/*
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

/*
 * BayesNet.java
 * Copyright (C) 2001 Remco Bouckaert
 * 
 */
package weka.classifiers.bayes;

import java.util.*;
import weka.core.*;
import weka.estimators.*;
import weka.filters.supervised.attribute.Discretize;
import weka.filters.unsupervised.attribute.ReplaceMissingValues;
import weka.classifiers.*;
import weka.classifiers.bayes.net.*;
import weka.classifiers.bayes.net.estimate.DiscreteEstimatorBayes;
import weka.classifiers.bayes.net.search.*;
import weka.classifiers.bayes.net.search.local.*;
import weka.classifiers.bayes.net.estimate.*;

/**
 * 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.
 * Works with nominal variables and no missing values only.
 * 
 * For further documentation, see 
 * <a href='http://www.cs.waikato.ac.nz/~remco/weka.pdf>Bayesian networks in Weka</a>
 * user documentation.
 * 
 * @author Remco Bouckaert (rrb@xm.co.nz)
 * @version $Revision: 1.21.2.4 $
 */
public class BayesNet extends Classifier implements OptionHandler, WeightedInstancesHandler, Drawable, AdditionalMeasureProducer {

    /**
     * The parent sets.
     */
    protected ParentSet[] m_ParentSets;

    /**
     * The attribute estimators containing CPTs.
     */
    public Estimator[][] m_Distributions;


   	/** filter used to quantize continuous variables, if any **/
    Discretize m_DiscretizeFilter = null;
    int m_nNonDiscreteAttribute = -1;

	/** filter used to fill in missing values, if any **/
	ReplaceMissingValues m_MissingValuesFilter = null;	
	
    /**
     * The number of classes
     */
    protected int m_NumClasses;

    /**
     * The dataset header for the purposes of printing out a semi-intelligible
     * model
     */
    public Instances m_Instances;

    /**
     * Datastructure containing ADTree representation of the database.
     * This may result in more efficient access to the data.
     */
    ADNode m_ADTree;

    /**
     * Bayes network to compare the structure with.
     */
    protected BIFReader m_otherBayesNet = null;

    /**
     * Use the experimental ADTree datastructure for calculating contingency tables
     */
    boolean m_bUseADTree = false;

    /**
     * Search algorithm used for learning the structure of a network.
     */
    SearchAlgorithm m_SearchAlgorithm = new K2();

    /**
     * Search algorithm used for learning the structure of a network.
     */
    BayesNetEstimator m_BayesNetEstimator = new SimpleEstimator();

    /**
     * Generates the classifier.
     * 
     * @param instances set of instances serving as training data
     * @exception Exception if the classifier has not been generated
     * successfully
     */
    public void buildClassifier(Instances instances) throws Exception {

        // Check that class is nominal
        if (!instances.classAttribute().isNominal()) {
            throw new UnsupportedClassTypeException("BayesNet: nominal class, please.");
        }

		// ensure we have a data set with discrete variables only and with no missing values
		instances = normalizeDataSet(instances);

        // Copy the instances
        m_Instances = new Instances(instances);

        // sanity check: need more than 1 variable in datat set
        m_NumClasses = instances.numClasses();

        // initialize ADTree
        if (m_bUseADTree) {
            m_ADTree = ADNode.makeADTree(instances);
            //      System.out.println("Oef, done!");
        }

        // build the network structure
        initStructure();

        // build the network structure
        buildStructure();

        // build the set of CPTs
        estimateCPTs();

        // Save space
        // m_Instances = new Instances(m_Instances, 0);
        m_ADTree = null;
    } // buildClassifier

	/** ensure that all variables are nominal and that there are no missing values
	 * @param instances: data set to check and quantize and/or fill in missing values
	 * @return filtered instances
	 * @throws Exception
	 */
	Instances normalizeDataSet(Instances instances) throws Exception {
		m_DiscretizeFilter = null;
		m_MissingValuesFilter = null;

		boolean bHasNonNominal = false;
		boolean bHasMissingValues = false;

		Enumeration enu = instances.enumerateAttributes();		
		while (enu.hasMoreElements()) {
			Attribute attribute = (Attribute) enu.nextElement();
			if (attribute.type() == Attribute.STRING) {
				throw new UnsupportedAttributeTypeException("BayesNet does not handle string variables, only nominal and continuous.");
			}
			if (attribute.type() == Attribute.DATE) {
				throw new UnsupportedAttributeTypeException("BayesNet does not handle date variables, only nominal and continuous.");
			}
		
			if (attribute.type() != Attribute.NOMINAL) {
				m_nNonDiscreteAttribute = attribute.index();
				bHasNonNominal = true;
				//throw new UnsupportedAttributeTypeException("BayesNet handles nominal variables only. Non-nominal variable in dataset detected.");
			}
			Enumeration enum2 = instances.enumerateInstances();
			while (enum2.hasMoreElements()) {
				if (((Instance) enum2.nextElement()).isMissing(attribute)) {
					bHasMissingValues = true;
					// throw new NoSupportForMissingValuesException("BayesNet: no missing values, please.");
				}
			}
		}
		        
		if (bHasNonNominal) {
			System.err.println("Warning: discretizing data set");
			m_DiscretizeFilter = new Discretize();
			m_DiscretizeFilter.setInputFormat(instances);
			instances = m_DiscretizeFilter.useFilter(instances, m_DiscretizeFilter);
		}

		if (bHasMissingValues) {
			System.err.println("Warning: filling in missing values in data set");
			m_MissingValuesFilter = new ReplaceMissingValues();
			m_MissingValuesFilter.setInputFormat(instances);
			instances = m_MissingValuesFilter.useFilter(instances, m_MissingValuesFilter);
		}
		return instances;
	} // normalizeDataSet

	/** ensure that all variables are nominal and that there are no missing values
	 * @param instance: instance to check and quantize and/or fill in missing values
	 * @return filtered instance
	 * @throws Exception
	 */
	Instance normalizeInstance(Instance instance) throws Exception {
		if ((m_DiscretizeFilter != null) &&
			(instance.attribute(m_nNonDiscreteAttribute).type() != Attribute.NOMINAL)) {
			m_DiscretizeFilter.input(instance);
			instance = m_DiscretizeFilter.output();
		}
		if (m_MissingValuesFilter != null) {
			m_MissingValuesFilter.input(instance);
			instance = m_MissingValuesFilter.output();
		} else {
			// is there a missing value in this instance?
			// this can happen when there is no missing value in the training set
			for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) {
				if (iAttribute != instance.classIndex() && instance.isMissing(iAttribute)) {
					System.err.println("Warning: Found missing value in test set, filling in values.");
					m_MissingValuesFilter = new ReplaceMissingValues();
					m_MissingValuesFilter.setInputFormat(m_Instances);
					m_MissingValuesFilter.useFilter(m_Instances, m_MissingValuesFilter);
					m_MissingValuesFilter.input(instance);
					instance = m_MissingValuesFilter.output();
					iAttribute = m_Instances.numAttributes();
				}
			}
		}
		return instance;
	} // normalizeInstance

    /**
     * Init structure initializes the structure to an empty graph or a Naive Bayes
     * graph (depending on the -N flag).
     */
    public void initStructure() throws Exception {

        // initialize topological ordering
        //    m_nOrder = new int[m_Instances.numAttributes()];
        //    m_nOrder[0] = m_Instances.classIndex();

        int nAttribute = 0;

        for (int iOrder = 1; iOrder < m_Instances.numAttributes(); iOrder++) {
            if (nAttribute == m_Instances.classIndex()) {
                nAttribute++;
            }

            //      m_nOrder[iOrder] = nAttribute++;
        }

        // reserve memory
        m_ParentSets = new ParentSet[m_Instances.numAttributes()];

        for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) {
            m_ParentSets[iAttribute] = new ParentSet(m_Instances.numAttributes());
        }
    } // initStructure

    /**
     * buildStructure determines the network structure/graph of the network.
     * The default behavior is creating a network where all nodes have the first
     * node as its parent (i.e., a BayesNet that behaves like a naive Bayes classifier).
     * This method can be overridden by derived classes to restrict the class
     * of network structures that are acceptable.
     */
    public void buildStructure() throws Exception {
        m_SearchAlgorithm.buildStructure(this, m_Instances);
    } // buildStructure

    /**
     * estimateCPTs estimates the conditional probability tables for the Bayes
     * Net using the network structure.
     */
    public void estimateCPTs() throws Exception {
        m_BayesNetEstimator.estimateCPTs(this);
    } // estimateCPTs

    public void initCPTs() throws Exception {
        m_BayesNetEstimator.initCPTs(this);
    } // estimateCPTs

    /**
     * Updates the classifier with the given instance.
     * 
     * @param instance the new training instance to include in the model
     * @exception Exception if the instance could not be incorporated in
     * the model.
     */
    public void updateClassifier(Instance instance) throws Exception {
		instance = normalizeInstance(instance);
    	m_BayesNetEstimator.updateClassifier(this, instance);
    } // updateClassifier

    /**
     * Calculates the class membership probabilities for the given test
     * instance.
     * 
     * @param instance the instance to be classified
     * @return predicted class probability distribution
     * @exception Exception if there is a problem generating the prediction
     */
    public double[] distributionForInstance(Instance instance) throws Exception {
    	instance = normalizeInstance(instance);
		return m_BayesNetEstimator.distributionForInstance(this, instance);
	} // distributionForInstance
   	
    /**
     * Calculates the counts for Dirichlet distribution for the 
     * class membership probabilities for the given test instance.
     * 
     * @param instance the instance to be classified
     * @return counts for Dirichlet distribution for class probability 
     * @exception Exception if there is a problem generating the prediction
     */
    public double[] countsForInstance(Instance instance) throws Exception {
        double[] fCounts = new double[m_NumClasses];

        for (int iClass = 0; iClass < m_NumClasses; iClass++) {
            fCounts[iClass] = 0.0;
        }

        for (int iClass = 0; iClass < m_NumClasses; iClass++) {
            double fCount = 0;

            for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) {
                double iCPT = 0;

                for (int iParent = 0; iParent < m_ParentSets[iAttribute].getNrOfParents(); iParent++) {
                    int nParent = m_ParentSets[iAttribute].getParent(iParent);

                    if (nParent == m_Instances.classIndex()) {
                        iCPT = iCPT * m_NumClasses + iClass;
                    } else {
                        iCPT = iCPT * m_Instances.attribute(nParent).numValues() + instance.value(nParent);
                    }
                }

                if (iAttribute == m_Instances.classIndex()) {
                    fCount += ((DiscreteEstimatorBayes) m_Distributions[iAttribute][(int) iCPT]).getCount(iClass);
                } else {
                    fCount
                        += ((DiscreteEstimatorBayes) m_Distributions[iAttribute][(int) iCPT]).getCount(
                            instance.value(iAttribute));
                }
            }

            fCounts[iClass] += fCount;
        }
        return fCounts;
    } // countsForInstance

    /**
     * Returns an enumeration describing the available options
     * 
     * @return an enumeration of all the available options
     */
    public Enumeration listOptions() {
        Vector newVector = new Vector(4);

        newVector.addElement(new Option("\tDo not use ADTree data structure\n", "D", 0, "-D"));
        newVector.addElement(new Option("\tBIF file to compare with\n", "B", 1, "-B <BIF file>"));
        newVector.addElement(new Option("\tSearch algorithm\n", "Q", 1, "-Q weka.classifiers.bayes.net.search.SearchAlgorithm"));
        newVector.addElement(new Option("\tEstimator algorithm\n", "E", 1, "-E weka.classifiers.bayes.net.estimate.SimpleEstimator"));

        return newVector.elements();
    } // listOptions

    /**
     * Parses a given list of options. Valid options are:<p>
     * 
     * @param options the list of options as an array of strings
     * @exception Exception if an option is not supported
     */
    public void setOptions(String[] options) throws Exception {
        m_bUseADTree = !(Utils.getFlag('D', options));

        String sBIFFile = Utils.getOption('B', options);
        if (sBIFFile != null && !sBIFFile.equals("")) {
            setBIFFile(sBIFFile);
        }

        String searchAlgorithmName = Utils.getOption('Q', options);
        if (searchAlgorithmName.length() != 0) {
          setSearchAlgorithm(
              (SearchAlgorithm) Utils.forName(
                  SearchAlgorithm.class,
                  searchAlgorithmName,
                  partitionOptions(options)));
        }
        else {
          setSearchAlgorithm(new K2());
        }


        String estimatorName = Utils.getOption('E', options);
        if (estimatorName.length() != 0) {
          setEstimator(
              (BayesNetEstimator) Utils.forName(
                  BayesNetEstimator.class,
                  estimatorName,
                  Utils.partitionOptions(options)));
        }
        else {
          setEstimator(new SimpleEstimator());
        }
        
        Utils.checkForRemainingOptions(options);
    } // setOptions

    /**
     * Returns the secondary set of options (if any) contained in
     * the supplied options array. The secondary set is defined to
     * be any options after the first "--" but before the "-E". These 
     * options are removed from the original options array.
     *
     * @param options the input array of options
     * @return the array of secondary options
     */
    public static String [] partitionOptions(String [] options) {

      for (int i = 0; i < options.length; i++) {
        if (options[i].equals("--")) {
        	// ensure it follows by a -E option
        	int j = i;
			while ((j < options.length) && !(options[j].equals("-E"))) {
			  j++;
			}
			if (j >= options.length) {
				return new String[0];
			}
  	options[i++] = "";
  	String [] result = new String [options.length - i];
	j = i;
  	while ((j < options.length) && !(options[j].equals("-E"))) {
  	  result[j - i] = options[j];
  	  options[j] = "";
	  j++;
  	}
	while(j < options.length) {
  	  result[j - i] = "";
	  j++;
  	}		 
  	return result;
        }
      }
      return new String [0];
    }

    
    /**
     * Gets the current settings of the classifier.
     * 
     * @return an array of strings suitable for passing to setOptions
     */
    public String[] getOptions() {
		String[] searchOptions = m_SearchAlgorithm.getOptions();
		String[] estimatorOptions = m_BayesNetEstimator.getOptions();
        String[] options = new String[11 + searchOptions.length + estimatorOptions.length];
        int current = 0;

        if (!m_bUseADTree) {
            options[current++] = "-D";
        }

        if (m_otherBayesNet != null) {
            options[current++] = "-B";
            options[current++] = ((BIFReader) m_otherBayesNet).getFileName();
        }

        options[current++] = "-Q";
        options[current++] = "" + getSearchAlgorithm().getClass().getName();
		options[current++] = "--";
		for (int iOption = 0; iOption < searchOptions.length; iOption++) {
			options[current++] = searchOptions[iOption];
		}

        options[current++] = "-E";
        options[current++] = "" + getEstimator().getClass().getName();
		options[current++] = "--";
		for (int iOption = 0; iOption < estimatorOptions.length; iOption++) {
			options[current++] = estimatorOptions[iOption];
		}

        // Fill up rest with empty strings, not nulls!
        while (current < options.length) {
            options[current++] = "";
        }

        return options;
    } // getOptions

    /**
    	* Set the SearchAlgorithm used in searching for network structures. 
    	* @param newSearchAlgorithm the SearchAlgorithm to use.
    	*/
    public void setSearchAlgorithm(SearchAlgorithm newSearchAlgorithm) {
        m_SearchAlgorithm = newSearchAlgorithm;
    }

    /**
    	* Get the SearchAlgorithm used as the search algorithm
    	* @return the SearchAlgorithm used as the search algorithm
    	*/
    public SearchAlgorithm getSearchAlgorithm() {
        return m_SearchAlgorithm;
    }

    /**
        * Set the Estimator Algorithm used in calculating the CPTs 
        * @param newEstimator the Estimator to use.
        */
    public void setEstimator(BayesNetEstimator newBayesNetEstimator) {
        m_BayesNetEstimator = newBayesNetEstimator;
    }

    /**
        * Get the BayesNetEstimator used for calculating the CPTs
        * @return the BayesNetEstimator used.
        */
    public BayesNetEstimator getEstimator() {
        return m_BayesNetEstimator;
    }

    /**
     * Set whether ADTree structure is used or not
     * @param bUseADTree
     */
    public void setUseADTree(boolean bUseADTree) {
        m_bUseADTree = bUseADTree;
    }

    /**
     * Method declaration
     * @return whether ADTree structure is used or not
     */
    public boolean getUseADTree() {
        return m_bUseADTree;
    }

    /**
     * Set name of network in BIF file to compare with
     * @param sBIFFile
     */
    public void setBIFFile(String sBIFFile) {
        try {
            m_otherBayesNet = new BIFReader().processFile(sBIFFile);
        } catch (Throwable t) {
            m_otherBayesNet = null;
        }
    }

    /**
     * Get name of network in BIF file to compare with
     * @return BIF file name
     */
    public String getBIFFile() {
        if (m_otherBayesNet != null) {
        	return m_otherBayesNet.getFileName();
        }
        return "";
    }


    /**
     * Returns a description of the classifier.
     * 
     * @return a description of the classifier as a string.
     */
    public String toString() {
        StringBuffer text = new StringBuffer();

        text.append("Bayes Network Classifier");
        text.append("\n" + (m_bUseADTree ? "Using " : "not using ") + "ADTree");

        if (m_Instances == null) {
            text.append(": No model built yet.");
        } else {

            // flatten BayesNet down to text
            text.append("\n#attributes=");
            text.append(m_Instances.numAttributes());
            text.append(" #classindex=");
            text.append(m_Instances.classIndex());
            text.append("\nNetwork structure (nodes followed by parents)\n");

            for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) {
                text.append(
                    m_Instances.attribute(iAttribute).name()
                        + "("
                        + m_Instances.attribute(iAttribute).numValues()
                        + "): ");

                for (int iParent = 0; iParent < m_ParentSets[iAttribute].getNrOfParents(); iParent++) {
                    text.append(m_Instances.attribute(m_ParentSets[iAttribute].getParent(iParent)).name() + " ");
                }

                text.append("\n");

                // Description of distributions tends to be too much detail, so it is commented out here
                // for (int iParent = 0; iParent < m_ParentSets[iAttribute].GetCardinalityOfParents(); iParent++) {
                // text.append('(' + m_Distributions[iAttribute][iParent].toString() + ')');
                // }
                // text.append("\n");
            }

			text.append("LogScore Bayes: " + measureBayesScore() + "\n");
			text.append("LogScore BDeu: " + measureBDeuScore() + "\n");
            text.append("LogScore MDL: " + measureMDLScore() + "\n");
            text.append("LogScore ENTROPY: " + measureEntropyScore() + "\n");
            text.append("LogScore AIC: " + measureAICScore() + "\n");

            if (m_otherBayesNet != null) {
                text.append(
                    "Missing: "
                        + m_otherBayesNet.missingArcs(this)
                        + " Extra: "
                        + m_otherBayesNet.extraArcs(this)
                        + " Reversed: "
                        + m_otherBayesNet.reversedArcs(this)
                        + "\n");
                text.append("Divergence: " + m_otherBayesNet.divergence(this) + "\n");
            }
        }

        return text.toString();
    } // toString


  /**
   *  Returns the type of graph this classifier
   *  represents.
   *  @return Drawable.TREE
   */   
  public int graphType() {
	  return Drawable.BayesNet;
  }

  /**
	 Returns a BayesNet graph in XMLBIF ver
	 0.3 format.
	 @return - String representing this
			   BayesNet in XMLBIF ver  0.3
  */
  public String graph() throws Exception {
	  return toXMLBIF03();
  }
       
  /**
   * Returns a description of the classifier in XML BIF 0.3 format.
   * See http://www-2.cs.cmu.edu/~fgcozman/Research/InterchangeFormat/
   * for details on XML BIF.
   * @return an XML BIF 0.3 description of the classifier as a string.
   */
  public String toXMLBIF03() {
    if (m_Instances == null) {
      return("<!--No model built yet-->");
    }
    
    StringBuffer text = new StringBuffer();
    
    text.append("<?xml version=\"1.0\"?>\n");
    text.append("<!-- DTD for the XMLBIF 0.3 format -->\n");
    text.append("<!DOCTYPE BIF [\n");
    text.append("	<!ELEMENT BIF ( NETWORK )*>\n");
    text.append("	      <!ATTLIST BIF VERSION CDATA #REQUIRED>\n");
    text.append("	<!ELEMENT NETWORK ( NAME, ( PROPERTY | VARIABLE | DEFINITION )* )>\n");
    text.append("	<!ELEMENT NAME (#PCDATA)>\n");
    text.append("	<!ELEMENT VARIABLE ( NAME, ( OUTCOME |  PROPERTY )* ) >\n");
    text.append("	      <!ATTLIST VARIABLE TYPE (nature|decision|utility) \"nature\">\n");
    text.append("	<!ELEMENT OUTCOME (#PCDATA)>\n");
    text.append("	<!ELEMENT DEFINITION ( FOR | GIVEN | TABLE | PROPERTY )* >\n");
    text.append("	<!ELEMENT FOR (#PCDATA)>\n");
    text.append("	<!ELEMENT GIVEN (#PCDATA)>\n");
    text.append("	<!ELEMENT TABLE (#PCDATA)>\n");
    text.append("	<!ELEMENT PROPERTY (#PCDATA)>\n");
    text.append("]>\n");
    text.append("\n");
    text.append("\n");
    text.append("<BIF VERSION=\"0.3\">\n");
    text.append("<NETWORK>\n");
    text.append("<NAME>" + XMLNormalize(m_Instances.relationName()) + "</NAME>\n");
    for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) {
      text.append("<VARIABLE TYPE=\"nature\">\n");
      text.append("<NAME>" + XMLNormalize(m_Instances.attribute(iAttribute).name()) + "</NAME>\n");
      for (int iValue = 0; iValue < m_Instances.attribute(iAttribute).numValues(); iValue++) {
        text.append("<OUTCOME>" + XMLNormalize(m_Instances.attribute(iAttribute).value(iValue)) + "</OUTCOME>\n");
      }
      text.append("</VARIABLE>\n");
    }
    
    for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) {
      text.append("<DEFINITION>\n");
      text.append("<FOR>" + XMLNormalize(m_Instances.attribute(iAttribute).name()) + "</FOR>\n");
      for (int iParent = 0; iParent < m_ParentSets[iAttribute].getNrOfParents(); iParent++) {
        text.append("<GIVEN>"
        + XMLNormalize(m_Instances.attribute(m_ParentSets[iAttribute].getParent(iParent)).name()) +
        "</GIVEN>\n");
      }
      text.append("<TABLE>\n");
      for (int iParent = 0; iParent < m_ParentSets[iAttribute].getCardinalityOfParents(); iParent++) {
        for (int iValue = 0; iValue < m_Instances.attribute(iAttribute).numValues(); iValue++) {
          text.append(m_Distributions[iAttribute][iParent].getProbability(iValue));
          text.append(' ');
        }
        text.append('\n');
      }
      text.append("</TABLE>\n");
      text.append("</DEFINITION>\n");
    }
    text.append("</NETWORK>\n");
    text.append("</BIF>\n");
    return text.toString();
  } // toXMLBIF03
  
  
  /** XMLNormalize converts the five standard XML entities in a string
   * g.e. the string V&D's is returned as V&amp;D&apos;s
   * @param sStr string to normalize
   * @return normalized string
   */
  String XMLNormalize(String sStr) {
    StringBuffer sStr2 = new StringBuffer();
    for (int iStr = 0; iStr < sStr.length(); iStr++) {
      char c = sStr.charAt(iStr);
      switch (c) {
        case '&': sStr2.append("&amp;"); break;
        case '\'': sStr2.append("&apos;"); break;
        case '\"': sStr2.append("&quot;"); break;
        case '<': sStr2.append("&lt;"); break;
        case '>': sStr2.append("&gt;"); break;
        default:
          sStr2.append(c);
      }
    }
    return sStr2.toString();
  } // XMLNormalize
  
  
    /**
     * @return a string to describe the UseADTreeoption.
     */
    public String useADTreeTipText() {
        return "When ADTree (the data structure for increasing speed on counts,"
            + " not to be confused with the classifier under the same name) is used"
            + " learning time goes down typically. However, because ADTrees are memory"
            + " intensive, memory problems may occur. Switching this option off makes"
            + " the structure learning algorithms slower, and run with less memory."
            + " By default, ADTrees are used.";
    }

    /**
     * @return a string to describe the SearchAlgorithm.
     */
    public String searchAlgorithmTipText() {
        return "Select method used for searching network structures.";
    }

    /**
     * This will return a string describing the BayesNetEstimator.
     * @return The string.
     */
    public String estimatorTipText() {
        return "Select Estimator algorithm for finding the conditional probability tables"
            + " of the Bayes Network.";
    }

    /**
     * @return a string to describe the BIFFile.
     */
    public String BIFFileTipText() {
        return "Set the name of a file in BIF XML format. A Bayes network learned"
            + " from data can be compared with the Bayes network represented by the BIF file."
            + " Statistics calculated are o.a. the number of missing and extra arcs.";
    }

    /**
     * This will return a string describing the classifier.
     * @return The string.
     */
    public String globalInfo() {
        return "Bayes Network learning using various search algorithms and quality measures.";
    }

    /**
     * Main method for testing this class.
     * 
     * @param argv the options
     */
    public static void main(String[] argv) {
        try {
            System.out.println(Evaluation.evaluateModel(new BayesNet(), argv));
        } catch (Exception e) {
            e.printStackTrace();
            System.err.println(e.getMessage());
        }
    } // main

    /** get name of the Bayes network
     * @return name of the Bayes net
     */
    public String getName() {
        return m_Instances.relationName();
    }

    /** get number of nodes in the Bayes network
     * @return number of nodes
     */
    public int getNrOfNodes() {
        return m_Instances.numAttributes();
    }

    /** get name of a node in the Bayes network
     * @param iNode: index of the node
     * @return name of the specified node
     */
    public String getNodeName(int iNode) {
        return m_Instances.attribute(iNode).name();
    }

    /** get number of values a node can take
     * @param iNode: index of the node
     * @return cardinality of the specified node
     */
    public int getCardinality(int iNode) {
        return m_Instances.attribute(iNode).numValues();
    }

    /** get name of a particular value of a node
     * @param iNode: index of the node
     * @param iValue: index of the value
     * @return cardinality of the specified node
     */
    public String getNodeValue(int iNode, int iValue) {
        return m_Instances.attribute(iNode).value(iValue);
    }

    /** get number of parents of a node in the network structure
     * @param iNode: index of the node
     * @return number of parents of the specified node
     */
    public int getNrOfParents(int iNode) {
        return m_ParentSets[iNode].getNrOfParents();
    }

    /** get node index of a parent of a node in the network structure
     * @param iNode: index of the node
     * @param iParent: index of the parents, e.g., 0 is the first parent, 1 the second parent, etc.
     * @return node index of the iParent's parent of the specified node
     */
    public int getParent(int iNode, int iParent) {
        return m_ParentSets[iNode].getParent(iParent);
    }

	/** Get full set of parent sets.
	 * @return parent sets;
	 */
	public ParentSet[] getParentSets() { 
		return m_ParentSets;
	}

	/** Get full set of estimators.
	 * @return estimators;
	 */
	public Estimator[][] getDistributions() {
		return m_Distributions;
	}

    /** get number of values the collection of parents of a node can take
     * @param iNode: index of the node
     * @return cardinality of the parent set of the specified node
     */
    public int getParentCardinality(int iNode) {
        return m_ParentSets[iNode].getCardinalityOfParents();
    }

    /** get particular probability of the conditional probability distribtion
     * of a node given its parents.
     * @param iNode: index of the node
     * @param iParent: index of the parent set, 0 <= iParent <= getParentCardinality(iNode)
     * @param iValue: index of the value, 0 <= iValue <= getCardinality(iNode)
     * @return probability
     */
    public double getProbability(int iNode, int iParent, int iValue) {
        return m_Distributions[iNode][iParent].getProbability(iValue);
    }

    /** get the parent set of a node 
     * @param iNode: index of the node
     * @return Parent set of the specified node.
     */
    public ParentSet getParentSet(int iNode) {
        return m_ParentSets[iNode];
    }

	/** get ADTree strucrture containing efficient representation of counts.
	 * @return ADTree strucrture
	 */
	public ADNode getADTree() { return m_ADTree;}

	// implementation of AdditionalMeasureProducer interface
	  /**
	   * Returns an enumeration of the measure names. Additional measures
	   * must follow the naming convention of starting with "measure", eg.
	   * double measureBlah()
	   * @return an enumeration of the measure names
	   */
	  public Enumeration enumerateMeasures() {
	    Vector newVector = new Vector(4);
	    newVector.addElement("measureExtraArcs");
	    newVector.addElement("measureMissingArcs");
	    newVector.addElement("measureReversedArcs");
	    newVector.addElement("measureDivergence");
	    newVector.addElement("measureBayesScore");
	    newVector.addElement("measureBDeuScore");
	    newVector.addElement("measureMDLScore");
	    newVector.addElement("measureAICScore");
	    newVector.addElement("measureEntropyScore");
	    return newVector.elements();
	  } // enumerateMeasures

	  public double measureExtraArcs() {
	  	if (m_otherBayesNet != null) {
	  		return m_otherBayesNet.extraArcs(this); 
	  	}
	  	return 0;
	  } // measureExtraArcs

	  public double measureMissingArcs() {
	  	if (m_otherBayesNet != null) {
	  		return m_otherBayesNet.missingArcs(this); 
	  	}
	  	return 0;
	  } // measureMissingArcs

  	  public double measureReversedArcs() {
	  	if (m_otherBayesNet != null) {
	  		return m_otherBayesNet.reversedArcs(this); 
	  	}
	  	return 0;
	  } // measureReversedArcs
	  	  
  	  public double measureDivergence() {
	  	if (m_otherBayesNet != null) {
	  		return m_otherBayesNet.divergence(this); 
	  	}
	  	return 0;
	  } // measureDivergence

  	  public double measureBayesScore() {
  	  	LocalScoreSearchAlgorithm s = new LocalScoreSearchAlgorithm(this, m_Instances);
  	  	return s.logScore(Scoreable.BAYES);
  	  } // measureBayesScore

  	  public double measureBDeuScore() {
  	  	LocalScoreSearchAlgorithm s = new LocalScoreSearchAlgorithm(this, m_Instances);
  	  	return s.logScore(Scoreable.BDeu);
  	  } // measureBDeuScore

  	  public double measureMDLScore() {
  	  	LocalScoreSearchAlgorithm s = new LocalScoreSearchAlgorithm(this, m_Instances);
  	  	return s.logScore(Scoreable.MDL);
  	  } // measureMDLScore

  	  public double measureAICScore() {
  	  	LocalScoreSearchAlgorithm s = new LocalScoreSearchAlgorithm(this, m_Instances);
  	  	return s.logScore(Scoreable.AIC);
  	  } // measureAICScore

  	  public double measureEntropyScore() {
  	  	LocalScoreSearchAlgorithm s = new LocalScoreSearchAlgorithm(this, m_Instances);
  	  	return s.logScore(Scoreable.ENTROPY);
  	  } // measureEntropyScore
  	  
  	  /**
	   * Returns the value of the named measure
	   * @param measureName the name of the measure to query for its value
	   * @return the value of the named measure
	   * @exception IllegalArgumentException if the named measure is not supported
	   */
	  public double getMeasure(String measureName) {
	  	if (measureName.equals("measureExtraArcs")) {
	  		return measureExtraArcs();
	  	}
	  	if (measureName.equals("measureMissingArcs")) {
	  		return measureMissingArcs();
	  	}
	  	if (measureName.equals("measureReversedArcs")) {
	  		return measureReversedArcs();
	  	}
	  	if (measureName.equals("measureDivergence")) {
	  		return measureDivergence();
	  	}
	  	if (measureName.equals("measureBayesScore")) {
	  		return measureBayesScore();
	  	}
	  	if (measureName.equals("measureBDeuScore")) {
	  		return measureBDeuScore();
	  	}
	  	if (measureName.equals("measureMDLScore")) {
	  		return measureMDLScore();
	  	}
	  	if (measureName.equals("measureAICScore")) {
	  		return measureAICScore();
	  	}
	  	if (measureName.equals("measureEntropyScore")) {
	  		return measureEntropyScore();
	  	}
	  	return 0;
	  } // getMeasure

} // class BayesNet