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EditableBayesNet.java

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1	package weka.classifiers.bayes.net;
2	/*
3	* This program is free software; you can redistribute it and/or modify
4	* it under the terms of the GNU General Public License as published by
5	* the Free Software Foundation; either version 2 of the License, or
6	* (at your option) any later version.
7	*
8	* This program is distributed in the hope that it will be useful,
9	* but WITHOUT ANY WARRANTY; without even the implied warranty of
10	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11	* GNU General Public License for more details.
12	*
13	* You should have received a copy of the GNU General Public License
14	* along with this program; if not, write to the Free Software
15	* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
16	*/
17
18	/*
19	* EditableBayesNet.java
20	*
21	*/
22
23	import java.io.Serializable;
24	import java.io.StringReader;
25	import java.util.StringTokenizer;
26
27	import javax.xml.parsers.DocumentBuilderFactory;
28
29	import org.w3c.dom.CharacterData;
30	import org.w3c.dom.Document;
31	import org.w3c.dom.Element;
32	import org.w3c.dom.Node;
33	import org.w3c.dom.NodeList;
34
35	import weka.classifiers.bayes.BayesNet;
36	import weka.classifiers.bayes.net.estimate.DiscreteEstimatorBayes;
37	import weka.core.Attribute;
38	import weka.core.FastVector;
39	import weka.core.Instances;
40	import weka.core.RevisionUtils;
41	import weka.core.SerializedObject;
42	import weka.estimators.Estimator;
43	import weka.filters.Filter;
44	import weka.filters.unsupervised.attribute.Reorder;
45
46
47	/**
48	<!-- globalinfo-start -->
49	* Bayes Network learning using various search algorithms and quality measures.<br/>
50	* Base class for a Bayes Network classifier. Provides datastructures (network structure, conditional probability distributions, etc.) and facilities common to Bayes Network learning algorithms like K2 and B.<br/>
51	* <br/>
52	* For more information see:<br/>
53	* <br/>
54	* http://www.cs.waikato.ac.nz/~remco/weka.pdf
55	* <p/>
56	<!-- globalinfo-end -->
57	*
58	<!-- options-start -->
59	* Valid options are: <p/>
60	*
61	* <pre> -D
62	* Do not use ADTree data structure
63	* </pre>
64	*
65	* <pre> -B <BIF file>
66	* BIF file to compare with
67	* </pre>
68	*
69	* <pre> -Q weka.classifiers.bayes.net.search.SearchAlgorithm
70	* Search algorithm
71	* </pre>
72	*
73	* <pre> -E weka.classifiers.bayes.net.estimate.SimpleEstimator
74	* Estimator algorithm
75	* </pre>
76	*
77	<!-- options-end -->
78	*
79	* @author Remco Bouckaert (rrb@xm.co.nz)
80	* @version $Revision: 4899 $
81	*/
82
83	public class EditableBayesNet extends BayesNet {
84	/** for serialization */
85	static final long serialVersionUID = 746037443258735954L;
86
87	/** location of nodes, used for graph drawing * */
88	protected FastVector m_nPositionX;
89
90	protected FastVector m_nPositionY;
91
92	/** marginal distributions * */
93	protected FastVector m_fMarginP;
94
95	/** evidence values, used for evidence propagation * */
96	protected FastVector m_nEvidence;
97
98	/** standard constructor * */
99	public EditableBayesNet() {
100	super();
101	m_nEvidence = new FastVector(0);
102	m_fMarginP = new FastVector(0);
103	m_nPositionX = new FastVector();
104	m_nPositionY = new FastVector();
105	clearUndoStack();
106	} // c'tor
107
108	/** constructor, creates empty network with nodes based on the attributes in a data set */
109	public EditableBayesNet(Instances instances) {
110	try {
111	if (instances.classIndex() < 0) {
112	instances.setClassIndex(instances.numAttributes() - 1);
113	}
114	m_Instances = normalizeDataSet(instances);
115	} catch (Exception e) {
116	e.printStackTrace();
117	}
118
119	int nNodes = getNrOfNodes();
120	m_ParentSets = new ParentSet[nNodes];
121	for (int i = 0; i < nNodes; i++) {
122	m_ParentSets[i] = new ParentSet();
123	}
124	m_Distributions = new Estimator[nNodes][];
125	for (int iNode = 0; iNode < nNodes; iNode++) {
126	m_Distributions[iNode] = new Estimator[1];
127	m_Distributions[iNode][0] = new DiscreteEstimatorBayes(getCardinality(iNode), 0.5);
128	}
129
130	m_nEvidence = new FastVector(nNodes);
131	for (int i = 0; i < nNodes; i++) {
132	m_nEvidence.addElement(-1);
133	}
134	m_fMarginP = new FastVector(nNodes);
135	for (int i = 0; i < nNodes; i++) {
136	double[] P = new double[getCardinality(i)];
137	m_fMarginP.addElement(P);
138	}
139
140	m_nPositionX = new FastVector(nNodes);
141	m_nPositionY = new FastVector(nNodes);
142	for (int iNode = 0; iNode < nNodes; iNode++) {
143	m_nPositionX.addElement(iNode%10 * 50);
144	m_nPositionY.addElement(((int)(iNode/10)) * 50);
145	}
146
147	} // c'tor
148
149	/** constructor, copies Bayesian network structure from a Bayesian network
150	* encapsulated in a BIFReader
151	*/
152	public EditableBayesNet(BIFReader other) {
153	m_Instances = other.m_Instances;
154	m_ParentSets = other.getParentSets();
155	m_Distributions = other.getDistributions();
156
157	int nNodes = getNrOfNodes();
158	m_nPositionX = new FastVector(nNodes);
159	m_nPositionY = new FastVector(nNodes);
160	for (int i = 0; i < nNodes; i++) {
161	m_nPositionX.addElement(other.m_nPositionX[i]);
162	m_nPositionY.addElement(other.m_nPositionY[i]);
163	}
164	m_nEvidence = new FastVector(nNodes);
165	for (int i = 0; i < nNodes; i++) {
166	m_nEvidence.addElement(-1);
167	}
168	m_fMarginP = new FastVector(nNodes);
169	for (int i = 0; i < nNodes; i++) {
170	double[] P = new double[getCardinality(i)];
171	m_fMarginP.addElement(P);
172	}
173	clearUndoStack();
174	} // c'tor
175
176	/**
177	* constructor that potentially initializes instances as well
178	*
179	* @param bSetInstances
180	* flag indicating whether to initialize instances or not
181	*/
182	public EditableBayesNet(boolean bSetInstances) {
183	super();
184	m_nEvidence = new FastVector(0);
185	m_fMarginP = new FastVector(0);
186	m_nPositionX = new FastVector();
187	m_nPositionY = new FastVector();
188	clearUndoStack();
189	if (bSetInstances) {
190	m_Instances = new Instances("New Network", new FastVector(0), 0);
191	}
192	} // c'tor
193
194
195	/** Assuming a network structure is defined and we want to learn from data,
196	* the data set must be put if correct order first and possibly discretized/missing
197	* values filled in before proceeding to CPT learning.
198	* @param instances data set to learn from
199	* @exception Exception when data sets are not compatible, e.g., a variable is missing
200	* or a variable has different nr of values.
201	*/
202	public void setData(Instances instances) throws Exception {
203	// sync order of variables
204	int [] order = new int [getNrOfNodes()];
205	for (int iNode = 0; iNode < getNrOfNodes(); iNode++) {
206	String sName = getNodeName(iNode);
207	int nNode = 0;
208	while (nNode < getNrOfNodes() && !sName.equals(instances.attribute(nNode).name())) {
209	nNode++;
210	}
211	if (nNode >= getNrOfNodes()) {
212	throw new Exception("Cannot find node named [[[" + sName + "]]] in the data");
213	}
214	order[iNode] = nNode;
215	}
216	Reorder reorderFilter = new Reorder();
217	reorderFilter.setAttributeIndicesArray(order);
218	reorderFilter.setInputFormat(instances);
219	instances = Filter.useFilter(instances, reorderFilter);
220	// filter using discretization/missing values filter
221	Instances newInstances = new Instances(m_Instances, 0);
222	if (m_DiscretizeFilter == null && m_MissingValuesFilter == null) {
223	newInstances = normalizeDataSet(instances);
224	} else {
225	for (int iInstance = 0; iInstance < instances.numInstances(); iInstance++) {
226	newInstances.add(normalizeInstance(instances.instance(iInstance)));
227	}
228	}
229	//sanity check
230	for (int iNode = 0; iNode < getNrOfNodes(); iNode++) {
231	if (newInstances.attribute(iNode).numValues() != getCardinality(iNode)) {
232	throw new Exception("Number of values of node [[[" + getNodeName(iNode) + "]]] differs in (discretized) dataset." );
233	}
234	}
235	// if we got this far, all is ok with the data set and
236	// we can replace data set of Bayes net
237	m_Instances = newInstances;
238	} // setData
239
240	/** returns index of node with given name, or -1 if no such node exists
241	* @param sNodeName name of the node to get index for
242	*/
243	public int getNode2(String sNodeName) {
244	int iNode = 0;
245	while (iNode < m_Instances.numAttributes()) {
246	if (m_Instances.attribute(iNode).name().equals(sNodeName)) {
247	return iNode;
248	}
249	iNode++;
250	}
251	return -1;
252	} // getNode2
253
254	/** returns index of node with given name. Throws exception if no such node exists
255	* @param sNodeName name of the node to get index for
256	*/
257	public int getNode(String sNodeName) throws Exception {
258	int iNode = getNode2(sNodeName);
259	if (iNode < 0) {
260	throw new Exception("Could not find node [[" + sNodeName + "]]");
261	}
262	return iNode;
263	} // getNode
264
265	/**
266	* Add new node to the network, initializing instances, parentsets,
267	* distributions. Used for manual manipulation of the Bayesian network.
268	*
269	* @param sName
270	* name of the node. If the name already exists, an x is appended
271	* to the name
272	* @param nCardinality
273	* number of values for this node
274	* @throws Exception
275	*/
276	public void addNode(String sName, int nCardinality) throws Exception {
277	addNode(sName, nCardinality, 100 + getNrOfNodes() * 10, 100 + getNrOfNodes() * 10);
278	} // addNode
279
280	/** Add node to network at a given position, initializing instances, parentsets,
281	* distributions. Used for manual manipulation of the Bayesian network.
282	*
283	* @param sName
284	* name of the node. If the name already exists, an x is appended
285	* to the name
286	* @param nCardinality
287	* number of values for this node
288	* @param nPosX x-coordiate of the position to place this node
289	* @param nPosY y-coordiate of the position to place this node
290	* @throws Exception
291	*/
292	public void addNode(String sName, int nCardinality, int nPosX, int nPosY) throws Exception {
293	if (getNode2(sName) >= 0) {
294	addNode(sName + "x", nCardinality);
295	return ;
296	}
297	// update instances
298	FastVector values = new FastVector(nCardinality);
299	for (int iValue = 0; iValue < nCardinality; iValue++) {
300	values.addElement("Value" + (iValue + 1));
301	}
302	Attribute att = new Attribute(sName, values);
303	m_Instances.insertAttributeAt(att, m_Instances.numAttributes());
304	int nAtts = m_Instances.numAttributes();
305	// update parentsets
306	ParentSet[] parentSets = new ParentSet[nAtts];
307	for (int iParentSet = 0; iParentSet < nAtts - 1; iParentSet++) {
308	parentSets[iParentSet] = m_ParentSets[iParentSet];
309	}
310	parentSets[nAtts - 1] = new ParentSet();
311	m_ParentSets = parentSets;
312	// update distributions
313	Estimator[][] distributions = new Estimator[nAtts][];
314	for (int iNode = 0; iNode < nAtts - 1; iNode++) {
315	distributions[iNode] = m_Distributions[iNode];
316	}
317	distributions[nAtts - 1] = new Estimator[1];
318	distributions[nAtts - 1][0] = new DiscreteEstimatorBayes(nCardinality, 0.5);
319	m_Distributions = distributions;
320	// update positions
321	m_nPositionX.addElement(nPosX);
322	m_nPositionY.addElement(nPosY);
323	// update evidence & margins
324	m_nEvidence.addElement(-1);
325	double[] fMarginP = new double[nCardinality];
326	for (int iValue = 0; iValue < nCardinality; iValue++) {
327	fMarginP[iValue] = 1.0 / nCardinality;
328	}
329	m_fMarginP.addElement(fMarginP);
330	// update undo stack
331	if (m_bNeedsUndoAction) {
332	addUndoAction(new AddNodeAction(sName, nCardinality, nPosX, nPosY));
333	}
334	} // addNode
335
336	/**
337	* Delete node from the network, updating instances, parentsets,
338	* distributions Conditional distributions are condensed by taking the
339	* values for the target node to be its first value. Used for manual
340	* manipulation of the Bayesian network.
341	*
342	* @param sName
343	* name of the node. If the name does not exists an exception is
344	* thrown
345	* @throws Exception
346	*/
347	public void deleteNode(String sName) throws Exception {
348	int nTargetNode = getNode(sName);
349	deleteNode(nTargetNode);
350	} // deleteNode
351
352	/**
353	* Delete node from the network, updating instances, parentsets,
354	* distributions Conditional distributions are condensed by taking the
355	* values for the target node to be its first value. Used for manual
356	* manipulation of the Bayesian network.
357	*
358	* @param nTargetNode
359	* index of the node to delete.
360	* @throws Exception
361	*/
362	public void deleteNode(int nTargetNode) throws Exception {
363	// update undo stack
364	if (m_bNeedsUndoAction) {
365	addUndoAction(new DeleteNodeAction(nTargetNode));
366	}
367	int nAtts = m_Instances.numAttributes() - 1;
368	int nTargetCard = m_Instances.attribute(nTargetNode).numValues();
369	// update distributions
370	Estimator[][] distributions = new Estimator[nAtts][];
371	for (int iNode = 0; iNode < nAtts; iNode++) {
372	int iNode2 = iNode;
373	if (iNode >= nTargetNode) {
374	iNode2++;
375	}
376	Estimator[] distribution = m_Distributions[iNode2];
377	if (m_ParentSets[iNode2].contains(nTargetNode)) {
378	// condense distribution, use values for targetnode = 0
379	int nParentCard = m_ParentSets[iNode2].getCardinalityOfParents();
380	nParentCard = nParentCard / nTargetCard;
381	Estimator[] distribution2 = new Estimator[nParentCard];
382	for (int iParent = 0; iParent < nParentCard; iParent++) {
383	distribution2[iParent] = distribution[iParent];
384	}
385	distribution = distribution2;
386	}
387	distributions[iNode] = distribution;
388	}
389	m_Distributions = distributions;
390	// update parentsets
391	ParentSet[] parentSets = new ParentSet[nAtts];
392	for (int iParentSet = 0; iParentSet < nAtts; iParentSet++) {
393	int iParentSet2 = iParentSet;
394	if (iParentSet >= nTargetNode) {
395	iParentSet2++;
396	}
397	ParentSet parentset = m_ParentSets[iParentSet2];
398	parentset.deleteParent(nTargetNode, m_Instances);
399	for (int iParent = 0; iParent < parentset.getNrOfParents(); iParent++) {
400	int nParent = parentset.getParent(iParent);
401	if (nParent > nTargetNode) {
402	parentset.SetParent(iParent, nParent - 1);
403	}
404	}
405	parentSets[iParentSet] = parentset;
406	}
407	m_ParentSets = parentSets;
408	// update instances
409	m_Instances.setClassIndex(-1);
410	m_Instances.deleteAttributeAt(nTargetNode);
411	m_Instances.setClassIndex(nAtts - 1);
412
413	// update positions
414	m_nPositionX.removeElementAt(nTargetNode);
415	m_nPositionY.removeElementAt(nTargetNode);
416	// update evidence & margins
417	m_nEvidence.removeElementAt(nTargetNode);
418	m_fMarginP.removeElementAt(nTargetNode);
419	} // deleteNode
420
421	/**
422	* Delete nodes with indexes in selection from the network, updating instances, parentsets,
423	* distributions Conditional distributions are condensed by taking the
424	* values for the target node to be its first value. Used for manual
425	* manipulation of the Bayesian network.
426	*
427	* @param nodes
428	* array of indexes of nodes to delete.
429	* @throws Exception
430	*/
431	public void deleteSelection(FastVector nodes) {
432	// sort before proceeding
433	for (int i = 0; i < nodes.size(); i++) {
434	for (int j = i + 1; j < nodes.size(); j++) {
435	if ((Integer) nodes.elementAt(i) > (Integer) nodes.elementAt(j)) {
436	int h = (Integer) nodes.elementAt(i);
437	nodes.setElementAt(nodes.elementAt(j), i);
438	nodes.setElementAt(h, j);
439	}
440	}
441	}
442	// update undo stack
443	if (m_bNeedsUndoAction) {
444	addUndoAction(new DeleteSelectionAction(nodes));
445	}
446	boolean bNeedsUndoAction = m_bNeedsUndoAction;
447	m_bNeedsUndoAction = false;
448	try {
449	for (int iNode = nodes.size() - 1; iNode >= 0; iNode--) {
450	deleteNode((Integer) nodes.elementAt(iNode));
451	}
452	} catch (Exception e) {
453	e.printStackTrace();
454	}
455	m_bNeedsUndoAction = bNeedsUndoAction;
456	} // deleteSelection
457
458	/** XML helper function for selecting elements under a node with a given name
459	* @param item XMLNode to select items from
460	* @param sElement name of the element to return
461	*/
462	FastVector selectElements(Node item, String sElement) throws Exception {
463	NodeList children = item.getChildNodes();
464	FastVector nodelist = new FastVector();
465	for (int iNode = 0; iNode < children.getLength(); iNode++) {
466	Node node = children.item(iNode);
467	if ((node.getNodeType() == Node.ELEMENT_NODE) && node.getNodeName().equals(sElement)) {
468	nodelist.addElement(node);
469	}
470	}
471	return nodelist;
472	} // selectElements
473
474	/**
475	* XML helper function. Returns all TEXT children of the given node in one string. Between the
476	* node values new lines are inserted.
477	*
478	* @param node
479	* the node to return the content for
480	* @return the content of the node
481	*/
482	public String getContent(Element node) {
483	NodeList list;
484	Node item;
485	int i;
486	String result;
487
488	result = "";
489	list = node.getChildNodes();
490
491	for (i = 0; i < list.getLength(); i++) {
492	item = list.item(i);
493	if (item.getNodeType() == Node.TEXT_NODE)
494	result += "\n" + item.getNodeValue();
495	}
496
497	return result;
498	}
499
500	/** XML helper function that returns DEFINITION element from a XMLBIF document
501	* for a node with a given name.
502	* @param doc XMLBIF document
503	* @param sName name of the node to get the definition for
504	*/
505	Element getDefinition(Document doc, String sName) throws Exception {
506	NodeList nodelist = doc.getElementsByTagName("DEFINITION");
507	for (int iNode = 0; iNode < nodelist.getLength(); iNode++) {
508	Node node = nodelist.item(iNode);
509	FastVector list = selectElements(node, "FOR");
510	if (list.size() > 0) {
511	Node forNode = (Node) list.elementAt(0);
512	if (getContent((Element) forNode).trim().equals(sName)) {
513	return (Element) node;
514	}
515	}
516	}
517	throw new Exception("Could not find definition for ((" + sName + "))");
518	} // getDefinition
519
520
521	/** Paste modes. This allows for verifying that a past action does not cause
522	* any problems before actually performing the paste operation.
523	*/
524	final static int TEST = 0;
525	final static int EXECUTE = 1;
526
527	/** Apply paste operation with XMLBIF fragment. This adds nodes in the XMLBIF fragment
528	* to the network, together with its parents. First, paste in test mode to verify
529	* no problems occur, then execute paste operation. If a problem occurs (e.g. parent
530	* does not exist) then a exception is thrown.
531	* @param sXML XMLBIF fragment to paste into the network
532	*/
533	public void paste(String sXML) throws Exception {
534	try {
535	paste(sXML, TEST);
536	} catch (Exception e) {
537	throw e;
538	}
539	paste(sXML, EXECUTE);
540	} // paste
541
542	/** Apply paste operation with XMLBIF fragment. Depending on the paste mode, the
543	* nodes are actually added to the network or it is just tested that the nodes can
544	* be added to the network.
545	* @param sXML XMLBIF fragment to paste into the network
546	* @param mode paste mode TEST or EXECUTE
547	*/
548	void paste(String sXML, int mode) throws Exception {
549	DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
550	factory.setValidating(true);
551	Document doc = factory.newDocumentBuilder().parse(new org.xml.sax.InputSource(new StringReader(sXML)));
552	doc.normalize();
553
554	// create nodes first
555	NodeList nodelist = doc.getElementsByTagName("VARIABLE");
556	FastVector sBaseNames = new FastVector();
557	Instances instances = new Instances(m_Instances, 0);
558	int nBase = instances.numAttributes();
559	for (int iNode = 0; iNode < nodelist.getLength(); iNode++) {
560	// Get element
561	FastVector valueslist;
562	// Get the name of the node
563	valueslist = selectElements(nodelist.item(iNode), "OUTCOME");
564
565	int nValues = valueslist.size();
566	// generate value strings
567	FastVector nomStrings = new FastVector(nValues + 1);
568	for (int iValue = 0; iValue < nValues; iValue++) {
569	Node node = ((Node) valueslist.elementAt(iValue)).getFirstChild();
570	String sValue = ((CharacterData) (node)).getData();
571	if (sValue == null) {
572	sValue = "Value" + (iValue + 1);
573	}
574	nomStrings.addElement(sValue);
575	}
576	FastVector nodelist2;
577	// Get the name of the network
578	nodelist2 = selectElements(nodelist.item(iNode), "NAME");
579	if (nodelist2.size() == 0) {
580	throw new Exception("No name specified for variable");
581	}
582	String sBaseName = ((CharacterData) (((Node) nodelist2.elementAt(0)).getFirstChild())).getData();
583	sBaseNames.addElement(sBaseName);
584	String sNodeName = sBaseName;
585	if (getNode2(sNodeName) >= 0) {
586	sNodeName = "Copy of " + sBaseName;
587	}
588	int iAttempt = 2;
589	while (getNode2(sNodeName) >= 0) {
590	sNodeName = "Copy (" + iAttempt + ") of " + sBaseName;
591	iAttempt++;
592	}
593
594	Attribute att = new Attribute(sNodeName, nomStrings);
595	instances.insertAttributeAt(att, instances.numAttributes());
596
597	valueslist = selectElements(nodelist.item(iNode), "PROPERTY");
598	nValues = valueslist.size();
599	// generate value strings
600	int nPosX = iAttempt * 10;
601	int nPosY = iAttempt * 10;
602	for (int iValue = 0; iValue < nValues; iValue++) {
603	// parsing for strings of the form "position = (73, 165)"
604	Node node = ((Node) valueslist.elementAt(iValue)).getFirstChild();
605	String sValue = ((CharacterData) (node)).getData();
606	if (sValue.startsWith("position")) {
607	int i0 = sValue.indexOf('(');
608	int i1 = sValue.indexOf(',');
609	int i2 = sValue.indexOf(')');
610	String sX = sValue.substring(i0 + 1, i1).trim();
611	String sY = sValue.substring(i1 + 1, i2).trim();
612	try {
613	nPosX = (Integer.parseInt(sX) + iAttempt * 10);
614	nPosY = (Integer.parseInt(sY) + iAttempt * 10);
615	} catch (NumberFormatException e) {
616	System.err.println("Wrong number format in position :(" + sX + "," + sY + ")");
617	}
618	}
619	}
620	if (mode == EXECUTE) {
621	m_nPositionX.addElement(nPosX);
622	m_nPositionY.addElement(nPosY);
623	}
624
625	}
626
627	FastVector nodelist2;
628	Estimator[][] distributions = new Estimator[nBase + sBaseNames.size()][];
629	ParentSet[] parentsets = new ParentSet[nBase + sBaseNames.size()];
630	for (int iNode = 0; iNode < nBase; iNode++) {
631	distributions[iNode] = m_Distributions[iNode];
632	parentsets[iNode] = m_ParentSets[iNode];
633	}
634	if (mode == EXECUTE) {
635	m_Instances = instances;
636	}
637	// create arrows & create distributions
638	for (int iNode = 0; iNode < sBaseNames.size(); iNode++) {
639	// find definition that goes with this node
640	String sName = (String) sBaseNames.elementAt(iNode);
641	Element definition = getDefinition(doc, sName);
642	parentsets[nBase + iNode] = new ParentSet();
643
644	// get the parents for this node
645	// resolve structure
646	nodelist2 = selectElements(definition, "GIVEN");
647	for (int iParent = 0; iParent < nodelist2.size(); iParent++) {
648	Node parentName = ((Node) nodelist2.elementAt(iParent)).getFirstChild();
649	String sParentName = ((CharacterData) (parentName)).getData();
650	int nParent = -1;
651	for (int iBase = 0; iBase < sBaseNames.size(); iBase++) {
652	if (sParentName.equals((String) sBaseNames.elementAt(iBase))) {
653	nParent = nBase + iBase;
654	}
655	}
656	if (nParent < 0) {
657	nParent = getNode(sParentName);
658	}
659	parentsets[nBase + iNode].addParent(nParent, instances);
660	}
661	// resolve conditional probability table
662	int nCardinality = parentsets[nBase + iNode].getCardinalityOfParents();
663	int nValues = instances.attribute(nBase + iNode).numValues();
664	distributions[nBase + iNode] = new Estimator[nCardinality];
665	for (int i = 0; i < nCardinality; i++) {
666	distributions[nBase + iNode][i] = new DiscreteEstimatorBayes(nValues, 0.0f);
667	}
668
669	String sTable = getContent((Element) selectElements(definition, "TABLE").elementAt(0));
670	sTable = sTable.replaceAll("\\n", " ");
671	StringTokenizer st = new StringTokenizer(sTable.toString());
672
673	for (int i = 0; i < nCardinality; i++) {
674	DiscreteEstimatorBayes d = (DiscreteEstimatorBayes) distributions[nBase + iNode][i];
675	for (int iValue = 0; iValue < nValues; iValue++) {
676	String sWeight = st.nextToken();
677	d.addValue(iValue, new Double(sWeight).doubleValue());
678	}
679	}
680	if (mode == EXECUTE) {
681	m_nEvidence.insertElementAt(-1, nBase + iNode);
682	m_fMarginP.insertElementAt(new double[getCardinality(nBase + iNode)], nBase + iNode);
683	}
684	}
685	if (mode == EXECUTE) {
686	m_Distributions = distributions;
687	m_ParentSets = parentsets;
688	}
689	// update undo stack
690	if (mode == EXECUTE && m_bNeedsUndoAction) {
691	addUndoAction(new PasteAction(sXML, nBase));
692	}
693	} // paste
694
695	/**
696	* Add arc between two nodes Distributions are updated by duplication for
697	* every value of the parent node.
698	*
699	* @param sParent
700	* name of the parent node
701	* @param sChild
702	* name of the child node
703	* @throws Exception
704	* if parent or child cannot be found in network
705	*/
706	public void addArc(String sParent, String sChild) throws Exception {
707	int nParent = getNode(sParent);
708	int nChild = getNode(sChild);
709	addArc(nParent, nChild);
710	} // addArc
711
712	/**
713	* Add arc between two nodes Distributions are updated by duplication for
714	* every value of the parent node.
715	*
716	* @param nParent
717	* index of the parent node
718	* @param nChild
719	* index of the child node
720	* @throws Exception
721	*/
722	public void addArc(int nParent, int nChild) throws Exception {
723	// update undo stack
724	if (m_bNeedsUndoAction) {
725	addUndoAction(new AddArcAction(nParent, nChild));
726	}
727	int nOldCard = m_ParentSets[nChild].getCardinalityOfParents();
728	// update parentsets
729	m_ParentSets[nChild].addParent(nParent, m_Instances);
730	// update distributions
731	int nNewCard = m_ParentSets[nChild].getCardinalityOfParents();
732	Estimator[] ds = new Estimator[nNewCard];
733	for (int iParent = 0; iParent < nNewCard; iParent++) {
734	ds[iParent] = Estimator.clone(m_Distributions[nChild][iParent % nOldCard]);
735	}
736	m_Distributions[nChild] = ds;
737	} // addArc
738
739	/**
740	* Add arc between parent node and each of the nodes in a given list.
741	* Distributions are updated as above.
742	*
743	* @param sParent
744	* name of the parent node
745	* @param nodes
746	* array of indexes of child nodes
747	* @throws Exception
748	*/
749	public void addArc(String sParent, FastVector nodes) throws Exception {
750	int nParent = getNode(sParent);
751	// update undo stack
752	if (m_bNeedsUndoAction) {
753	addUndoAction(new AddArcAction(nParent, nodes));
754	}
755	boolean bNeedsUndoAction = m_bNeedsUndoAction;
756	m_bNeedsUndoAction = false;
757	for (int iNode = 0; iNode < nodes.size(); iNode++) {
758	int nNode = (Integer) nodes.elementAt(iNode);
759	addArc(nParent, nNode);
760	}
761	m_bNeedsUndoAction = bNeedsUndoAction;
762	} // addArc
763
764	/**
765	* Delete arc between two nodes. Distributions are updated by condensing for
766	* the parent node taking its first value.
767	*
768	* @param sParent
769	* name of the parent node
770	* @param sChild
771	* name of the child node
772	* @throws Exception
773	* if parent or child cannot be found in network
774	*/
775	public void deleteArc(String sParent, String sChild) throws Exception {
776	int nParent = getNode(sParent);
777	int nChild = getNode(sChild);
778	deleteArc(nParent, nChild);
779	} // deleteArc
780
781	/**
782	* Delete arc between two nodes. Distributions are updated by condensing for
783	* the parent node taking its first value.
784	*
785	* @param nParent
786	* index of the parent node
787	* @param nChild
788	* index of the child node
789	* @throws Exception
790	*/
791	public void deleteArc(int nParent, int nChild) throws Exception {
792	// update undo stack
793	if (m_bNeedsUndoAction) {
794	addUndoAction(new DeleteArcAction(nParent, nChild));
795	}
796	// update distributions
797	// condense distribution, use values for targetnode = 0
798	int nParentCard = m_ParentSets[nChild].getCardinalityOfParents();
799	int nTargetCard = m_Instances.attribute(nChild).numValues();
800	nParentCard = nParentCard / nTargetCard;
801	Estimator[] distribution2 = new Estimator[nParentCard];
802	for (int iParent = 0; iParent < nParentCard; iParent++) {
803	distribution2[iParent] = m_Distributions[nChild][iParent];
804	}
805	m_Distributions[nChild] = distribution2;
806	// update parentsets
807	m_ParentSets[nChild].deleteParent(nParent, m_Instances);
808	} // deleteArc
809
810
811	/** specify distribution of a node
812	* @param sName name of the node to specify distribution for
813	* @param P matrix representing distribution with P[i][j] = P(node = j \| parent configuration = i)
814	* @throws Exception
815	* if parent or child cannot be found in network
816	*/
817	public void setDistribution(String sName, double[][] P) throws Exception {
818	int nTargetNode = getNode(sName);
819	setDistribution(nTargetNode, P);
820	} // setDistribution
821
822	/** specify distribution of a node
823	* @param nTargetNode index of the node to specify distribution for
824	* @param P matrix representing distribution with P[i][j] = P(node = j \| parent configuration = i)
825	* @throws Exception
826	* if parent or child cannot be found in network
827	*/
828	public void setDistribution(int nTargetNode, double[][] P) throws Exception {
829	// update undo stack
830	if (m_bNeedsUndoAction) {
831	addUndoAction(new SetDistributionAction(nTargetNode, P));
832	}
833	Estimator[] distributions = m_Distributions[nTargetNode];
834	for (int iParent = 0; iParent < distributions.length; iParent++) {
835	DiscreteEstimatorBayes distribution = new DiscreteEstimatorBayes(P[0].length, 0);
836	for (int iValue = 0; iValue < distribution.getNumSymbols(); iValue++) {
837	distribution.addValue(iValue, P[iParent][iValue]);
838	}
839	distributions[iParent] = distribution;
840	}
841	// m_Distributions[nTargetNode] = distributions;
842	} // setDistribution
843
844	/** returns distribution of a node in matrix form with matrix representing distribution
845	* with P[i][j] = P(node = j \| parent configuration = i)
846	* @param sName name of the node to get distribution from
847	*/
848	public double[][] getDistribution(String sName) {
849	int nTargetNode = getNode2(sName);
850	return getDistribution(nTargetNode);
851	} // getDistribution
852
853	/** returns distribution of a node in matrix form with matrix representing distribution
854	* with P[i][j] = P(node = j \| parent configuration = i)
855	* @param nTargetNode index of the node to get distribution from
856	*/
857	public double[][] getDistribution(int nTargetNode) {
858	int nParentCard = m_ParentSets[nTargetNode].getCardinalityOfParents();
859	int nCard = m_Instances.attribute(nTargetNode).numValues();
860	double[][] P = new double[nParentCard][nCard];
861	for (int iParent = 0; iParent < nParentCard; iParent++) {
862	for (int iValue = 0; iValue < nCard; iValue++) {
863	P[iParent][iValue] = m_Distributions[nTargetNode][iParent].getProbability(iValue);
864	}
865	}
866	return P;
867	} // getDistribution
868
869	/** returns array of values of a node
870	* @param sName name of the node to get values from
871	*/
872	public String[] getValues(String sName) {
873	int nTargetNode = getNode2(sName);
874	return getValues(nTargetNode);
875	} // getValues
876
877	/** returns array of values of a node
878	* @param nTargetNode index of the node to get values from
879	*/
880	public String[] getValues(int nTargetNode) {
881	String[] values = new String[getCardinality(nTargetNode)];
882	for (int iValue = 0; iValue < values.length; iValue++) {
883	values[iValue] = m_Instances.attribute(nTargetNode).value(iValue);
884	}
885	return values;
886	} // getValues
887
888	/** returns value of a node
889	* @param nTargetNode index of the node to get values from
890	* @param iValue index of the value
891	*/
892	public String getValueName(int nTargetNode, int iValue) {
893	return m_Instances.attribute(nTargetNode).value(iValue);
894	} // getNodeValue
895
896	/** change the name of a node
897	* @param nTargetNode index of the node to set name for
898	* @param sName new name to assign
899	*/
900	public void setNodeName(int nTargetNode, String sName) {
901	// update undo stack
902	if (m_bNeedsUndoAction) {
903	addUndoAction(new RenameAction(nTargetNode, getNodeName(nTargetNode), sName));
904	}
905	Attribute att = m_Instances.attribute(nTargetNode);
906	int nCardinality = att.numValues();
907	FastVector values = new FastVector(nCardinality);
908	for (int iValue = 0; iValue < nCardinality; iValue++) {
909	values.addElement(att.value(iValue));
910	}
911	replaceAtt(nTargetNode, sName, values);
912	} // setNodeName
913
914	/** change the name of a value of a node
915	* @param nTargetNode index of the node to set name for
916	* @param sValue current name of the value
917	* @param sNewValue new name of the value
918	*/
919	public void renameNodeValue(int nTargetNode, String sValue, String sNewValue) {
920	// update undo stack
921	if (m_bNeedsUndoAction) {
922	addUndoAction(new RenameValueAction(nTargetNode, sValue, sNewValue));
923	}
924	Attribute att = m_Instances.attribute(nTargetNode);
925	int nCardinality = att.numValues();
926	FastVector values = new FastVector(nCardinality);
927	for (int iValue = 0; iValue < nCardinality; iValue++) {
928	if (att.value(iValue).equals(sValue)) {
929	values.addElement(sNewValue);
930	} else {
931	values.addElement(att.value(iValue));
932	}
933	}
934	replaceAtt(nTargetNode, att.name(), values);
935	} // renameNodeValue
936
937
938	/** Add node value to a node. Distributions for the node assign zero probability
939	* to the new value. Child nodes duplicate CPT conditioned on the new value.
940	* @param nTargetNode index of the node to add value for
941	* @param sNewValue name of the value
942	*/
943	public void addNodeValue(int nTargetNode, String sNewValue) {
944	// update undo stack
945	if (m_bNeedsUndoAction) {
946	addUndoAction(new AddValueAction(nTargetNode, sNewValue));
947	}
948	Attribute att = m_Instances.attribute(nTargetNode);
949	int nCardinality = att.numValues();
950	FastVector values = new FastVector(nCardinality);
951	for (int iValue = 0; iValue < nCardinality; iValue++) {
952	values.addElement(att.value(iValue));
953	}
954	values.addElement(sNewValue);
955	replaceAtt(nTargetNode, att.name(), values);
956
957	// update distributions of this node
958	Estimator[] distributions = m_Distributions[nTargetNode];
959	int nNewCard = values.size();
960	for (int iParent = 0; iParent < distributions.length; iParent++) {
961	DiscreteEstimatorBayes distribution = new DiscreteEstimatorBayes(nNewCard, 0);
962	for (int iValue = 0; iValue < nNewCard - 1; iValue++) {
963	distribution.addValue(iValue, distributions[iParent].getProbability(iValue));
964	}
965	distributions[iParent] = distribution;
966	}
967
968	// update distributions of all children
969	for (int iNode = 0; iNode < getNrOfNodes(); iNode++) {
970	if (m_ParentSets[iNode].contains(nTargetNode)) {
971	distributions = m_Distributions[iNode];
972	ParentSet parentSet = m_ParentSets[iNode];
973	int nParentCard = parentSet.getFreshCardinalityOfParents(m_Instances);
974	Estimator[] newDistributions = new Estimator[nParentCard];
975	int nCard = getCardinality(iNode);
976	int nParents = parentSet.getNrOfParents();
977	int[] values2 = new int[nParents];
978	int iOldPos = 0;
979	int iTargetNode = 0;
980	while (parentSet.getParent(iTargetNode) != nTargetNode) {
981	iTargetNode++;
982	}
983	for (int iPos = 0; iPos < nParentCard; iPos++) {
984	DiscreteEstimatorBayes distribution = new DiscreteEstimatorBayes(nCard, 0);
985	for (int iValue = 0; iValue < nCard; iValue++) {
986	distribution.addValue(iValue, distributions[iOldPos].getProbability(iValue));
987	}
988	newDistributions[iPos] = distribution;
989	// update values
990	int i = 0;
991	values2[i]++;
992	while (i < nParents && values2[i] == getCardinality(parentSet.getParent(i))) {
993	values2[i] = 0;
994	i++;
995	if (i < nParents) {
996	values2[i]++;
997	}
998	}
999	if (values2[iTargetNode] != nNewCard - 1) {
1000	iOldPos++;
1001	}
1002	}
1003	m_Distributions[iNode] = newDistributions;
1004	}
1005	}
1006	} // addNodeValue
1007
1008
1009	/** Delete node value from a node. Distributions for the node are scaled
1010	* up proportional to existing distribution
1011	* (or made uniform if zero probability is assigned to remainder of values).
1012	.* Child nodes delete CPTs conditioned on the new value.
1013	* @param nTargetNode index of the node to delete value from
1014	* @param sValue name of the value to delete
1015	*/
1016	public void delNodeValue(int nTargetNode, String sValue) throws Exception {
1017	// update undo stack
1018	if (m_bNeedsUndoAction) {
1019	addUndoAction(new DelValueAction(nTargetNode, sValue));
1020	}
1021	Attribute att = m_Instances.attribute(nTargetNode);
1022	int nCardinality = att.numValues();
1023	FastVector values = new FastVector(nCardinality);
1024	int nValue = -1;
1025	for (int iValue = 0; iValue < nCardinality; iValue++) {
1026	if (att.value(iValue).equals(sValue)) {
1027	nValue = iValue;
1028	} else {
1029	values.addElement(att.value(iValue));
1030	}
1031	}
1032	if (nValue < 0) {
1033	// could not find value
1034	throw new Exception("Node " + nTargetNode + " does not have value (" + sValue + ")");
1035	}
1036	replaceAtt(nTargetNode, att.name(), values);
1037
1038	// update distributions
1039	Estimator[] distributions = m_Distributions[nTargetNode];
1040	int nCard = values.size();
1041	for (int iParent = 0; iParent < distributions.length; iParent++) {
1042	DiscreteEstimatorBayes distribution = new DiscreteEstimatorBayes(nCard, 0);
1043	double sum = 0;
1044	for (int iValue = 0; iValue < nCard; iValue++) {
1045	sum += distributions[iParent].getProbability(iValue);
1046	}
1047	if (sum > 0) {
1048	for (int iValue = 0; iValue < nCard; iValue++) {
1049	distribution.addValue(iValue, distributions[iParent].getProbability(iValue) / sum);
1050	}
1051	} else {
1052	for (int iValue = 0; iValue < nCard; iValue++) {
1053	distribution.addValue(iValue, 1.0 / nCard);
1054	}
1055	}
1056	distributions[iParent] = distribution;
1057	}
1058
1059	// update distributions of all children
1060	for (int iNode = 0; iNode < getNrOfNodes(); iNode++) {
1061	if (m_ParentSets[iNode].contains(nTargetNode)) {
1062	ParentSet parentSet = m_ParentSets[iNode];
1063	distributions = m_Distributions[iNode];
1064	Estimator[] newDistributions = new Estimator[distributions.length * nCard / (nCard + 1)];
1065	int iCurrentDist = 0;
1066
1067	int nParents = parentSet.getNrOfParents();
1068	int[] values2 = new int[nParents];
1069	// fill in the values
1070	int nParentCard = parentSet.getFreshCardinalityOfParents(m_Instances) * (nCard + 1) / nCard;
1071	int iTargetNode = 0;
1072	while (parentSet.getParent(iTargetNode) != nTargetNode) {
1073	iTargetNode++;
1074	}
1075	int[] nCards = new int[nParents];
1076	for (int iParent = 0; iParent < nParents; iParent++) {
1077	nCards[iParent] = getCardinality(parentSet.getParent(iParent));
1078	}
1079	nCards[iTargetNode]++;
1080	for (int iPos = 0; iPos < nParentCard; iPos++) {
1081	if (values2[iTargetNode] != nValue) {
1082	newDistributions[iCurrentDist++] = distributions[iPos];
1083	}
1084	// update values
1085	int i = 0;
1086	values2[i]++;
1087	while (i < nParents && values2[i] == nCards[i]) {
1088	values2[i] = 0;
1089	i++;
1090	if (i < nParents) {
1091	values2[i]++;
1092	}
1093	}
1094	}
1095
1096	m_Distributions[iNode] = newDistributions;
1097	}
1098	}
1099	// update evidence
1100	if (getEvidence(nTargetNode) > nValue) {
1101	setEvidence(nTargetNode, getEvidence(nTargetNode) - 1);
1102	}
1103	} // delNodeValue
1104
1105	/** set position of node
1106	* @param iNode index of node to set position for
1107	* @param nX x position of new position
1108	* @param nY y position of new position
1109	*/
1110	public void setPosition(int iNode, int nX, int nY) {
1111	// update undo stack
1112	if (m_bNeedsUndoAction) {
1113	boolean isUpdate = false;
1114	UndoAction undoAction = null;
1115	try {
1116	if (m_undoStack.size() > 0) {
1117	undoAction = (UndoAction) m_undoStack.elementAt(m_undoStack.size() - 1);
1118	SetPositionAction posAction = (SetPositionAction) undoAction;
1119	if (posAction.m_nTargetNode == iNode) {
1120	isUpdate = true;
1121	posAction.setUndoPosition(nX, nY);
1122	}
1123	}
1124	} catch (Exception e) {
1125	// ignore. it's not a SetPositionAction
1126	}
1127	if (!isUpdate) {
1128	addUndoAction(new SetPositionAction(iNode, nX, nY));
1129	}
1130	}
1131	m_nPositionX.setElementAt(nX, iNode);
1132	m_nPositionY.setElementAt(nY, iNode);
1133	} // setPosition
1134
1135	/** Set position of node. Move set of nodes with the same displacement
1136	* as a specified node.
1137	* @param nNode index of node to set position for
1138	* @param nX x position of new position
1139	* @param nY y position of new position
1140	* @param nodes array of indexes of nodes to move
1141	*/
1142	public void setPosition(int nNode, int nX, int nY, FastVector nodes) {
1143	int dX = nX - getPositionX(nNode);
1144	int dY = nY - getPositionY(nNode);
1145	// update undo stack
1146	if (m_bNeedsUndoAction) {
1147	boolean isUpdate = false;
1148	try {
1149	UndoAction undoAction = null;
1150	if (m_undoStack.size() > 0) {
1151	undoAction = (UndoAction) m_undoStack.elementAt(m_undoStack.size() - 1);
1152	SetGroupPositionAction posAction = (SetGroupPositionAction) undoAction;
1153	isUpdate = true;
1154	int iNode = 0;
1155	while (isUpdate && iNode < posAction.m_nodes.size()) {
1156	if ((Integer)posAction.m_nodes.elementAt(iNode) != (Integer) nodes.elementAt(iNode)) {
1157	isUpdate = false;
1158	}
1159	iNode++;
1160	}
1161	if (isUpdate == true) {
1162	posAction.setUndoPosition(dX, dY);
1163	}
1164	}
1165	} catch (Exception e) {
1166	// ignore. it's not a SetPositionAction
1167	}
1168	if (!isUpdate) {
1169	addUndoAction(new SetGroupPositionAction(nodes, dX, dY));
1170	}
1171	}
1172	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1173	nNode = (Integer) nodes.elementAt(iNode);
1174	m_nPositionX.setElementAt(getPositionX(nNode) + dX, nNode);
1175	m_nPositionY.setElementAt(getPositionY(nNode) + dY, nNode);
1176	}
1177	} // setPosition
1178
1179	/** set positions of all nodes
1180	* @param nPosX new x positions for all nodes
1181	* @param nPosY new y positions for all nodes
1182	*/
1183	public void layoutGraph(FastVector nPosX, FastVector nPosY) {
1184	if (m_bNeedsUndoAction) {
1185	addUndoAction(new LayoutGraphAction(nPosX, nPosY));
1186	}
1187	m_nPositionX = nPosX;
1188	m_nPositionY = nPosY;
1189	} // layoutGraph
1190
1191	/** get x position of a node
1192	* @param iNode index of node of interest
1193	*/
1194	public int getPositionX(int iNode) {
1195	return (Integer) (m_nPositionX.elementAt(iNode));
1196	}
1197
1198	/** get y position of a node
1199	* @param iNode index of node of interest
1200	*/
1201	public int getPositionY(int iNode) {
1202	return (Integer) (m_nPositionY.elementAt(iNode));
1203	}
1204
1205	/** align set of nodes with the left most node in the list
1206	* @param nodes list of indexes of nodes to align
1207	*/
1208	public void alignLeft(FastVector nodes) {
1209	// update undo stack
1210	if (m_bNeedsUndoAction) {
1211	addUndoAction(new alignLeftAction(nodes));
1212	}
1213	int nMinX = -1;
1214	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1215	int nX = getPositionX((Integer) nodes.elementAt(iNode));
1216	if (nX < nMinX \|\| iNode == 0) {
1217	nMinX = nX;
1218	}
1219	}
1220	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1221	int nNode = (Integer) nodes.elementAt(iNode);
1222	m_nPositionX.setElementAt(nMinX, nNode);
1223	}
1224	} // alignLeft
1225
1226	/** align set of nodes with the right most node in the list
1227	* @param nodes list of indexes of nodes to align
1228	*/
1229	public void alignRight(FastVector nodes) {
1230	// update undo stack
1231	if (m_bNeedsUndoAction) {
1232	addUndoAction(new alignRightAction(nodes));
1233	}
1234	int nMaxX = -1;
1235	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1236	int nX = getPositionX((Integer) nodes.elementAt(iNode));
1237	if (nX > nMaxX \|\| iNode == 0) {
1238	nMaxX = nX;
1239	}
1240	}
1241	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1242	int nNode = (Integer) nodes.elementAt(iNode);
1243	m_nPositionX.setElementAt(nMaxX, nNode);
1244	}
1245	} // alignRight
1246
1247	/** align set of nodes with the top most node in the list
1248	* @param nodes list of indexes of nodes to align
1249	*/
1250	public void alignTop(FastVector nodes) {
1251	// update undo stack
1252	if (m_bNeedsUndoAction) {
1253	addUndoAction(new alignTopAction(nodes));
1254	}
1255	int nMinY = -1;
1256	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1257	int nY = getPositionY((Integer) nodes.elementAt(iNode));
1258	if (nY < nMinY \|\| iNode == 0) {
1259	nMinY = nY;
1260	}
1261	}
1262	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1263	int nNode = (Integer) nodes.elementAt(iNode);
1264	m_nPositionY.setElementAt(nMinY, nNode);
1265	}
1266	} // alignTop
1267
1268	/** align set of nodes with the bottom most node in the list
1269	* @param nodes list of indexes of nodes to align
1270	*/
1271	public void alignBottom(FastVector nodes) {
1272	// update undo stack
1273	if (m_bNeedsUndoAction) {
1274	addUndoAction(new alignBottomAction(nodes));
1275	}
1276	int nMaxY = -1;
1277	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1278	int nY = getPositionY((Integer) nodes.elementAt(iNode));
1279	if (nY > nMaxY \|\| iNode == 0) {
1280	nMaxY = nY;
1281	}
1282	}
1283	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1284	int nNode = (Integer) nodes.elementAt(iNode);
1285	m_nPositionY.setElementAt(nMaxY, nNode);
1286	}
1287	} // alignBottom
1288
1289	/** center set of nodes half way between left and right most node in the list
1290	* @param nodes list of indexes of nodes to center
1291	*/
1292	public void centerHorizontal(FastVector nodes) {
1293	// update undo stack
1294	if (m_bNeedsUndoAction) {
1295	addUndoAction(new centerHorizontalAction(nodes));
1296	}
1297	int nMinY = -1;
1298	int nMaxY = -1;
1299	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1300	int nY = getPositionY((Integer) nodes.elementAt(iNode));
1301	if (nY < nMinY \|\| iNode == 0) {
1302	nMinY = nY;
1303	}
1304	if (nY > nMaxY \|\| iNode == 0) {
1305	nMaxY = nY;
1306	}
1307	}
1308	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1309	int nNode = (Integer) nodes.elementAt(iNode);
1310	m_nPositionY.setElementAt((nMinY + nMaxY) / 2, nNode);
1311	}
1312	} // centerHorizontal
1313
1314	/** center set of nodes half way between top and bottom most node in the list
1315	* @param nodes list of indexes of nodes to center
1316	*/
1317	public void centerVertical(FastVector nodes) {
1318	// update undo stack
1319	if (m_bNeedsUndoAction) {
1320	addUndoAction(new centerVerticalAction(nodes));
1321	}
1322	int nMinX = -1;
1323	int nMaxX = -1;
1324	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1325	int nX = getPositionX((Integer) nodes.elementAt(iNode));
1326	if (nX < nMinX \|\| iNode == 0) {
1327	nMinX = nX;
1328	}
1329	if (nX > nMaxX \|\| iNode == 0) {
1330	nMaxX = nX;
1331	}
1332	}
1333	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1334	int nNode = (Integer) nodes.elementAt(iNode);
1335	m_nPositionX.setElementAt((nMinX + nMaxX) / 2, nNode);
1336	}
1337	} // centerVertical
1338
1339	/** space out set of nodes evenly between left and right most node in the list
1340	* @param nodes list of indexes of nodes to space out
1341	*/
1342	public void spaceHorizontal(FastVector nodes) {
1343	// update undo stack
1344	if (m_bNeedsUndoAction) {
1345	addUndoAction(new spaceHorizontalAction(nodes));
1346	}
1347	int nMinX = -1;
1348	int nMaxX = -1;
1349	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1350	int nX = getPositionX((Integer) nodes.elementAt(iNode));
1351	if (nX < nMinX \|\| iNode == 0) {
1352	nMinX = nX;
1353	}
1354	if (nX > nMaxX \|\| iNode == 0) {
1355	nMaxX = nX;
1356	}
1357	}
1358	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1359	int nNode = (Integer) nodes.elementAt(iNode);
1360	m_nPositionX.setElementAt((int) (nMinX + iNode * (nMaxX - nMinX) / (nodes.size() - 1.0)), nNode);
1361	}
1362	} // spaceHorizontal
1363
1364	/** space out set of nodes evenly between top and bottom most node in the list
1365	* @param nodes list of indexes of nodes to space out
1366	*/
1367	public void spaceVertical(FastVector nodes) {
1368	// update undo stack
1369	if (m_bNeedsUndoAction) {
1370	addUndoAction(new spaceVerticalAction(nodes));
1371	}
1372	int nMinY = -1;
1373	int nMaxY = -1;
1374	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1375	int nY = getPositionY((Integer) nodes.elementAt(iNode));
1376	if (nY < nMinY \|\| iNode == 0) {
1377	nMinY = nY;
1378	}
1379	if (nY > nMaxY \|\| iNode == 0) {
1380	nMaxY = nY;
1381	}
1382	}
1383	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1384	int nNode = (Integer) nodes.elementAt(iNode);
1385	m_nPositionY.setElementAt((int) (nMinY + iNode * (nMaxY - nMinY) / (nodes.size() - 1.0)), nNode);
1386	}
1387	} // spaceVertical
1388
1389
1390	/** replace attribute with specified name and values
1391	* @param nTargetNode index of node the replace specification for
1392	* @param sName new name of the node
1393	* @param values array of values of the node
1394	*/
1395	void replaceAtt(int nTargetNode, String sName, FastVector values) {
1396	Attribute newAtt = new Attribute(sName, values);
1397	if (m_Instances.classIndex() == nTargetNode) {
1398	m_Instances.setClassIndex(-1);
1399	m_Instances.insertAttributeAt(newAtt, nTargetNode);
1400	m_Instances.deleteAttributeAt(nTargetNode + 1);
1401	m_Instances.setClassIndex(nTargetNode);
1402	} else {
1403	m_Instances.insertAttributeAt(newAtt, nTargetNode);
1404	m_Instances.deleteAttributeAt(nTargetNode + 1);
1405	}
1406	} // replaceAtt
1407
1408	/** return marginal distibution for a node
1409	* @param iNode index of node of interest
1410	*/
1411	public double[] getMargin(int iNode) {
1412	return (double[]) m_fMarginP.elementAt(iNode);
1413	};
1414
1415	/** set marginal distibution for a node
1416	* @param iNode index of node to set marginal distribution for
1417	* @param fMarginP marginal distribution
1418	*/
1419	public void setMargin(int iNode, double[] fMarginP) {
1420	m_fMarginP.setElementAt(fMarginP, iNode);
1421	}
1422
1423	/** get evidence state of a node. -1 represents no evidence set, otherwise
1424	* the index of a value of the node
1425	* @param iNode index of node of interest
1426	*/
1427	public int getEvidence(int iNode) {
1428	return (Integer) m_nEvidence.elementAt(iNode);
1429	}
1430
1431	/** set evidence state of a node. -1 represents no evidence set, otherwise
1432	* the index of a value of the node
1433	* @param iNode index of node of interest
1434	* @param iValue evidence value to set
1435	*/
1436	public void setEvidence(int iNode, int iValue) {
1437	m_nEvidence.setElementAt(iValue, iNode);
1438	}
1439
1440	/** return list of children of a node
1441	* @param nTargetNode index of node of interest
1442	*/
1443	public FastVector getChildren(int nTargetNode) {
1444	FastVector children = new FastVector();
1445	for (int iNode = 0; iNode < getNrOfNodes(); iNode++) {
1446	if (m_ParentSets[iNode].contains(nTargetNode)) {
1447	children.addElement(iNode);
1448	}
1449	}
1450	return children;
1451	} // getChildren
1452
1453	/** returns network in XMLBIF format
1454	*/
1455	public String toXMLBIF03() {
1456	if (m_Instances == null) {
1457	return ("<!--No model built yet-->");
1458	}
1459
1460	StringBuffer text = new StringBuffer();
1461	text.append(getBIFHeader());
1462	text.append("\n");
1463	text.append("\n");
1464	text.append("<BIF VERSION=\"0.3\">\n");
1465	text.append("<NETWORK>\n");
1466	text.append("<NAME>" + XMLNormalize(m_Instances.relationName()) + "</NAME>\n");
1467	for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) {
1468	text.append("<VARIABLE TYPE=\"nature\">\n");
1469	text.append("<NAME>" + XMLNormalize(m_Instances.attribute(iAttribute).name()) + "</NAME>\n");
1470	for (int iValue = 0; iValue < m_Instances.attribute(iAttribute).numValues(); iValue++) {
1471	text.append("<OUTCOME>" + XMLNormalize(m_Instances.attribute(iAttribute).value(iValue))
1472	+ "</OUTCOME>\n");
1473	}
1474	text.append("<PROPERTY>position = (" + getPositionX(iAttribute) + "," + getPositionY(iAttribute)
1475	+ ")</PROPERTY>\n");
1476	text.append("</VARIABLE>\n");
1477	}
1478
1479	for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) {
1480	text.append("<DEFINITION>\n");
1481	text.append("<FOR>" + XMLNormalize(m_Instances.attribute(iAttribute).name()) + "</FOR>\n");
1482	for (int iParent = 0; iParent < m_ParentSets[iAttribute].getNrOfParents(); iParent++) {
1483	text.append("<GIVEN>"
1484	+ XMLNormalize(m_Instances.attribute(m_ParentSets[iAttribute].getParent(iParent)).name())
1485	+ "</GIVEN>\n");
1486	}
1487	text.append("<TABLE>\n");
1488	for (int iParent = 0; iParent < m_ParentSets[iAttribute].getCardinalityOfParents(); iParent++) {
1489	for (int iValue = 0; iValue < m_Instances.attribute(iAttribute).numValues(); iValue++) {
1490	text.append(m_Distributions[iAttribute][iParent].getProbability(iValue));
1491	text.append(' ');
1492	}
1493	text.append('\n');
1494	}
1495	text.append("</TABLE>\n");
1496	text.append("</DEFINITION>\n");
1497	}
1498	text.append("</NETWORK>\n");
1499	text.append("</BIF>\n");
1500	return text.toString();
1501	} // toXMLBIF03
1502
1503	/** return fragment of network in XMLBIF format
1504	* @param nodes array of indexes of nodes that should be in the fragment
1505	*/
1506	public String toXMLBIF03(FastVector nodes) {
1507	StringBuffer text = new StringBuffer();
1508	text.append(getBIFHeader());
1509	text.append("\n");
1510	text.append("\n");
1511	text.append("<BIF VERSION=\"0.3\">\n");
1512	text.append("<NETWORK>\n");
1513	text.append("<NAME>" + XMLNormalize(m_Instances.relationName()) + "</NAME>\n");
1514	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1515	int nNode = (Integer) nodes.elementAt(iNode);
1516	text.append("<VARIABLE TYPE=\"nature\">\n");
1517	text.append("<NAME>" + XMLNormalize(m_Instances.attribute(nNode).name()) + "</NAME>\n");
1518	for (int iValue = 0; iValue < m_Instances.attribute(nNode).numValues(); iValue++) {
1519	text.append("<OUTCOME>" + XMLNormalize(m_Instances.attribute(nNode).value(iValue)) + "</OUTCOME>\n");
1520	}
1521	text.append("<PROPERTY>position = (" + getPositionX(nNode) + "," + getPositionY(nNode) + ")</PROPERTY>\n");
1522	text.append("</VARIABLE>\n");
1523	}
1524
1525	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1526	int nNode = (Integer) nodes.elementAt(iNode);
1527	text.append("<DEFINITION>\n");
1528	text.append("<FOR>" + XMLNormalize(m_Instances.attribute(nNode).name()) + "</FOR>\n");
1529	for (int iParent = 0; iParent < m_ParentSets[nNode].getNrOfParents(); iParent++) {
1530	text.append("<GIVEN>"
1531	+ XMLNormalize(m_Instances.attribute(m_ParentSets[nNode].getParent(iParent)).name())
1532	+ "</GIVEN>\n");
1533	}
1534	text.append("<TABLE>\n");
1535	for (int iParent = 0; iParent < m_ParentSets[nNode].getCardinalityOfParents(); iParent++) {
1536	for (int iValue = 0; iValue < m_Instances.attribute(nNode).numValues(); iValue++) {
1537	text.append(m_Distributions[nNode][iParent].getProbability(iValue));
1538	text.append(' ');
1539	}
1540	text.append('\n');
1541	}
1542	text.append("</TABLE>\n");
1543	text.append("</DEFINITION>\n");
1544	}
1545	text.append("</NETWORK>\n");
1546	text.append("</BIF>\n");
1547	return text.toString();
1548	} // toXMLBIF03
1549
1550	/** undo stack for undoin edit actions, or redo edit actions */
1551	FastVector m_undoStack = new FastVector();
1552
1553	/** current action in undo stack */
1554	int m_nCurrentEditAction = -1;
1555
1556	/** action that the network is saved */
1557	int m_nSavedPointer = -1;
1558
1559	/***************************************************************************
1560	* flag to indicate whether an edit action needs to introduce an undo
1561	* action. This is only false when an undo or redo action is performed.
1562	**************************************************************************/
1563	boolean m_bNeedsUndoAction = true;
1564
1565	/** return whether there is something on the undo stack that can be performed */
1566	public boolean canUndo() {
1567	return m_nCurrentEditAction >= 0;
1568	}
1569
1570	/** return whether there is something on the undo stack that can be performed */
1571	public boolean canRedo() {
1572	return m_nCurrentEditAction < m_undoStack.size() - 1;
1573	}
1574
1575	/** return true when current state differs from the state the network was last saved */
1576	public boolean isChanged() {
1577	return m_nCurrentEditAction != m_nSavedPointer;
1578	}
1579
1580	/** indicate the network state was saved */
1581	public void isSaved() {
1582	m_nSavedPointer = m_nCurrentEditAction;
1583	}
1584
1585	/** get message representing the last action performed on the network */
1586	public String lastActionMsg() {
1587	if (m_undoStack.size() == 0) {
1588	return "";
1589	}
1590	return ((UndoAction) m_undoStack.lastElement()).getRedoMsg();
1591	} // lastActionMsg
1592
1593
1594	/** undo the last edit action performed on the network.
1595	* returns message representing the action performed.
1596	*/
1597	public String undo() {
1598	if (!canUndo()) {
1599	return "";
1600	}
1601	UndoAction undoAction = (UndoAction) m_undoStack.elementAt(m_nCurrentEditAction);
1602	m_bNeedsUndoAction = false;
1603	undoAction.undo();
1604	m_bNeedsUndoAction = true;
1605	m_nCurrentEditAction--;
1606
1607	// undo stack debugging
1608	/*
1609	if (m_nCurrentEditAction>0) {
1610	String sXML = (String) m_sXMLStack.elementAt(m_nCurrentEditAction);
1611	String sXMLCurrent = toXMLBIF03();
1612	if (!sXML.equals(sXMLCurrent)) {
1613	String sDiff = "";
1614	String sDiff2 = "";
1615	for (int i = 0; i < sXML.length() && sDiff.length() < 80; i++) {
1616	if (sXML.charAt(i) != sXMLCurrent.charAt(i)) {
1617	sDiff += sXML.charAt(i);
1618	sDiff2 += sXMLCurrent.charAt(i);
1619	}
1620	}
1621
1622	JOptionPane.showMessageDialog(null,"Undo error\n" + sDiff + " \n" + sDiff2);
1623	}
1624	}
1625	*/
1626	return undoAction.getUndoMsg();
1627	} // undo
1628
1629	/** redo the last edit action performed on the network.
1630	* returns message representing the action performed.
1631	*/
1632	public String redo() {
1633	if (!canRedo()) {
1634	return "";
1635	}
1636	m_nCurrentEditAction++;
1637	UndoAction undoAction = (UndoAction) m_undoStack.elementAt(m_nCurrentEditAction);
1638	m_bNeedsUndoAction = false;
1639	undoAction.redo();
1640	m_bNeedsUndoAction = true;
1641
1642	// undo stack debugging
1643	/*
1644	if (m_nCurrentEditAction < m_sXMLStack.size()) {
1645	String sXML = (String) m_sXMLStack.elementAt(m_nCurrentEditAction);
1646	String sXMLCurrent = toXMLBIF03();
1647	if (!sXML.equals(sXMLCurrent)) {
1648	String sDiff = "";
1649	String sDiff2 = "";
1650	for (int i = 0; i < sXML.length() && sDiff.length() < 80; i++) {
1651	if (sXML.charAt(i) != sXMLCurrent.charAt(i)) {
1652	sDiff += sXML.charAt(i);
1653	sDiff2 += sXMLCurrent.charAt(i);
1654	}
1655	}
1656
1657	JOptionPane.showMessageDialog(null,"redo error\n" + sDiff + " \n" + sDiff2);
1658	}
1659	}
1660	*/
1661	return undoAction.getRedoMsg();
1662	} // redo
1663
1664	/** add undo action to the undo stack.
1665	* @param action operation that needs to be added to the undo stack
1666	*/
1667	void addUndoAction(UndoAction action) {
1668	int iAction = m_undoStack.size() - 1;
1669	while (iAction > m_nCurrentEditAction) {
1670	m_undoStack.removeElementAt(iAction--);
1671	}
1672	if (m_nSavedPointer > m_nCurrentEditAction) {
1673	m_nSavedPointer = -2;
1674	}
1675	m_undoStack.addElement(action);
1676	//m_sXMLStack.addElement(toXMLBIF03());
1677	m_nCurrentEditAction++;
1678	} // addUndoAction
1679
1680	/** remove all actions from the undo stack */
1681	public void clearUndoStack() {
1682	m_undoStack = new FastVector();
1683	//m_sXMLStack = new FastVector();
1684	m_nCurrentEditAction = -1;
1685	m_nSavedPointer = -1;
1686	} // clearUndoStack
1687
1688	/** base class for actions representing operations on the Bayesian network
1689	* that can be undone/redone
1690	*/
1691	class UndoAction implements Serializable {
1692	/** for serialization */
1693	static final long serialVersionUID = 1;
1694	public void undo() {
1695	}
1696
1697	public void redo() {
1698	}
1699
1700	public String getUndoMsg() {
1701	return getMsg();
1702	}
1703
1704	public String getRedoMsg() {
1705	return getMsg();
1706	}
1707	String getMsg() {
1708	String sStr = toString();
1709	int iStart = sStr.indexOf('$');
1710	int iEnd = sStr.indexOf('@');
1711	StringBuffer sBuffer = new StringBuffer();
1712	for(int i= iStart + 1; i < iEnd; i++) {
1713	char c = sStr.charAt(i);
1714	if (Character.isUpperCase(c)) {
1715	sBuffer.append(' ');
1716	}
1717	sBuffer.append(sStr.charAt(i));
1718	}
1719	return sBuffer.toString();
1720	} // getMsg
1721	} // class UndoAction
1722
1723	class AddNodeAction extends UndoAction {
1724	/** for serialization */
1725	static final long serialVersionUID = 1;
1726	String m_sName;
1727	int m_nPosX;
1728	int m_nPosY;
1729
1730	int m_nCardinality;
1731
1732	AddNodeAction(String sName, int nCardinality, int nPosX, int nPosY) {
1733	m_sName = sName;
1734	m_nCardinality = nCardinality;
1735	m_nPosX = nPosX;
1736	m_nPosY = nPosY;
1737	} // c'tor
1738
1739	public void undo() {
1740	try {
1741	deleteNode(getNrOfNodes() - 1);
1742	} catch (Exception e) {
1743	e.printStackTrace();
1744	}
1745	} // undo
1746
1747	public void redo() {
1748	try {
1749	addNode(m_sName, m_nCardinality, m_nPosX, m_nPosY);
1750	} catch (Exception e) {
1751	e.printStackTrace();
1752	}
1753	} // redo
1754	} // class AddNodeAction
1755
1756	class DeleteNodeAction extends UndoAction {
1757	/** for serialization */
1758	static final long serialVersionUID = 1;
1759	int m_nTargetNode;
1760
1761	Attribute m_att;
1762
1763	Estimator[] m_CPT;
1764
1765	ParentSet m_ParentSet;
1766
1767	FastVector m_deleteArcActions;
1768
1769	int m_nPosX;
1770
1771	int m_nPosY;
1772
1773	DeleteNodeAction(int nTargetNode) {
1774	m_nTargetNode = nTargetNode;
1775	m_att = m_Instances.attribute(nTargetNode);
1776	try {
1777	SerializedObject so = new SerializedObject(m_Distributions[nTargetNode]);
1778	m_CPT = (Estimator[]) so.getObject();
1779	;
1780	so = new SerializedObject(m_ParentSets[nTargetNode]);
1781	m_ParentSet = (ParentSet) so.getObject();
1782	} catch (Exception e) {
1783	e.printStackTrace();
1784	}
1785	m_deleteArcActions = new FastVector();
1786	for (int iNode = 0; iNode < getNrOfNodes(); iNode++) {
1787	if (m_ParentSets[iNode].contains(nTargetNode)) {
1788	m_deleteArcActions.addElement(new DeleteArcAction(nTargetNode, iNode));
1789	}
1790	}
1791	m_nPosX = getPositionX(m_nTargetNode);
1792	m_nPosY = getPositionY(m_nTargetNode);
1793	} // c'tor
1794
1795	public void undo() {
1796	try {
1797	m_Instances.insertAttributeAt(m_att, m_nTargetNode);
1798	int nAtts = m_Instances.numAttributes();
1799	// update parentsets
1800	ParentSet[] parentSets = new ParentSet[nAtts];
1801	int nX = 0;
1802	for (int iParentSet = 0; iParentSet < nAtts; iParentSet++) {
1803	if (iParentSet == m_nTargetNode) {
1804	SerializedObject so = new SerializedObject(m_ParentSet);
1805	parentSets[iParentSet] = (ParentSet) so.getObject();
1806	nX = 1;
1807	} else {
1808	parentSets[iParentSet] = m_ParentSets[iParentSet - nX];
1809	for (int iParent = 0; iParent < parentSets[iParentSet].getNrOfParents(); iParent++) {
1810	int nParent = parentSets[iParentSet].getParent(iParent);
1811	if (nParent >= m_nTargetNode) {
1812	parentSets[iParentSet].SetParent(iParent, nParent + 1);
1813	}
1814	}
1815	}
1816	}
1817	m_ParentSets = parentSets;
1818	// update distributions
1819	Estimator[][] distributions = new Estimator[nAtts][];
1820	nX = 0;
1821	for (int iNode = 0; iNode < nAtts; iNode++) {
1822	if (iNode == m_nTargetNode) {
1823	SerializedObject so = new SerializedObject(m_CPT);
1824	distributions[iNode] = (Estimator[]) so.getObject();
1825	nX = 1;
1826	} else {
1827	distributions[iNode] = m_Distributions[iNode - nX];
1828	}
1829	}
1830	m_Distributions = distributions;
1831
1832	for (int deletedArc = 0; deletedArc < m_deleteArcActions.size(); deletedArc++) {
1833	DeleteArcAction action = (DeleteArcAction) m_deleteArcActions.elementAt(deletedArc);
1834	action.undo();
1835	}
1836	m_nPositionX.insertElementAt(m_nPosX, m_nTargetNode);
1837	m_nPositionY.insertElementAt(m_nPosY, m_nTargetNode);
1838	m_nEvidence.insertElementAt(-1, m_nTargetNode);
1839	m_fMarginP.insertElementAt(new double[getCardinality(m_nTargetNode)], m_nTargetNode);
1840	} catch (Exception e) {
1841	e.printStackTrace();
1842	}
1843	} // undo
1844
1845	public void redo() {
1846	try {
1847	deleteNode(m_nTargetNode);
1848	} catch (Exception e) {
1849	e.printStackTrace();
1850	}
1851	} // redo
1852	} // class DeleteNodeAction
1853
1854	class DeleteSelectionAction extends UndoAction {
1855	/** for serialization */
1856	static final long serialVersionUID = 1;
1857	FastVector m_nodes;
1858
1859	Attribute[] m_att;
1860
1861	Estimator[][] m_CPT;
1862
1863	ParentSet[] m_ParentSet;
1864
1865	FastVector m_deleteArcActions;
1866
1867	int[] m_nPosX;
1868
1869	int[] m_nPosY;
1870
1871	public DeleteSelectionAction(FastVector nodes) {
1872	m_nodes = new FastVector();
1873	int nNodes = nodes.size();
1874	m_att = new Attribute[nNodes];
1875	m_CPT = new Estimator[nNodes][];
1876	m_ParentSet = new ParentSet[nNodes];
1877	m_nPosX = new int[nNodes];
1878	m_nPosY = new int[nNodes];
1879	m_deleteArcActions = new FastVector();
1880	for (int iNode = 0; iNode < nodes.size(); iNode++) {
1881	int nTargetNode = (Integer) nodes.elementAt(iNode);
1882	m_nodes.addElement(nTargetNode);
1883	m_att[iNode] = m_Instances.attribute(nTargetNode);
1884	try {
1885	SerializedObject so = new SerializedObject(m_Distributions[nTargetNode]);
1886	m_CPT[iNode] = (Estimator[]) so.getObject();
1887	;
1888	so = new SerializedObject(m_ParentSets[nTargetNode]);
1889	m_ParentSet[iNode] = (ParentSet) so.getObject();
1890	} catch (Exception e) {
1891	e.printStackTrace();
1892	}
1893	m_nPosX[iNode] = getPositionX(nTargetNode);
1894	m_nPosY[iNode] = getPositionY(nTargetNode);
1895	for (int iNode2 = 0; iNode2 < getNrOfNodes(); iNode2++) {
1896	if (!nodes.contains(iNode2) && m_ParentSets[iNode2].contains(nTargetNode)) {
1897	m_deleteArcActions.addElement(new DeleteArcAction(nTargetNode, iNode2));
1898	}
1899	}
1900	}
1901	} // c'tor
1902
1903	public void undo() {
1904	try {
1905	for (int iNode = 0; iNode < m_nodes.size(); iNode++) {
1906	int nTargetNode = (Integer) m_nodes.elementAt(iNode);
1907	m_Instances.insertAttributeAt(m_att[iNode], nTargetNode);
1908	}
1909	int nAtts = m_Instances.numAttributes();
1910	// update parentsets
1911	ParentSet[] parentSets = new ParentSet[nAtts];
1912	int[] offset = new int[nAtts];
1913	for (int iNode = 0; iNode < nAtts; iNode++) {
1914	offset[iNode] = iNode;
1915	}
1916	for (int iNode = m_nodes.size() - 1; iNode >= 0; iNode--) {
1917	int nTargetNode = (Integer) m_nodes.elementAt(iNode);
1918	for (int i = nTargetNode; i < nAtts - 1; i++) {
1919	offset[i] = offset[i + 1];
1920	}
1921	}
1922
1923	int iTargetNode = 0;
1924	for (int iParentSet = 0; iParentSet < nAtts; iParentSet++) {
1925	if (iTargetNode < m_nodes.size()
1926	&& (Integer) m_nodes.elementAt(iTargetNode) == (Integer) iParentSet) {
1927	SerializedObject so = new SerializedObject(m_ParentSet[iTargetNode]);
1928	parentSets[iParentSet] = (ParentSet) so.getObject();
1929	iTargetNode++;
1930	} else {
1931	parentSets[iParentSet] = m_ParentSets[iParentSet - iTargetNode];
1932	for (int iParent = 0; iParent < parentSets[iParentSet].getNrOfParents(); iParent++) {
1933	int nParent = parentSets[iParentSet].getParent(iParent);
1934	parentSets[iParentSet].SetParent(iParent, offset[nParent]);
1935	}
1936	}
1937	}
1938	m_ParentSets = parentSets;
1939	// update distributions
1940	Estimator[][] distributions = new Estimator[nAtts][];
1941	iTargetNode = 0;
1942	for (int iNode = 0; iNode < nAtts; iNode++) {
1943	if (iTargetNode < m_nodes.size() && (Integer) m_nodes.elementAt(iTargetNode) == (Integer) iNode) {
1944	SerializedObject so = new SerializedObject(m_CPT[iTargetNode]);
1945	distributions[iNode] = (Estimator[]) so.getObject();
1946	iTargetNode++;
1947	} else {
1948	distributions[iNode] = m_Distributions[iNode - iTargetNode];
1949	}
1950	}
1951	m_Distributions = distributions;
1952
1953	for (int iNode = 0; iNode < m_nodes.size(); iNode++) {
1954	int nTargetNode = (Integer) m_nodes.elementAt(iNode);
1955	m_nPositionX.insertElementAt(m_nPosX[iNode], nTargetNode);
1956	m_nPositionY.insertElementAt(m_nPosY[iNode], nTargetNode);
1957	m_nEvidence.insertElementAt(-1, nTargetNode);
1958	m_fMarginP.insertElementAt(new double[getCardinality(nTargetNode)], nTargetNode);
1959	}
1960	for (int deletedArc = 0; deletedArc < m_deleteArcActions.size(); deletedArc++) {
1961	DeleteArcAction action = (DeleteArcAction) m_deleteArcActions.elementAt(deletedArc);
1962	action.undo();
1963	}
1964	} catch (Exception e) {
1965	e.printStackTrace();
1966	}
1967	} // undo
1968
1969	public void redo() {
1970	try {
1971	for (int iNode = m_nodes.size() - 1; iNode >= 0; iNode--) {
1972	int nNode = (Integer) m_nodes.elementAt(iNode);
1973	deleteNode(nNode);
1974	}
1975	} catch (Exception e) {
1976	e.printStackTrace();
1977	}
1978	} // redo
1979	} // class DeleteSelectionAction
1980
1981	class AddArcAction extends UndoAction {
1982	/** for serialization */
1983	static final long serialVersionUID = 1;
1984	//int m_nChild;
1985	FastVector m_children;
1986
1987	int m_nParent;
1988
1989	Estimator[][] m_CPT;
1990
1991	AddArcAction(int nParent, int nChild) {
1992	try {
1993	m_nParent = nParent;
1994	m_children = new FastVector();
1995	m_children.addElement(nChild);
1996	//m_nChild = nChild;
1997	SerializedObject so = new SerializedObject(m_Distributions[nChild]);
1998	m_CPT = new Estimator[1][];
1999	m_CPT[0] = (Estimator[]) so.getObject();
2000	;
2001	} catch (Exception e) {
2002	e.printStackTrace();
2003	}
2004	} // c'tor
2005
2006	AddArcAction(int nParent, FastVector children) {
2007	try {
2008	m_nParent = nParent;
2009	m_children = new FastVector();
2010	m_CPT = new Estimator[children.size()][];
2011	for (int iChild = 0; iChild < children.size(); iChild++) {
2012	int nChild = (Integer) children.elementAt(iChild);
2013	m_children.addElement(nChild);
2014	SerializedObject so = new SerializedObject(m_Distributions[nChild]);
2015	m_CPT[iChild] = (Estimator[]) so.getObject();
2016	}
2017	} catch (Exception e) {
2018	e.printStackTrace();
2019	}
2020	} // c'tor
2021
2022	public void undo() {
2023	try {
2024	for (int iChild = 0; iChild < m_children.size(); iChild++) {
2025	int nChild = (Integer) m_children.elementAt(iChild);
2026	deleteArc(m_nParent, nChild);
2027	SerializedObject so = new SerializedObject(m_CPT[iChild]);
2028	m_Distributions[nChild] = (Estimator[]) so.getObject();
2029	}
2030	} catch (Exception e) {
2031	e.printStackTrace();
2032	}
2033	} // undo
2034
2035	public void redo() {
2036	try {
2037	for (int iChild = 0; iChild < m_children.size(); iChild++) {
2038	int nChild = (Integer) m_children.elementAt(iChild);
2039	addArc(m_nParent, nChild);
2040	}
2041	} catch (Exception e) {
2042	e.printStackTrace();
2043	}
2044	} // redo
2045	} // class AddArcAction
2046
2047	class DeleteArcAction extends UndoAction {
2048	/** for serialization */
2049	static final long serialVersionUID = 1;
2050	int[] m_nParents;
2051	int m_nChild;
2052	int m_nParent;
2053	Estimator[] m_CPT;
2054
2055	DeleteArcAction(int nParent, int nChild) {
2056	try {
2057	m_nChild = nChild;
2058	m_nParent = nParent;
2059	m_nParents = new int[getNrOfParents(nChild)];
2060	for (int iParent = 0; iParent < m_nParents.length; iParent++) {
2061	m_nParents[iParent] = getParent(nChild, iParent);
2062	}
2063	SerializedObject so = new SerializedObject(m_Distributions[nChild]);
2064	m_CPT = (Estimator[]) so.getObject();
2065	} catch (Exception e) {
2066	e.printStackTrace();
2067	}
2068	} // c'tor
2069
2070	public void undo() {
2071	try {
2072	SerializedObject so = new SerializedObject(m_CPT);
2073	m_Distributions[m_nChild] = (Estimator[]) so.getObject();
2074	ParentSet parentSet = new ParentSet();
2075	for (int iParent = 0; iParent < m_nParents.length; iParent++) {
2076	parentSet.addParent(m_nParents[iParent], m_Instances);
2077	}
2078	m_ParentSets[m_nChild] = parentSet;
2079	} catch (Exception e) {
2080	e.printStackTrace();
2081	}
2082	} // undo
2083
2084	public void redo() {
2085	try {
2086	deleteArc(m_nParent, m_nChild);
2087	} catch (Exception e) {
2088	e.printStackTrace();
2089	}
2090	} // redo
2091	} // class DeleteArcAction
2092
2093	class SetDistributionAction extends UndoAction {
2094	/** for serialization */
2095	static final long serialVersionUID = 1;
2096	int m_nTargetNode;
2097
2098	Estimator[] m_CPT;
2099
2100	double[][] m_P;
2101
2102	SetDistributionAction(int nTargetNode, double[][] P) {
2103	try {
2104	m_nTargetNode = nTargetNode;
2105	SerializedObject so = new SerializedObject(m_Distributions[nTargetNode]);
2106	m_CPT = (Estimator[]) so.getObject();
2107	;
2108	m_P = P;
2109	} catch (Exception e) {
2110	e.printStackTrace();
2111	}
2112	} // c'tor
2113
2114	public void undo() {
2115	try {
2116	SerializedObject so = new SerializedObject(m_CPT);
2117	m_Distributions[m_nTargetNode] = (Estimator[]) so.getObject();
2118	} catch (Exception e) {
2119	e.printStackTrace();
2120	}
2121	} // undo
2122
2123	public void redo() {
2124	try {
2125	setDistribution(m_nTargetNode, m_P);
2126	} catch (Exception e) {
2127	e.printStackTrace();
2128	}
2129	} // redo
2130
2131	public String getUndoMsg() {
2132	return "Distribution of node " + getNodeName(m_nTargetNode) + " changed";
2133	}
2134
2135	public String getRedoMsg() {
2136	return "Distribution of node " + getNodeName(m_nTargetNode) + " changed";
2137	}
2138	} // class SetDistributionAction
2139
2140	class RenameAction extends UndoAction {
2141	/** for serialization */
2142	static final long serialVersionUID = 1;
2143	int m_nTargetNode;
2144
2145	String m_sNewName;
2146
2147	String m_sOldName;
2148
2149	RenameAction(int nTargetNode, String sOldName, String sNewName) {
2150	m_nTargetNode = nTargetNode;
2151	m_sNewName = sNewName;
2152	m_sOldName = sOldName;
2153	} // c'tor
2154
2155	public void undo() {
2156	setNodeName(m_nTargetNode, m_sOldName);
2157	} // undo
2158
2159	public void redo() {
2160	setNodeName(m_nTargetNode, m_sNewName);
2161	} // redo
2162	} // class RenameAction
2163
2164	class RenameValueAction extends RenameAction {
2165	/** for serialization */
2166	static final long serialVersionUID = 1;
2167	RenameValueAction(int nTargetNode, String sOldName, String sNewName) {
2168	super(nTargetNode, sOldName, sNewName);
2169	} // c'tor
2170
2171	public void undo() {
2172	renameNodeValue(m_nTargetNode, m_sNewName, m_sOldName);
2173	} // undo
2174
2175	public void redo() {
2176	renameNodeValue(m_nTargetNode, m_sOldName, m_sNewName);
2177	} // redo
2178
2179	public String getUndoMsg() {
2180	return "Value of node " + getNodeName(m_nTargetNode) + " changed from " + m_sNewName + " to " + m_sOldName;
2181	}
2182
2183	public String getRedoMsg() {
2184	return "Value of node " + getNodeName(m_nTargetNode) + " changed from " + m_sOldName + " to " + m_sNewName;
2185	}
2186	} // class RenameValueAction
2187
2188	class AddValueAction extends UndoAction {
2189	/** for serialization */
2190	static final long serialVersionUID = 1;
2191	int m_nTargetNode;
2192
2193	String m_sValue;
2194
2195	AddValueAction(int nTargetNode, String sValue) {
2196	m_nTargetNode = nTargetNode;
2197	m_sValue = sValue;
2198	} // c'tor
2199
2200	public void undo() {
2201	try {
2202	delNodeValue(m_nTargetNode, m_sValue);
2203	} catch (Exception e) {
2204	e.printStackTrace();
2205	}
2206	} // undo
2207
2208	public void redo() {
2209	addNodeValue(m_nTargetNode, m_sValue);
2210	} // redo
2211
2212	public String getUndoMsg() {
2213	return "Value " + m_sValue + " removed from node " + getNodeName(m_nTargetNode);
2214	}
2215
2216	public String getRedoMsg() {
2217	return "Value " + m_sValue + " added to node " + getNodeName(m_nTargetNode);
2218	}
2219	} // class AddValueAction
2220
2221	class DelValueAction extends UndoAction {
2222	/** for serialization */
2223	static final long serialVersionUID = 1;
2224	int m_nTargetNode;
2225
2226	String m_sValue;
2227
2228	Estimator[] m_CPT;
2229
2230	FastVector m_children;
2231
2232	Estimator[][] m_childAtts;
2233
2234	Attribute m_att;
2235
2236	DelValueAction(int nTargetNode, String sValue) {
2237	try {
2238	m_nTargetNode = nTargetNode;
2239	m_sValue = sValue;
2240	m_att = m_Instances.attribute(nTargetNode);
2241	SerializedObject so = new SerializedObject(m_Distributions[nTargetNode]);
2242	m_CPT = (Estimator[]) so.getObject();
2243	;
2244	m_children = new FastVector();
2245	for (int iNode = 0; iNode < getNrOfNodes(); iNode++) {
2246	if (m_ParentSets[iNode].contains(nTargetNode)) {
2247	m_children.addElement(iNode);
2248	}
2249	}
2250	m_childAtts = new Estimator[m_children.size()][];
2251	for (int iChild = 0; iChild < m_children.size(); iChild++) {
2252	int nChild = (Integer) m_children.elementAt(iChild);
2253	m_childAtts[iChild] = m_Distributions[nChild];
2254	}
2255	} catch (Exception e) {
2256	e.printStackTrace();
2257	}
2258	} // c'tor
2259
2260	public void undo() {
2261	try {
2262	m_Instances.insertAttributeAt(m_att, m_nTargetNode);
2263	SerializedObject so = new SerializedObject(m_CPT);
2264	m_Distributions[m_nTargetNode] = (Estimator[]) so.getObject();
2265	for (int iChild = 0; iChild < m_children.size(); iChild++) {
2266	int nChild = (Integer) m_children.elementAt(iChild);
2267	m_Instances.insertAttributeAt(m_att, m_nTargetNode);
2268	so = new SerializedObject(m_childAtts[iChild]);
2269	m_Distributions[nChild] = (Estimator[]) so.getObject();
2270	}
2271	} catch (Exception e) {
2272	e.printStackTrace();
2273	}
2274	} // undo
2275
2276	public void redo() {
2277	try {
2278	delNodeValue(m_nTargetNode, m_sValue);
2279	} catch (Exception e) {
2280	e.printStackTrace();
2281	}
2282	} // redo
2283
2284	public String getUndoMsg() {
2285	return "Value " + m_sValue + " added to node " + getNodeName(m_nTargetNode);
2286	}
2287
2288	public String getRedoMsg() {
2289	return "Value " + m_sValue + " removed from node " + getNodeName(m_nTargetNode);
2290	}
2291	} // class DelValueAction
2292
2293	class alignAction extends UndoAction {
2294	/** for serialization */
2295	static final long serialVersionUID = 1;
2296	FastVector m_nodes;
2297
2298	FastVector m_posX;
2299
2300	FastVector m_posY;
2301
2302	alignAction(FastVector nodes) {
2303	m_nodes = new FastVector(nodes.size());
2304	m_posX = new FastVector(nodes.size());
2305	m_posY = new FastVector(nodes.size());
2306	for (int iNode = 0; iNode < nodes.size(); iNode++) {
2307	int nNode = (Integer) nodes.elementAt(iNode);
2308	m_nodes.addElement(nNode);
2309	m_posX.addElement(getPositionX(nNode));
2310	m_posY.addElement(getPositionY(nNode));
2311	}
2312	} // c'tor
2313
2314	public void undo() {
2315	try {
2316	for (int iNode = 0; iNode < m_nodes.size(); iNode++) {
2317	int nNode = (Integer) m_nodes.elementAt(iNode);
2318	setPosition(nNode, (Integer) m_posX.elementAt(iNode), (Integer) m_posY.elementAt(iNode));
2319	}
2320	} catch (Exception e) {
2321	e.printStackTrace();
2322	}
2323	} // undo
2324	} // class alignAction
2325
2326	class alignLeftAction extends alignAction {
2327	/** for serialization */
2328	static final long serialVersionUID = 1;
2329	public alignLeftAction(FastVector nodes) {
2330	super(nodes);
2331	} // c'tor
2332
2333	public void redo() {
2334	try {
2335	alignLeft(m_nodes);
2336	} catch (Exception e) {
2337	e.printStackTrace();
2338	}
2339	} // redo
2340
2341	public String getUndoMsg() {
2342	return "Returning " + m_nodes.size() + " from aliging nodes to the left.";
2343	}
2344
2345	public String getRedoMsg() {
2346	return "Aligning " + m_nodes.size() + " nodes to the left.";
2347	}
2348	} // class alignLeftAction
2349
2350	class alignRightAction extends alignAction {
2351	/** for serialization */
2352	static final long serialVersionUID = 1;
2353	public alignRightAction(FastVector nodes) {
2354	super(nodes);
2355	} // c'tor
2356
2357	public void redo() {
2358	try {
2359	alignRight(m_nodes);
2360	} catch (Exception e) {
2361	e.printStackTrace();
2362	}
2363	} // redo
2364
2365	public String getUndoMsg() {
2366	return "Returning " + m_nodes.size() + " from aliging nodes to the right.";
2367	}
2368
2369	public String getRedoMsg() {
2370	return "Aligning " + m_nodes.size() + " nodes to the right.";
2371	}
2372	} // class alignLeftAction
2373
2374	class alignTopAction extends alignAction {
2375	/** for serialization */
2376	static final long serialVersionUID = 1;
2377	public alignTopAction(FastVector nodes) {
2378	super(nodes);
2379	} // c'tor
2380
2381	public void redo() {
2382	try {
2383	alignTop(m_nodes);
2384	} catch (Exception e) {
2385	e.printStackTrace();
2386	}
2387	} // redo
2388
2389	public String getUndoMsg() {
2390	return "Returning " + m_nodes.size() + " from aliging nodes to the top.";
2391	}
2392
2393	public String getRedoMsg() {
2394	return "Aligning " + m_nodes.size() + " nodes to the top.";
2395	}
2396	} // class alignTopAction
2397
2398	class alignBottomAction extends alignAction {
2399	/** for serialization */
2400	static final long serialVersionUID = 1;
2401	public alignBottomAction(FastVector nodes) {
2402	super(nodes);
2403	} // c'tor
2404
2405	public void redo() {
2406	try {
2407	alignBottom(m_nodes);
2408	} catch (Exception e) {
2409	e.printStackTrace();
2410	}
2411	} // redo
2412
2413	public String getUndoMsg() {
2414	return "Returning " + m_nodes.size() + " from aliging nodes to the bottom.";
2415	}
2416
2417	public String getRedoMsg() {
2418	return "Aligning " + m_nodes.size() + " nodes to the bottom.";
2419	}
2420	} // class alignBottomAction
2421
2422	class centerHorizontalAction extends alignAction {
2423	/** for serialization */
2424	static final long serialVersionUID = 1;
2425	public centerHorizontalAction(FastVector nodes) {
2426	super(nodes);
2427	} // c'tor
2428
2429	public void redo() {
2430	try {
2431	centerHorizontal(m_nodes);
2432	} catch (Exception e) {
2433	e.printStackTrace();
2434	}
2435	} // redo
2436
2437	public String getUndoMsg() {
2438	return "Returning " + m_nodes.size() + " from centering horizontally.";
2439	}
2440
2441	public String getRedoMsg() {
2442	return "Centering " + m_nodes.size() + " nodes horizontally.";
2443	}
2444	} // class centerHorizontalAction
2445
2446	class centerVerticalAction extends alignAction {
2447	/** for serialization */
2448	static final long serialVersionUID = 1;
2449	public centerVerticalAction(FastVector nodes) {
2450	super(nodes);
2451	} // c'tor
2452
2453	public void redo() {
2454	try {
2455	centerVertical(m_nodes);
2456	} catch (Exception e) {
2457	e.printStackTrace();
2458	}
2459	} // redo
2460
2461	public String getUndoMsg() {
2462	return "Returning " + m_nodes.size() + " from centering vertically.";
2463	}
2464
2465	public String getRedoMsg() {
2466	return "Centering " + m_nodes.size() + " nodes vertically.";
2467	}
2468	} // class centerVerticalAction
2469
2470	class spaceHorizontalAction extends alignAction {
2471	/** for serialization */
2472	static final long serialVersionUID = 1;
2473	public spaceHorizontalAction(FastVector nodes) {
2474	super(nodes);
2475	} // c'tor
2476
2477	public void redo() {
2478	try {
2479	spaceHorizontal(m_nodes);
2480	} catch (Exception e) {
2481	e.printStackTrace();
2482	}
2483	} // redo
2484
2485	public String getUndoMsg() {
2486	return "Returning " + m_nodes.size() + " from spaceing horizontally.";
2487	}
2488
2489	public String getRedoMsg() {
2490	return "spaceing " + m_nodes.size() + " nodes horizontally.";
2491	}
2492	} // class spaceHorizontalAction
2493
2494	class spaceVerticalAction extends alignAction {
2495	/** for serialization */
2496	static final long serialVersionUID = 1;
2497	public spaceVerticalAction(FastVector nodes) {
2498	super(nodes);
2499	} // c'tor
2500
2501	public void redo() {
2502	try {
2503	spaceVertical(m_nodes);
2504	} catch (Exception e) {
2505	e.printStackTrace();
2506	}
2507	} // redo
2508
2509	public String getUndoMsg() {
2510	return "Returning " + m_nodes.size() + " from spaceng vertically.";
2511	}
2512
2513	public String getRedoMsg() {
2514	return "Spaceng " + m_nodes.size() + " nodes vertically.";
2515	}
2516	} // class spaceVerticalAction
2517
2518	class SetPositionAction extends UndoAction {
2519	/** for serialization */
2520	static final long serialVersionUID = 1;
2521	int m_nTargetNode;
2522
2523	int m_nX;
2524
2525	int m_nY;
2526
2527	int m_nX2;
2528
2529	int m_nY2;
2530
2531	SetPositionAction(int nTargetNode, int nX, int nY) {
2532	m_nTargetNode = nTargetNode;
2533	m_nX2 = nX;
2534	m_nY2 = nY;
2535	m_nX = getPositionX(nTargetNode);
2536	m_nY = getPositionY(nTargetNode);
2537	} // c'tor
2538
2539	public void undo() {
2540	setPosition(m_nTargetNode, m_nX, m_nY);
2541	} // undo
2542
2543	public void redo() {
2544	setPosition(m_nTargetNode, m_nX2, m_nY2);
2545	} // redo
2546
2547	public void setUndoPosition(int nX, int nY) {
2548	m_nX2 = nX;
2549	m_nY2 = nY;
2550	} // setPosition
2551	} // class SetPositionAction
2552
2553	class SetGroupPositionAction extends UndoAction {
2554	/** for serialization */
2555	static final long serialVersionUID = 1;
2556	FastVector m_nodes;
2557	int m_dX;
2558	int m_dY;
2559
2560	SetGroupPositionAction(FastVector nodes, int dX, int dY) {
2561	m_nodes = new FastVector(nodes.size());
2562	for (int iNode = 0; iNode < nodes.size(); iNode++) {
2563	m_nodes.addElement(nodes.elementAt(iNode));
2564	}
2565	m_dX = dX;
2566	m_dY = dY;
2567	} // c'tor
2568
2569	public void undo() {
2570	for (int iNode = 0; iNode < m_nodes.size(); iNode++) {
2571	int nNode = (Integer) m_nodes.elementAt(iNode);
2572	setPosition(nNode, getPositionX(nNode) - m_dX, getPositionY(nNode) - m_dY);
2573	}
2574	} // undo
2575
2576	public void redo() {
2577	for (int iNode = 0; iNode < m_nodes.size(); iNode++) {
2578	int nNode = (Integer) m_nodes.elementAt(iNode);
2579	setPosition(nNode, getPositionX(nNode) + m_dX, getPositionY(nNode) + m_dY);
2580	}
2581	} // redo
2582	public void setUndoPosition(int dX, int dY) {
2583	m_dX += dX;
2584	m_dY += dY;
2585	} // setPosition
2586	} // class SetGroupPositionAction
2587
2588	class LayoutGraphAction extends UndoAction {
2589	/** for serialization */
2590	static final long serialVersionUID = 1;
2591	FastVector m_nPosX;
2592	FastVector m_nPosY;
2593	FastVector m_nPosX2;
2594	FastVector m_nPosY2;
2595
2596	LayoutGraphAction(FastVector nPosX, FastVector nPosY) {
2597	m_nPosX = new FastVector(nPosX.size());
2598	m_nPosY = new FastVector(nPosX.size());
2599	m_nPosX2 = new FastVector(nPosX.size());
2600	m_nPosY2 = new FastVector(nPosX.size());
2601	for (int iNode = 0; iNode < nPosX.size(); iNode++) {
2602	m_nPosX.addElement(m_nPositionX.elementAt(iNode));
2603	m_nPosY.addElement(m_nPositionY.elementAt(iNode));
2604	m_nPosX2.addElement(nPosX.elementAt(iNode));
2605	m_nPosY2.addElement(nPosY.elementAt(iNode));
2606	}
2607	} // c'tor
2608
2609	public void undo() {
2610	for (int iNode = 0; iNode < m_nPosX.size(); iNode++) {
2611	setPosition(iNode, (Integer) m_nPosX.elementAt(iNode), (Integer) m_nPosY.elementAt(iNode));
2612	}
2613	} // undo
2614
2615	public void redo() {
2616	for (int iNode = 0; iNode < m_nPosX.size(); iNode++) {
2617	setPosition(iNode, (Integer) m_nPosX2.elementAt(iNode), (Integer) m_nPosY2.elementAt(iNode));
2618	}
2619	} // redo
2620	} // class LayoutGraphAction
2621
2622	class PasteAction extends UndoAction {
2623	/** for serialization */
2624	static final long serialVersionUID = 1;
2625	int m_nBase;
2626
2627	String m_sXML;
2628
2629	PasteAction(String sXML, int nBase) {
2630	m_sXML = sXML;
2631	m_nBase = nBase;
2632	} // c'tor
2633
2634	public void undo() {
2635	try {
2636	int iNode = getNrOfNodes() - 1;
2637	while (iNode >= m_nBase) {
2638	deleteNode(iNode);
2639	iNode--;
2640	}
2641	} catch (Exception e) {
2642	e.printStackTrace();
2643	}
2644	} // undo
2645
2646	public void redo() {
2647	try {
2648	paste(m_sXML, EXECUTE);
2649	} catch (Exception e) {
2650	e.printStackTrace();
2651	}
2652	} // redo
2653	} // class PasteAction
2654
2655	/**
2656	* Returns the revision string.
2657	*
2658	* @return the revision
2659	*/
2660	public String getRevision() {
2661	return RevisionUtils.extract("$Revision: 4899 $");
2662	}
2663
2664	/**
2665	* @param args
2666	*/
2667	public static void main(String[] args) {
2668	} // main
2669	} // class EditableBayesNet
2670

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source: branches/MetisMQI/src/main/java/weka/classifiers/bayes/net/EditableBayesNet.java

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