src/clustal/util.c File Reference

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <time.h>
#include "log.h"
#include "util.h"

Include dependency graph for util.c:

Data Structures
struct	sortwithindex_t
Functions
int	CheckIfFileExists (char *pcFilename)
	Copy of squid's FileExists(). Copied here to make squid independent.
void *	CkMalloc (size_t bytes, const char *function, const int line)
	Allocates memory (malloc).
void *	CkCalloc (size_t count, size_t size, const char *function, const int line)
	Allocates memory (calloc). Memory will be set to zero.
void *	CkRealloc (void *ptr, size_t bytes, const char *function, const int line)
	Reallocates memory.
void *	CkFree (void *ptr, const char *function, const int line)
	Frees memory.
char *	CkStrdup (const char *src)
	safe version of strdup
void	PermutationArray (int **perm, const int len)
	Creates an int array of size len with len-1 random but unique integers with values 0--len-1. This is "a modified version of Fisher-Yates known as Durstenfeld-Fisher-Yates or Knuth-Fisher-Yates". See http://stackoverflow.com/questions/196017/unique-random-numbers-in-o1.
void	RandomUniqueIntArray (int *array, const int array_len, const int max_value)
	Creates an array filled with random, but unique ints of given range. Implementation of the Floyd algorithm. See http://stackoverflow.com/questions/1608181/unique-random-numbers-in-an-integer-array-in-the-c-programming-language Assuming M is the length of the desired array and N is the numeric range: "This approach has the complexity of about O(M) (depends on the search structure used), so it is better suitable when M << N. This approach keeps track of already generated random numbers, so it requires extra memory. However, the beauty of it is that it does not make any of those horrendous "trial and error" iterations, trying to find an unused random number. This algorithm is guaranteed to generate one unique random number after each single call to the random number generator.".
int	IntCmp (const void *a, const void *b)
	int comparison function for qsort
int	SortAndTrackIndexCmpAsc (const void *a, const void *b)
	Compare two sortwithindex_t pointers and return the difference between the int value of the 1st sortwithindex_t and the 2nd. Used for ascending sort order in QSortWithIndexes()/.
int	SortAndTrackIndexCmpDesc (const void *a, const void *b)
	Compare two sortwithindex_t pointers and return the difference between the int value of the 2nd sortwithindex_t and the 1st. Used for descending sort order in QSortWithIndexes().
void	QSortAndTrackIndex (int *piSortedIndices, int *piArrayToSort, const int iArrayLen, const char cOrder, const bool bOverwriteArrayToSort)
	Sort a given int array in ascending or descending order, while keeping track of the element order.
bool	FileIsWritable (char *pcFileName)
	Test if file is writable. File may or may not exist.

---

Function Documentation

int CheckIfFileExists

(

char *

pcFilename

)

Copy of squid's FileExists(). Copied here to make squid independent.

void* CkCalloc	(	size_t	count,
		size_t	size,
		const char *	function,
		const int	line
	)

Allocates memory (calloc). Memory will be set to zero.

Parameters:

[in]	count	Allocate space for count objects
[in]	size	Objects are of this size
[in]	function	calling function name
[in]	line	calling function line

Returns:

void pointer to the newly allocated and zeroed memory (calloc).

Note:

use provided macro CKCALLOC() which automatically adds function name and line number

void* CkFree	(	void *	ptr,
		const char *	function,
		const int	line
	)

Frees memory.

Parameters:

[in]	ptr	Pointer to memory to be freed
[in]	function	calling function name
[in]	line	calling function line

Returns:

void pointer to the now zeroed memory

Note:

use provided macro CKFREE()

void* CkMalloc	(	size_t	bytes,
		const char *	function,
		const int	line
	)

Allocates memory (malloc).

Parameters:

[in]	bytes	bytes to allocated
[in]	function	calling function name
[in]	line	calling function line

Returns:

void pointer to the newly allocated memory

Note:

use provided macro CKMALLOC() which automatically adds function name and line number

void* CkRealloc	(	void *	ptr,
		size_t	bytes,
		const char *	function,
		const int	line
	)

Reallocates memory.

Parameters:

[in]	ptr	Pointer to memory to be reallocated
[in]	bytes	bytes to allocated
[in]	function	calling function name
[in]	line	calling function line

Returns:

void pointer to the newly allocated memory

Note:

use provided macro CKREALLOC() which automatically adds function name and line number

char* CkStrdup

(

const char *

src

)

safe version of strdup

Parameters:

[in]

src

String to copy from

Returns:

copy of string

Note:

src is not allowed to be NULL.

bool FileIsWritable

(

char *

pcFileName

)

Test if file is writable. File may or may not exist.

Parameters:

[in]

pcFileName

Filename to check

Returns:

True if file is writable at the time of calling

int IntCmp	(	const void *	a,
		const void *	b
	)

int comparison function for qsort

void PermutationArray	(	int **	perm,
		const int	len
	)

Creates an int array of size len with len-1 random but unique integers with values 0--len-1. This is "a modified version of Fisher-Yates known as Durstenfeld-Fisher-Yates or Knuth-Fisher-Yates". See http://stackoverflow.com/questions/196017/unique-random-numbers-in-o1.

Parameters:

[in]	perm	The permutation array. Has to be preallocated
[out]	len	Length of the permutation array

void QSortAndTrackIndex	(	int *	piSortedIndices,
		int *	piArrayToSort,
		const int	iArrayLen,
		const char	cOrder,
		const bool	bOverwriteArrayToSort
	)

Sort a given int array in ascending or descending order, while keeping track of the element order.

Parameters:

[out]	piSortedIndices	Will contain the indices of the sorted elements. Has to be preallocated.
[out]	piArrayToSort	Array with values to sort. Will only be overwritten if bOverwriteArrayToSort it true.
[in]	iArrayLen	Number of elements in piArrayToSort.
[in]	cOrder	Sort order. 'a' for ascending, 'd' for descending.
[in]	bOverwriteArrayToSort	If false do not overwrite the array to sort.

< aux

void RandomUniqueIntArray	(	int *	array,
		const int	array_len,
		const int	max_value
	)

Creates an array filled with random, but unique ints of given range. Implementation of the Floyd algorithm. See http://stackoverflow.com/questions/1608181/unique-random-numbers-in-an-integer-array-in-the-c-programming-language Assuming M is the length of the desired array and N is the numeric range: "This approach has the complexity of about O(M) (depends on the search structure used), so it is better suitable when M << N. This approach keeps track of already generated random numbers, so it requires extra memory. However, the beauty of it is that it does not make any of those horrendous "trial and error" iterations, trying to find an unused random number. This algorithm is guaranteed to generate one unique random number after each single call to the random number generator.".

Warning:

This won't work if max_value<=array_len. Only use for cases where array_len<<max_value

Parameters:

[in]	array	Preallocated int array whose values will be set
[in]	array_len	Size of array
[in]	max_value

int SortAndTrackIndexCmpAsc	(	const void *	a,
		const void *	b
	)

Compare two sortwithindex_t pointers and return the difference between the int value of the 1st sortwithindex_t and the 2nd. Used for ascending sort order in QSortWithIndexes()/.

See also:

SortAndTrackIndexCmpDesc() and QSortAndTrackIndex()

int SortAndTrackIndexCmpDesc	(	const void *	a,
		const void *	b
	)

Compare two sortwithindex_t pointers and return the difference between the int value of the 2nd sortwithindex_t and the 1st. Used for descending sort order in QSortWithIndexes().

See also:

SortAndTrackIndexCmpDesc() and QSortAndTrackIndex()