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

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	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 medin 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 <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 int[]	rank(double[] values, boolean sameRank) Ranks the values in values, where the greatest value obtains the lowest rank.
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 double[][]	transpose(double[][] sp) Transpose a double matrix.

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 medin 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

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

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

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