/**
   * Computes average class values for each attribute and value
   *
   * @throws Exception
   */
  private void computeAverageClassValues() throws Exception {

    double totalCounts, sum;
    M5Instance instance;
    double[] counts;

    double[][] avgClassValues = new double[getInputFormat().numAttributes()][0];
    m_Indices = new int[getInputFormat().numAttributes()][0];
    for (int j = 0; j < getInputFormat().numAttributes(); j++) {
      M5Attribute att = getInputFormat().attribute(j);
      if (att.isNominal()) {
        avgClassValues[j] = new double[att.numValues()];
        counts = new double[att.numValues()];
        for (int i = 0; i < getInputFormat().numInstances(); i++) {
          instance = getInputFormat().instance(i);
          if (!instance.classIsMissing() && (!instance.isMissing(j))) {
            counts[(int) instance.value(j)] += instance.weight();
            avgClassValues[j][(int) instance.value(j)] += instance.weight() * instance.classValue();
          }
        }
        sum = M5StaticUtils.sum(avgClassValues[j]);
        totalCounts = M5StaticUtils.sum(counts);
        if (M5StaticUtils.gr(totalCounts, 0)) {
          for (int k = 0; k < att.numValues(); k++) {
            if (M5StaticUtils.gr(counts[k], 0)) {
              avgClassValues[j][k] /= (double) counts[k];
            } else {
              avgClassValues[j][k] = sum / (double) totalCounts;
            }
          }
        }
        m_Indices[j] = M5StaticUtils.sort(avgClassValues[j]);
      }
    }
  }
  /**
   * Parses the options for this object. Valid options are:
   *
   * <p>-N <br>
   * If binary attributes are to be coded as nominal ones.
   *
   * <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 {

    setBinaryAttributesNominal(M5StaticUtils.getFlag('N', options));

    if (getInputFormat() != null) {
      setInputFormat(getInputFormat());
    }
  }
  /**
   * Method for testing filters ability to process multiple batches.
   *
   * @param options should contain the following arguments:<br>
   *     -i (first) input file <br>
   *     -o (first) output file <br>
   *     -r (second) input file <br>
   *     -s (second) output file <br>
   *     -c class_index <br>
   *     or -h for help on options
   * @exception Exception if something goes wrong or the user requests help on command options
   */
  public static void batchFilterFile(NominalToBinaryFilter filter, String[] options)
      throws Exception {

    M5Instances firstData = null;
    M5Instances secondData = null;
    Reader firstInput = null;
    Reader secondInput = null;
    PrintWriter firstOutput = null;
    PrintWriter secondOutput = null;
    boolean helpRequest;
    try {
      helpRequest = M5StaticUtils.getFlag('h', options);

      String fileName = M5StaticUtils.getOption('i', options);
      if (fileName.length() != 0) {
        firstInput = new BufferedReader(new FileReader(fileName));
      } else {
        throw new Exception("No first input file given.\n");
      }

      fileName = M5StaticUtils.getOption('r', options);
      if (fileName.length() != 0) {
        secondInput = new BufferedReader(new FileReader(fileName));
      } else {
        throw new Exception("No second input file given.\n");
      }

      fileName = M5StaticUtils.getOption('o', options);
      if (fileName.length() != 0) {
        firstOutput = new PrintWriter(new FileOutputStream(fileName));
      } else {
        firstOutput = new PrintWriter(System.out);
      }

      fileName = M5StaticUtils.getOption('s', options);
      if (fileName.length() != 0) {
        secondOutput = new PrintWriter(new FileOutputStream(fileName));
      } else {
        secondOutput = new PrintWriter(System.out);
      }
      String classIndex = M5StaticUtils.getOption('c', options);

      if (filter instanceof NominalToBinaryFilter) {
        ((NominalToBinaryFilter) filter).setOptions(options);
      }
      M5StaticUtils.checkForRemainingOptions(options);

      if (helpRequest) {
        throw new Exception("Help requested.\n");
      }
      firstData = new M5Instances(firstInput, 1);
      secondData = new M5Instances(secondInput, 1);
      if (!secondData.equalHeaders(firstData)) {
        throw new Exception("Input file formats differ.\n");
      }
      if (classIndex.length() != 0) {
        if (classIndex.equals("first")) {
          firstData.setClassIndex(0);
          secondData.setClassIndex(0);
        } else if (classIndex.equals("last")) {
          firstData.setClassIndex(firstData.numAttributes() - 1);
          secondData.setClassIndex(secondData.numAttributes() - 1);
        } else {
          firstData.setClassIndex(Integer.parseInt(classIndex) - 1);
          secondData.setClassIndex(Integer.parseInt(classIndex) - 1);
        }
      }
    } catch (Exception ex) {
      String filterOptions = "";
      // Output the error and also the valid options
      if (filter instanceof NominalToBinaryFilter) {
        filterOptions += "\nFilter options:\n\n";
        Enumeration enume = ((NominalToBinaryFilter) filter).listOptions();
        while (enume.hasMoreElements()) {
          Information option = (Information) enume.nextElement();
          filterOptions += option.synopsis() + '\n' + option.description() + "\n";
        }
      }

      String genericOptions =
          "\nGeneral options:\n\n"
              + "-h\n"
              + "\tGet help on available options.\n"
              + "-i <filename>\n"
              + "\tThe file containing first input instances.\n"
              + "-o <filename>\n"
              + "\tThe file first output instances will be written to.\n"
              + "-r <filename>\n"
              + "\tThe file containing second input instances.\n"
              + "-s <filename>\n"
              + "\tThe file second output instances will be written to.\n"
              + "-c <class index>\n"
              + "\tThe number of the attribute to use as the class.\n"
              + "\t\"first\" and \"last\" are also valid entries.\n"
              + "\tIf not supplied then no class is assigned.\n";

      throw new Exception('\n' + ex.getMessage() + filterOptions + genericOptions);
    }
    boolean printedHeader = false;
    if (filter.setInputFormat(firstData)) {
      firstOutput.println(filter.getOutputFormat().toString());
      printedHeader = true;
    }

    // Pass all the instances to the filter
    while (firstData.readInstance(firstInput)) {
      if (filter.input(firstData.instance(0))) {
        if (!printedHeader) {
          throw new Error("Filter didn't return true from setInputFormat() " + "earlier!");
        }
        firstOutput.println(filter.output().toString());
      }
      firstData.delete(0);
    }

    // Say that input has finished, and print any pending output instances
    if (filter.batchFinished()) {
      if (!printedHeader) {
        firstOutput.println(filter.getOutputFormat().toString());
      }
      while (filter.numPendingOutput() > 0) {
        firstOutput.println(filter.output().toString());
      }
    }

    if (firstOutput != null) {
      firstOutput.close();
    }
    printedHeader = false;
    if (filter.isOutputFormatDefined()) {
      secondOutput.println(filter.getOutputFormat().toString());
      printedHeader = true;
    }
    // Pass all the second instances to the filter
    while (secondData.readInstance(secondInput)) {
      if (filter.input(secondData.instance(0))) {
        if (!printedHeader) {
          throw new Error("Filter didn't return true from" + " isOutputFormatDefined() earlier!");
        }
        secondOutput.println(filter.output().toString());
      }
      secondData.delete(0);
    }

    // Say that input has finished, and print any pending output instances
    if (filter.batchFinished()) {
      if (!printedHeader) {
        secondOutput.println(filter.getOutputFormat().toString());
      }
      while (filter.numPendingOutput() > 0) {
        secondOutput.println(filter.output().toString());
      }
    }
    if (secondOutput != null) {
      secondOutput.close();
    }
  }
  /**
   * Method for testing filters.
   *
   * @param options should contain the following arguments: <br>
   *     -i input_file <br>
   *     -o output_file <br>
   *     -c class_index <br>
   *     or -h for help on options
   * @exception Exception if something goes wrong or the user requests help on command options
   */
  public static void filterFile(NominalToBinaryFilter filter, String[] options) throws Exception {

    boolean debug = false;
    M5Instances data = null;
    Reader input = null;
    PrintWriter output = null;
    boolean helpRequest;

    try {
      helpRequest = M5StaticUtils.getFlag('h', options);

      if (M5StaticUtils.getFlag('d', options)) {
        debug = true;
      }
      String infileName = M5StaticUtils.getOption('i', options);
      String outfileName = M5StaticUtils.getOption('o', options);
      String classIndex = M5StaticUtils.getOption('c', options);

      if (filter instanceof NominalToBinaryFilter) {
        ((NominalToBinaryFilter) filter).setOptions(options);
      }

      M5StaticUtils.checkForRemainingOptions(options);
      if (helpRequest) {
        throw new Exception("Help requested.\n");
      }
      if (infileName.length() != 0) {
        input = new BufferedReader(new FileReader(infileName));
      } else {
        input = new BufferedReader(new InputStreamReader(System.in));
      }
      if (outfileName.length() != 0) {
        output = new PrintWriter(new FileOutputStream(outfileName));
      } else {
        output = new PrintWriter(System.out);
      }

      data = new M5Instances(input, 1);
      if (classIndex.length() != 0) {
        if (classIndex.equals("first")) {
          data.setClassIndex(0);
        } else if (classIndex.equals("last")) {
          data.setClassIndex(data.numAttributes() - 1);
        } else {
          data.setClassIndex(Integer.parseInt(classIndex) - 1);
        }
      }
    } catch (Exception ex) {
      String filterOptions = "";
      // Output the error and also the valid options
      if (filter instanceof NominalToBinaryFilter) {
        filterOptions += "\nFilter options:\n\n";
        Enumeration enuma = ((NominalToBinaryFilter) filter).listOptions();
        while (enuma.hasMoreElements()) {
          Information option = (Information) enuma.nextElement();
          filterOptions += option.synopsis() + '\n' + option.description() + "\n";
        }
      }

      String genericOptions =
          "\nGeneral options:\n\n"
              + "-h\n"
              + "\tGet help on available options.\n"
              + "\t(use -b -h for help on batch mode.)\n"
              + "-i <file>\n"
              + "\tThe name of the file containing input instances.\n"
              + "\tIf not supplied then instances will be read from stdin.\n"
              + "-o <file>\n"
              + "\tThe name of the file output instances will be written to.\n"
              + "\tIf not supplied then instances will be written to stdout.\n"
              + "-c <class index>\n"
              + "\tThe number of the attribute to use as the class.\n"
              + "\t\"first\" and \"last\" are also valid entries.\n"
              + "\tIf not supplied then no class is assigned.\n";

      throw new Exception('\n' + ex.getMessage() + filterOptions + genericOptions);
    }

    if (debug) {
      System.err.println("Setting input format");
    }
    boolean printedHeader = false;
    if (filter.setInputFormat(data)) {
      if (debug) {
        System.err.println("Getting output format");
      }
      output.println(filter.getOutputFormat().toString());
      printedHeader = true;
    }

    // Pass all the instances to the filter
    while (data.readInstance(input)) {
      if (debug) {
        System.err.println("Input instance to filter");
      }
      if (filter.input(data.instance(0))) {
        if (debug) {
          System.err.println("Filter said collect immediately");
        }
        if (!printedHeader) {
          throw new Error("Filter didn't return true from setInputFormat() " + "earlier!");
        }
        if (debug) {
          System.err.println("Getting output instance");
        }
        output.println(filter.output().toString());
      }
      data.delete(0);
    }

    // Say that input has finished, and print any pending output instances
    if (debug) {
      System.err.println("Setting end of batch");
    }
    if (filter.batchFinished()) {
      if (debug) {
        System.err.println("Filter said collect output");
      }
      if (!printedHeader) {
        if (debug) {
          System.err.println("Getting output format");
        }
        output.println(filter.getOutputFormat().toString());
      }
      if (debug) {
        System.err.println("Getting output instance");
      }
      while (filter.numPendingOutput() > 0) {
        output.println(filter.output().toString());
        if (debug) {
          System.err.println("Getting output instance");
        }
      }
    }
    if (debug) {
      System.err.println("Done");
    }

    if (output != null) {
      output.close();
    }
  }