de.jstacs.utils
Class ToolBox

java.lang.Object
  de.jstacs.utils.ToolBox

public class ToolBox
extends Object

This class is a collection of methods which might be useful for the programmer.

Author:

Jens Keilwagen, Jan Grau

Nested Class Summary

static class

ToolBox.TiedRanks Handling of tied ranks in rank(double[], TiedRanks).

Constructor Summary

ToolBox()

Method Summary

static int	getMaxIndex(double[] w) Returns the index with maximal value in a double array.
static int	getMaxIndex(int start, int end, double[] w) Returns the index with maximal value in a double array.
static double[]	getUniqueHueValues(int number) Creates an array of hue values that can be used for the representation of probabilities.
static double	max(double... array) This method returns the maximum of the elements of an array.
static double	max(int start, int end, double[] array) This method returns the maximum of the elements of an array between start and end.
static double	mean(int start, int end, double[] array) This method returns the mean of the elements of an array between start and end.
static double	median(double... array) This method returns the median of the elements of array.
static double	median(int start, int end, double[] array) This method returns the median of the elements of an array between start and end.
static double	min(double... array) This method returns the minimum of the elements of an array.
static double	min(int start, int end, double[] array) This method returns the minimum of the elements of an array between start and end.
static int[]	order(double[] values, boolean ascending) This method computes the order of the elements to obtain a sorted array.
static <K> Hashtable<K,Integer>	parseHashSet2IndexHashtable(HashSet<K> set) This method converts a HashSet in a Hashtable with unique indices starting at 0.
static double	pearsonCorrelation(double[] v1, double[] v2) The method computes the Pearson correlation of two vectors.
static double	pearsonCorrelation(double[] v1, double[] v2, int off1, int off2) The method computes the Pearson correlation of two vectors beginning at specific offsets.
static double	pearsonCorrelation(double[] v1, double[] v2, int off1, int off2, int length) The method computes the Pearson correlation of two vectors beginning at specific offsets and using a given number of entries.
static double	percentile(double[] array, double percent) Returns the percent percentile of the array, i.e., returns the element at percent*(array.length) of the sorted array.
static double	percentile(int start, int end, double[] array, double percent) Returns the percent percentile of the array between start and end, i.e., returns the element at percent*(end-start) of the sorted sub-array.
static int[]	rank(double[] values, boolean sameRank) Ranks the values in values, where the greatest value obtains the lowest rank.
static int[]	rank(double[] values, ToolBox.TiedRanks ties) Ranks the values in values, where the greatest value obtains the lowest rank.
static double	sd(int start, int end, double[] array) This method returns the standard deviation of the elements of an array between start and end.
static void	sortAlongWith(double[] arrayToBeSorted, double[]... alongWith) This method implements a sort algorithm on the array arrayToBeSorted.
static double	spearmanCorrelation(double[] v1, double[] v2) The method computes the Spearman correlation of two vectors.
static double	sum(double... array) Computes the sum of the values in array
static double	sum(int start, int end, double[] array) Computes the sum of the values in array starting at start until end.
static String	toString(double[] array, NumberFormat nf) This methods returns a String representation of a double array using the specified NumberFormat.
static double[][]	transpose(double[][] sp) Transpose a double matrix.
static double	weightPercentile(double[] array, double percent) Returns the element in the sorted variant of array (considered in descending order) that yields percent of the cumulative value of array elements.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ToolBox

public ToolBox()

Method Detail

parseHashSet2IndexHashtable

public static <K> Hashtable<K,Integer> parseHashSet2IndexHashtable(HashSet<K> set)

This method converts a HashSet in a Hashtable with unique indices starting at 0. The indices are derived from the order of the Iterator of the HashSet.

Type Parameters:

K - the type of the keys

Parameters:

set - the set of keys

Returns:

a Hashtable with keys and unique indices starting at 0

max

public static double max(double... array)

This method returns the maximum of the elements of an array.

Parameters:

array - the array of values

Returns:

the maximum

min

public static double min(double... array)

This method returns the minimum of the elements of an array.

Parameters:

array - the array of values

Returns:

the minimum

max

public static double max(int start,
                         int end,
                         double[] array)

This method returns the maximum of the elements of an array between start and end.

Parameters:

start - start position (inclusive)

end - end position (exclusive)

array - the array of values

Returns:

the maximum

min

public static double min(int start,
                         int end,
                         double[] array)

This method returns the minimum of the elements of an array between start and end.

Parameters:

start - start position (inclusive)

end - end position (exclusive)

array - the array of values

Returns:

the minimum

getMaxIndex

public static final int getMaxIndex(double[] w)

Returns the index with maximal value in a double array.

Parameters:

w - the given double array

Returns:

the index

getMaxIndex

public static final int getMaxIndex(int start,
                                    int end,
                                    double[] w)

Returns the index with maximal value in a double array.

Parameters:

w - the given double array

start - start position (inclusive)

end - end position (exclusive)

Returns:

the index

median

public static double median(double... array)

This method returns the median of the elements of array.

Parameters:

array - the array of values

Returns:

the median

median

public static double median(int start,
                            int end,
                            double[] array)

This method returns the median of the elements of an array between start and end.

Parameters:

start - start position (inclusive)

end - end position (exclusive)

array - the array of values

Returns:

the median

mean

public static double mean(int start,
                          int end,
                          double[] array)

This method returns the mean of the elements of an array between start and end.

Parameters:

start - start position (inclusive)

end - end position (exclusive)

array - the array of values

Returns:

the mean

sd

public static double sd(int start,
                        int end,
                        double[] array)

This method returns the standard deviation of the elements of an array between start and end.

Parameters:

start - start position (inclusive)

end - end position (exclusive)

array - the array of values

Returns:

the standard deviation

percentile

public static double percentile(double[] array,
                                double percent)

Returns the percent percentile of the array, i.e., returns the element at percent*(array.length) of the sorted array.

Parameters:

array - the array

percent - the percentage

Returns:

the percentile value

percentile

public static double percentile(int start,
                                int end,
                                double[] array,
                                double percent)

Returns the percent percentile of the array between start and end, i.e., returns the element at percent*(end-start) of the sorted sub-array.

Parameters:

start - the first index to consider

end - the end index (exclusive)

array - the array

percent - the percentage

Returns:

the percentile value

weightPercentile

public static double weightPercentile(double[] array,
                                      double percent)

Returns the element in the sorted variant of array (considered in descending order) that yields percent of the cumulative value of array elements.

Parameters:

array - the array

percent - the percentage

Returns:

the element

rank

public static final int[] rank(double[] values,
                               boolean sameRank)

Ranks the values in values, where the greatest value obtains the lowest rank. The boolean sameRank allows to decide whether tied values should obtain the same rank.

Parameters:

values - the values

sameRank - a switch whether tied values obtain the same rank.

Returns:

the ranks

order

public static final int[] order(double[] values,
                                boolean ascending)

This method computes the order of the elements to obtain a sorted array.

Parameters:

values - the array

ascending - a switch whether the array should be sorted ascending or descending

Returns:

the array containing the indices of the elements to obtain a sorted array

rank

public static final int[] rank(double[] values,
                               ToolBox.TiedRanks ties)

Ranks the values in values, where the greatest value obtains the lowest rank. The enum ties allows to choose how tied ranks are handled.

Parameters:

values - the values

ties - a switch how to handle tied ranks

Returns:

the ranks

See Also:

ToolBox.TiedRanks

spearmanCorrelation

public static double spearmanCorrelation(double[] v1,
                                         double[] v2)
                                  throws Exception

The method computes the Spearman correlation of two vectors.

Parameters:

v1 - the first vector

v2 - the second vector

Returns:

the Spearman correlation of the two vectors

Throws:

Exception - if the vectors have different length

pearsonCorrelation

public static double pearsonCorrelation(double[] v1,
                                        double[] v2)
                                 throws Exception

The method computes the Pearson correlation of two vectors.

Parameters:

v1 - the first vector

v2 - the second vector

Returns:

the Pearson correlation of the two vectors

Throws:

Exception - if the vectors have different length

pearsonCorrelation

public static double pearsonCorrelation(double[] v1,
                                        double[] v2,
                                        int off1,
                                        int off2)
                                 throws Exception

The method computes the Pearson correlation of two vectors beginning at specific offsets.

Parameters:

v1 - the first vector

v2 - the second vector

off1 - the offset for the first vector

off2 - the offset for the second vector

Returns:

the Pearson correlation of the two vectors

Throws:

Exception - if the vectors have different length

pearsonCorrelation

public static double pearsonCorrelation(double[] v1,
                                        double[] v2,
                                        int off1,
                                        int off2,
                                        int length)
                                 throws Exception

The method computes the Pearson correlation of two vectors beginning at specific offsets and using a given number of entries.

Parameters:

v1 - the first vector

v2 - the second vector

off1 - the offset for the first vector

off2 - the offset for the second vector

length - the number of elements to be used for computing the correlation

Returns:

the Pearson correlation of the two vectors

Throws:

Exception - if the vectors have different length

sum

public static double sum(double... array)

Computes the sum of the values in array

Parameters:

array - the array

Returns:

the sum of the elements in array

sum

public static double sum(int start,
                         int end,
                         double[] array)

Computes the sum of the values in array starting at start until end.

Parameters:

start - the index of the first element in the sum (inclusive)

end - the end index (exclusive)

array - the array

Returns:

the sum of the elements in array from start to end

transpose

public static double[][] transpose(double[][] sp)
                            throws Exception

Transpose a double matrix.

Parameters:

sp - the array

Returns:

the transposed array

Throws:

Exception - if sp is no matrix

getUniqueHueValues

public static double[] getUniqueHueValues(int number)

Creates an array of hue values that can be used for the representation of probabilities. The first four hues are always equal to those of the sequence-logo colors.

Parameters:

number - the number of colors

Returns:

the hue values

sortAlongWith

public static void sortAlongWith(double[] arrayToBeSorted,
                                 double[]... alongWith)

This method implements a sort algorithm on the array arrayToBeSorted. However, the entries of the array alongWith are reordered in the same way asarrayToBeSorted.

Parameters:

arrayToBeSorted - the array to be sorted

alongWith - a series of arrays that is in the same way reordered as arrayToBeSorted.

See Also:

Arrays.sort(Object[], Comparator), DoubleArrayComparator

toString

public static String toString(double[] array,
                              NumberFormat nf)

This methods returns a String representation of a double array using the specified NumberFormat.

Parameters:

array - the array to be represented

nf - the NumberFormat to be used

Returns:

a String representation