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

Nested Classes
Modifier and Type Class and Description

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

Nested Classes
Modifier and Type	Class and Description
`static class`	`ToolBox.TiedRanks` Handling of tied ranks in `rank(double[], TiedRanks)`.

Constructor Summary

Constructors
Constructor and Description

ToolBox()

Constructors
Constructor and Description
`ToolBox()`

Method Summary

Methods
Modifier and Type	Method and Description
`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 int`	`getMinIndex(double[] w)` Returns the index with minimum value in a `double` array.
`static int`	`getMinIndex(int start, int end, double[] w)` Returns the index with minimum 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 descending)` 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 double[]`	`permute(double[] values)` Creates and returns a permutation of the values in `values`.
`static double[]`	`permute(double[] values, double[] permutation)` Creates a new permutation of the values in `values`.
`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 int`	`sum(boolean[] bools)` Counts the number of `true` values in `bools` (similar to sum on booleans in R).
`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 descending)
```
    This method computes the order of the elements to obtain a sorted array.
    
    Parameters:
    values - the array
    descending - 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
  - permute
```
public static double[] permute(double[] values)
```
    Creates and returns a permutation of the values in values.
    
    Parameters:
    values - the values
    
    Returns:
    the permutation
  - permute
```
public static double[] permute(double[] values,
               double[] permutation)
```
    Creates a new permutation of the values in values. If the array supplied as permutation has the same dimension as values and is not null, the values are returned in this array (and, additionally, as return value), which may save memory in multiple successive calls to this method.
    
    Parameters:
    values - the values
    permutation - the permutation (may be null)
    
    Returns:
    the permutation
  - sum
```
public static int sum(boolean[] bools)
```
    Counts the number of true values in bools (similar to sum on booleans in R).
    
    Parameters:
    bools - the boolean values
    
    Returns:
    the number of trues
  - getMinIndex
```
public static int getMinIndex(double[] w)
```
    Returns the index with minimum value in a double array.
    
    Parameters:
    w - the given double array
    
    Returns:
    the index
  - getMinIndex
```
public static int getMinIndex(int start,
              int end,
              double[] w)
```
    Returns the index with minimum value in a double array.
    
    Parameters:
    w - the given double array
    start - start position (inclusive)
    end - end position (exclusive)
    
    Returns:
    the index

Class ToolBox

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ToolBox

Method Detail

parseHashSet2IndexHashtable

max

min

max

min

getMaxIndex

getMaxIndex

median

median

mean

sd

percentile

percentile

weightPercentile

rank

order

rank

spearmanCorrelation

pearsonCorrelation

pearsonCorrelation

pearsonCorrelation

sum

sum

transpose

getUniqueHueValues

sortAlongWith

toString

permute

permute

sum

getMinIndex

getMinIndex