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weka.classifiers.bayes.NaiveBayes Maven / Gradle / Ivy

/*
 *   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 3 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, see .
 */

/*
 *    NaiveBayes.java
 *    Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.classifiers.bayes;

import java.util.Collections;
import java.util.Enumeration;
import java.util.Vector;

import weka.classifiers.AbstractClassifier;
import weka.core.*;
import weka.core.Capabilities.Capability;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;
import weka.estimators.DiscreteEstimator;
import weka.estimators.Estimator;
import weka.estimators.KernelEstimator;
import weka.estimators.NormalEstimator;

/**
 *  Class for a Naive Bayes classifier using estimator
 * classes. Numeric estimator precision values are chosen based on analysis of
 * the training data. For this reason, the classifier is not an
 * UpdateableClassifier (which in typical usage are initialized with zero
 * training instances) -- if you need the UpdateableClassifier functionality,
 * use the NaiveBayesUpdateable classifier. The NaiveBayesUpdateable classifier
 * will use a default precision of 0.1 for numeric attributes when
 * buildClassifier is called with zero training instances.

 * 

 * For more information on Naive Bayes classifiers, see

 * 

 * George H. John, Pat Langley: Estimating Continuous Distributions in Bayesian
 * Classifiers. In: Eleventh Conference on Uncertainty in Artificial
 * Intelligence, San Mateo, 338-345, 1995.
 * 

 * 
 * 
 *  BibTeX:
 * 
 * 
 * @inproceedings{John1995,
 *    address = {San Mateo},
 *    author = {George H. John and Pat Langley},
 *    booktitle = {Eleventh Conference on Uncertainty in Artificial Intelligence},
 *    pages = {338-345},
 *    publisher = {Morgan Kaufmann},
 *    title = {Estimating Continuous Distributions in Bayesian Classifiers},
 *    year = {1995}
 * }
 * 
 * 

 * 
 * 
 *  Valid options are:
 * 

 * 
 * 
 * -K
 *  Use kernel density estimator rather than normal
 *  distribution for numeric attributes
 * 
 * 
 * 
 * -D
 *  Use supervised discretization to process numeric attributes
 * 
 * 
 * 
 * -O
 *  Display model in old format (good when there are many classes)
 * 
 * 
 * 
 * 
 * @author Len Trigg ([email protected])
 * @author Eibe Frank ([email protected])
 * @version $Revision: 14501 $
 */
public class NaiveBayes extends AbstractClassifier implements OptionHandler,
  WeightedInstancesHandler, WeightedAttributesHandler, TechnicalInformationHandler,
  Aggregateable {

  /** for serialization */
  static final long serialVersionUID = 5995231201785697655L;

  /** The attribute estimators. */
  protected Estimator[][] m_Distributions;

  /** The class estimator. */
  protected Estimator m_ClassDistribution;

  /**
   * Whether to use kernel density estimator rather than normal distribution for
   * numeric attributes
   */
  protected boolean m_UseKernelEstimator = false;

  /**
   * Whether to use discretization than normal distribution for numeric
   * attributes
   */
  protected boolean m_UseDiscretization = false;

  /** The number of classes (or 1 for numeric class) */
  protected int m_NumClasses;

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

  /*** The precision parameter used for numeric attributes */
  protected static final double DEFAULT_NUM_PRECISION = 0.01;

  /**
   * The discretization filter.
   */
  protected weka.filters.supervised.attribute.Discretize m_Disc = null;

  protected boolean m_displayModelInOldFormat = false;

  /**
   * Returns a string describing this classifier
   * 
   * @return a description of the classifier suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String globalInfo() {
    return "Class for a Naive Bayes classifier using estimator classes. Numeric"
      + " estimator precision values are chosen based on analysis of the "
      + " training data. For this reason, the classifier is not an"
      + " UpdateableClassifier (which in typical usage are initialized with zero"
      + " training instances) -- if you need the UpdateableClassifier functionality,"
      + " use the NaiveBayesUpdateable classifier. The NaiveBayesUpdateable"
      + " classifier will  use a default precision of 0.1 for numeric attributes"
      + " when buildClassifier is called with zero training instances.\n\n"
      + "For more information on Naive Bayes classifiers, see\n\n"
      + getTechnicalInformation().toString();
  }

  /**
   * Returns an instance of a TechnicalInformation object, containing detailed
   * information about the technical background of this class, e.g., paper
   * reference or book this class is based on.
   * 
   * @return the technical information about this class
   */
  @Override
  public TechnicalInformation getTechnicalInformation() {
    TechnicalInformation result;

    result = new TechnicalInformation(Type.INPROCEEDINGS);
    result.setValue(Field.AUTHOR, "George H. John and Pat Langley");
    result.setValue(Field.TITLE,
      "Estimating Continuous Distributions in Bayesian Classifiers");
    result.setValue(Field.BOOKTITLE,
      "Eleventh Conference on Uncertainty in Artificial Intelligence");
    result.setValue(Field.YEAR, "1995");
    result.setValue(Field.PAGES, "338-345");
    result.setValue(Field.PUBLISHER, "Morgan Kaufmann");
    result.setValue(Field.ADDRESS, "San Mateo");

    return result;
  }

  /**
   * Returns default capabilities of the classifier.
   * 
   * @return the capabilities of this classifier
   */
  @Override
  public Capabilities getCapabilities() {
    Capabilities result = super.getCapabilities();
    result.disableAll();

    // attributes
    result.enable(Capability.NOMINAL_ATTRIBUTES);
    result.enable(Capability.NUMERIC_ATTRIBUTES);
    result.enable( Capability.MISSING_VALUES );

    // class
    result.enable(Capability.NOMINAL_CLASS);
    result.enable(Capability.MISSING_CLASS_VALUES);

    // instances
    result.setMinimumNumberInstances(0);

    return result;
  }

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

    // can classifier handle the data?
    getCapabilities().testWithFail(instances);

    // remove instances with missing class
    instances = new Instances(instances);
    instances.deleteWithMissingClass();

    m_NumClasses = instances.numClasses();

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

    // Discretize instances if required
    if (m_UseDiscretization) {
      m_Disc = new weka.filters.supervised.attribute.Discretize();
      m_Disc.setInputFormat(m_Instances);
      m_Instances = weka.filters.Filter.useFilter(m_Instances, m_Disc);
    } else {
      m_Disc = null;
    }

    // Reserve space for the distributions
    m_Distributions = new Estimator[m_Instances.numAttributes() - 1][m_Instances
      .numClasses()];
    m_ClassDistribution = new DiscreteEstimator(m_Instances.numClasses(), true);
    int attIndex = 0;
    Enumeration enu = m_Instances.enumerateAttributes();
    while (enu.hasMoreElements()) {
      Attribute attribute = enu.nextElement();

      // If the attribute is numeric, determine the estimator
      // numeric precision from differences between adjacent values
      double numPrecision = DEFAULT_NUM_PRECISION;
      if (attribute.type() == Attribute.NUMERIC) {
        m_Instances.sort(attribute);
        if ((m_Instances.numInstances() > 0)
          && !m_Instances.instance(0).isMissing(attribute)) {
          double lastVal = m_Instances.instance(0).value(attribute);
          double currentVal, deltaSum = 0;
          int distinct = 0;
          for (int i = 1; i < m_Instances.numInstances(); i++) {
            Instance currentInst = m_Instances.instance(i);
            if (currentInst.isMissing(attribute)) {
              break;
            }
            currentVal = currentInst.value(attribute);
            if (currentVal != lastVal) {
              deltaSum += currentVal - lastVal;
              lastVal = currentVal;
              distinct++;
            }
          }
          if (distinct > 0) {
            numPrecision = deltaSum / distinct;
          }
        }
      }

      for (int j = 0; j < m_Instances.numClasses(); j++) {
        switch (attribute.type()) {
        case Attribute.NUMERIC:
          if (m_UseKernelEstimator) {
            m_Distributions[attIndex][j] = new KernelEstimator(numPrecision);
          } else {
            m_Distributions[attIndex][j] = new NormalEstimator(numPrecision);
          }
          break;
        case Attribute.NOMINAL:
          m_Distributions[attIndex][j] = new DiscreteEstimator(
            attribute.numValues(), true);
          break;
        default:
          throw new Exception("Attribute type unknown to NaiveBayes");
        }
      }
      attIndex++;
    }

    // Compute counts
    Enumeration enumInsts = m_Instances.enumerateInstances();
    while (enumInsts.hasMoreElements()) {
      Instance instance = enumInsts.nextElement();
      updateClassifier(instance);
    }

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

  /**
   * 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 {

    if (!instance.classIsMissing()) {
      Enumeration enumAtts = m_Instances.enumerateAttributes();
      int attIndex = 0;
      while (enumAtts.hasMoreElements()) {
        Attribute attribute = enumAtts.nextElement();
        if (!instance.isMissing(attribute)) {
          m_Distributions[attIndex][(int) instance.classValue()].addValue(
            instance.value(attribute), instance.weight());
        }
        attIndex++;
      }
      m_ClassDistribution.addValue(instance.classValue(), instance.weight());
    }
  }

  /**
   * 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
   */
  @Override
  public double[] distributionForInstance(Instance instance) throws Exception {

    if (m_UseDiscretization) {
      m_Disc.input(instance);
      instance = m_Disc.output();
    }
    double[] probs = new double[m_NumClasses];
    for (int j = 0; j < m_NumClasses; j++) {
      probs[j] = m_ClassDistribution.getProbability(j);
    }
    Enumeration enumAtts = instance.enumerateAttributes();
    int attIndex = 0;
    while (enumAtts.hasMoreElements()) {
      Attribute attribute = enumAtts.nextElement();
      if (!instance.isMissing(attribute)) {
        double temp, max = 0;
        for (int j = 0; j < m_NumClasses; j++) {
          temp = Math.max(1e-75, Math.pow(m_Distributions[attIndex][j]
            .getProbability(instance.value(attribute)),
            m_Instances.attribute(attIndex).weight()));
          probs[j] *= temp;
          if (probs[j] > max) {
            max = probs[j];
          }
          if (Double.isNaN(probs[j])) {
            throw new Exception("NaN returned from estimator for attribute "
              + attribute.name() + ":\n"
              + m_Distributions[attIndex][j].toString());
          }
        }
        if ((max > 0) && (max < 1e-75)) { // Danger of probability underflow
          for (int j = 0; j < m_NumClasses; j++) {
            probs[j] *= 1e75;
          }
        }
      }
      attIndex++;
    }

    // Display probabilities
    Utils.normalize(probs);
    return probs;
  }

  /**
   * Returns an enumeration describing the available options.
   * 
   * @return an enumeration of all the available options.
   */
  @Override
  public Enumeration listOptions() {

    Vector newVector = new Vector(3);

    newVector.addElement(new Option(
      "\tUse kernel density estimator rather than normal\n"
        + "\tdistribution for numeric attributes", "K", 0, "-K"));
    newVector.addElement(new Option(
      "\tUse supervised discretization to process numeric attributes\n", "D",
      0, "-D"));

    newVector
      .addElement(new Option(
        "\tDisplay model in old format (good when there are "
          + "many classes)\n", "O", 0, "-O"));

    newVector.addAll(Collections.list(super.listOptions()));

    return newVector.elements();
  }

  /**
   * Parses a given list of options.
   * 

   * 
   *  Valid options are:
   * 

   * 
   * 
   * -K
   *  Use kernel density estimator rather than normal
   *  distribution for numeric attributes
   * 
   * 
   * 
   * -D
   *  Use supervised discretization to process numeric attributes
   * 
   * 
   * 
   * -O
   *  Display model in old format (good when there are many classes)
   * 
   * 
   * 
   * 
   * @param options the list of options as an array of strings
   * @exception Exception if an option is not supported
   */
  @Override
  public void setOptions(String[] options) throws Exception {

    super.setOptions(options);
    boolean k = Utils.getFlag('K', options);
    boolean d = Utils.getFlag('D', options);
    if (k && d) {
      throw new IllegalArgumentException("Can't use both kernel density "
        + "estimation and discretization!");
    }
    setUseSupervisedDiscretization(d);
    setUseKernelEstimator(k);
    setDisplayModelInOldFormat(Utils.getFlag('O', options));
    Utils.checkForRemainingOptions(options);
  }

  /**
   * Gets the current settings of the classifier.
   * 
   * @return an array of strings suitable for passing to setOptions
   */
  @Override
  public String[] getOptions() {

    Vector options = new Vector();

    Collections.addAll(options, super.getOptions());

    if (m_UseKernelEstimator) {
      options.add("-K");
    }

    if (m_UseDiscretization) {
      options.add("-D");
    }

    if (m_displayModelInOldFormat) {
      options.add("-O");
    }

    return options.toArray(new String[0]);
  }

  /**
   * Returns a description of the classifier.
   * 
   * @return a description of the classifier as a string.
   */
  @Override
  public String toString() {
    if (m_displayModelInOldFormat) {
      return toStringOriginal();
    }

    StringBuffer temp = new StringBuffer();
    temp.append("Naive Bayes Classifier");
    if (m_Instances == null) {
      temp.append(": No model built yet.");
    } else {

      int maxWidth = 0;
      int maxAttWidth = 0;
      boolean containsKernel = false;

      // set up max widths
      // class values
      for (int i = 0; i < m_Instances.numClasses(); i++) {
        if (m_Instances.classAttribute().value(i).length() > maxWidth) {
          maxWidth = m_Instances.classAttribute().value(i).length();
        }
      }
      // attributes
      for (int i = 0; i < m_Instances.numAttributes(); i++) {
        if (i != m_Instances.classIndex()) {
          Attribute a = m_Instances.attribute(i);
          if (a.name().length() > maxAttWidth) {
            maxAttWidth = m_Instances.attribute(i).name().length();
          }
          if (a.isNominal()) {
            // check values
            for (int j = 0; j < a.numValues(); j++) {
              String val = a.value(j) + "  ";
              if (val.length() > maxAttWidth) {
                maxAttWidth = val.length();
              }
            }
          }
        }
      }

      for (Estimator[] m_Distribution : m_Distributions) {
        for (int j = 0; j < m_Instances.numClasses(); j++) {
          if (m_Distribution[0] instanceof NormalEstimator) {
            // check mean/precision dev against maxWidth
            NormalEstimator n = (NormalEstimator) m_Distribution[j];
            double mean = Math.log(Math.abs(n.getMean())) / Math.log(10.0);
            double precision = Math.log(Math.abs(n.getPrecision()))
              / Math.log(10.0);
            double width = (mean > precision) ? mean : precision;
            if (width < 0) {
              width = 1;
            }
            // decimal + # decimal places + 1
            width += 6.0;
            if ((int) width > maxWidth) {
              maxWidth = (int) width;
            }
          } else if (m_Distribution[0] instanceof KernelEstimator) {
            containsKernel = true;
            KernelEstimator ke = (KernelEstimator) m_Distribution[j];
            int numK = ke.getNumKernels();
            String temps = "K" + numK + ": mean (weight)";
            if (maxAttWidth < temps.length()) {
              maxAttWidth = temps.length();
            }
            // check means + weights against maxWidth
            if (ke.getNumKernels() > 0) {
              double[] means = ke.getMeans();
              double[] weights = ke.getWeights();
              for (int k = 0; k < ke.getNumKernels(); k++) {
                String m = Utils.doubleToString(means[k], maxWidth, 4).trim();
                m += " ("
                  + Utils.doubleToString(weights[k], maxWidth, 1).trim() + ")";
                if (maxWidth < m.length()) {
                  maxWidth = m.length();
                }
              }
            }
          } else if (m_Distribution[0] instanceof DiscreteEstimator) {
            DiscreteEstimator d = (DiscreteEstimator) m_Distribution[j];
            for (int k = 0; k < d.getNumSymbols(); k++) {
              String size = "" + d.getCount(k);
              if (size.length() > maxWidth) {
                maxWidth = size.length();
              }
            }
            int sum = ("" + d.getSumOfCounts()).length();
            if (sum > maxWidth) {
              maxWidth = sum;
            }
          }
        }
      }

      // Check width of class labels
      for (int i = 0; i < m_Instances.numClasses(); i++) {
        String cSize = m_Instances.classAttribute().value(i);
        if (cSize.length() > maxWidth) {
          maxWidth = cSize.length();
        }
      }

      // Check width of class priors
      for (int i = 0; i < m_Instances.numClasses(); i++) {
        String priorP = Utils.doubleToString(
          ((DiscreteEstimator) m_ClassDistribution).getProbability(i),
          maxWidth, 2).trim();
        priorP = "(" + priorP + ")";
        if (priorP.length() > maxWidth) {
          maxWidth = priorP.length();
        }
      }

      if (maxAttWidth < "Attribute".length()) {
        maxAttWidth = "Attribute".length();
      }

      if (maxAttWidth < "  weight sum".length()) {
        maxAttWidth = "  weight sum".length();
      }

      if (containsKernel) {
        if (maxAttWidth < "  [precision]".length()) {
          maxAttWidth = "  [precision]".length();
        }
      }

      maxAttWidth += 2;

      temp.append("\n\n");
      temp.append(pad("Class", " ",
        (maxAttWidth + maxWidth + 1) - "Class".length(), true));

      temp.append("\n");
      temp.append(pad("Attribute", " ", maxAttWidth - "Attribute".length(),
        false));
      // class labels
      for (int i = 0; i < m_Instances.numClasses(); i++) {
        String classL = m_Instances.classAttribute().value(i);
        temp.append(pad(classL, " ", maxWidth + 1 - classL.length(), true));
      }
      temp.append("\n");
      // class priors
      temp.append(pad("", " ", maxAttWidth, true));
      for (int i = 0; i < m_Instances.numClasses(); i++) {
        String priorP = Utils.doubleToString(
          ((DiscreteEstimator) m_ClassDistribution).getProbability(i),
          maxWidth, 2).trim();
        priorP = "(" + priorP + ")";
        temp.append(pad(priorP, " ", maxWidth + 1 - priorP.length(), true));
      }
      temp.append("\n");
      temp.append(pad(
        "",
        "=",
        maxAttWidth + (maxWidth * m_Instances.numClasses())
          + m_Instances.numClasses() + 1, true));
      temp.append("\n");

      // loop over the attributes
      int counter = 0;
      for (int i = 0; i < m_Instances.numAttributes(); i++) {
        if (i == m_Instances.classIndex()) {
          continue;
        }
        String attName = m_Instances.attribute(i).name();
        temp.append(attName + "\n");

        if (m_Distributions[counter][0] instanceof NormalEstimator) {
          String meanL = "  mean";
          temp.append(pad(meanL, " ", maxAttWidth + 1 - meanL.length(), false));
          for (int j = 0; j < m_Instances.numClasses(); j++) {
            // means
            NormalEstimator n = (NormalEstimator) m_Distributions[counter][j];
            String mean = Utils.doubleToString(n.getMean(), maxWidth, 4).trim();
            temp.append(pad(mean, " ", maxWidth + 1 - mean.length(), true));
          }
          temp.append("\n");
          // now do std deviations
          String stdDevL = "  std. dev.";
          temp.append(pad(stdDevL, " ", maxAttWidth + 1 - stdDevL.length(),
            false));
          for (int j = 0; j < m_Instances.numClasses(); j++) {
            NormalEstimator n = (NormalEstimator) m_Distributions[counter][j];
            String stdDev = Utils.doubleToString(n.getStdDev(), maxWidth, 4)
              .trim();
            temp.append(pad(stdDev, " ", maxWidth + 1 - stdDev.length(), true));
          }
          temp.append("\n");
          // now the weight sums
          String weightL = "  weight sum";
          temp.append(pad(weightL, " ", maxAttWidth + 1 - weightL.length(),
            false));
          for (int j = 0; j < m_Instances.numClasses(); j++) {
            NormalEstimator n = (NormalEstimator) m_Distributions[counter][j];
            String weight = Utils.doubleToString(n.getSumOfWeights(), maxWidth,
              4).trim();
            temp.append(pad(weight, " ", maxWidth + 1 - weight.length(), true));
          }
          temp.append("\n");
          // now the precisions
          String precisionL = "  precision";
          temp.append(pad(precisionL, " ",
            maxAttWidth + 1 - precisionL.length(), false));
          for (int j = 0; j < m_Instances.numClasses(); j++) {
            NormalEstimator n = (NormalEstimator) m_Distributions[counter][j];
            String precision = Utils.doubleToString(n.getPrecision(), maxWidth,
              4).trim();
            temp.append(pad(precision, " ", maxWidth + 1 - precision.length(),
              true));
          }
          temp.append("\n\n");

        } else if (m_Distributions[counter][0] instanceof DiscreteEstimator) {
          Attribute a = m_Instances.attribute(i);
          for (int j = 0; j < a.numValues(); j++) {
            String val = "  " + a.value(j);
            temp.append(pad(val, " ", maxAttWidth + 1 - val.length(), false));
            for (int k = 0; k < m_Instances.numClasses(); k++) {
              DiscreteEstimator d = (DiscreteEstimator) m_Distributions[counter][k];
              String count = "" + d.getCount(j);
              temp.append(pad(count, " ", maxWidth + 1 - count.length(), true));
            }
            temp.append("\n");
          }
          // do the totals
          String total = "  [total]";
          temp.append(pad(total, " ", maxAttWidth + 1 - total.length(), false));
          for (int k = 0; k < m_Instances.numClasses(); k++) {
            DiscreteEstimator d = (DiscreteEstimator) m_Distributions[counter][k];
            String count = "" + d.getSumOfCounts();
            temp.append(pad(count, " ", maxWidth + 1 - count.length(), true));
          }
          temp.append("\n\n");
        } else if (m_Distributions[counter][0] instanceof KernelEstimator) {
          String kL = "  [# kernels]";
          temp.append(pad(kL, " ", maxAttWidth + 1 - kL.length(), false));
          for (int k = 0; k < m_Instances.numClasses(); k++) {
            KernelEstimator ke = (KernelEstimator) m_Distributions[counter][k];
            String nk = "" + ke.getNumKernels();
            temp.append(pad(nk, " ", maxWidth + 1 - nk.length(), true));
          }
          temp.append("\n");
          // do num kernels, std. devs and precisions
          String stdDevL = "  [std. dev]";
          temp.append(pad(stdDevL, " ", maxAttWidth + 1 - stdDevL.length(),
            false));
          for (int k = 0; k < m_Instances.numClasses(); k++) {
            KernelEstimator ke = (KernelEstimator) m_Distributions[counter][k];
            String stdD = Utils.doubleToString(ke.getStdDev(), maxWidth, 4)
              .trim();
            temp.append(pad(stdD, " ", maxWidth + 1 - stdD.length(), true));
          }
          temp.append("\n");
          String precL = "  [precision]";
          temp.append(pad(precL, " ", maxAttWidth + 1 - precL.length(), false));
          for (int k = 0; k < m_Instances.numClasses(); k++) {
            KernelEstimator ke = (KernelEstimator) m_Distributions[counter][k];
            String prec = Utils.doubleToString(ke.getPrecision(), maxWidth, 4)
              .trim();
            temp.append(pad(prec, " ", maxWidth + 1 - prec.length(), true));
          }
          temp.append("\n");
          // first determine max number of kernels accross the classes
          int maxK = 0;
          for (int k = 0; k < m_Instances.numClasses(); k++) {
            KernelEstimator ke = (KernelEstimator) m_Distributions[counter][k];
            if (ke.getNumKernels() > maxK) {
              maxK = ke.getNumKernels();
            }
          }
          for (int j = 0; j < maxK; j++) {
            // means first
            String meanL = "  K" + (j + 1) + ": mean (weight)";
            temp
              .append(pad(meanL, " ", maxAttWidth + 1 - meanL.length(), false));
            for (int k = 0; k < m_Instances.numClasses(); k++) {
              KernelEstimator ke = (KernelEstimator) m_Distributions[counter][k];
              double[] means = ke.getMeans();
              double[] weights = ke.getWeights();
              String m = "--";
              if (ke.getNumKernels() == 0) {
                m = "" + 0;
              } else if (j < ke.getNumKernels()) {
                m = Utils.doubleToString(means[j], maxWidth, 4).trim();
                m += " ("
                  + Utils.doubleToString(weights[j], maxWidth, 1).trim() + ")";
              }
              temp.append(pad(m, " ", maxWidth + 1 - m.length(), true));
            }
            temp.append("\n");
          }
          temp.append("\n");
        }

        counter++;
      }
    }

    return temp.toString();
  }

  /**
   * Returns a description of the classifier in the old format.
   * 
   * @return a description of the classifier as a string.
   */
  protected String toStringOriginal() {

    StringBuffer text = new StringBuffer();

    text.append("Naive Bayes Classifier");
    if (m_Instances == null) {
      text.append(": No model built yet.");
    } else {
      try {
        for (int i = 0; i < m_Distributions[0].length; i++) {
          text.append("\n\nClass " + m_Instances.classAttribute().value(i)
            + ": Prior probability = "
            + Utils.doubleToString(m_ClassDistribution.getProbability(i), 4, 2)
            + "\n\n");
          Enumeration enumAtts = m_Instances.enumerateAttributes();
          int attIndex = 0;
          while (enumAtts.hasMoreElements()) {
            Attribute attribute = enumAtts.nextElement();
            if (attribute.weight() > 0) {
              text.append(attribute.name() + ":  "
                + m_Distributions[attIndex][i]);
            }
            attIndex++;
          }
        }
      } catch (Exception ex) {
        text.append(ex.getMessage());
      }
    }

    return text.toString();
  }

  private String pad(String source, String padChar, int length, boolean leftPad) {
    StringBuffer temp = new StringBuffer();

    if (leftPad) {
      for (int i = 0; i < length; i++) {
        temp.append(padChar);
      }
      temp.append(source);
    } else {
      temp.append(source);
      for (int i = 0; i < length; i++) {
        temp.append(padChar);
      }
    }
    return temp.toString();
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String useKernelEstimatorTipText() {
    return "Use a kernel estimator for numeric attributes rather than a "
      + "normal distribution.";
  }

  /**
   * Gets if kernel estimator is being used.
   * 
   * @return Value of m_UseKernelEstimatory.
   */
  public boolean getUseKernelEstimator() {

    return m_UseKernelEstimator;
  }

  /**
   * Sets if kernel estimator is to be used.
   * 
   * @param v Value to assign to m_UseKernelEstimatory.
   */
  public void setUseKernelEstimator(boolean v) {

    m_UseKernelEstimator = v;
    if (v) {
      setUseSupervisedDiscretization(false);
    }
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String useSupervisedDiscretizationTipText() {
    return "Use supervised discretization to convert numeric attributes to nominal "
      + "ones.";
  }

  /**
   * Get whether supervised discretization is to be used.
   * 
   * @return true if supervised discretization is to be used.
   */
  public boolean getUseSupervisedDiscretization() {

    return m_UseDiscretization;
  }

  /**
   * Set whether supervised discretization is to be used.
   * 
   * @param newblah true if supervised discretization is to be used.
   */
  public void setUseSupervisedDiscretization(boolean newblah) {

    m_UseDiscretization = newblah;
    if (newblah) {
      setUseKernelEstimator(false);
    }
  }

  /**
   * Returns the tip text for this property
   * 
   * @return tip text for this property suitable for displaying in the
   *         explorer/experimenter gui
   */
  public String displayModelInOldFormatTipText() {
    return "Use old format for model output. The old format is "
      + "better when there are many class values. The new format "
      + "is better when there are fewer classes and many attributes.";
  }

  /**
   * Set whether to display model output in the old, original format.
   * 
   * @param d true if model ouput is to be shown in the old format
   */
  public void setDisplayModelInOldFormat(boolean d) {
    m_displayModelInOldFormat = d;
  }

  /**
   * Get whether to display model output in the old, original format.
   * 
   * @return true if model ouput is to be shown in the old format
   */
  public boolean getDisplayModelInOldFormat() {
    return m_displayModelInOldFormat;
  }

  /**
   * Return the header that this classifier was trained with
   *
   * @return the header that this classifier was trained with
   */
  public Instances getHeader() {
    return m_Instances;
  }

  /**
   * Get all the conditional estimators.
   *
   * @return all the conditional estimators.
   */
  public Estimator[][] getConditionalEstimators() {
    return m_Distributions;
  }

  /**
   * Get the class estimator.
   *
   * @return the class estimator
   */
  public Estimator getClassEstimator() {
    return m_ClassDistribution;
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 14501 $");
  }

  @SuppressWarnings({ "rawtypes", "unchecked" })
  @Override
  public NaiveBayes aggregate(NaiveBayes toAggregate) throws Exception {

    // Highly unlikely that discretization intervals will match between the
    // two classifiers
    if (m_UseDiscretization || toAggregate.getUseSupervisedDiscretization()) {
      throw new Exception("Unable to aggregate when supervised discretization "
        + "has been turned on");
    }

    if (!m_Instances.equalHeaders(toAggregate.m_Instances)) {
      throw new Exception("Can't aggregate - data headers don't match: "
        + m_Instances.equalHeadersMsg(toAggregate.m_Instances));
    }

    ((Aggregateable) m_ClassDistribution)
      .aggregate(toAggregate.m_ClassDistribution);

    // aggregate all conditional estimators
    for (int i = 0; i < m_Distributions.length; i++) {
      for (int j = 0; j < m_Distributions[i].length; j++) {
        ((Aggregateable) m_Distributions[i][j])
          .aggregate(toAggregate.m_Distributions[i][j]);
      }
    }

    return this;
  }

  @Override
  public void finalizeAggregation() throws Exception {
    // nothing to do
  }

  /**
   * Main method for testing this class.
   * 
   * @param argv the options
   */
  public static void main(String[] argv) {
    runClassifier(new NaiveBayes(), argv);
  }
}