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## weka.core
Class Utils

    java.lang.Object
      weka.core.Utils

All Implemented Interfaces:
  RevisionHandler

    public final class Utils

extends java.lang.Object
implements RevisionHandler

Class implementing some simple utility methods.

Version:
  $Revision: 9389 $
Author:
  Eibe Frank, Yong Wang, Len Trigg, Julien Prados

Field Summary
`static double` | `log2` The natural logarithm of 2.
`static double` | `SMALL` The small deviation allowed in double comparisons.

Constructor Summary
`Utils()`

Method Summary
`static java.lang.String` | `arrayToString(java.lang.Object array)` Returns the given Array in a string representation.
`static java.lang.String` | `backQuoteChars(java.lang.String string)` Converts carriage returns and new lines in a string into \r and \n.
`static void` | `checkForRemainingOptions(java.lang.String[] options)` Checks if the given array contains any non-empty options.
`static java.lang.String` | `convertNewLines(java.lang.String string)` Converts carriage returns and new lines in a string into \r and \n.
`static java.io.File` | `convertToRelativePath(java.io.File absolute)` Converts a File's absolute path to a path relative to the user (ie start) directory.
`static double` | `correlation(double[] y1, double[] y2, int n)` Returns the correlation coefficient of two double vectors.
`static java.lang.String` | `doubleToString(double value, int afterDecimalPoint)` Rounds a double and converts it into String.
`static java.lang.String` | `doubleToString(double value, int width, int afterDecimalPoint)` Rounds a double and converts it into a formatted decimal-justified String.
`static boolean` | `eq(double a, double b)` Tests if a is equal to b.
`static java.lang.Object` | `forName(java.lang.Class classType, java.lang.String className, java.lang.String[] options)` Creates a new instance of an object given it's class name and (optional) arguments to pass to it's setOptions method.
`static java.lang.Class` | `getArrayClass(java.lang.Class c)` Returns the basic class of an array class (handles multi-dimensional arrays).
`static int` | `getArrayDimensions(java.lang.Class array)` Returns the dimensions of the given array.
`static int` | `getArrayDimensions(java.lang.Object array)` Returns the dimensions of the given array.
`static boolean` | `getFlag(char flag, java.lang.String[] options)` Checks if the given array contains the flag "-Char".
`static boolean` | `getFlag(java.lang.String flag, java.lang.String[] options)` Checks if the given array contains the flag "-String".
`static java.lang.String` | `getOption(char flag, java.lang.String[] options)` Gets an option indicated by a flag "-Char" from the given array of strings.
`static java.lang.String` | `getOption(java.lang.String flag, java.lang.String[] options)` Gets an option indicated by a flag "-String" from the given array of strings.
`static int` | `getOptionPos(char flag, java.lang.String[] options)` Gets the index of an option or flag indicated by a flag "-Char" from the given array of strings.
`static int` | `getOptionPos(java.lang.String flag, java.lang.String[] options)` Gets the index of an option or flag indicated by a flag "-String" from the given array of strings.
`java.lang.String` | `getRevision()` Returns the revision string.
`static boolean` | `gr(double a, double b)` Tests if a is greater than b.
`static boolean` | `grOrEq(double a, double b)` Tests if a is greater or equal to b.
`static double` | `info(int[] counts)` Computes entropy for an array of integers.
`static java.lang.String` | `joinOptions(java.lang.String[] optionArray)` Joins all the options in an option array into a single string, as might be used on the command line.
`static double` | `kthSmallestValue(double[] array, int k)` Returns the kth-smallest value in the array
`static int` | `kthSmallestValue(int[] array, int k)` Returns the kth-smallest value in the array.
`static double` | `log2(double a)` Returns the logarithm of a for base 2.
`static double[]` | `logs2probs(double[] a)` Converts an array containing the natural logarithms of probabilities stored in a vector back into probabilities.
`static void` | `main(java.lang.String[] ops)` Main method for testing this class.
`static int` | `maxIndex(double[] doubles)` Returns index of maximum element in a given array of doubles.
`static int` | `maxIndex(int[] ints)` Returns index of maximum element in a given array of integers.
`static double` | `mean(double[] vector)` Computes the mean for an array of doubles.
`static int` | `minIndex(double[] doubles)` Returns index of minimum element in a given array of doubles.
`static int` | `minIndex(int[] ints)` Returns index of minimum element in a given array of integers.
`static void` | `normalize(double[] doubles)` Normalizes the doubles in the array by their sum.
`static void` | `normalize(double[] doubles, double sum)` Normalizes the doubles in the array using the given value.
`static java.lang.String` | `padLeft(java.lang.String inString, int length)` Pads a string to a specified length, inserting spaces on the left as required.
`static java.lang.String` | `padRight(java.lang.String inString, int length)` Pads a string to a specified length, inserting spaces on the right as required.
`static java.lang.String[]` | `partitionOptions(java.lang.String[] options)` Returns the secondary set of options (if any) contained in the supplied options array.
`static int` | `probRound(double value, java.util.Random rand)` Rounds a double to the next nearest integer value in a probabilistic fashion (e.g.
`static double` | `probToLogOdds(double prob)` Returns the log-odds for a given probabilitiy.
`static java.lang.String` | `quote(java.lang.String string)` Quotes a string if it contains special characters.
`static java.util.Properties` | `readProperties(java.lang.String resourceName)` Reads properties that inherit from three locations.
`static java.lang.String` | `removeSubstring(java.lang.String inString, java.lang.String substring)` Removes all occurrences of a string from another string.
`static void` | `replaceMissingWithMAX_VALUE(double[] array)` Replaces all "missing values" in the given array of double values with MAX_VALUE.
`static java.lang.String` | `replaceSubstring(java.lang.String inString, java.lang.String subString, java.lang.String replaceString)` Replaces with a new string, all occurrences of a string from another string.
`static java.lang.String` | `revertNewLines(java.lang.String string)` Reverts \r and \n in a string into carriage returns and new lines.
`static int` | `round(double value)` Rounds a double to the next nearest integer value.
`static double` | `roundDouble(double value, int afterDecimalPoint)` Rounds a double to the given number of decimal places.
`static boolean` | `sm(double a, double b)` Tests if a is smaller than b.
`static boolean` | `smOrEq(double a, double b)` Tests if a is smaller or equal to b.
`static int[]` | `sort(double[] array)` Sorts a given array of doubles in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array.
`static int[]` | `sort(int[] array)` Sorts a given array of integers in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array.
`static int[]` | `sortWithNoMissingValues(double[] array)` Sorts a given array of doubles in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array.
`static java.lang.String[]` | `splitOptions(java.lang.String quotedOptionString)` Split up a string containing options into an array of strings, one for each option.
`static int[]` | `stableSort(double[] array)` Sorts a given array of doubles in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array.
`static double` | `sum(double[] doubles)` Computes the sum of the elements of an array of doubles.
`static int` | `sum(int[] ints)` Computes the sum of the elements of an array of integers.
`static java.lang.String` | `unbackQuoteChars(java.lang.String string)` The inverse operation of backQuoteChars().
`static java.lang.String` | `unquote(java.lang.String string)` unquotes are previously quoted string (but only if necessary), i.e., it removes the single quotes around it.
`static double` | `variance(double[] vector)` Computes the variance for an array of doubles.
`static double` | `xlogx(int c)` Returns c*log2(c) for a given integer value c.

Methods inherited from class java.lang.Object
`equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

### log2

    public static double log2

  The natural logarithm of 2.

### SMALL

    public static double SMALL

  The small deviation allowed in double comparisons.

Constructor Detail

### Utils

    public Utils()

Method Detail

### readProperties

    public static java.util.Properties readProperties(java.lang.String resourceName)
                                               throws java.lang.Exception

  Reads properties that inherit from three locations. Properties are first defined in the system resource location (i.e. in the CLASSPATH). These default properties must exist. Properties defined in the users home directory (optional) override default settings. Properties defined in the current directory (optional) override all these settings.

  Parameters:
    `resourceName` - the location of the resource that should be loaded. e.g.: "weka/core/Utils.props". (The use of hardcoded forward slashes here is OK - see jdk1.1/docs/guide/misc/resources.html) This routine will also look for the file (in this case) "Utils.props" in the users home directory and the current directory.
  Returns:
    the Properties
  Throws:
    `java.lang.Exception` - if no default properties are defined, or if an error occurs reading the properties files.

### correlation

    public static final double correlation(double[] y1,
                                           double[] y2,
                                           int n)

  Returns the correlation coefficient of two double vectors.

  Parameters:
    `y1` - double vector 1
    `y2` - double vector 2
    `n` - the length of two double vectors
  Returns:
    the correlation coefficient

### removeSubstring

    public static java.lang.String removeSubstring(java.lang.String inString,
                                                   java.lang.String substring)

  Removes all occurrences of a string from another string.

  Parameters:
    `inString` - the string to remove substrings from.
    `substring` - the substring to remove.
  Returns:
    the input string with occurrences of substring removed.

### replaceSubstring

    public static java.lang.String replaceSubstring(java.lang.String inString,
                                                    java.lang.String subString,
                                                    java.lang.String replaceString)

  Replaces with a new string, all occurrences of a string from another string.

  Parameters:
    `inString` - the string to replace substrings in.
    `subString` - the substring to replace.
    `replaceString` - the replacement substring
  Returns:
    the input string with occurrences of substring replaced.

### padLeft

    public static java.lang.String padLeft(java.lang.String inString,
                                           int length)

  Pads a string to a specified length, inserting spaces on the left as required. If the string is too long, characters are removed (from the right).

  Parameters:
    `inString` - the input string
    `length` - the desired length of the output string
  Returns:
    the output string

### padRight

    public static java.lang.String padRight(java.lang.String inString,
                                            int length)

  Pads a string to a specified length, inserting spaces on the right as required. If the string is too long, characters are removed (from the right).

  Parameters:
    `inString` - the input string
    `length` - the desired length of the output string
  Returns:
    the output string

### doubleToString

    public static java.lang.String doubleToString(double value,
                                                  int afterDecimalPoint)

  Rounds a double and converts it into String.

  Parameters:
    `value` - the double value
    `afterDecimalPoint` - the (maximum) number of digits permitted after the decimal point
  Returns:
    the double as a formatted string

### doubleToString

    public static java.lang.String doubleToString(double value,
                                                  int width,
                                                  int afterDecimalPoint)

  Rounds a double and converts it into a formatted decimal-justified String. Trailing 0's are replaced with spaces.

  Parameters:
    `value` - the double value
    `width` - the width of the string
    `afterDecimalPoint` - the number of digits after the decimal point
  Returns:
    the double as a formatted string

### getArrayClass

    public static java.lang.Class getArrayClass(java.lang.Class c)

  Returns the basic class of an array class (handles multi-dimensional arrays).

  Parameters:
    `c` - the array to inspect
  Returns:
    the class of the innermost elements

### getArrayDimensions

    public static int getArrayDimensions(java.lang.Class array)

  Returns the dimensions of the given array. Even though the parameter is of type "Object" one can hand over primitve arrays, e.g. int[3] or double[2][4].

  Parameters:
    `array` - the array to determine the dimensions for
  Returns:
    the dimensions of the array

### getArrayDimensions

    public static int getArrayDimensions(java.lang.Object array)

  Returns the dimensions of the given array. Even though the parameter is of type "Object" one can hand over primitve arrays, e.g. int[3] or double[2][4].

  Parameters:
    `array` - the array to determine the dimensions for
  Returns:
    the dimensions of the array

### arrayToString

    public static java.lang.String arrayToString(java.lang.Object array)

  Returns the given Array in a string representation. Even though the parameter is of type "Object" one can hand over primitve arrays, e.g. int[3] or double[2][4].

  Parameters:
    `array` - the array to return in a string representation
  Returns:
    the array as string

### eq

    public static boolean eq(double a,
                             double b)

  Tests if a is equal to b.

  Parameters:
    `a` - a double
    `b` - a double

### checkForRemainingOptions

    public static void checkForRemainingOptions(java.lang.String[] options)
                                         throws java.lang.Exception

  Checks if the given array contains any non-empty options.

  Parameters:
    `options` - an array of strings
  Throws:
    `java.lang.Exception` - if there are any non-empty options

### getFlag

    public static boolean getFlag(char flag,
                                  java.lang.String[] options)
                           throws java.lang.Exception

  Checks if the given array contains the flag "-Char". Stops searching at the first marker "--". If the flag is found, it is replaced with the empty string.

  Parameters:
    `flag` - the character indicating the flag.
    `options` - the array of strings containing all the options.
  Returns:
    true if the flag was found
  Throws:
    `java.lang.Exception` - if an illegal option was found

### getFlag

    public static boolean getFlag(java.lang.String flag,
                                  java.lang.String[] options)
                           throws java.lang.Exception

  Checks if the given array contains the flag "-String". Stops searching at the first marker "--". If the flag is found, it is replaced with the empty string.

  Parameters:
    `flag` - the String indicating the flag.
    `options` - the array of strings containing all the options.
  Returns:
    true if the flag was found
  Throws:
    `java.lang.Exception` - if an illegal option was found

### getOption

    public static java.lang.String getOption(char flag,
                                             java.lang.String[] options)
                                      throws java.lang.Exception

  Gets an option indicated by a flag "-Char" from the given array of strings. Stops searching at the first marker "--". Replaces flag and option with empty strings.

  Parameters:
    `flag` - the character indicating the option.
    `options` - the array of strings containing all the options.
  Returns:
    the indicated option or an empty string
  Throws:
    `java.lang.Exception` - if the option indicated by the flag can't be found

### getOption

    public static java.lang.String getOption(java.lang.String flag,
                                             java.lang.String[] options)
                                      throws java.lang.Exception

  Gets an option indicated by a flag "-String" from the given array of strings. Stops searching at the first marker "--". Replaces flag and option with empty strings.

  Parameters:
    `flag` - the String indicating the option.
    `options` - the array of strings containing all the options.
  Returns:
    the indicated option or an empty string
  Throws:
    `java.lang.Exception` - if the option indicated by the flag can't be found

### getOptionPos

    public static int getOptionPos(char flag,
                                   java.lang.String[] options)

  Gets the index of an option or flag indicated by a flag "-Char" from the given array of strings. Stops searching at the first marker "--".

  Parameters:
    `flag` - the character indicating the option.
    `options` - the array of strings containing all the options.
  Returns:
    the position if found, or -1 otherwise

### getOptionPos

    public static int getOptionPos(java.lang.String flag,
                                   java.lang.String[] options)

  Gets the index of an option or flag indicated by a flag "-String" from the given array of strings. Stops searching at the first marker "--".

  Parameters:
    `flag` - the String indicating the option.
    `options` - the array of strings containing all the options.
  Returns:
    the position if found, or -1 otherwise

### quote

    public static java.lang.String quote(java.lang.String string)

  Quotes a string if it contains special characters. The following rules are applied: A character is backquoted version of it is one of `" ' % \ \n \r \t` . A string is enclosed within single quotes if a character has been backquoted using the previous rule above or contains `{ }` or is exactly equal to the strings `, ? space or ""` (empty string). A quoted question mark distinguishes it from the missing value which is represented as an unquoted question mark in arff files.

  Parameters:
    `string` - the string to be quoted
  Returns:
    the string (possibly quoted)
  See Also:
    `unquote(String)`

### unquote

    public static java.lang.String unquote(java.lang.String string)

  unquotes are previously quoted string (but only if necessary), i.e., it removes the single quotes around it. Inverse to quote(String).

  Parameters:
    `string` - the string to process
  Returns:
    the unquoted string
  See Also:
    `quote(String)`

### backQuoteChars

    public static java.lang.String backQuoteChars(java.lang.String string)

  Converts carriage returns and new lines in a string into \r and \n. Backquotes the following characters: ` " \ \t and %

  Parameters:
    `string` - the string
  Returns:
    the converted string
  See Also:
    `unbackQuoteChars(String)`

### convertNewLines

    public static java.lang.String convertNewLines(java.lang.String string)

  Converts carriage returns and new lines in a string into \r and \n.

  Parameters:
    `string` - the string
  Returns:
    the converted string

### revertNewLines

    public static java.lang.String revertNewLines(java.lang.String string)

  Reverts \r and \n in a string into carriage returns and new lines.

  Parameters:
    `string` - the string
  Returns:
    the converted string

### partitionOptions

    public static java.lang.String[] partitionOptions(java.lang.String[] options)

  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.

  Parameters:
    `options` - the input array of options
  Returns:
    the array of secondary options

### unbackQuoteChars

    public static java.lang.String unbackQuoteChars(java.lang.String string)

  The inverse operation of backQuoteChars(). Converts back-quoted carriage returns and new lines in a string to the corresponding character ('\r' and '\n'). Also "un"-back-quotes the following characters: ` " \ \t and %

  Parameters:
    `string` - the string
  Returns:
    the converted string
  See Also:
    `backQuoteChars(String)`

### splitOptions

    public static java.lang.String[] splitOptions(java.lang.String quotedOptionString)
                                           throws java.lang.Exception

  Split up a string containing options into an array of strings, one for each option.

  Parameters:
    `quotedOptionString` - the string containing the options
  Returns:
    the array of options
  Throws:
    `java.lang.Exception` - in case of an unterminated string, unknown character or a parse error

### joinOptions

    public static java.lang.String joinOptions(java.lang.String[] optionArray)

  Joins all the options in an option array into a single string, as might be used on the command line.

  Parameters:
    `optionArray` - the array of options
  Returns:
    the string containing all options.

### forName

    public static java.lang.Object forName(java.lang.Class classType,
                                           java.lang.String className,
                                           java.lang.String[] options)
                                    throws java.lang.Exception

  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:

  ``

       String classifierName = Utils.getOption('W', options);
       Classifier c = (Classifier)Utils.forName(Classifier.class,
                                                classifierName,
                                                options);
       setClassifier(c);

  Parameters:
    `classType` - the class that the instantiated object should be assignable to -- an exception is thrown if this is not the case
    `className` - the fully qualified class name of the object
    `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.
  Returns:
    the newly created object, ready for use.
  Throws:
    `java.lang.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

### info

    public static double info(int[] counts)

  Computes entropy for an array of integers.

  Parameters:
    `counts` - array of counts
  Returns:
    - a log2 a - b log2 b - c log2 c + (a+b+c) log2 (a+b+c) when given array [a b c]

### smOrEq

    public static boolean smOrEq(double a,
                                 double b)

  Tests if a is smaller or equal to b.

  Parameters:
    `a` - a double
    `b` - a double

### grOrEq

    public static boolean grOrEq(double a,
                                 double b)

  Tests if a is greater or equal to b.

  Parameters:
    `a` - a double
    `b` - a double

### sm

    public static boolean sm(double a,
                             double b)

  Tests if a is smaller than b.

  Parameters:
    `a` - a double
    `b` - a double

### gr

    public static boolean gr(double a,
                             double b)

  Tests if a is greater than b.

  Parameters:
    `a` - a double
    `b` - a double

### kthSmallestValue

    public static int kthSmallestValue(int[] array,
                                       int k)

  Returns the kth-smallest value in the array.

  Parameters:
    `array` - the array of integers
    `k` - the value of k
  Returns:
    the kth-smallest value

### kthSmallestValue

    public static double kthSmallestValue(double[] array,
                                          int k)

  Returns the kth-smallest value in the array

  Parameters:
    `array` - the array of double
    `k` - the value of k
  Returns:
    the kth-smallest value

### log2

    public static double log2(double a)

  Returns the logarithm of a for base 2.

  Parameters:
    `a` - a double
  Returns:
    the logarithm for base 2

### maxIndex

    public static int maxIndex(double[] doubles)

  Returns index of maximum element in a given array of doubles. First maximum is returned.

  Parameters:
    `doubles` - the array of doubles
  Returns:
    the index of the maximum element

### maxIndex

    public static int maxIndex(int[] ints)

  Returns index of maximum element in a given array of integers. First maximum is returned.

  Parameters:
    `ints` - the array of integers
  Returns:
    the index of the maximum element

### mean

    public static double mean(double[] vector)

  Computes the mean for an array of doubles.

  Parameters:
    `vector` - the array
  Returns:
    the mean

### minIndex

    public static int minIndex(int[] ints)

  Returns index of minimum element in a given array of integers. First minimum is returned.

  Parameters:
    `ints` - the array of integers
  Returns:
    the index of the minimum element

### minIndex

    public static int minIndex(double[] doubles)

  Returns index of minimum element in a given array of doubles. First minimum is returned.

  Parameters:
    `doubles` - the array of doubles
  Returns:
    the index of the minimum element

### normalize

    public static void normalize(double[] doubles)

  Normalizes the doubles in the array by their sum.

  Parameters:
    `doubles` - the array of double
  Throws:
    `java.lang.IllegalArgumentException` - if sum is Zero or NaN

### normalize

    public static void normalize(double[] doubles,
                                 double sum)

  Normalizes the doubles in the array using the given value.

  Parameters:
    `doubles` - the array of double
    `sum` - the value by which the doubles are to be normalized
  Throws:
    `java.lang.IllegalArgumentException` - if sum is zero or NaN

### logs2probs

    public static double[] logs2probs(double[] a)

  Converts an array containing the natural logarithms of probabilities stored in a vector back into probabilities. The probabilities are assumed to sum to one.

  Parameters:
    `a` - an array holding the natural logarithms of the probabilities
  Returns:
    the converted array

### probToLogOdds

    public static double probToLogOdds(double prob)

  Returns the log-odds for a given probabilitiy.

  Parameters:
    `prob` - the probabilitiy
  Returns:
    the log-odds after the probability has been mapped to [Utils.SMALL, 1-Utils.SMALL]

### round

    public static int round(double value)

  Rounds a double to the next nearest integer value. The JDK version of it doesn't work properly.

  Parameters:
    `value` - the double value
  Returns:
    the resulting integer value

### probRound

    public static int probRound(double value,
                                java.util.Random rand)

  Rounds a double to the next nearest integer value in a probabilistic fashion (e.g. 0.8 has a 20% chance of being rounded down to 0 and a 80% chance of being rounded up to 1). In the limit, the average of the rounded numbers generated by this procedure should converge to the original double.

  Parameters:
    `value` - the double value
    `rand` - the random number generator
  Returns:
    the resulting integer value

### replaceMissingWithMAX_VALUE

    public static void replaceMissingWithMAX_VALUE(double[] array)

  Replaces all "missing values" in the given array of double values with MAX_VALUE.

  Parameters:
    `array` - the array to be modified.

### roundDouble

    public static double roundDouble(double value,
                                     int afterDecimalPoint)

  Rounds a double to the given number of decimal places.

  Parameters:
    `value` - the double value
    `afterDecimalPoint` - the number of digits after the decimal point
  Returns:
    the double rounded to the given precision

### sort

    public static int[] sort(int[] array)

  Sorts a given array of integers in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array. The sort is stable. (Equal elements remain in their original order.)

  Parameters:
    `array` - this array is not changed by the method!
  Returns:
    an array of integers with the positions in the sorted array.

### sort

    public static int[] sort(double[] array)

  Sorts a given array of doubles in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array. NOTE THESE CHANGES: the sort is no longer stable and it doesn't use safe floating-point comparisons anymore. Occurrences of Double.NaN are treated as Double.MAX_VALUE.

  Parameters:
    `array` - this array is not changed by the method!
  Returns:
    an array of integers with the positions in the sorted array.

### sortWithNoMissingValues

    public static int[] sortWithNoMissingValues(double[] array)

  Sorts a given array of doubles in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array. Missing values in the given array are replaced by Double.MAX_VALUE, so the array is modified in that case!

  Parameters:
    `array` - the array to be sorted, which is modified if it has missing values
  Returns:
    an array of integers with the positions in the sorted array.

### stableSort

    public static int[] stableSort(double[] array)

  Sorts a given array of doubles in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array. The sort is stable (Equal elements remain in their original order.) Occurrences of Double.NaN are treated as Double.MAX_VALUE

  Parameters:
    `array` - this array is not changed by the method!
  Returns:
    an array of integers with the positions in the sorted array.

### variance

    public static double variance(double[] vector)

  Computes the variance for an array of doubles.

  Parameters:
    `vector` - the array
  Returns:
    the variance

### sum

    public static double sum(double[] doubles)

  Computes the sum of the elements of an array of doubles.

  Parameters:
    `doubles` - the array of double
  Returns:
    the sum of the elements

### sum

    public static int sum(int[] ints)

  Computes the sum of the elements of an array of integers.

  Parameters:
    `ints` - the array of integers
  Returns:
    the sum of the elements

### xlogx

    public static double xlogx(int c)

  Returns c*log2(c) for a given integer value c.

  Parameters:
    `c` - an integer value
  Returns:
    c*log2(c) (but is careful to return 0 if c is 0)

### convertToRelativePath

    public static java.io.File convertToRelativePath(java.io.File absolute)
                                              throws java.lang.Exception

  Converts a File's absolute path to a path relative to the user (ie start) directory. Includes an additional workaround for Cygwin, which doesn't like upper case drive letters.

  Parameters:
    `absolute` - the File to convert to relative path
  Returns:
    a File with a path that is relative to the user's directory
  Throws:
    `java.lang.Exception` - if the path cannot be constructed

### getRevision

    public java.lang.String getRevision()

  Returns the revision string.

  Specified by:
    `getRevision` in interface `RevisionHandler`
  Returns:
    the revision

### main

    public static void main(java.lang.String[] ops)

  Main method for testing this class.

  Parameters:
    `ops` - some dummy options

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