utils.java

wekaUT是 university texas austin 开发的基于weka的半指导学习(semi supervised learning)的分类器

	    if (i + 1 == options.length) {
	      throw new Exception("No value given for -" + flag + " option.");
	    }
	    options[i] = "";
	    newString = new String(options[i + 1]);
	    options[i + 1] = "";
	    return newString;
	  }
	  if (options[i].charAt(1) == '-') {
	    return "";
	  }
	}
      }
    }
    return "";
  }

  /**
   * Quotes a string if it contains special characters.
   * 
   * The following rules are applied:
   *
   * A character is backquoted version of it is one 
   * of <tt>" ' % \ \n \r \t</tt>.
   *
   * A string is enclosed within single quotes if a character has been
   * backquoted using the previous rule above or contains 
   * <tt>{ }</tt> or is exactly equal to the strings 
   * <tt>, ? space or ""</tt> (empty string).
   *
   * A quoted question mark distinguishes it from the missing value which
   * is represented as an unquoted question mark in arff files.
   *
   * @param string the string to be quoted
   * @return the string (possibly quoted)
   */
  public static String quote(String string) {
      boolean quote = false;

      // backquote the following characters 
      if ((string.indexOf('\n') != -1) || (string.indexOf('\r') != -1) || 
	  (string.indexOf('\'') != -1) || (string.indexOf('"') != -1) || 
	  (string.indexOf('\\') != -1) || 
	  (string.indexOf('\t') != -1) || (string.indexOf('%') != -1)) {
	  string = backQuoteChars(string);
	  quote = true;
      }

      // Enclose the string in 's if the string contains a recently added
      // backquote or contains one of the following characters.
      if((quote == true) || 
	 (string.indexOf('{') != -1) || (string.indexOf('}') != -1) ||
	 (string.indexOf(',') != -1) || (string.equals("?")) ||
	 (string.indexOf(' ') != -1) || (string.equals(""))) {
	  string = ("'".concat(string)).concat("'");
      }

      return string;
  }

  /**
   * Converts carriage returns and new lines in a string into \r and \n.
   * Backquotes the following characters: ` " \ \t and %
   * @param string the string
   * @return the converted string
   */
  public static String backQuoteChars(String string) {

    int index;
    StringBuffer newStringBuffer;

    // replace each of the following characters with the backquoted version
    char   charsFind[] =    {'\\',   '\'',  '\t',  '"',    '%'};
    String charsReplace[] = {"\\\\", "\\'", "\\t", "\\\"", "\\%"};
    for(int i = 0; i < charsFind.length; i++) {
	if (string.indexOf(charsFind[i]) != -1 ) {
	    newStringBuffer = new StringBuffer();
	    while ((index = string.indexOf(charsFind[i])) != -1) {
		if (index > 0) {
		    newStringBuffer.append(string.substring(0, index));
		}
		newStringBuffer.append(charsReplace[i]);
		if ((index + 1) < string.length()) {
		    string = string.substring(index + 1);
		} else {
		    string = "";
		}
	    }
	    newStringBuffer.append(string);
	    string = newStringBuffer.toString();
	}
    }

    return Utils.convertNewLines(string);
  }

  /**
   * Converts carriage returns and new lines in a string into \r and \n.
   * @param string the string
   * @return the converted string
   */
  public static String convertNewLines(String string) {
    
    int index;

    // Replace with \n
    StringBuffer newStringBuffer = new StringBuffer();
    while ((index = string.indexOf('\n')) != -1) {
      if (index > 0) {
	newStringBuffer.append(string.substring(0, index));
      }
      newStringBuffer.append('\\');
      newStringBuffer.append('n');
      if ((index + 1) < string.length()) {
	string = string.substring(index + 1);
      } else {
	string = "";
      }
    }
    newStringBuffer.append(string);
    string = newStringBuffer.toString();

    // Replace with \r
    newStringBuffer = new StringBuffer();
    while ((index = string.indexOf('\r')) != -1) {
      if (index > 0) {
	newStringBuffer.append(string.substring(0, index));
      }
      newStringBuffer.append('\\');
      newStringBuffer.append('r');
      if ((index + 1) < string.length()){
	string = string.substring(index + 1);
      } else {
	string = "";
      }
    }
    newStringBuffer.append(string);
    return newStringBuffer.toString();
  }
    

  /**
   * 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 "--". 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("--")) {
	options[i++] = "";
	String [] result = new String [options.length - i];
	for (int j = i; j < options.length; j++) {
	  result[j - i] = options[j];
	  options[j] = "";
	}
	return result;
      }
    }
    return new String [0];
  }

  /**
   * Split up a string containing options into an array of strings,
   * one for each option.
   *
   * @param optionString the string containing the options
   * @return the array of options
   */
  public static String [] splitOptions(String optionString) {

    FastVector optionsVec = new FastVector();
    StringTokenizer st = new StringTokenizer(optionString);
    while (st.hasMoreTokens())
      optionsVec.addElement(st.nextToken());

    String [] options = new String[optionsVec.size()];
    for (int i = 0; i < optionsVec.size(); i++) {
      options[i] = (String)optionsVec.elementAt(i);
    }
    return options;
  }

  /**
   * Joins all the options in an option array into a single string,
   * as might be used on the command line.
   *
   * @param optionArray the array of options
   * @return the string containing all options.
   */
  public static String joinOptions(String [] optionArray) {

    String optionString = "";
    for (int i = 0; i < optionArray.length; i++) {
      if (optionArray[i].equals("")) {
	continue;
      }
      if (optionArray[i].indexOf(' ') != -1) {
	optionString += '"' + optionArray[i] + '"';
      } else {
	optionString += optionArray[i];
      }
      optionString += " ";
    }
    return optionString.trim();
  }
  
  /**
   * Creates a new instance of an object given it's class name and
   * (optional) arguments to pass to it's setOptions method. If the
   * object implements OptionHandler and the options parameter is
   * non-null, the object will have it's options set. Example use:<p>
   *
   * <code> <pre>
   * String classifierName = Utils.getOption('W', options);
   * Classifier c = (Classifier)Utils.forName(Classifier.class,
   *                                          classifierName,
   *                                          options);
   * setClassifier(c);
   * </pre></code>
   *
   * @param classType the class that the instantiated object should
   * be assignable to -- an exception is thrown if this is not the case
   * @param className the fully qualified class name of the object
   * @param options an array of options suitable for passing to setOptions. May
   * be null. Any options accepted by the object will be removed from the
   * array.
   * @return the newly created object, ready for use.
   * @exception Exception if the class name is invalid, or if the
   * class is not assignable to the desired class type, or the options
   * supplied are not acceptable to the object
   */
  public static Object forName(Class classType,
			       String className,
			       String [] options) throws Exception {

    Class c = null;
    try {
      c = Class.forName(className);
    } catch (Exception ex) {
      throw new Exception("Can't find class called: " + className);
    }
    if (!classType.isAssignableFrom(c)) {
      throw new Exception(classType.getName() + " is not assignable from "
			  + className);
    }
    Object o = c.newInstance();
    if ((o instanceof OptionHandler)
	&& (options != null)) {
      ((OptionHandler)o).setOptions(options);
      Utils.checkForRemainingOptions(options);
    }
    return o;
  }

  /**
   * Computes entropy for an array of integers.
   *
   * @param counts array of counts
   * @return - a log2 a - b log2 b - c log2 c + (a+b+c) log2 (a+b+c)
   * when given array [a b c]
   */
  public static double info(int counts[]) {
    
    int total = 0; int c;
    double x = 0;
    for (int j = 0; j < counts.length; j++) {
      x -= xlogx(counts[j]);
      total += counts[j];
    }
    return x + xlogx(total);
  }

  /**
   * Tests if a is smaller or equal to b.
   *
   * @param a a double
   * @param b a double
   */
  public static boolean smOrEq(double a,double b) {
    
    return (a-b < SMALL);
  }

  /**
   * Tests if a is greater or equal to b.
   *
   * @param a a double
   * @param b a double
   */
  public static boolean grOrEq(double a,double b) {
    
    return (b-a < SMALL);
  }
  
  /**
   * Tests if a is smaller than b.
   *
   * @param a a double
   * @param b a double
   */
  public static boolean sm(double a,double b) {
    
    return (b-a > SMALL);
  }

  /**
   * Tests if a is smaller than b.
   *
   * @param a a double
   * @param b a double 
   */
  public static boolean gr(double a,double b) {
    
    return (a-b > SMALL);
  }

  /**
   * Returns the logarithm of a for base 2.
   *
   * @param a a double
   */
  public static double log2(double a) {
    
    return Math.log(a) / log2;
  }

  /**
   * Returns index of maximum element in a given
   * array of doubles. First maximum is returned.
   *
   * @param doubles the array of doubles
   * @return the index of the maximum element
   */
  public static int maxIndex(double [] doubles) {

    double maximum = 0;
    int maxIndex = 0;

    for (int i = 0; i < doubles.length; i++) {
      if ((i == 0) || (doubles[i] > maximum)) {
	maxIndex = i;
	maximum = doubles[i];
      }
    }

    return maxIndex;
  }

  /**
   * Returns index of maximum element in a given
   * array of integers. First maximum is returned.
   *
   * @param ints the array of integers
   * @return the index of the maximum element
   */
  public static int maxIndex(int [] ints) {

    int maximum = 0;
    int maxIndex = 0;

    for (int i = 0; i < ints.length; i++) {
      if ((i == 0) || (ints[i] > maximum)) {
	maxIndex = i;
	maximum = ints[i];
      }
    }

    return maxIndex;
  }

  /**
   * Computes the mean for an array of doubles.
   *
   * @param vector the array
   * @return the mean
   */
  public static double mean(double[] vector) {
  
    double sum = 0;

    if (vector.length == 0) {
      return 0;
    }
    for (int i = 0; i < vector.length; i++) {
      sum += vector[i];
    }
    return sum / (double) vector.length;
  }

  /**
   * Returns index of minimum element in a given
   * array of integers. First minimum is returned.
   *
   * @param ints the array of integers
   * @return the index of the minimum element
   */
  public static int minIndex(int [] ints) {

    int minimum = 0;
    int minIndex = 0;

    for (int i = 0; i < ints.length; i++) {
      if ((i == 0) || (ints[i] < minimum)) {
	minIndex = i;
	minimum = ints[i];
      }
    }

    return minIndex;
  }

  /**
   * Returns index of minimum element in a given
   * array of doubles. First minimum is returned.
   *
   * @param doubles the array of doubles
   * @return the index of the minimum element
   */
  public static int minIndex(double [] doubles) {

    double minimum = 0;
    int minIndex = 0;

    for (int i = 0; i < doubles.length; i++) {
      if ((i == 0) || (doubles[i] < minimum)) {
	minIndex = i;
	minimum = doubles[i];
      }
    }

    return minIndex;
  }

  /**
   * Normalizes the doubles in the array by their sum.
   *
   * @param doubles the array of double
   * @exception IllegalArgumentException if sum is Zero or NaN
   */
  public static void normalize(double[] doubles) {

    double sum = 0;
    for (int i = 0; i < doubles.length; i++) {
      sum += doubles[i];
    }
    normalize(doubles, sum);
  }

  /**
   * Normalizes the doubles in the array using the given value.
   *
   * @param doubles the array of double
   * @param sum the value by which the doubles are to be normalized
   * @exception IllegalArgumentException if sum is zero or NaN
   */
  public static void normalize(double[] doubles, double sum) {

    if (Double.isNaN(sum)) {
      throw new IllegalArgumentException("Can't normalize array. Sum is NaN.");
    }
    if (sum == 0) {
      // Maybe this should just be a return.
      throw new IllegalArgumentException("Can't normalize array. Sum is zero.");
    }
    for (int i = 0; i < doubles.length; i++) {
      doubles[i] /= sum;
    }
  }

  /**