActionLearn
822
823	class ActionLearnCPT extends MyAction {
824	/** for serialization */
825	private static final long serialVersionUID = -2022211085935516L;
826
827	public ActionLearnCPT() {
828	super("Learn CPT", "Learn conditional probability tables", "learncpt", "");
829	setEnabled(false);
830	} // c'tor
831
832	public void actionPerformed(ActionEvent ae) {
833	if (m_Instances == null) {
834	JOptionPane.showMessageDialog(null, "Select instances to learn from first (menu Tools/Set Data)");
835	return;
836	}
837	try {
838	m_BayesNet.setData(m_Instances);
839	} catch (Exception e) {
840	JOptionPane.showMessageDialog(null, "Data set is not compatible with network.\n"+e.getMessage() + "\nChoose other instances (menu Tools/Set Data)");
841	return;
842	}
843	try {
844	m_BayesNet.estimateCPTs();
845	m_BayesNet.clearUndoStack();
846	} catch (Exception e) {
847	e.printStackTrace();
848	}
849	updateStatus();
850	} // actionPerformed
851	} // class ActionLearnCPT
852
853	class ActionSetData extends MyAction {
854	/** for serialization */
855	private static final long serialVersionUID = -2038911085935519L;
856
857	public ActionSetData() {
858	super("Set Data", "Set Data File", "setdata", "ctrl A");
859	} // c'tor
860
861	public void actionPerformed(ActionEvent ae) {
862	ConverterFileChooser fc = new ConverterFileChooser(System.getProperty("user.dir"));
863	fc.setDialogTitle("Set Data File");
864	int rval = fc.showOpenDialog(GUI.this);
865
866	if (rval == JFileChooser.APPROVE_OPTION) {
867	AbstractFileLoader loader = fc.getLoader();
868	try {
869	if (loader != null)
870	m_Instances = loader.getDataSet();
871	if (m_Instances.classIndex() == -1)
872	m_Instances.setClassIndex(m_Instances.numAttributes() - 1);
873	a_learn.setEnabled(true);
874	a_learnCPT.setEnabled(true);
875	repaint();
876	} catch (Exception e) {
877	e.printStackTrace();
878	}
879	}
880	}
881	} // class ActionSetData
882
883	class ActionUndo extends MyAction {
884	/** for serialization */
885	private static final long serialVersionUID = -3038910085935519L;
886
887	public ActionUndo() {
888	super("Undo", "Undo", "undo", "ctrl Z");
889	setEnabled(false);
890	} // c'tor
891
892	public boolean isEnabled() {
893	return m_BayesNet.canUndo();
894	}
895
896	public void actionPerformed(ActionEvent ae) {
897	String sMsg = m_BayesNet.undo();
898	m_jStatusBar.setText("Undo action performed: " + sMsg);
899	//if (!sMsg.equals("")) {
900	// JOptionPane.showMessageDialog(null, sMsg, "Undo action successful", JOptionPane.INFORMATION_MESSAGE);
901	//}
902	a_redo.setEnabled(m_BayesNet.canRedo());
903	a_undo.setEnabled(m_BayesNet.canUndo());
904	m_Selection.clear();
905	updateStatus();
906	repaint();
907	}
908	} // ActionUndo
909
910	class ActionRedo extends MyAction {
911	/** for serialization */
912	private static final long serialVersionUID = -4038910085935519L;
913
914	public ActionRedo() {
915	super("Redo", "Redo", "redo", "ctrl Y");
916	setEnabled(false);
917	} // c'tor
918
919	public boolean isEnabled() {
920	return m_BayesNet.canRedo();
921	}
922
923	public void actionPerformed(ActionEvent ae) {
924	String sMsg = m_BayesNet.redo();
925	m_jStatusBar.setText("Redo action performed: " + sMsg);
926	//if (!sMsg.equals("")) {
927	// JOptionPane.showMessageDialog(null, sMsg, "Redo action successful", JOptionPane.INFORMATION_MESSAGE);
928	//}
929	m_Selection.clear();
930	updateStatus();
931	repaint();
932	}
933	} // ActionRedo
934
935	class ActionAddNode extends MyAction {
936	/** for serialization */
937	private static final long serialVersionUID = -2038910085935519L;
938
939	public ActionAddNode() {
940	super("Add Node", "Add Node", "addnode", "");
941	} // c'tor
942
943	JDialog dlg = null;
944
945	JTextField jTfName = new JTextField(20);
946
947	JTextField jTfCard = new JTextField(3);
948
949	int m_X = Integer.MAX_VALUE;
950	int m_Y;
951	public void addNode(int nX, int nY) {
952	m_X = nX;
953	m_Y = nY;
954	addNode();
955	} // addNode
956
957	void addNode() {
958	if (dlg == null) {
959	dlg = new JDialog();
960	dlg.setTitle("Add node");
961	JLabel jLbName = new JLabel("Name");
962	jTfName.setHorizontalAlignment(JTextField.CENTER);
963	JLabel jLbCard = new JLabel("Cardinality");
964	jTfCard.setHorizontalAlignment(JTextField.CENTER);
965	jTfCard.setText("2");
966
967	JButton jBtCancel;
968	jBtCancel = new JButton("Cancel");
969	jBtCancel.setMnemonic('C');
970	jBtCancel.addActionListener(new ActionListener() {
971	public void actionPerformed(ActionEvent ae) {
972	dlg.setVisible(false);
973	}
974	});
975	JButton jBtOk = new JButton("Ok");
976	jBtOk.setMnemonic('O');
977	jBtOk.addActionListener(new ActionListener() {
978	public void actionPerformed(ActionEvent ae) {
979	String sName = jTfName.getText();
980	if (sName.length() <= 0) {
981	JOptionPane.showMessageDialog(null, "Name should have at least one character");
982	return;
983	}
984	int nCard = new Integer(jTfCard.getText()).intValue();
985	if (nCard <= 1) {
986	JOptionPane.showMessageDialog(null, "Cardinality should be larger than 1");
987	return;
988	}
989	try {
990	if (m_X < Integer.MAX_VALUE) {
991	m_BayesNet.addNode(sName, nCard, m_X, m_Y);
992	} else {
993	m_BayesNet.addNode(sName, nCard);
994	}
995	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
996	a_undo.setEnabled(true);
997	a_redo.setEnabled(false);
998	//GraphNode n = new GraphNode("id" + m_nodes.size(), sName);
999	//n.probs = m_BayesNet.getDistribution(sName);
1000	//n.outcomes = m_BayesNet.getValues(sName);
1001	//n.x = 100 + m_nodes.size() * 10;
1002	//n.y = 100 + m_nodes.size() * 10;
1003	//m_nodes.addElement(n);
1004	} catch (Exception e) {
1005	e.printStackTrace();
1006	}
1007	repaint();
1008	dlg.setVisible(false);
1009	}
1010	});
1011	dlg.setLayout(new GridLayout(3, 2, 10, 10));
1012	dlg.add(jLbName);
1013	dlg.add(jTfName);
1014	dlg.add(jLbCard);
1015	dlg.add(jTfCard);
1016	dlg.add(jBtOk);
1017	dlg.add(jBtCancel);
1018	dlg.setSize(dlg.getPreferredSize());
1019	}
1020	jTfName.setText("Node" + (m_BayesNet.getNrOfNodes() + 1));
1021	dlg.setVisible(true);
1022	} // addNode
1023
1024	public void actionPerformed(ActionEvent ae) {
1025	m_X = Integer.MAX_VALUE;
1026	addNode();
1027	}
1028	} // class ActionAddNode
1029
1030	class ActionDeleteNode extends MyAction {
1031	/** for serialization */
1032	private static final long serialVersionUID = -2038912085935519L;
1033
1034	public ActionDeleteNode() {
1035	super("Delete Node", "Delete Node", "delnode", "DELETE");
1036	} // c'tor
1037
1038	public void actionPerformed(ActionEvent ae) {
1039	if (m_Selection.getSelected().size() > 0) {
1040	m_BayesNet.deleteSelection(m_Selection.getSelected());
1041	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1042	m_Selection.clear();
1043	updateStatus();
1044	repaint();
1045	} else {
1046	String[] options = new String[m_BayesNet.getNrOfNodes()];
1047	for (int i = 0; i < options.length; i++) {
1048	options[i] = m_BayesNet.getNodeName(i);
1049	}
1050	String sResult = (String) JOptionPane.showInputDialog(null, "Select node to delete", "Nodes", 0, null,
1051	options, options[0]);
1052	if (sResult != null && !sResult.equals("")) {
1053	int iNode = m_BayesNet.getNode2(sResult);
1054	deleteNode(iNode);
1055	}
1056	}
1057	}
1058	} // class ActionDeleteNode
1059
1060	class ActionCopyNode extends MyAction {
1061	/** for serialization */
1062	private static final long serialVersionUID = -2038732085935519L;
1063
1064	public ActionCopyNode() {
1065	super("Copy", "Copy Nodes", "copy", "ctrl C");
1066	} // c'tor
1067
1068	public ActionCopyNode(String sName, String sToolTipText, String sIcon, String sAcceleratorKey) {
1069	super(sName, sToolTipText, sIcon, sAcceleratorKey);
1070	} // c'rot
1071
1072	public void actionPerformed(ActionEvent ae) {
1073	copy();
1074	}
1075
1076	public void copy() {
1077	String sXML = m_BayesNet.toXMLBIF03(m_Selection.getSelected());
1078	m_clipboard.setText(sXML);
1079	} // copy
1080	} // class ActionCopyNode
1081
1082	class ActionCutNode extends ActionCopyNode {
1083	/** for serialization */
1084	private static final long serialVersionUID = -2038822085935519L;
1085
1086	public ActionCutNode() {
1087	super("Cut", "Cut Nodes", "cut", "ctrl X");
1088	} // c'tor
1089
1090	public void actionPerformed(ActionEvent ae) {
1091	copy();
1092	m_BayesNet.deleteSelection(m_Selection.getSelected());
1093	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1094	m_Selection.clear();
1095	a_undo.setEnabled(true);
1096	a_redo.setEnabled(false);
1097	repaint();
1098	}
1099	} // class ActionCutNode
1100
1101	class ActionPasteNode extends MyAction {
1102	/** for serialization */
1103	private static final long serialVersionUID = -2038732085935519L;
1104
1105	public ActionPasteNode() {
1106	super("Paste", "Paste Nodes", "paste", "ctrl V");
1107	} // c'tor
1108
1109	public void actionPerformed(ActionEvent ae) {
1110	try {
1111	m_BayesNet.paste(m_clipboard.getText());
1112	updateStatus();
1113	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1114	} catch (Exception e) {
1115	e.printStackTrace();
1116	}
1117	}
1118	public boolean isEnabled() {
1119	return m_clipboard.hasText();
1120	}
1121	} // class ActionPasteNode
1122
1123	class ActionSelectAll extends MyAction {
1124	/** for serialization */
1125	private static final long serialVersionUID = -2038642085935519L;
1126
1127	public ActionSelectAll() {
1128	super("Select All", "Select All Nodes", "selectall", "ctrl A");
1129	} // c'tor
1130
1131	public void actionPerformed(ActionEvent ae) {
1132	m_Selection.selectAll();
1133	repaint();
1134	}
1135	} // class ActionSelectAll
1136
1137	class ActionExport extends MyAction {
1138	boolean m_bIsExporting = false;
1139	/** for serialization */
1140	private static final long serialVersionUID = -3027642085935519L;
1141
1142	public ActionExport() {
1143	super("Export", "Export to graphics file", "export", "");
1144	} // c'tor
1145
1146	public void actionPerformed(ActionEvent ae) {
1147	m_bIsExporting = true;
1148	m_GraphPanel.saveComponent();
1149	m_bIsExporting = false;
1150	repaint();
1151	}
1152	public boolean isExporting() {return m_bIsExporting;}
1153	} // class ActionExport
1154
1155	class ActionAlignLeft extends MyAction {
1156	/** for serialization */
1157	private static final long serialVersionUID = -3138642085935519L;
1158
1159	public ActionAlignLeft() {
1160	super("Align Left", "Align Left", "alignleft", "");
1161	} // c'tor
1162
1163	public void actionPerformed(ActionEvent ae) {
1164	m_BayesNet.alignLeft(m_Selection.getSelected());
1165	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1166	a_undo.setEnabled(true);
1167	a_redo.setEnabled(false);
1168	repaint();
1169	}
1170	} // class ActionAlignLeft
1171
1172	class ActionAlignRight extends MyAction {
1173	/** for serialization */
1174	private static final long serialVersionUID = -4238642085935519L;
1175
1176	public ActionAlignRight() {
1177	super("Align Right", "Align Right", "alignright", "");
1178	} // c'tor
1179
1180	public void actionPerformed(ActionEvent ae) {
1181	m_BayesNet.alignRight(m_Selection.getSelected());
1182	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1183	a_undo.setEnabled(true);
1184	a_redo.setEnabled(false);
1185	repaint();
1186	}
1187	} // class ActionAlignRight
1188
1189	class ActionAlignTop extends MyAction {
1190	/** for serialization */
1191	private static final long serialVersionUID = -5338642085935519L;
1192
1193	public ActionAlignTop() {
1194	super("Align Top", "Align Top", "aligntop", "");
1195	} // c'tor
1196
1197	public void actionPerformed(ActionEvent ae) {
1198	m_BayesNet.alignTop(m_Selection.getSelected());
1199	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1200	a_undo.setEnabled(true);
1201	a_redo.setEnabled(false);
1202	repaint();
1203	}
1204	} // class ActionAlignTop
1205
1206	class ActionAlignBottom extends MyAction {
1207	/** for serialization */
1208	private static final long serialVersionUID = -6438642085935519L;
1209
1210	public ActionAlignBottom() {
1211	super("Align Bottom", "Align Bottom", "alignbottom", "");
1212	} // c'tor
1213
1214	public void actionPerformed(ActionEvent ae) {
1215	m_BayesNet.alignBottom(m_Selection.getSelected());
1216	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1217	a_undo.setEnabled(true);
1218	a_redo.setEnabled(false);
1219	repaint();
1220	}
1221	} // class ActionAlignBottom
1222
1223	class ActionCenterHorizontal extends MyAction {
1224	/** for serialization */
1225	private static final long serialVersionUID = -7538642085935519L;
1226
1227	public ActionCenterHorizontal() {
1228	super("Center Horizontal", "Center Horizontal", "centerhorizontal", "");
1229	} // c'tor
1230
1231	public void actionPerformed(ActionEvent ae) {
1232	m_BayesNet.centerHorizontal(m_Selection.getSelected());
1233	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1234	a_undo.setEnabled(true);
1235	a_redo.setEnabled(false);
1236	repaint();
1237	}
1238	} // class ActionCenterHorizontal
1239
1240	class ActionCenterVertical extends MyAction {
1241	/** for serialization */
1242	private static final long serialVersionUID = -8638642085935519L;
1243
1244	public ActionCenterVertical() {
1245	super("Center Vertical", "Center Vertical", "centervertical", "");
1246	} // c'tor
1247
1248	public void actionPerformed(ActionEvent ae) {
1249	m_BayesNet.centerVertical(m_Selection.getSelected());
1250	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1251	a_undo.setEnabled(true);
1252	a_redo.setEnabled(false);
1253	repaint();
1254	}
1255	} // class ActionCenterVertical
1256
1257	class ActionSpaceHorizontal extends MyAction {
1258	/** for serialization */
1259	private static final long serialVersionUID = -9738642085935519L;
1260
1261	public ActionSpaceHorizontal() {
1262	super("Space Horizontal", "Space Horizontal", "spacehorizontal", "");
1263	} // c'tor
1264
1265	public void actionPerformed(ActionEvent ae) {
1266	m_BayesNet.spaceHorizontal(m_Selection.getSelected());
1267	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1268	a_undo.setEnabled(true);
1269	a_redo.setEnabled(false);
1270	repaint();
1271	}
1272	} // class ActionSpaceHorizontal
1273
1274	class ActionSpaceVertical extends MyAction {
1275	/** for serialization */
1276	private static final long serialVersionUID = -838642085935519L;
1277
1278	public ActionSpaceVertical() {
1279	super("Space Vertical", "Space Vertical", "spacevertical", "");
1280	} // c'tor
1281
1282	public void actionPerformed(ActionEvent ae) {
1283	m_BayesNet.spaceVertical(m_Selection.getSelected());
1284	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
1285	a_undo.setEnabled(true);
1286	a_redo.setEnabled(false);
1287	repaint();
1288	}
1289	} // class ActionSpaceVertical
1290
1291	class ActionAddArc extends MyAction {
1292	/** for serialization */
1293	private static final long serialVersionUID = -2038913085935519L;
1294
1295	public ActionAddArc() {
1296	super("Add Arc", "Add Arc", "addarc", "");
1297	} // c'tor
1298
1299	public void actionPerformed(ActionEvent ae) {
1300	try {
1301	String[] options = new String[m_BayesNet.getNrOfNodes()];
1302	for (int i = 0; i < options.length; i++) {
1303	options[i] = m_BayesNet.getNodeName(i);
1304	}
1305	String sChild = (String) JOptionPane.showInputDialog(null, "Select child node", "Nodes", 0, null,
1306	options, options[0]);
1307	if (sChild == null \|\| sChild.equals("")) {
1308	return;
1309	}
1310	int iChild = m_BayesNet.getNode(sChild);
1311	addArcInto(iChild);
1312	} catch (Exception e) {
1313	e.printStackTrace();
1314	}
1315	}
1316	} // class ActionAddArc
1317
1318	class ActionDeleteArc extends MyAction {
1319	/** for serialization */
1320	private static final long serialVersionUID = -2038914085935519L;
1321
1322	public ActionDeleteArc() {
1323	super("Delete Arc", "Delete Arc", "delarc", "");
1324	} // c'tor
1325
1326	public void actionPerformed(ActionEvent ae) {
1327	int nEdges = 0;
1328	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
1329	nEdges += m_BayesNet.getNrOfParents(iNode);
1330	}
1331	String[] options = new String[nEdges];
1332	int i = 0;
1333	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
1334	for (int iParent = 0; iParent < m_BayesNet.getNrOfParents(iNode); iParent++) {
1335	int nParent = m_BayesNet.getParent(iNode, iParent);
1336	String sEdge = m_BayesNet.getNodeName(nParent);
1337	sEdge += " -> ";
1338	sEdge += m_BayesNet.getNodeName(iNode);
1339	options[i++] = sEdge;
1340	}
1341
1342	}
1343	deleteArc(options);
1344	}
1345	} // class ActionDeleteArc
1346
1347	class ActionNew extends MyAction {
1348	/** for serialization */
1349	private static final long serialVersionUID = -2038911085935515L;
1350
1351	public ActionNew() {
1352	super("New", "New Network", "new", "");
1353	} // c'tor
1354
1355	public void actionPerformed(ActionEvent ae) {
1356	m_sFileName = "";
1357	m_BayesNet = new EditableBayesNet(true);
1358	updateStatus();
1359	layoutGraph();
1360	a_datagenerator.setEnabled(false);
1361	m_BayesNet.clearUndoStack();
1362	m_jStatusBar.setText("New Network");
1363	m_Selection = new Selection();
1364	repaint();
1365	}
1366	} // class ActionNew
1367
1368	class ActionLoad extends MyAction {
1369	/** for serialization */
1370	private static final long serialVersionUID = -2038911085935515L;
1371
1372	public ActionLoad() {
1373	super("Load", "Load Graph", "open", "ctrl O");
1374	} // c'tor
1375
1376	public void actionPerformed(ActionEvent ae) {
1377	JFileChooser fc = new JFileChooser(System.getProperty("user.dir"));
1378	ExtensionFileFilter ef1 = new ExtensionFileFilter(".arff", "ARFF files");
1379	ExtensionFileFilter ef2 = new ExtensionFileFilter(".xml", "XML BIF files");
1380	fc.addChoosableFileFilter(ef1);
1381	fc.addChoosableFileFilter(ef2);
1382	fc.setDialogTitle("Load Graph");
1383	int rval = fc.showOpenDialog(GUI.this);
1384
1385	if (rval == JFileChooser.APPROVE_OPTION) {
1386	String sFileName = fc.getSelectedFile().toString();
1387	if (sFileName.endsWith(ef1.getExtensions()[0])) {
1388	initFromArffFile(sFileName);
1389	} else {
1390	try {
1391	readBIFFromFile(sFileName);
1392	} catch (Exception e) {
1393	e.printStackTrace();
1394	}
1395	}
1396	m_jStatusBar.setText("Loaded " + sFileName);
1397	updateStatus();
1398	}
1399	}
1400	} // class ActionLoad
1401
1402
1403	class ActionViewStatusbar extends MyAction {
1404	/** for serialization */
1405	private static final long serialVersionUID = -20389330812354L;
1406
1407	public ActionViewStatusbar() {
1408	super("View statusbar", "View statusbar", "statusbar", "");
1409	} // c'tor
1410
1411	public void actionPerformed(ActionEvent ae) {
1412	m_jStatusBar.setVisible(!m_jStatusBar.isVisible());
1413	} // actionPerformed
1414	} // class ActionViewStatusbar
1415
1416	class ActionViewToolbar extends MyAction {
1417	/** for serialization */
1418	private static final long serialVersionUID = -20389110812354L;
1419
1420	public ActionViewToolbar() {
1421	super("View toolbar", "View toolbar", "toolbar", "");
1422	} // c'tor
1423
1424	public void actionPerformed(ActionEvent ae) {
1425	m_jTbTools.setVisible(!m_jTbTools.isVisible());
1426	} // actionPerformed
1427	} // class ActionViewToolbar
1428
1429	class ActionSave extends MyAction {
1430	/** for serialization */
1431	private static final long serialVersionUID = -20389110859355156L;
1432
1433	public ActionSave() {
1434	super("Save", "Save Graph", "save", "ctrl S");
1435	} // c'tor
1436
1437	public ActionSave(String sName, String sToolTipText, String sIcon, String sAcceleratorKey) {
1438	super(sName, sToolTipText, sIcon, sAcceleratorKey);
1439	} // c'tor
1440
1441	public void actionPerformed(ActionEvent ae) {
1442	if (!m_sFileName.equals("")) {
1443	saveFile(m_sFileName);
1444	m_BayesNet.isSaved();
1445	m_jStatusBar.setText("Saved as " + m_sFileName);
1446	} else {
1447	if (saveAs()) {
1448	m_BayesNet.isSaved();
1449	m_jStatusBar.setText("Saved as " + m_sFileName);
1450	}
1451	}
1452	} // actionPerformed
1453
1454
1455	ExtensionFileFilter ef1 = new ExtensionFileFilter(".xml", "XML BIF files");
1456
1457	boolean saveAs() {
1458	JFileChooser fc = new JFileChooser(System.getProperty("user.dir"));
1459	fc.addChoosableFileFilter(ef1);
1460	fc.setDialogTitle("Save Graph As");
1461	if (!m_sFileName.equals("")) {
1462	// can happen on actionQuit
1463	fc.setSelectedFile(new File(m_sFileName));
1464	}
1465	int rval = fc.showSaveDialog(GUI.this);
1466
1467	if (rval == JFileChooser.APPROVE_OPTION) {
1468	// System.out.println("Saving to file \""+
1469	// f.getAbsoluteFile().toString()+"\"");
1470	String sFileName = fc.getSelectedFile().toString();
1471	if (!sFileName.endsWith(".xml"))
1472	sFileName = sFileName.concat(".xml");
1473	saveFile(sFileName);
1474	return true;
1475	}
1476	return false;
1477	} // saveAs
1478
1479	protected void saveFile(String sFileName) {
1480	try {
1481	FileWriter outfile = new FileWriter(sFileName);
1482	outfile.write(m_BayesNet.toXMLBIF03());
1483	outfile.close();
1484	m_sFileName = sFileName;
1485	m_jStatusBar.setText("Saved as " + m_sFileName);
1486	}
1487	catch(IOException e) {
1488	e.printStackTrace();
1489	}
1490	} // saveFile
1491	} // class ActionSave
1492
1493	class ActionSaveAs extends ActionSave {
1494	/** for serialization */
1495	private static final long serialVersionUID = -20389110859354L;
1496
1497	public ActionSaveAs() {
1498	super("Save As", "Save Graph As", "saveas", "");
1499	} // c'tor
1500
1501	public void actionPerformed(ActionEvent ae) {
1502	saveAs();
1503	} // actionPerformed
1504	} // class ActionSaveAs
1505
1506	class ActionPrint extends ActionSave {
1507	/** for serialization */
1508	private static final long serialVersionUID = -20389001859354L;
1509	boolean m_bIsPrinting = false;
1510	public ActionPrint() {
1511	super("Print", "Print Graph", "print", "ctrl P");
1512	} // c'tor
1513
1514	public void actionPerformed(ActionEvent ae) {
1515	PrinterJob printJob = PrinterJob.getPrinterJob();
1516	printJob.setPrintable(m_GraphPanel);
1517	if (printJob.printDialog())
1518	try {
1519	m_bIsPrinting = true;
1520	printJob.print();
1521	m_bIsPrinting = false;
1522	} catch(PrinterException pe) {
1523	m_jStatusBar.setText("Error printing: " + pe);
1524	m_bIsPrinting = false;
1525	}
1526	m_jStatusBar.setText("Print");
1527	} // actionPerformed
1528	public boolean isPrinting() {return m_bIsPrinting;}
1529
1530	} // class ActionPrint
1531
1532	class ActionQuit extends ActionSave {
1533	/** for serialization */
1534	private static final long serialVersionUID = -2038911085935515L;
1535
1536	public ActionQuit() {
1537	super("Exit", "Exit Program", "exit", "");
1538	} // c'tor
1539
1540	public void actionPerformed(ActionEvent ae) {
1541	if (m_BayesNet.isChanged()) {
1542	int result = JOptionPane.showConfirmDialog(null, "Network changed. Do you want to save it?", "Save before closing?", JOptionPane.YES_NO_CANCEL_OPTION);
1543	if (result == JOptionPane.CANCEL_OPTION) {
1544	return;
1545	}
1546	if (result == JOptionPane.YES_OPTION) {
1547	if (!saveAs()) {
1548	return;
1549	}
1550	}
1551	}
1552	System.exit(0);
1553	}
1554	} // class ActionQuit
1555
1556	class ActionHelp extends MyAction {
1557	/** for serialization */
1558	private static final long serialVersionUID = -20389110859354L;
1559
1560	public ActionHelp() {
1561	super("Help", "Bayesian Network Workbench Help", "help", "");
1562	} // c'tor
1563
1564	public void actionPerformed(ActionEvent ae) {
1565	JOptionPane.showMessageDialog(null, "See Weka Homepage\nhttp://www.cs.waikato.ac.nz/ml", "Help Message",
1566	JOptionPane.PLAIN_MESSAGE);
1567	}
1568	} // class ActionHelp
1569
1570	class ActionAbout extends MyAction {
1571	/** for serialization */
1572	private static final long serialVersionUID = -20389110859353L;
1573
1574	public ActionAbout() {
1575	super("About", "Help about", "about", "");
1576	} // c'tor
1577
1578	public void actionPerformed(ActionEvent ae) {
1579	JOptionPane.showMessageDialog(null, "Bayesian Network Workbench\nPart of Weka\n2007", "About Message",
1580	JOptionPane.PLAIN_MESSAGE);
1581	}
1582	} // class ActionAbout
1583
1584	class ActionZoomIn extends MyAction {
1585	/** for serialization */
1586	private static final long serialVersionUID = -2038911085935515L;
1587
1588	public ActionZoomIn() {
1589	super("Zoom in", "Zoom in", "zoomin", "+");
1590	} // c'tor
1591
1592	public void actionPerformed(ActionEvent ae) {
1593	int i = 0, s = (int) (m_fScale * 100);
1594	if (s < 300)
1595	i = s / 25;
1596	else if (s < 700)
1597	i = 6 + s / 50;
1598	else
1599	i = 13 + s / 100;
1600
1601	if (s >= 999) {
1602	setEnabled(false);
1603	return;
1604	} else if (s >= 10) {
1605	if (i >= 22) {
1606	setEnabled(false);
1607	}
1608	if (s == 10 && !a_zoomout.isEnabled()) {
1609	a_zoomout.setEnabled(true);
1610	}
1611	m_jTfZoom.setText(m_nZoomPercents[i + 1] + "%");
1612	m_fScale = m_nZoomPercents[i + 1] / 100D;
1613	} else {
1614	if (!a_zoomout.isEnabled())
1615	a_zoomout.setEnabled(true);
1616	m_jTfZoom.setText(m_nZoomPercents[0] + "%");
1617	m_fScale = m_nZoomPercents[0] / 100D;
1618	}
1619	setAppropriateSize();
1620	m_GraphPanel.repaint();
1621	m_GraphPanel.invalidate();
1622	m_jScrollPane.revalidate();
1623	m_jStatusBar.setText("Zooming in");
1624	}
1625	} // class ActionZoomIn
1626
1627	class ActionZoomOut extends MyAction {
1628	/** for serialization */
1629	private static final long serialVersionUID = -203891108593551L;
1630
1631	public ActionZoomOut() {
1632	super("Zoom out", "Zoom out", "zoomout", "-");
1633	} // c'tor
1634
1635	public void actionPerformed(ActionEvent ae) {
1636	int i = 0, s = (int) (m_fScale * 100);
1637	if (s < 300)
1638	i = (int) Math.ceil(s / 25D);
1639	else if (s < 700)
1640	i = 6 + (int) Math.ceil(s / 50D);
1641	else
1642	i = 13 + (int) Math.ceil(s / 100D);
1643
1644	if (s <= 10) {
1645	setEnabled(false);
1646	} else if (s < 999) {
1647	if (i <= 1) {
1648	setEnabled(false);
1649	}
1650	m_jTfZoom.setText(m_nZoomPercents[i - 1] + "%");
1651	m_fScale = m_nZoomPercents[i - 1] / 100D;
1652	} else {
1653	if (!a_zoomin.isEnabled())
1654	a_zoomin.setEnabled(true);
1655	m_jTfZoom.setText(m_nZoomPercents[22] + "%");
1656	m_fScale = m_nZoomPercents[22] / 100D;
1657	}
1658	setAppropriateSize();
1659	m_GraphPanel.repaint();
1660	m_GraphPanel.invalidate();
1661	m_jScrollPane.revalidate();
1662	m_jStatusBar.setText("Zooming out");
1663	}
1664	} // class ActionZoomOut
1665
1666	class ActionLayout extends MyAction {
1667	/** for serialization */
1668	private static final long serialVersionUID = -203891108593551L;
1669
1670	public ActionLayout() {
1671	super("Layout", "Layout Graph", "layout", "ctrl L");
1672	} // c'tor
1673
1674	JDialog dlg = null;
1675
1676	public void actionPerformed(ActionEvent ae) {
1677	if (dlg == null) {
1678	dlg = new JDialog();
1679	dlg.setTitle("Graph Layout Options");
1680	final JCheckBox jCbCustomNodeSize = new JCheckBox("Custom Node Size");
1681	final JLabel jLbNodeWidth = new JLabel("Width");
1682	final JLabel jLbNodeHeight = new JLabel("Height");
1683
1684	m_jTfNodeWidth.setHorizontalAlignment(JTextField.CENTER);
1685	m_jTfNodeWidth.setText("" + m_nNodeWidth);
1686	m_jTfNodeHeight.setHorizontalAlignment(JTextField.CENTER);
1687	m_jTfNodeHeight.setText("" + m_nNodeHeight);
1688	jLbNodeWidth.setEnabled(false);
1689	m_jTfNodeWidth.setEnabled(false);
1690	jLbNodeHeight.setEnabled(false);
1691	m_jTfNodeHeight.setEnabled(false);
1692
1693	jCbCustomNodeSize.addActionListener(new ActionListener() {
1694	public void actionPerformed(ActionEvent ae) {
1695	if (((JCheckBox) ae.getSource()).isSelected()) {
1696	jLbNodeWidth.setEnabled(true);
1697	m_jTfNodeWidth.setEnabled(true);
1698	jLbNodeHeight.setEnabled(true);
1699	m_jTfNodeHeight.setEnabled(true);
1700	} else {
1701	jLbNodeWidth.setEnabled(false);
1702	m_jTfNodeWidth.setEnabled(false);
1703	jLbNodeHeight.setEnabled(false);
1704	m_jTfNodeHeight.setEnabled(false);
1705	setAppropriateSize();
1706	setAppropriateNodeSize();
1707	}
1708	}
1709	});
1710	JButton jBtLayout;
1711	jBtLayout = new JButton("Layout Graph");
1712	jBtLayout.setMnemonic('L');
1713
1714	jBtLayout.addActionListener(new ActionListener() {
1715	public void actionPerformed(ActionEvent ae) {
1716	int tmpW, tmpH;
1717
1718	if (jCbCustomNodeSize.isSelected()) {
1719	try {
1720	tmpW = Integer.parseInt(m_jTfNodeWidth.getText());
1721	} catch (NumberFormatException ne) {
1722	JOptionPane.showMessageDialog(GUI.this.getParent(),
1723	"Invalid integer entered for node width.", "Error", JOptionPane.ERROR_MESSAGE);
1724	tmpW = m_nNodeWidth;
1725	m_jTfNodeWidth.setText("" + m_nNodeWidth);
1726
1727	}
1728	try {
1729	tmpH = Integer.parseInt(m_jTfNodeHeight.getText());
1730	} catch (NumberFormatException ne) {
1731	JOptionPane.showMessageDialog(GUI.this.getParent(),
1732	"Invalid integer entered for node height.", "Error", JOptionPane.ERROR_MESSAGE);
1733	tmpH = m_nNodeHeight;
1734	m_jTfNodeWidth.setText("" + m_nNodeHeight);
1735	}
1736
1737	if (tmpW != m_nNodeWidth \|\| tmpH != m_nNodeHeight) {
1738	m_nNodeWidth = tmpW;
1739	m_nPaddedNodeWidth = m_nNodeWidth + PADDING;
1740	m_nNodeHeight = tmpH;
1741	}
1742	}
1743	// JButton bt = (JButton) ae.getSource();
1744	// bt.setEnabled(false);
1745	dlg.setVisible(false);
1746	updateStatus();
1747	layoutGraph();
1748	m_jStatusBar.setText("Laying out Bayes net");
1749	}
1750	});
1751	JButton jBtCancel;
1752	jBtCancel = new JButton("Cancel");
1753	jBtCancel.setMnemonic('C');
1754	jBtCancel.addActionListener(new ActionListener() {
1755	public void actionPerformed(ActionEvent ae) {
1756	dlg.setVisible(false);
1757	}
1758	});
1759	GridBagConstraints gbc = new GridBagConstraints();
1760	dlg.setLayout(new GridBagLayout());
1761	//dlg.add(m_le.getControlPanel());
1762
1763	Container c = new Container();
1764	c.setLayout(new GridBagLayout());
1765
1766	gbc.gridwidth = 1;
1767	gbc.insets = new Insets(8, 0, 0, 0);
1768	gbc.anchor = GridBagConstraints.NORTHWEST;
1769	gbc.gridwidth = GridBagConstraints.REMAINDER;
1770	c.add(jCbCustomNodeSize, gbc);
1771	gbc.gridwidth = GridBagConstraints.RELATIVE;
1772	c.add(jLbNodeWidth, gbc);
1773	gbc.gridwidth = GridBagConstraints.REMAINDER;
1774	c.add(m_jTfNodeWidth, gbc);
1775	gbc.gridwidth = GridBagConstraints.RELATIVE;
1776	c.add(jLbNodeHeight, gbc);
1777	gbc.gridwidth = GridBagConstraints.REMAINDER;
1778	c.add(m_jTfNodeHeight, gbc);
1779	gbc.fill = GridBagConstraints.HORIZONTAL;
1780	dlg.add(c, gbc);
1781	dlg.add(jBtLayout);
1782	gbc.gridwidth = GridBagConstraints.REMAINDER;
1783	dlg.add(jBtCancel);
1784	}
1785	dlg.setLocation(100, 100);
1786	dlg.setVisible(true);
1787	dlg.setSize(dlg.getPreferredSize());
1788	dlg.setVisible(false);
1789	dlg.setVisible(true);
1790	dlg.repaint();
1791	}
1792	} // class ActionLayout
1793
1794	/**
1795	* Constructor<br>
1796	* Sets up the gui and initializes all the other previously uninitialized
1797	* variables.
1798	*/
1799	public GUI() {
1800	m_GraphPanel = new GraphPanel();
1801	m_jScrollPane = new JScrollPane(m_GraphPanel);
1802
1803	// creating a new layout engine and adding this class as its listener
1804	// to receive layoutComplete events
1805
1806	m_jTfZoom = new JTextField("100%");
1807	m_jTfZoom.setMinimumSize(m_jTfZoom.getPreferredSize());
1808	m_jTfZoom.setHorizontalAlignment(JTextField.CENTER);
1809	m_jTfZoom.setToolTipText("Zoom");
1810
1811	m_jTfZoom.addActionListener(new ActionListener() {
1812	public void actionPerformed(ActionEvent ae) {
1813	JTextField jt = (JTextField) ae.getSource();
1814	try {
1815	int i = -1;
1816	i = jt.getText().indexOf('%');
1817	if (i == -1)
1818	i = Integer.parseInt(jt.getText());
1819	else
1820	i = Integer.parseInt(jt.getText().substring(0, i));
1821
1822	if (i <= 999)
1823	m_fScale = i / 100D;
1824
1825	jt.setText((int) (m_fScale * 100) + "%");
1826	if (m_fScale > 0.1) {
1827	if (!a_zoomout.isEnabled())
1828	a_zoomout.setEnabled(true);
1829	} else
1830	a_zoomout.setEnabled(false);
1831	if (m_fScale < 9.99) {
1832	if (!a_zoomin.isEnabled())
1833	a_zoomin.setEnabled(true);
1834	} else
1835	a_zoomin.setEnabled(false);
1836	setAppropriateSize();
1837	// m_GraphPanel.clearBuffer();
1838	m_GraphPanel.repaint();
1839	m_GraphPanel.invalidate();
1840	m_jScrollPane.revalidate();
1841	} catch (NumberFormatException ne) {
1842	JOptionPane.showMessageDialog(GUI.this.getParent(),
1843	"Invalid integer entered for zoom.", "Error", JOptionPane.ERROR_MESSAGE);
1844	jt.setText((m_fScale * 100) + "%");
1845	}
1846	}
1847	});
1848
1849	GridBagConstraints gbc = new GridBagConstraints();
1850
1851	final JPanel p = new JPanel(new GridBagLayout());
1852	p.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createTitledBorder("ExtraControls"), BorderFactory
1853	.createEmptyBorder(4, 4, 4, 4)));
1854	p.setPreferredSize(new Dimension(0, 0));
1855
1856	m_jTbTools = new JToolBar();
1857	m_jTbTools.setFloatable(false);
1858	m_jTbTools.setLayout(new GridBagLayout());
1859	gbc.anchor = GridBagConstraints.NORTHWEST;
1860	gbc.gridwidth = GridBagConstraints.REMAINDER;
1861	gbc.insets = new Insets(0, 0, 0, 0);
1862	m_jTbTools.add(p, gbc);
1863	gbc.gridwidth = 1;
1864
1865
1866	m_jTbTools.add(a_new);
1867	m_jTbTools.add(a_save);
1868	m_jTbTools.add(a_load);
1869	m_jTbTools.addSeparator(new Dimension(2, 2));
1870	m_jTbTools.add(a_cutnode);
1871	m_jTbTools.add(a_copynode);
1872	m_jTbTools.add(a_pastenode);
1873	m_jTbTools.addSeparator(new Dimension(2, 2));
1874	m_jTbTools.add(a_undo);
1875	m_jTbTools.add(a_redo);
1876	m_jTbTools.addSeparator(new Dimension(2, 2));
1877	m_jTbTools.add(a_alignleft);
1878	m_jTbTools.add(a_alignright);
1879	m_jTbTools.add(a_aligntop);
1880	m_jTbTools.add(a_alignbottom);
1881	m_jTbTools.add(a_centerhorizontal);
1882	m_jTbTools.add(a_centervertical);
1883	m_jTbTools.add(a_spacehorizontal);
1884	m_jTbTools.add(a_spacevertical);
1885
1886
1887	m_jTbTools.addSeparator(new Dimension(2, 2));
1888	m_jTbTools.add(a_zoomin);
1889
1890	gbc.fill = GridBagConstraints.VERTICAL;
1891	gbc.weighty = 1;
1892	JPanel p2 = new JPanel(new BorderLayout());
1893	p2.setPreferredSize(m_jTfZoom.getPreferredSize());
1894	p2.setMinimumSize(m_jTfZoom.getPreferredSize());
1895	p2.add(m_jTfZoom, BorderLayout.CENTER);
1896	m_jTbTools.add(p2, gbc);
1897	gbc.weighty = 0;
1898	gbc.fill = GridBagConstraints.NONE;
1899
1900	m_jTbTools.add(a_zoomout);
1901	m_jTbTools.addSeparator(new Dimension(2, 2));
1902
1903	// jTbTools.add(jBtExtraControls, gbc);
1904	m_jTbTools.add(a_layout);
1905	m_jTbTools.addSeparator(new Dimension(4, 2));
1906	gbc.weightx = 1;
1907	gbc.fill = GridBagConstraints.BOTH;
1908	//jTbTools.add(m_layoutEngine.getProgressBar(), gbc);
1909	m_jStatusBar = new JLabel("Status bar");
1910
1911	this.setLayout(new BorderLayout());
1912	this.add(m_jTbTools, BorderLayout.NORTH);
1913	this.add(m_jScrollPane, BorderLayout.CENTER);
1914	this.add(m_jStatusBar, BorderLayout.SOUTH);
1915
1916	updateStatus();
1917	a_datagenerator.setEnabled(false);
1918
1919	makeMenuBar();
1920	}
1921
1922	/**
1923	* Get the menu bar for this application.
1924	*
1925	* @return the menu bar
1926	*/
1927	public JMenuBar getMenuBar() {
1928	return m_menuBar;
1929	}
1930
1931	private void makeMenuBar() {
1932	m_menuBar = new JMenuBar();
1933	JMenu fileMenu = new JMenu("File");
1934	fileMenu.setMnemonic('F');
1935
1936	m_menuBar.add(fileMenu);
1937	fileMenu.add(a_new);
1938	fileMenu.add(a_load);
1939	fileMenu.add(a_save);
1940	fileMenu.add(a_saveas);
1941	fileMenu.addSeparator();
1942	fileMenu.add(a_print);
1943	fileMenu.add(a_export);
1944	fileMenu.addSeparator();
1945	fileMenu.add(a_quit);
1946	JMenu editMenu = new JMenu("Edit");
1947	editMenu.setMnemonic('E');
1948	m_menuBar.add(editMenu);
1949	editMenu.add(a_undo);
1950	editMenu.add(a_redo);
1951	editMenu.addSeparator();
1952	editMenu.add(a_selectall);
1953	editMenu.add(a_delnode);
1954	editMenu.add(a_cutnode);
1955	editMenu.add(a_copynode);
1956	editMenu.add(a_pastenode);
1957	editMenu.addSeparator();
1958	editMenu.add(a_addnode);
1959	editMenu.add(a_addarc);
1960	editMenu.add(a_delarc);
1961	editMenu.addSeparator();
1962	editMenu.add(a_alignleft);
1963	editMenu.add(a_alignright);
1964	editMenu.add(a_aligntop);
1965	editMenu.add(a_alignbottom);
1966	editMenu.add(a_centerhorizontal);
1967	editMenu.add(a_centervertical);
1968	editMenu.add(a_spacehorizontal);
1969	editMenu.add(a_spacevertical);
1970
1971	JMenu toolMenu = new JMenu("Tools");
1972	toolMenu.setMnemonic('T');
1973	toolMenu.add(a_networkgenerator);
1974	toolMenu.add(a_datagenerator);
1975	toolMenu.add(a_datasetter);
1976	toolMenu.add(a_learn);
1977	toolMenu.add(a_learnCPT);
1978	toolMenu.addSeparator();
1979	toolMenu.add(a_layout);
1980	toolMenu.addSeparator();
1981	final JCheckBoxMenuItem viewMargins = new JCheckBoxMenuItem("Show Margins", false);
1982	viewMargins.addActionListener(new ActionListener() {
1983	public void actionPerformed(ActionEvent ae) {
1984	boolean bPrev = m_bViewMargins;
1985	m_bViewMargins = viewMargins.getState();
1986	if (bPrev == false && viewMargins.getState() == true) {
1987	updateStatus();
1988	}
1989	repaint();
1990	}
1991	});
1992	toolMenu.add(viewMargins);
1993	final JCheckBoxMenuItem viewCliques = new JCheckBoxMenuItem("Show Cliques", false);
1994	viewCliques.addActionListener(new ActionListener() {
1995	public void actionPerformed(ActionEvent ae) {
1996	boolean bPrev = m_bViewCliques;
1997	m_bViewCliques = viewCliques.getState();
1998	if (bPrev == false && viewCliques.getState() == true) {
1999	updateStatus();
2000	}
2001	repaint();
2002	}
2003	});
2004	toolMenu.add(viewCliques);
2005
2006	m_menuBar.add(toolMenu);
2007	JMenu viewMenu = new JMenu("View");
2008	viewMenu.setMnemonic('V');
2009	m_menuBar.add(viewMenu);
2010	viewMenu.add(a_zoomin);
2011	viewMenu.add(a_zoomout);
2012	viewMenu.addSeparator();
2013	viewMenu.add(a_viewtoolbar);
2014	viewMenu.add(a_viewstatusbar);
2015
2016	JMenu helpMenu = new JMenu("Help");
2017	helpMenu.setMnemonic('H');
2018	m_menuBar.add(helpMenu);
2019	helpMenu.add(a_help);
2020	helpMenu.add(a_about);
2021	}
2022
2023	/**
2024	* This method sets the node size that is appropriate considering the
2025	* maximum label size that is present. It is used internally when custom
2026	* node size checkbox is unchecked.
2027	*/
2028	protected void setAppropriateNodeSize() {
2029	int strWidth;
2030	FontMetrics fm = this.getFontMetrics(this.getFont());
2031	int nMaxStringWidth = DEFAULT_NODE_WIDTH;
2032	if (nMaxStringWidth == 0)
2033	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
2034	strWidth = fm.stringWidth(m_BayesNet.getNodeName(iNode));
2035	if (strWidth > nMaxStringWidth)
2036	nMaxStringWidth = strWidth;
2037	}
2038	m_nNodeWidth = nMaxStringWidth + 4;
2039	m_nPaddedNodeWidth = m_nNodeWidth + PADDING;
2040	m_jTfNodeWidth.setText("" + m_nNodeWidth);
2041
2042	m_nNodeHeight = 2 * fm.getHeight();
2043	m_jTfNodeHeight.setText("" + m_nNodeHeight);
2044	}
2045
2046	/**
2047	* Sets the preferred size for m_GraphPanel GraphPanel to the minimum size that is
2048	* neccessary to display the graph.
2049	*/
2050	public void setAppropriateSize() {
2051	int maxX = 0, maxY = 0;
2052
2053	m_GraphPanel.setScale(m_fScale, m_fScale);
2054
2055	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
2056	int nPosX = m_BayesNet.getPositionX(iNode);
2057	int nPosY = m_BayesNet.getPositionY(iNode);
2058	if (maxX < nPosX)
2059	maxX = nPosX + 100;
2060	if (maxY < nPosY)
2061	maxY = nPosY;
2062	}
2063	m_GraphPanel.setPreferredSize(new Dimension((int) ((maxX + m_nPaddedNodeWidth + 2) * m_fScale),
2064	(int) ((maxY + m_nNodeHeight + 2) * m_fScale)));
2065	m_GraphPanel.revalidate();
2066	} // setAppropriateSize
2067
2068	/**
2069	* This method is an implementation for LayoutCompleteEventListener class.
2070	* It sets the size appropriate for m_GraphPanel GraphPanel and and revalidates it's
2071	* container JScrollPane once a LayoutCompleteEvent is received from the
2072	* LayoutEngine. Also, it updates positions of the Bayesian network stored
2073	* in m_BayesNet.
2074	*/
2075	public void layoutCompleted(LayoutCompleteEvent le) {
2076	LayoutEngine layoutEngine = m_layoutEngine; // (LayoutEngine) le.getSource();
2077	FastVector nPosX = new FastVector(m_BayesNet.getNrOfNodes());
2078	FastVector nPosY = new FastVector(m_BayesNet.getNrOfNodes());
2079	for (int iNode = 0; iNode < layoutEngine.getNodes().size(); iNode++) {
2080	GraphNode gNode = (GraphNode) layoutEngine.getNodes().elementAt(iNode);
2081	if (gNode.nodeType == GraphNode.NORMAL) {
2082	nPosX.addElement(gNode.x);
2083	nPosY.addElement(gNode.y);
2084	}
2085	}
2086	m_BayesNet.layoutGraph(nPosX, nPosY);
2087	m_jStatusBar.setText("Graph layed out");
2088	a_undo.setEnabled(true);
2089	a_redo.setEnabled(false);
2090	setAppropriateSize();
2091	m_GraphPanel.invalidate();
2092	m_jScrollPane.revalidate();
2093	m_GraphPanel.repaint();
2094	} // layoutCompleted
2095
2096
2097	/**
2098	* BIF reader<br>
2099	* Reads a graph description in XMLBIF03 from an file
2100	* with name sFileName
2101	*/
2102	public void readBIFFromFile(String sFileName) throws BIFFormatException, IOException {
2103	m_sFileName = sFileName;
2104	try {
2105
2106	BIFReader bayesNet = new BIFReader();
2107	bayesNet.processFile(sFileName);
2108	m_BayesNet = new EditableBayesNet(bayesNet);
2109	updateStatus();
2110	a_datagenerator.setEnabled(m_BayesNet.getNrOfNodes() > 0);
2111	m_BayesNet.clearUndoStack();
2112	} catch (Exception ex) {
2113	ex.printStackTrace();
2114	return;
2115	}
2116
2117	setAppropriateNodeSize();
2118	setAppropriateSize();
2119	} // readBIFFromFile
2120
2121	/* read arff file from file sFileName
2122	* and start new Bayesian network with nodes
2123	* representing attributes in data set.
2124	*/
2125	void initFromArffFile(String sFileName) {
2126	try {
2127	Instances instances = new Instances(new FileReader(sFileName));
2128	m_BayesNet = new EditableBayesNet(instances);
2129	m_Instances = instances;
2130	a_learn.setEnabled(true);
2131	a_learnCPT.setEnabled(true);
2132	setAppropriateNodeSize();
2133	setAppropriateSize();
2134	} catch (Exception ex) {
2135	ex.printStackTrace();
2136	return;
2137	}
2138	} // initFromArffFile
2139
2140	/**
2141	* The panel which contains the actual Bayeian network.
2142	*/
2143	private class GraphPanel extends PrintablePanel implements Printable {
2144
2145	/** for serialization */
2146	private static final long serialVersionUID = -3562813603236753173L;
2147
2148	/** node drawing modes */
2149	final static int HIGHLIGHTED = 1;
2150	final static int NORMAL = 0;
2151
2152	public GraphPanel() {
2153	super();
2154	this.addMouseListener(new GraphVisualizerMouseListener());
2155	this.addMouseMotionListener(new GraphVisualizerMouseMotionListener());
2156	this.setToolTipText("");
2157	} // c'tor
2158
2159	/* For showing instructions when hovering over a node
2160	* (non-Javadoc)
2161	* @see javax.swing.JComponent#getToolTipText(java.awt.event.MouseEvent)
2162	*/
2163	public String getToolTipText(MouseEvent me) {
2164	int x, y;
2165	Rectangle r;
2166	x = y = 0;
2167
2168	r = new Rectangle(0, 0, (int) (m_nPaddedNodeWidth * m_fScale), (int) (m_nNodeHeight * m_fScale));
2169	x += me.getX();
2170	y += me.getY();
2171
2172	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
2173	r.x = (int) (m_BayesNet.getPositionX(iNode) * m_fScale);
2174	r.y = (int) (m_BayesNet.getPositionY(iNode) * m_fScale);
2175	if (r.contains(x, y)) {
2176	return m_BayesNet.getNodeName(iNode) + " (right click to manipulate this node)";
2177	}
2178	}
2179	return null;
2180	} // getToolTipText
2181
2182	/* Code for showing the graph in the panel.
2183	* (non-Javadoc)
2184	* @see javax.swing.JComponent#paintComponent(java.awt.Graphics)
2185	*/
2186	public void paintComponent(Graphics gr) {
2187	Graphics2D g = (Graphics2D) gr;
2188	RenderingHints rh = new RenderingHints(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
2189	rh.put(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED);
2190	g.setRenderingHints(rh);
2191	g.scale(m_fScale, m_fScale);
2192	Rectangle r = g.getClipBounds();
2193	g.clearRect(r.x, r.y, r.width, r.height);
2194
2195	if (m_bViewCliques) {
2196	m_nClique = 1;
2197	viewCliques(g, m_marginCalculator.m_root);
2198	}
2199	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
2200	drawNode(g, iNode, NORMAL);
2201	}
2202	if (!a_export.isExporting() && !a_print.isPrinting()) {
2203	m_Selection.draw(g);
2204	}
2205	if (m_nSelectedRect != null) {
2206	g.drawRect((int)(m_nSelectedRect.x/ m_fScale),
2207	(int)(m_nSelectedRect.y/ m_fScale),
2208	(int)(m_nSelectedRect.width/ m_fScale),
2209	(int)(m_nSelectedRect.height/ m_fScale));
2210	}
2211	} // paintComponent
2212
2213	/** number of the clique being drawn. Used for selecting the color of the clique */
2214	int m_nClique = 1;
2215
2216	/* draws cliques in junction tree.
2217	*
2218	*/
2219	void viewCliques(Graphics g, JunctionTreeNode node) {
2220	int [] nodes = node.m_nNodes;
2221	g.setColor(
2222	new Color(m_nClique % 7 * 256 /7,
2223	(m_nClique % 2 * 256 / 2),
2224	(m_nClique % 3 * 256 / 3))
2225	);
2226	int dX = m_nPaddedNodeWidth / 2 + m_nClique;
2227	int dY = m_nNodeHeight / 2;
2228	int nPosX = 0;
2229	int nPosY = 0;
2230	String sStr = "";
2231	for (int j = 0; j < nodes.length; j++) {
2232	nPosX += m_BayesNet.getPositionX(nodes[j]);
2233	nPosY += m_BayesNet.getPositionY(nodes[j]);
2234	sStr += " " + nodes[j];
2235	for (int k = j+1; k < nodes.length; k++) {
2236	g.drawLine(
2237	m_BayesNet.getPositionX(nodes[j]) + dX,
2238	m_BayesNet.getPositionY(nodes[j]) + dY,
2239	m_BayesNet.getPositionX(nodes[k]) + dX,
2240	m_BayesNet.getPositionY(nodes[k]) + dY
2241	);
2242	}
2243	}
2244	m_nClique++;
2245	nPosX /= nodes.length;
2246	nPosY /= nodes.length;
2247	g.drawString("Clique " + m_nClique + "("+sStr+")", nPosX, nPosY);
2248	for (int iChild = 0; iChild < node.m_children.size(); iChild++) {
2249	viewCliques(g, (JunctionTreeNode) node.m_children.elementAt(iChild));
2250	}
2251	} // viewCliques
2252
2253
2254	/* Draw a node with index iNode on Graphics g at position
2255	* Drawing mode can be NORMAL or HIGHLIGHTED.
2256	*/
2257	protected void drawNode(Graphics g, int iNode, int mode) {
2258	int nPosX = m_BayesNet.getPositionX(iNode);
2259	int nPosY = m_BayesNet.getPositionY(iNode);
2260	g.setColor(this.getBackground().darker().darker());
2261	FontMetrics fm = getFontMetrics(getFont());
2262
2263	if (mode == HIGHLIGHTED) {
2264	g.setXORMode(Color.green); // g.setColor(Color.green);
2265	}
2266	g.fillOval(nPosX + m_nPaddedNodeWidth - m_nNodeWidth - (m_nPaddedNodeWidth - m_nNodeWidth) / 2, nPosY,
2267	m_nNodeWidth, m_nNodeHeight);
2268	g.setColor(Color.white);
2269	if (mode == HIGHLIGHTED) {
2270	g.setXORMode(Color.red);
2271	}
2272
2273	// Draw the node's label if it can fit inside the node's
2274	// current width otherwise just display its node nr
2275	// if it can fit in node's current width
2276	if (fm.stringWidth(m_BayesNet.getNodeName(iNode)) <= m_nNodeWidth) {
2277	g.drawString(m_BayesNet.getNodeName(iNode), nPosX + m_nPaddedNodeWidth / 2
2278	- fm.stringWidth(m_BayesNet.getNodeName(iNode)) / 2, nPosY + m_nNodeHeight / 2
2279	+ fm.getHeight() / 2 - 2);
2280	} else if (fm.stringWidth("" + iNode) <= m_nNodeWidth) {
2281	g.drawString("" + iNode, nPosX + m_nPaddedNodeWidth / 2 - fm.stringWidth("" + iNode) / 2,
2282	nPosY + m_nNodeHeight / 2 + fm.getHeight() / 2 - 2);
2283	}
2284
2285	if (mode == HIGHLIGHTED) {
2286	g.setXORMode(Color.green);
2287	}
2288
2289	if (m_bViewMargins) {
2290	if (m_BayesNet.getEvidence(iNode) < 0) {
2291	g.setColor(new Color(0, 128, 0));
2292	} else {
2293	g.setColor(new Color(128, 0, 0));
2294	}
2295	double[] P = m_BayesNet.getMargin(iNode);
2296	for (int iValue = 0; iValue < P.length; iValue++) {
2297	String sP = P[iValue] + "";
2298	if (sP.charAt(0) == '0') {
2299	sP = sP.substring(1);
2300	}
2301	if (sP.length() > 5) {
2302	sP = sP.substring(1, 5);
2303	}
2304	g.fillRect(nPosX + m_nPaddedNodeWidth, nPosY + iValue * 10 + 2, (int) (P[iValue] * 100), 8);
2305	g.drawString(m_BayesNet.getNodeValue(iNode, iValue) + " " + sP, nPosX + m_nPaddedNodeWidth
2306	+ (int) (P[iValue] * 100), nPosY + iValue * 10 + 10);
2307
2308	}
2309	}
2310	if (m_bViewCliques) {
2311	return;
2312	}
2313	g.setColor(Color.black);
2314	// Drawing all incoming edges into the node,
2315	for (int iParent = 0; iParent < m_BayesNet.getNrOfParents(iNode); iParent++) {
2316	int nParent = m_BayesNet.getParent(iNode, iParent);
2317	int nPosX1 = nPosX + m_nPaddedNodeWidth / 2;
2318	int nPosY1 = nPosY + m_nNodeHeight;
2319	int nPosX2 = m_BayesNet.getPositionX(nParent);
2320	int nPosY2 = m_BayesNet.getPositionY(nParent);
2321	int nPosX2b = nPosX2 + m_nPaddedNodeWidth / 2;
2322	int nPosY2b = nPosY2;
2323
2324	double phi = Math.atan2((nPosX2b - nPosX1 + 0.0) * m_nNodeHeight, (nPosY2b - nPosY1 + 0.0) * m_nNodeWidth);
2325	nPosX1 = (int) (nPosX + m_nPaddedNodeWidth / 2 + Math.sin(phi) * m_nNodeWidth / 2);
2326	nPosY1 = (int) (nPosY + m_nNodeHeight / 2 + Math.cos(phi) * m_nNodeHeight / 2);
2327	nPosX2b = (int) (nPosX2 + m_nPaddedNodeWidth / 2 - Math.sin(phi) * m_nNodeWidth / 2);
2328	nPosY2b = (int) (nPosY2 + m_nNodeHeight / 2 - Math.cos(phi) * m_nNodeHeight / 2);
2329	drawArrow(g, nPosX2b, nPosY2b, nPosX1, nPosY1);
2330	}
2331	if (mode == HIGHLIGHTED) {
2332	FastVector children = m_BayesNet.getChildren(iNode);
2333	for (int iChild = 0; iChild < children.size(); iChild++) {
2334	int nChild = (Integer) children.elementAt(iChild);
2335	int nPosX1 = nPosX + m_nPaddedNodeWidth / 2;
2336	int nPosY1 = nPosY;
2337	int nPosX2 = m_BayesNet.getPositionX(nChild);
2338	int nPosY2 = m_BayesNet.getPositionY(nChild);
2339	int nPosX2b = nPosX2 + m_nPaddedNodeWidth / 2;
2340	int nPosY2b = nPosY2 + m_nNodeHeight;
2341
2342	double phi = Math.atan2((nPosX2b - nPosX1 + 0.0) * m_nNodeHeight, (nPosY2b - nPosY1 + 0.0) * m_nNodeWidth);
2343	nPosX1 = (int) (nPosX + m_nPaddedNodeWidth / 2 + Math.sin(phi) * m_nNodeWidth / 2);
2344	nPosY1 = (int) (nPosY + m_nNodeHeight / 2 + Math.cos(phi) * m_nNodeHeight / 2);
2345	nPosX2b = (int) (nPosX2 + m_nPaddedNodeWidth / 2 - Math.sin(phi) * m_nNodeWidth / 2);
2346	nPosY2b = (int) (nPosY2 + m_nNodeHeight / 2 - Math.cos(phi) * m_nNodeHeight / 2);
2347	drawArrow(g, nPosX1, nPosY1, nPosX2b, nPosY2b);
2348	}
2349	}
2350	} // drawNode
2351
2352
2353	/**
2354	* This method draws an arrow on a line from (x1,y1) to (x2,y2). The
2355	* arrow head is seated on (x2,y2) and is in the direction of the line.
2356	* If the arrow is needed to be drawn in the opposite direction then
2357	* simply swap the order of (x1, y1) and (x2, y2) when calling this
2358	* function.
2359	*/
2360	protected void drawArrow(Graphics g, int nPosX1, int nPosY1, int nPosX2, int nPosY2) {
2361	g.drawLine(nPosX1, nPosY1, nPosX2, nPosY2);
2362
2363	if (nPosX1 == nPosX2) {
2364	if (nPosY1 < nPosY2) {
2365	g.drawLine(nPosX2, nPosY2, nPosX2 + 4, nPosY2 - 8);
2366	g.drawLine(nPosX2, nPosY2, nPosX2 - 4, nPosY2 - 8);
2367	} else {
2368	g.drawLine(nPosX2, nPosY2, nPosX2 + 4, nPosY2 + 8);
2369	g.drawLine(nPosX2, nPosY2, nPosX2 - 4, nPosY2 + 8);
2370	}
2371	} else {
2372	// theta=line's angle from base, beta=angle of arrow's side from
2373	// line
2374	double hyp = 0, base = 0, perp = 0, theta, beta;
2375	int nPosX3 = 0, nPosY3 = 0;
2376
2377	if (nPosX2 < nPosX1) {
2378	base = nPosX1 - nPosX2;
2379	hyp = Math.sqrt((nPosX2 - nPosX1) * (nPosX2 - nPosX1) + (nPosY2 - nPosY1) * (nPosY2 - nPosY1));
2380	theta = Math.acos(base / hyp);
2381	} else { // x1>x2 as we already checked x1==x2 before
2382	base = nPosX1 - nPosX2;
2383	hyp = Math.sqrt((nPosX2 - nPosX1) * (nPosX2 - nPosX1) + (nPosY2 - nPosY1) * (nPosY2 - nPosY1));
2384	theta = Math.acos(base / hyp);
2385	}
2386	beta = 30 * Math.PI / 180;
2387
2388	hyp = 8;
2389	base = Math.cos(theta - beta) * hyp;
2390	perp = Math.sin(theta - beta) * hyp;
2391
2392	nPosX3 = (int) (nPosX2 + base);
2393	if (nPosY1 < nPosY2)
2394	nPosY3 = (int) (nPosY2 - perp);
2395	else
2396	nPosY3 = (int) (nPosY2 + perp);
2397
2398	g.drawLine(nPosX2, nPosY2, nPosX3, nPosY3);
2399
2400	base = Math.cos(theta + beta) * hyp;
2401	perp = Math.sin(theta + beta) * hyp;
2402
2403	nPosX3 = (int) (nPosX2 + base);
2404	if (nPosY1 < nPosY2)
2405	nPosY3 = (int) (nPosY2 - perp);
2406	else
2407	nPosY3 = (int) (nPosY2 + perp);
2408	g.drawLine(nPosX2, nPosY2, nPosX3, nPosY3);
2409	}
2410	} // drawArrow
2411
2412	/**
2413	* This method highlights a given node and all its incoming and outgoing arcs
2414	*/
2415	public void highLight(int iNode) {
2416	Graphics2D g = (Graphics2D) this.getGraphics();
2417	RenderingHints rh = new RenderingHints(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
2418	rh.put(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED);
2419	g.setRenderingHints(rh);
2420	g.setPaintMode();
2421	g.scale(m_fScale, m_fScale);
2422	drawNode(g, iNode, HIGHLIGHTED);
2423	} // highlight
2424
2425	/** implementation of Printable, used for printing
2426	* @see Printable
2427	*/
2428	public int print(Graphics g, PageFormat pageFormat, int pageIndex) {
2429	if (pageIndex > 0) {
2430	return(NO_SUCH_PAGE);
2431	} else {
2432	Graphics2D g2d = (Graphics2D)g;
2433	g2d.translate(pageFormat.getImageableX(), pageFormat.getImageableY());
2434	double fHeight = pageFormat.getImageableHeight();
2435	double fWidth = pageFormat.getImageableWidth();
2436	int xMax = 1;
2437	int yMax = 1;
2438	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
2439	if (xMax < m_BayesNet.getPositionX(iNode)) {
2440	xMax = m_BayesNet.getPositionX(iNode);
2441	}
2442	if (yMax < m_BayesNet.getPositionY(iNode)) {
2443	yMax = m_BayesNet.getPositionY(iNode);
2444	}
2445	}
2446	double fCurrentScale = m_fScale;
2447	xMax += m_nPaddedNodeWidth + 100;
2448	if (fWidth/xMax < fHeight/yMax) {
2449	m_fScale = fWidth/xMax;
2450	} else {
2451	m_fScale = fHeight/yMax;
2452	}
2453
2454	// Turn off double buffering
2455	paint(g2d);
2456	m_fScale = fCurrentScale;
2457	// Turn double buffering back on
2458	return(PAGE_EXISTS);
2459	}
2460	} // print
2461
2462	} // class GraphPanel
2463
2464	/**
2465	* Table Model for the Table for editing CPTs
2466	*/
2467	private class GraphVisualizerTableModel extends AbstractTableModel {
2468
2469	/** for serialization */
2470	private static final long serialVersionUID = -4789813491347366596L;
2471	/** labels for the columns */
2472	final String [] m_sColumnNames;
2473	/ probability table data /
2474	final double [][] m_fProbs;
2475	/** nr of node for currently editted CPT */
2476	int m_iNode;
2477
2478	public GraphVisualizerTableModel(int iNode) {
2479	m_iNode = iNode;
2480	double [][] probs = m_BayesNet.getDistribution(iNode);
2481	m_fProbs = new double[probs.length][probs[0].length];
2482	for (int i = 0; i < probs.length; i++) {
2483	for (int j = 0; j < probs[0].length; j++) {
2484	m_fProbs[i][j] = probs[i][j];
2485	}
2486	}
2487	m_sColumnNames = m_BayesNet.getValues(iNode);
2488	} // c'tor
2489
2490	/** method that generates random CPTs
2491	*/
2492	public void randomize() {
2493	int nProbs = m_fProbs[0].length;
2494	Random random = new Random();
2495	for (int i = 0; i < m_fProbs.length; i++) {
2496	// get random nrs
2497	for (int j = 0; j < nProbs-1; j++) {
2498	m_fProbs[i][j] = random.nextDouble();
2499	}
2500	// sort
2501	for (int j = 0; j < nProbs-1; j++) {
2502	for (int k = j+1; k < nProbs-1; k++) {
2503	if (m_fProbs[i][j] > m_fProbs[i][k]) {
2504	double h = m_fProbs[i][j];
2505	m_fProbs[i][j] = m_fProbs[i][k];
2506	m_fProbs[i][k] = h;
2507	}
2508	}
2509	}
2510	double sum = m_fProbs[i][0];
2511	for (int j = 1; j < nProbs-1; j++) {
2512	m_fProbs[i][j] = m_fProbs[i][j] - sum;
2513	sum += m_fProbs[i][j];
2514	}
2515	m_fProbs[i][nProbs - 1] = 1.0 - sum;
2516	}
2517	} // randomize
2518
2519	public void setData() {}
2520
2521	/** return nr of colums */
2522	public int getColumnCount() {
2523	return m_sColumnNames.length;
2524	}
2525
2526	/** return nr of rows */
2527	public int getRowCount() {
2528	return m_fProbs.length;
2529	}
2530
2531	/** return name of specified colum
2532	* @param iCol index of the column
2533	*/
2534	public String getColumnName(int iCol) {
2535	return m_sColumnNames[iCol];
2536	}
2537	/** return data point
2538	* @param iRow index of row in table
2539	* @param iCol index of column in table
2540	*/
2541	public Object getValueAt(int iRow, int iCol) {
2542	return new Double(m_fProbs[iRow][iCol]);
2543	}
2544
2545	/** Set data point, assigns value to CPT entry
2546	* specified by row and column. The remainder of the
2547	* CPT is normalized so that the values add up to 1.
2548	* IF a value below zero of over 1 is given, no changes
2549	* take place.
2550	* @param oProb data point
2551	* @param iRow index of row in table
2552	* @param iCol index of column in table
2553	*/
2554	public void setValueAt(Object oProb, int iRow, int iCol) {
2555	Double fProb = (Double) oProb;
2556	if (fProb < 0 \|\| fProb > 1) {
2557	return;
2558	}
2559	m_fProbs[iRow][iCol] = (double) fProb;
2560	double sum = 0;
2561	for (int i = 0; i < m_fProbs[iRow].length; i++) {
2562	sum += m_fProbs[iRow][i];
2563	}
2564
2565	if (sum > 1) {
2566	// handle overflow
2567	int i = m_fProbs[iRow].length - 1;
2568	while (sum > 1) {
2569	if (i != iCol) {
2570	if (m_fProbs[iRow][i] > sum - 1) {
2571	m_fProbs[iRow][i] -= sum - 1;
2572	sum = 1;
2573	} else {
2574	sum -= m_fProbs[iRow][i];
2575	m_fProbs[iRow][i] = 0;
2576	}
2577	}
2578	i--;
2579	}
2580	} else {
2581	// handle underflow
2582	int i = m_fProbs[iRow].length - 1;
2583	while (sum < 1) {
2584	if (i != iCol) {
2585	m_fProbs[iRow][i] += 1 - sum;
2586	sum = 1;
2587	}
2588	i--;
2589	}
2590
2591	}
2592	validate();
2593	} // setData
2594
2595	/*
2596	* JTable uses this method to determine the default renderer/ editor for
2597	* each cell.
2598	*/
2599	public Class getColumnClass(int c) {
2600	return getValueAt(0, c).getClass();
2601	}
2602
2603	/*
2604	* Implemented this to make sure the table is uneditable.
2605	*/
2606	public boolean isCellEditable(int row, int col) {
2607	return true;
2608	}
2609	} // class GraphVisualizerTableModel
2610
2611	/**
2612	* Listener class for processing mouseClicked
2613	*/
2614	private class GraphVisualizerMouseListener extends MouseAdapter {
2615
2616	/** A left mouseclick on a node adds node to selection (depending
2617	* on shift and ctrl keys).
2618	* A right mouseclick on a node pops up menu with actions to be
2619	* performed on the node.
2620	* A right mouseclick outside another node pops up menu.
2621	*/
2622	public void mouseClicked(MouseEvent me) {
2623	int x, y;
2624
2625	Rectangle r = new Rectangle(0, 0, (int) (m_nPaddedNodeWidth * m_fScale), (int) (m_nNodeHeight * m_fScale));
2626	x = me.getX();
2627	y = me.getY();
2628
2629	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
2630	r.x = (int) (m_BayesNet.getPositionX(iNode) * m_fScale);
2631	r.y = (int) (m_BayesNet.getPositionY(iNode) * m_fScale);
2632	if (r.contains(x, y)) {
2633	m_nCurrentNode = iNode;
2634	if (me.getButton() == MouseEvent.BUTTON3) {
2635	handleRightNodeClick(me);
2636	}
2637	if (me.getButton() == MouseEvent.BUTTON1) {
2638	if ((me.getModifiersEx() & MouseEvent.CTRL_DOWN_MASK) != 0) {
2639	m_Selection.toggleSelection(m_nCurrentNode);
2640	} else if ((me.getModifiersEx() & MouseEvent.SHIFT_DOWN_MASK) != 0) {
2641	m_Selection.addToSelection(m_nCurrentNode);
2642	} else {
2643	m_Selection.clear();
2644	m_Selection.addToSelection(m_nCurrentNode);
2645	}
2646	repaint();
2647	}
2648	return;
2649	}
2650	}
2651	if (me.getButton() == MouseEvent.BUTTON3) {
2652	handleRightClick(me, (int)(x/m_fScale), (int)(y/m_fScale));
2653	}
2654	} // mouseClicked
2655
2656	/* update selection
2657	* (non-Javadoc)
2658	* @see java.awt.event.MouseListener#mouseReleased(java.awt.event.MouseEvent)
2659	*/
2660	public void mouseReleased(MouseEvent me) {
2661	if (m_nSelectedRect != null) {
2662	if ((me.getModifiersEx() & MouseEvent.CTRL_DOWN_MASK) != 0) {
2663	m_Selection.toggleSelection(m_nSelectedRect);
2664	} else if ((me.getModifiersEx() & MouseEvent.SHIFT_DOWN_MASK) != 0) {
2665	m_Selection.addToSelection(m_nSelectedRect);
2666	} else {
2667	m_Selection.clear();
2668	m_Selection.addToSelection(m_nSelectedRect);
2669	}
2670	m_nSelectedRect = null;
2671	repaint();
2672	}
2673	} // mouseReleased
2674
2675	/** position clicked on */
2676	int m_nPosX = 0, m_nPosY = 0;
2677
2678	/* pop up menu with actions that apply in general or to selection (if any exists)
2679	*/
2680	void handleRightClick(MouseEvent me, int nPosX, int nPosY) {
2681
2682	ActionListener act = new ActionListener() {
2683	public void actionPerformed(ActionEvent ae) {
2684	if (ae.getActionCommand().equals("Add node")) {
2685	a_addnode.addNode(m_nPosX, m_nPosY);
2686	return;
2687	}
2688	repaint();
2689	}
2690	};
2691	JPopupMenu popupMenu = new JPopupMenu("Choose a value");
2692
2693	JMenuItem addNodeItem = new JMenuItem("Add node");
2694	addNodeItem.addActionListener(act);
2695	popupMenu.add(addNodeItem);
2696
2697	FastVector selected = m_Selection.getSelected();
2698	JMenu addArcMenu = new JMenu("Add parent");
2699	popupMenu.add(addArcMenu);
2700	if (selected.size() == 0) {
2701	addArcMenu.setEnabled(false);
2702	} else {
2703	int nNodes = m_BayesNet.getNrOfNodes();
2704	boolean[] isNotAllowedAsParent = new boolean[nNodes];
2705	// prevent it being a parent of itself
2706	for (int iNode = 0; iNode < selected.size(); iNode++) {
2707	isNotAllowedAsParent[(Integer) selected.elementAt(iNode)] = true;
2708	}
2709	// prevent a descendant being a parent, since it introduces cycles
2710	for (int i = 0; i < nNodes; i++) {
2711	for (int iNode = 0; iNode < nNodes; iNode++) {
2712	for (int iParent = 0; iParent < m_BayesNet.getNrOfParents(iNode); iParent++) {
2713	if (isNotAllowedAsParent[m_BayesNet.getParent(iNode, iParent)]) {
2714	isNotAllowedAsParent[iNode] = true;
2715	}
2716	}
2717	}
2718	}
2719	// prevent nodes that are already a parent
2720	for (int iNode = 0; iNode < selected.size(); iNode++) {
2721	int nNode = (Integer) selected.elementAt(iNode);
2722	for (int iParent = 0; iParent < m_BayesNet.getNrOfParents(nNode); iParent++) {
2723	isNotAllowedAsParent[m_BayesNet.getParent(nNode, iParent)] = true;
2724	}
2725	}
2726	ActionListener addParentAction = new ActionListener() {
2727	public void actionPerformed(ActionEvent ae) {
2728	try {
2729	m_BayesNet.addArc(ae.getActionCommand(), m_Selection.getSelected());
2730	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
2731	updateStatus();
2732	} catch (Exception e) {
2733	e.printStackTrace();
2734	}
2735	}
2736	};
2737	// count nr of remaining candidates
2738	int nCandidates = 0;
2739	for (int i = 0; i < nNodes; i++) {
2740	if (!isNotAllowedAsParent[i]) {
2741	JMenuItem item = new JMenuItem(m_BayesNet.getNodeName(i));
2742	item.addActionListener(addParentAction);
2743	addArcMenu.add(item);
2744	nCandidates++;
2745	}
2746	}
2747	if (nCandidates == 0) {
2748	addArcMenu.setEnabled(false);
2749	}
2750	}
2751	m_nPosX = nPosX;
2752	m_nPosY = nPosY;
2753	popupMenu.setLocation(me.getX(), me.getY());
2754	popupMenu.show(m_GraphPanel, me.getX(), me.getY());
2755	} // handleRightClick
2756
2757	/* pop up menu with actions that apply to node that was clicked on
2758	*/
2759	void handleRightNodeClick(MouseEvent me) {
2760	m_Selection.clear();
2761	repaint();
2762	ActionListener renameValueAction = new ActionListener() {
2763	public void actionPerformed(ActionEvent ae) {
2764	renameValue(m_nCurrentNode, ae.getActionCommand());
2765	}
2766	};
2767	ActionListener delValueAction = new ActionListener() {
2768	public void actionPerformed(ActionEvent ae) {
2769	delValue(m_nCurrentNode, ae.getActionCommand());
2770	}
2771	};
2772	ActionListener addParentAction = new ActionListener() {
2773	public void actionPerformed(ActionEvent ae) {
2774	try {
2775	m_BayesNet.addArc(ae.getActionCommand(), m_BayesNet.getNodeName(m_nCurrentNode));
2776	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
2777	updateStatus();
2778	} catch (Exception e) {
2779	e.printStackTrace();
2780	}
2781	}
2782	};
2783	ActionListener delParentAction = new ActionListener() {
2784	public void actionPerformed(ActionEvent ae) {
2785	deleteArc(m_nCurrentNode, ae.getActionCommand());
2786	}
2787	};
2788	ActionListener delChildAction = new ActionListener() {
2789	public void actionPerformed(ActionEvent ae) {
2790	deleteArc(ae.getActionCommand(), m_nCurrentNode);
2791	}
2792	};
2793	ActionListener setAvidenceAction = new ActionListener() {
2794	public void actionPerformed(ActionEvent ae) {
2795	try {
2796	String [] outcomes = m_BayesNet.getValues(m_nCurrentNode);
2797	int iValue = 0;
2798	while (iValue < outcomes.length && !outcomes[iValue].equals(ae.getActionCommand())) {
2799	iValue++;
2800	}
2801
2802	if (iValue == outcomes.length) {
2803	iValue = -1;
2804	}
2805	if (iValue < outcomes.length) {
2806	m_jStatusBar.setText("Set evidence for " + m_BayesNet.getNodeName(m_nCurrentNode));
2807	if (m_BayesNet.getEvidence(m_nCurrentNode) < 0 && iValue >= 0) {
2808	m_BayesNet.setEvidence(m_nCurrentNode, iValue);
2809	m_marginCalculatorWithEvidence.setEvidence(m_nCurrentNode, iValue);
2810	} else {
2811	m_BayesNet.setEvidence(m_nCurrentNode, iValue);
2812	SerializedObject so = new SerializedObject(m_marginCalculator);
2813	m_marginCalculatorWithEvidence = (MarginCalculator) so.getObject();
2814	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
2815	if (m_BayesNet.getEvidence(iNode) >= 0) {
2816	m_marginCalculatorWithEvidence.setEvidence(iNode, m_BayesNet.getEvidence(iNode));
2817	}
2818	}
2819	}
2820	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
2821	m_BayesNet.setMargin(iNode, m_marginCalculatorWithEvidence.getMargin(iNode));
2822	}
2823	}
2824	} catch (Exception e) {
2825	e.printStackTrace();
2826	}
2827	repaint();
2828	}
2829	};
2830
2831	ActionListener act = new ActionListener() {
2832	public void actionPerformed(ActionEvent ae) {
2833	if (ae.getActionCommand().equals("Rename")) {
2834	renameNode(m_nCurrentNode);
2835	return;
2836	}
2837	if (ae.getActionCommand().equals("Add parent")) {
2838	addArcInto(m_nCurrentNode);
2839	return;
2840	}
2841	if (ae.getActionCommand().equals("Add value")) {
2842	addValue();
2843	return;
2844	}
2845	if (ae.getActionCommand().equals("Delete node")) {
2846	deleteNode(m_nCurrentNode);
2847	return;
2848	}
2849	if (ae.getActionCommand().equals("Edit CPT")) {
2850	editCPT(m_nCurrentNode);
2851	return;
2852	}
2853	repaint();
2854	}
2855	};
2856	try {
2857	JPopupMenu popupMenu = new JPopupMenu("Choose a value");
2858
2859	JMenu setEvidenceMenu = new JMenu("Set evidence");
2860	String [] outcomes = m_BayesNet.getValues(m_nCurrentNode);
2861	for (int iValue = 0; iValue < outcomes.length; iValue++) {
2862	JMenuItem item = new JMenuItem(outcomes[iValue]);
2863	item.addActionListener(setAvidenceAction);
2864	setEvidenceMenu.add(item);
2865	}
2866	setEvidenceMenu.addSeparator();
2867	JMenuItem item = new JMenuItem("Clear");
2868	item.addActionListener(setAvidenceAction);
2869	setEvidenceMenu.add(item);
2870	popupMenu.add(setEvidenceMenu);
2871
2872	setEvidenceMenu.setEnabled(m_bViewMargins);
2873
2874	popupMenu.addSeparator();
2875
2876	JMenuItem renameItem = new JMenuItem("Rename");
2877	renameItem.addActionListener(act);
2878	popupMenu.add(renameItem);
2879
2880	JMenuItem delNodeItem = new JMenuItem("Delete node");
2881	delNodeItem.addActionListener(act);
2882	popupMenu.add(delNodeItem);
2883
2884	JMenuItem editCPTItem = new JMenuItem("Edit CPT");
2885	editCPTItem.addActionListener(act);
2886	popupMenu.add(editCPTItem);
2887
2888	popupMenu.addSeparator();
2889
2890	JMenu addArcMenu = new JMenu("Add parent");
2891	popupMenu.add(addArcMenu);
2892	int nNodes = m_BayesNet.getNrOfNodes();
2893	boolean[] isNotAllowedAsParent = new boolean[nNodes];
2894	// prevent it being a parent of itself
2895	isNotAllowedAsParent[m_nCurrentNode] = true;
2896	// prevent a descendant being a parent, since it introduces cycles
2897	for (int i = 0; i < nNodes; i++) {
2898	for (int iNode = 0; iNode < nNodes; iNode++) {
2899	for (int iParent = 0; iParent < m_BayesNet.getNrOfParents(iNode); iParent++) {
2900	if (isNotAllowedAsParent[m_BayesNet.getParent(iNode, iParent)]) {
2901	isNotAllowedAsParent[iNode] = true;
2902	}
2903	}
2904	}
2905	}
2906	// prevent nodes that are already a parent
2907	for (int iParent = 0; iParent < m_BayesNet.getNrOfParents(m_nCurrentNode); iParent++) {
2908	isNotAllowedAsParent[m_BayesNet.getParent(m_nCurrentNode, iParent)] = true;
2909	}
2910	// count nr of remaining candidates
2911	int nCandidates = 0;
2912	for (int i = 0; i < nNodes; i++) {
2913	if (!isNotAllowedAsParent[i]) {
2914	item = new JMenuItem(m_BayesNet.getNodeName(i));
2915	item.addActionListener(addParentAction);
2916	addArcMenu.add(item);
2917	nCandidates++;
2918	}
2919	}
2920	if (nCandidates == 0) {
2921	addArcMenu.setEnabled(false);
2922	}
2923
2924	JMenu delArcMenu = new JMenu("Delete parent");
2925	popupMenu.add(delArcMenu);
2926	if (m_BayesNet.getNrOfParents(m_nCurrentNode) == 0) {
2927	delArcMenu.setEnabled(false);
2928	}
2929	for (int iParent = 0; iParent < m_BayesNet.getNrOfParents(m_nCurrentNode); iParent++) {
2930	item = new JMenuItem(m_BayesNet.getNodeName(m_BayesNet.getParent(m_nCurrentNode, iParent)));
2931	item.addActionListener(delParentAction);
2932	delArcMenu.add(item);
2933	}
2934	JMenu delChildMenu = new JMenu("Delete child");
2935	popupMenu.add(delChildMenu);
2936	FastVector nChildren = m_BayesNet.getChildren(m_nCurrentNode);
2937	if (nChildren.size() == 0) {
2938	delChildMenu.setEnabled(false);
2939	}
2940	for (int iChild = 0; iChild < nChildren.size(); iChild++) {
2941	item = new JMenuItem(m_BayesNet.getNodeName((Integer) nChildren.elementAt(iChild)));
2942	item.addActionListener(delChildAction);
2943	delChildMenu.add(item);
2944	}
2945
2946	popupMenu.addSeparator();
2947
2948	JMenuItem addValueItem = new JMenuItem("Add value");
2949	addValueItem.addActionListener(act);
2950	popupMenu.add(addValueItem);
2951
2952	JMenu renameValue = new JMenu("Rename value");
2953	popupMenu.add(renameValue);
2954	for (int iValue = 0; iValue < outcomes.length; iValue++) {
2955	item = new JMenuItem(outcomes[iValue]);
2956	item.addActionListener(renameValueAction);
2957	renameValue.add(item);
2958	}
2959
2960	JMenu delValue = new JMenu("Delete value");
2961	popupMenu.add(delValue);
2962	if (m_BayesNet.getCardinality(m_nCurrentNode) <= 2) {
2963	delValue.setEnabled(false);
2964	}
2965	for (int iValue = 0; iValue < outcomes.length; iValue++) {
2966	JMenuItem delValueItem = new JMenuItem(outcomes[iValue]);
2967	delValueItem.addActionListener(delValueAction);
2968	delValue.add(delValueItem);
2969	}
2970
2971	popupMenu.setLocation(me.getX(), me.getY());
2972	popupMenu.show(m_GraphPanel, me.getX(), me.getY());
2973	} catch (Exception e) {
2974	e.printStackTrace();
2975	}
2976	} // handleRightNodeClick
2977	} // class GraphVisualizerMouseListener
2978
2979	/**
2980	* private class for handling mouseMoved events to highlight nodes if the
2981	* the mouse is moved on one, move it around or move selection around
2982	*/
2983	private class GraphVisualizerMouseMotionListener extends MouseMotionAdapter {
2984
2985	/* last node moved over. Used for turning highlight on and off */
2986	int m_nLastNode = -1;
2987	/* current mouse position clicked */
2988	int m_nPosX, m_nPosY;
2989
2990	/* identify the node under the mouse
2991	* @returns node index of node under mouse, or -1 if there is no such node
2992	*/
2993	int getGraphNode(MouseEvent me) {
2994	m_nPosX = m_nPosY = 0;
2995
2996	Rectangle r = new Rectangle(0, 0, (int) (m_nPaddedNodeWidth * m_fScale), (int) (m_nNodeHeight * m_fScale));
2997	m_nPosX += me.getX();
2998	m_nPosY += me.getY();
2999
3000	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
3001	r.x = (int) (m_BayesNet.getPositionX(iNode) * m_fScale);
3002	r.y = (int) (m_BayesNet.getPositionY(iNode) * m_fScale);
3003	if (r.contains(m_nPosX, m_nPosY)) {
3004	return iNode;
3005	}
3006	}
3007	return -1;
3008	} // getGraphNode
3009
3010	/* handle mouse dragging event
3011	* (non-Javadoc)
3012	* @see java.awt.event.MouseMotionListener#mouseDragged(java.awt.event.MouseEvent)
3013	*/
3014	public void mouseDragged(MouseEvent me) {
3015	if (m_nSelectedRect != null) {
3016	m_nSelectedRect.width = me.getPoint().x - m_nSelectedRect.x;
3017	m_nSelectedRect.height = me.getPoint().y - m_nSelectedRect.y;
3018	repaint();
3019	return;
3020	}
3021	int iNode = getGraphNode(me);
3022	if (iNode >= 0) {
3023	if (m_Selection.getSelected().size() > 0) {
3024	if (m_Selection.getSelected().contains(iNode)) {
3025	m_BayesNet.setPosition(iNode, (int) ((m_nPosX / m_fScale - m_nPaddedNodeWidth / 2)),
3026	(int) ((m_nPosY / m_fScale - m_nNodeHeight / 2)), m_Selection.getSelected());
3027	} else {
3028	m_Selection.clear();
3029	m_BayesNet.setPosition(iNode, (int) ((m_nPosX / m_fScale - m_nPaddedNodeWidth / 2)),
3030	(int) ((m_nPosY / m_fScale - m_nNodeHeight / 2)));
3031	}
3032	repaint();
3033	} else {
3034	m_BayesNet.setPosition(iNode, (int) ((m_nPosX / m_fScale - m_nPaddedNodeWidth / 2)),
3035	(int) ((m_nPosY / m_fScale - m_nNodeHeight / 2)));
3036	}
3037	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3038	a_undo.setEnabled(true);
3039	a_redo.setEnabled(false);
3040	m_GraphPanel.highLight(iNode);
3041	}
3042	if (iNode < 0) {
3043	if (m_nLastNode >= 0) {
3044	m_GraphPanel.repaint();
3045	m_nLastNode = -1;
3046	} else {
3047	m_nSelectedRect = new Rectangle(me.getPoint().x, me.getPoint().y, 1, 1);
3048	m_GraphPanel.repaint();
3049	}
3050	}
3051	} // mouseDragged
3052
3053	/* handles mouse move event
3054	* (non-Javadoc)
3055	* @see java.awt.event.MouseMotionListener#mouseMoved(java.awt.event.MouseEvent)
3056	*/
3057	public void mouseMoved(MouseEvent me) {
3058	int iNode = getGraphNode(me);
3059	if (iNode >= 0) {
3060	if (iNode != m_nLastNode) {
3061	m_GraphPanel.highLight(iNode);
3062	if (m_nLastNode >= 0) {
3063	m_GraphPanel.highLight(m_nLastNode);
3064	}
3065	m_nLastNode = iNode;
3066	}
3067	}
3068	if (iNode < 0 && m_nLastNode >= 0) {
3069	m_GraphPanel.repaint();
3070	m_nLastNode = -1;
3071	}
3072	} // mouseMoved
3073
3074	} // class GraphVisualizerMouseMotionListener
3075
3076	/* apply graph layout algorithm to Bayesian network
3077	*/
3078	void layoutGraph() {
3079	if (m_BayesNet.getNrOfNodes() == 0) {
3080	return;
3081	}
3082	try {
3083	FastVector m_nodes = new FastVector();
3084	FastVector m_edges = new FastVector();
3085	BIFParser bp = new BIFParser(m_BayesNet.toXMLBIF03(), m_nodes, m_edges);
3086	bp.parse();
3087	updateStatus();
3088	m_layoutEngine = new HierarchicalBCEngine(m_nodes, m_edges, m_nPaddedNodeWidth, m_nNodeHeight);
3089	m_layoutEngine.addLayoutCompleteEventListener(this);
3090	m_layoutEngine.layoutGraph();
3091	} catch (Exception e) {
3092	e.printStackTrace();
3093	}
3094	} // layoutGraph
3095
3096	/* Update status of various items that need regular updating
3097	* such as enabled status of some menu items, marginal distributions
3098	* if shown, repainting of graph.
3099	*/
3100	void updateStatus() {
3101	a_undo.setEnabled(m_BayesNet.canUndo());
3102	a_redo.setEnabled(m_BayesNet.canRedo());
3103
3104	a_datagenerator.setEnabled(m_BayesNet.getNrOfNodes() > 0);
3105
3106	if (!m_bViewMargins && !m_bViewCliques) {
3107	repaint();
3108	return;
3109	}
3110
3111	try {
3112	m_marginCalculator = new MarginCalculator();
3113	m_marginCalculator.calcMargins(m_BayesNet);
3114	SerializedObject so = new SerializedObject(m_marginCalculator);
3115	m_marginCalculatorWithEvidence = (MarginCalculator) so.getObject();
3116	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
3117	if (m_BayesNet.getEvidence(iNode) >= 0) {
3118	m_marginCalculatorWithEvidence.setEvidence(iNode, m_BayesNet.getEvidence(iNode));
3119	}
3120	}
3121	for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
3122	m_BayesNet.setMargin(iNode, m_marginCalculatorWithEvidence.getMargin(iNode));
3123	}
3124	} catch (Exception e) {
3125	e.printStackTrace();
3126	}
3127	repaint();
3128	} // updateStatus
3129
3130	/* add arc with node iChild as child.
3131	* This pops up a selection list with potential parents for the child.
3132	* All decendants and current parents are excluded from the list as is
3133	* the child node itself.
3134	* @param iChild index of the node for which to add an arc
3135	*/
3136	void addArcInto(int iChild) {
3137	String sChild = m_BayesNet.getNodeName(iChild);
3138	try {
3139	int nNodes = m_BayesNet.getNrOfNodes();
3140	boolean[] isNotAllowedAsParent = new boolean[nNodes];
3141	// prevent it being a parent of itself
3142	isNotAllowedAsParent[iChild] = true;
3143	// prevent a descendant being a parent, since it introduces cycles
3144	for (int i = 0; i < nNodes; i++) {
3145	for (int iNode = 0; iNode < nNodes; iNode++) {
3146	for (int iParent = 0; iParent < m_BayesNet.getNrOfParents(iNode); iParent++) {
3147	if (isNotAllowedAsParent[m_BayesNet.getParent(iNode, iParent)]) {
3148	isNotAllowedAsParent[iNode] = true;
3149	}
3150	}
3151	}
3152	}
3153	// prevent nodes that are already a parent
3154	for (int iParent = 0; iParent < m_BayesNet.getNrOfParents(iChild); iParent++) {
3155	isNotAllowedAsParent[m_BayesNet.getParent(iChild, iParent)] = true;
3156	}
3157	// count nr of remaining candidates
3158	int nCandidates = 0;
3159	for (int i = 0; i < nNodes; i++) {
3160	if (!isNotAllowedAsParent[i]) {
3161	nCandidates++;
3162	}
3163	}
3164	if (nCandidates == 0) {
3165	JOptionPane.showMessageDialog(null, "No potential parents available for this node (" + sChild
3166	+ "). Choose another node as child node.");
3167	return;
3168	}
3169	String[] options = new String[nCandidates];
3170	int k = 0;
3171	for (int i = 0; i < nNodes; i++) {
3172	if (!isNotAllowedAsParent[i]) {
3173	options[k++] = m_BayesNet.getNodeName(i);
3174	}
3175	}
3176	String sParent = (String) JOptionPane.showInputDialog(null, "Select parent node for " + sChild, "Nodes", 0,
3177	null, options, options[0]);
3178	if (sParent == null \|\| sParent.equals("")) {
3179	return;
3180	}
3181	// update all data structures
3182	m_BayesNet.addArc(sParent, sChild);
3183	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3184	updateStatus();
3185	} catch (Exception e) {
3186	e.printStackTrace();
3187	}
3188	} // addArcInto
3189
3190	/* deletes arc from node with name sParent into child with index iChild
3191	*
3192	*/
3193	void deleteArc(int iChild, String sParent) {
3194	try {
3195	m_BayesNet.deleteArc(m_BayesNet.getNode(sParent), iChild);
3196	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3197	} catch (Exception e) {
3198	e.printStackTrace();
3199	}
3200	updateStatus();
3201	} // deleteArc
3202
3203	/* deletes arc from node with index iParent into child with name sChild
3204	*
3205	*/
3206	void deleteArc(String sChild, int iParent) {
3207	try {
3208	m_BayesNet.deleteArc(iParent, m_BayesNet.getNode(sChild));
3209	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3210	} catch (Exception e) {
3211	e.printStackTrace();
3212	}
3213	updateStatus();
3214	} // deleteArc
3215
3216	/* deletes arc. Pops up list of arcs listed in 'options' as
3217	* "<Node1> -> <Node2>".
3218	*/
3219	void deleteArc(String[] options) {
3220	String sResult = (String) JOptionPane.showInputDialog(null, "Select arc to delete", "Arcs", 0, null, options,
3221	options[0]);
3222	if (sResult != null && !sResult.equals("")) {
3223	int nPos = sResult.indexOf(" -> ");
3224	String sParent = sResult.substring(0, nPos);
3225	String sChild = sResult.substring(nPos + 4);
3226	try {
3227	m_BayesNet.deleteArc(sParent, sChild);
3228	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3229	} catch (Exception e) {
3230	e.printStackTrace();
3231	}
3232	updateStatus();
3233	}
3234	} // deleteArc
3235
3236	/* Rename node with index nTargetNode.
3237	* Pops up window that allwos for entering a new name.
3238	*/
3239	void renameNode(int nTargetNode) {
3240	String sName = (String) JOptionPane.showInputDialog(null, m_BayesNet.getNodeName(nTargetNode), "New name for node",
3241	JOptionPane.OK_CANCEL_OPTION);
3242	if (sName == null \|\| sName.equals("")) {
3243	return;
3244	}
3245	try {
3246	while (m_BayesNet.getNode2(sName) >= 0) {
3247	sName = (String) JOptionPane.showInputDialog(null, "Cannot rename to " + sName
3248	+ ".\nNode with that name already exists.");
3249	if (sName == null \|\| sName.equals("")) {
3250	return;
3251	}
3252	}
3253	m_BayesNet.setNodeName(nTargetNode, sName);
3254	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3255	} catch (Exception e) {
3256	e.printStackTrace();
3257	}
3258	repaint();
3259	} // renameNode
3260
3261	/* Rename value with name sValeu of a node with index nTargetNode.
3262	* Pops up window that allows entering a new name.
3263	*/
3264	void renameValue(int nTargetNode, String sValue) {
3265	String sNewValue = (String) JOptionPane.showInputDialog(null, "New name for value " + sValue, "Node "
3266	+ m_BayesNet.getNodeName(nTargetNode), JOptionPane.OK_CANCEL_OPTION);
3267	if (sNewValue == null \|\| sNewValue.equals("")) {
3268	return;
3269	}
3270	m_BayesNet.renameNodeValue(nTargetNode, sValue, sNewValue);
3271	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3272	a_undo.setEnabled(true);
3273	a_redo.setEnabled(false);
3274	repaint();
3275	} // renameValue
3276
3277	/* delete a single node with index iNode */
3278	void deleteNode(int iNode) {
3279	try {
3280	m_BayesNet.deleteNode(iNode);
3281	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3282	} catch (Exception e) {
3283	e.printStackTrace();
3284	}
3285	updateStatus();
3286	} // deleteNode
3287
3288	/* Add a value to currently selected node.
3289	* Shows window that allows to enter the name of the value.
3290	*/
3291	void addValue() {
3292	//GraphNode n = (GraphNode) m_nodes.elementAt(m_nCurrentNode);
3293	String sValue = "Value" + (m_BayesNet.getCardinality(m_nCurrentNode) + 1);
3294	String sNewValue = (String) JOptionPane.showInputDialog(null, "New value " + sValue, "Node " + m_BayesNet.getNodeName(m_nCurrentNode),
3295	JOptionPane.OK_CANCEL_OPTION);
3296	if (sNewValue == null \|\| sNewValue.equals("")) {
3297	return;
3298	}
3299	try {
3300	m_BayesNet.addNodeValue(m_nCurrentNode, sNewValue);
3301	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3302	//n.outcomes = m_BayesNet.getValues(m_nCurrentNode);
3303	//for (int iNode = 0; iNode < m_BayesNet.getNrOfNodes(); iNode++) {
3304	// n = (GraphNode) m_nodes.elementAt(iNode);
3305	// n.probs = m_BayesNet.getDistribution(iNode);
3306	//}
3307	} catch (Exception e) {
3308	e.printStackTrace();
3309	}
3310	updateStatus();
3311	} // addValue
3312
3313	/* remove value with name sValue from the node with index nTargetNode
3314	*/
3315	void delValue(int nTargetNode, String sValue) {
3316	try {
3317	m_BayesNet.delNodeValue(nTargetNode, sValue);
3318	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3319	} catch (Exception e) {
3320	e.printStackTrace();
3321	}
3322	updateStatus();
3323	} // delValue
3324
3325	/* Edits CPT of node with index nTargetNode.
3326	* Pops up table with probability table that the user can change or just view.
3327	*/
3328	void editCPT(int nTargetNode) {
3329	m_nCurrentNode = nTargetNode;
3330	final GraphVisualizerTableModel tm = new GraphVisualizerTableModel(nTargetNode);
3331
3332	JTable jTblProbs = new JTable(tm);
3333
3334	JScrollPane js = new JScrollPane(jTblProbs);
3335
3336	int nParents = m_BayesNet.getNrOfParents(nTargetNode);
3337	if (nParents > 0) {
3338	GridBagConstraints gbc = new GridBagConstraints();
3339	JPanel jPlRowHeader = new JPanel(new GridBagLayout());
3340
3341	// indices of the parent nodes in the Vector
3342	int[] idx = new int[nParents];
3343	// max length of values of each parent
3344	int[] lengths = new int[nParents];
3345
3346	// Adding labels for rows
3347	gbc.anchor = GridBagConstraints.NORTHWEST;
3348	gbc.fill = GridBagConstraints.HORIZONTAL;
3349	gbc.insets = new Insets(0, 1, 0, 0);
3350	int addNum = 0, temp = 0;
3351	boolean dark = false;
3352	while (true) {
3353	gbc.gridwidth = 1;
3354	for (int k = 0; k < nParents; k++) {
3355	int iParent2 = m_BayesNet.getParent(nTargetNode, k);
3356	JLabel lb = new JLabel(m_BayesNet.getValueName(iParent2,idx[k]));
3357	lb.setFont(new Font("Dialog", Font.PLAIN, 12));
3358	lb.setOpaque(true);
3359	lb.setBorder(BorderFactory.createEmptyBorder(1, 2, 1, 1));
3360	lb.setHorizontalAlignment(JLabel.CENTER);
3361	if (dark) {
3362	lb.setBackground(lb.getBackground().darker());
3363	lb.setForeground(Color.white);
3364	} else
3365	lb.setForeground(Color.black);
3366
3367	temp = lb.getPreferredSize().width;
3368	lb.setPreferredSize(new Dimension(temp, jTblProbs.getRowHeight()));
3369	if (lengths[k] < temp)
3370	lengths[k] = temp;
3371	temp = 0;
3372
3373	if (k == nParents - 1) {
3374	gbc.gridwidth = GridBagConstraints.REMAINDER;
3375	dark = (dark == true) ? false : true;
3376	}
3377	jPlRowHeader.add(lb, gbc);
3378	addNum++;
3379	}
3380
3381	for (int k = nParents - 1; k >= 0; k--) {
3382	int iParent2 = m_BayesNet.getParent(m_nCurrentNode, k);
3383	if (idx[k] == m_BayesNet.getCardinality(iParent2) - 1 && k != 0) {
3384	idx[k] = 0;
3385	continue;
3386	} else {
3387	idx[k]++;
3388	break;
3389	}
3390	}
3391
3392	int iParent2 = m_BayesNet.getParent(m_nCurrentNode, 0);
3393	if (idx[0] == m_BayesNet.getCardinality(iParent2)) {
3394	JLabel lb = (JLabel) jPlRowHeader.getComponent(addNum - 1);
3395	jPlRowHeader.remove(addNum - 1);
3396	lb.setPreferredSize(new Dimension(lb.getPreferredSize().width, jTblProbs
3397	.getRowHeight()));
3398	gbc.gridwidth = GridBagConstraints.REMAINDER;
3399	gbc.weighty = 1;
3400	jPlRowHeader.add(lb, gbc);
3401	gbc.weighty = 0;
3402	break;
3403	}
3404	}
3405
3406	gbc.gridwidth = 1;
3407	// The following panel contains the names of the
3408	// parents
3409	// and is displayed above the row names to identify
3410	// which value belongs to which parent
3411	JPanel jPlRowNames = new JPanel(new GridBagLayout());
3412	for (int j = 0; j < nParents; j++) {
3413	JLabel lb2;
3414	JLabel lb1 = new JLabel(m_BayesNet.getNodeName(m_BayesNet.getParent(nTargetNode, j)));
3415	lb1.setBorder(BorderFactory.createEmptyBorder(1, 2, 1, 1));
3416	Dimension tempd = lb1.getPreferredSize();
3417	if (tempd.width < lengths[j]) {
3418	lb1.setPreferredSize(new Dimension(lengths[j], tempd.height));
3419	lb1.setHorizontalAlignment(JLabel.CENTER);
3420	lb1.setMinimumSize(new Dimension(lengths[j], tempd.height));
3421	} else if (tempd.width > lengths[j]) {
3422	lb2 = (JLabel) jPlRowHeader.getComponent(j);
3423	lb2.setPreferredSize(new Dimension(tempd.width, lb2.getPreferredSize().height));
3424	}
3425	jPlRowNames.add(lb1, gbc);
3426	}
3427	js.setRowHeaderView(jPlRowHeader);
3428	js.setCorner(JScrollPane.UPPER_LEFT_CORNER, jPlRowNames);
3429	}
3430
3431	final JDialog dlg = new JDialog((Frame) GUI.this.getTopLevelAncestor(),
3432	"Probability Distribution Table For " + m_BayesNet.getNodeName(nTargetNode), true);
3433	dlg.setSize(500, 400);
3434	dlg.setLocation(GUI.this.getLocation().x + GUI.this.getWidth() / 2
3435	- 250, GUI.this.getLocation().y + GUI.this.getHeight() / 2
3436	- 200);
3437
3438	dlg.getContentPane().setLayout(new BorderLayout());
3439	dlg.getContentPane().add(js, BorderLayout.CENTER);
3440
3441	JButton jBtRandomize = new JButton("Randomize");
3442	jBtRandomize.setMnemonic('R');
3443	jBtRandomize.addActionListener(new ActionListener() {
3444	public void actionPerformed(ActionEvent ae) {
3445	tm.randomize();
3446	dlg.repaint();
3447	}
3448	});
3449
3450	JButton jBtOk = new JButton("Ok");
3451	jBtOk.setMnemonic('O');
3452	jBtOk.addActionListener(new ActionListener() {
3453	public void actionPerformed(ActionEvent ae) {
3454	tm.setData();
3455	try {
3456	m_BayesNet.setDistribution(m_nCurrentNode, tm.m_fProbs);
3457	m_jStatusBar.setText(m_BayesNet.lastActionMsg());
3458	updateStatus();
3459	} catch (Exception e) {
3460	e.printStackTrace();
3461	}
3462	dlg.setVisible(false);
3463	}
3464	});
3465	JButton jBtCancel = new JButton("Cancel");
3466	jBtCancel.setMnemonic('C');
3467	jBtCancel.addActionListener(new ActionListener() {
3468	public void actionPerformed(ActionEvent ae) {
3469	dlg.setVisible(false);
3470	}
3471	});
3472	Container c = new Container();
3473	c.setLayout(new GridBagLayout());
3474	c.add(jBtRandomize);
3475	c.add(jBtOk);
3476	c.add(jBtCancel);
3477
3478	dlg.getContentPane().add(c, BorderLayout.SOUTH);
3479	dlg.setVisible(true);
3480	} // editCPT
3481
3482	/**
3483	* Main method. Builds up menus and reads from file if one is specified.
3484	*/
3485	public static void main(String[] args) {
3486
3487	weka.core.logging.Logger.log(weka.core.logging.Logger.Level.INFO, "Logging started");
3488
3489	LookAndFeel.setLookAndFeel();
3490
3491	JFrame jf = new JFrame("Bayes Network Editor");
3492	final GUI g = new GUI();
3493	JMenuBar menuBar = g.getMenuBar();
3494
3495	if (args.length>0) {
3496	try {
3497	g.readBIFFromFile(args[0]);
3498	} catch (IOException ex) {
3499	ex.printStackTrace();
3500	} catch (BIFFormatException bf) {
3501	bf.printStackTrace();
3502	System.exit(-1);
3503	}
3504	}
3505
3506
3507
3508
3509	jf.setJMenuBar(menuBar);
3510	jf.getContentPane().add(g);
3511	jf.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
3512	jf.setSize(800, 600);
3513	jf.setVisible(true);
3514	g.m_Selection.updateGUI();
3515	GenericObjectEditor.registerEditors();
3516	} // main
3517
3518	} // end of class

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